Module Index

Module: CPlot2D_wrapper_module

Files: - extlibs/CPlot2D/simple_CPlot2D_wrapper.f90

Uses: - simple_core_module_api

Public symbols: - CDataPoint_type — type

Private symbols: - C_CDataPoint__delete — subroutine - C_CDataPoint__new2 — function - C_CDataSet__AddDataPoint — subroutine - C_CDataSet__delete — subroutine - C_CDataSet__new — function - C_CDataSet__SetDashedLine — subroutine - C_CDataSet__SetDatasetColor — subroutine - C_CDataSet__SetDrawLine — subroutine - C_CDataSet__SetDrawMarker — subroutine - C_CDataSet__SetFillArea — subroutine - C_CDataSet__SetLineWidth — subroutine - C_CDataSet__SetMarkerSize — subroutine - C_CPlot2D__AddDataSet — subroutine - C_CPlot2D__delete — subroutine - C_CPlot2D__new — function - C_CPlot2D__OutputPostScriptPlot — subroutine - C_CPlot2D__SetDrawLegend — subroutine - C_CPlot2D__SetDrawXAxisGridLines — subroutine - C_CPlot2D__SetDrawYAxisGridLines — subroutine - C_CPlot2D__SetFlipY — subroutine - C_CPlot2D__SetXAxisSize — subroutine - C_CPlot2D__SetXAxisTitle — subroutine - C_CPlot2D__SetYAxisSize — subroutine - C_CPlot2D__SetYAxisTitle — subroutine - CDataPoint__delete — subroutine - CDataPoint__new2 — subroutine - CDataSet__AddDataPoint — subroutine - CDataSet__delete — subroutine - CDataSet__new — subroutine - CDataSet__SetDashedLine — subroutine - CDataSet__SetDatasetColor — subroutine - CDataSet__SetDrawLine — subroutine - CDataSet__SetDrawMarker — subroutine - CDataSet__SetFillArea — subroutine - CDataSet__SetLineWidth — subroutine - CDataSet__SetMarkerSize — subroutine - CDataSet_addpoint — subroutine - CDataSet_type — type - CPlot2D__AddDataSet — subroutine - CPlot2D__delete — subroutine - CPlot2D__new — subroutine - CPlot2D__OutputPostScriptPlot — subroutine - CPlot2D__SetDrawLegend — subroutine - CPlot2D__SetDrawXAxisGridLines — subroutine - CPlot2D__SetDrawYAxisGridLines — subroutine - CPlot2D__SetFlipY — subroutine - CPlot2D__SetXAxisSize — subroutine - CPlot2D__SetXAxisTitle — subroutine - CPlot2D__SetYAxisSize — subroutine - CPlot2D__SetYAxisTitle — subroutine - CPlot2D_type — type - plot2D — subroutine - test_CPlot2D — subroutine

---

Module: curl

Files: - extlibs/curl/src/curl.f90

---

Module: curl_easy

Files: - extlibs/curl/src/curl_easy.f90

Public symbols: - curl_easy_cleanup — subroutine - curl_easy_init — function - curl_easy_pause — function - curl_easy_perform — function - curl_free — subroutine - curl_global_cleanup — subroutine - curl_mime_addpart — function - curl_mime_data — function - curl_mime_free — subroutine - curl_mime_headers — function - curl_mime_init — function - curl_mime_subparts — function - curl_slist_free_all — subroutine - curl_version_now — function

Private symbols: - curl_easy_escape_ — function - curl_easy_getinfo_c_double — function - curl_easy_getinfo_c_long — function - curl_easy_getinfo_c_ptr — function - curl_easy_setopt_c_char — function - curl_easy_setopt_c_funptr — function - curl_easy_setopt_c_long — function - curl_easy_setopt_c_ptr — function - curl_easy_strerror_ — function - curl_easy_unescape_ — function - curl_escape_ — function - curl_global_init_ — function - curl_mime_encoder_ — function - curl_mime_filedata_ — function - curl_mime_filename_ — function - curl_mime_name_ — function - curl_mime_type_ — function - curl_slist — type - curl_slist_append_ — function - curl_unescape_ — function - curl_version_ — function - curl_version_info_ — function - curl_version_info_data — type

---

Module: curl_multi

Files: - extlibs/curl/src/curl_multi.f90

Public symbols: - curl_multi_add_handle — function - curl_multi_cleanup — function - curl_multi_info_read — function - curl_multi_init — function - curl_multi_perform — function - curl_multi_poll — function - curl_multi_remove_handle — function - curl_multi_strerror — function - curl_multi_timeout — function - curl_multi_wakeup — function

Private symbols: - curl_msg — type - curl_multi_strerror_ — function

---

Module: curl_urlapi

Files: - extlibs/curl/src/curl_urlapi.f90

Public symbols: - curl_url — function - curl_url_cleanup — subroutine - curl_url_dup — function - curl_url_get — function - curl_url_set — function - curl_url_strerror — function

Private symbols: - curl_url_get_ — function - curl_url_set_ — function - curl_url_strerror_ — function

---

Module: curl_util

Files: - extlibs/curl/src/curl_util.f90

Public symbols: - c_f_str_ptr — subroutine

Private symbols: - c_strlen — function

---

Module: elemental

Files: - main/image/simple_image.f90 - main/image/simple_image_access.f90 - main/image/simple_image_arith.f90

---

Module: FoX_common

Files: - extlibs/xml/common/FoX_common.F90

Uses: - fox_m_fsys_array_str - fox_m_fsys_count_parse_input - fox_m_fsys_format - fox_m_fsys_parse_input - m_common_attrs - m_common_error

---

Module: FoX_dom

Files: - extlibs/xml/dom/FoX_dom.f90

Uses: - fox_m_fsys_array_str - fox_m_fsys_format - m_dom_dom - m_dom_error - m_dom_extras - m_dom_parse - m_dom_utils

---

Module: fox_m_fsys_abort_flush

Files: - extlibs/xml/fsys/fox_m_fsys_abort_flush.F90

Uses: - f90_unix_io - f90_unix_proc

Public symbols: - abort — subroutine - pure_pxfabort — function - pxfabort — subroutine - pxfflush — subroutine

---

Module: fox_m_fsys_array_str

Files: - extlibs/xml/fsys/fox_m_fsys_array_str.F90

---

Module: fox_m_fsys_count_parse_input

Files: - extlibs/xml/fsys/fox_m_fsys_count_parse_input.F90

Uses: - fox_m_fsys_realtypes

---

Module: fox_m_fsys_format

Files: - extlibs/xml/fsys/fox_m_fsys_format.F90

Uses: - fox_m_fsys_abort_flush - fox_m_fsys_realtypes

---

Module: fox_m_fsys_parse_input

Files: - extlibs/xml/fsys/fox_m_fsys_parse_input.F90

Uses: - fox_m_fsys_realtypes

---

Module: fox_m_fsys_realtypes

Files: - extlibs/xml/fsys/fox_m_fsys_realtypes.f90

---

Module: fox_m_fsys_string

Files: - extlibs/xml/fsys/fox_m_fsys_string.F90

Public symbols: - toLower — function

---

Module: fox_m_fsys_string_list

Files: - extlibs/xml/fsys/fox_m_fsys_string_list.F90

Uses: - fox_m_fsys_array_str

---

Module: fox_m_utils_mtprng

Files: - extlibs/xml/utils/fox_m_utils_mtprng.F90

Private symbols: - mtprng_init — subroutine - mtprng_init_by_array — subroutine - mtprng_rand — function - mtprng_rand64 — function - mtprng_rand_range — function - mtprng_rand_real1 — function - mtprng_rand_real2 — function - mtprng_rand_real3 — function

---

Module: fox_m_utils_uri

Files: - extlibs/xml/utils/fox_m_utils_uri.F90

Uses: - fox_m_fsys_array_str - fox_m_fsys_format - fox_m_fsys_string

Public symbols: - copyURI — function - destroyURI — subroutine - dumpURI — subroutine - expressURI — function - getAuthority — function - getFragment — function - getHost — function - getPath — function - getPort — function - getQuery — function - getScheme — function - getUserinfo — function - hasAuthority — function - hasFragment — function - hasHost — function - hasPort — function - hasQuery — function - hasScheme — function - hasUserinfo — function - isAbsoluteURI — function - parseURI — function - rebaseURI — function

Private symbols: - appendPaths — function - checkAuthority — function - checkFragment — function - checkHost — function - checkIpvX — function - checkNonOpaquePath — function - checkOpaquePart — function - checkPath — function - checkPathSegment — function - checkQuery — function - checkScheme — function - cleanUp — subroutine - expressSegments — function - expressURI_len — function - normalizepath — function - pctEncode — function - pctEncode_len — function - produceResult — subroutine - unEscape_alloc — function - verifyWithPctEncoding — function

---

Module: fox_m_utils_uuid

Files: - extlibs/xml/utils/fox_m_utils_uuid.F90

Uses: - fox_m_utils_mtprng

Public symbols: - generate_uuid — function

Private symbols: - get_utc_since_1582 — function - int32ToHexOctets — function - int64ToHexOctets — function - isLeapYear — function

---

Module: FoX_sax

Files: - extlibs/xml/sax/FoX_sax.f90

Uses: - fox_common - m_sax_operate

---

Module: FoX_utils

Files: - extlibs/xml/utils/FoX_utils.f90

Uses: - fox_m_utils_uri - fox_m_utils_uuid

---

Module: FoX_wcml

Files: - extlibs/xml/wcml/FoX_wcml.f90

Uses: - fox_wxml - m_wcml_coma - m_wcml_core - m_wcml_geometry - m_wcml_lattice - m_wcml_lists - m_wcml_metadata - m_wcml_molecule - m_wcml_parameter - m_wcml_property - m_wcml_stml

---

Module: FoX_wkml

Files: - extlibs/xml/wkml/FoX_wkml.f90

Uses: - fox_wxml - m_wkml_chart - m_wkml_color - m_wkml_contours - m_wkml_core - m_wkml_coverage - m_wkml_features - m_wkml_lowlevel - m_wkml_styling

---

Module: FoX_wxml

Files: - extlibs/xml/wxml/FoX_wxml.f90

Uses: - m_wxml_core - m_wxml_overloads

---

Module: function

Files: - main/image/simple_image.f90 - main/image/simple_image_access.f90 - main/image/simple_image_arith.f90 - main/image/simple_image_calc.f90 - main/image/simple_image_checks.f90 - main/image/simple_image_fft.f90 - main/image/simple_image_filt.f90 - main/image/simple_image_freq_anal.f90 - main/image/simple_image_geom.f90 - main/image/simple_image_seg.f90 - main/nu_filt/simple_nu_filter.f90 - main/nu_filt/simple_nu_filter_state.f90 - main/ori/simple_oris.f90 - main/ori/simple_oris_dists.f90 - main/ori/simple_oris_getters.f90 - main/ori/simple_oris_life.f90 - main/ori/simple_oris_neig.f90 - main/ori/simple_oris_sampling.f90 - main/ori/simple_oris_stats.f90 - main/params/simple_parameters.f90 - main/params/simple_parameters_core.f90 - main/pftc/simple_polarft_access.f90 - main/pftc/simple_polarft_calc.f90 - main/project/simple_sp_project.f90 - main/project/simple_sp_project_cls.f90 - main/project/simple_sp_project_core.f90 - main/project/simple_sp_project_io.f90 - main/project/simple_sp_project_mic.f90 - main/project/simple_sp_project_stk.f90 - main/simple_abinitio_controller.f90 - main/simple_abinitio_utils.f90

Uses: - simple_online_var

---

Module: gnufor2

Files: - extlibs/gnufor/gnufor2.f90

---

Module: integer

Files: - main/nu_filt/simple_nu_filter.f90 - main/nu_filt/simple_nu_filter_bank.f90 - main/nu_filt/simple_nu_filter_potts.f90 - main/nu_filt/simple_nu_filter_state.f90 - main/pftc/simple_polarft_access.f90 - main/pftc/simple_polarft_calc.f90 - main/project/simple_sp_project.f90 - main/project/simple_sp_project_core.f90 - main/project/simple_sp_project_mic.f90 - main/project/simple_sp_project_ptcl.f90 - main/project/simple_sp_project_stk.f90

---

Module: json_file_module

Files: - extlibs/json/json_file_module.f90

Uses: - json_kinds - json_parameters - json_string_utilities - json_value_module

Private symbols: - json_file — type

---

Module: json_kinds

Files: - extlibs/json/json_kinds.f90

---

Module: json_module

Files: - extlibs/json/json_module.f90

Uses: - json_file_module - json_kinds - json_parameters - json_string_utilities - json_value_module

---

Module: json_parameters

Files: - extlibs/json/json_parameters.f90

Uses: - json_kinds

---

Module: json_string_utilities

Files: - extlibs/json/json_string_utilities.f90

Uses: - json_kinds - json_parameters

---

Module: json_value_module

Files: - extlibs/json/json_value_module.f90

Uses: - json_kinds - json_parameters - json_string_utilities

Private symbols: - json_core — type - json_value — type

---

Module: logical

Files: - main/image/simple_image.f90 - main/image/simple_image_calc.f90 - main/image/simple_image_checks.f90 - main/nu_filt/simple_nu_filter.f90 - main/nu_filt/simple_nu_filter_potts.f90 - main/nu_filt/simple_nu_filter_state.f90 - main/pftc/simple_polarft_access.f90 - main/pftc/simple_polarft_calc.f90 - main/project/simple_sp_project.f90 - main/project/simple_sp_project_mic.f90 - main/project/simple_sp_project_out.f90 - main/project/simple_sp_project_ptcl.f90

---

Module: m_common_attrs

Files: - extlibs/xml/common/m_common_attrs.F90

Uses: - fox_m_fsys_array_str - m_common_element - m_common_error

---

Module: m_common_buffer

Files: - extlibs/xml/common/m_common_buffer.F90

Uses: - fox_m_fsys_format - m_common_charset - m_common_error

---

Module: m_common_charset

Files: - extlibs/xml/common/m_common_charset.F90

Uses: - fox_m_fsys_string

Public symbols: - allowed_encoding — function - checkChars — function - isInitialNameChar — function - isInitialNCNameChar — function - isLegalChar — function - isLegalCharRef — function - isNameChar — function - isNCNameChar — function - isRepCharRef — function - isUSASCII — function - isXML1_0_NameChar — function - isXML1_1_NameChar — function

---

Module: m_common_content_model

Files: - extlibs/xml/common/m_common_content_model.F90

Uses: - fox_m_fsys_array_str

Public symbols: - checkCP — function - checkCPToEnd — function - destroyCPtree — subroutine - dumpCPtree — subroutine - elementContentCP — function - emptyContentCP — function - newCP — function - transformCPPlus — subroutine

Private symbols: - copyCP — function - copyCPtree — function - destroyCP — subroutine - dumpCP — subroutine - nextCPafterfail — function - nextCPaftermatch — function - nextCPMustMatch — function

---

Module: m_common_element

Files: - extlibs/xml/common/m_common_element.F90

Uses: - fox_m_fsys_array_str - fox_m_fsys_string_list - m_common_charset - m_common_content_model - m_common_error - m_common_namecheck

---

Module: m_common_elstack

Files: - extlibs/xml/common/m_common_elstack.F90

Uses: - fox_m_fsys_array_str - m_common_content_model - m_common_error

Private symbols: - elstack_item — type - elstack_t — type

---

Module: m_common_entities

Files: - extlibs/xml/common/m_common_entities.F90

Uses: - fox_m_fsys_array_str - fox_m_fsys_format - fox_m_utils_uri - m_common_charset - m_common_error

---

Module: m_common_entity_expand

Files: - extlibs/xml/common/m_common_entity_expand.F90

Uses: - fox_m_fsys_array_str - m_common_entities - m_common_error - m_common_namecheck - m_common_struct

Public symbols: - expand_entity_value_alloc — function

---

Module: m_common_error

Files: - extlibs/xml/common/m_common_error.F90

Uses: - fox_m_fsys_abort_flush - fox_m_fsys_array_str

---

Module: m_common_io

Files: - extlibs/xml/common/m_common_io.F90

Uses: - f90_iostat - m_common_error

Public symbols: - get_unit — subroutine - setup_io — subroutine

Private symbols: - find_eor_eof — subroutine

---

Module: m_common_namecheck

Files: - extlibs/xml/common/m_common_namecheck.F90

Uses: - fox_m_fsys_format - fox_m_fsys_string - m_common_charset

Public symbols: - checkAttValue — function - checkCharacterEntityReference — function - checkEncName — function - checkName — function - checkNames — function - checkNCName — function - checkNCNames — function - checkNmtoken — function - checkNmtokens — function - checkPEDef — function - checkPITarget — function - checkPseudoAttValue — function - checkPublicId — function - checkQName — function - checkQNames — function - checkRepCharEntityReference — function - likeCharacterEntityReference — function - localpartOfQname — function - prefixOfQName — function

---

Module: m_common_namespaces

Files: - extlibs/xml/common/m_common_namespaces.F90

Uses: - fox_m_fsys_array_str - fox_m_utils_uri - m_common_attrs - m_common_charset - m_common_error - m_common_namecheck - m_common_struct

---

Module: m_common_notations

Files: - extlibs/xml/common/m_common_notations.F90

Uses: - fox_m_fsys_array_str - m_common_error

Public symbols: - add_notation — subroutine - destroy_notation_list — subroutine - init_notation_list — subroutine - notation_exists — function

---

Module: m_common_struct

Files: - extlibs/xml/common/m_common_struct.F90

Uses: - fox_utils - m_common_charset - m_common_element - m_common_entities - m_common_notations

Public symbols: - destroy_xml_doc_state — subroutine - init_xml_doc_state — subroutine - register_external_GE — subroutine - register_external_PE — subroutine - register_internal_GE — subroutine - register_internal_PE — subroutine

---

Module: m_contours

Files: - extlibs/xml/wkml/m_contours.F90

Uses: - fox_common - m_common_error

Public symbols: - destroy_contourObject — subroutine - make_contours_on_a_complex_grid — function - make_contours_on_a_simple_grid — function - make_contours_on_simplest_grid — function

Private symbols: - add_line — subroutine - add_point — subroutine - add_polygon — subroutine - addLinesToContourObject — subroutine - addLineToLineList — subroutine - addPolygonsToContourObject — subroutine - addPolygonToPolygonList — subroutine - checkPointOnPolygon — function - complexScalePoints — subroutine - concatenate_lines — subroutine - destroy_contourLines — subroutine - draw — subroutine - GCONTR — subroutine - init_contourObject — subroutine - init_line — subroutine - joinUpLines — subroutine - nextLineOnEdge — function - pointInPolygon — function - polygonsInPolygons — subroutine - scale_contours_complex — subroutine - scale_contours_simple — subroutine - setpnew — subroutine - shave_polygon — subroutine - shave_polygons — subroutine - simpleScalePoints — subroutine - whichLevel — function

---

Module: m_dom_dom

Files: - extlibs/xml/dom/m_dom_dom.F90

Uses: - fox_m_fsys_array_str - fox_m_fsys_format - fox_m_fsys_string - fox_m_utils_uri - m_common_charset - m_common_element - m_common_namecheck - m_common_struct - m_dom_error

---

Module: m_dom_error

Files: - extlibs/xml/dom/m_dom_error.f90

Uses: - fox_m_fsys_abort_flush - m_common_error

Public symbols: - dom_error — subroutine - getExceptionCode — function - inException — function - internal_error — subroutine - throw_exception — subroutine

Private symbols: - destroyDOMException — subroutine - errorString — function

---

Module: m_dom_extras

Files: - extlibs/xml/dom/m_dom_extras.F90

Uses: - fox_m_fsys_parse_input - fox_m_fsys_realtypes - m_dom_dom - m_dom_error

---

Module: m_dom_parse

Files: - extlibs/xml/dom/m_dom_parse.f90

Uses: - fox_common - fox_m_fsys_array_str - fox_m_utils_uri - fox_sax - m_common_attrs - m_common_entities - m_common_error - m_common_struct - m_dom_dom - m_dom_error - m_sax_parser

Public symbols: - parsefile — function - parsestring — function

Private symbols: - characters_handler — subroutine - comment_handler — subroutine - endCdata_handler — subroutine - endDocument_Handler — subroutine - endDTD_handler — subroutine - endElement_handler — subroutine - endEntity_handler — subroutine - entityErrorHandler — subroutine - externalEntityDecl_handler — subroutine - FoX_endDTD_handler — subroutine - ignorableWhitespace_handler — subroutine - internalEntityDecl_handler — subroutine - normalErrorHandler — subroutine - notationDecl_handler — subroutine - processingInstruction_handler — subroutine - runParser — subroutine - skippedEntity_handler — subroutine - startCdata_handler — subroutine - startDocument_handler — subroutine - startDTD_handler — subroutine - startElement_handler — subroutine - startEntity_handler — subroutine - unparsedEntityDecl_handler — subroutine

---

Module: m_dom_utils

Files: - extlibs/xml/dom/m_dom_utils.f90

Uses: - fox_m_fsys_array_str - fox_m_fsys_format - fox_wxml - m_common_attrs - m_common_element - m_common_struct - m_dom_dom - m_dom_error

Public symbols: - dumpTree — subroutine - serialize — subroutine

Private symbols: - dump2 — subroutine - iter_dmp_xml — subroutine

---

Module: m_ieee

Files: - extlibs/xml/fsys/m_ieee.f90

Public symbols: - generate_nan — function

---

Module: m_sax_operate

Files: - extlibs/xml/sax/m_sax_operate.F90

Uses: - fox_common - m_common_error - m_sax_parser - m_sax_reader - m_sax_types

Public symbols: - close_xml_t — subroutine - open_xml_file — subroutine - open_xml_string — subroutine - parse — subroutine - stop_parser — subroutine

Private symbols: - attributeDecl_handler — subroutine - characters_handler — subroutine - comment_handler — subroutine - elementDecl_handler — subroutine - endCdata_handler — subroutine - endDocument_handler — subroutine - endDTD_handler — subroutine - endElement_handler — subroutine - endEntity_handler — subroutine - endPrefixMapping_handler — subroutine - error_handler — subroutine - externalEntityDecl_handler — subroutine - fatalError_handler — subroutine - ignorableWhitespace_handler — subroutine - internalEntityDecl_handler — subroutine - notationDecl_handler — subroutine - processingInstruction_handler — subroutine - skippedEntity_handler — subroutine - startCdata_handler — subroutine - startDocument_handler — subroutine - startDTD_handler — subroutine - startElement_handler — subroutine - startEntity_handler — subroutine - startPrefixMapping_handler — subroutine - unparsedEntityDecl_handler — subroutine - warning_handler — subroutine

---

Module: m_sax_parser

Files: - extlibs/xml/sax/m_sax_parser.F90

Uses: - fox_common - fox_m_fsys_array_str - fox_m_fsys_string_list - fox_utils - m_common_attrs - m_common_charset - m_common_element - m_common_elstack - m_common_entities - m_common_entity_expand - m_common_error - m_common_namecheck - m_common_namespaces - m_common_notations - m_common_struct - m_sax_reader - m_sax_tokenizer - m_sax_types

Public symbols: - getNSDict — function - sax_parse — subroutine - sax_parser_destroy — subroutine - sax_parser_init — subroutine

Private symbols: - add_entity — subroutine - attributeDecl_handler — subroutine - characters_handler — subroutine - checkAttributes — subroutine - checkIdRefs — subroutine - checkXMLAttributes — subroutine - close_tag — subroutine - comment_handler — subroutine - elementDecl_handler — subroutine - endCdata_handler — subroutine - endDocument_handler — subroutine - endDTD_handler — subroutine - endDTDchecks — subroutine - endElement_handler — subroutine - endEntity_handler — subroutine - endPrefixMapping_handler — subroutine - error_handler — subroutine - error_handler — subroutine - externalEntityDecl_handler — subroutine - fatalError_handler — subroutine - FoX_endDTD_handler — subroutine - getDefaultAttributes — subroutine - getLocalNameofQName — function - getURIofQName — function - ignorableWhitespace_handler — subroutine - internalEntityDecl_handler — subroutine - notationDecl_handler — subroutine - open_tag — subroutine - parseDTD — subroutine - processingInstruction_handler — subroutine - sax_error — subroutine - skippedEntity_handler — subroutine - startCdata_handler — subroutine - startDocument_handler — subroutine - startDTD_handler — subroutine - startElement_handler — subroutine - startEntity_handler — subroutine - startPrefixMapping_handler — subroutine - unparsedEntityDecl_handler — subroutine - URIlength — function - warning_handler — subroutine

---

Module: m_sax_reader

Files: - extlibs/xml/sax/m_sax_reader.F90

Uses: - fox_m_fsys_array_str - fox_m_fsys_format - fox_utils - m_common_charset - m_common_error - m_common_io - m_sax_xml_source

Public symbols: - close_file — subroutine - column — function - get_all_characters — function - get_character — function - line — function - open_file — subroutine - open_new_file — subroutine - open_new_string — subroutine - parse_text_declaration — subroutine - parse_xml_declaration — subroutine - pop_buffer_stack — subroutine - push_chars — subroutine - reading_first_entity — function - reading_main_file — function

Private symbols: - close_actual_file — subroutine - open_actual_file — subroutine

---

Module: m_sax_tokenizer

Files: - extlibs/xml/sax/m_sax_tokenizer.F90

Uses: - fox_m_fsys_array_str - fox_m_utils_uri - m_common_charset - m_common_entities - m_common_error - m_common_namecheck - m_sax_reader - m_sax_types

Public symbols: - expand_pe_text — function - normalize_attribute_text — function - sax_tokenize — subroutine

Private symbols: - tokenizeDTD — subroutine

---

Module: m_sax_types

Files: - extlibs/xml/sax/m_sax_types.F90

Uses: - m_common_attrs - m_common_elstack - m_common_entities - m_common_error - m_common_namespaces - m_common_notations - m_common_struct - m_sax_reader

---

Module: m_sax_xml_source

Files: - extlibs/xml/sax/m_sax_xml_source.F90

Uses: - fox_m_fsys_array_str - fox_m_fsys_format - fox_utils - m_common_charset - m_common_error - m_common_io

Public symbols: - get_char_from_file — function - parse_declaration — subroutine - push_file_chars — subroutine

Private symbols: - read_single_char — function - rewind_source — subroutine

---

Module: m_wcml_coma

Files: - extlibs/xml/wcml/m_wcml_coma.F90

Uses: - fox_m_fsys_realtypes - fox_wxml - m_wcml_stml - m_wxml_overloads

---

Module: m_wcml_core

Files: - extlibs/xml/wcml/m_wcml_core.F90

Uses: - fox_common - fox_utils - fox_wxml - m_common_error - m_wcml_metadata

Public symbols: - cmlAddNamespace — subroutine - cmlBeginFile — subroutine - cmlEndCml — subroutine - cmlFinishFile — subroutine - cmlStartCml — subroutine

---

Module: m_wcml_geometry

Files: - extlibs/xml/wcml/m_wcml_geometry.F90

Uses: - fox_m_fsys_realtypes - fox_wxml - m_wxml_overloads

---

Module: m_wcml_lattice

Files: - extlibs/xml/wcml/m_wcml_lattice.F90

Uses: - fox_m_fsys_realtypes - fox_wxml - m_wxml_overloads

---

Module: m_wcml_lists

Files: - extlibs/xml/wcml/m_wcml_lists.F90

Uses: - fox_common - fox_wxml

Public symbols: - cmlEndbandList — subroutine - cmlEndkpointList — subroutine - cmlEndmetadataList — subroutine - cmlEndmodule — subroutine - cmlEndparameterList — subroutine - cmlEndpropertyList — subroutine - cmlEndStep — subroutine - cmlStartbandList — subroutine - cmlStartkpointList — subroutine - cmlStartmetadataList — subroutine - cmlStartmodule — subroutine - cmlStartparameterList — subroutine - cmlStartpropertyList — subroutine - cmlStartStep — subroutine

---

Module: m_wcml_metadata

Files: - extlibs/xml/wcml/m_wcml_metadata.F90

Uses: - fox_wxml

Public symbols: - cmlAddMetadata — subroutine

---

Module: m_wcml_molecule

Files: - extlibs/xml/wcml/m_wcml_molecule.F90

Uses: - fox_m_fsys_format - fox_m_fsys_realtypes - fox_wxml - m_common_error - m_wxml_overloads

---

Module: m_wcml_parameter

Files: - extlibs/xml/wcml/m_wcml_parameter.F90

Uses: - fox_m_fsys_realtypes - fox_wxml - m_wcml_stml - m_wxml_overloads

---

Module: m_wcml_property

Files: - extlibs/xml/wcml/m_wcml_property.F90

Uses: - fox_m_fsys_realtypes - fox_wxml - m_wcml_stml - m_wxml_overloads

---

Module: m_wcml_stml

Files: - extlibs/xml/wcml/m_wcml_stml.F90

Uses: - fox_wxml - m_wxml_overloads

---

Module: m_wkml_chart

Files: - extlibs/xml/wkml/m_wkml_chart.F90

Uses: - fox_common - fox_wxml - m_common_error - m_wkml_lowlevel

---

Module: m_wkml_color

Files: - extlibs/xml/wkml/m_wkml_color.F90

Uses: - fox_common - fox_wxml - m_common_error - m_wkml_color_def

---

Module: m_wkml_color_def

Files: - extlibs/xml/wkml/m_wkml_color_def.F90

---

Module: m_wkml_contours

Files: - extlibs/xml/wkml/m_wkml_contours.F90

Uses: - fox_common - fox_m_fsys_realtypes - fox_wxml - m_common_error - m_contours - m_wkml_color - m_wkml_features - m_wkml_lowlevel - m_wkml_styling

---

Module: m_wkml_core

Files: - extlibs/xml/wkml/m_wkml_core.F90

Uses: - fox_wxml - m_common_error - m_wkml_lowlevel

Public symbols: - kmlAddNamespace — subroutine - kmlBeginFile — subroutine - kmlFinishFile — subroutine

---

Module: m_wkml_coverage

Files: - extlibs/xml/wkml/m_wkml_coverage.F90

Uses: - fox_common - fox_m_fsys_realtypes - fox_wxml - m_common_error - m_wkml_chart - m_wkml_color - m_wkml_features - m_wkml_lowlevel - m_wkml_styling

---

Module: m_wkml_features

Files: - extlibs/xml/wkml/m_wkml_features.F90

Uses: - fox_common - fox_m_fsys_realtypes - fox_wxml - m_common_error - m_wkml_chart - m_wkml_color - m_wkml_lowlevel - m_wkml_styling

---

Module: m_wkml_lowlevel

Files: - extlibs/xml/wkml/m_wkml_lowlevel.F90

Uses: - fox_common - fox_m_fsys_realtypes - fox_utils - fox_wxml - m_common_error

---

Module: m_wkml_styling

Files: - extlibs/xml/wkml/m_wkml_styling.F90

Uses: - fox_m_fsys_realtypes - fox_wxml - m_common_error - m_wkml_color - m_wkml_lowlevel

---

Module: m_wxml_core

Files: - extlibs/xml/wxml/m_wxml_core.F90

Uses: - fox_m_fsys_abort_flush - fox_m_fsys_array_str - fox_m_fsys_string - fox_m_utils_uri - m_common_attrs - m_common_buffer - m_common_charset - m_common_element - m_common_elstack - m_common_entities - m_common_error - m_common_io - m_common_namecheck - m_common_namespaces - m_common_notations - m_common_struct - m_wxml_escape

---

Module: m_wxml_escape

Files: - extlibs/xml/wxml/m_wxml_escape.F90

Uses: - fox_m_fsys_format - m_common_charset - m_common_error

Public symbols: - escape_string — function - escape_string_len — function

---

Module: m_wxml_overloads

Files: - extlibs/xml/wxml/m_wxml_overloads.F90

Uses: - fox_m_fsys_format - fox_m_fsys_realtypes - m_wxml_core

---

Module: mod_phasecorr

Files: - main/commanders/test/simple_test_mod_phasecorr.f90

Uses: - simple_image

Public symbols: - alloc — subroutine - gen_images — subroutine - kill — subroutine - new — subroutine - run — subroutine - t_phasecorr — type - vis_imgs — subroutine

---

Module: procedure

Files: - defs/simple_type_defs.f90 - extlibs/curl/src/curl_easy.f90 - extlibs/gnufor/gnufor2.f90 - extlibs/json/json_file_module.f90 - extlibs/json/json_string_utilities.f90 - extlibs/json/json_value_module.f90 - extlibs/unix/src/unix.f90 - extlibs/xml/common/m_common_attrs.F90 - extlibs/xml/common/m_common_buffer.F90 - extlibs/xml/common/m_common_element.F90 - extlibs/xml/common/m_common_elstack.F90 - extlibs/xml/common/m_common_entities.F90 - extlibs/xml/common/m_common_error.F90 - extlibs/xml/common/m_common_namespaces.F90 - extlibs/xml/dom/m_dom_dom.F90 - extlibs/xml/dom/m_dom_extras.F90 - extlibs/xml/fsys/fox_m_fsys_array_str.F90 - extlibs/xml/fsys/fox_m_fsys_count_parse_input.F90 - extlibs/xml/fsys/fox_m_fsys_format.F90 - extlibs/xml/fsys/fox_m_fsys_parse_input.F90 - extlibs/xml/fsys/fox_m_fsys_string_list.F90 - extlibs/xml/wcml/m_wcml_coma.F90 - extlibs/xml/wcml/m_wcml_geometry.F90 - extlibs/xml/wcml/m_wcml_lattice.F90 - extlibs/xml/wcml/m_wcml_molecule.F90 - extlibs/xml/wcml/m_wcml_parameter.F90 - extlibs/xml/wcml/m_wcml_property.F90 - extlibs/xml/wcml/m_wcml_stml.F90 - extlibs/xml/wkml/m_wkml_chart.F90 - extlibs/xml/wkml/m_wkml_color.F90 - extlibs/xml/wkml/m_wkml_contours.F90 - extlibs/xml/wkml/m_wkml_coverage.F90 - extlibs/xml/wkml/m_wkml_features.F90 - extlibs/xml/wkml/m_wkml_lowlevel.F90 - extlibs/xml/wkml/m_wkml_styling.F90 - extlibs/xml/wxml/m_wxml_core.F90 - extlibs/xml/wxml/m_wxml_overloads.F90 - fileio/simple_fileio.f90 - main/ctf/simple_ctf.f90 - main/image/simple_ftiter.f90 - main/image/simple_image.f90 - main/interp/simple_edges_sqwins.f90 - main/interp/simple_kbinterpol.f90 - main/interp/simple_winfuns.f90 - main/ori/simple_ori.f90 - main/ori/simple_oris.f90 - main/simple_abinitio_controller.f90 - main/simple_eul_prob_tab_utils.f90 - main/simple_sym.f90 - main/strategies/search/simple_matcher_ptcl_io.f90 - main/stream/simple_stream_watcher.f90 - utils/filter/simple_butterworth.f90 - utils/filter/simple_opt_filter.f90 - utils/math/simple_linalg.f90 - utils/math/simple_math.f90 - utils/math/simple_math_ft.f90 - utils/math/simple_neighs.f90 - utils/math/simple_ran_tabu.f90 - utils/math/simple_rnd.f90 - utils/math/simple_srch_sort_loc.f90 - utils/math/simple_stat.f90 - utils/qsys/simple_qsys_ctrl.f90 - utils/qsys/simple_qsys_funs.f90 - utils/simple_corrmat.f90 - utils/simple_gauss2Dfit.f90 - utils/simple_gpu_utils.f90 - utils/simple_imgarr_utils.f90 - utils/simple_is_check_assert.f90 - utils/simple_jiffys.f90 - utils/simple_magic_boxes.f90 - utils/simple_sauron.f90 - utils/simple_segmentation.f90 - utils/simple_string.f90 - utils/simple_string_utils.f90 - utils/structs/simple_chash.f90 - utils/structs/simple_hash.f90

Uses: - fox_common - fox_wxml - iso_fortran_env - m_wkml_color - simple_cmdline - simple_image - simple_math - simple_qsys_local - simple_rnd - simple_sauron - simple_string - simple_syslib - simple_type_defs

Public symbols: - add2fbody_1 — function - add2fbody_2 — function - add2fbody_3 — function - add_error — subroutine - addDefaultNS — subroutine - addPrefixedNS — subroutine - adoptNode — function - alloc_imgarr — subroutine - append2basename_1 — function - append2basename_2 — function - appendChild — function - appendData — subroutine - arr2file_dp — subroutine - arr2file_sp — subroutine - arr2txtfile_1 — subroutine - arr2txtfile_2 — subroutine - assert_eq2 — function - assert_eq3 — function - assert_eq4 — function - assert_eqn — function - automatic_thresh_sobel — subroutine - autoscale — subroutine - basename — function - batch_gauss2Dfit_1 — subroutine - batch_gauss2Dfit_2 — subroutine - c_f_str_chars — subroutine - c_f_str_ptr — subroutine - c_int32_to_uint16 — function - c_int64_to_uint32 — function - c_uint16_to_int32 — function - c_uint32_to_int64 — function - calc_cartesian_corrmat_1 — subroutine - calc_cartesian_corrmat_2 — subroutine - calc_inpl_invariant_cc_nomirr — function - canny — subroutine - canny_edge — subroutine - check4nans2D_1 — subroutine - check4nans2D_2 — subroutine - check4nans3D_1 — subroutine - check4nans3D_2 — subroutine - check4nans_1 — subroutine - check4nans_2 — subroutine - cloneNode — function - cmlEndMolecule — subroutine - cmlStartMolecule — subroutine - copy_imgarr — function - copyDOMConfig — subroutine - createAttribute — function - createAttributeNS — function - createCdataSection — function - createComment — function - createDocument — function - createDocumentFragment — function - createDocumentType — function - createElement — function - createElementNS — function - createEmptyDocument — function - createEmptyEntityReference — function - createEntity — function - createEntityReference — function - createNamespaceNode — function - createNotation — function - createProcessingInstruction — function - createTextNode — function - dealloc_imgarr — subroutine - decode_rfc6901 — function - del_files_1 — subroutine - del_files_2 — subroutine - deleteData — subroutine - destroy_error_stack — subroutine - destroyAllNodesRecursively — subroutine - destroyDocument — subroutine - destroyNamedNodeMap — subroutine - destroyNodeList — subroutine - detect_peak_thres_1 — subroutine - detect_peak_thres_2 — subroutine - detect_peak_thres_fdr — subroutine - detect_peak_thres_for_npeaks — subroutine - detect_peak_thres_sortmeans — subroutine - dist_avg — function - dist_btw_farthest — function - dist_btw_nearest — function - double_thresh — subroutine - dumpnsdict — subroutine - encode_rfc6901 — function - escape_string — subroutine - extract_imgarr — function - f_c_str_chars — subroutine - f_readdir — function - f_strerror — function - fclose — subroutine - file2drarr — function - file2imat — subroutine - file2lmat — subroutine - file2rarr — function - file2rmat — subroutine - fileiochk — subroutine - filelength — function - filepath_1 — function - filepath_2 — function - filepath_3 — function - filepath_4 — function - find_larger_magic_box — function - find_magic_box — function - find_magic_boxes4scale — function - fname2ext — function - fname2format — function - fname_new_ext_1 — function - fname_new_ext_2 — function - fopen — subroutine - FoX_error_base — subroutine - FoX_fatal_base — subroutine - FoX_get_fatal_errors — function - FoX_get_fatal_warnings — function - FoX_set_fatal_errors — subroutine - FoX_set_fatal_warnings — subroutine - FoX_warning_base — subroutine - funit_size — function - gauss2Dfit — subroutine - get_fbody_1 — function - get_fbody_2 — function - get_fpath — function - get_open_funits — subroutine - get_relative_path — function - getAttribute — function - getAttributeNode — function - getAttributeNodeNS — function - getAttributeNS — function - getAttributes — function - getBaseURI — function - getchildNodes — function - getdata — function - getdocType — function - getdocumentElement — function - getdocumentURI — function - getdomConfig — function - getElementById — function - getElementsByTagName — function - getElementsByTagNameNS — function - getEntities — function - getEntityByIndex — function - getEntityByName — function - getfirstChild — function - getFoX_checks — function - getillFormed — function - getImplementation — function - getInputEncoding — function - getInternalSubset — function - getisElementContentWhitespace — function - getlastChild — function - getliveNodeLists — function - getLocalName — function - getname — function - getNamedItem — function - getNamedItemNS — function - getnamespaceNodes — function - getNamespaceURI — function - getnextSibling — function - getnodeName — function - getNodePath — function - getnodeType — function - getNodeValue — function - getnotationName — function - getNotations — function - getNumberOfPrefixes — function - getOwnerDocument — function - getownerElement — function - getParameter — function - getParameterNames — function - getparentNode — function - getPrefix — function - getPrefixByIndex — function - getpreviousSibling — function - getpublicId — function - getreadonly — function - getspecified — function - getstrictErrorChecking — function - getstringValue — function - getsystemId — function - gettagName — function - getTarget — function - getTextContent — function - getXds — function - getXmlEncoding — function - getxmlStandalone — function - getXmlVersion — function - hasAttribute — function - hasAttributeNS — function - hasAttributes — function - hasChildNodes — function - hasFeature — function - hough_line — subroutine - imat2file — subroutine - importNode — function - in_error — function - init_error_stack — subroutine - insertBefore — function - insertData — subroutine - integer_to_string — subroutine - is_even_2 — function - isDefaultNamespace — function - isDefaultNSInForce — function - isEqualNode — function - isPrefixInForce — function - isSameNode — function - isSupported — function - join_imgarrs — function - kmlAddLegend — subroutine - kmlCloseInnerBoundaryIs — subroutine - kmlCloseLinearRing — subroutine - kmlCloseLineString — subroutine - kmlCloseouterBoundaryIs — subroutine - kmlClosePolygon — subroutine - kmlCloseStyle — subroutine - kmlCreateLineStyle — subroutine - kmlCreatePolygonStyle — subroutine - kmlEndRegion — subroutine - kmlGetColorHex — function - kmlMakeColorMap — function - kmlOpenInnerBoundaryIs — subroutine - kmlOpenLinearRing — subroutine - kmlOpenLineString — subroutine - kmlOpenOuterBoundaryIs — subroutine - kmlOpenPolygon — subroutine - kmlOpenStyle — subroutine - kmlSetCustomColor — subroutine - lmat2file — subroutine - lookupNamespaceURI — function - lookupPrefix — function - lowercase_string — function - make_dirnames — function - make_filenames — function - move_files2dir — subroutine - move_files_in_cwd — subroutine - namespaceFixup — subroutine - newDOMConfig — function - nlines — function - non_max_supp — subroutine - normalize — subroutine - normalizeDocument — subroutine - otsu_img — subroutine - otsu_robust_fast — subroutine - pack_imgarr — function - pop_nl — function - print_magic_box_range — subroutine - read_cavgs_into_imgarr — function - read_exit_code — subroutine - read_filetable — subroutine - read_stk_into_imgarr — function - real_to_string — subroutine - refine_peak_thres_sortmeans — subroutine - remove_nl — function - removeAttribute — subroutine - removeAttributeNode — function - removeAttributeNodeNS — function - removeAttributeNS — subroutine - removeChild — function - removeDefaultNS — subroutine - removeNamedItem — function - removeNamedItemNS — function - removePrefixedNS — subroutine - renameNode — function - replace_string — subroutine - replaceChild — function - replaceData — subroutine - rm_from_fbody — function - rmat2file — subroutine - sauvola — subroutine - setAttribute — subroutine - setAttributeNode — function - setAttributeNodeNS — function - setAttributeNS — subroutine - setData — subroutine - setDocType — subroutine - setDocumentElement — subroutine - setdocumentURI — subroutine - setdomConfig — subroutine - setFoX_checks — subroutine - setGCstate — subroutine - setIdAttribute — subroutine - setIdAttributeNode — subroutine - setIdAttributeNS — subroutine - setillFormed — subroutine - setIsElementContentWhitespace — subroutine - setliveNodeLists — subroutine - setNamedItem — function - setNamedItemNS — function - setNodeValue — subroutine - setParameter — subroutine - setPrefix — subroutine - setReadOnlyMap — subroutine - setReadOnlyNode — subroutine - setspecified — subroutine - setstrictErrorChecking — subroutine - setstringValue — subroutine - setTextContent — subroutine - setValue — subroutine - setXds — subroutine - setxmlStandalone — subroutine - setXmlVersion — subroutine - simple_copy_file — subroutine - sobel — subroutine - splitText — function - stemname — function - str_to_int_10 — function - str_to_int_16 — function - str_vs — function - string — type - string_to_integer — subroutine - string_to_real — subroutine - subStringData — function - swap_suffix_1 — function - swap_suffix_2 — function - threshold_for_no_peaks — subroutine - threshold_for_npeaks — subroutine - unescape_string — subroutine - valid_json_hex — function - vs_str — function - vs_str_alloc — function - vs_vs_alloc — function - wait_for_closure — subroutine - write_filetable — subroutine - write_imgarr_1 — subroutine - write_imgarr_2 — subroutine - write_imgarr_3 — subroutine - write_junk_cavgs — subroutine - write_selected_cavgs — subroutine - write_singlelineoftext — subroutine

Private symbols: - add2history_1 — subroutine - add2history_2 — subroutine - add2watchdirs — subroutine - add_attribute — function - add_element — function - add_entity — subroutine - add_eol — subroutine - add_external_entity — subroutine - add_internal_entity — subroutine - add_item_to_dict — subroutine - add_string — subroutine - add_to_buffer — subroutine - add_to_path — subroutine - add_to_stream_stack — subroutine - add_to_streaming — subroutine - addBondArray — subroutine - addcoords_x3_dp — subroutine - addcoords_x3_sp — subroutine - addcoords_xfrac_dp — subroutine - addcoords_xfrac_sp — subroutine - addcoords_xyz3_dp — subroutine - addcoords_xyz3_sp — subroutine - addcoords_xyzfrac_dp — subroutine - addcoords_xyzfrac_sp — subroutine - addDlpolyMatrix_3_dp — subroutine - addDlpolyMatrix_3_sp — subroutine - addDlpolyMatrix_dp — subroutine - addDlpolyMatrix_sp — subroutine - addPrefix — subroutine - addPrefixedURI — subroutine - alloc_chash — subroutine - alloc_hash — subroutine - alloc_str — type - analyze_smat — subroutine - ang2vox — function - angle_sampling_1 — function - angle_sampling_2 — function - annotate_invalid_json — subroutine - apod — function - apod_fast — function - apod_fast_device — function - apod_kb15_a2 — function - apod_mat_2d — subroutine - apod_mat_2d_fast — subroutine - apod_mat_3d — subroutine - apod_mat_3d_fast — subroutine - append — function - append_candidate — subroutine - append_limited_char — subroutine - append_nl — subroutine - append_nnm — subroutine - append_or_replace_candidate — subroutine - append_ori — subroutine - append_text — subroutine - appendNSNode — subroutine - apply2all — subroutine - apply_1 — subroutine - apply_2 — subroutine - apply_convention — subroutine - apply_refine3D_search_overrides — subroutine - apply_sym_with_shift — subroutine - arg — function - arpack_stop — subroutine - arraytocomplexdp — subroutine - arraytocomplexsp — subroutine - arraytointeger — subroutine - arraytological — subroutine - arraytorealdp — subroutine - arraytorealsp — subroutine - arraytostring — subroutine - assign — subroutine - att_value_normalize — function - att_value_normalize_len — function - attribute_has_default — function - AttributeArrayCh — subroutine - AttributeArrayCmplxDp — subroutine - AttributeArrayCmplxSp — subroutine - AttributeArrayInt — subroutine - AttributeArrayLg — subroutine - AttributeArrayRealDp — subroutine - AttributeArrayRealSp — subroutine - attributeDecl_handler — subroutine - AttributeMatrixCh — subroutine - AttributeMatrixCmplxDp — subroutine - AttributeMatrixCmplxSp — subroutine - AttributeMatrixInt — subroutine - AttributeMatrixLg — subroutine - AttributeMatrixRealDp — subroutine - AttributeMatrixRealSp — subroutine - AttributeScalarCmplxDp — subroutine - AttributeScalarCmplxSp — subroutine - AttributeScalarInt — subroutine - AttributeScalarLg — subroutine - AttributeScalarRealDp — subroutine - AttributeScalarRealSp — subroutine - augment_partition_job_descr — subroutine - avg_frac_smallest — function - avg_sdev_1 — subroutine - avg_sdev_2 — subroutine - avg_sdev_3 — subroutine - avg_sdev_4 — subroutine - balanced — subroutine - bessi0 — function - bman_apod — function - bman_instr — function - bounds_from_mask3D — subroutine - buffer_length — function - buffer_to_chararray — function - buffer_to_str — function - build_eullims — subroutine - build_pind_lookup — subroutine - build_refine3D_stage_cfg — subroutine - build_refspiral — subroutine - butterworth — function - butterworth_filter_1 — subroutine - butterworth_filter_2 — subroutine - butterworth_filter_3 — subroutine - butterworth_filter_4 — subroutine - butterworth_filter_5 — subroutine - calc_ap_pref — function - calc_athres — function - calc_graphene_mask — function - calc_num2sample — subroutine - calc_offset2D — subroutine - calc_score_thres — function - calc_stats — subroutine - canSetParameter_ch — function - canSetParameter_log — function - cast_str_types — function - char2str — function - CharactersArrayCh — subroutine - CharactersArrayCmplxDp — subroutine - CharactersArrayCmplxSp — subroutine - CharactersArrayInt — subroutine - CharactersArrayLg — subroutine - CharactersArrayRealDp — subroutine - CharactersArrayRealSp — subroutine - CharactersMatrixCh — subroutine - CharactersMatrixCmplxDp — subroutine - CharactersMatrixCmplxSp — subroutine - CharactersMatrixInt — subroutine - CharactersMatrixLg — subroutine - CharactersMatrixRealDp — subroutine - CharactersMatrixRealSp — subroutine - CharactersScalarCmplxDp — subroutine - CharactersScalarCmplxSp — subroutine - CharactersScalarInt — subroutine - CharactersScalarLg — subroutine - CharactersScalarRealDp — subroutine - CharactersScalarRealSp — subroutine - chash2ori — subroutine - chash2str — function - check_buffer — subroutine - check_duplicates — function - check_if_valid — subroutine - check_xf — subroutine - checkBondIdRefs — subroutine - checkColorHex — function - checkContentModel — function - checkContentModelToEnd — function - checkEndNamespaces — subroutine - checkExistingRefs — function - checkExistingRefsInAttValue — function - checkFmt — function - checkNamespaces — subroutine - checkNamespacesWriting — subroutine - checkParsedRefsInAttValue — function - clear_history — subroutine - clear_partition_job_descr — subroutine - clear_stack — subroutine - close_start_tag — subroutine - cmlAddAngle_dp — subroutine - cmlAddAngle_sp — subroutine - cmlAddAtoms_3_dp — subroutine - cmlAddAtoms_3_dp_sh — subroutine - cmlAddAtoms_3_sp — subroutine - cmlAddAtoms_3_sp_sh — subroutine - cmlAddAtomsdp — subroutine - cmlAddAtomsdp_sh — subroutine - cmlAddAtomssp — subroutine - cmlAddAtomssp_sh — subroutine - cmlAddBandListdp — subroutine - cmlAddBandListsp — subroutine - cmlAddCoords_dp — subroutine - cmlAddCoords_sp — subroutine - cmlAddCrystaldp — subroutine - cmlAddCrystalsp — subroutine - cmlAddEigenValuedp — subroutine - cmlAddEigenValuesp — subroutine - cmlAddEigenValueVectorCmplxdp — subroutine - cmlAddEigenValueVectorCmplxsp — subroutine - cmlAddEigenValueVectordp — subroutine - cmlAddEigenValueVectorsp — subroutine - cmlAddKPointdp — subroutine - cmlAddKPointsp — subroutine - cmlAddLatticedp — subroutine - cmlAddLatticesp — subroutine - cmlAddLength_dp — subroutine - cmlAddLength_sp — subroutine - cmlAddMolecule_3_dp — subroutine - cmlAddMolecule_3_dp_sh — subroutine - cmlAddMolecule_3_sp — subroutine - cmlAddMolecule_3_sp_sh — subroutine - cmlAddMoleculedp — subroutine - cmlAddMoleculedp_sh — subroutine - cmlAddMoleculesp — subroutine - cmlAddMoleculesp_sh — subroutine - cmlAddParticles_3_dp — subroutine - cmlAddParticles_3_dp_sh — subroutine - cmlAddParticles_3_sp — subroutine - cmlAddParticles_3_sp_sh — subroutine - cmlAddParticlesdp — subroutine - cmlAddParticlesdp_sh — subroutine - cmlAddParticlessp — subroutine - cmlAddParticlessp_sh — subroutine - cmlAddSymmetrydp — subroutine - cmlAddSymmetryNoOps — subroutine - cmlAddSymmetrysp — subroutine - cmlAddTorsion_dp — subroutine - cmlAddTorsion_sp — subroutine - cmlEndBand — subroutine - cmlEndKpoint — subroutine - cmlStartBand — subroutine - cmlStartKPointdp — subroutine - cmlStartKPointsp — subroutine - cnt_recs_per_line — function - comp_addr_logi — function - comp_addr_phys1 — function - comp_addr_phys2 — function - comp_addr_phys3 — function - comp_addr_phys_orig — function - compact — subroutine - compact_real_string — subroutine - compeuler — subroutine - compose2dshift3d — subroutine - compose3d2d — subroutine - concat_complex_dp_str — function - concat_complex_sp_str — function - concat_int_str — function - concat_logical_str — function - concat_real_dp_str — function - concat_real_sp_str — function - concat_str_complex_dp — function - concat_str_complex_sp — function - concat_str_int — function - concat_str_logical — function - concat_str_real_dp — function - concat_str_real_sp — function - constructor — function - constructor — function - constructor — function - constructor — function - constructor — function - constructor — function - constructor — function - constructor — function - constructor — function - constructor — function - constructor_1 — function - constructor_1 — function - constructor_2 — function - constructor_2 — function - conv2rank_weights — subroutine - convert — subroutine - copy — subroutine - copy — subroutine - copy — subroutine - copy — subroutine - copyURIMapping — subroutine - corrs2weights — function - cosedge_1 — function - cosedge_2 — function - cosedge_inner_1 — function - cosedge_inner_2 — function - cosedge_r2_2d — function - cosedge_r2_3d — function - countcomplexdp — function - countcomplexsp — function - countinteger — function - countlogical — function - countrealdp — function - countrealsp — function - countstring — function - create_hist_vector — subroutine - createEmptyElement — function - createEmptyElementNS — function - createNode — function - cross — function - csq_1 — function - csq_2 — function - csv_field — function - curl_easy_escape — function - curl_easy_getinfo_char — function - curl_easy_getinfo_double — function - curl_easy_getinfo_int — function - curl_easy_getinfo_long — function - curl_easy_getinfo_ptr — function - curl_easy_setopt_char — function - curl_easy_setopt_funptr — function - curl_easy_setopt_int — function - curl_easy_setopt_long — function - curl_easy_setopt_ptr — function - curl_easy_strerror — function - curl_easy_unescape — function - curl_escape — function - curl_global_init — function - curl_mime_encoder — function - curl_mime_filedata — function - curl_mime_filename — function - curl_mime_name — function - curl_mime_type — function - curl_slist_append — function - curl_unescape — function - curl_version — function - curl_version_info — function - cyci_1d — function - cyci_1d_static — function - dble2str — function - dealloc_chash — subroutine - dealloc_hash — subroutine - declare_coarray_jobs_finished — subroutine - declared_element — function - default_comp_ucs4 — function - default_join_ucs4 — function - default_neq_ucs4 — function - deg2rad_dp — function - deg2rad_sp — function - delete — subroutine - delete — subroutine - delete_2Dclustering — subroutine - delete_3Dalignment — subroutine - delete_entry — subroutine - destroy_attribute_list — subroutine - destroy_attribute_t — subroutine - destroy_dict — subroutine - destroy_dict_item — subroutine - destroy_element_list — subroutine - destroy_elstack — subroutine - destroy_entity — subroutine - destroy_entity_list — subroutine - destroy_json_core — subroutine - destroy_json_data — subroutine - destroy_string_list — subroutine - destroy_vs — subroutine - destroyDocumentType — subroutine - destroyDOMConfig — subroutine - destroyElementOrAttribute — subroutine - destroyEntityOrNotation — subroutine - destroyNamespaceDictionary — subroutine - destroyNode — subroutine - destroyNodeContents — subroutine - detect_and_add_dirs — subroutine - dgelss — subroutine - dgelsy — subroutine - dgesvd — subroutine - dgetrf — subroutine - dgetri — subroutine - discrete_read_imgbatch — subroutine - discrete_read_imgbatch_source — subroutine - dispatch_task_to_persistent_worker — subroutine - dist_eval_fun — function - dists2order — function - dists2scores_percen — subroutine - dmat2smat — function - dnrm2 — function - dposv — subroutine - dsyev — subroutine - dump_buffer — subroutine - duplicate_key_func — subroutine - dynfind — function - e1get — function - e1set — subroutine - e2get — function - e2set — subroutine - e3get — function - e3set — subroutine - eigh_sp — subroutine - eigsrt_dp — subroutine - eigsrt_sp — subroutine - elementContent — function - elim_dup — subroutine - ellipse — subroutine - emit_refine3D_stage_cfg — subroutine - emptyContent — function - end_prefix_handler — subroutine - end_prefix_handler — subroutine - ensure_capacity — subroutine - equispaced_vals — function - estimate_lplim3D — subroutine - estimate_lplim_1 — subroutine - estimate_lplim_2 — subroutine - estimate_lplims2D — subroutine - euclid_dp — function - euclid_sp_1 — function - euclid_sp_2 — function - euldist — function - eulprob_corr_switch — function - eulprob_dist_switch — function - eval_apod — function - eval_instr — function - existing_attribute — function - existing_element — function - existing_entity — function - exists — function - expand_char_entity — function - expand_char_entity_len — function - expand_entity — function - expand_entity_len — function - expand_entity_text — function - expand_entity_text_len — function - express_att_decl_len — function - express_attribute_declaration — function - extractDataAttNSChArr — subroutine - extractDataAttNSChMat — subroutine - extractDataAttNSChSca — subroutine - extractDataAttNSCmplxDpArr — subroutine - extractDataAttNSCmplxDpMat — subroutine - extractDataAttNSCmplxDpSca — subroutine - extractDataAttNSCmplxSpArr — subroutine - extractDataAttNSCmplxSpMat — subroutine - extractDataAttNSCmplxSpSca — subroutine - extractDataAttNSIntArr — subroutine - extractDataAttNSIntMat — subroutine - extractDataAttNSIntSca — subroutine - extractDataAttNSLgArr — subroutine - extractDataAttNSLgMat — subroutine - extractDataAttNSLgSca — subroutine - extractDataAttNSRealDpArr — subroutine - extractDataAttNSRealDpMat — subroutine - extractDataAttNSRealDpSca — subroutine - extractDataAttNSRealSpArr — subroutine - extractDataAttNSRealSpMat — subroutine - extractDataAttNSRealSpSca — subroutine - extractDataAttributeChArr — subroutine - extractDataAttributeChMat — subroutine - extractDataAttributeChSca — subroutine - extractDataAttributeCmplxDpArr — subroutine - extractDataAttributeCmplxDpMat — subroutine - extractDataAttributeCmplxDpSca — subroutine - extractDataAttributeCmplxSpArr — subroutine - extractDataAttributeCmplxSpMat — subroutine - extractDataAttributeCmplxSpSca — subroutine - extractDataAttributeIntArr — subroutine - extractDataAttributeIntMat — subroutine - extractDataAttributeIntSca — subroutine - extractDataAttributeLgArr — subroutine - extractDataAttributeLgMat — subroutine - extractDataAttributeLgSca — subroutine - extractDataAttributeRealDpArr — subroutine - extractDataAttributeRealDpMat — subroutine - extractDataAttributeRealDpSca — subroutine - extractDataAttributeRealSpArr — subroutine - extractDataAttributeRealSpMat — subroutine - extractDataAttributeRealSpSca — subroutine - extractDataContentChArr — subroutine - extractDataContentChMat — subroutine - extractDataContentChSca — subroutine - extractDataContentCmplxDpArr — subroutine - extractDataContentCmplxDpMat — subroutine - extractDataContentCmplxDpSca — subroutine - extractDataContentCmplxSpArr — subroutine - extractDataContentCmplxSpMat — subroutine - extractDataContentCmplxSpSca — subroutine - extractDataContentIntArr — subroutine - extractDataContentIntMat — subroutine - extractDataContentIntSca — subroutine - extractDataContentLgArr — subroutine - extractDataContentLgMat — subroutine - extractDataContentLgSca — subroutine - extractDataContentRealDpArr — subroutine - extractDataContentRealDpMat — subroutine - extractDataContentRealDpSca — subroutine - extractDataContentRealSpArr — subroutine - extractDataContentRealSpMat — subroutine - extractDataContentRealSpSca — subroutine - fdim — function - find_1 — subroutine - find_2 — subroutine - find_closest_proj — function - find_medoids — subroutine - findloc_str_1 — function - findloc_str_2 — function - fit_lsq_plane — subroutine - fit_straight_line — subroutine - fmtsymstr — function - fortran_logical — function - fortran_quote — function - fortran_symbol_from_string — function - FoX_error — subroutine - fplane_get_cmplx — function - fplane_get_ctfsq — function - free_all_cunits — subroutine - funcs — function - funcs — function - funcs — function - funcs — function - gasdev_2 — function - gasdev_3 — function - gau_rnd_shift — subroutine - gauwfun — function - gcd — function - gen_c1 — subroutine - gen_job_descr — subroutine - generate_array_script — subroutine - generate_script_1 — subroutine - generate_script_2 — subroutine - generate_script_3 — subroutine - generate_script_4 — subroutine - generate_scripts_subprojects — subroutine - geodesic_dist_trace — function - get_1 — function - get_2 — function - get_2Dshift — function - get_3Dshift — function - get_all_subgrps_descr — function - get_att_index_pointer — subroutine - get_att_type_enum — function - get_attdecl_by_index — function - get_attdecl_by_name — function - get_attlist_size — function - get_attribute — function - get_axis_angle — subroutine - get_chars_from_array — subroutine - get_chars_from_array — subroutine - get_ctfvars — function - get_ctfvars — function - get_current_line_from_file_sequential — subroutine - get_current_line_from_file_stream — subroutine - get_double_from_array — subroutine - get_element — function - get_euler — function - get_eullims — function - get_find — function - get_find_at_crit — function - get_find_at_res — function - get_int_from_array — subroutine - get_jobs_status — subroutine - get_json_core_in_file — subroutine - get_key — function - get_key — function - get_key — function - get_key_index — function - get_key_index_ns — function - get_key_len — function - get_keys — function - get_keys — function - get_last_string — function - get_ldim — function - get_lfny — function - get_lhp — function - get_llp — function - get_localName_by_index — function - get_localName_by_keyname — function - get_localname_by_keyname_len — function - get_logical_from_array — subroutine - get_lp — function - get_mat — function - get_normal — function - get_nsubgrp — function - get_nsURI_by_index — function - get_nsURI_by_keyname — function - get_nsURI_by_keyname_len — function - get_pgrp — function - get_pixel_pos — subroutine - get_prefix_by_index — function - get_prefix_by_keyname — function - get_prefix_by_keyname_len — function - get_resarr — function - get_spat_freq — function - get_static — subroutine - get_static — subroutine - get_str — function - get_stream_done_stack — subroutine - get_stream_fail_stack — subroutine - get_string_lengths — subroutine - get_subgrp — function - get_subgrp_descr — function - get_sym_rmat — subroutine - get_symori — subroutine - get_top_elstack — function - get_value_by_index — function - get_value_by_index_len — function - get_value_by_key — function - get_value_by_key_len — function - get_value_by_key_ns — function - get_value_by_key_ns_len — function - get_Whalf — function - getAttribute_len — function - getAttributesNS_len — function - getBase — function - getBase_len — function - getdata_len — function - getdocumentURI_len — function - getEntityNameByIndex — function - getevensym — subroutine - getGCstate — function - getInputEncoding_len — function - getInternalSubset_len — function - getIsId_by_index — function - getisId_DOM — function - getLength — function - getLength_characterdata — function - getLength_nl — function - getLength_nnm — function - getLocalName_len — function - getname_len — function - getNamespaceURI_len — function - getnodeName_len — function - getNodeValue_len — function - getnotationName_len — function - getPrefix_len — function - getPrefixIndex — function - getpublicId_len — function - getstringValue_len — function - getsystemId_len — function - gettagName_len — function - getTarget_len — function - getter_1 — subroutine - getter_1 — subroutine - getter_2 — subroutine - getter_2 — subroutine - getter_3 — subroutine - getter_3 — subroutine - getTextContent_len — function - getType_by_index — function - getType_by_index_len — function - getType_by_keyname — function - getType_by_keyname_len — function - getURIofDefaultNS — function - getURIofPrefixedNS — function - getValue_DOM — function - getWhitespaceHandling — function - getXmlEncoding_len — function - getXmlVersionEnum — function - great_circle_samples — function - greedy_sampling_1 — function - greedy_sampling_2 — function - hac_1d — subroutine - hac_1d_fast — subroutine - hac_med_thres — subroutine - haloween_end — subroutine - hann_apod — function - hann_instr — function - hardedge_1 — function - hardedge_2 — function - hardedge_3 — function - hardedge_4 — function - hardedge_inner_1 — function - hardedge_inner_2 — function - hardedge_inner_3 — function - hardedge_inner_4 — function - hardedge_r2_2d — function - hardedge_r2_3d — function - has_key — function - has_key_ns — function - has_subgrp — function - hash2str — function - hermitian_eigh_z — subroutine - hermitian_invert_dp — subroutine - hermitian_invert_z — subroutine - hermitian_solve_dp — subroutine - hermitian_solve_z — subroutine - hist — subroutine - hpsort_1 — subroutine - hpsort_2 — subroutine - hpsort_3 — subroutine - hpsort_4 — subroutine - hpsort_5 — subroutine - hpsort_6 — subroutine - image_1 — subroutine - image_2 — subroutine - image_3 — subroutine - image_4 — subroutine - image_5 — subroutine - image_6 — subroutine - image_stack — type - init — subroutine - init_attribute_list — subroutine - init_dict — subroutine - init_element_list — subroutine - init_elstack — subroutine - init_entity_list — subroutine - init_refine3D_iteration — subroutine - init_string_list — subroutine - initialize_json_core — function - initialize_json_core_in_file — subroutine - initialize_json_file — function - initialize_json_file_v2 — function - initNamespaceDictionary — subroutine - inplrotdist — function - insert — subroutine - instr — function - int2str — function - int2str — function - int2str_pad — function - irnd — function - irnd_gasdev — function - irnd_gau — function - irnd_pair — subroutine - irnd_uni — function - irnd_uni_pair — function - is — function - is_child_of_callback — subroutine - is_empty_elstack — function - is_external_entity — function - is_particle — function - is_unparsed_entity_ — function - is_unparsed_entity_from_list — function - isCharData — function - isDeclared_by_index — function - isDeclared_by_key — function - isDeclared_by_keyNS — function - isSpecified_by_index — function - isSpecified_by_key — function - isSpecified_by_keyNS — function - isthere — function - isthere — function - item_nl — function - item_nnm — function - jacobi_dp — subroutine - jacobi_sp — subroutine - json_add_double_by_path — subroutine - json_add_double_vec_by_path — subroutine - json_add_integer_by_path — subroutine - json_add_integer_vec_by_path — subroutine - json_add_logical_by_path — subroutine - json_add_logical_vec_by_path — subroutine - json_add_member_by_path — subroutine - json_add_string_by_path — subroutine - json_add_string_by_path_path_ascii — subroutine - json_add_string_by_path_value_ascii — subroutine - json_add_string_vec_by_path — subroutine - json_add_string_vec_by_path_path_ascii — subroutine - json_add_string_vec_by_path_value_ascii — subroutine - json_array_callback_func — subroutine - json_check_all_for_duplicate_keys — subroutine - json_check_children_for_duplicate_keys — subroutine - json_check_for_errors — subroutine - json_clear_exceptions — subroutine - json_clone — subroutine - json_count — function - json_create_by_path — subroutine - json_failed — function - json_file_add_double — subroutine - json_file_add_double_vec — subroutine - json_file_add_integer — subroutine - json_file_add_integer_vec — subroutine - json_file_add_logical — subroutine - json_file_add_logical_vec — subroutine - json_file_add_object — subroutine - json_file_add_string — subroutine - json_file_add_string_path_ascii — subroutine - json_file_add_string_value_ascii — subroutine - json_file_add_string_vec — subroutine - json_file_add_string_vec_path_ascii — subroutine - json_file_add_string_vec_vec_ascii — subroutine - json_file_check_for_errors — subroutine - json_file_clear_exceptions — subroutine - json_file_destroy — subroutine - json_file_failed — function - json_file_get_alloc_string_vec — subroutine - json_file_get_double — subroutine - json_file_get_double_vec — subroutine - json_file_get_integer — subroutine - json_file_get_integer_vec — subroutine - json_file_get_logical — subroutine - json_file_get_logical_vec — subroutine - json_file_get_object — subroutine - json_file_get_root — subroutine - json_file_get_string — subroutine - json_file_get_string_vec — subroutine - json_file_load — subroutine - json_file_load_from_string — subroutine - json_file_move_pointer — subroutine - json_file_print_1 — subroutine - json_file_print_2 — subroutine - json_file_print_error_message — subroutine - json_file_print_to_console — subroutine - json_file_print_to_string — subroutine - json_file_remove — subroutine - json_file_rename — subroutine - json_file_rename_name_ascii — subroutine - json_file_rename_path_ascii — subroutine - json_file_traverse — subroutine - json_file_update_integer — subroutine - json_file_update_logical — subroutine - json_file_update_real — subroutine - json_file_update_string — subroutine - json_file_update_string_name_ascii — subroutine - json_file_update_string_val_ascii — subroutine - json_file_valid_path — function - json_file_valid_path_op — function - json_file_variable_info — subroutine - json_file_variable_matrix_info — subroutine - json_get_alloc_string_vec — subroutine - json_get_alloc_string_vec_by_path — subroutine - json_get_array — subroutine - json_get_array_by_path — subroutine - json_get_by_path — subroutine - json_get_by_path_default — subroutine - json_get_by_path_jsonpath_bracket — subroutine - json_get_by_path_rfc6901 — subroutine - json_get_double — subroutine - json_get_double_by_path — subroutine - json_get_double_vec — subroutine - json_get_double_vec_by_path — subroutine - json_get_integer — subroutine - json_get_integer_by_path — subroutine - json_get_integer_vec — subroutine - json_get_integer_vec_by_path — subroutine - json_get_logical — subroutine - json_get_logical_by_path — subroutine - json_get_logical_vec — subroutine - json_get_logical_vec_by_path — subroutine - json_get_next — subroutine - json_get_parent — subroutine - json_get_path — subroutine - json_get_previous — subroutine - json_get_string — subroutine - json_get_string_by_path — subroutine - json_get_string_vec — subroutine - json_get_string_vec_by_path — subroutine - json_get_tail — subroutine - json_info — subroutine - json_info_by_path — subroutine - json_initialize — subroutine - json_matrix_info — subroutine - json_matrix_info_by_path — subroutine - json_parse_file — subroutine - json_parse_string — subroutine - json_print_error_message — subroutine - json_print_to_filename — subroutine - json_print_to_unit — subroutine - json_print_value_fast — subroutine - json_print_value_fast_impl — subroutine - json_rename_by_path — subroutine - json_rename_by_path_name_ascii — subroutine - json_rename_by_path_path_ascii — subroutine - json_string_info — subroutine - json_throw_exception — subroutine - json_traverse — subroutine - json_traverse_callback_func — subroutine - json_update_double — subroutine - json_update_integer — subroutine - json_update_logical — subroutine - json_update_string — subroutine - json_update_string_name_ascii — subroutine - json_update_string_val_ascii — subroutine - json_valid_path — function - json_value_add_double — subroutine - json_value_add_double_vec — subroutine - json_value_add_integer — subroutine - json_value_add_integer_vec — subroutine - json_value_add_logical — subroutine - json_value_add_logical_vec — subroutine - json_value_add_member — subroutine - json_value_add_null — subroutine - json_value_add_string — subroutine - json_value_add_string_name_ascii — subroutine - json_value_add_string_val_ascii — subroutine - json_value_add_string_vec — subroutine - json_value_add_string_vec_name_ascii — subroutine - json_value_add_string_vec_val_ascii — subroutine - json_value_clone_func — subroutine - json_value_create — subroutine - json_value_create_array — subroutine - json_value_create_double — subroutine - json_value_create_integer — subroutine - json_value_create_logical — subroutine - json_value_create_null — subroutine - json_value_create_object — subroutine - json_value_create_string — subroutine - json_value_destroy — subroutine - json_value_get_child — subroutine - json_value_get_child_by_index — subroutine - json_value_get_child_by_name — subroutine - json_value_insert_after — subroutine - json_value_insert_after_child_by_index — subroutine - json_value_is_child_of — function - json_value_print — subroutine - json_value_remove — subroutine - json_value_remove_if_present — subroutine - json_value_rename — subroutine - json_value_replace — subroutine - json_value_reverse — subroutine - json_value_swap — subroutine - json_value_to_string — subroutine - json_value_to_string_fast — subroutine - json_value_validate — subroutine - kb_apod — function - kb_instr — function - kill — subroutine - kill — subroutine - kill — subroutine - kill — subroutine - kill — subroutine - kill — subroutine - kill — subroutine - kill — subroutine - kill_candidate_buffer — subroutine - kill_candidate_store — subroutine - kill_chash — subroutine - kill_hash — subroutine - killimgbatch — subroutine - kmlAddaddress — subroutine - kmlAddaltitude — subroutine - kmlAddaltitudeMode — subroutine - kmlAddBalloonStyle — subroutine - kmlAddbegin — subroutine - kmlAddBgColor_c — subroutine - kmlAddBgColor_h — subroutine - kmlAddChart_dp — subroutine - kmlAddChart_sp — subroutine - kmlAddColor_c — subroutine - kmlAddColor_h — subroutine - kmlAddcolorMode — subroutine - kmlAddcookie — subroutine - kmlAddCoordinates_array_dp — subroutine - kmlAddCoordinates_array_sp — subroutine - kmlAddcoordinates_dp — subroutine - kmlAddcoordinates_sp — subroutine - kmlAdddescription_ch — subroutine - kmlAdddescription_dp — subroutine - kmlAdddescription_sp — subroutine - kmlAdddrawOrder — subroutine - kmlAddeast — subroutine - kmlAddend — subroutine - kmlAddextrude — subroutine - kmlAddfill — subroutine - kmlAddflyToView — subroutine - kmlAddheading — subroutine - kmlAddhref — subroutine - kmlAddIcon_href — subroutine - kmlAddIcon_refresh — subroutine - kmlAddIcon_view — subroutine - kmlAddInnerBoundary_1d_dp — subroutine - kmlAddInnerBoundary_1d_sp — subroutine - kmlAddInnerBoundary_2d_dp — subroutine - kmlAddInnerBoundary_2d_sp — subroutine - kmlAddkey — subroutine - kmlAddLabelStyle_color — subroutine - kmlAddLabelStyle_scale — subroutine - kmlAddlatitude_dp — subroutine - kmlAddlatitude_sp — subroutine - kmlAddLineStyle — subroutine - kmlAddlinkDescription — subroutine - kmlAddlinkName — subroutine - kmlAddlistItemType — subroutine - kmlAddListStyle_bgcolor — subroutine - kmlAddlongitude_dp — subroutine - kmlAddlongitude_sp — subroutine - kmlAddmaxAltitude — subroutine - kmlAddmaxFadeExtent — subroutine - kmlAddmaxLodPixels — subroutine - kmlAddmessage — subroutine - kmlAddminAltitude — subroutine - kmlAddminFadeExtent — subroutine - kmlAddminLodPixels — subroutine - kmlAddminRefreshPeriod — subroutine - kmlAddname — subroutine - kmlAddNamespace — subroutine - kmlAddnorth — subroutine - kmlAddopen — subroutine - kmlAddoutline — subroutine - kmlAddphoneNumber — subroutine - kmlAddPoint_dp — subroutine - kmlAddPoint_sp — subroutine - kmlAddPointStyle_s_dp — subroutine - kmlAddPointStyle_s_int — subroutine - kmlAddPointStyle_s_none_hd_dp — subroutine - kmlAddPointStyle_s_none_hd_int — subroutine - kmlAddPointStyle_s_none_hd_none — subroutine - kmlAddPointStyle_s_none_hd_sp — subroutine - kmlAddPointStyle_s_sp — subroutine - kmlAddrange — subroutine - kmlAddrefreshInterval — subroutine - kmlAddrefreshMode — subroutine - kmlAddrefreshVisibility — subroutine - kmlAddrequest — subroutine - kmlAddroll — subroutine - kmlAddrotation — subroutine - kmlAddScale_dp — subroutine - kmlAddScale_int — subroutine - kmlAddScale_sp — subroutine - kmlAddsouth — subroutine - kmlAddstate — subroutine - kmlAddstyleUrl — subroutine - kmlAddtargetHref — subroutine - kmlAddtessellate — subroutine - kmlAddTextColor_c — subroutine - kmlAddTextColor_h — subroutine - kmlAddtilt — subroutine - kmlAddviewBoundScale — subroutine - kmlAddviewrefreshMode — subroutine - kmlAddviewRefreshTime — subroutine - kmlAddvisibility — subroutine - kmlAddwest — subroutine - kmlAddwhen — subroutine - kmlAddwidth — subroutine - kmlCloseAddressDetail — subroutine - kmlCloseBalloonStyle — subroutine - kmlCloseChange — subroutine - kmlCloseColorStyle — subroutine - kmlCloseContainer — subroutine - kmlClosecoordinates — subroutine - kmlCloseCreate — subroutine - kmlCloseDelete — subroutine - kmlCloseDocument — subroutine - kmlCloseFeature — subroutine - kmlCloseFolder — subroutine - kmlCloseGeometry — subroutine - kmlCloseGeometryCollection — subroutine - kmlCloseGroundOverlay — subroutine - kmlCloseIcon — subroutine - kmlCloseIconStyle — subroutine - kmlCloseItemIcon — subroutine - kmlCloseLabelStyle — subroutine - kmlCloseLatLonAltBox — subroutine - kmlCloseLatLonBox — subroutine - kmlCloseLineStyle — subroutine - kmlCloseLink — subroutine - kmlCloseListStyle — subroutine - kmlCloseLocation — subroutine - kmlCloseLod — subroutine - kmlCloseLookAt — subroutine - kmlCloseModel — subroutine - kmlCloseMultiGeometry — subroutine - kmlCloseNetworkLink — subroutine - kmlCloseNetworkLinkControl — subroutine - kmlCloseObjArrayField — subroutine - kmlCloseObject — subroutine - kmlCloseObjField — subroutine - kmlCloseOrientation — subroutine - kmlCloseOverlay — subroutine - kmlClosePair — subroutine - kmlClosePlacemark — subroutine - kmlClosePoint — subroutine - kmlClosePolyStyle — subroutine - kmlCloseRegion — subroutine - kmlCloseResponse — subroutine - kmlCloseScale — subroutine - kmlCloseSchema — subroutine - kmlCloseSchemaField — subroutine - kmlCloseScreenOverlay — subroutine - kmlCloseSimpleArrayField — subroutine - kmlCloseSimpleField — subroutine - kmlCloseSnippet — subroutine - kmlCloseStatus — subroutine - kmlCloseStyleMap — subroutine - kmlCloseStyleSelector — subroutine - kmlCloseTimePrimitive — subroutine - kmlCloseTimeSpan — subroutine - kmlCloseTimeStamp — subroutine - kmlCloseUpdate — subroutine - kmlCloseUrl — subroutine - kmlcreateCells3_dp — subroutine - kmlcreateCells3_sp — subroutine - kmlCreateCells_dp — subroutine - kmlCreateCells_longlat2_dp — subroutine - kmlCreateCells_longlat2_sp — subroutine - kmlCreateCells_longlat_dp — subroutine - kmlCreateCells_longlat_sp — subroutine - kmlCreateCells_sp — subroutine - kmlCreateContours_longlat2_sp — subroutine - kmlCreateContours_longlat_sp — subroutine - kmlCreateContours_old — subroutine - kmlCreateContours_sp — subroutine - kmlCreateLine_1d_dp — subroutine - kmlCreateLine_1d_sp — subroutine - kmlCreateLine_2d_dp — subroutine - kmlCreateLine_2d_sp — subroutine - kmlCreateLine_seg_sh_dp — subroutine - kmlCreateLineStyle_old — subroutine - kmlCreatePoints_0d_dp — subroutine - kmlCreatePoints_0d_sp — subroutine - kmlCreatePoints_1d_dp — subroutine - kmlCreatePoints_1d_sp — subroutine - kmlCreatePoints_2d_dp — subroutine - kmlCreatePoints_2d_sp — subroutine - kmlCreatePointStyleOld — subroutine - kmlCreateRGBCells_dp — subroutine - kmlCreateRGBCells_sp — subroutine - kmlGetColor_byName — function - kmlGetColor_index — function - kmlOpenAddressDetail — subroutine - kmlOpenBalloonStyle — subroutine - kmlOpenChange — subroutine - kmlOpenColorStyle — subroutine - kmlOpenContainer — subroutine - kmlOpencoordinates — subroutine - kmlOpenCreate — subroutine - kmlOpenDelete — subroutine - kmlOpenDocument — subroutine - kmlOpenFeature — subroutine - kmlOpenFolder — subroutine - kmlOpenGeometry — subroutine - kmlOpenGeometryCollection — subroutine - kmlOpenGroundOverlay — subroutine - kmlOpenIcon — subroutine - kmlOpenIconStyle — subroutine - kmlOpenItemIcon — subroutine - kmlOpenLabelStyle — subroutine - kmlOpenLatLonAltBox — subroutine - kmlOpenLatLonBox — subroutine - kmlOpenLineStyle — subroutine - kmlOpenLink — subroutine - kmlOpenListStyle — subroutine - kmlOpenLocation — subroutine - kmlOpenLod — subroutine - kmlOpenLookAt — subroutine - kmlOpenModel — subroutine - kmlOpenMultiGeometry — subroutine - kmlOpenNetworkLink — subroutine - kmlOpenNetworkLinkControl — subroutine - kmlOpenObjArrayField — subroutine - kmlOpenObject — subroutine - kmlOpenObjField — subroutine - kmlOpenOrientation — subroutine - kmlOpenOverlay — subroutine - kmlOpenPair — subroutine - kmlOpenPlacemark — subroutine - kmlOpenPoint — subroutine - kmlOpenPolyStyle — subroutine - kmlOpenRegion — subroutine - kmlOpenResponse — subroutine - kmlOpenScale — subroutine - kmlOpenSchema — subroutine - kmlOpenSchemaField — subroutine - kmlOpenScreenOverlay — subroutine - kmlOpenSimpleArrayField — subroutine - kmlOpenSimpleField — subroutine - kmlOpenSnippet — subroutine - kmlOpenStatus — subroutine - kmlOpenStyleMap — subroutine - kmlOpenStyleSelector — subroutine - kmlOpenTimePrimitive — subroutine - kmlOpenTimeSpan — subroutine - kmlOpenTimeStamp — subroutine - kmlOpenUpdate — subroutine - kmlOpenUrl — subroutine - kmlOutputContours — subroutine - kmlStartPolygon_1d_dp — subroutine - kmlStartPolygon_1d_sp — subroutine - kmlStartPolygon_2d_dp — subroutine - kmlStartPolygon_2d_sp — subroutine - kstwo — subroutine - l1dist_dp — function - l1dist_sp — function - lapack_stop — subroutine - lcg — function - lex_sort_1 — subroutine - lex_sort_2 — subroutine - lin_apod — function - lin_instr — function - list_of_ints2arr — function - locate_1 — function - locate_2 — function - lookup — function - lookupNamespaceURI_len — function - lookupPrefix_len — function - loop_lims — function - lowercase — function - make_c_and_d — subroutine - make_i_relion — subroutine - make_i_spider — subroutine - make_o — subroutine - make_t — subroutine - make_token_group — function - make_token_group_len — function - map3dshift22d — subroutine - map_str_nrs — function - mask2inds — function - masked_swap_rm — subroutine - masked_swap_rs — subroutine - masked_swap_rv — subroutine - matcreate — function - materialize_seed_shift — subroutine - matextract — function - matinv_dp — subroutine - matinv_sp — subroutine - matrixtocomplexdp — subroutine - matrixtocomplexsp — subroutine - matrixtointeger — subroutine - matrixtological — subroutine - matrixtorealdp — subroutine - matrixtorealsp — subroutine - matrixtostring — subroutine - maxheap_sift_down — subroutine - maxnloc — function - median — function - median_nocopy — function - medoid_from_dmat — subroutine - medoid_from_smat — subroutine - medoid_ranking_from_smat — subroutine - merge_dmats_1 — function - merge_dmats_2 — function - merge_idx — subroutine - merge_idx — subroutine - merge_smats — function - mergesort_idx — subroutine - mergesort_idx — subroutine - min3 — function - minnloc — function - mirror2d — subroutine - mirror3d — subroutine - mnomal — function - mnorm_smp — function - mode — subroutine - moment_1 — subroutine - moment_2 — subroutine - moment_3 — subroutine - moment_4 — subroutine - moment_serial — subroutine - mostOfLineStyle — subroutine - mostOfPointStyle — subroutine - move_key_to_front_1 — subroutine - move_key_to_front_2 — subroutine - multinomal — function - my_date_and_time — function - myacos_dp — function - myacos_sp — function - mycabs — function - name_equal — function - name_strings_equal — function - ne_mnomal_iarr — subroutine - ne_ran_iarr — subroutine - nearest_proj_neighbors_1 — subroutine - nearest_proj_neighbors_2 — subroutine - nearest_sym_neighbors — subroutine - neigh_4_3D_1 — subroutine - neigh_4_3D_2 — subroutine - neigh_8_1 — subroutine - neigh_8_2 — subroutine - neigh_8_3 — subroutine - neigh_8_3D_0 — subroutine - neigh_8_3D_1 — subroutine - neigh_8_3D_2 — subroutine - new — subroutine - new — subroutine - new — subroutine - new — subroutine - new_1 — subroutine - new_1 — subroutine - new_2 — subroutine - new_2 — subroutine - new_fixed_candidate_store — subroutine - new_ori — subroutine - new_ragged_candidate_store — subroutine - nextPow2 — function - nn_apod — function - nn_instr — function - norm_2_dp — function - norm_2_sp — function - norm_corr — function - norm_corr_8 — function - norm_key — function - normal_solve — subroutine - normalize_1 — subroutine - normalize_2 — subroutine - normalize_3 — subroutine - normalize_4 — subroutine - normalize_minmax_1 — subroutine - normalize_minmax_2 — subroutine - normalize_sigm_1 — subroutine - normalize_sigm_2 — subroutine - normalize_sigm_3 — subroutine - number_of_items — function - ori2chash — function - ori2json — subroutine - ori2prec — subroutine - ori2str — function - ori_from_rotmat — subroutine - otsu_1 — subroutine - otsu_2 — subroutine - otsu_3 — subroutine - outerprod_d — function - outerprod_r — function - output_terminal — function - outputContourLines — subroutine - outputContourRegions — subroutine - p1_lt_p2 — function - parameterChArrSh — subroutine - parameterChArrSi — subroutine - parameterChMatSh — subroutine - parameterChMatSi — subroutine - parameterChSca — subroutine - parameterCmplxDpArrSh — subroutine - parameterCmplxDpArrSi — subroutine - parameterCmplxDpMatSh — subroutine - parameterCmplxDpMatSi — subroutine - parameterCmplxDpSca — subroutine - parameterCmplxSpArrSh — subroutine - parameterCmplxSpArrSi — subroutine - parameterCmplxSpMatSh — subroutine - parameterCmplxSpMatSi — subroutine - parameterCmplxSpSca — subroutine - parameterIntArrSh — subroutine - parameterIntArrSi — subroutine - parameterIntMatSh — subroutine - parameterIntMatSi — subroutine - parameterIntSca — subroutine - parameterLgArrSh — subroutine - parameterLgArrSi — subroutine - parameterLgMatSh — subroutine - parameterLgMatSi — subroutine - parameterLgSca — subroutine - parameterRealDpArrSh — subroutine - parameterRealDpArrSi — subroutine - parameterRealDpMatSh — subroutine - parameterRealDpMatSi — subroutine - parameterRealDpSca — subroutine - parameterRealSpArrSh — subroutine - parameterRealSpArrSi — subroutine - parameterRealSpMatSh — subroutine - parameterRealSpMatSi — subroutine - parameterRealSpSca — subroutine - parse_array — subroutine - parse_cmdline — subroutine - parse_dtd_attlist — subroutine - parse_dtd_element — subroutine - parse_for_chars — subroutine - parse_number — subroutine - parse_object — subroutine - parse_string — subroutine - parse_value — subroutine - parsestr — subroutine - partial_shuffle_1 — subroutine - partial_shuffle_2 — subroutine - peakfinder — function - pearsn_1 — function - pearsn_2 — function - pearsn_3 — function - pearsn_serial — function - pearsn_serial_8 — function - phase_angle — function - pixels_dist_1 — function - pixels_dist_2 — function - plane_from_points — function - plot3d — subroutine - plot_1 — subroutine - plot_2 — subroutine - plot_3 — subroutine - plot_4 — subroutine - pop_char — subroutine - pop_elstack — function - pop_entity_list — function - power_sampling — subroutine - pparms2str — function - prec2ori — subroutine - prep_part_jobs — subroutine - prepare_tree_sub_distmat — subroutine - prepimgbatch — subroutine - print — subroutine - print — subroutine - print_buffer — subroutine - print_dict — subroutine - print_elstack — subroutine - print_entity_list — subroutine - print_gpu_specs — subroutine - print_jobs_status — subroutine - print_key_val_pair_1 — subroutine - print_key_val_pair_2 — subroutine - print_key_val_pairs — subroutine - print_mat — subroutine - print_ori — subroutine - probks — function - progress — subroutine - progress_gfortran — subroutine - projz — subroutine - propertyChArrSh — subroutine - propertyChArrSi — subroutine - propertyChMatSh — subroutine - propertyChMatSi — subroutine - propertyChSca — subroutine - propertyCmplxDpArrSh — subroutine - propertyCmplxDpArrSi — subroutine - propertyCmplxDpMatSh — subroutine - propertyCmplxDpMatSi — subroutine - propertyCmplxDpSca — subroutine - propertyCmplxSpArrSh — subroutine - propertyCmplxSpArrSi — subroutine - propertyCmplxSpMatSh — subroutine - propertyCmplxSpMatSi — subroutine - propertyCmplxSpSca — subroutine - propertyIntArrSh — subroutine - propertyIntArrSi — subroutine - propertyIntMatSh — subroutine - propertyIntMatSi — subroutine - propertyIntSca — subroutine - propertyLgArrSh — subroutine - propertyLgArrSi — subroutine - propertyLgMatSh — subroutine - propertyLgMatSi — subroutine - propertyLgSca — subroutine - propertyRealDpArrSh — subroutine - propertyRealDpArrSi — subroutine - propertyRealDpMatSh — subroutine - propertyRealDpMatSi — subroutine - propertyRealDpSca — subroutine - propertyRealSpArrSh — subroutine - propertyRealSpArrSi — subroutine - propertyRealSpMatSh — subroutine - propertyRealSpMatSi — subroutine - propertyRealSpSca — subroutine - PseudoAttributeArrayCh — subroutine - PseudoAttributeArrayCmplxDp — subroutine - PseudoAttributeArrayCmplxSp — subroutine - PseudoAttributeArrayInt — subroutine - PseudoAttributeArrayLg — subroutine - PseudoAttributeArrayRealDp — subroutine - PseudoAttributeArrayRealSp — subroutine - PseudoAttributeMatrixCh — subroutine - PseudoAttributeMatrixCmplxDp — subroutine - PseudoAttributeMatrixCmplxSp — subroutine - PseudoAttributeMatrixInt — subroutine - PseudoAttributeMatrixLg — subroutine - PseudoAttributeMatrixRealDp — subroutine - PseudoAttributeMatrixRealSp — subroutine - PseudoAttributeScalarCmplxDp — subroutine - PseudoAttributeScalarCmplxSp — subroutine - PseudoAttributeScalarInt — subroutine - PseudoAttributeScalarLg — subroutine - PseudoAttributeScalarRealDp — subroutine - PseudoAttributeScalarRealSp — subroutine - push_1 — subroutine - push_1 — subroutine - push_2 — subroutine - push_2 — subroutine - push_3 — subroutine - push_char — subroutine - push_elstack — subroutine - put_last — subroutine - putNodesInDocument — subroutine - pythag_dp — function - pythag_sp — function - qr_solve — subroutine - qsys_cleanup — subroutine - qsys_declare_part_finished — subroutine - qsys_job_finished — subroutine - qsys_subproject_job_finished — subroutine - qsys_watcher_1 — subroutine - qsys_watcher_2 — subroutine - qsys_watcher_diag — subroutine - quadri — function - quantize_vec — subroutine - quantize_vec_serial — subroutine - r8po_fa — subroutine - rad2deg_1 — function - rad2deg_2 — function - ran3 — function - ran3arr_1 — subroutine - ran3arr_2 — subroutine - randn_1 — function - randn_2 — function - rank_centroid_weights — subroutine - rank_exponent_weights — subroutine - rank_inverse_weights — subroutine - rank_sum_weights — subroutine - raw — function - read — subroutine - read_imgbatch_1 — subroutine - read_imgbatch_2 — subroutine - read_imgbatch_3 — subroutine - read_seed_shift_table — subroutine - readfile — subroutine - readline — subroutine - real2str — function - real_dp_str — function - real_sp_str — function - realdp2str — function - realloc_chash — subroutine - realloc_hash — subroutine - realsp2str — function - registered_string — function - reject — subroutine - remove — subroutine - remove_key_by_index — subroutine - remove_last_string — subroutine - remove_node_nl — subroutine - removeNodesFromDocument — subroutine - removePrefix — subroutine - removePrefixedURI — subroutine - removepunct — subroutine - removesp — subroutine - reorder_1 — subroutine - reorder_2 — subroutine - report_declarations — subroutine - resang — function - reset — subroutine - reset — subroutine - reset_buffer — subroutine - reset_dict — subroutine - reset_elstack — subroutine - reset_entity_list — subroutine - reset_pparms — subroutine - resetParameter — subroutine - resize_elstack — subroutine - reverse_drarr — subroutine - reverse_f — subroutine - reverse_iarr — subroutine - reverse_rarr — subroutine - reverselookup — function - ring_stats — subroutine - rm_substr — subroutine - rnd_4dim_sphere_pnt — function - rnd_euler_1 — subroutine - rnd_euler_1 — subroutine - rnd_euler_2 — subroutine - rnd_euler_2 — subroutine - rnd_euler_3 — subroutine - rnd_euler_3 — subroutine - rnd_euler_4 — subroutine - rnd_euler_5 — subroutine - rnd_inds — function - rnd_inpl — subroutine - rnd_ori — subroutine - rnd_shift — subroutine - robust_normalization — subroutine - robust_normalize_minmax — subroutine - robust_scaling — subroutine - robust_sigma_thres — function - robust_z_scores — function - rot_to_asym — subroutine - rotall_to_asym — subroutine - rotate_vec — function - rotmat2d — subroutine - round2even — function - round2odd — function - round_shifts — subroutine - rpl_substr — subroutine - run_gnuplot — subroutine - same_energy_euclid — function - sample_bounded_dist — subroutine - sample_likelihood_dist — subroutine - sample_likelihood_index — subroutine - sample_power_dist — subroutine - sauron_ori_parser_1 — subroutine - sauron_ori_parser_2 — subroutine - savgol — subroutine - SavitzkyGolay_filter — subroutine - scalartocomplexdp — subroutine - scalartocomplexsp — subroutine - scalartointeger — subroutine - scalartological — subroutine - scalartorealdp — subroutine - scalartorealsp — subroutine - scalartostring — subroutine - schedule_array_jobs — subroutine - schedule_jobs — subroutine - schedule_streaming — subroutine - schedule_subproject_jobs — subroutine - scores2order — function - scores2scores_percen — subroutine - seed_rnd — subroutine - service_persistent_worker_warmup — subroutine - set_1 — subroutine - set_1 — subroutine - set_1 — subroutine - set_2 — subroutine - set_2 — subroutine - set_2 — subroutine - set_3 — subroutine - set_3 — subroutine - set_3 — subroutine - set_4 — subroutine - set_5 — subroutine - set_class — subroutine - set_ctfvars — subroutine - set_dble — subroutine - set_dfx — subroutine - set_dfy — subroutine - set_euler — subroutine - set_hp — subroutine - set_int — subroutine - set_jobs_status — subroutine - set_json_core_in_file — subroutine - set_localName_by_index_s — subroutine - set_localName_by_index_vs — subroutine - set_nsURI_by_index — subroutine - set_offload_device_1 — subroutine - set_offload_device_2 — subroutine - set_ogid — subroutine - set_prefix_by_index — subroutine - set_real — subroutine - set_refine3D_automsk_policy — subroutine - set_refine3D_balance_policy — subroutine - set_refine3D_filtering_policy — subroutine - set_refine3D_gauref_policy — subroutine - set_refine3D_mode_policy — subroutine - set_refine3D_stage_controls — subroutine - set_refine3D_symmetry_policy — subroutine - set_refine3D_trailrec_policy — subroutine - set_refine3D_update_policy — subroutine - set_shift — subroutine - set_state — subroutine - set_stkind — subroutine - set_subgrps — subroutine - setBase — subroutine - setDeclared — subroutine - setIsId_by_index — subroutine - setisId_DOM — subroutine - setnamespaceURI — subroutine - setownerDocument — subroutine - setSpecified — subroutine - sgelsy — subroutine - sgesvd — subroutine - sgetrf — subroutine - sgetri — subroutine - shallow_copy_entity — function - shcloc — function - shell_quote — function - shft — subroutine - shift — subroutine - shuffle_1 — subroutine - shuffle_1 — subroutine - shuffle_2 — subroutine - shuffle_2 — subroutine - sigma_array — type - simple_end — subroutine - simple_print_git_version — subroutine - simple_print_timer — subroutine - sinc — function - sinc_apod — function - sinc_instr — function - sinhc — function - size_el — function - smat2dmat — function - sniff_folders_SJ — subroutine - snrm2 — function - sort — subroutine - sortAttrs — subroutine - sortmeans — subroutine - spaces — function - sparse_eigh — subroutine - spear — function - split_1 — subroutine - split_2 — subroutine - split_str — subroutine - squared_sampling — subroutine - sqwin_1d_1 — subroutine - sqwin_1d_2 — subroutine - sqwin_2d_1 — subroutine - sqwin_2d_2 — subroutine - sqwin_3d_1 — subroutine - sqwin_3d_2 — subroutine - ssaupd — subroutine - sseupd — subroutine - ssyev — subroutine - ssyevr — subroutine - stage_coarray_jobs — subroutine - start_prefix_handler — subroutine - stmAddChArr — subroutine - stmAddChMat — subroutine - stmAddChSca — subroutine - stmAddCmplxDpArr — subroutine - stmAddCmplxDpMat — subroutine - stmAddCmplxDpSca — subroutine - stmAddCmplxSpArr — subroutine - stmAddCmplxSpMat — subroutine - stmAddCmplxSpSca — subroutine - stmAddIntArr — subroutine - stmAddIntMat — subroutine - stmAddIntSca — subroutine - stmAddLgArr — subroutine - stmAddLgMat — subroutine - stmAddLgSca — subroutine - stmAddRealDpArr — subroutine - stmAddRealDpMat — subroutine - stmAddRealDpSca — subroutine - stmAddRealSpArr — subroutine - stmAddRealSpMat — subroutine - stmAddRealSpSca — subroutine - str2format_1 — subroutine - str2format_2 — subroutine - str2ori — subroutine - str2real_1 — function - str2real_2 — function - str2realdp_local — subroutine - str_complex_dp — function - str_complex_dp_array — function - str_complex_dp_array_fmt — function - str_complex_dp_array_fmt_chk — function - str_complex_dp_array_fmt_len — function - str_complex_dp_array_len — function - str_complex_dp_fmt — function - str_complex_dp_fmt_chk — function - str_complex_dp_fmt_len — function - str_complex_dp_len — function - str_complex_dp_matrix — function - str_complex_dp_matrix_fmt — function - str_complex_dp_matrix_fmt_chk — function - str_complex_dp_matrix_fmt_len — function - str_complex_dp_matrix_len — function - str_complex_sp — function - str_complex_sp_array — function - str_complex_sp_array_fmt — function - str_complex_sp_array_fmt_chk — function - str_complex_sp_array_fmt_len — function - str_complex_sp_array_len — function - str_complex_sp_fmt — function - str_complex_sp_fmt_chk — function - str_complex_sp_fmt_len — function - str_complex_sp_len — function - str_complex_sp_matrix — function - str_complex_sp_matrix_fmt — function - str_complex_sp_matrix_fmt_chk — function - str_complex_sp_matrix_fmt_len — function - str_complex_sp_matrix_len — function - str_integer — function - str_integer_array — function - str_integer_array_fmt — function - str_integer_array_fmt_len — function - str_integer_array_len — function - str_integer_base_len — function - str_integer_fmt — function - str_integer_fmt_len — function - str_integer_len — function - str_integer_matrix — function - str_integer_matrix_fmt — function - str_integer_matrix_fmt_len — function - str_integer_matrix_len — function - str_logical — function - str_logical_array — function - str_logical_array_len — function - str_logical_len — function - str_logical_matrix — function - str_logical_matrix_len — function - str_pad — function - str_real_dp — function - str_real_dp_array — function - str_real_dp_array_fmt — function - str_real_dp_array_fmt_chk — function - str_real_dp_array_fmt_len — function - str_real_dp_array_len — function - str_real_dp_fmt — function - str_real_dp_fmt_chk — function - str_real_dp_fmt_len — function - str_real_dp_len — function - str_real_dp_matrix — function - str_real_dp_matrix_fmt — function - str_real_dp_matrix_fmt_chk — function - str_real_dp_matrix_fmt_len — function - str_real_dp_matrix_len — function - str_real_sp — function - str_real_sp_array — function - str_real_sp_array_fmt — function - str_real_sp_array_fmt_chk — function - str_real_sp_array_fmt_len — function - str_real_sp_array_len — function - str_real_sp_fmt — function - str_real_sp_fmt_chk — function - str_real_sp_fmt_len — function - str_real_sp_len — function - str_real_sp_matrix — function - str_real_sp_matrix_fmt — function - str_real_sp_matrix_fmt_chk — function - str_real_sp_matrix_fmt_len — function - str_real_sp_matrix_len — function - str_string — function - str_string_array — function - str_string_array_len — function - str_string_matrix — function - str_string_matrix_len — function - string_to_dble — function - string_to_int — function - strip_spaces — function - submit_coarray_jobs — subroutine - submit_script — subroutine - submit_scripts — subroutine - substr_remove — function - substr_replace — subroutine - surf_1 — subroutine - surf_2 — subroutine - surf_3 — subroutine - svbksb_dp — subroutine - svbksb_sp — subroutine - svd_multifit_dp — subroutine - svd_multifit_sp — subroutine - svd_solve — subroutine - svdcmp_dp — subroutine - svdcmp_sp — subroutine - svdfit_dp — subroutine - svdfit_sp — subroutine - svdvar — subroutine - swap_c — subroutine - swap_cm — subroutine - swap_cv — subroutine - swap_i — subroutine - swap_pointers — subroutine - swap_r — subroutine - swap_rv — subroutine - swape1e3 — subroutine - sym_dists_1 — subroutine - sym_dists_2 — subroutine - sym_tester — subroutine - symrandomize — subroutine - test_addr — subroutine - test_eigh — subroutine - test_ftiter — subroutine - test_image — subroutine - test_image_local — subroutine - to_array — subroutine - to_char_1 — function - to_char_2 — function - to_cstring — function - to_double — subroutine - to_fnv1a_hash64 — function - to_integer — subroutine - to_logical — subroutine - to_lower — function - to_null — subroutine - to_object — subroutine - to_static_1 — subroutine - to_static_2 — subroutine - to_string — subroutine - to_uni — function - to_uni_vec — function - tokenize_and_add_strings — subroutine - tokenize_to_string_list — function - trace — function - transfer_2Dparams — subroutine - transfer_3Dparams — subroutine - transfmat2inpls — subroutine - transp — subroutine - traverse — subroutine - ucs4_comp_default — function - ucs4_join_default — function - ucs4_neq_default — function - unique — subroutine - unmemoize_mask_coords — subroutine - unmemoize_powspec_coords — subroutine - update_queue — subroutine - updateNodeLists — subroutine - updatestack — subroutine - updateTextContentLength — subroutine - uppercase — function - upsample_sigma2 — subroutine - vabs_dp — function - vabs_sp — function - vector_angle_norm — function - vis_2Dinteger_mat — subroutine - vis_2Dreal_mat — subroutine - vis_3Dinteger_mat — subroutine - vis_3Dreal_mat — subroutine - vox2ang — function - vs_s_concat — function - watch — subroutine - watchdirs — subroutine - which — function - workout_directory_structure — subroutine - wrap_json_add_double_by_path — subroutine - wrap_json_add_double_vec_by_path — subroutine - wrap_json_add_integer_by_path — subroutine - wrap_json_add_integer_vec_by_path — subroutine - wrap_json_add_logical_by_path — subroutine - wrap_json_add_logical_vec_by_path — subroutine - wrap_json_add_member_by_path — subroutine - wrap_json_add_string_by_path — subroutine - wrap_json_add_string_vec_by_path — subroutine - wrap_json_create_by_path — subroutine - wrap_json_file_add_double — subroutine - wrap_json_file_add_double_vec — subroutine - wrap_json_file_add_integer — subroutine - wrap_json_file_add_integer_vec — subroutine - wrap_json_file_add_logical — subroutine - wrap_json_file_add_logical_vec — subroutine - wrap_json_file_add_object — subroutine - wrap_json_file_add_string — subroutine - wrap_json_file_add_string_vec — subroutine - wrap_json_file_get_alloc_string_vec — subroutine - wrap_json_file_get_double — subroutine - wrap_json_file_get_double_vec — subroutine - wrap_json_file_get_integer — subroutine - wrap_json_file_get_integer_vec — subroutine - wrap_json_file_get_logical — subroutine - wrap_json_file_get_logical_vec — subroutine - wrap_json_file_get_object — subroutine - wrap_json_file_get_string — subroutine - wrap_json_file_get_string_vec — subroutine - wrap_json_file_load_from_string — subroutine - wrap_json_file_remove — subroutine - wrap_json_file_rename — subroutine - wrap_json_file_update_integer — subroutine - wrap_json_file_update_logical — subroutine - wrap_json_file_update_real — subroutine - wrap_json_file_update_string — subroutine - wrap_json_file_valid_path — function - wrap_json_file_valid_path_op — function - wrap_json_file_variable_info — subroutine - wrap_json_file_variable_matrix_info — subroutine - wrap_json_get_alloc_string_vec_by_path — subroutine - wrap_json_get_array_by_path — subroutine - wrap_json_get_by_path — subroutine - wrap_json_get_double_by_path — subroutine - wrap_json_get_double_vec_by_path — subroutine - wrap_json_get_integer_by_path — subroutine - wrap_json_get_integer_vec_by_path — subroutine - wrap_json_get_logical_by_path — subroutine - wrap_json_get_logical_vec_by_path — subroutine - wrap_json_get_path — subroutine - wrap_json_get_string_by_path — subroutine - wrap_json_get_string_vec_by_path — subroutine - wrap_json_info_by_path — subroutine - wrap_json_matrix_info_by_path — subroutine - wrap_json_parse_string — subroutine - wrap_json_rename_by_path — subroutine - wrap_json_throw_exception — subroutine - wrap_json_update_double — subroutine - wrap_json_update_integer — subroutine - wrap_json_update_logical — subroutine - wrap_json_update_string — subroutine - wrap_json_valid_path — function - wrap_json_value_add_double — subroutine - wrap_json_value_add_double_vec — subroutine - wrap_json_value_add_integer — subroutine - wrap_json_value_add_integer_vec — subroutine - wrap_json_value_add_logical — subroutine - wrap_json_value_add_logical_vec — subroutine - wrap_json_value_add_null — subroutine - wrap_json_value_add_string — subroutine - wrap_json_value_add_string_vec — subroutine - wrap_json_value_create_array — subroutine - wrap_json_value_create_double — subroutine - wrap_json_value_create_integer — subroutine - wrap_json_value_create_logical — subroutine - wrap_json_value_create_null — subroutine - wrap_json_value_create_object — subroutine - wrap_json_value_create_string — subroutine - wrap_json_value_get_child_by_name — subroutine - wrap_json_value_remove_if_present — subroutine - wrap_json_value_rename — subroutine - write — subroutine - write2bild — subroutine - write_attributes — subroutine - write_checkpoint — subroutine - write_it — subroutine - write_it_fast — subroutine - write_seed_shift_table — subroutine - writeline — subroutine - wxml_error_xf — subroutine - wxml_fatal_xf — subroutine - wxml_warning_xf — subroutine - xml_AddAttlistToDTD — subroutine - xml_AddAttribute_Ch — subroutine - xml_AddCharacters_ch — subroutine - xml_AddComment — subroutine - xml_AddDOCTYPE — subroutine - xml_AddElementToDTD — subroutine - xml_AddEntityReference — subroutine - xml_AddExternalEntity — subroutine - xml_AddInternalEntity — subroutine - xml_AddNewline — subroutine - xml_AddNotation — subroutine - xml_AddParameterEntity — subroutine - xml_AddPEReferenceToDTD — subroutine - xml_AddPseudoAttribute_Ch — subroutine - xml_AddXMLDeclaration — subroutine - xml_AddXMLPI — subroutine - xml_AddXMLStylesheet — subroutine - xml_Close — subroutine - xml_DeclareNamespace — subroutine - xml_EndElement — subroutine - xml_NewElement — subroutine - xml_OpenFile — subroutine - xml_UndeclareNamespace — subroutine - xmlf_GetPretty_print — function - xmlf_name — function - xmlf_opentag — function - xmlf_opentag_len — function - xmlf_SetPretty_print — subroutine - z_scores — function - zheev — subroutine - zposv — subroutine

---

Module: pure

Files: - main/class/simple_classaverager.f90 - main/class/simple_classaverager_restore.f90 - main/image/simple_image.f90 - main/image/simple_image_access.f90 - main/image/simple_image_arith.f90 - main/image/simple_image_calc.f90 - main/image/simple_image_checks.f90 - main/ori/simple_oris.f90 - main/ori/simple_oris_dists.f90 - main/ori/simple_oris_getters.f90 - main/pftc/simple_polarft_access.f90 - main/pftc/simple_polarft_calc.f90 - main/pftc/simple_polarft_core.f90 - main/pftc/simple_polarft_geom.f90

Public symbols: - backup_previous_cavgs — subroutine

---

Module: real

Files: - main/image/simple_image.f90 - main/image/simple_image_calc.f90 - main/nu_filt/simple_nu_filter.f90 - main/nu_filt/simple_nu_filter_bank.f90 - main/nu_filt/simple_nu_filter_potts.f90 - main/nu_filt/simple_nu_filter_state.f90 - main/nu_filt/simple_nu_filter_stats.f90 - main/ori/simple_oris.f90 - main/ori/simple_oris_neig.f90 - main/pftc/simple_polarft_calc.f90 - main/pftc/simple_polarft_corr.f90 - main/project/simple_sp_project.f90 - main/project/simple_sp_project_core.f90

Public symbols: - test_oris — subroutine

---

Module: recursive

Files: - main/image/simple_image.f90 - main/image/simple_image_geom.f90

---

Module: simple_abinitio2D_controller

Files: - main/simple_abinitio2D_controller.f90

Uses: - simple_cmdline - simple_core_module_api - simple_parameters

Public symbols: - determine_abinitio2D_stages — subroutine - mskdiam2lplimits_cluster2D — subroutine - set_abinitio2D_sampling_policy — subroutine - set_cline_cluster2D_stage — subroutine

Private symbols: - build_cluster2D_stage_cfg — subroutine - emit_cluster2D_stage_cfg — subroutine - set_cluster2D_stage_iteration_policy — subroutine - set_cluster2D_stage_objfun_policy — subroutine - set_cluster2D_stage_phase_policy — subroutine - set_cluster2D_stage_reference_policy — subroutine - set_cluster2D_stage_regular_refs — subroutine - set_cluster2D_stage_search_policy — subroutine

---

Module: simple_abinitio_utils

Files: - main/simple_abinitio_utils.f90

Uses: - simple_class_frcs - simple_cluster_seed - simple_commanders_api - simple_commanders_rec - simple_commanders_volops - simple_euclid_sigma2 - simple_matcher_refvol_utils - simple_parameters - simple_refine3d_fnames

---

Module: simple_aff_prop

Files: - utils/clustering/simple_aff_prop.f90

Uses: - simple_core_module_api

Public symbols: - test_aff_prop — subroutine

Private symbols: - calc_exemplar_mask — subroutine - kill — subroutine - new — subroutine - propagate — subroutine

---

Module: simple_ansi_ctrls

Files: - defs/simple_ansi_ctrls.f90

Public symbols: - format_str — function

---

Module: simple_atoms

Files: - main/nano/simple_atoms.f90

Uses: - simple_core_module_api - simple_defs_atoms - simple_image - simple_molecule_data

Public symbols: - atoms — type - test_atoms — subroutine

Private symbols: - assert_close — subroutine - assert_int_eq — subroutine - assert_true — subroutine - assert_vec3_close — subroutine - atom_validate — subroutine - cc_res — function - center_inbox — subroutine - center_pdbcoord — subroutine - cif2mrc — subroutine - cif2pdb — subroutine - convolve — subroutine - copy — subroutine - extract_atom — subroutine - find_masscen — function - fit_bfactors — subroutine - geometry_analysis_pdb — subroutine - get_beta — function - get_coord — function - get_geom_center — function - guess_an_element — subroutine - guess_element — subroutine - kill — subroutine - map_validate — subroutine - model_validate — subroutine - model_validate_eo — subroutine - new_from_cif — subroutine - new_from_file — subroutine - new_from_molecule — subroutine - new_from_pdb — subroutine - new_instance — subroutine - pdb2mrc — subroutine - print_atom — subroutine - rotate — subroutine - scan_cif — subroutine - set_atom_corr — subroutine - set_beta — subroutine - set_chain — subroutine - set_coord — subroutine - set_element — subroutine - set_name — subroutine - set_num — subroutine - set_occupancy — subroutine - set_resnum — subroutine - split_tokens — subroutine - strip_digits — function - translate — subroutine - writepdb — subroutine - writepdb_aniso — subroutine - Z_and_radius_from_name — subroutine

---

Module: simple_binary_tree

Files: - utils/structs/simple_binary_tree.f90

Uses: - simple_error

Public symbols: - binary_tree — type - bt_node — type - deserialize_tree — subroutine - serialize_tree — subroutine

Private symbols: - build_balanced_index_tree — subroutine - build_from_hclust — subroutine - build_range — function - get_node — function - get_root_node — function - int_list — type - kill — subroutine

---

Module: simple_binary_tree_tester

Files: - utils/structs/simple_binary_tree_tester.f90

Uses: - simple_binary_tree - simple_test_utils

Public symbols: - run_all_tree_tests — subroutine

Private symbols: - assert_idx_valid — subroutine - build_test_tree — subroutine - test_build_balanced_index_tree_deterministic — subroutine - test_build_from_hclust_basic_invariants — subroutine - test_get_node_copy_semantics — subroutine - test_initial_state — subroutine - test_kill_and_rebuild — subroutine - to_str — function

---

Module: simple_binoris

Files: - fileio/simple_binoris.f90

Uses: - simple_defs - simple_defs_ori - simple_fileio - simple_map_reduce - simple_ori - simple_oris - simple_string - simple_string_utils - simple_syslib - simple_type_defs

Private symbols: - add_segment_1 — subroutine - add_segment_2 — subroutine - byte_manager4seg_inside_1 — subroutine - byte_manager4seg_inside_2 — subroutine - clear_segments — subroutine - close — subroutine - get_fromto — function - get_segments_info — subroutine - open — subroutine - open_local — subroutine - read_first_segment_record — subroutine - read_header — subroutine - read_record — subroutine - read_segment_1 — subroutine - read_segment_2 — subroutine - update_byte_ranges — subroutine - write_header — subroutine - write_segment_1 — subroutine - write_segment_2 — subroutine - write_segment_inside_1 — subroutine - write_segment_inside_2 — subroutine

---

Module: simple_binoris_io

Files: - fileio/simple_binoris_io.f90

Uses: - simple_core_module_api - simple_sp_project

Public symbols: - binread_ctfparams_state_eo — subroutine - binread_nlines — function - binread_oritab — subroutine - binwrite_oritab — subroutine

---

Module: simple_block_tree

Files: - utils/simple_block_tree.f90

Uses: - simple_binary_tree - simple_core_module_api - simple_eulspace_neigh_map - simple_multi_dendro - simple_parameters

Public symbols: - gen_block_index_tree — function - gen_eulspace_block_tree — function - gen_eulspace_block_tree_map — function - gen_multi_block_index_tree — function - gen_single_block_index_tree — function - srch_eul_bl_tree — subroutine - srch_eul_bl_tree_exhaustive — subroutine - srch_eul_bl_tree_prob — subroutine

Private symbols: - push_stack — subroutine - sample_two — function

---

Module: simple_block_tree_corr

Files: - utils/simple_block_tree_corr.f90

Uses: - simple_aff_prop - simple_core_module_api - simple_corrmat - simple_eulspace_neigh_map - simple_hclust - simple_image - simple_multi_dendro - simple_parameters

Public symbols: - gen_corr_block_tree_aff_prop — function - gen_corr_block_tree_hac — function - gen_eulspace_block_tree_corr — function

---

Module: simple_block_tree_io

Files: - fileio/simple_block_tree_io.f90

Uses: - simple_error - simple_fileio - simple_multi_dendro - simple_string_utils

Public symbols: - read_block_tree — subroutine - test_io — subroutine - write_block_tree — subroutine

---

Module: simple_bspline_smoother

Files: - utils/filter/simple_bspline_smoother.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - bspline_smoother — type - test_bspline_smoother — subroutine - test_bspline_smoother_3d — subroutine

Private symbols: - a0xy — function - a2xy — function - b3 — function - b3_help — function - fill_b — subroutine - fill_b_3d — subroutine - fill_r — subroutine - fill_r_3d — subroutine - kill_bspline_smoother — subroutine - new_bspline_smoother — subroutine - new_bspline_smoother_img — subroutine - smooth — subroutine - smooth_3d — subroutine

---

Module: simple_builder

Files: - main/simple_builder.f90

Uses: - simple_binoris_io - simple_class_frcs - simple_cmdline - simple_core_module_api - simple_euclid_sigma2 - simple_image - simple_parameters - simple_polarft_calc - simple_projector - simple_reconstructor_eo - simple_sp_project - simple_srchspace_map - simple_ui

Public symbols: - builder — type

Private symbols: - build_general_tbox — subroutine - build_rec_eo_tbox — subroutine - build_spproj — subroutine - build_strategy2D_tbox — subroutine - build_strategy3D_tbox — subroutine - init_params_and_build_general_tbox — subroutine - init_params_and_build_spproj — subroutine - init_params_and_build_strategy2D_tbox — subroutine - init_params_and_build_strategy3D_tbox — subroutine - init_params_spproj_tbox2D — subroutine - kill_general_tbox — subroutine - kill_rec_eo_tbox — subroutine - kill_strategy2D_tbox — subroutine - kill_strategy3D_tbox — subroutine - set_field_ptr — subroutine

---

Module: simple_butterworth

Files: - utils/filter/simple_butterworth.f90

Uses: - simple_core_module_api

---

Module: simple_calc_pspec_strategy

Files: - main/strategies/parallelization/simple_calc_pspec_strategy.f90

Uses: - simple_builder - simple_cmdline - simple_commanders_euclid_distr - simple_core_module_api - simple_image - simple_matcher_ptcl_io - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_ran_tabu - simple_sigma2_binfile

Public symbols: - calc_pspec_distr_strategy — type - calc_pspec_inmem_strategy — type - calc_pspec_strategy — type - create_calc_pspec_strategy — function

Private symbols: - cleanup_calc_pspec_outputs — subroutine - cleanup_interface — subroutine - compute_pspec_channel — subroutine - distr_cleanup — subroutine - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - ensure_calc_pspec_eo_partition — subroutine - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - read_sigma2_bootstrap_selection — subroutine - sanity_check_calc_pspec_input — subroutine - write_sigma2_bootstrap_selection — subroutine

---

Module: simple_cavg_quality_analysis

Files: - main/cavg_quality/simple_cavg_quality_analysis.f90

Uses: - simple_cavg_quality_feats - simple_cavg_quality_model - simple_cavg_quality_relations - simple_cavg_quality_stats - simple_cavg_quality_types - simple_defs - simple_error - simple_image - simple_oris - simple_parameters

Public symbols: - evaluate_cavg_quality — subroutine - evaluate_cavg_quality_hard_reject — subroutine - prepare_cavg_quality — subroutine - write_cavg_quality_feature_table — subroutine - write_cavg_quality_training_table — subroutine

Private symbols: - calc_best_thresholds — subroutine - eval_threshold — subroutine - write_analysis_class_header — subroutine - write_analysis_class_row — subroutine - write_feature_table_class_row — subroutine - write_model_as_analysis_comments — subroutine - write_one_threshold — subroutine - write_threshold_scan_comments — subroutine

---

Module: simple_cavg_quality_feats

Files: - main/cavg_quality/simple_cavg_quality_feats.f90

Uses: - simple_cavg_quality_types - simple_defs - simple_error - simple_image - simple_image_bin - simple_oris - simple_segmentation - simple_stat

Public symbols: - cavg_quality_feature_description — function - cavg_quality_feature_direction — function - cavg_quality_feature_family — function - cavg_quality_feature_name — function - extract_cavg_quality_features — subroutine - normalize_cavg_quality_features — subroutine - write_cavg_quality_feature_inventory — subroutine

Private symbols: - measure_cavg_foreground_geometry — subroutine - measure_cavg_image_metrics — subroutine - validate_quality_context — subroutine

---

Module: simple_cavg_quality_helpers

Files: - main/cavg_quality/simple_cavg_quality_helpers.f90

Uses: - simple_cavg_quality_types - simple_string

Public symbols: - cavg_rejection_reason_string — function

---

Module: simple_cavg_quality_learn

Files: - main/cavg_quality/simple_cavg_quality_learn.f90

Uses: - simple_cavg_quality_feats - simple_cavg_quality_model - simple_cavg_quality_relations - simple_cavg_quality_stats - simple_cavg_quality_types - simple_defs - simple_error - simple_opt_factory - simple_opt_spec - simple_optimizer - simple_srch_sort_loc - simple_string - simple_string_utils

Public symbols: - evaluate_cavg_quality_model — subroutine - evaluate_cavg_quality_result — subroutine - learn_cavg_quality_model — subroutine

Private symbols: - abinitio_learn_base_spec — function - append_feature_family — subroutine - apply_feature_policy — subroutine - best_score_threshold_balacc — subroutine - best_tie_minsep_span — subroutine - build_logistic_problem — subroutine - build_policy_caches — subroutine - calc_suggested_training_weights — subroutine - cavg_quality_logistic_problem — type - classify_training_dataset — subroutine - classify_training_dataset_cached_detail — subroutine - classify_training_dataset_detail — subroutine - collect_learn_diagnostics — subroutine - consider_model_candidate — subroutine - dataset_learn_role_name — function - dataset_short_name — function - evaluate_candidate_spec — subroutine - evaluate_policy_grid — subroutine - feature_auc_summary — subroutine - feature_policy_indices — subroutine - feature_policy_mask — subroutine - feature_policy_name — function - fit_logistic_problem — subroutine - kill_logistic_problem — subroutine - kill_policy_caches — subroutine - kill_training_datasets — subroutine - learn_cavg_quality_pairwise_logistic_model — subroutine - load_quality_training_datasets — subroutine - lodo_feature_policy_weights — subroutine - logistic_cost_wrapper — function - logistic_dataset_class_weights — subroutine - logistic_fdf_wrapper — subroutine - logistic_gradient_wrapper — subroutine - logistic_problem_fdf — subroutine - logistic_solution_to_model — subroutine - map_analysis_columns — subroutine - min_accept_policy_level — function - parse_training_metadata_line — subroutine - policy_level — function - read_quality_training_dataset — subroutine - record_top_model_candidate — subroutine - require_analysis_columns — subroutine - require_relational_training_datasets — subroutine - rescue_policy_level — function - score_dataset_feature_policy — subroutine - select_preferred_best_tie — subroutine - sort_real_prefix_ascending — subroutine - validate_quality_context — subroutine - validate_training_dataset_schemas — subroutine - write_bool_grid_diagnostic — subroutine - write_candidate_row — subroutine - write_candidate_table_header — subroutine - write_cavg_quality_evaluate_report — subroutine - write_cavg_quality_learn_report — subroutine - write_cavg_quality_logistic_learn_report — subroutine - write_dataset_metric_table — subroutine - write_evaluate_diagnostic — subroutine - write_evaluate_diagnostics — subroutine - write_feature_drop_diagnostics — subroutine - write_feature_policy_grid — subroutine - write_feature_policy_lodo_row — subroutine - write_feature_policy_screen — subroutine - write_feature_screen_diagnostics — subroutine - write_feature_signal_diagnostics — subroutine - write_fixed_model_summary — subroutine - write_grid_position_diagnostic — subroutine - write_learn_search_diagnostics — subroutine - write_logical_list — subroutine - write_logistic_coefficient_table — subroutine - write_minsep_diagnostic — subroutine - write_otsu_ablation_diagnostics — subroutine - write_policy_parameter_diagnostics — subroutine - write_real_list — subroutine - write_search_diagnostic — subroutine

---

Module: simple_cavg_quality_model

Files: - main/cavg_quality/simple_cavg_quality_model.f90

Uses: - simple_cavg_quality_feats - simple_cavg_quality_stats - simple_cavg_quality_types - simple_clustering_utils - simple_defs - simple_error - simple_srch_sort_loc - simple_string_utils

Public symbols: - apply_cached_decision_to_quality — subroutine - build_classify_cache — subroutine - cached_decision_confusion — subroutine - cavg_quality_classify_cache — type - cavg_quality_model — type - kill_classify_cache — subroutine - write_cavg_quality_model_builtin_code — subroutine

Private symbols: - accept_fit_as_single_cluster — subroutine - accumulate_accept_all_confusion — subroutine - apply_pairwise_logistic — subroutine - builtin_names — function - builtin_spec — function - cavg_quality_cached_decision — type - choose_tied_good_label — subroutine - chunk100mics_model_spec — function - classify — subroutine - forced_reason_name — function - get_spec — function - init_preset — subroutine - init_spec — subroutine - kill_model — subroutine - mark_threshold_accepts_all — subroutine - normalize — subroutine - otsu_score_threshold — subroutine - parse_feature_weight_values — subroutine - parse_model_key_value — subroutine - parse_real_values — subroutine - pool_model_spec — function - prepare_cached_decision — subroutine - read_feature_weights — subroutine - read_interaction_terms — subroutine - read_model — subroutine - read_real_values_keyed — subroutine - set_pairwise_interactions_for_feature_count — subroutine - sieve_model_spec — function - write_interaction_terms — subroutine - write_logistic_spec_assignments — subroutine - write_model — subroutine - write_model_real_list — subroutine - write_model_spec_function — subroutine - write_real_array_assignment — subroutine - write_weights_assignment — subroutine

---

Module: simple_cavg_quality_relations

Files: - main/cavg_quality/simple_cavg_quality_relations.f90

Uses: - simple_cavg_quality_types - simple_error - simple_image - simple_imgarr_utils - simple_parameters - simple_srch_sort_loc - simple_stat - simple_strategy2d_utils - simple_test_utils - simple_type_defs

Public symbols: - cavg_quality_relation_analysis — type - test_cavg_quality_relations — subroutine

Private symbols: - calculate_promoted_feature — subroutine - calculate_relation_analysis — subroutine - kill_relation_analysis — subroutine - normalize_relation_feature — subroutine - sorted_cc_neighbours — subroutine

---

Module: simple_cavg_quality_stats

Files: - main/cavg_quality/simple_cavg_quality_stats.f90

Uses: - simple_cavg_quality_types - simple_error - simple_stat

Public symbols: - calc_binary_metrics — subroutine - calc_confusion — subroutine - normalize_quality_dmat — subroutine

---

Module: simple_cavg_quality_types

Files: - main/cavg_quality/simple_cavg_quality_types.f90

Uses: - simple_defs - simple_string

Public symbols: - cavg_quality_feature_def — type - cavg_quality_learn_diagnostics — type - cavg_quality_model_spec — type - cavg_quality_result — type - cavg_quality_training_dataset — type - reset_cavg_quality_result — subroutine

---

Module: simple_chash

Files: - utils/structs/simple_chash.f90

Uses: - simple_ansi_ctrls - simple_defs - simple_error - simple_fileio - simple_string - simple_string_utils - simple_syslib

Public symbols: - chash — type

---

Module: simple_chash_tester

Files: - utils/structs/simple_chash_tester.f90

Uses: - simple_chash - simple_defs - simple_fileio - simple_string - simple_test_utils

Public symbols: - run_all_chash_tests — subroutine

Private symbols: - test_chash2str_and_strlen — subroutine - test_construction_and_kill — subroutine - test_delete — subroutine - test_get_by_key_and_index — subroutine - test_isthere_lookup_reverse — subroutine - test_move_key_to_front — subroutine - test_push_and_set_basic — subroutine - test_set_replaces_existing — subroutine - test_sort — subroutine

---

Module: simple_class_compatibility

Files: - main/class/simple_class_compatibility.f90

Uses: - simple_defs - simple_error - simple_image - simple_image_bin - simple_imgarr_utils - simple_segmentation - simple_sp_project - simple_srch_sort_loc - simple_string - simple_string_utils

Public symbols: - class_compatibility — type - support_model_metrics — type

Private symbols: - apply_support_model — subroutine - get_support_model_metrics — subroutine - infer — subroutine - kill — subroutine - kill_support_model — subroutine - new — subroutine - new_support_training_set — subroutine - preprocess_img — subroutine - support_model — type - support_model_training_set — type - train_1 — subroutine - train_2 — subroutine - update_support_model — subroutine

---

Module: simple_class_compatibility_tester

Files: - main/class/simple_class_compatibility_tester.f90

Uses: - simple_class_compatibility - simple_core_module_api - simple_image - simple_imgarr_utils - simple_sp_project - simple_string - simple_test_utils

Public symbols: - run_all_class_compatibility_tests — subroutine

Private symbols: - init_project_for_cavgs — subroutine - make_blob_stack — subroutine - paint_square_blob — subroutine - test_defaults_and_lifecycle — subroutine - test_infer_rejects_size_outliers — subroutine - test_infer_without_valid_model_preserves_selection — subroutine - test_kill_support_model_resets_after_fit — subroutine - test_train_1_from_project_sets_valid_fit — subroutine - test_train_1_too_small_set_no_fit — subroutine - test_train_2_retrain_sets_delta_and_convergence — subroutine

---

Module: simple_class_frcs

Files: - main/class/simple_class_frcs.f90

Uses: - simple_core_module_api - simple_fsc

Public symbols: - resample_filter — function

Private symbols: - avg_frc_getter — subroutine - bound_res — subroutine - crop — subroutine - estimate_find_for_eoavg — function - estimate_lp_for_align — function - estimate_res — subroutine - frc_getter — subroutine - get_frc — function - getter — subroutine - kill — subroutine - new — subroutine - pad — subroutine - plot_frcs — subroutine - print_frcs — subroutine - raise_exception — subroutine - read — subroutine - set_frc — subroutine - write — subroutine

---

Module: simple_class_sample_io

Files: - fileio/simple_class_sample_io.f90

Uses: - simple_error - simple_fileio - simple_string_utils - simple_syslib - simple_type_defs

Public symbols: - class_samples_same — function - deallocate_class_samples — subroutine - print_class_sample — subroutine - read_class_samples — subroutine - write_class_samples — subroutine

Private symbols: - serialize_class_sample — function - unserialize_class_sample — function

---

Module: simple_classaverager

Files: - main/class/simple_classaverager.f90

Uses: - simple_builder - simple_core_module_api - simple_ctf - simple_euclid_sigma2 - simple_fftw3 - simple_ftiter - simple_image - simple_imgfile - simple_memoize_ft_maps - simple_parameters

Public symbols: - fourier_2d_accumulator — type

Private symbols: - matrix_ptrs — type - stack — type

---

Module: simple_cls_split_strategy

Files: - main/strategies/parallelization/simple_cls_split_strategy.f90

Uses: - simple_builder - simple_classaverager - simple_clustering_utils - simple_cmdline - simple_core_module_api - simple_default_clines - simple_defs_fname - simple_diff_map_graphs - simple_diffusion_maps - simple_exec_helpers - simple_image - simple_image_msk - simple_imgarr_utils - simple_imgproc - simple_kpca_svd - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_sp_project - simple_srch_sort_loc - simple_srchspace_map2d_io

Public symbols: - cls_split_master_strategy — type - cls_split_shmem_strategy — type - cls_split_strategy — type - cls_split_worker_strategy — type - create_cls_split_strategy — function

Private symbols: - apply_defaults — subroutine - apply_split_project_updates — subroutine - cleanup_interface — subroutine - collect_split_classes — subroutine - count_data_lines — subroutine - determine_phase_flip — subroutine - determine_split_label — subroutine - estimate_icm_rank_stats — subroutine - exec_interface — subroutine - finalize_interface — subroutine - init_common — subroutine - init_interface — subroutine - make_split_embedding — subroutine - master_cleanup — subroutine - master_execute — subroutine - master_finalize_run — subroutine - master_initialize — subroutine - merge_worker_outputs — subroutine - prepare_class_partitions — subroutine - read_int_file — subroutine - read_part_map — subroutine - run_icm_rank_seed — subroutine - run_local_split — subroutine - sanitize_distance_matrix — subroutine - sanitize_embedding_coords — subroutine - select_kmedoids_by_silhouette — subroutine - shmem_cleanup — subroutine - shmem_execute — subroutine - shmem_finalize_run — subroutine - shmem_initialize — subroutine - sort_combined_maps — subroutine - sort_order_by_weight_desc — subroutine - split_one_parent_class — subroutine - trim_split_embedding — subroutine - update_icm_rank_site — subroutine - validate_cls_split — subroutine - worker_cleanup — subroutine - worker_execute — subroutine - worker_finalize_run — subroutine - worker_initialize — subroutine

---

Module: simple_cluster2D_strategy

Files: - main/strategies/parallelization/simple_cluster2D_strategy.f90

Uses: - simple_builder - simple_cmdline - simple_commanders_euclid - simple_commanders_imgops - simple_commanders_mkcavgs - simple_commanders_prob - simple_convergence - simple_core_module_api - simple_euclid_sigma2 - simple_exec_helpers - simple_gui_utils - simple_matcher_smpl_and_lplims - simple_parameters - simple_procimgstk - simple_progress - simple_qsys_env - simple_qsys_funs - simple_starproject - simple_strategy2d_matcher - simple_stream_utils

Public symbols: - cluster2D_distr_strategy — type - cluster2D_inmem_strategy — type - cluster2D_strategy — type - create_cluster2D_strategy — function

Private symbols: - apply_stream_iteration_policy — subroutine - cleanup_distributed_iteration_artifacts — subroutine - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_execute_iteration — subroutine - distr_finalize_iteration — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - exec_iter_interface — subroutine - execute_make_cavgs — subroutine - finalize_iter_interface — subroutine - finalize_run_interface — subroutine - gen_jpeg — subroutine - init_cluster2D_refs — subroutine - init_interface — subroutine - init_standard_refs — subroutine - init_tseries_refs — subroutine - inmem_cleanup — subroutine - inmem_execute_iteration — subroutine - inmem_finalize_iteration — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - run_distributed_cavg_assembly — subroutine

---

Module: simple_cluster_seed

Files: - utils/clustering/simple_cluster_seed.f90

Uses: - simple_core_module_api

Public symbols: - gen_labelling — subroutine

Private symbols: - draw — subroutine - draw_ranked — subroutine - draw_ranked_uniform — subroutine - draw_squared — subroutine - draw_squared_uniform — subroutine - draw_squared_uniform_projdir — subroutine - draw_uniform — subroutine - draw_uniform_corr — subroutine

---

Module: simple_clustering_utils

Files: - utils/clustering/simple_clustering_utils.f90

Uses: - simple_aff_prop - simple_core_module_api - simple_hclust - simple_kmedoids - simple_stat

Public symbols: - aggregate — subroutine - cluster_dmat — subroutine - labels2smat — function

Private symbols: - merge_if_necessary — subroutine

---

Module: simple_cmdline

Files: - main/simple_cmdline.f90

Uses: - simple_args - simple_core_module_api - simple_private_prgs - simple_ui - simple_ui_program

Public symbols: - cmdline_err — subroutine

Private symbols: - assign — subroutine - check — subroutine - checkvar — subroutine - copy — subroutine - defined — function - delete — subroutine - gen_job_descr — subroutine - get_carg — function - get_keys — function - get_rarg — function - kill — subroutine - lookup — function - parse — subroutine - parse_command_line_value — subroutine - parse_oldschool — subroutine - parse_private — subroutine - parse_private_line — subroutine - printline — subroutine - read — subroutine - set_1 — subroutine - set_2 — subroutine - set_3 — subroutine - set_4 — subroutine - set_5 — subroutine - set_6 — subroutine - writeline — subroutine

---

Module: simple_cmdline_tester

Files: - main/simple_cmdline_tester.f90

Uses: - simple_chash - simple_cmdline - simple_defs - simple_string - simple_string_utils - simple_test_utils

Public symbols: - run_all_cmdline_tests — subroutine

Private symbols: - test_copy_and_assignment — subroutine - test_defined_and_lookup — subroutine - test_delete_behavior — subroutine - test_gen_job_descr — subroutine - test_get_keys — subroutine - test_read_parsing — subroutine - test_set_and_get_char_and_string — subroutine - test_set_and_get_numeric — subroutine

---

Module: simple_commander_base

Files: - main/commanders/simple/simple_commander_base.f90

Uses: - simple_cmdline - simple_core_module_api - simple_defs

Public symbols: - commander_base — type

Private symbols: - generic_execute — subroutine

---

Module: simple_commanders_abinitio

Files: - main/commanders/simple/simple_commanders_abinitio.f90

Uses: - simple_abinitio_utils - simple_cluster_seed - simple_commanders_api - simple_commanders_cavgs - simple_commanders_project_core - simple_commanders_rec - simple_commanders_refine3d - simple_commanders_reproject - simple_estimate_ssnr - simple_procimgstk - simple_refine3d_fnames

Public symbols: - commander_abinitio3D — type - commander_abinitio3D_cavgs — type

Private symbols: - clean_ptcl3D_sampling — subroutine - configure_cavgs_distributed_clines — subroutine - conv_eo — subroutine - conv_eo_states — subroutine - del_pproc_vols — subroutine - ensure_docked_multistate_particle_assignments — subroutine - ensure_multistate_particle_assignments — subroutine - exec_abinitio3D — subroutine - exec_abinitio3D_cavgs — subroutine - ini3D_from_cavgs — subroutine - prepare_state_continue_project — subroutine - rank_cavgs — subroutine - read_multistate_assignment_coverage — subroutine - reset_ptcl3D_from_ptcl2D_selection — subroutine - rndstart — subroutine - run_multistate_missing_update — subroutine - strip_distributed_child — subroutine - sync_distributed_child — subroutine - validate_cavg_ini_ext_states — subroutine

---

Module: simple_commanders_abinitio2D

Files: - main/commanders/simple/simple_commanders_abinitio2D.f90

Uses: - simple_abinitio2d_controller - simple_class_frcs - simple_classaverager - simple_commanders_api - simple_commanders_cavgs - simple_commanders_cluster2d - simple_commanders_imgops - simple_commanders_volops - simple_procimgstk - simple_timer

Public symbols: - commander_abinitio2D — type

Private symbols: - exec_abinitio2D — subroutine - execute_cluster2D — subroutine - execute_terminal_prob_pass — subroutine - gen_final_cavgs — subroutine - inirefs — subroutine - output_stats — subroutine - prep_command_lines — subroutine - set_dims — subroutine - set_lplims — subroutine - set_sampling — subroutine - write_abinitio_benchmark — subroutine

---

Module: simple_commanders_api

Files: - main/apis/simple_commanders_api.f90

Uses: - simple_binoris_io - simple_builder - simple_cmdline - simple_commander_base - simple_core_module_api - simple_default_clines - simple_euclid_sigma2 - simple_exec_helpers - simple_image - simple_image_bin - simple_image_msk - simple_nice - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_sp_project - simple_stack_io - simple_stream_utils

---

Module: simple_commanders_atoms

Files: - main/commanders/simple/simple_commanders_atoms.f90

Uses: - simple_atoms - simple_commanders_api - simple_commanders_resolest - simple_commanders_sim - simple_commanders_volops - simple_nanoparticle - simple_nanoparticle_utils

Public symbols: - commander_atoms_register — type - commander_atoms_rmsd — type - commander_atoms_stats — type - commander_cif2mrc — type - commander_cif2pdb — type - commander_conv_atom_denoise — type - commander_core_atoms_analysis — type - commander_crys_score — type - commander_detect_atoms — type - commander_map2model_fsc — type - commander_map_validate — type - commander_model_validate — type - commander_model_validate_eo — type - commander_pdb2mrc — type - common_atoms — type - compute_stats — subroutine - exec_atoms_register — subroutine - exec_atoms_rmsd — subroutine - exec_atoms_stats — subroutine - exec_cif2mrc — subroutine - exec_cif2pdb — subroutine - exec_conv_atom_denoise — subroutine - exec_core_atoms_analysis — subroutine - exec_crys_score — subroutine - exec_detect_atoms — subroutine - exec_map2model_fsc — subroutine - exec_map_validate — subroutine - exec_model_validate — subroutine - exec_model_validate_eo — subroutine - exec_pdb2mrc — subroutine - sort_cluster — subroutine

---

Module: simple_commanders_cavgs

Files: - main/commanders/simple/simple_commanders_cavgs.f90

Uses: - simple_cavg_quality_analysis - simple_cavg_quality_learn - simple_cavg_quality_model - simple_cavg_quality_relations - simple_cavg_quality_types - simple_clustering_utils - simple_commanders_api - simple_corrmat - simple_imgarr_utils - simple_projfile_utils - simple_srch_sort_loc - simple_strategy2d_utils - simple_string_utils

Public symbols: - annotate_project — subroutine - build_temp_project_from_stack — subroutine - commander_cluster_cavgs — type - commander_cluster_cavgs_selection — type - commander_map_cavgs_selection — type - commander_map_cavgs_states — type - commander_match_cavgs — type - commander_model_cavgs_rejection — type - commander_rank_cavgs — type - commander_select_clusters — type - commander_shape_rank_cavgs — type - exec_cluster_cavgs — subroutine - exec_cluster_cavgs_selection — subroutine - exec_map_cavgs_selection — subroutine - exec_map_cavgs_states — subroutine - exec_match_cavgs — subroutine - exec_model_cavgs_rejection — subroutine - exec_rank_cavgs — subroutine - exec_select_clusters — subroutine - exec_shape_rank_cavgs — subroutine - find_label_state — function - p1_lt_p2 — function - prep_stack4clust — subroutine - resolve_quality_context — function - update_project — subroutine - write_hard_gate_stack — subroutine - write_quality_stack — subroutine - write_ranked_quality_stack — subroutine

---

Module: simple_commanders_checks

Files: - main/commanders/simple/simple_commanders_checks.f90

Uses: - simple_commanders_api - simple_decay_funs - simple_ori - simple_rnd

Public symbols: - check_euler_shift — subroutine - commander_check_box — type - commander_check_nptcls — type - commander_check_stoch_update — type - commander_check_update_frac — type - commander_info_image — type - commander_info_stktab — type - exec_check_box — subroutine - exec_check_nptcls — subroutine - exec_check_stoch_update — subroutine - exec_check_update_frac — subroutine - exec_info_image — subroutine - exec_info_stktab — subroutine

---

Module: simple_commanders_cluster2D

Files: - main/commanders/simple/simple_commanders_cluster2D.f90

Uses: - simple_classaverager - simple_cluster2d_strategy - simple_commanders_api - simple_commanders_cavgs - simple_commanders_euclid - simple_commanders_imgops - simple_commanders_mkcavgs - simple_gui_utils - simple_imgproc - simple_kpca_svd - simple_matcher_smpl_and_lplims - simple_pca - simple_pca_svd - simple_pftc_srch_api - simple_ppca - simple_procimgstk - simple_progress - simple_strategy2d_matcher

Public symbols: - commander_cluster2D — type - commander_cluster2D_distr_worker — type - commander_ppca_denoise_classes — type - exec_cluster2D — subroutine - exec_cluster2D_distr_worker — subroutine - exec_ppca_denoise_classes — subroutine - log_ppca_rank_scan — subroutine

---

Module: simple_commanders_denoise

Files: - main/commanders/simple/simple_commanders_denoise.f90

Uses: - simple_cls_split_strategy - simple_commanders_api - simple_commanders_mkcavgs - simple_denoise_project_strategy - simple_ori - simple_oris

Public symbols: - build_den2raw_map — subroutine - commander_cls_split — type - commander_denoise_project — type - commander_map_params_from_den — type - copy_assignment_keys — subroutine - exec_cls_split — subroutine - exec_denoise_project — subroutine - exec_map_params_from_den — subroutine - validate_den2raw_map — subroutine

---

Module: simple_commanders_distr

Files: - main/commanders/simple/simple_commanders_distr.f90

Uses: - simple_commanders_api - simple_map_reduce

Public symbols: - commander_split — type - exec_split — subroutine

---

Module: simple_commanders_euclid

Files: - main/commanders/simple/simple_commanders_euclid.f90

Uses: - simple_calc_pspec_strategy - simple_commanders_api - simple_sigma2_binfile

Public symbols: - commander_calc_group_sigmas — type - commander_calc_pspec — type - consolidate_channel — subroutine - exec_calc_group_sigmas — subroutine - exec_calc_pspec — subroutine

---

Module: simple_commanders_euclid_distr

Files: - main/commanders/simple/simple_commanders_euclid_distr.f90

Uses: - simple_commanders_api - simple_sigma2_binfile

Public symbols: - commander_calc_pspec_assemble — type - exec_calc_pspec_assemble — subroutine - remove_negative_sigmas — subroutine

---

Module: simple_commanders_flex_analysis

Files: - main/commanders/simple/simple_commanders_flex_analysis.f90

Uses: - simple_commanders_api - simple_flex_analysis_strategy

Public symbols: - commander_flex_analysis — type - exec_flex_analysis — subroutine

---

Module: simple_commanders_imgops

Files: - main/commanders/simple/simple_commanders_imgops.f90

Uses: - simple_bspline_smoother - simple_commanders_api - simple_diff_map_denoise - simple_diff_map_graphs - simple_imgarr_utils - simple_imgproc - simple_kpca_svd - simple_pca - simple_pca_svd - simple_ppca - simple_procimgstk - simple_segmentation

Public symbols: - commander_binarize — type - commander_edge_detect — type - commander_filter — type - commander_normalize — type - commander_ppca_denoise — type - commander_scale — type - doit — subroutine - doit — subroutine - exec_binarize — subroutine - exec_edge_detect — subroutine - exec_filter — subroutine - exec_normalize — subroutine - exec_ppca_denoise — subroutine - exec_scale — subroutine

---

Module: simple_commanders_imgproc

Files: - main/commanders/simple/simple_commanders_imgproc.f90

Uses: - simple_commanders_api - simple_ctf - simple_estimate_ssnr - simple_fileio - simple_matcher_ptcl_io - simple_memoize_ft_maps - simple_ori - simple_procimgstk - simple_segmentation

Public symbols: - commander_ctf_correct — type - commander_ctfops — type - commander_estimate_diam — type - correct_particles_batch — subroutine - exec_ctf_correct — subroutine - exec_ctfops — subroutine - exec_estimate_diam — subroutine - update_local_project_copy — subroutine

---

Module: simple_commanders_mask

Files: - main/commanders/simple/simple_commanders_mask.f90

Uses: - simple_atoms - simple_commanders_api - simple_procimgstk

Public symbols: - commander_auto_spher_mask — type - commander_automask — type - commander_automask2D — type - commander_mask — type - exec_auto_spher_mask — subroutine - exec_automask — subroutine - exec_automask2D — subroutine - exec_mask — subroutine

---

Module: simple_commanders_misc

Files: - main/commanders/simple/simple_commanders_misc.f90

Uses: - simple_class_frcs - simple_commanders_api - simple_fsc - simple_micrograph_generator - simple_motion_correct_utils - simple_simple_volinterp - simple_starproject

Public symbols: - commander_fractionate_movies — type - commander_fractionate_movies_distr — type - commander_kstest — type - commander_mkdir — type - commander_pearsn — type - commander_print_dose_weights — type - commander_print_fsc — type - commander_print_magic_boxes — type - exec_fractionate_movies — subroutine - exec_fractionate_movies_distr — subroutine - exec_kstest — subroutine - exec_mkdir — subroutine - exec_pearsn — subroutine - exec_print_dose_weights — subroutine - exec_print_fsc — subroutine - exec_print_magic_boxes — subroutine - read_nrs_dat — subroutine

---

Module: simple_commanders_mkcavgs

Files: - main/commanders/simple/simple_commanders_mkcavgs.f90

Uses: - simple_classaverager - simple_cmdline - simple_commanders_api - simple_make_cavgs_strategy - simple_parameters - simple_pftc_srch_api - simple_timer

Public symbols: - append_bootstrap_row — subroutine - append_skipped_class — subroutine - build_bootstrap_project — subroutine - clear_parent_sample — subroutine - collect_bootstrap_classes — subroutine - commander_bootstrap_cavgs — type - commander_cavgassemble — type - commander_make_cavgs — type - commander_make_cavgs_distr — type - commander_unbootstrap_cavgs — type - commander_write_classes — type - derive_bootstrap_output_names — subroutine - exec_bootstrap_cavgs — subroutine - exec_cavgassemble — subroutine - exec_make_cavgs — subroutine - exec_make_cavgs_distr — subroutine - exec_unbootstrap_cavgs — subroutine - exec_write_classes — subroutine - make_cavgs_exec_cavgassemble — subroutine - report_bootstrap_class_accounting — subroutine - run_make_cavgs_workflow — subroutine - select_bootstrap_anchor — subroutine - set_bootstrap_class_row — subroutine - shuffle_ints — subroutine - validate_evenodd_present — subroutine - write_bootstrap_outputs — subroutine

---

Module: simple_commanders_ori

Files: - main/commanders/simple/simple_commanders_ori.f90

Uses: - simple_commanders_api

Public symbols: - check_states — subroutine - commander_check_states — type - commander_make_oris — type - commander_oriconsensus — type - commander_oriops — type - commander_oristats — type - commander_rotmats2oris — type - commander_vizoris — type - exec_make_oris — subroutine - exec_oriconsensus — subroutine - exec_oriops — subroutine - exec_oristats — subroutine - exec_rotmats2oris — subroutine - exec_vizoris — subroutine - generate_perm — subroutine - read_state_order — subroutine

---

Module: simple_commanders_pick

Files: - main/commanders/simple/simple_commanders_pick.f90

Uses: - simple_cmdline - simple_commanders_api - simple_core_module_api - simple_extract_strategy - simple_parameters - simple_pick_strategy - simple_picker_iter - simple_reextract_strategy

Public symbols: - commander_extract — type - commander_make_pickrefs — type - commander_pick — type - commander_pick_extract — type - commander_reextract — type

Private symbols: - exec_extract — subroutine - exec_make_pickrefs — subroutine - exec_pick — subroutine - exec_pick_extract — subroutine - exec_reextract — subroutine

---

Module: simple_commanders_preprocess

Files: - main/commanders/simple/simple_commanders_preprocess.f90

Uses: - simple_cmdline - simple_commanders_api - simple_core_module_api - simple_ctf_estimate_strategy - simple_gen_pspecs_and_thumbs_strategy - simple_mini_stream_utils - simple_motion_correct_strategy - simple_motion_correct_utils - simple_parameters - simple_preprocess_strategy

Public symbols: - commander_ctf_estimate — type - commander_gen_pspecs_and_thumbs — type - commander_motion_correct — type - commander_preprocess — type - exec_ctf_estimate — subroutine - exec_gen_pspecs_and_thumbs — subroutine - exec_motion_correct — subroutine - exec_preprocess — subroutine

---

Module: simple_commanders_prob

Files: - main/commanders/simple/simple_commanders_prob.f90

Uses: - simple_builder - simple_classaverager - simple_commanders_api - simple_eul_prob_tab - simple_eul_prob_tab2d - simple_eul_prob_tab_neigh - simple_imgarr_utils - simple_matcher_2dprep - simple_matcher_pftc_prep - simple_matcher_ptcl_batch - simple_matcher_refvol_utils - simple_matcher_smpl_and_lplims - simple_pftc_srch_api - simple_strategy2d_matcher

Public symbols: - cleanup_prob_align_outputs — subroutine - cleanup_prob_neigh_workspace — subroutine - commander_prob_align — type - commander_prob_align2D — type - commander_prob_align_neigh — type - commander_prob_tab — type - commander_prob_tab2D — type - commander_prob_tab_neigh — type - exec_prob_align — subroutine - exec_prob_align2D — subroutine - exec_prob_align_neigh — subroutine - exec_prob_tab — subroutine - exec_prob_tab2D — subroutine - exec_prob_tab_neigh — subroutine - prepare_prob_neigh_workspace — subroutine - run_prob_tab_neigh_batch — subroutine

---

Module: simple_commanders_project_cls

Files: - main/commanders/simple/simple_commanders_project_cls.f90

Uses: - simple_commanders_api

Public symbols: - commander_export_cavgs — type - commander_import_cavgs — type - commander_sample_classes — type - exec_export_cavgs — subroutine - exec_import_cavgs — subroutine - exec_sample_classes — subroutine

---

Module: simple_commanders_project_core

Files: - main/commanders/simple/simple_commanders_project_core.f90

Uses: - simple_commanders_api - simple_commanders_project_ptcl - simple_imgarr_utils - simple_projfile_utils - simple_strategy2d_utils - simple_stream_communicator

Public symbols: - apply_consensus — subroutine - best_state_mapping — subroutine - build_agreement — subroutine - build_consensus — subroutine - cleanup — subroutine - commander_aggregate_chunks — type - commander_concatenate_projects — type - commander_extract_subproj — type - commander_merge_projects — type - commander_new_project — type - commander_print_project_field — type - commander_print_project_info — type - commander_print_project_vals — type - commander_ptcl3D_state_consensus — type - commander_replace_project_field — type - commander_selection — type - commander_update_project — type - commander_validate_projfile — type - exec_aggregate_chunks — subroutine - exec_concatenate_projects — subroutine - exec_extract_subproj — subroutine - exec_merge_projects — subroutine - exec_new_project — subroutine - exec_print_project_field — subroutine - exec_print_project_info — subroutine - exec_print_project_vals — subroutine - exec_ptcl3D_state_consensus — subroutine - exec_replace_project_field — subroutine - exec_selection — subroutine - exec_update_project — subroutine - exec_validate_projfile — subroutine - generate_mapping — subroutine - map_state_correspondence — subroutine - sanitize_source_labels — subroutine - write_consensus_report — subroutine

---

Module: simple_commanders_project_mov

Files: - main/commanders/simple/simple_commanders_project_mov.f90

Uses: - simple_commanders_api - simple_stream_watcher

Public symbols: - commander_import_movies — type - commander_write_mic_filetab — type - exec_import_movies — subroutine - exec_write_mic_filetab — subroutine

---

Module: simple_commanders_project_ptcl

Files: - main/commanders/simple/simple_commanders_project_ptcl.f90

Uses: - simple_commanders_api - simple_starproject - simple_stream_watcher

Public symbols: - commander_import_boxes — type - commander_import_particles — type - commander_prune_project — type - commander_prune_project_distr — type - commander_reimport_particles — type - commander_scale_project — type - commander_split_stack — type - commander_zero_project_shifts — type - exec_import_boxes — subroutine - exec_import_particles — subroutine - exec_prune_project — subroutine - exec_prune_project_distr — subroutine - exec_reimport_particles — subroutine - exec_scale_project — subroutine - exec_split_stack — subroutine - exec_zero_project_shifts — subroutine - validate_denoised_stack_pair — subroutine

---

Module: simple_commanders_rec

Files: - main/commanders/simple/simple_commanders_rec.f90

Uses: - simple_builder - simple_commanders_api - simple_matcher_2dprep - simple_matcher_3drec - simple_parameters - simple_rec3d_strategy - simple_refine3d_fnames

Public symbols: - accumulate_bootstrap_eo_counts — subroutine - calc_bootstrap_state_scales — subroutine - commander_bootstrap_rec3D — type - commander_rec3D — type - commander_rec3D_worker — type - condition_bootstrap_sigma2 — subroutine - exec_bootstrap_rec3D — subroutine - exec_random_rec — subroutine - exec_rec3D — subroutine - exec_rec3D_distr_worker — subroutine - prepare_bootstrap_rec_cline — subroutine - random_rec_commander — type - register_bootstrap_rec_outputs — subroutine - warn_for_forced_bootstrap_overrides — subroutine - write_bootstrap_sigma2_from_halfmaps — subroutine

---

Module: simple_commanders_rec_distr

Files: - main/commanders/simple/simple_commanders_rec_distr.f90

Uses: - simple_commanders_api - simple_fsc - simple_gridding - simple_nu_filter - simple_reconstructor_eo - simple_refine3d_fnames - simple_vol_pproc_policy

Public symbols: - commander_volassemble — type

Private symbols: - assemble_state — subroutine - build_nonuniform_mask — subroutine - capture_nonuniform_source_halves — subroutine - carry_forward_dropped_state — subroutine - cleanup_context — subroutine - cleanup_nonuniform_state — subroutine - cleanup_nu_aux_images — subroutine - cleanup_restore_state — subroutine - collect_restore_timings — subroutine - determine_dropped_states — subroutine - determine_trailing_update_fraction — subroutine - exec_volassemble — subroutine - initialize_bench_timers — subroutine - initialize_context — subroutine - log_nonuniform_filter_stats — subroutine - log_nu_alignment_lowpass_summary — subroutine - nu_highres_steps_fname — function - postprocess_state — subroutine - prepare_grid_correction — subroutine - read_previous_halfmaps — subroutine - record_nu_alignment_lowpass_limit — subroutine - reduce_partials — subroutine - refine_nonuniform_filter_bank — subroutine - refresh_state_populations — subroutine - release_nonuniform_aux_inputs — subroutine - release_nonuniform_base_inputs — subroutine - resolution_outfile_fbody — function - resolve_fsc_txt_fname — function - restore_eos_and_write_fsc — subroutine - restore_merged_volume — subroutine - restore_state_from_parts — subroutine - restore_timings_t — type - run_state_automask — subroutine - run_state_nonuniform_filter — subroutine - set_state_filenames — subroutine - setup_nonuniform_filter — subroutine - sum_eos_after_density_correction_if_needed — subroutine - sum_eos_before_density_correction_if_needed — subroutine - trail_restored_halves_if_needed — subroutine - update_project_nu_alignment_lowpass — subroutine - update_project_resolution_metadata — subroutine - write_benchmark — subroutine - write_nonuniform_outputs — subroutine - write_nu_highres_steps_for_state — subroutine

---

Module: simple_commanders_reconstruct3D_pcg

Files: - main/commanders/simple/simple_commanders_reconstruct3D_pcg.f90

Uses: - simple_commanders_api - simple_matcher_ptcl_io - simple_math_ft - simple_reconstructor_pcg - simple_sigma2_files

Public symbols: - commander_reconstruct3D_pcg — type

Private symbols: - exec_reconstruct3D_pcg — subroutine

---

Module: simple_commanders_refine3D

Files: - main/commanders/simple/simple_commanders_refine3D.f90

Uses: - simple_abinitio_utils - simple_commanders_api - simple_commanders_rec - simple_core_module_api - simple_estimate_ssnr - simple_nu_filter - simple_pftc_srch_api - simple_refine3d_fnames - simple_refine3d_strategy - simple_strategy3d_matcher

Public symbols: - cleanup_init_vols — subroutine - commander_refine3D — type - commander_refine3D_auto — type - commander_refine3D_distr_worker — type - commander_refine3D_multi — type - configure_refine3D_multi_stages — subroutine - ensure_all_active_particles_updated — subroutine - exec_nspace — subroutine - exec_refine3D — subroutine - exec_refine3D_auto — subroutine - exec_refine3D_distr_worker — subroutine - exec_refine3D_multi — subroutine - initialize_state_volumes — subroutine - make_projdir_class_samples — subroutine - nspace_commander — type - prepare_external_init_vol — subroutine - prepare_nu_bootstrap_refs_from_raw_halves — subroutine - prepare_refine3D_multi_class_sampling — subroutine - prepare_startup_reconstruct3D_cline — subroutine - read_update_coverage — subroutine - run_refine3D_multi_missing_update — subroutine - run_refine3D_multi_stage — subroutine - seed_refine3D_auto_nonuniform_lpset — subroutine - set_refine3D_auto_sampling — subroutine - set_refine3D_multi_downscaling — subroutine - set_refine3D_multi_nstates — subroutine - set_refine3D_multi_sampling — subroutine - validate_input_volumes — subroutine - validate_refine3D_multi_combine_eo — subroutine - validate_refine3D_multi_filtering — subroutine - validate_refine3D_multi_mode — subroutine - validate_refine3D_multi_prob_neigh_mode — subroutine

---

Module: simple_commanders_relion

Files: - main/commanders/simple/simple_commanders_relion.f90

Uses: - simple_commanders_api - simple_relion

Public symbols: - commander_export_relion — type - exec_export_relion — subroutine

---

Module: simple_commanders_reproject

Files: - main/commanders/simple/simple_commanders_reproject.f90

Uses: - simple_commanders_api - simple_imgarr_utils - simple_projector - simple_simple_volinterp

Public symbols: - commander_reproject — type - exec_reproject — subroutine

---

Module: simple_commanders_resolest

Files: - main/commanders/simple/simple_commanders_resolest.f90

Uses: - simple_commanders_api - simple_commanders_euclid - simple_fsc - simple_nu_filter - simple_opt_filter - simple_pftc_srch_api - simple_refine3d_fnames

Public symbols: - calc_lplim_final_stage — function - commander_estimate_lpstages — type - commander_fsc — type - commander_fsc_area_score — type - commander_icm2D — type - commander_icm3D — type - commander_nu_filt3D — type - commander_uniform_filter2D — type - commander_uniform_filter3D — type - exec_estimate_lpstages — subroutine - exec_fsc — subroutine - exec_fsc_area_score — subroutine - exec_icm2D — subroutine - exec_icm3D — subroutine - exec_nu_filt3D — subroutine - exec_uniform_filter2D — subroutine - exec_uniform_filter3D — subroutine

---

Module: simple_commanders_sieve

Files: - main/commanders/simple/simple_commanders_sieve.f90

Uses: - simple_commanders_api - simple_ptcl_sieve - simple_ptcl_sieve_utils - simple_rec_list

Public symbols: - commander_sieve_ptcls — type - exec_sieve_ptcls — subroutine

---

Module: simple_commanders_sim

Files: - main/commanders/simple/simple_commanders_sim.f90

Uses: - simple_atoms - simple_commanders_api - simple_ctf - simple_defs_atoms - simple_matcher_ptcl_io - simple_memoize_ft_maps - simple_projector - simple_simple_volinterp - simple_simulator

Public symbols: - commander_simulate_movie — type - commander_simulate_nanoparticle — type - commander_simulate_noise — type - commander_simulate_particles — type - commander_simulate_subtomogram — type - exec_simulate_movie — subroutine - exec_simulate_nanoparticle — subroutine - exec_simulate_noise — subroutine - exec_simulate_particles — subroutine - exec_simulate_subtomogram — subroutine - gen_ptcl_pos — function

---

Module: simple_commanders_starproject

Files: - main/commanders/simple/simple_commanders_starproject.f90

Uses: - simple_commanders_api - simple_jiffys - simple_starproject

Public symbols: - commander_assign_optics_groups — type - commander_export_manifoldem_starproject — type - commander_export_starproject — type - commander_import_starproject — type - exec_assign_optics_groups — subroutine - exec_export_manifoldem_starproject — subroutine - exec_export_starproject — subroutine - exec_import_starproject — subroutine

---

Module: simple_commanders_stkops

Files: - main/commanders/simple/simple_commanders_stkops.f90

Uses: - simple_clustering_utils - simple_commanders_api - simple_imgarr_utils - simple_procimgstk - simple_stackops - simple_strategy2d_utils

Public symbols: - commander_cluster_stack — type - commander_convert — type - commander_match_stacks — type - commander_stack — type - commander_stackops — type - exec_cluster_stack — subroutine - exec_convert — subroutine - exec_match_stacks — subroutine - exec_stack — subroutine - exec_stackops — subroutine - finish_cleanup — subroutine - handle_random_selection — subroutine - handle_state_class_selection — subroutine

---

Module: simple_commanders_test_class

Files: - main/commanders/test/simple_commanders_test_class.f90

Uses: - simple_aff_prop - simple_atoms - simple_binary_tree_tester - simple_bspline_smoother - simple_chash_tester - simple_cmdline_tester - simple_commanders_api - simple_fileio_tester - simple_forked_process_tester - simple_ftexp_shsrch - simple_ftiter - simple_gui_assembler_tester - simple_gui_metadata_tester - simple_hash_tester - simple_hclust - simple_http_post_tester - simple_image - simple_imghead - simple_ipc_tcp_socket_tester - simple_linked_list_tester - simple_motion_gain_tester - simple_multi_dendro_tester - simple_online_var - simple_ori_tester - simple_oris - simple_oris_tester - simple_persistent_worker_message_tester - simple_persistent_worker_server_tester - simple_project_merge_tester - simple_rec_list_tester - simple_starfile_tester - simple_strategy2d_utils - simple_stream_api - simple_string_tester - simple_syslib_tester - simple_test_utils - simple_ui - simple_ui_hash - simple_vrefhash_tester

Public symbols: - commander_test_strategy2D — type - commander_test_ui_hash_test — type - commander_test_units — type - exec_test_strategy2D — subroutine - exec_test_ui_hash_test — subroutine - exec_test_units — subroutine - simple_test_fit_line — subroutine - test_euler_shift — subroutine - test_multinomal — subroutine

---

Module: simple_commanders_test_fft

Files: - main/commanders/test/simple_commanders_test_fft.f90

Uses: - gnufor2 - mod_phasecorr - simple_builder - simple_commanders_api - simple_core_module_api - simple_ftexp_shsrch - simple_matcher_smpl_and_lplims - simple_pftc_shsrch_grad - simple_pftc_srch_api - simple_projector_pft - simple_timer

Public symbols: - commander_test_corrs2weights_test — type - commander_test_eval_polarftcc — type - commander_test_ft_expanded — type - commander_test_gencorrs_fft — type - commander_test_order_corr — type - commander_test_phasecorr — type - commander_test_rank_weights — type - commander_test_rotate_ref — type - exec_test_corrs2weights_test — subroutine - exec_test_eval_polarftcc — subroutine - exec_test_ft_expanded — subroutine - exec_test_gencorrs_fft — subroutine - exec_test_order_corr — subroutine - exec_test_phasecorr — subroutine - exec_test_rank_weights — subroutine - exec_test_rotate_ref — subroutine - fast_rotate_ref — subroutine - rotate_ref — subroutine - rotate_ref_2 — subroutine - rotate_ref_t — subroutine

---

Module: simple_commanders_test_geometry

Files: - main/commanders/test/simple_commanders_test_geometry.f90

Uses: - json_kinds - json_module - simple_cmdline - simple_commanders_api - simple_commanders_project_core - simple_core_module_api - simple_sp_project - simple_sym

Public symbols: - commander_test_angres — type - commander_test_ori_test — type - commander_test_oris_test — type - commander_test_sym_test — type - commander_test_uniform_euler — type - commander_test_uniform_rot — type - exec_test_angres — subroutine - exec_test_ori_test — subroutine - exec_test_oris_test — subroutine - exec_test_sym_test — subroutine - exec_test_uniform_euler — subroutine - exec_test_uniform_rot — subroutine - rgauss — subroutine

---

Module: simple_commanders_test_highlevel

Files: - main/commanders/test/simple_commanders_test_highlevel.f90

Uses: - simple_atoms - simple_commanders_abinitio - simple_commanders_abinitio2d - simple_commanders_api - simple_commanders_pick - simple_commanders_preprocess - simple_commanders_project_core - simple_commanders_project_mov - simple_commanders_project_ptcl - simple_commanders_reproject - simple_commanders_sim - simple_commanders_stkops - simple_commanders_validate - simple_imghead - simple_micproc - simple_molecule_data - simple_projfile_utils - simple_qsys_env - simple_reconstructor_pcg - simple_stream_api - simple_string_utils - simple_sym - simple_ui

Public symbols: - commander_test_mini_stream — type - commander_test_pcg_recon — type - commander_test_ptcls_ppca_subproject_distr — type - commander_test_reproject — type - commander_test_simulate_particles — type - commander_test_simulated_workflow — type - commander_test_subproject_distr — type - exec_test_mini_stream — subroutine - exec_test_pcg_recon — subroutine - exec_test_ptcls_ppca_subproject_distr — subroutine - exec_test_reproject — subroutine - exec_test_simulate_particles — subroutine - exec_test_simulated_workflow — subroutine - exec_test_subproject_distr — subroutine - return_to_stage_root — subroutine - update_project_path — subroutine

---

Module: simple_commanders_test_io

Files: - main/commanders/test/simple_commanders_test_io.f90

Uses: - simple_cmdline - simple_commanders_api - simple_image - simple_imgfile - simple_jpg - simple_parameters - simple_sp_project - simple_stack_io - simple_starfile - simple_starfile_wrappers - simple_starproject_tester

Public symbols: - commander_test_imgfile — type - commander_test_inside_write — type - commander_test_io — type - commander_test_io_parallel — type - commander_test_mrc2jpeg — type - commander_test_mrc_validate — type - commander_test_stack_io — type - commander_test_star_export — type - commander_test_starfile_test — type - exec_test_imgfile — subroutine - exec_test_inside_write — subroutine - exec_test_io — subroutine - exec_test_io_parallel — subroutine - exec_test_mrc2jpeg — subroutine - exec_test_mrc_validate — subroutine - exec_test_stack_io — subroutine - exec_test_star_export — subroutine - exec_test_starfile_test — subroutine

---

Module: simple_commanders_test_masks

Files: - main/commanders/test/simple_commanders_test_masks.f90

Uses: - simple_cmdline - simple_commanders_api - simple_commanders_atoms - simple_image - simple_image_msk - simple_imgarr_utils - simple_math - simple_parameters - simple_projector

Public symbols: - commander_test_bounds_from_mask3D_test — type - commander_test_graphene_mask — type - commander_test_image_bin — type - commander_test_mask — type - commander_test_msk_routines — type - commander_test_nano_mask — type - commander_test_otsu_test — type - commander_test_ptcl_center — type - exec_test_bounds_from_mask3D_test — subroutine - exec_test_graphene_mask — subroutine - exec_test_image_bin — subroutine - exec_test_mask — subroutine - exec_test_msk_routines — subroutine - exec_test_nano_mask — subroutine - exec_test_otsu_test — subroutine - exec_test_ptcl_center — subroutine - test_center — subroutine

---

Module: simple_commanders_test_network

Files: - main/commanders/test/simple_commanders_test_network.f90

Uses: - json_kinds - json_module - simple_commanders_api - simple_distr_comm - simple_socket_comm - simple_string_utils - unix

Public symbols: - commander_test_socket_client — type - commander_test_socket_comm_distr — type - commander_test_socket_io — type - commander_test_socket_server — type - exec_test_socket_client — subroutine - exec_test_socket_comm_distr — subroutine - exec_test_socket_io — subroutine - exec_test_socket_server — subroutine - socket_server — subroutine

---

Module: simple_commanders_test_numerics

Files: - main/commanders/test/simple_commanders_test_numerics.f90

Uses: - simple_commanders_api - simple_kbinterpol - simple_linalg - simple_test_utils - simple_timer

Public symbols: - commander_test_eigh_test — type - commander_test_kbinterpol_fast — type - commander_test_maxnloc_test — type - commander_test_neigh — type - exec_test_eigh_test — subroutine - exec_test_kbinterpol_fast — subroutine - exec_test_maxnloc_test — subroutine - exec_test_neigh — subroutine - rnd_romat — subroutine

---

Module: simple_commanders_test_optimize

Files: - main/commanders/test/simple_commanders_test_optimize.f90

Uses: - simple_builder - simple_butterworth - simple_cmdline - simple_commanders_api - simple_commanders_atoms - simple_commanders_reproject - simple_image - simple_math - simple_opt_factory - simple_opt_spec - simple_optimizer - simple_parameters

Public symbols: - commander_test_lbfgsb — type - commander_test_lbfgsb_cosine — type - commander_test_lplims — type - commander_test_lpstages_test — type - commander_test_opt_lp — type - costfct — function - costfct — function - exec_test_lbfgsb — subroutine - exec_test_lbfgsb_cosine — subroutine - exec_test_lplims — subroutine - exec_test_lpstages_test — subroutine - exec_test_opt_lp — subroutine - gradfct — subroutine - gradfct — subroutine

---

Module: simple_commanders_test_parallel

Files: - main/commanders/test/simple_commanders_test_parallel.f90

Uses: - simple_commanders_api - simple_commanders_sim - simple_image - simple_timer

Public symbols: - commander_test_coarrays — type - commander_test_openacc — type - commander_test_openmp — type - commander_test_simd — type - exec_test_coarrays — subroutine - exec_test_openacc — subroutine - exec_test_openmp — subroutine - exec_test_simd — subroutine

---

Module: simple_commanders_test_single

Files: - main/commanders/test/simple_commanders_test_single.f90

Uses: - simple_commanders_api - simple_commanders_atoms - simple_commanders_project_core - simple_commanders_reproject - simple_commanders_sim - single_commanders_nano3d - single_commanders_trajectory

Public symbols: - commander_test_atoms_stats — type - commander_test_detect_atoms — type - commander_test_simulate_nanoparticle — type - commander_test_single_workflow — type - exec_test_atoms_stats — subroutine - exec_test_detect_atoms — subroutine - exec_test_simulate_nanoparticle — subroutine - exec_test_single_workflow — subroutine

---

Module: simple_commanders_test_stats

Files: - main/commanders/test/simple_commanders_test_stats.f90

Uses: - simple_aff_prop - simple_binoris_io - simple_class_sample_io - simple_cmdline - simple_commanders_api - simple_ctf - simple_decay_funs - simple_image - simple_kpca_svd - simple_linalg - simple_memoize_ft_maps - simple_parameters - simple_pca_svd - simple_ppca - simple_refine3d_fnames - simple_rnd - simple_sp_project

Public symbols: - commander_test_class_sample_test — type - commander_test_clustering — type - commander_test_ctf_test — type - commander_test_eo_diff — type - commander_test_extr_frac — type - commander_test_multinomal_test — type - commander_test_pca_all — type - commander_test_pca_imgvar — type - commander_test_sp_project — type - exec_test_class_sample_test — subroutine - exec_test_clustering — subroutine - exec_test_ctf_test — subroutine - exec_test_eo_diff — subroutine - exec_test_extr_frac — subroutine - exec_test_multinomal_test — subroutine - exec_test_pca_all — subroutine - exec_test_pca_imgvar — subroutine - exec_test_sp_project — subroutine - make_cs — subroutine

---

Module: simple_commanders_test_utils

Files: - main/commanders/test/simple_commanders_test_utils.f90

Uses: - simple_ansi_ctrls - simple_atoms - simple_cmdline - simple_commanders_api - simple_defs_fname - simple_image - simple_imghead - simple_molecule_data - simple_nice - simple_ppca - simple_segmentation - simple_stackops - simple_test_utils - simple_testfuns

Public symbols: - commander_test_ansi_colors — type - commander_test_binoris_io_test — type - commander_test_binoris_test — type - commander_test_cif2mrc — type - commander_test_cif2pdb — type - commander_test_cmdline — type - commander_test_install — type - commander_test_nice — type - commander_test_pdb2mrc — type - commander_test_peak_thres_fdr — type - commander_test_serialize — type - commander_test_stringmatch — type - exec_test_ansi_colors — subroutine - exec_test_binoris_io_test — subroutine - exec_test_binoris_test — subroutine - exec_test_cif2mrc — subroutine - exec_test_cif2pdb — subroutine - exec_test_cmdline — subroutine - exec_test_install — subroutine - exec_test_nice — subroutine - exec_test_pdb2mrc — subroutine - exec_test_peak_thres_fdr — subroutine - exec_test_serialize — subroutine - exec_test_stringmatch — subroutine

---

Module: simple_commanders_validate

Files: - main/commanders/simple/simple_commanders_validate.f90

Uses: - simple_commanders_abinitio2d - simple_commanders_api - simple_commanders_cavgs - simple_commanders_pick - simple_commanders_preprocess - simple_commanders_project_core - simple_commanders_project_mov - simple_mini_stream_utils

Public symbols: - commander_check_refpick — type - commander_mini_stream — type - exec_check_refpick — subroutine - exec_mini_stream — subroutine

Private symbols: - transfer_phase_fit_args — subroutine

---

Module: simple_commanders_volops

Files: - main/commanders/simple/simple_commanders_volops.f90

Uses: - simple_atoms - simple_clustering_utils - simple_commanders_api - simple_commanders_reproject - simple_dock_vols - simple_image_msk - simple_imgproc - simple_kpca_svd - simple_pca - simple_pca_svd - simple_ppca - simple_procimgstk - simple_projector - simple_segmentation - simple_simple_volinterp - simple_strategy2d_utils - simple_symanalyzer - simple_volanalyzer - simple_volcluster - simple_volpft_symsrch

Public symbols: - commander_centervol — type - commander_dock_volpair — type - commander_noisevol — type - commander_postprocess — type - commander_ppca_volvar — type - commander_sharpvol — type - commander_symaxis_search — type - commander_symmetrize_map — type - commander_symmetry_test — type - commander_volanalyze — type - commander_volcluster — type - commander_volops — type - exec_centervol — subroutine - exec_dock_volpair — subroutine - exec_noisevol — subroutine - exec_postprocess — subroutine - exec_ppca_volvar — subroutine - exec_sharpvol — subroutine - exec_symaxis_search — subroutine - exec_symmetrize_map — subroutine - exec_symmetry_test — subroutine - exec_volanalyze — subroutine - exec_volcluster — subroutine - exec_volops — subroutine - postprocess_volume_from_files — subroutine

---

Module: simple_complex_ppca

Files: - main/pca/simple_complex_ppca.f90

Uses: - simple_core_module_api

Public symbols: - complex_ppca — type

Private symbols: - denoise_complex_ppca — subroutine - fit_covariance_complex_ppca — subroutine - generate_complex_ppca — subroutine - get_eigvals_complex_ppca — function - get_feat_complex_ppca — function - get_mean_complex_ppca — function - hermitian_jacobi — subroutine - kill_complex_ppca — subroutine - master_complex_ppca — subroutine - new_complex_ppca — subroutine - outer_hermitian — function - reconstruct_external_complex_ppca — subroutine - sort_eigs_desc — subroutine - stream_finalize_complex_ppca — subroutine - stream_reset_complex_ppca — subroutine - stream_update_complex_ppca — subroutine

---

Module: simple_convergence

Files: - main/simple_convergence.f90

Uses: - cplot2d_wrapper_module - simple_cmdline - simple_core_module_api - simple_parameters - simple_progress

Private symbols: - append_stats — subroutine - check_conv2D — function - check_conv3D — function - plot_projdirs — subroutine - print_iteration — subroutine - read — subroutine

---

Module: simple_core_module_api

Files: - main/apis/simple_core_api.f90

Uses: - simple_binoris - simple_chash - simple_class_sample_io - simple_defs - simple_defs_conv - simple_defs_fname - simple_defs_stream - simple_edges_sqwins - simple_error - simple_estimate_ssnr - simple_fileio - simple_hash - simple_imghead - simple_is_check_assert - simple_jiffys - simple_kbinterpol - simple_linalg - simple_magic_boxes - simple_map_reduce - simple_math - simple_math_ft - simple_nrtxtfile - simple_ori - simple_ori_utils - simple_oris - simple_ran_tabu - simple_rnd - simple_srch_sort_loc - simple_stat - simple_string - simple_string_utils - simple_sym - simple_syslib - simple_timer - simple_type_defs

---

Module: simple_corrmat

Files: - utils/simple_corrmat.f90

Uses: - simple_builder - simple_defs - simple_pftc_shsrch_grad - simple_pftc_srch_api

---

Module: simple_ctf

Files: - main/ctf/simple_ctf.f90

Uses: - simple_core_module_api

---

Module: simple_ctf_estimate_cost

Files: - main/ctf/simple_ctf_estimate_cost.f90

Uses: - simple_core_module_api - simple_ctf - simple_image - simple_opt_de - simple_opt_factory - simple_opt_spec - simple_optimizer

Private symbols: - df_costfun — subroutine - fdf — subroutine - fdf_costfun — subroutine - init1D — subroutine - init2D — subroutine - init4Dcont — subroutine - kill1D — subroutine - kill2D — subroutine - kill4Dcont — subroutine - minimize — subroutine - minimize4Dcont — subroutine

---

Module: simple_ctf_estimate_fit

Files: - main/ctf/simple_ctf_estimate_fit.f90

Uses: - cplot2d_wrapper_module - simple_core_module_api - simple_ctf - simple_ctf_estimate_cost - simple_image - simple_starfile_wrappers - simple_timer

Private symbols: - calc_ctfres — subroutine - calc_frc — subroutine - calc_icefrac — subroutine - calc_pspec_stats — subroutine - calc_tilt — subroutine - ctf2pspecimg — subroutine - fit — subroutine - fit_patches — subroutine - fit_polynomial — subroutine - ft2img — subroutine - gen_profiles — subroutine - gen_resmsk — subroutine - gen_roavspec1d — subroutine - gen_tiles — subroutine - get_parms — subroutine - get_pspec — subroutine - kill — subroutine - mask_central_disc — subroutine - mic2spec — subroutine - new — subroutine - norm_pspec — subroutine - pix2poly — subroutine - pix2polyvals — subroutine - plot_ctf — subroutine - poly — function - rank_spec — subroutine - read_doc — subroutine - refine — subroutine - srch — subroutine - subtr_backgr — subroutine - write_diagnostic — subroutine - write_doc — subroutine - write_star — subroutine

---

Module: simple_ctf_estimate_iter

Files: - main/ctf/simple_ctf_estimate_iter.f90

Uses: - simple_core_module_api - simple_ctf_estimate_fit - simple_image - simple_parameters

Public symbols: - ctf_estimate_iter — type

Private symbols: - gen_thumbnail — subroutine - iterate — subroutine - kill — subroutine

---

Module: simple_ctf_estimate_strategy

Files: - main/strategies/parallelization/simple_ctf_estimate_strategy.f90

Uses: - simple_binoris_io - simple_cmdline - simple_commanders_api - simple_ctf_estimate_iter - simple_parameters - simple_qsys_env - simple_sp_project

Public symbols: - create_ctf_estimate_strategy — function - ctf_estimate_distr_strategy — type - ctf_estimate_inmem_strategy — type - ctf_estimate_strategy — type

Private symbols: - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_end_message — function - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_end_message — function - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - set_ctf_estimate_defaults — subroutine

---

Module: simple_decay_funs

Files: - utils/math/simple_decay_funs.f90

Uses: - simple_core_module_api

Public symbols: - calc_nsampl_fromto — function - calc_update_frac — function - calc_update_frac_dyn — function - cos_decay — function - inv_cos_decay — function - inv_nsampl_decay — function - nsampl_decay — function

---

Module: simple_default_clines

Files: - defs/simple_default_clines.f90

Uses: - simple_cmdline - simple_defs - simple_estimate_ssnr

Public symbols: - set_automask2D_defaults — subroutine - set_cluster2D_defaults — subroutine

---

Module: simple_defs

Files: - defs/simple_defs.f90

---

Module: simple_defs_atoms

Files: - defs/simple_defs_atoms.f90

Public symbols: - get_element_Z_and_radius — subroutine - get_lattice_params — subroutine

---

Module: simple_defs_conv

Files: - defs/simple_defs_conv.f90

---

Module: simple_defs_environment

Files: - defs/simple_defs_environment.f90

---

Module: simple_defs_fname

Files: - defs/simple_defs_fname.f90

---

Module: simple_defs_ori

Files: - defs/simple_defs_ori.f90

Public symbols: - get_oriparam_flag — function

---

Module: simple_defs_stream

Files: - defs/simple_defs_stream.f90

---

Module: simple_defs_string

Files: - defs/simple_defs_string.f90

---

Module: simple_denoise_movies

Files: - main/motion/simple_denoise_movies.f90

Uses: - simple_core_module_api - simple_diff_map_denoise - simple_diff_map_graphs - simple_diffusion_maps - simple_image

Public symbols: - diffmap_denoise_image_stack — subroutine

Private symbols: - validate_realspace_2d_stack — subroutine

---

Module: simple_denoise_project_strategy

Files: - main/strategies/parallelization/simple_denoise_project_strategy.f90

Uses: - simple_builder - simple_classaverager - simple_cmdline - simple_core_module_api - simple_default_clines - simple_diff_map_graphs - simple_diffusion_maps - simple_eulspace_neigh_map - simple_exec_helpers - simple_image - simple_image_msk - simple_imgarr_utils - simple_imgfile - simple_imgproc - simple_linalg - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_sp_project - simple_srch_sort_loc

Public symbols: - create_denoise_project_strategy — function - denoise_project_master_strategy — type - denoise_project_shmem_strategy — type - denoise_project_strategy — type - denoise_project_worker_strategy — type

Private symbols: - apply_defaults — subroutine - assign_global_so3_mixtures — subroutine - build_diffmap_so3_mixture_graphs — subroutine - calc_diffmap_reconstruction_error — subroutine - calc_diffmap_residual_energy_ratio — subroutine - cleanup_interface — subroutine - count_data_lines — subroutine - estimate_diffmap_denoise_icm_rank_stats — subroutine - estimate_diffmap_denoise_rank — subroutine - exec_interface — subroutine - filter_classes_by_assignment — subroutine - finalize_diffmap_worker_outputs — subroutine - finalize_interface — subroutine - graph_nystrom_residual_preimage — subroutine - init_common — subroutine - init_interface — subroutine - master_cleanup — subroutine - master_execute — subroutine - master_finalize_run — subroutine - master_initialize — subroutine - pack_diffmap_so3_mixture_pinds — subroutine - prepare_class_partitions — subroutine - preserve_diffmap_frc2D — subroutine - read_diffmap_worker_maps — subroutine - read_int_file — subroutine - run_denoise_project — subroutine - run_diffmap_denoise_icm_rank_seed — subroutine - run_diffmap_so3_mixture_graphs — subroutine - select_diffmap_denoise_rank_icm — subroutine - setup_diffmap_so3_mixture_map — subroutine - shmem_cleanup — subroutine - shmem_execute — subroutine - shmem_finalize_run — subroutine - shmem_initialize — subroutine - sort_order_by_weight_desc — subroutine - update_diffmap_denoise_icm_rank_site — subroutine - validate_denoise_project — subroutine - worker_cleanup — subroutine - worker_execute — subroutine - worker_finalize_run — subroutine - worker_initialize — subroutine - write_diffmap_denoised_class — subroutine - write_diffmap_partial_project — subroutine - write_diffmap_project — subroutine - write_diffmap_stack_image — subroutine

---

Module: simple_diff_map_denoise

Files: - main/pca/simple_diff_map_denoise.f90

Uses: - simple_core_module_api - simple_diff_map_graphs - simple_diffusion_maps - simple_image - simple_imgarr_utils - simple_linalg - simple_parameters - simple_polarft_calc

Public symbols: - calc_diffmap_reconstruction_error — subroutine - calc_diffmap_residual_energy_ratio — subroutine - estimate_diffmap_denoise_rank — subroutine - graph_coeffproj_denoise — subroutine - graph_nystrom_residual_preimage — subroutine - select_spectral_rank_icm — subroutine

Private symbols: - accumulate_pft_angular_mode — subroutine - estimate_diffmap_denoise_icm_rank_stats — subroutine - extract_pft_angular_mode — subroutine - prepare_steerable_pft_params — subroutine - project_pft_angular_mode — subroutine - run_diffmap_denoise_icm_rank_seed — subroutine - scatter_fourier_sample — subroutine - so2_coeffproj_denoise — subroutine - synthesize_pft_residual — subroutine - update_diffmap_denoise_icm_rank_site — subroutine

---

Module: simple_diff_map_graphs

Files: - main/pca/simple_diff_map_graphs.f90

Uses: - simple_core_module_api - simple_ori - simple_parameters - simple_sp_project - simple_srch_sort_loc

Public symbols: - build_cls_split_graph — subroutine - build_euclidean_knn_graph — subroutine - build_gated_euclidean_graph_from_neighbors — subroutine - build_gated_euclidean_knn_graph — subroutine - build_orientation_knn_graph — subroutine - diffmap_graph — type - find_gated_euclidean_neighbors_rows — subroutine - graph_matvec — subroutine - projection_occupancy_weights — subroutine

Private symbols: - diffmap_graph_degree — subroutine - estimate_ferguson_bandwidth — subroutine - find_euclidean_neighbors — subroutine - find_orientation_neighbors — subroutine - insert_neighbor — subroutine - kill_diffmap_graph — subroutine - make_singleton_graph — subroutine - normalize_diffmap_graph — subroutine - pack_scalar_knn_to_csr — subroutine

---

Module: simple_diffusion_maps

Files: - main/pca/simple_diffusion_maps.f90

Uses: - simple_core_module_api - simple_diff_map_graphs - simple_linalg

Public symbols: - diffusion_map_embedder — type - embed_graph — subroutine - normalize_coords — subroutine

Private symbols: - embed — subroutine - set_params — subroutine

---

Module: simple_discrete_stack_io

Files: - fileio/simple_discrete_stack_io.f90

Uses: - simple_core_module_api - simple_image - simple_imgfile

Private symbols: - cache_stack_info — subroutine - clear_stack_cache — subroutine - get_stack_info — subroutine - kill — subroutine - new — subroutine - open_1 — subroutine - read — subroutine

---

Module: simple_distr_comm

Files: - utils/comm/simple_distr_comm.f90

Uses: - simple_socket_comm - unix

Public symbols: - distr_comm — type

Private symbols: - init — subroutine - server — subroutine - thread_comm — type

---

Module: simple_dock_vols

Files: - main/volume/simple_dock_vols.f90

Uses: - simple_core_module_api - simple_image - simple_projector - simple_simple_volinterp - simple_volpft_corrcalc

Private symbols: - get_dock_info — subroutine - kill — subroutine - new — subroutine - rotate_target — subroutine - rotpeak_interp — subroutine - set_dock_info — subroutine - set_ref — subroutine - set_target — subroutine - setup_srch_spaces — subroutine - srch — subroutine - srch_rots — subroutine - srch_shift — subroutine

---

Module: simple_edges_sqwins

Files: - main/interp/simple_edges_sqwins.f90

Uses: - simple_defs - simple_error

---

Module: simple_eer_factory

Files: - fileio/simple_eer_factory.f90

Uses: - simple_core_module_api - simple_image - simple_tifflib

Private symbols: - decode — subroutine - decode_frame_7bit_16k — subroutine - decode_frame_7bit_4k — subroutine - decode_frame_7bit_8k — subroutine - decode_frame_8bit_16k — subroutine - decode_frame_8bit_4k — subroutine - decode_frame_8bit_8k — subroutine - decode_frames — subroutine - get_ldim — function - kill — subroutine - new — subroutine - prep_gainref — subroutine - read — subroutine - set_dims — subroutine

---

Module: simple_error

Files: - fileio/simple_error.f90

Uses: - simple_defs

Public symbols: - simple_error_check — subroutine - simple_exception — subroutine

---

Module: simple_estimate_ssnr

Files: - utils/filter/simple_estimate_ssnr.f90

Uses: - simple_defs - simple_defs_conv - simple_defs_stream - simple_fileio - simple_magic_boxes - simple_math_ft - simple_srch_sort_loc - simple_string_utils - simple_syslib - simple_type_defs

Public symbols: - calc_dose_weights — subroutine - fsc2optlp — function - fsc2optlp_sub — subroutine - fsc2ssnr — function - fsc2wiener_regularizer — function - gaussian_filter — subroutine - get_resolution — subroutine - get_resolution_at_fsc — subroutine - lowpass_from_klim — subroutine - lpstages — subroutine - lpstages_fast — subroutine - lpstages_setlims — subroutine - mskdiam2lplimits — subroutine - mskdiam2streamresthreshold — subroutine - ssnr2fsc — function - ssnr2optlp — function

Private symbols: - calc_lpinfo — subroutine - calc_scaleinfo — subroutine - calc_scaleinfo — subroutine - print_lpinfo — subroutine - print_scaleinfo — subroutine

---

Module: simple_euclid_sigma2

Files: - main/simple_euclid_sigma2.f90

Uses: - simple_core_module_api - simple_parameters - simple_polarft_calc - simple_sigma2_binfile - simple_starfile_wrappers

Public symbols: - average_sigma2_groups — subroutine - consolidate_sigma2_groups — subroutine - fill_sigma2_before_nyq — subroutine - sigma2_star_from_iter — function - split_sigma2_into_groups — subroutine - test_unit — subroutine - write_groups_starfile — subroutine

Private symbols: - allocate_ptcls — subroutine - calc_sigma2 — subroutine - consolidate_sigma2_history — subroutine - get_kfromto — function - init_from_group_header — subroutine - kill — subroutine - new — subroutine - parse_key_int_pair — subroutine - parse_key_string_pair — subroutine - read_groups — subroutine - read_groups_starfile — subroutine - read_part — subroutine - read_sigma2_groups — subroutine - write_info — subroutine - write_sigma2 — subroutine

---

Module: simple_eul_prob_tab

Files: - main/simple_eul_prob_tab.f90

Uses: - simple_builder - simple_eul_prob_tab_utils - simple_pftc_shsrch_grad - simple_pftc_srch_api - simple_type_defs

Public symbols: - eul_prob_tab — type

Private symbols: - advance_ref_head — subroutine - advance_state_head — subroutine - assign_candidate — subroutine - assign_current_ref — subroutine - assign_greedy_state_labels — subroutine - assign_refs_for_state — subroutine - begin_write — subroutine - estimate_shift_seed — subroutine - fill_tab — subroutine - fill_tab_range — subroutine - fill_tab_state_only — subroutine - fill_tab_state_only_range — subroutine - flush_candidate_buffers — subroutine - gather_active_refs — subroutine - get_particle_context — subroutine - initialize_storage — subroutine - kill — subroutine - make_ref_candidate — function - new_assignment — subroutine - new_common — subroutine - new_compact_global — subroutine - new_global — subroutine - new_state — subroutine - new_worker — subroutine - prepare_ref_score_vectors — subroutine - process_particle_with_shift — subroutine - process_particle_without_shift — subroutine - read_assignment — subroutine - read_state_tab — subroutine - read_tab_to_glob — subroutine - record_ref_eval — subroutine - ref_assign — subroutine - refine_best_refs — subroutine - replace_ref_eval — subroutine - reset_ref_frontier — subroutine - score_ref — subroutine - state_assign — subroutine - write_assignment — subroutine - write_state_tab — subroutine - write_tab — subroutine

---

Module: simple_eul_prob_tab2D

Files: - main/simple_eul_prob_tab2D.f90

Uses: - simple_builder - simple_decay_funs - simple_eul_prob_tab_utils - simple_pftc_shsrch_grad - simple_pftc_srch_api

Public symbols: - eul_prob_tab2D — type

Private symbols: - advance_class_head — subroutine - assign_frontier_ws — type - assign_graph_ws — type - assign_particles_from_frontier — subroutine - assign_remaining_particles — subroutine - begin_write — subroutine - build_sparse_assignment_graph — subroutine - commit_selected_assignment — subroutine - dealloc_eval2D_sparse_ws — subroutine - eval2D_sparse_ws — type - fill_tab — subroutine - fill_tab_prob_snhc — subroutine - fill_tab_prob_snhc_range — subroutine - fill_tab_range — subroutine - finalize_assignment — subroutine - finalize_candidate_assignment — subroutine - flush_candidate_buffers — subroutine - init_eval2D_sparse_ws — subroutine - init_frontier — subroutine - initialize_storage — subroutine - kill — subroutine - new_assignment — subroutine - new_common — subroutine - new_global — subroutine - new_worker — subroutine - process_particle — subroutine - read_assignment — subroutine - read_sparse_tab_to_glob — subroutine - read_tab_to_glob — subroutine - read_tabs_to_glob — subroutine - record_sparse_eval — subroutine - ref_assign_likelihood — subroutine - ref_assign_sparse_likelihood — subroutine - refine_best_classes — subroutine - sample_frontier_likelihood — subroutine - score_class — subroutine - sync_frontier_class — subroutine - update_frontier_after_assignment — subroutine - write_assignment — subroutine - write_tab — subroutine

---

Module: simple_eul_prob_tab_neigh

Files: - main/simple_eul_prob_tab_neigh.f90

Uses: - simple_builder - simple_decay_funs - simple_eul_prob_tab - simple_eul_prob_tab_utils - simple_ori - simple_pftc_shsrch_grad - simple_pftc_srch_api

Public symbols: - eul_prob_tab_neigh — type

Private symbols: - add_pooled_subspace — subroutine - advance_ref_head — subroutine - alloc_coarse_ws — subroutine - alloc_eval_stoch_ws — subroutine - alloc_eval_subspace_ws — subroutine - assign_frontier_ws — type - assign_graph_ws — type - assign_greedy_state_labels — subroutine - assign_particles_for_state — subroutine - assign_particles_globally — subroutine - assign_particles_single_state — subroutine - assign_remaining_particles_from_best_touched_ref — subroutine - build_geometric_neighborhood — subroutine - build_pooled_neighborhood — subroutine - build_sparse_assignment_graph — subroutine - calc_previous_corr — subroutine - coarse_search_ws — type - commit_selected_assignment — subroutine - consider_peak_subspace — subroutine - dealloc_coarse_ws — subroutine - dealloc_eval_ws — subroutine - estimate_shift_seed — subroutine - eval_ws — type - evaluate_direct_stochastic_refs — subroutine - evaluate_neighborhood — subroutine - fill_tab_neigh — subroutine - fill_tab_neigh_range — subroutine - fill_tab_stoch_range — subroutine - fill_tab_subspace_range — subroutine - find_peak_subspaces — subroutine - get_particle_context — subroutine - init_eval_stoch_ws — subroutine - init_eval_subspace_ws — subroutine - init_frontier — subroutine - kill_neigh — subroutine - new_neigh — subroutine - new_neigh_global — subroutine - process_particle_stoch — subroutine - process_particle_subspace — subroutine - read_sparse_tab_to_glob — subroutine - read_tabs_to_glob — subroutine - record_sparse_eval — subroutine - ref_assign_neigh — subroutine - refine_best_neighbors — subroutine - score_direct_ref — subroutine - score_subspace_ref — subroutine - seed_fallback_if_empty — subroutine - sync_frontier_ref — subroutine - update_frontier_after_assignment — subroutine - validate_neigh_mode — subroutine

---

Module: simple_eul_prob_tab_utils

Files: - main/simple_eul_prob_tab_utils.f90

Uses: - simple_defs - simple_error - simple_math - simple_oris - simple_rnd - simple_type_defs

Public symbols: - prob_candidate — type - prob_candidate_buffer — type - prob_candidate_store — type

---

Module: simple_eulspace_neigh_map

Files: - utils/simple_eulspace_neigh_map.f90

Uses: - simple_core_module_api - simple_srchspace_map

Public symbols: - eulspace_neigh_map — type

Private symbols: - get_full2sub_map — function - get_neighbors_list — subroutine - get_neighbors_mask — subroutine - get_neighbors_mask_pooled — subroutine - kill — subroutine - new_from_labels — subroutine - new_from_spaces — subroutine

---

Module: simple_exec_abinitio3D

Files: - main/exec/simple_exec_abinitio3D.f90

Uses: - simple_cmdline - simple_commanders_abinitio - simple_commanders_resolest - simple_commanders_volops - simple_exec_helpers - simple_string

Public symbols: - exec_abinitio3D_commander — subroutine

---

Module: simple_exec_api

Files: - main/apis/simple_exec_api.f90

Uses: - iso_fortran_env - simple_cmdline - simple_core_module_api - simple_exec_abinitio3d - simple_exec_cavgproc - simple_exec_cluster2d - simple_exec_denoise - simple_exec_dock - simple_exec_filter - simple_exec_helpers - simple_exec_image - simple_exec_mask - simple_exec_ori - simple_exec_other - simple_exec_preproc - simple_exec_print - simple_exec_project - simple_exec_refine3d - simple_exec_res - simple_exec_sieve - simple_exec_sim - simple_exec_sym - simple_exec_validate - simple_exec_volume - simple_jiffys - simple_ui - simple_ui_program

---

Module: simple_exec_cavgproc

Files: - main/exec/simple_exec_cavgproc.f90

Uses: - simple_cmdline - simple_commanders_cavgs - simple_commanders_stkops

Public symbols: - exec_cavgproc_commander — subroutine

---

Module: simple_exec_cluster2D

Files: - main/exec/simple_exec_cluster2D.f90

Uses: - simple_cmdline - simple_commanders_abinitio2d - simple_commanders_cavgs - simple_commanders_cluster2d - simple_commanders_mkcavgs - simple_commanders_project_cls - simple_exec_helpers - simple_stream_abinitio2d_chunks - simple_string

Public symbols: - exec_cluster2D_commander — subroutine

---

Module: simple_exec_denoise

Files: - main/exec/simple_exec_denoise.f90

Uses: - simple_cmdline - simple_commanders_cluster2d - simple_commanders_denoise - simple_commanders_flex_analysis - simple_commanders_imgops - simple_commanders_resolest - simple_commanders_volops

Public symbols: - exec_denoise_commander — subroutine

---

Module: simple_exec_dock

Files: - main/exec/simple_exec_dock.f90

Uses: - simple_cmdline - simple_commanders_volops

Public symbols: - exec_dock_commander — subroutine

---

Module: simple_exec_filter

Files: - main/exec/simple_exec_filter.f90

Uses: - simple_cmdline - simple_commanders_imgops - simple_commanders_resolest

Public symbols: - exec_filter_commander — subroutine

---

Module: simple_exec_helpers

Files: - utils/simple_exec_helpers.f90

Uses: - simple_cmdline - simple_core_module_api - simple_parameters - simple_qsys_env - simple_sp_project

Public symbols: - async_exec — subroutine - copy_project_file_to_root_dir — subroutine - exec_screen — subroutine - gen_exec_cmd — function - restarted_exec — subroutine - script_exec — subroutine - set_master_num_threads — subroutine - update_job_descriptions_in_project — subroutine

---

Module: simple_exec_image

Files: - main/exec/simple_exec_image.f90

Uses: - simple_cmdline - simple_commanders_imgops - simple_commanders_imgproc - simple_commanders_stkops

Public symbols: - exec_image_commander — subroutine

---

Module: simple_exec_mask

Files: - main/exec/simple_exec_mask.f90

Uses: - simple_cmdline - simple_commanders_mask

Public symbols: - exec_mask_commander — subroutine

---

Module: simple_exec_ori

Files: - main/exec/simple_exec_ori.f90

Uses: - simple_cmdline - simple_commanders_ori

Public symbols: - exec_ori_commander — subroutine

---

Module: simple_exec_other

Files: - main/exec/simple_exec_other.f90

Uses: - simple_cmdline - simple_commanders_atoms - simple_commanders_distr - simple_commanders_misc - simple_commanders_project_ptcl

Public symbols: - exec_other_commander — subroutine

---

Module: simple_exec_preproc

Files: - main/exec/simple_exec_preproc.f90

Uses: - simple_cmdline - simple_commanders_pick - simple_commanders_preprocess - simple_commanders_starproject

Public symbols: - exec_preproc_commander — subroutine

---

Module: simple_exec_print

Files: - main/exec/simple_exec_print.f90

Uses: - simple_cmdline - simple_commanders_checks - simple_commanders_misc

Public symbols: - exec_print_commander — subroutine

---

Module: simple_exec_project

Files: - main/exec/simple_exec_project.f90

Uses: - simple_cmdline - simple_commanders_project_cls - simple_commanders_project_core - simple_commanders_project_mov - simple_commanders_project_ptcl - simple_commanders_relion - simple_commanders_starproject - single_commanders_trajectory

Public symbols: - exec_project_commander — subroutine

---

Module: simple_exec_refine3D

Files: - main/exec/simple_exec_refine3D.f90

Uses: - simple_cmdline - simple_commanders_mask - simple_commanders_rec - simple_commanders_refine3d - simple_commanders_volops - simple_exec_helpers - simple_string

Public symbols: - exec_refine3D_commander — subroutine

---

Module: simple_exec_res

Files: - main/exec/simple_exec_res.f90

Uses: - simple_cmdline - simple_commanders_resolest

Public symbols: - exec_res_commander — subroutine

---

Module: simple_exec_sieve

Files: - main/exec/simple_exec_sieve.f90

Uses: - simple_cmdline - simple_commanders_sieve

Public symbols: - exec_sieve_commander — subroutine

---

Module: simple_exec_sim

Files: - main/exec/simple_exec_sim.f90

Uses: - simple_cmdline - simple_commanders_atoms - simple_commanders_sim

Public symbols: - exec_sim_commander — subroutine

---

Module: simple_exec_sym

Files: - main/exec/simple_exec_sym.f90

Uses: - simple_cmdline - simple_commanders_volops

Public symbols: - exec_sym_commander — subroutine

---

Module: simple_exec_validate

Files: - main/exec/simple_exec_validate.f90

Uses: - simple_cmdline - simple_commanders_atoms - simple_commanders_validate

Public symbols: - exec_validate_commander — subroutine

---

Module: simple_exec_volume

Files: - main/exec/simple_exec_volume.f90

Uses: - simple_cmdline - simple_commanders_reconstruct3d_pcg - simple_commanders_reproject - simple_commanders_volops

Public symbols: - exec_volume_commander — subroutine

---

Module: simple_extract_strategy

Files: - main/strategies/parallelization/simple_extract_strategy.f90

Uses: - simple_cmdline - simple_commanders_api - simple_ctf_estimate_fit - simple_parameters - simple_particle_extractor - simple_qsys_env - simple_sp_project

Public symbols: - create_extract_strategy — function - extract_distr_strategy — type - extract_inmem_strategy — type - extract_strategy — type

Private symbols: - apply_defaults_interface — subroutine - cleanup_interface — subroutine - distr_apply_defaults — subroutine - distr_cleanup — subroutine - distr_end_message — function - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_apply_defaults — subroutine - inmem_cleanup — subroutine - inmem_end_message — function - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - killimgbatch — subroutine - prepimgbatch — subroutine - set_extract_defaults — subroutine

---

Module: simple_fftw3

Files: - defs/simple_fftw3.f90

Public symbols: - fftw_cleanup — subroutine - fftw_cleanup_threads — subroutine - fftw_destroy_plan — subroutine - fftw_execute_dft — subroutine - fftw_execute_dft_c2r — subroutine - fftw_execute_dft_r2c — subroutine - fftw_execute_r2r — subroutine - fftw_execute_split_dft — subroutine - fftw_execute_split_dft_c2r — subroutine - fftw_execute_split_dft_r2c — subroutine - fftw_export_wisdom — subroutine - fftw_export_wisdom_to_file — subroutine - fftw_flops — subroutine - fftw_forget_wisdom — subroutine - fftw_fprint_plan — subroutine - fftw_free — subroutine - fftw_free_str — subroutine - fftw_iodim — type - fftw_iodim64 — type - fftw_plan_with_nthreads — subroutine - fftw_print_plan — subroutine - fftw_set_timelimit — subroutine - fftwf_cleanup — subroutine - fftwf_cleanup_threads — subroutine - fftwf_destroy_plan — subroutine - fftwf_execute_dft — subroutine - fftwf_execute_dft_c2r — subroutine - fftwf_execute_dft_r2c — subroutine - fftwf_execute_r2r — subroutine - fftwf_execute_split_dft — subroutine - fftwf_execute_split_dft_c2r — subroutine - fftwf_execute_split_dft_r2c — subroutine - fftwf_export_wisdom — subroutine - fftwf_export_wisdom_to_file — subroutine - fftwf_flops — subroutine - fftwf_forget_wisdom — subroutine - fftwf_fprint_plan — subroutine - fftwf_free — subroutine - fftwf_iodim — type - fftwf_iodim64 — type - fftwf_plan_with_nthreads — subroutine - fftwf_print_plan — subroutine - fftwf_set_timelimit — subroutine

---

Module: simple_fileio

Files: - fileio/simple_fileio.f90

Uses: - simple_defs - simple_error - simple_string - simple_string_utils - simple_syslib

---

Module: simple_fileio_tester

Files: - fileio/simple_fileio_tester.f90

Uses: - simple_defs - simple_fileio - simple_string - simple_string_utils - simple_syslib - simple_test_utils

Public symbols: - run_all_fileio_tests — subroutine

Private symbols: - test_add2fbody_rm_swap_getfbody — subroutine - test_arr2file_sp_dp_roundtrip — subroutine - test_arr2txtfile_roundtrip — subroutine - test_filepath_overloads — subroutine - test_fname2ext_and_basename — subroutine - test_fname2format — subroutine - test_fname2iter — subroutine - test_fopen_and_fclose_basic — subroutine - test_get_fpath_and_stemname — subroutine - test_get_relative_path — subroutine - test_make_dir_and_file_names — subroutine - test_nlines_and_filelength — subroutine - test_read_write_filetable — subroutine - test_rmat_lmat_roundtrip — subroutine - test_simple_copy_file — subroutine - test_simple_list_files_and_regexp — subroutine - test_simple_mkdir_dir_exists_chdir_getcwd_rmdir — subroutine - test_simple_touch_rename_abspath — subroutine - test_write_singlelineoftext_and_read_exit_code — subroutine

---

Module: simple_finch

Files: - utils/clustering/simple_finch.f90

Uses: - simple_core_module_api - simple_kd_tree

Public symbols: - finch_hierarchy — type - finch_partition_from_first_neighbors — subroutine - finch_representatives — subroutine - fit_finch — subroutine - refine_finch_level — subroutine - select_finch_level — subroutine

Private symbols: - append_level — subroutine - finch_get_coarsest_labels — subroutine - finch_get_finest_labels — subroutine - finch_get_labels — subroutine - grow_ward_heap — subroutine - initialize_refinement_nodes — subroutine - kill_finch_hierarchy — subroutine - kill_ward_heap — subroutine - reserve_ward_heap — subroutine - swap_ward_edges — subroutine - trim_hierarchy — subroutine - union_components — subroutine - ward_edge_heap — type - ward_heap_pop — subroutine - ward_heap_push — subroutine - weighted_cluster_centroids — subroutine

---

Module: simple_flex_analysis_strategy

Files: - main/flex/simple_flex_analysis_strategy.f90

Uses: - simple_builder - simple_cmdline - simple_core_module_api - simple_diff_map_denoise - simple_diff_map_graphs - simple_diffusion_maps - simple_flex_diffmap_features - simple_flex_diffmap_preimage - simple_flex_diffmap_rec3d - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_sigma2_files - simple_sp_project

Public symbols: - create_flex_analysis_strategy — function - fit_flex_analysis_embedding — subroutine - flex_analysis_master_strategy — type - flex_analysis_shmem_strategy — type - flex_analysis_strategy — type - flex_analysis_worker_strategy — type - flex_embedding_result — type

Private symbols: - apply_defaults — subroutine - build_flex_diffmap_graph — subroutine - capture_result — subroutine - cleanup_distributed_analysis_parts — subroutine - cleanup_interface — subroutine - collect_target_coefficients — subroutine - embed_flex_graph — subroutine - ensure_flex_sigma_support — subroutine - exec_interface — subroutine - finalize_interface — subroutine - finish_analysis_outputs — subroutine - init_common — subroutine - init_interface — subroutine - init_model_context — subroutine - kill_flex_embedding_result — subroutine - log_flex_coordinate_scales — subroutine - master_cleanup — subroutine - master_execute — subroutine - master_finalize_run — subroutine - master_initialize — subroutine - prepare_particle_partitions — subroutine - prepare_reconstruction_partitions — subroutine - read_flex_reconstruction_assignment — subroutine - read_graph_parts — subroutine - read_int_file — subroutine - run_flex_analysis — subroutine - select_flex_spectral_rank — subroutine - select_particles — subroutine - shmem_cleanup — subroutine - shmem_execute — subroutine - shmem_finalize_run — subroutine - shmem_initialize — subroutine - validate_inputs — subroutine - validate_selected_particles — subroutine - worker_cleanup — subroutine - worker_execute — subroutine - worker_finalize_run — subroutine - worker_initialize — subroutine - write_coordinates — subroutine - write_discrete_state_project — subroutine - write_graph_part — subroutine - write_graph_summary — subroutine - write_preimage_particle_map — subroutine - write_spectrum — subroutine

---

Module: simple_flex_diffmap_features

Files: - main/flex/simple_flex_diffmap_features.f90

Uses: - simple_builder - simple_classaverager - simple_core_module_api - simple_ctf - simple_image - simple_imgarr_utils - simple_math_ft - simple_memoize_ft_maps - simple_ori - simple_parameters - simple_simple_volinterp - simple_sp_project - simple_stack_io

Public symbols: - assemble_flex_diffmap_feature_parts — subroutine - flex_projection_directions — subroutine - map_flex_registered_to_native_project — subroutine - prepare_flex_diffmap_feature_part — subroutine - prepare_flex_diffmap_features — subroutine - read_flex_diffmap_feature_parts — subroutine - write_flex_mean_projection_stack — subroutine

Private symbols: - apply_sigma_shell_whitening — subroutine - read_mean_projection_stack — subroutine - write_registered_project — subroutine

---

Module: simple_flex_diffmap_preimage

Files: - main/flex/simple_flex_diffmap_preimage.f90

Uses: - simple_clustering_utils - simple_core_module_api - simple_srch_sort_loc

Public symbols: - build_flex_preimage_kernel_weights — subroutine - select_flex_diffmap_preimages — subroutine - test_flex_preimage_bandwidth_decoupling — subroutine

Private symbols: - dense_bandwidth — function - median_default_real — function - median_positive_d2 — function - raw_neff_state — function

---

Module: simple_flex_diffmap_rec3D

Files: - main/flex/simple_flex_diffmap_rec3D.f90

Uses: - simple_builder - simple_core_module_api - simple_flex_projected_latent_model - simple_flex_reconstructor_latent_ops - simple_gridding - simple_image - simple_matcher_3drec - simple_matcher_ptcl_io - simple_parameters - simple_reconstructor - simple_sp_project

Public symbols: - cleanup_flex_diffmap_rec_parts — subroutine - reconstruct_flex_diffmap_local_linear_states — subroutine - reconstruct_flex_diffmap_states — subroutine - reconstruct_flex_diffmap_weighted_states — subroutine - reduce_flex_diffmap_rec_parts — subroutine - test_flex_local_linear_preimage — subroutine - write_flex_diffmap_rec_parts — subroutine

Private symbols: - cleanup_reconstructors — subroutine - flex_part_fname — function - init_basis_reconstructor — subroutine - init_mean_reconstructor — subroutine - ll_solve — subroutine - ll_solve_intercept — function - ll_solve_slope — function - prepare_project_fsc_lowpass_filters — subroutine - prepare_unfiltered_model_params — subroutine - validate_model_tables — subroutine - write_preimage_states — subroutine - write_state — subroutine

---

Module: simple_flex_projected_latent_model

Files: - main/flex/simple_flex_projected_latent_model.f90

Uses: - simple_builder - simple_core_module_api - simple_flex_reconstructor_latent_ops - simple_gridding - simple_image - simple_imgarr_utils - simple_linalg - simple_map_reduce - simple_matcher_3drec - simple_matcher_ptcl_io - simple_math - simple_memoize_ft_maps - simple_parameters - simple_reconstructor - simple_rnd

Public symbols: - basis_fourier_energy — function - canonicalize_projected_latent_basis — subroutine - cleanup_planes — subroutine - infer_latents_from_basis — subroutine - initialize_latents — subroutine - latent_covariance — subroutine - latent_sdev — function - orthonormalize_latents — subroutine - prep_imgs4projected_model — subroutine - projected_model_kfromto — function - reduce_estep_latent_part_files — subroutine - solve_coupled_basis_exp — subroutine - test_projected_latent_canonicalization — subroutine - test_projected_latent_mstep_stats_io — subroutine - update_basis_from_latents — subroutine - update_basis_from_mstep_stats_part_files — subroutine - write_estep_latent_part_file — subroutine - write_mstep_stats_part_file — subroutine

Private symbols: - accumulate_projected_latent_mstep_2d_block — subroutine - cap_fplane_for_projected_model — subroutine - cleanup_plane — subroutine - cleanup_runtime_batch — subroutine - compute_canonical_transform — subroutine - finalize_basis_for_projection — subroutine - hermitian_plane_inner_product — function - init_projected_latent_estep_part — subroutine - init_projected_latent_mstep_2d_block — subroutine - init_projected_latent_mstep_stats — subroutine - insert_projected_latent_mstep_2d_block — subroutine - kill_projected_latent_estep_part — subroutine - kill_projected_latent_mstep_2d_block — subroutine - kill_projected_latent_mstep_stats — subroutine - log_comp_seconds — subroutine - log_seconds — subroutine - mix_projected_latent_basis — subroutine - plane_energy — function - prepare_projected_latent_estep_part — subroutine - prepare_projected_latent_mstep_2d_block — subroutine - projected_latent_estep_part — type - projected_latent_mstep_2d_block — type - projected_latent_mstep_stats — type - projected_model_log_prefix — function - read_particles — subroutine - read_projected_latent_estep_part — subroutine - reduce_projected_latent_estep_part — subroutine - reduce_projected_latent_mstep_stats_file — subroutine - regularize_basis_volume — subroutine - reseed_latent_column — subroutine - reset_projected_latent_estep_part — subroutine - reset_projected_latent_mstep_2d_block — subroutine - solve_latent_least_squares — subroutine - solve_real_spd_complex — subroutine - subtract_plane — subroutine - subtract_scaled_plane — subroutine - write_projected_latent_estep_part — subroutine - write_projected_latent_mstep_stats — subroutine

---

Module: simple_flex_reconstructor_latent_ops

Files: - main/flex/simple_flex_reconstructor_latent_ops.f90

Uses: - simple_core_module_api - simple_ftiter - simple_math - simple_parameters - simple_reconstructor - simple_sp_project

Public symbols: - accumulate_plane_oversamp_coupled_stats — subroutine - accumulate_planes_oversamp_coupled_stats_batch — subroutine - insert_plane_oversamp_coupled_scaled — subroutine - insert_plane_oversamp_multi_scaled — subroutine - insert_planes_oversamp_coupled_batch_scaled — subroutine - project_fplane_mean — subroutine - project_fplanes_mean_basis — subroutine - test_cartesian_projection_contract — subroutine - test_coupled_batch_accumulation — subroutine

Private symbols: - cleanup_test_plane — subroutine - ensure_latent_projection_plane — subroutine - kb_apod_vecs_3d_fast — subroutine - kb_apod_vecs_3d_fast — subroutine - kb_apod_vecs_3d_fast — subroutine - kb_apod_vecs_3d_fast — subroutine - kb_apod_vecs_3d_fast — subroutine - latent_projection_weights — subroutine - weighted_expanded_cmat — function

---

Module: simple_forked_process

Files: - utils/simple_forked_process.f90

Uses: - simple_cmdline - simple_defs - simple_error - simple_fileio - simple_memory_monitor - simple_string - simple_string_utils - simple_syslib - unix

Public symbols: - forked_process — type

Private symbols: - await_final_status — subroutine - destroy — subroutine - execute_test — subroutine - get_failtime — function - get_nrestarts — function - get_pid — function - get_queuetime — function - get_starttime — function - get_stoptime — function - kill — subroutine - sigterm_handler — subroutine - skip — subroutine - start — subroutine - status — function - terminate — subroutine

---

Module: simple_forked_process_tester

Files: - utils/simple_forked_process_tester.f90

Uses: - simple_forked_process - simple_string - simple_syslib - simple_test_utils - unix

Public symbols: - run_all_forked_process_tests — subroutine

Private symbols: - test_destroy — subroutine - test_fail_timestamps — subroutine - test_kill — subroutine - test_logfile_redirection — subroutine - test_restart — subroutine - test_start — subroutine - test_terminate — subroutine - test_timestamps — subroutine

---

Module: simple_fsc

Files: - utils/filter/simple_fsc.f90

Uses: - cplot2d_wrapper_module - simple_core_module_api - simple_image

Public symbols: - fsc_area_score_result — type - phase_rand_fsc — subroutine - plot_fsc — subroutine - plot_fsc2 — subroutine - plot_fsc_area_score — subroutine - plot_phrand_fsc — subroutine - write_fsc_area_score_outputs — subroutine

Private symbols: - add_crossing_bars — subroutine - add_curve — subroutine - add_curve_segment — subroutine - add_filled_band — subroutine - add_filled_band_segment — subroutine - add_filled_rect — subroutine - add_invisible_bounds — subroutine - add_segment — subroutine - bar_edges — subroutine - calc_fsc_area_score — subroutine - fibonacci_sphere_dirs — subroutine - kill — subroutine - new — subroutine - score_cfsc_curve — subroutine

---

Module: simple_ft_expanded

Files: - main/image/simple_ft_expanded.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - ft_expanded — type - ftexp_transfmat_init — subroutine - ftexp_transfmat_kill — subroutine

Private symbols: - add — subroutine - add2cmat — subroutine - add_uncond — subroutine - alloc_and_calc_tmp_cmat12 — subroutine - copy — subroutine - corr — function - corr_fdfshifted_cost_8 — subroutine - corr_gshifted_cost_8 — subroutine - corr_normalize_dp — subroutine - corr_normalize_sp — subroutine - corr_shifted_cost_8 — function - corr_unnorm — function - corr_unnorm_serial — function - dealloc_tmp_cmat12 — subroutine - div — subroutine - get_flims — function - get_hp_lp — subroutine - kill — subroutine - new — subroutine - normalize_mat — subroutine - set_cmat — subroutine - shift — subroutine - shift_and_add — subroutine - subtr — subroutine - zero — subroutine

---

Module: simple_ftexp_shsrch

Files: - main/image/simple_ftexp_shsrch.f90

Uses: - simple_core_module_api - simple_ft_expanded - simple_image - simple_opt_factory - simple_opt_spec - simple_optimizer

Public symbols: - ftexp_shsrch — type - test_ftexp_shsrch — subroutine - test_ftexp_shsrch2 — subroutine

Private symbols: - ftexp_shsrch_cost_8 — function - ftexp_shsrch_fdfcost_8 — subroutine - ftexp_shsrch_gcost_8 — subroutine - ftexp_shsrch_kill — subroutine - ftexp_shsrch_minimize — function - ftexp_shsrch_new — subroutine - profile_corrs — subroutine - set_factr_pgtol — subroutine - set_shsrch_tol — subroutine - test_shifted_correlator — subroutine

---

Module: simple_ftiter

Files: - main/image/simple_ftiter.f90

Uses: - simple_core_module_api

Public symbols: - ftiter — type

---

Module: simple_gauss2Dfit

Files: - utils/simple_gauss2Dfit.f90

Uses: - simple_core_module_api - simple_image

---

Module: simple_gen_pspecs_and_thumbs_strategy

Files: - main/strategies/parallelization/simple_gen_pspecs_and_thumbs_strategy.f90

Uses: - simple_binoris_io - simple_cmdline - simple_commanders_api - simple_parameters - simple_pspec_thumb_iter - simple_qsys_env - simple_sp_project

Public symbols: - create_gen_pspecs_and_thumbs_strategy — function - gen_pspecs_and_thumbs_distr_strategy — type - gen_pspecs_and_thumbs_inmem_strategy — type - gen_pspecs_and_thumbs_strategy — type

Private symbols: - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_end_message — function - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_end_message — function - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - set_gen_pspecs_and_thumbs_defaults — subroutine

---

Module: simple_gpu_utils

Files: - utils/simple_gpu_utils.f90

Uses: - simple_core_module_api

Public symbols: - cuda_device_prop — type

---

Module: simple_gridding

Files: - main/interp/simple_gridding.f90

Uses: - simple_core_module_api - simple_image - simple_projector

Public symbols: - prep2D_inv_instrfun4mul — function - prep3D_inv_instrfun4mul — function

---

Module: simple_gui_assembler

Files: - utils/gui/simple_gui_assembler.f90

Uses: - simple_forked_process - simple_gui_metadata_api - simple_string - unix

Public symbols: - gui_assembler — type

Private symbols: - assemble_stream_heartbeat — subroutine - assemble_stream_initial_picking — subroutine - assemble_stream_opening2D — subroutine - assemble_stream_optics_assignment — subroutine - assemble_stream_particle_sieving — subroutine - assemble_stream_pool2D — subroutine - assemble_stream_preprocess — subroutine - assemble_stream_reference_picking — subroutine - clear_hashes — subroutine - forked_process_status — subroutine - is_associated — function - kill — subroutine - new — subroutine - set_stoptime — subroutine - to_string — function

---

Module: simple_gui_assembler_tester

Files: - utils/gui/simple_gui_assembler_tester.f90

Uses: - simple_gui_assembler - simple_gui_metadata_api - simple_string - simple_test_utils

Public symbols: - run_all_gui_assembler_tests — subroutine

Private symbols: - test_clear_hashes — subroutine - test_initial_picking — subroutine - test_new_kill — subroutine - test_new_kill_reuse — subroutine - test_opening2D — subroutine - test_optics_assignment — subroutine - test_particle_sieving — subroutine - test_pool2D — subroutine - test_preprocess — subroutine - test_reference_picking — subroutine - test_set_stoptime — subroutine

---

Module: simple_gui_metadata_api

Files: - main/apis/simple_gui_metadata_api.f90

Uses: - json_kinds - json_module - simple_core_module_api - simple_gui_metadata_base - simple_gui_metadata_cavg2d - simple_gui_metadata_histogram - simple_gui_metadata_micrograph - simple_gui_metadata_optics_group - simple_gui_metadata_stream_opening2d - simple_gui_metadata_stream_optics_assignment - simple_gui_metadata_stream_particle_sieving - simple_gui_metadata_stream_picking - simple_gui_metadata_stream_pool2d - simple_gui_metadata_stream_pool2d_snapshot - simple_gui_metadata_stream_preprocess - simple_gui_metadata_stream_update - simple_gui_metadata_timeplot - simple_gui_metadata_types

---

Module: simple_gui_metadata_base

Files: - utils/gui/metadata/simple_gui_metadata_base.f90

Uses: - json_module - simple_error

Public symbols: - gui_metadata_base — type

Private symbols: - assigned — function - initialized — function - jsonise — function - kill — subroutine - new — subroutine - serialise — subroutine - type — function

---

Module: simple_gui_metadata_cavg2D

Files: - utils/gui/metadata/simple_gui_metadata_cavg2D.f90

Uses: - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_gui_metadata_types - simple_string

Public symbols: - gui_metadata_cavg2D — type - sprite_sheet_pos — type

Private symbols: - get — function - get_i — function - get_i_max — function - get_idx — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_histogram

Files: - utils/gui/metadata/simple_gui_metadata_histogram.f90

Uses: - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string

Public symbols: - gui_metadata_histogram — type

Private symbols: - get — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_micrograph

Files: - utils/gui/metadata/simple_gui_metadata_micrograph.f90

Uses: - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string

Public symbols: - gui_metadata_micrograph — type

Private symbols: - clear_coordinates — subroutine - get — function - get_i — function - get_i_max — function - jsonise_override — function - set — subroutine - set_coordinate — subroutine

---

Module: simple_gui_metadata_optics_group

Files: - utils/gui/metadata/simple_gui_metadata_optics_group.f90

Uses: - json_module - simple_error - simple_gui_metadata_base

Public symbols: - gui_metadata_optics_group — type

Private symbols: - get — function - get_i — function - get_i_max — function - get_max_points — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_stream_opening2D

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_opening2D.f90

Uses: - json_kinds - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string - unix

Public symbols: - gui_metadata_stream_opening2D — type

Private symbols: - get — function - jsonise_override — function - set — subroutine - set_user_input — subroutine

---

Module: simple_gui_metadata_stream_optics_assignment

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_optics_assignment.f90

Uses: - json_kinds - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string - unix

Public symbols: - gui_metadata_stream_optics_assignment — type

Private symbols: - get — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_stream_particle_sieving

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_particle_sieving.f90

Uses: - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string - unix

Public symbols: - gui_metadata_stream_particle_sieving — type

Private symbols: - clear_selection — subroutine - get — function - jsonise_override — function - set — subroutine - set_selection — subroutine - set_user_input — subroutine

---

Module: simple_gui_metadata_stream_picking

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_picking.f90

Uses: - json_kinds - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string - unix

Public symbols: - gui_metadata_stream_picking — type

Private symbols: - get — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_stream_pool2D

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_pool2D.f90

Uses: - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string - unix

Public symbols: - gui_metadata_stream_pool2D — type

Private symbols: - get — function - jsonise_override — function - set — subroutine - set_initial_ref_selection — subroutine - set_user_input — subroutine

---

Module: simple_gui_metadata_stream_pool2D_snapshot

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_pool2D_snapshot.f90

Uses: - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string - unix

Public symbols: - gui_metadata_stream_pool2D_snapshot — type

Private symbols: - get — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_stream_preprocess

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_preprocess.f90

Uses: - json_kinds - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string

Public symbols: - gui_metadata_stream_preprocess — type

Private symbols: - get — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_stream_update

Files: - utils/gui/metadata/stream/simple_gui_metadata_stream_update.f90

Uses: - json_kinds - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string

Public symbols: - gui_metadata_stream_update — type

Private symbols: - get_astigmatism_update — function - get_ctfres_update — function - get_icescore_update — function - get_increase_nmics — function - get_mskdiam2D_update — function - get_pickrefs_clusters — function - get_pickrefs_selection — function - get_pickrefs_selection_length — function - get_sieverefs_selection — function - get_sieverefs_selection_length — function - get_snapshot2D_update — subroutine - has_snapshot2D_update — function - set_astigmatism_update — subroutine - set_ctfres_update — subroutine - set_icescore_update — subroutine - set_increase_nmics — subroutine - set_mskdiam2D_update — subroutine - set_pickrefs_clusters — subroutine - set_pickrefs_selection — subroutine - set_pickrefs_selection_length — subroutine - set_sieverefs_selection — subroutine - set_sieverefs_selection_length — subroutine - set_snapshot2D_update — subroutine

---

Module: simple_gui_metadata_tester

Files: - utils/gui/metadata/simple_gui_metadata_tester.f90

Uses: - simple_gui_metadata_api - simple_test_utils

Public symbols: - run_all_gui_metadata_tests — subroutine

Private symbols: - test_jsonise_cavg2D — subroutine - test_jsonise_histogram — subroutine - test_jsonise_micrograph — subroutine - test_jsonise_optics_group — subroutine - test_jsonise_stream_initial_picking — subroutine - test_jsonise_stream_opening2D — subroutine - test_jsonise_stream_optics_assignment — subroutine - test_jsonise_stream_particle_sieving — subroutine - test_jsonise_stream_pool2D — subroutine - test_jsonise_stream_pool2D_snapshot — subroutine - test_jsonise_stream_preprocess — subroutine - test_jsonise_stream_reference_picking — subroutine - test_jsonise_stream_update — subroutine - test_jsonise_timeplot — subroutine - test_new_kill — subroutine - test_serialise — subroutine - test_serialise_cavg2D — subroutine - test_serialise_histogram — subroutine - test_serialise_micrograph — subroutine - test_serialise_optics_group — subroutine - test_serialise_stream_initial_picking — subroutine - test_serialise_stream_opening2D — subroutine - test_serialise_stream_optics_assignment — subroutine - test_serialise_stream_particle_sieving — subroutine - test_serialise_stream_pool2D — subroutine - test_serialise_stream_pool2D_snapshot — subroutine - test_serialise_stream_preprocess — subroutine - test_serialise_stream_reference_picking — subroutine - test_serialise_stream_update — subroutine - test_serialise_timeplot — subroutine - test_set_get_cavg2D — subroutine - test_set_get_histogram — subroutine - test_set_get_micrograph — subroutine - test_set_get_optics_group — subroutine - test_set_get_stream_initial_picking — subroutine - test_set_get_stream_opening2D — subroutine - test_set_get_stream_optics_assignment — subroutine - test_set_get_stream_particle_sieving — subroutine - test_set_get_stream_pool2D — subroutine - test_set_get_stream_pool2D_snapshot — subroutine - test_set_get_stream_preprocess — subroutine - test_set_get_stream_reference_picking — subroutine - test_set_get_stream_update — subroutine - test_set_get_timeplot — subroutine

---

Module: simple_gui_metadata_timeplot

Files: - utils/gui/metadata/simple_gui_metadata_timeplot.f90

Uses: - json_module - simple_defs - simple_error - simple_gui_metadata_base - simple_string

Public symbols: - gui_metadata_timeplot — type

Private symbols: - get — function - jsonise_override — function - set — subroutine

---

Module: simple_gui_metadata_types

Files: - utils/gui/metadata/simple_gui_metadata_types.f90

---

Module: simple_gui_metadata_utils

Files: - utils/gui/metadata/simple_gui_metadata_utils.f90

Uses: - simple_gui_metadata_api

Public symbols: - max_metadata_size — function

---

Module: simple_gui_utils

Files: - utils/gui/simple_gui_utils.f90

Uses: - simple_core_module_api - simple_image - simple_stack_io

Public symbols: - mic2thumb — subroutine - mrc2jpeg_tiled — subroutine

---

Module: simple_guistats

Files: - utils/gui/simple_guistats.f90

Uses: - json_module - simple_core_module_api - simple_image

Private symbols: - create_section_array — subroutine - deactivate_section — subroutine - delete — subroutine - ensure_section — subroutine - generate_2D_jpeg — subroutine - generate_2D_thumbnail — subroutine - get_1 — subroutine - get_keyline — function - hide — subroutine - init — subroutine - kill — subroutine - merge — subroutine - new_section — subroutine - set_1 — subroutine - set_2 — subroutine - set_3 — subroutine - set_now — subroutine - write — subroutine - write_json — subroutine

---

Module: simple_hash

Files: - utils/structs/simple_hash.f90

Uses: - simple_defs - simple_error - simple_string - simple_string_utils

Public symbols: - hash — type

---

Module: simple_hash_tester

Files: - utils/structs/simple_hash_tester.f90

Uses: - simple_defs - simple_hash - simple_string - simple_string_utils - simple_test_utils

Public symbols: - run_all_hash_tests — subroutine

Private symbols: - test_constructor_and_kill — subroutine - test_copy_and_realloc — subroutine - test_delete — subroutine - test_get_keys_and_get_str — subroutine - test_getters_numeric — subroutine - test_hash2str_and_strlen — subroutine - test_lookup_and_isthere — subroutine - test_push_and_set — subroutine

---

Module: simple_hclust

Files: - utils/clustering/simple_hclust.f90

Uses: - simple_core_module_api

Public symbols: - test_hclust — subroutine

Private symbols: - cluster — subroutine - cut_tree — subroutine - get_medoids — subroutine - kill — subroutine - new — subroutine

---

Module: simple_histogram

Files: - utils/math/simple_histogram.f90

Uses: - cplot2d_wrapper_module - simple_core_module_api - simple_image

Public symbols: - histogram — type

Private symbols: - add — subroutine - div — subroutine - kill — subroutine - new_1 — subroutine - new_2 — subroutine - new_3 — subroutine - new_4 — subroutine - new_5 — subroutine - plot — subroutine - quantize — subroutine - reset — subroutine - smooth — subroutine - topdf — subroutine - update — subroutine - zero — subroutine

---

Module: simple_http_post

Files: - utils/comm/simple_http_post.f90

Uses: - curl - simple_error - simple_string

Public symbols: - http_post — type - http_response — type

Private symbols: - initialised — function - kill — subroutine - new — subroutine - request — function - response_callback — function

---

Module: simple_http_post_tester

Files: - utils/comm/simple_http_post_tester.f90

Uses: - simple_http_post - simple_string - simple_test_utils

Public symbols: - run_all_http_post_tests — subroutine

Private symbols: - test_create_and_kill — subroutine - test_request_no_body — subroutine - test_request_with_body — subroutine - test_response_reset — subroutine

---

Module: simple_image

Files: - main/image/simple_image.f90

Uses: - gnufor2 - simple_core_module_api - simple_ctf - simple_fftw3 - simple_ftiter - simple_imgfile - simple_neighs - simple_winfuns

Public symbols: - image — type

---

Module: simple_image_bin

Files: - main/image/simple_image_bin.f90

Uses: - simple_core_module_api - simple_image - simple_neighs

Public symbols: - image_bin — type

Private symbols: - apply_mask — subroutine - border_mask — subroutine - cc2bin — subroutine - copy_bimg — subroutine - cos_edge — subroutine - dequeue — subroutine - diameter_bin — subroutine - diameter_cc — subroutine - dilate — subroutine - elim_cc — subroutine - elim_ccs — subroutine - elim_largestcc — subroutine - empty_queue — subroutine - enqueue — subroutine - erode — subroutine - feret_minmax — subroutine - find_ccs — subroutine - flood_fill — subroutine - get_imat — subroutine - get_nccs — subroutine - grow_bins — subroutine - inv_bimg — subroutine - is_empty — function - kill_bimg — subroutine - masscen_cc — subroutine - max_dist — subroutine - new_bimg — subroutine - order_ccs — subroutine - polish_ccs — subroutine - read_bimg — subroutine - set_edgecc2background — subroutine - set_imat — subroutine - set_largestcc2background — subroutine - size_ccs — function - transfer2bimg — subroutine - update_img_rmat — subroutine - update_mask_2d — subroutine - update_mask_3d — subroutine - write_bimg — subroutine

---

Module: simple_image_msk

Files: - main/image/simple_image_msk.f90

Uses: - simple_core_module_api - simple_image - simple_image_bin - simple_parameters - simple_segmentation

Public symbols: - automask2D — subroutine - automask2D_support_pix — subroutine - density_inoutside_mask — subroutine - image_msk — type

Private symbols: - automask2D_binary_one — subroutine - automask3D_1 — subroutine - automask3D_2 — subroutine - automask3D_binarize — subroutine - automask3D_filter — subroutine - automask3D_keep_largest_cc — subroutine - binary_imat_to_pix — subroutine - env_rproject — subroutine - estimate_spher_mask_diam — subroutine

---

Module: simple_imgarr_utils

Files: - utils/simple_imgarr_utils.f90

Uses: - simple_core_module_api - simple_image - simple_sp_project - simple_stack_io

---

Module: simple_imgfile

Files: - fileio/simple_imgfile.f90

Uses: - gnufor2 - iso_fortran_env - simple_core_module_api - simple_string_utils - simple_tifflib

Private symbols: - close — subroutine - getDim — function - getDims — function - open — subroutine - open_local — subroutine - rSlices — subroutine - rTiffSlices — subroutine - setDims — subroutine - setIform — subroutine - setMean — subroutine - setMinMax — subroutine - setMode — subroutine - setPixSz — subroutine - setRMSD — subroutine - slice2bytepos — subroutine - slice2recpos — subroutine - update_MRC_stats — subroutine - wmrcSlices — subroutine - wSlices — subroutine

---

Module: simple_imghead

Files: - fileio/simple_imghead.f90

Uses: - simple_defs - simple_error - simple_fileio - simple_string - simple_string_utils - simple_syslib - simple_tifflib

Public symbols: - find_ldim_nptcls — subroutine - get_mrcfile_info — subroutine - MrcImgHead — type - SpiImgHead — type - test_imghead — subroutine - TiffImgHead — type - update_stack_nimgs — subroutine

Private symbols: - CloseTiff — subroutine - get_eerfile_info — subroutine - get_spifile_info — subroutine - get_tiffile_info — subroutine - getDim — function - getDims — function - getIform — function - getLabbyt — function - getLabrec — function - getLenbyt — function - getMaxim — function - getMode — function - is_even — function - kill — subroutine - new — subroutine - print_imghead — subroutine - print_spihed — subroutine - read — subroutine - read_spihed — subroutine - read_tiff — subroutine - reset2default — subroutine - setDim — subroutine - setDims — subroutine - setIform — subroutine - setMaxim — subroutine - setMaxPixVal — subroutine - setMean — subroutine - setMinimal — subroutine - setMinPixVal — subroutine - setMode — subroutine - setPixSz — subroutine - setRMSD — subroutine - transfer_byte_array2obj — subroutine - transfer_obj2byte_array — subroutine - write — subroutine

---

Module: simple_imgproc

Files: - utils/simple_imgproc.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - make_pcavecs — subroutine - make_pcavol — subroutine

---

Module: simple_ipc_tcp_socket_client

Files: - utils/comm/simple_ipc_tcp_socket_client.f90

Uses: - iso_c_binding - simple_core_module_api - simple_ipc_tcp_socket_helpers - unix

Public symbols: - ipc_tcp_socket_client — type - tcp_sockaddr_in — type

Private symbols: - c_timeval — type - connect — subroutine - kill — subroutine - new — subroutine - send_recv_msg — subroutine

---

Module: simple_ipc_tcp_socket_helpers

Files: - utils/comm/simple_ipc_tcp_socket_helpers.f90

Uses: - iso_c_binding - unix

Public symbols: - accept_connection — function - c_pollfd — type - poll_fds — subroutine

Private symbols: - c_poll — function - c_recv — function

---

Module: simple_ipc_tcp_socket_server

Files: - utils/comm/simple_ipc_tcp_socket_server.f90

Uses: - iso_c_binding - simple_core_module_api - simple_error - simple_ipc_tcp_socket_helpers - unix

Public symbols: - ipc_tcp_socket_server — type - listener_args — type - recv_msg — subroutine - repl_msg — subroutine - tcp_sockaddr_in — type

Private symbols: - find_server_ips — subroutine - get_server_ips — function - join_listener — subroutine - kill — subroutine - new — subroutine - start_listener — subroutine

---

Module: simple_ipc_tcp_socket_tester

Files: - utils/comm/simple_ipc_tcp_socket_tester.f90

Uses: - iso_c_binding - simple_core_module_api - simple_ipc_tcp_socket_client - simple_ipc_tcp_socket_helpers - simple_ipc_tcp_socket_server - simple_test_utils - unix

Public symbols: - run_all_ipc_tcp_socket_tests — subroutine

Private symbols: - assert_port_in_range — subroutine - destroy_listener_args — subroutine - init_listener_args — subroutine - listener_echo_ok_once — subroutine - listener_ready_once — subroutine - poke_server_port — subroutine - test_client_send_recv_without_server_fails — subroutine - test_client_server_roundtrip — subroutine - test_helpers_accept_connection_invalid_fd — subroutine - test_helpers_constants — subroutine - test_helpers_fd_is_healthy_invalid_fd — subroutine - test_helpers_poll_fds_bounds_and_zero — subroutine - test_server_find_ips_and_port_range — subroutine - test_server_new_kill_lifecycle — subroutine - test_server_start_join_lifecycle — subroutine

---

Module: simple_is_check_assert

Files: - utils/simple_is_check_assert.f90

Uses: - simple_defs - simple_error

---

Module: simple_jiffys

Files: - utils/simple_jiffys.f90

Uses: - simple_defs - simple_defs_fname - simple_timer

---

Module: simple_jpg

Files: - extlibs/jpg/simple_jpg.f90

Uses: - simple_core_module_api

Public symbols: - test_jpg_export — subroutine

Private symbols: - constructor — subroutine - load_jpeg_i4 — function - load_jpeg_r4 — function - montage — function - read_jpeg — subroutine - save_jpeg_i4 — function - save_jpeg_r4 — function - save_jpeg_r4_3D — function - setColorspace — subroutine - setGamma — subroutine - setHeight — subroutine - setNormalised — subroutine - setQuality — subroutine - setup_jpeg — subroutine - setWidth — subroutine - write_jpeg — subroutine

---

Module: simple_kbinterpol

Files: - main/interp/simple_kbinterpol.f90

Uses: - iso_c_binding - simple_defs - simple_edges_sqwins

Public symbols: - kbinterpol — type

---

Module: simple_kd_tree

Files: - utils/structs/simple_kd_tree.f90

Uses: - simple_core_module_api

Public symbols: - kd_tree — type - knn_table — type

Private symbols: - build_kd_tree — subroutine - build_node — subroutine - grow_nodes — subroutine - heap_consider — subroutine - heap_sift_down — subroutine - kill_kd_tree — subroutine - kill_knn_table — subroutine - query_all_kd_tree — subroutine - query_kd_tree — subroutine - query_node — subroutine - reserve_nodes — subroutine - select_kth — subroutine - sort_neighbor_pairs — subroutine - swap_int — subroutine - swap_pair — subroutine - validate_query — subroutine

---

Module: simple_kmedoids

Files: - utils/clustering/simple_kmedoids.f90

Uses: - simple_core_module_api

Private symbols: - assign_labels — subroutine - cluster — subroutine - find_medoid — subroutine - find_medoids — subroutine - get_labels — subroutine - get_medoids — subroutine - init — subroutine - kill — subroutine - merge — subroutine - merge_ranked — subroutine - new_1 — subroutine - new_2 — subroutine

---

Module: simple_kpca_svd

Files: - main/pca/simple_kpca_svd.f90

Uses: - simple_core_module_api - simple_pca

Public symbols: - kpca_svd — type

Private symbols: - center_columns — subroutine - choose_nystrom_inds_from_data — subroutine - compute_eigvecs — subroutine - cosine_kernel — subroutine - dense_mm — subroutine - dense_tmm — subroutine - generate_kpca — subroutine - get_eigvals_kpca — function - get_feat_kpca — function - gram_symmetric — subroutine - kernel_center — subroutine - kill_kpca — subroutine - master_kpca — subroutine - master_nystrom — subroutine - new_kpca — subroutine - orthonormalize_cols — subroutine - partial_eigh_sym — subroutine - projected_kernel_col — subroutine - rbf_kernel — subroutine - select_local_support_inds — subroutine - select_nystrom_inds — subroutine - set_params_kpca — subroutine

---

Module: simple_linalg

Files: - utils/math/simple_linalg.f90

Uses: - simple_defs - simple_is_check_assert

Private symbols: - sparse_matvec_sp_proc — subroutine

---

Module: simple_linked_list

Files: - utils/structs/simple_linked_list.f90

Uses: - simple_core_module_api

Public symbols: - linked_list — type - list_iterator — type

Private symbols: - advance — subroutine - append — function - assign — subroutine - at — subroutine - at_char — subroutine - at_complex — subroutine - at_int — subroutine - at_logical — subroutine - at_real — subroutine - back — subroutine - begin — function - end — function - end_iter — function - front — subroutine - getter — subroutine - kill — subroutine - kill_node — subroutine - next — subroutine - node — type - pop_front — subroutine - push_back — subroutine - push_back_char — subroutine - push_back_complex — subroutine - push_back_int — subroutine - push_back_logical — subroutine - push_back_real — subroutine - push_front — subroutine - replace_at — subroutine - replace_iterator — subroutine - replace_with — subroutine - slice — subroutine

---

Module: simple_linked_list_tester

Files: - utils/structs/simple_linked_list_tester.f90

Uses: - simple_linked_list - simple_test_utils

Public symbols: - run_all_list_tests — subroutine

Private symbols: - particle — type - test_append — subroutine - test_assign_and_copy_semantics — subroutine - test_complex — subroutine - test_derived_type_independence — subroutine - test_derived_type_values — subroutine - test_end_iterator_behavior — subroutine - test_front_back_at — subroutine - test_intrinsic_integer — subroutine - test_iteration — subroutine - test_iterator_index_and_advance — subroutine - test_kill — subroutine - test_logical — subroutine - test_move_semantics — subroutine - test_nested_allocations — subroutine - test_pop_front — subroutine - test_push_and_size — subroutine - test_real — subroutine - test_replace_iterator_stability — subroutine - test_slice — subroutine - test_string_values — subroutine - test_type_safe_wrappers — subroutine

---

Module: simple_magic_boxes

Files: - utils/simple_magic_boxes.f90

Uses: - simple_defs - simple_error - simple_math

---

Module: simple_make_cavgs_strategy

Files: - main/strategies/parallelization/simple_make_cavgs_strategy.f90

Uses: - simple_builder - simple_classaverager - simple_cmdline - simple_core_module_api - simple_exec_helpers - simple_parameters - simple_qsys_env - simple_qsys_funs

Public symbols: - create_make_cavgs_strategy — function - make_cavgs_hooks — type - make_cavgs_master_strategy — type - make_cavgs_shmem_strategy — type - make_cavgs_strategy — type - make_cavgs_worker_strategy — type

Private symbols: - apply_defaults_interface — subroutine - apply_distr_entry_defaults — subroutine - base_after_end — subroutine - cavgassemble_hook — subroutine - cavger_prepare_and_assemble — subroutine - cleanup_interface — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - generate_cluster_centers — subroutine - init_interface — subroutine - master_apply_defaults — subroutine - master_cleanup — subroutine - master_end_message — function - master_execute — subroutine - master_finalize_run — subroutine - master_initialize — subroutine - print_raw_source_verification — subroutine - setup_evenodd — subroutine - shmem_apply_defaults — subroutine - shmem_bookkeeping — subroutine - shmem_cleanup — subroutine - shmem_end_message — function - shmem_execute — subroutine - shmem_finalize_run — subroutine - shmem_initialize — subroutine - worker_apply_defaults — subroutine - worker_cleanup — subroutine - worker_end_message — function - worker_execute — subroutine - worker_finalize_run — subroutine - worker_initialize — subroutine - write_oritype_segment_for_compute — subroutine

---

Module: simple_map_reduce

Files: - utils/simple_map_reduce.f90

Uses: - simple_defs - simple_fileio - simple_jiffys - simple_srch_sort_loc - simple_string - simple_string_utils

Public symbols: - split_nobjs_even — function - split_pairs_in_parts — subroutine

---

Module: simple_matcher_2Dprep

Files: - main/strategies/search/simple_matcher_2Dprep.f90

Uses: - simple_builder - simple_butterworth - simple_matcher_ptcl_io - simple_matcher_smpl_and_lplims - simple_pftc_srch_api - simple_projector - simple_strategy2d_utils - simple_timer

Public symbols: - calc_2Dref_offset — subroutine - prep2Dref — subroutine - prepimg4align — subroutine

---

Module: simple_matcher_3Drec

Files: - main/strategies/search/simple_matcher_3Drec.f90

Uses: - simple_builder - simple_classaverager - simple_cmdline - simple_core_module_api - simple_image - simple_imgarr_utils - simple_matcher_ptcl_io - simple_memoize_ft_maps - simple_parameters - simple_reconstructor - simple_refine3d_fnames - simple_timer

Public symbols: - calc_3Drec — subroutine - calc_projdir3Drec — subroutine - cleanup_rec_buffers — subroutine - init_rec — subroutine - prep_imgs4rec — subroutine - write_state_partial — subroutine

Private symbols: - group_pinds_by_state_eo — subroutine - init_state_half_rec — subroutine - kill_state_half_rec — subroutine - mark_empty_state — subroutine - set_state_vol_output — subroutine - update_state_half_rec — subroutine - write_state_half_partial — subroutine

---

Module: simple_matcher_pftc_prep

Files: - main/strategies/search/simple_matcher_pftc_prep.f90

Uses: - simple_builder - simple_classaverager - simple_core_module_api - simple_image - simple_matcher_2dprep - simple_matcher_ptcl_batch - simple_parameters - simple_strategy2d_alloc

Public symbols: - prep_pftc4align2D — subroutine

---

Module: simple_matcher_ptcl_batch

Files: - main/strategies/search/simple_matcher_ptcl_batch.f90

Uses: - simple_builder - simple_euclid_sigma2 - simple_imgarr_utils - simple_matcher_2dprep - simple_matcher_ptcl_io - simple_pftc_srch_api

Public symbols: - alloc_ptcl_imgs — subroutine - build_batch_particles2D — subroutine - build_batch_particles3D — subroutine - clean_batch_particles2D — subroutine - clean_batch_particles3D — subroutine - prep_sigmas_objfun — subroutine

Private symbols: - polarize_batch_particles3D — subroutine - polarize_batch_particles3D_den — subroutine

---

Module: simple_matcher_ptcl_io

Files: - main/strategies/search/simple_matcher_ptcl_io.f90

Uses: - simple_builder - simple_discrete_stack_io - simple_imghead - simple_pftc_srch_api

---

Module: simple_matcher_refvol_utils

Files: - main/strategies/search/simple_matcher_refvol_utils.f90

Uses: - simple_builder - simple_cmdline - simple_core_module_api - simple_image - simple_opt_filter - simple_parameters - simple_polarft_calc - simple_refine3d_fnames

Public symbols: - adopt_reprojection_model_range — subroutine - estimate_lp_from_refs — subroutine - materialize_reprojection_model_from_volumes — subroutine - pick_lp_est_state — subroutine - read_mask_filter_reproject_refvols — subroutine - read_reprojection_model — subroutine - remove_ref_section_files — subroutine

Private symbols: - blend_lowres_eo_for_registration — subroutine - calcrefvolshift_and_mapshifts2ptcls — subroutine - read_mask_filter_refvols — subroutine - read_reprojection_model_file_header — subroutine - read_reprojection_model_header — subroutine - regularize_ref_with_noise — subroutine

---

Module: simple_matcher_smpl_and_lplims

Files: - main/strategies/search/simple_matcher_smpl_and_lplims.f90

Uses: - simple_abinitio2d_controller - simple_builder - simple_pftc_srch_api - simple_refine3d_fnames

Public symbols: - sample_ptcls4fillin — subroutine - sample_ptcls4missing3D — subroutine - sample_ptcls4update2D — subroutine - sample_ptcls4update3D — subroutine - set_bp_range2D — subroutine - set_bp_range3D — subroutine

---

Module: simple_math

Files: - utils/math/simple_math.f90

Uses: - simple_defs - simple_error - simple_is_check_assert - simple_linalg - simple_srch_sort_loc

---

Module: simple_math_ctf

Files: - utils/math/simple_math_ctf.f90

Uses: - simple_defs - simple_memoize_ft_maps

---

Module: simple_math_ft

Files: - utils/math/simple_math_ft.f90

Uses: - simple_defs - simple_error - simple_is_check_assert - simple_srch_sort_loc

---

Module: simple_mem_estimator

Files: - utils/simple_mem_estimator.f90

Uses: - simple_core_module_api - simple_parameters

Public symbols: - estimate_mem_usage — subroutine - estimate_mem_usage_2D — function - estimate_mem_usage_ctf_estimation — function - estimate_mem_usage_extract — function - estimate_mem_usage_motion_corr — function - estimate_mem_usage_pick — function - estimate_mem_usage_preprocess — function - estimate_mem_usage_pspec — function - estimate_mem_usage_scale — function

---

Module: simple_memoize_ft_maps

Files: - utils/simple_memoize_ft_maps.f90

Uses: - simple_core_module_api - simple_ftiter

Public symbols: - forget_ft_maps — subroutine - ft_map_get_farray_shape — function - memoize_ft_maps — subroutine

---

Module: simple_memory_monitor

Files: - utils/simple_memory_monitor.f90

Uses: - simple_cmdline - simple_defs - simple_string - simple_syslib

Public symbols: - mem_monitor_finish — subroutine - mem_monitor_init — subroutine - mem_report — subroutine

Private symbols: - log_sample — subroutine - start_monitor — subroutine

---

Module: simple_micproc

Files: - utils/simple_micproc.f90

Uses: - simple_bspline_smoother - simple_core_module_api - simple_histogram - simple_image - simple_image_bin

Public symbols: - binarize_mic_den — subroutine - bs_smoother — subroutine - bs_smoother_biomol — subroutine - cascade_filter — subroutine - cascade_filter_biomol — subroutine - cluster — subroutine - clustering_rejection — subroutine - flag_amorphous_carbon — subroutine - flag_ice — subroutine - read_mic — subroutine - read_mic_subtr_backgr — subroutine - read_mic_subtr_backgr_shrink — subroutine - sample_filetab — function

---

Module: simple_micrograph_generator

Files: - main/simple_micrograph_generator.f90

Uses: - simple_core_module_api - simple_eer_factory - simple_image - simple_motion_correct_utils - simple_ori - simple_starfile_wrappers - simple_string

Public symbols: - mic_generator — type

Private symbols: - cure_outliers_1 — subroutine - cure_outliers_2 — subroutine - display — subroutine - generate_micrographs — subroutine - get_moviename — function - kill — subroutine - new — subroutine - parse_movie_metadata — subroutine - parse_string — subroutine - write_star — subroutine

---

Module: simple_mini_stream_utils

Files: - main/stream/simple_mini_stream_utils.f90

Uses: - simple_cmdline - simple_core_module_api - simple_gui_utils - simple_image - simple_image_bin - simple_micproc - simple_nrtxtfile - simple_parameters - simple_picksegdiam - simple_sp_project

Public symbols: - ensure_real_capacity — subroutine - print_diam_stats — subroutine - segdiampick_mics — subroutine - segdiampick_mics_multi — subroutine - segdiampick_preprocess — subroutine

---

Module: simple_molecule_data

Files: - main/nano/simple_molecule_data.f90

Public symbols: - betagal_1jyx — function - molecule_data — type - sars_cov2_spkgp_6vxx — function

---

Module: simple_motion_align_hybrid

Files: - main/motion/simple_motion_align_hybrid.f90

Uses: - simple_core_module_api - simple_ft_expanded - simple_ftexp_shsrch - simple_image - simple_parameters

Public symbols: - motion_align_hybrid — type

Private symbols: - align — subroutine - align_corr — subroutine - align_dcorr — subroutine - align_discrete — subroutine - calc_shifts — subroutine - dealloc_ftexps — subroutine - dealloc_images — subroutine - fit_polynomial — subroutine - gen_weights — subroutine - get_coords — subroutine - get_corrs — subroutine - get_opt_shifts — subroutine - get_shifts_toplot — subroutine - get_weights — subroutine - init_ftexps — subroutine - init_images — subroutine - kill — subroutine - new — subroutine - poly — function - polynomial2shift — subroutine - recenter_shifts — subroutine - refine — subroutine - set_bfactor — subroutine - set_coords — subroutine - set_fitshifts — subroutine - set_fixed_frame — subroutine - set_maxits — subroutine - set_rand_init_shifts — subroutine - set_reslims — subroutine - set_shsrch_tol — subroutine - set_trs — subroutine - set_weights — subroutine

---

Module: simple_motion_align_nano

Files: - main/motion/simple_motion_align_nano.f90

Uses: - simple_core_module_api - simple_image - simple_parameters

Public symbols: - motion_align_nano — type

Private symbols: - align — subroutine - align_dcorr — subroutine - calc_shifts — subroutine - dealloc_images — subroutine - gen_weights — subroutine - get_opt_shifts — subroutine - get_reference — subroutine - init_images — subroutine - kill — subroutine - new — subroutine - set_bfactor — subroutine - set_reslims — subroutine - set_trs — subroutine - shift_frames_gen_ref — subroutine

---

Module: simple_motion_correct

Files: - main/motion/simple_motion_correct.f90

Uses: - simple_core_module_api - simple_eer_factory - simple_ft_expanded - simple_image - simple_motion_align_hybrid - simple_motion_correct_utils - simple_motion_patched - simple_opt_image_weights - simple_parameters - simple_starfile_wrappers

Public symbols: - motion_correct_calc_bid — subroutine - motion_correct_calc_opt_weights — subroutine - motion_correct_iso — subroutine - motion_correct_iso_calc_sums — subroutine - motion_correct_iso_kill — subroutine - motion_correct_iso_shift_frames — subroutine - motion_correct_kill_common — subroutine - motion_correct_mic2spec — subroutine - motion_correct_patched — subroutine - motion_correct_patched_calc_sums — subroutine - motion_correct_patched_kill — subroutine - motion_correct_write2star — subroutine - motion_correct_write_poly — subroutine

Private symbols: - cure_outliers — subroutine - motion_correct_init — subroutine

---

Module: simple_motion_correct_iter

Files: - main/motion/simple_motion_correct_iter.f90

Uses: - simple_cmdline - simple_core_module_api - simple_image - simple_motion_correct - simple_parameters - simple_stackops

Public symbols: - motion_correct_iter — type

Private symbols: - calc_npatches — subroutine - get_moviename — function - iterate — subroutine

---

Module: simple_motion_correct_strategy

Files: - main/strategies/parallelization/simple_motion_correct_strategy.f90

Uses: - simple_binoris_io - simple_cmdline - simple_commanders_api - simple_motion_correct_iter - simple_motion_correct_utils - simple_parameters - simple_qsys_env - simple_sp_project

Public symbols: - create_motion_correct_strategy — function - motion_correct_distr_strategy — type - motion_correct_inmem_strategy — type - motion_correct_strategy — type

Private symbols: - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_end_message — function - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_end_message — function - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - set_motion_correct_defaults — subroutine

---

Module: simple_motion_correct_utils

Files: - main/motion/simple_motion_correct_utils.f90

Uses: - simple_cmdline - simple_core_module_api - simple_eer_factory - simple_image

Public symbols: - calc_eer_fraction — subroutine - correct_gain — subroutine - flip_gain — subroutine

---

Module: simple_motion_gain_analysis

Files: - main/motion/simple_motion_gain_analysis.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - gain_flip_analyzer — type

Private symbols: - analyze_if_due — subroutine - analyzer_kill — subroutine - analyzer_new — subroutine

---

Module: simple_motion_gain_helpers

Files: - main/motion/simple_motion_gain_helpers.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - normalized_inverse_average_intensity — subroutine - read_movies_and_sum_frames — subroutine

---

Module: simple_motion_gain_tester

Files: - main/motion/simple_motion_gain_tester.f90

Uses: - simple_core_module_api - simple_image - simple_motion_gain_analysis - simple_motion_gain_helpers - simple_test_utils

Public symbols: - run_all_motion_gain_tests — subroutine

Private symbols: - create_constant_image — subroutine - create_gainref — subroutine - create_movie_stack — subroutine - test_gain_flip_analyzer_batch_updates — subroutine - test_read_movies_and_sum_frames_counts — subroutine

---

Module: simple_motion_patched

Files: - main/motion/simple_motion_patched.f90

Uses: - cplot2d_wrapper_module - simple_core_module_api - simple_ft_expanded - simple_image - simple_motion_align_hybrid - simple_motion_correct_utils - simple_opt_factory - simple_opt_lbfgsb - simple_opt_spec - simple_optimizer - simple_parameters

Public symbols: - motion_patched — type

Private symbols: - allocate_patches — subroutine - apply_patch_poly — function - correct — subroutine - deallocate_patches — subroutine - det_shifts — subroutine - det_shifts_refine — subroutine - fit_polynomial — subroutine - gen_micrograph — subroutine - gen_patch — subroutine - get_local_shift — subroutine - get_poly4star — subroutine - get_poly_coeffs — subroutine - get_polyfit_rmsd — function - kill — subroutine - new — subroutine - patch_poly — function - pix2polycoords — subroutine - plot_shifts — subroutine - robust_fit_polynomial — subroutine - set_bfactor — subroutine - set_fitshifts — subroutine - set_fixed_frame — subroutine - set_frameweights — subroutine - set_interp_fixed_frame — subroutine - set_nframes — subroutine - set_poly_coeffs — subroutine - set_size_frames_ref — subroutine

---

Module: simple_multi_dendro

Files: - utils/structs/simple_multi_dendro.f90

Uses: - simple_binary_tree - simple_core_module_api - simple_hclust - simple_srch_sort_loc

Public symbols: - deserialize_multi_dendro — subroutine - multi_dendro — type - serialize_multi_dendro — subroutine

Private symbols: - build_tree_balanced — subroutine - build_tree_from_subdistmat — subroutine - get_full2sub_map — function - get_node — function - get_root_node — function - get_sub2full_map — function - get_tree_refs — function - get_tree_refs_static — subroutine - kill — subroutine - new — subroutine - new_multi_balanced — subroutine

---

Module: simple_multi_dendro_tester

Files: - utils/structs/simple_multi_dendro_tester.f90

Uses: - simple_binary_tree - simple_multi_dendro - simple_test_utils

Public symbols: - run_all_multi_dendro_tests — subroutine

Private symbols: - assert_int_in_set — subroutine - build_tree_from_full_dist — subroutine - make_distmat_two_pairs — subroutine - make_distmat_two_triples — subroutine - test_build_tree_balanced_two_triples — subroutine - test_build_tree_pairs_basic_structure — subroutine - test_build_tree_singletons — subroutine - test_build_tree_two_triples_basic_structure — subroutine - test_get_tree_refs — subroutine - test_initial_state — subroutine - test_kill_and_reuse — subroutine - test_new_counts_and_getters — subroutine - test_new_multi_balanced_single_tree — subroutine

---

Module: simple_nanoparticle

Files: - main/nano/simple_nanoparticle.f90

Uses: - simple_atoms - simple_core_module_api - simple_defs_atoms - simple_image - simple_image_bin - simple_image_msk - simple_nanoparticle_utils - simple_parameters

Public symbols: - nanoparticle — type

Private symbols: - atom_stats — type - atominfo2centers — function - atominfo2centers_A — function - binarize_and_find_centers — subroutine - calc_anisotropic_disp — subroutine - calc_cn_stats — subroutine - calc_isotropic_disp — subroutine - calc_longest_atm_dist — subroutine - calc_zscore — subroutine - center_on_atom — subroutine - check_neighbors_cn — subroutine - conv_denoise — subroutine - discard_atoms — subroutine - discard_small_ccs — subroutine - fillin_atominfo — subroutine - find_centers — subroutine - get_img — subroutine - get_img_raw — subroutine - get_ldim — subroutine - get_natoms — function - get_valid_corrs — function - identify_atomic_pos — subroutine - identify_lattice_params — subroutine - kill — subroutine - masscen — function - new — subroutine - pack_instance4stats — subroutine - remove_lowly_contacted — subroutine - remove_small_and_lowly_contacted — subroutine - set_atm_info — subroutine - set_atom — subroutine - set_atomic_coords_from_pdb — subroutine - set_atomic_coords_from_xyz — subroutine - set_coords4stats — subroutine - set_img — subroutine - set_ncc — subroutine - simulate_atoms — subroutine - split_atom — subroutine - split_atoms — subroutine - update_ncc — subroutine - validate_atoms — subroutine - write_2D_slice — subroutine - write_atominfo — subroutine - write_centers_1 — subroutine - write_centers_2 — subroutine - write_centers_aniso — subroutine - write_cn_atoms — subroutine - write_cn_stats — subroutine - write_csv_files — subroutine - write_individual_atoms — subroutine - write_np_stats — subroutine

---

Module: simple_nanoparticle_utils

Files: - main/nano/simple_nanoparticle_utils.f90

Uses: - simple_atoms - simple_core_module_api - simple_defs_atoms - simple_image - simple_linalg

Public symbols: - atm_rmsd_stats — function - atoms_register — subroutine - calc_contact_scores — subroutine - dists_btw_common — function - find_atoms_subset — subroutine - find_couples — subroutine - find_rMax — function - fit_lattice — subroutine - Kabsch_algo — subroutine - phasecorr_one_atom — subroutine - read_pdb2matrix — subroutine - remove_atoms — subroutine - run_cn_analysis — subroutine - strain_analysis — subroutine - thres_detect_conv_atom_denoised — subroutine - write_matrix2pdb — subroutine

Private symbols: - gaussian_kernel — subroutine - nnbdl_lat — subroutine - qr — subroutine - write_ideal_lattice_pdb — subroutine

---

Module: simple_neighs

Files: - utils/math/simple_neighs.f90

Uses: - simple_core_module_api

---

Module: simple_nice

Files: - utils/gui/simple_nice.f90

Uses: - json_kinds - json_module - simple_core_module_api - simple_histogram - simple_socket_comm - simple_sp_project - unix

Public symbols: - add_headline_cls2D — subroutine - add_headline_micrographs — subroutine - add_histograms_cls2D — subroutine - add_histograms_micrographs — subroutine - add_plot_optics — subroutine - add_view_cls2D — subroutine - add_view_ini3D — subroutine - add_view_micrographs — subroutine - add_view_optics — subroutine - add_view_pick — subroutine - add_view_vols — subroutine - bar_plot_object — subroutine - calculate_checksum — function - create_interactive_plot — subroutine - cycle — subroutine - datestr — function - doughnut_plot_object — subroutine - fsc_object — subroutine - generate_stat_json — subroutine - get_real_keys_json — subroutine - get_stat_json — subroutine - image_thumbnail_object — subroutine - init_1 — subroutine - init_2 — subroutine - nice_plot_bar — type - nice_plot_doughnut — type - nice_stat_root — type - nice_stat_thumb_image — type - nice_stat_thumb_image_meta — type - nice_thread_comm_message — type - nice_view_cls2D — type - nice_view_ini3D — type - nice_view_micrographs — type - nice_view_optics — type - nice_view_pick — type - nice_view_vols — type - remote_heartbeat — subroutine - simple_nice_comm — type - start_comm_thread — subroutine - terminate — subroutine - terminate_comm_thread — subroutine - text_data_object_1 — subroutine - text_data_object_2 — subroutine - text_data_object_3 — subroutine - update_cls2D — subroutine - update_from_project — subroutine - update_ini3D — subroutine - update_micrographs — subroutine - update_optics — subroutine - update_pick — subroutine - update_vols — subroutine

---

Module: simple_nrtxtfile

Files: - fileio/simple_nrtxtfile.f90

Uses: - simple_defs - simple_error - simple_fileio - simple_string - simple_string_utils - simple_syslib

Public symbols: - nrtxtfile — type

Private symbols: - kill — subroutine - new — subroutine - readNextDataLine — subroutine - writeCommentLine — subroutine - writeDataLineInt — subroutine - writeDataLineReal — subroutine

---

Module: simple_nu_filter

Files: - main/nu_filt/simple_nu_filter.f90

Uses: - simple_butterworth - simple_core_module_api - simple_image - simple_neighs - simple_tent_smooth

Private symbols: - nu_highres_extension_stats — type

---

Module: simple_online_var

Files: - utils/math/simple_online_var.f90

Uses: - simple_defs - simple_rnd - simple_stat

Public symbols: - online_var — type - test_online_var — subroutine

Private symbols: - add_1 — subroutine - add_2 — subroutine - get_mean — function - get_var — function - reset_mean — subroutine - serialize — function - unserialize — subroutine

---

Module: simple_opt_bfgs

Files: - main/opt/simple_opt_bfgs.f90

Uses: - simple_core_module_api - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_bfgs — type

Private symbols: - bfgs_minimize — subroutine - bfgsmin — subroutine - kill_opt_bfgs — subroutine - new_opt_bfgs — subroutine

---

Module: simple_opt_bfgs2

Files: - main/opt/simple_opt_bfgs2.f90

Uses: - simple_core_module_api - simple_opt_helpers - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_bfgs2 — type

Private symbols: - bfgs2_iterate — function - bfgs2_minimize — subroutine - bfgs2_set — subroutine - bfgs2_wrapper — type - bfgs2min — subroutine - change_direction — subroutine - check_extremum — subroutine - cubic — function - interp_cubic — function - interp_quad — function - interpolate — function - kill_opt_bfgs2 — subroutine - linear_minimize — function - moveto — subroutine - new_opt_bfgs2 — subroutine - prepare_wrapper — subroutine - slope — function - solve_quadratic — function - update_position — subroutine - wrap_df — function - wrap_f — function - wrap_fdf — subroutine

---

Module: simple_opt_bforce

Files: - main/opt/simple_opt_bforce.f90

Uses: - simple_core_module_api - simple_opt_spec - simple_optimizer

Public symbols: - opt_bforce — type

Private symbols: - bforce_minimize — subroutine - kill_opt_bforce — subroutine - new_opt_bforce — subroutine - srch_not_done — function

---

Module: simple_opt_de

Files: - main/opt/simple_opt_de.f90

Uses: - simple_core_module_api - simple_opt_spec - simple_optimizer

Public symbols: - opt_de — type

Private symbols: - de_minimize — subroutine - kill_de — subroutine - new_de — subroutine

---

Module: simple_opt_factory

Files: - main/opt/simple_opt_factory.f90

Uses: - simple_core_module_api - simple_opt_bfgs2 - simple_opt_bforce - simple_opt_de - simple_opt_lbfgsb - simple_opt_simplex - simple_opt_spec - simple_opt_stde - simple_optimizer

Public symbols: - opt_factory — type

Private symbols: - new — subroutine

---

Module: simple_opt_filter

Files: - utils/filter/simple_opt_filter.f90

Uses: - simple_butterworth - simple_core_module_api - simple_image

---

Module: simple_opt_fr_cg

Files: - main/opt/simple_opt_fr_cg.f90

Uses: - simple_core_module_api - simple_opt_helpers - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_fr_cg — type

Private symbols: - fr_cg_iterate — function - fr_cg_minimize — subroutine - fr_cg_set — subroutine - fr_cgmin — subroutine - kill_opt_fr_cg — subroutine - new_opt_fr_cg — subroutine

---

Module: simple_opt_helpers

Files: - main/opt/simple_opt_helpers.f90

Uses: - simple_core_module_api - simple_opt_spec

Public symbols: - intermediate_point — subroutine - minimize — subroutine - take_step — subroutine - test_gradient — function

---

Module: simple_opt_image_weights

Files: - main/motion/simple_opt_image_weights.f90

Uses: - simple_core_module_api - simple_ft_expanded - simple_ftexp_shsrch - simple_image - simple_opt_factory - simple_opt_spec - simple_optimizer

Public symbols: - opt_image_weights — type

Private symbols: - calc_Dmat — subroutine - calc_opt_weights — subroutine - create_ftexp_objs — subroutine - dealloc_ftexp_objs — subroutine - get_weights — function - kill — subroutine - new — subroutine - opt_image_weights_cost_Dmat — function - opt_image_weights_cost_Ref — function - opt_image_weights_cost_sp_wrapper — function - opt_image_weights_cost_wrapper — function - opt_image_weights_fdf_Dmat — subroutine - opt_image_weights_fdf_Ref — subroutine - opt_image_weights_fdf_wrapper — subroutine - opt_image_weights_gcost — subroutine - opt_image_weights_gcost_Dmat — subroutine - opt_image_weights_gcost_Ref — subroutine - opt_image_weights_gcost_wrapper — subroutine - set_Nrestarts — subroutine

---

Module: simple_opt_lbfgsb

Files: - main/opt/simple_opt_lbfgsb.f90

Uses: - simple_core_module_api - simple_opt_helpers - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_lbfgsb — type

Private symbols: - active — subroutine - bmv — subroutine - cauchy — subroutine - cmprlb — subroutine - daxpy — subroutine - dcopy — subroutine - dcsrch — subroutine - dcstep — subroutine - ddot — function - dpofa — subroutine - dscal — subroutine - dtrsl — subroutine - errclb — subroutine - formk — subroutine - formt — subroutine - freev — subroutine - hpsolb — subroutine - kill_opt_lbfgsb — subroutine - lbfgsb_minimize — subroutine - lbfgsbmin — subroutine - lnsrlb — subroutine - mainlb — subroutine - matupd — subroutine - new_opt_lbfgsb — subroutine - projgr — subroutine - setulb — subroutine - subsm — subroutine

---

Module: simple_opt_mask

Files: - utils/simple_opt_mask.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - estimate_spher_mask — subroutine

---

Module: simple_opt_particle_swarm

Files: - main/opt/simple_opt_particle_swarm.f90

Uses: - simple_core_module_api - simple_opt_spec - simple_optimizer

Public symbols: - opt_particle_swarm — type

Private symbols: - init — subroutine - kill_particle_swarm — subroutine - new_particle_swarm — subroutine - particle_swarm_minimize — subroutine - update_particle — subroutine

---

Module: simple_opt_powell

Files: - main/opt/simple_opt_powell.f90

Uses: - simple_core_module_api - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_powell — type

Private symbols: - kill_opt_powell — subroutine - new_opt_powell — subroutine - powell — subroutine - powell_minimize — subroutine

---

Module: simple_opt_pr_cg

Files: - main/opt/simple_opt_pr_cg.f90

Uses: - simple_core_module_api - simple_opt_helpers - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_pr_cg — type

Private symbols: - kill_opt_pr_cg — subroutine - new_opt_pr_cg — subroutine - pr_cg_iterate — function - pr_cg_minimize — subroutine - pr_cg_set — subroutine - pr_cgmin — subroutine

---

Module: simple_opt_simplex

Files: - main/opt/simple_opt_simplex.f90

Uses: - simple_core_module_api - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_simplex — type

Private symbols: - init — subroutine - kill_opt_simplex — subroutine - new_opt_simplex — subroutine - simplex_minimize — subroutine

---

Module: simple_opt_spec

Files: - main/opt/simple_opt_spec.f90

Uses: - simple_core_module_api

Public symbols: - costfun — function - opt_spec — type

Private symbols: - change_opt — subroutine - costfun_8 — function - eval_df_4 — subroutine - eval_df_8 — subroutine - eval_f_4 — function - eval_f_8 — function - eval_fdf_4 — subroutine - eval_fdf_8 — subroutine - fdfcostfun — subroutine - fdfcostfun_8 — subroutine - fun — function - fun — subroutine - fun — subroutine - fun — function - fun — subroutine - fun — subroutine - gcostfun — subroutine - gcostfun_8 — subroutine - kill — subroutine - opt_callback — subroutine - set_costfun — subroutine - set_costfun_8 — subroutine - set_fdfcostfun — subroutine - set_fdfcostfun_8 — subroutine - set_gcostfun — subroutine - set_gcostfun_8 — subroutine - set_inipop — subroutine - set_limits — subroutine - set_limits_init — subroutine - specify — subroutine

---

Module: simple_opt_stde

Files: - main/opt/simple_opt_stde.f90

Uses: - simple_core_module_api - simple_opt_helpers - simple_opt_spec - simple_opt_subs - simple_optimizer

Public symbols: - opt_stde — type

Private symbols: - kill_opt_stde — subroutine - new_opt_stde — subroutine - stde_iterate — function - stde_minimize — subroutine - stde_set — subroutine - stdemin — subroutine

---

Module: simple_opt_subs

Files: - main/opt/simple_opt_subs.f90

Uses: - simple_core_module_api - simple_opt_spec

Public symbols: - amoeba — subroutine - check_and_correct_vec — subroutine - linmin — subroutine - lnsrch — subroutine - shc_selector — function

Private symbols: - amoeba_private — subroutine - amotry — function - brent — function - eval_move — function - mnbrak — subroutine

---

Module: simple_optimizer

Files: - main/opt/simple_optimizer.f90

Uses: - simple_opt_spec

Public symbols: - optimizer — type

Private symbols: - generic_kill — subroutine - generic_minimize — subroutine - generic_new — subroutine

---

Module: simple_ori

Files: - main/ori/simple_ori.f90

Uses: - simple_ori_api

Public symbols: - ori — type

---

Module: simple_ori_api

Files: - main/apis/simple_ori_api.f90

Uses: - json_kinds - json_module - simple_chash - simple_defs - simple_defs_ori - simple_error - simple_fileio - simple_hash - simple_is_check_assert - simple_linalg - simple_math - simple_math_ft - simple_nrtxtfile - simple_ori_utils - simple_ran_tabu - simple_rnd - simple_srch_sort_loc - simple_stat - simple_string - simple_string_utils - simple_type_defs

---

Module: simple_ori_tester

Files: - main/ori/simple_ori_tester.f90

Uses: - simple_defs - simple_ori - simple_ori_utils - simple_string - simple_test_utils

Public symbols: - run_all_ori_tests — subroutine

Private symbols: - test_2Dshift_set_get_and_rounding — subroutine - test_copy_nonptcl_to_ptcl — subroutine - test_copy_ptcl_to_nonptcl — subroutine - test_copy_ptcl_to_ptcl — subroutine - test_ctor_and_flags — subroutine - test_delete_2Dclustering — subroutine - test_delete_3Dalignment — subroutine - test_euler_basic_set_get — subroutine - test_euler_compose_vs_compeuler — subroutine - test_euler_matrix_roundtrip — subroutine - test_geodesic_metrics — subroutine - test_get_dfx_dfy_and_setters — subroutine - test_isthere_and_ischar — subroutine - test_mirror2d_involution — subroutine - test_mirror3d_involution — subroutine - test_normal_and_mat_consistency — subroutine - test_ori2str_and_str2ori_roundtrip — subroutine - test_state_class_proj_eo_sampled_updatecnt — subroutine - test_transfer_2Dparams — subroutine - test_transfer_3Dparams — subroutine - test_transp_involution — subroutine

---

Module: simple_ori_utils

Files: - main/ori/simple_ori_utils.f90

Uses: - simple_defs - simple_linalg - simple_math - simple_rnd

Public symbols: - dm2euler — function - euler2m — function - euler_compose — subroutine - euler_mirror — subroutine - m2euler — function - make_transfmat — function - rnd_romat — subroutine

Private symbols: - drotmat — function - euler2dm — subroutine - euler_normal — function - rotmat — function

---

Module: simple_oris

Files: - main/ori/simple_oris.f90

Uses: - simple_ori - simple_ori_api

Public symbols: - oris — type

---

Module: simple_oris_tester

Files: - main/ori/simple_oris_tester.f90

Uses: - simple_core_module_api - simple_test_utils

Public symbols: - run_all_oris_tests — subroutine

Private symbols: - test_compress_and_masks — subroutine - test_constructors_and_basic_props — subroutine - test_extract_and_copy — subroutine - test_getters_setters — subroutine - test_misc_flags — subroutine - test_proj_space_and_remap — subroutine - test_randomization_and_symmetry — subroutine - test_rotations_and_errors — subroutine - test_sample4update_cnt_large — subroutine - test_sampling_and_updatecnt — subroutine - test_stats_and_ordering — subroutine

---

Module: simple_parameters

Files: - main/params/simple_parameters.f90

Uses: - simple_atoms - simple_cmdline - simple_core_module_api - simple_decay_funs - simple_parameters_registry - simple_ui - simple_ui_program

Public symbols: - parameters — type

---

Module: simple_parameters_registry

Files: - main/params/simple_parameters_registry.f90

Uses: - simple_cmdline - simple_core_module_api

Public symbols: - param_registry — type

Private symbols: - add_char_fixed — subroutine - add_char_string — subroutine - add_dir — subroutine - add_file — subroutine - add_int — subroutine - add_real — subroutine - apply_cmdline — subroutine - char_binding — type - clear — subroutine - dir_binding — type - ensure_char_capacity — subroutine - ensure_dir_capacity — subroutine - ensure_file_capacity — subroutine - ensure_int_capacity — subroutine - ensure_real_capacity — subroutine - ensure_string_capacity — subroutine - file_binding — type - int_binding — type - real_binding — type - string_binding — type

---

Module: simple_particle_extractor

Files: - main/simple_particle_extractor.f90

Uses: - simple_core_module_api - simple_eer_factory - simple_image - simple_motion_correct_utils - simple_ori - simple_starfile_wrappers

Public symbols: - ptcl_extractor — type

Private symbols: - cure_outliers — subroutine - display — subroutine - extract_particles — subroutine - extract_particles_from_mic — subroutine - extract_ptcl — subroutine - get_local_shift — subroutine - init_mask — subroutine - init_mic — subroutine - init_mov — subroutine - kill — subroutine - parse_movie_metadata — subroutine - parse_string — subroutine - pix2polycoords — subroutine - post_process — subroutine

---

Module: simple_pca

Files: - main/pca/simple_pca.f90

Public symbols: - pca — type

Private symbols: - generic_generate — subroutine - generic_get_feat — function - generic_kill — subroutine - generic_master — subroutine - generic_new — subroutine

---

Module: simple_pca_svd

Files: - main/pca/simple_pca_svd.f90

Uses: - simple_core_module_api - simple_pca

Public symbols: - pca_svd — type

Private symbols: - generate_svd — subroutine - get_feat_svd — function - kill_svd — subroutine - master_ori — subroutine - master_svd — subroutine - master_T — subroutine - new_svd — subroutine

---

Module: simple_persistent_worker_message_base

Files: - utils/persistent_worker/message/simple_persistent_worker_message_base.f90

Public symbols: - qsys_persistent_worker_message_base — type

Private symbols: - kill_qsys_persistent_worker_message_base — subroutine - new_qsys_persistent_worker_message_base — subroutine - serialise — subroutine

---

Module: simple_persistent_worker_message_heartbeat

Files: - utils/persistent_worker/message/simple_persistent_worker_message_heartbeat.f90

Uses: - simple_persistent_worker_message_base - simple_persistent_worker_message_types

Public symbols: - qsys_persistent_worker_message_heartbeat — type

Private symbols: - kill_qsys_persistent_worker_message_heartbeat — subroutine - new_qsys_persistent_worker_message_heartbeat — subroutine - serialise_qsys_persistent_worker_message_heartbeat — subroutine

---

Module: simple_persistent_worker_message_status

Files: - utils/persistent_worker/message/simple_persistent_worker_message_status.f90

Uses: - simple_defs - simple_persistent_worker_message_base - simple_persistent_worker_message_types

Public symbols: - qsys_persistent_worker_message_status — type

Private symbols: - kill_qsys_persistent_worker_message_status — subroutine - new_qsys_persistent_worker_message_status — subroutine - serialise_qsys_persistent_worker_message_status — subroutine

---

Module: simple_persistent_worker_message_task

Files: - utils/persistent_worker/message/simple_persistent_worker_message_task.f90

Uses: - simple_defs - simple_persistent_worker_message_base - simple_persistent_worker_message_types

Public symbols: - qsys_persistent_worker_message_task — type

Private symbols: - kill_qsys_persistent_worker_message_task — subroutine - new_qsys_persistent_worker_message_task — subroutine - serialise_qsys_persistent_worker_message_task — subroutine

---

Module: simple_persistent_worker_message_terminate

Files: - utils/persistent_worker/message/simple_persistent_worker_message_terminate.f90

Uses: - simple_defs - simple_persistent_worker_message_base - simple_persistent_worker_message_types

Public symbols: - qsys_persistent_worker_message_terminate — type

Private symbols: - kill_qsys_persistent_worker_message_terminate — subroutine - new_qsys_persistent_worker_message_terminate — subroutine - serialise_qsys_persistent_worker_message_terminate — subroutine

---

Module: simple_persistent_worker_message_tester

Files: - utils/persistent_worker/message/simple_persistent_worker_message_tester.f90

Uses: - simple_persistent_worker_message_base - simple_persistent_worker_message_heartbeat - simple_persistent_worker_message_status - simple_persistent_worker_message_task - simple_persistent_worker_message_terminate - simple_persistent_worker_message_types - simple_test_utils

Public symbols: - run_all_persistent_worker_message_tests — subroutine

Private symbols: - test_base_message_new_kill_and_serialise — subroutine - test_heartbeat_new_kill_and_serialise — subroutine - test_message_type_enum_values — subroutine - test_status_new_kill_and_serialise — subroutine - test_task_new_kill_and_serialise — subroutine - test_terminate_new_kill_and_serialise — subroutine

---

Module: simple_persistent_worker_message_types

Files: - utils/persistent_worker/message/simple_persistent_worker_message_types.f90

---

Module: simple_persistent_worker_server

Files: - utils/persistent_worker/simple_persistent_worker_server.f90

Uses: - iso_c_binding - simple_core_module_api - simple_ipc_tcp_socket_client - simple_ipc_tcp_socket_helpers - simple_ipc_tcp_socket_server - simple_persistent_worker_message_heartbeat - simple_persistent_worker_message_status - simple_persistent_worker_message_task - simple_persistent_worker_message_terminate - simple_persistent_worker_message_types - simple_string - unix

Private symbols: - claim_warmup_worker_ids — subroutine - clear_registry_entry_by_fd — subroutine - clear_stale_registry_entry — subroutine - get_host_ips — function - get_port — function - get_queue_pressure_workers_required — function - handle_heartbeat_msg — subroutine - handle_new_task_msg — subroutine - handle_terminate_msg — subroutine - handle_unknown_msg — subroutine - is_running — function - kill — subroutine - mark_worker_slots_launch_pending — subroutine - new — subroutine - pack_task_queue — subroutine - queue_task — function - send_idle_reply — subroutine - set_warmup_cooldown_enabled — subroutine - set_warmup_request — subroutine - signal_ready — subroutine - update_queue_pressure — subroutine - update_worker_registry — subroutine - worker_listener_thread — subroutine

---

Module: simple_persistent_worker_server_tester

Files: - utils/persistent_worker/simple_persistent_worker_server_tester.f90

Uses: - simple_persistent_worker_message_task - simple_persistent_worker_server - simple_string - simple_test_utils

Public symbols: - run_all_persistent_worker_server_tests — subroutine

Private symbols: - build_test_task — subroutine - test_claim_warmup_marks_launch_pending_and_clears_requests — subroutine - test_get_host_ips_default_empty — subroutine - test_mark_worker_slots_launch_pending_sets_flags — subroutine - test_module_defaults_and_constants — subroutine - test_new_and_kill_lifecycle — subroutine - test_new_client_only_invalid_address_rejected — subroutine - test_new_client_only_valid_address_parse — subroutine - test_new_invalid_args_do_not_start — subroutine - test_new_is_idempotent_while_running — subroutine - test_queue_task_eventually_rejects_when_full — subroutine - test_queue_task_priority_requests — subroutine - test_server_default_state — subroutine - test_startup_pending_prevents_duplicate_warmup_claim — subroutine

---

Module: simple_pftc_api

Files: - main/apis/simple_pftc_api.f90

Uses: - gnufor2 - simple_class_frcs - simple_cmdline - simple_core_module_api - simple_ctf - simple_fftw3 - simple_image - simple_imgarr_utils - simple_parameters - simple_sp_project

---

Module: simple_pftc_shsrch_grad

Files: - main/pftc/simple_pftc_shsrch_grad.f90

Uses: - iso_fortran_env - simple_builder - simple_core_module_api - simple_opt_factory - simple_opt_spec - simple_optimizer

Public symbols: - bounded_shift_trial — function - pftc_shsrch_grad — type

Private symbols: - coarse_search — subroutine - coarse_search_opt_angle — subroutine - grad_shsrch_costfun — function - grad_shsrch_fdfcostfun — subroutine - grad_shsrch_gcostfun — subroutine - grad_shsrch_get_profile — subroutine - grad_shsrch_kill — subroutine - grad_shsrch_minimize — function - grad_shsrch_minimize_direct — function - grad_shsrch_new — subroutine - grad_shsrch_optimize_angle — subroutine - grad_shsrch_optimize_angle_wrapper — subroutine - grad_shsrch_reset_profile — subroutine - grad_shsrch_set_indices — subroutine - set_limits — subroutine

---

Module: simple_pftc_srch_api

Files: - main/apis/simple_pftc_srch_api.f90

Uses: - simple_class_frcs - simple_cmdline - simple_core_module_api - simple_ctf - simple_image - simple_imgarr_utils - simple_memoize_ft_maps - simple_parameters - simple_polarft_calc - simple_sigma2_binfile - simple_sp_project - simple_stack_io - simple_starproject - simple_stat

---

Module: simple_pick_strategy

Files: - main/strategies/parallelization/simple_pick_strategy.f90

Uses: - simple_binoris_io - simple_cmdline - simple_commanders_api - simple_commanders_cavgs - simple_default_clines - simple_gui_utils - simple_image - simple_image_msk - simple_imghead - simple_parameters - simple_picker_iter - simple_qsys_env - simple_sp_project - simple_stack_io - simple_syslib

Public symbols: - create_pick_strategy — function - make_pickrefs_impl — subroutine - pick_distr_strategy — type - pick_inmem_strategy — type - pick_strategy — type

Private symbols: - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_end_message — function - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_end_message — function - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - set_pick_defaults — subroutine - validate_pick_mode — subroutine

---

Module: simple_picker_iter

Files: - main/pick/simple_picker_iter.f90

Uses: - simple_cmdline - simple_core_module_api - simple_image - simple_parameters - simple_picker_utils

Public symbols: - picker_iter — type

Private symbols: - iterate — subroutine - kill — subroutine - read_pickrefs — subroutine

---

Module: simple_picker_utils

Files: - main/pick/simple_picker_utils.f90

Uses: - simple_core_module_api - simple_image - simple_imgarr_utils - simple_parameters - simple_pickref - simple_pickseg - simple_picksegdiam - simple_string_utils

Public symbols: - exec_gaupick — subroutine - exec_refpick — subroutine - exec_segdiampick — subroutine - exec_segpick — subroutine

---

Module: simple_pickref

Files: - main/pick/simple_pickref.f90

Uses: - simple_core_module_api - simple_gui_utils - simple_image - simple_micproc - simple_segmentation

Public symbols: - multiref_merge — subroutine - read_mic_raw_pickref — subroutine

Private symbols: - detect_peaks — subroutine - distance_filter — subroutine - get_loc_sdevs — subroutine - get_nboxes — function - get_positions — subroutine - get_scores — subroutine - kill — subroutine - match_boximgs — subroutine - new — subroutine - peak_vs_nonpeak_stats — subroutine - refine_upscaled — subroutine - refpick — subroutine - remove_outliers — subroutine - report_boxfile — subroutine - report_thumb_den — subroutine - setup_iterators — subroutine - write_boxfile — subroutine

---

Module: simple_pickseg

Files: - main/pick/simple_pickseg.f90

Uses: - simple_bspline_smoother - simple_core_module_api - simple_image - simple_image_bin - simple_parameters - simple_segmentation

Private symbols: - center_mass_cc — function - get_boxsize — function - get_ldim — function - get_nboxes — function - get_positions — subroutine - get_smpd_shrink — function - pick — subroutine - report_boxfile — subroutine

---

Module: simple_picksegdiam

Files: - main/pick/simple_picksegdiam.f90

Uses: - simple_core_module_api - simple_image - simple_image_bin - simple_linked_list - simple_micproc - simple_nrtxtfile

Private symbols: - dealloc_objs — subroutine - dealloc_objs — subroutine - get_diameters — subroutine - kill — subroutine - pick_1 — subroutine - pick_2 — subroutine - pick_3 — subroutine - write_diameters — subroutine - write_pos_and_diams — subroutine

---

Module: simple_polarft_calc

Files: - main/pftc/simple_polarft_calc.f90

Uses: - simple_pftc_api

Public symbols: - polarft_calc — type

---

Module: simple_ppca

Files: - main/pca/simple_ppca.f90

Uses: - simple_core_module_api - simple_math - simple_pca - simple_rnd

Public symbols: - ppca — type

Private symbols: - calc_eigvals — subroutine - em_opt — subroutine - generate_ppca — subroutine - get_eigvals_ppca — function - get_feat_ppca — function - get_signal_eigvals_ppca — function - init — subroutine - kill_ppca — subroutine - master_ppca — subroutine - new_ppca — subroutine - reconstruct_external_ppca — subroutine - set_verbose_ppca — subroutine - slim_ppca — subroutine

---

Module: simple_preprocess_strategy

Files: - main/strategies/parallelization/simple_preprocess_strategy.f90

Uses: - fox_dom - simple_binoris_io - simple_cmdline - simple_commanders_api - simple_ctf_estimate_iter - simple_mini_stream_utils - simple_motion_correct_iter - simple_motion_correct_utils - simple_parameters - simple_qsys_env - simple_sp_project

Public symbols: - create_preprocess_strategy — function - preprocess_distr_strategy — type - preprocess_inmem_strategy — type - preprocess_strategy — type

Private symbols: - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_end_message — function - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_end_message — function - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - set_preprocess_defaults — subroutine

---

Module: simple_private_exec_api

Files: - main/apis/simple_private_exec_api.f90

Uses: - simple_cmdline - simple_commanders_cavgs - simple_commanders_checks - simple_commanders_cluster2d - simple_commanders_denoise - simple_commanders_distr - simple_commanders_euclid - simple_commanders_euclid_distr - simple_commanders_flex_analysis - simple_commanders_imgops - simple_commanders_mask - simple_commanders_misc - simple_commanders_ori - simple_commanders_pick - simple_commanders_preprocess - simple_commanders_prob - simple_commanders_project_cls - simple_commanders_project_core - simple_commanders_project_ptcl - simple_commanders_rec - simple_commanders_rec_distr - simple_commanders_refine3d - simple_commanders_volops - simple_core_module_api - simple_jiffys - simple_private_prgs - simple_symanalyzer - simple_syslib - simple_ui - single_commanders_trajectory - single_commanders_tseries

---

Module: simple_private_prgs

Files: - utils/simple_private_prgs.f90

Uses: - simple_core_module_api

Public symbols: - get_n_private_keys_required — function - get_private_keys_required — function - make_private_ui — subroutine - print_cmdline_oldschool — subroutine - print_private_cmdline — subroutine

Private symbols: - get_n_private_keys_optional — function - get_private_keys_optional — function - init_cmd_dict — subroutine - new_private_prgs — subroutine - push_opt_key — subroutine - push_req_key — subroutine - set_name — subroutine

---

Module: simple_procimgstk

Files: - utils/simple_procimgstk.f90

Uses: - simple_bspline_smoother - simple_core_module_api - simple_ctf - simple_denoise_movies - simple_image - simple_sp_project - simple_stack_io

Public symbols: - add_noise_imgfile — subroutine - apply_ctf_imgfile — subroutine - bp_imgfile — subroutine - bs_smoother_imgfile — subroutine - clip_imgfile — subroutine - copy_imgfile — subroutine - diffmap_denoise_imgfile — subroutine - icm_imgfile — subroutine - loc_sdev_imgfile — subroutine - mask_imgfile — subroutine - mirror_imgfile — subroutine - neg_imgfile — subroutine - nlmean_imgfile — subroutine - noise_imgfile — subroutine - noise_norm_imgfile — subroutine - norm_imgfile — subroutine - pad_imgfile — subroutine - phase_rand_imgfile — subroutine - quantize_imgfile — subroutine - raise_exception_imgfile — subroutine - random_cls_from_imgfile — subroutine - random_selection_from_imgfile — subroutine - real_filter_imgfile — subroutine - roavg_imgfile — subroutine - scale_and_clip_imgfile — subroutine - scale_imgfile — subroutine - selection_from_tseries_imgfile — subroutine - shift_imgfile — subroutine - taper_edges_imgfile — subroutine

---

Module: simple_progress

Files: - utils/simple_progress.f90

Uses: - simple_core_module_api

Public symbols: - lastfoundfile_update — subroutine - progress_estimate_2D — function - progress_estimate_preprocess_stream — function - progressfile_complete_parts — subroutine - progressfile_init — subroutine - progressfile_init_part — subroutine - progressfile_init_parts — subroutine - progressfile_update — subroutine - progressfile_update_part — subroutine

---

Module: simple_project_merge_tester

Files: - main/project/simple_project_merge_tester.f90

Uses: - simple_oris - simple_projfile_utils - simple_sp_project - simple_string - simple_syslib - simple_test_utils

Public symbols: - run_all_project_merge_tests — subroutine

Private symbols: - cleanup_files — subroutine - fill_class_row — subroutine - fill_particle_row — subroutine - make_project — subroutine - test_merge_pruned_stack_indexing_heterogeneous_ctf — subroutine - test_validate_projfile_normalizes_legacy_stack_indices — subroutine

---

Module: simple_projector

Files: - main/image/simple_projector.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - projector — type

Private symbols: - expand_cmat — subroutine - fproject — subroutine - fproject_serial — subroutine - get_kbwin — function - interp_fcomp — function - interp_fcomp_oversamp — function - kill_expanded — subroutine - reset_expanded — subroutine

---

Module: simple_projector_pft

Files: - main/image/simple_projector_pft.f90

Uses: - simple_core_module_api - simple_polarft_calc - simple_projector

Public symbols: - fproject_polar — subroutine - fproject_polar_oversamp — subroutine

---

Module: simple_projector_pft_batch

Files: - main/image/simple_projector_pft_batch.f90

Uses: - simple_core_module_api - simple_kbinterpol - simple_polarft_calc - simple_projector

Public symbols: - fproject_polar_batch — subroutine - fproject_polar_batch_mirr — subroutine - fproject_polar_batch_opt — subroutine

Private symbols: - fproject_polar_batch_opt_kernel — subroutine

---

Module: simple_projfile_utils

Files: - fileio/simple_projfile_utils.f90

Uses: - simple_class_frcs - simple_core_module_api - simple_euclid_sigma2 - simple_image - simple_oris - simple_sp_project

Public symbols: - absolutize_project_stack_paths — subroutine - copy_particle_row — subroutine - err — subroutine - make_prefix_offsets — subroutine - merge_chunk_projfiles — subroutine - merge_selected_project_files — subroutine - remap_row_ogid — subroutine - repair — subroutine - repair_particle_segment — subroutine - repair_stack_counts_without_particles — subroutine - repair_stack_nptcls_stk — subroutine - repair_stack_ranges — subroutine - require_row_field — subroutine - set_stack_int_if_changed — subroutine - validate_and_repair_project_file — subroutine - validate_field_presence — subroutine - validate_mic_sampling — subroutine - validate_particle_field — subroutine - validate_source_project — subroutine - validate_stack_dimensions — subroutine - validate_stack_particle_ranges — subroutine - warn — subroutine

---

Module: simple_pspec_thumb_iter

Files: - main/simple_pspec_thumb_iter.f90

Uses: - simple_cmdline - simple_core_module_api - simple_image - simple_parameters

Public symbols: - pspec_thumb_iter — type

Private symbols: - iterate — subroutine

---

Module: simple_pspecs

Files: - main/simple_pspecs.f90

Uses: - simple_core_module_api - simple_fsc - simple_image - simple_oris

Private symbols: - calc_distmat_1 — function - calc_distmat_2 — function - get_nspecs — function - kill — subroutine - new — subroutine

---

Module: simple_ptcl_sieve

Files: - main/sieve/simple_ptcl_sieve.f90

Uses: - simple_cavg_quality_analysis - simple_cavg_quality_feats - simple_cavg_quality_helpers - simple_cavg_quality_model - simple_cavg_quality_types - simple_class_compatibility - simple_cmdline - simple_commanders_cavgs - simple_defs - simple_defs_fname - simple_error - simple_fileio - simple_gui_utils - simple_image - simple_image_bin - simple_imgarr_utils - simple_parameters - simple_projfile_utils - simple_qsys_env - simple_rec_list - simple_segmentation - simple_sp_project - simple_string - simple_string_utils - simple_syslib - simple_timer - unix

Public symbols: - ptcl_sieve — type

Private symbols: - append_chunk_coarse — subroutine - append_chunk_fine — subroutine - chunk2D_coarse_defaults — type - chunk2D_fine_defaults — type - chunk2D_state — type - cleanup_chunk — subroutine - collect_and_reject — subroutine - combine_completed_chunks — subroutine - cycle — subroutine - draw_reason_key_swatches — subroutine - generate_chunk_coarse_cline — subroutine - generate_chunk_fine_cline — subroutine - generate_chunks_coarse — subroutine - generate_chunks_fine — subroutine - import_existing_chunks_coarse — subroutine - import_existing_chunks_fine — subroutine - kill — subroutine - merge_and_clear — subroutine - new — subroutine - paint_mask_outline — subroutine - paint_reason_border — subroutine - reject_cavgs — subroutine - remove_duplicates — function - set_final_ingestion — subroutine - submit — subroutine - timer_stop — subroutine - unset_final_ingestion — subroutine - write_rejection_reason_overlay_jpg — subroutine

---

Module: simple_ptcl_sieve_tester

Files: - main/sieve/simple_ptcl_sieve_tester.f90

Uses: - simple_cmdline - simple_core_module_api - simple_defs_fname - simple_parameters - simple_ptcl_sieve - simple_rec_list - simple_sp_project - simple_string - simple_test_utils

Public symbols: - run_all_ptcl_sieve_tests — subroutine

Private symbols: - init_test_params — subroutine - make_chunk_project — subroutine - setup_workspace — subroutine - teardown_workspace — subroutine - test_cycle_empty_project_list — subroutine - test_finished_semantics — subroutine - test_import_existing_chunks_and_counts — subroutine - test_new_accepts_tuning_overrides — subroutine - test_new_kill_and_empty_queries — subroutine - test_single_pass_ignores_incomplete_fine — subroutine

---

Module: simple_ptcl_sieve_utils

Files: - main/sieve/simple_ptcl_sieve_utils.f90

Uses: - simple_cmdline - simple_core_module_api - simple_parameters - simple_sp_project - simple_stream_api - simple_string - simple_string_utils - simple_type_defs

Public symbols: - generate_sieve_projects — subroutine

---

Module: simple_qsys_base

Files: - utils/qsys/simple_qsys_base.f90

Uses: - simple_chash - simple_string

Public symbols: - qsys_base — type

Private symbols: - generic_kill — subroutine - generic_new — subroutine - generic_submit_cmd — function - generic_write_array_instr — subroutine - generic_write_instr — subroutine

---

Module: simple_qsys_coarray

Files: - utils/qsys/simple_qsys_coarray.f90

Uses: - simple_core_module_api - simple_qsys_base

Public symbols: - qsys_coarray — type

Private symbols: - get_coarray_submit_cmd — function - kill_coarray_env — subroutine - new_coarray_env — subroutine - write_coarray_array_header — subroutine - write_coarray_header — subroutine

---

Module: simple_qsys_ctrl

Files: - utils/qsys/simple_qsys_ctrl.f90

Uses: - simple_cmdline - simple_core_module_api - simple_mem_estimator - simple_parameters - simple_persistent_worker_message_task - simple_persistent_worker_server - simple_qsys_base - simple_qsys_coarray - simple_qsys_lsf - simple_qsys_persistent_worker - simple_qsys_slurm - simple_syslib

Private symbols: - worker_warmup_callback — subroutine

---

Module: simple_qsys_env

Files: - utils/qsys/simple_qsys_env.f90

Uses: - simple_cmdline - simple_core_module_api - simple_defs_environment - simple_parameters - simple_persistent_worker_server - simple_qsys_base - simple_qsys_coarray - simple_qsys_ctrl - simple_qsys_factory - simple_qsys_funs - simple_qsys_local - simple_qsys_lsf - simple_qsys_pbs - simple_qsys_persistent_worker - simple_qsys_sge - simple_qsys_slurm - simple_sp_project

Public symbols: - qsys_env — type

Private symbols: - diagnose_parallelism — subroutine - exec_simple_prg_in_queue — subroutine - exec_simple_prg_in_queue_async — subroutine - exec_simple_prgs_in_queue_async — subroutine - exists — function - gen_script — subroutine - gen_scripts_and_schedule_jobs — subroutine - gen_subproject_scripts_and_schedule — subroutine - get_exec_bin — function - get_persistent_worker_server_address — function - get_qsys — function - init_qdescr_from_runtime — subroutine - kill — subroutine - new — subroutine - persistent_worker_warmup_callback — subroutine - schedule_subproject_jobs — subroutine - service_persistent_worker_warmup — subroutine - standard_exec_path — subroutine - start_persistent_workers — subroutine - validate_requested_qsys — subroutine

---

Module: simple_qsys_factory

Files: - utils/qsys/simple_qsys_factory.f90

Uses: - simple_core_module_api - simple_qsys_base - simple_qsys_coarray - simple_qsys_local - simple_qsys_lsf - simple_qsys_pbs - simple_qsys_persistent_worker - simple_qsys_sge - simple_qsys_slurm

Public symbols: - qsys_factory — type

Private symbols: - kill — subroutine - new — subroutine

---

Module: simple_qsys_funs

Files: - utils/qsys/simple_qsys_funs.f90

Uses: - simple_core_module_api - simple_parameters

---

Module: simple_qsys_local

Files: - utils/qsys/simple_qsys_local.f90

Uses: - simple_core_module_api - simple_qsys_base

Public symbols: - qsys_local — type

Private symbols: - get_local_submit_cmd — function - kill_local_env — subroutine - new_local_env — subroutine - write_local_array_header — subroutine - write_local_header — subroutine

---

Module: simple_qsys_lsf

Files: - utils/qsys/simple_qsys_lsf.f90

Uses: - simple_core_module_api - simple_qsys_base

Public symbols: - qsys_lsf — type

Private symbols: - get_lsf_submit_cmd — function - kill_lsf_env — subroutine - new_lsf_env — subroutine - write_lsf_array_header — subroutine - write_lsf_header — subroutine

---

Module: simple_qsys_pbs

Files: - utils/qsys/simple_qsys_pbs.f90

Uses: - simple_core_module_api - simple_qsys_base

Public symbols: - qsys_pbs — type

Private symbols: - get_pbs_submit_cmd — function - kill_pbs_env — subroutine - new_pbs_env — subroutine - write_formatted — subroutine - write_pbs_array_header — subroutine - write_pbs_header — subroutine

---

Module: simple_qsys_persistent_worker

Files: - utils/qsys/simple_qsys_persistent_worker.f90

Uses: - simple_core_module_api - simple_persistent_worker_server - simple_qsys_base

Public symbols: - qsys_persistent_worker — type

Private symbols: - get_worker_submit_cmd — function - kill_worker_env — subroutine - new_worker_env — subroutine - write_worker_array_header — subroutine - write_worker_header — subroutine

---

Module: simple_qsys_sge

Files: - utils/qsys/simple_qsys_sge.f90

Uses: - simple_core_module_api - simple_qsys_base

Public symbols: - qsys_sge — type

Private symbols: - get_sge_submit_cmd — function - kill_sge_env — subroutine - new_sge_env — subroutine - write_sge_array_header — subroutine - write_sge_header — subroutine

---

Module: simple_qsys_slurm

Files: - utils/qsys/simple_qsys_slurm.f90

Uses: - simple_core_module_api - simple_qsys_base

Public symbols: - qsys_slurm — type

Private symbols: - get_slurm_submit_cmd — function - kill_slurm_env — subroutine - new_slurm_env — subroutine - write_slurm_array_header — subroutine - write_slurm_header — subroutine

---

Module: simple_r8lib

Files: - utils/math/simple_r8lib.f90

Public symbols: - r8mat_cholesky_factor — subroutine - r8mat_cholesky_solve — subroutine

Private symbols: - r8mat_l_solve — subroutine - r8mat_lt_solve — subroutine

---

Module: simple_ran_tabu

Files: - utils/math/simple_ran_tabu.f90

Uses: - simple_defs - simple_error - simple_rnd

Public symbols: - ran_tabu — type

---

Module: simple_rec3D_strategy

Files: - main/strategies/parallelization/simple_rec3D_strategy.f90

Uses: - simple_builder - simple_cmdline - simple_commanders_rec_distr - simple_commanders_volops - simple_core_module_api - simple_exec_helpers - simple_matcher_3drec - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_refine3d_fnames

Public symbols: - create_rec3D_strategy — function - rec3D_distr_strategy — type - rec3D_inmem_strategy — type - rec3D_strategy — type

Private symbols: - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - maybe_postprocess_reconstruct3D — subroutine - sync_resolved_rec_params — subroutine

---

Module: simple_rec_list

Files: - utils/structs/simple_rec_list.f90

Uses: - simple_core_module_api - simple_linked_list

Public symbols: - chunk_rec — type - process_rec — type - project_rec — type - rec — type - rec_iterator — type - rec_list — type

Private symbols: - append — function - assign — subroutine - at_chunk_rec — subroutine - at_process_rec — subroutine - at_project_rec — subroutine - at_rec — subroutine - begin — function - end — function - end_iter — function - get_busy_flags — function - get_ids — function - get_included_flags — function - get_nptcls — function - get_processed_flags — function - get_projfiles — function - get_projnames — function - iter_advance — subroutine - iter_get_chunk_rec — subroutine - iter_get_process_rec — subroutine - iter_get_project_rec — subroutine - iter_get_rec — subroutine - iter_next — subroutine - iter_replace — subroutine - kill — subroutine - print_file — subroutine - print_proc — subroutine - print_proj — subroutine - push2chunk_list — subroutine - push2project_list — subroutine - push_back — subroutine - rec_print — subroutine - replace_at — subroutine - replace_iterator — subroutine - replace_with — subroutine - set_included_flags — subroutine - slice — subroutine - subset_to — subroutine

---

Module: simple_rec_list_tester

Files: - utils/structs/simple_rec_list_tester.f90

Uses: - simple_defs - simple_rec_list - simple_string - simple_test_utils

Public symbols: - run_all_rec_list_tests — subroutine

Private symbols: - test_append_operator — subroutine - test_assign_semantics — subroutine - test_default_and_size — subroutine - test_flag_included — subroutine - test_included_mask — subroutine - test_iterator_replace — subroutine - test_iterator_traversal — subroutine - test_kill_behavior — subroutine - test_particle_sums — subroutine - test_push_back_and_at — subroutine - test_replace_at — subroutine - test_slice_subset — subroutine

---

Module: simple_reconstructor

Files: - main/volume/simple_reconstructor.f90

Uses: - simple_core_module_api - simple_fftw3 - simple_fsc - simple_image - simple_kbinterpol - simple_math - simple_parameters - simple_sp_project

Public symbols: - reconstructor — type

Private symbols: - add_conical_invtausq2rho — subroutine - add_invtausq2rho — subroutine - alloc_rho — subroutine - apply_weight — subroutine - compress_exp — subroutine - dealloc_exp — subroutine - dealloc_rho — subroutine - expand_exp — subroutine - get_kbwin — function - insert_plane_oversamp — subroutine - insert_plane_oversamp_opt — subroutine - interp_cmat_exp — function - kb_apod_vecs_3d_fast — subroutine - kernel — subroutine - pad_with_zeros — subroutine - project_fplane — subroutine - project_polar — subroutine - read_raw_rho — subroutine - read_rho — subroutine - reset — subroutine - reset_exp — subroutine - sampl_dens_correct — subroutine - set_sh_lim — subroutine - sum_reduce — subroutine - write_absfc_as_mrc — subroutine - write_rho — subroutine - write_rho_as_mrc — subroutine

---

Module: simple_reconstructor_eo

Files: - main/volume/simple_reconstructor_eo.f90

Uses: - simple_core_module_api - simple_fsc - simple_image - simple_image_msk - simple_imgfile - simple_parameters - simple_reconstructor - simple_refine3d_fnames - simple_sp_project - simple_vol_pproc_policy

Public symbols: - reconstructor_eo — type

Private symbols: - apply_weight — subroutine - calc_fsc4sampl_dens_correct — subroutine - compress_exp — subroutine - expand_exp — subroutine - get_kbwin — function - get_res — subroutine - grid_plane — subroutine - grid_plane_compact — subroutine - kill — subroutine - kill_exp — subroutine - load_state_mask_or_fallback — subroutine - new — subroutine - project_polar — subroutine - read_eos — subroutine - read_eos_parallel_io — subroutine - read_even — subroutine - read_odd — subroutine - reset_all — subroutine - reset_eoexp — subroutine - reset_eos — subroutine - reset_even — subroutine - reset_odd — subroutine - reset_sum — subroutine - sampl_dens_correct_eos — subroutine - sampl_dens_correct_sum — subroutine - set_sh_lim — subroutine - sum_eos — subroutine - sum_reduce — subroutine - write_eos — subroutine - write_even — subroutine - write_fsc2txt — subroutine - write_odd — subroutine

---

Module: simple_reconstructor_openmpoffload

Files: - main/volume/simple_reconstructor_openmpoffload.f90

Uses: - simple_builder - simple_cmdline - simple_core_module_api - simple_kbinterpol - simple_matcher_3drec - simple_matcher_ptcl_io - simple_math - simple_parameters

Public symbols: - calc_3Drec_gpu — subroutine

Private symbols: - insert_all_slices — subroutine - insert_slices_batch — subroutine - prep_batch — subroutine - update_ptcls_arrays — subroutine

---

Module: simple_reconstructor_pcg

Files: - main/volume/simple_reconstructor_pcg.f90

Uses: - simple_core_module_api - simple_ctf - simple_image

Public symbols: - reconstructor_pcg — type

Private symbols: - absT2_plane — subroutine - accumulate_absT2 — subroutine - accumulate_batch — subroutine - accumulate_rhs — subroutine - adjoint_plane_add — subroutine - apply_adjoint_all — function - apply_normal — function - apply_normal_kernel — function - apply_normal_matrixfree — function - apply_precond — function - begin_accum — subroutine - build_env — subroutine - build_hk_luts — subroutine - build_kernel — subroutine - build_operators — subroutine - build_precond — subroutine - build_transfer — function - calibrate_kernel — subroutine - crop_vol — function - deapod_mul — subroutine - dot_real_volume — function - end_accum — subroutine - ensure_wimg — subroutine - extract_native_plane — function - finalize_khat — subroutine - fold_accum_to_khat — subroutine - fold_and_ifft — function - forward_plane — subroutine - fourier_dot — function - get_env — function - get_invenv — function - get_lims2 — function - get_lims3 — function - get_rhs — subroutine - kill — subroutine - mask_mul — subroutine - measure_kernel_scale — function - new — subroutine - pad_vol — function - precond_from_accum — subroutine - prep_particles — subroutine - report_profile — subroutine - reset_profile — subroutine - scatter_plane — subroutine - scatter_window — subroutine - scatter_window_cmplx_nowrap — subroutine - scatter_window_nowrap — subroutine - set_deapod — subroutine - set_mask — subroutine - set_op_mode — subroutine - set_sym — subroutine - set_volume — subroutine - solve — subroutine - solve_accum — subroutine - solve_core — subroutine - transfer_plane_cmplx — subroutine

---

Module: simple_reextract_strategy

Files: - main/strategies/parallelization/simple_reextract_strategy.f90

Uses: - simple_builder - simple_cmdline - simple_commanders_api - simple_parameters - simple_particle_extractor - simple_qsys_env - simple_sp_project

Public symbols: - create_reextract_strategy — function - reextract_distr_strategy — type - reextract_inmem_strategy — type - reextract_strategy — type

Private symbols: - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_end_message — function - distr_execute — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - endmsg_interface — function - exec_interface — subroutine - finalize_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_end_message — function - inmem_execute — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - killimgbatch_local — subroutine - prepimgbatch_local — subroutine - set_reextract_defaults — subroutine - validate_reextract_cline — subroutine

---

Module: simple_refine3D_fnames

Files: - defs/simple_refine3D_fnames.f90

Uses: - simple_defs_fname - simple_string - simple_string_utils

Public symbols: - refine3D_partial_rec_glob — function

---

Module: simple_refine3D_strategy

Files: - main/strategies/parallelization/simple_refine3D_strategy.f90

Uses: - simple_builder - simple_cluster_seed - simple_cmdline - simple_commanders_euclid - simple_commanders_prob - simple_commanders_rec - simple_commanders_rec_distr - simple_commanders_volops - simple_convergence - simple_core_module_api - simple_decay_funs - simple_euclid_sigma2 - simple_exec_helpers - simple_fsc - simple_image - simple_image_msk - simple_matcher_refvol_utils - simple_matcher_smpl_and_lplims - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_refine3d_fnames - simple_sp_project - simple_strategy3d_matcher

Public symbols: - create_refine3D_strategy — function - refine3D_distr_strategy — type - refine3D_inmem_strategy — type - refine3D_strategy — type

Private symbols: - activate_ptcl3D_states_from_selection — subroutine - assert_multistate_populations — subroutine - cleanup_interface — subroutine - distr_cleanup — subroutine - distr_execute_iteration — subroutine - distr_finalize_iteration — subroutine - distr_finalize_run — subroutine - distr_initialize — subroutine - exec_iter_interface — subroutine - finalize_iter_interface — subroutine - finalize_run_interface — subroutine - init_interface — subroutine - inmem_cleanup — subroutine - inmem_execute_iteration — subroutine - inmem_finalize_iteration — subroutine - inmem_finalize_run — subroutine - inmem_initialize — subroutine - invalidate_fresh_start_refs_from_volumes — subroutine - materialize_reprojection_model — subroutine - prepare_assembly_cline — subroutine - refine3D_bench_state — type - refine3D_stage_bench_state — type - refresh_matching_lp_from_project — subroutine - refresh_resolution_fields_from_fsc — subroutine - remove_partial_rec_files — subroutine - reset_refine3D_bench — subroutine - seed_multistate_startup_labels — subroutine - write_stage_bench_report — subroutine - write_strategy_bench_report — subroutine

---

Module: simple_relion

Files: - main/star/simple_relion.f90

Uses: - cplot2d_wrapper_module - fox_dom - simple_cmdline - simple_core_module_api - simple_sp_project - simple_starfile_wrappers

Private symbols: - allocate_opticsgroups — subroutine - create — subroutine - find_movienames — subroutine - generate_epu_tiltgroups — subroutine - generate_single_tiltgroup — subroutine - generate_xml_tiltgroups — subroutine - h_clust — subroutine - write_corrected_micrographs_star — subroutine - write_micrographs_star — subroutine - write_particles2D_star — subroutine

---

Module: simple_rnd

Files: - utils/math/simple_rnd.f90

Uses: - simple_defs - simple_error - simple_syslib

---

Module: simple_sauron

Files: - utils/simple_sauron.f90

Uses: - simple_chash - simple_defs - simple_defs_ori - simple_hash - simple_string_utils

---

Module: simple_segmentation

Files: - utils/simple_segmentation.f90

Uses: - simple_core_module_api - simple_image - simple_image_bin - simple_neighs

---

Module: simple_sigma2_binfile

Files: - fileio/simple_sigma2_binfile.f90

Uses: - simple_core_module_api

Private symbols: - create_empty — subroutine - get_resrange — subroutine - kill — subroutine - new — subroutine - new_from_file — subroutine - open_and_check_header — function - read — subroutine - read_header — subroutine - write — subroutine - write_info — subroutine

---

Module: simple_sigma2_files

Files: - fileio/simple_sigma2_files.f90

Uses: - simple_cmdline - simple_core_module_api - simple_euclid_sigma2 - simple_parameters - simple_polarft_calc - simple_sp_project

Public symbols: - carry_over_prior_sigma_files — subroutine - load_sigma2_groups — subroutine - pick_sigma_group_file — subroutine

Private symbols: - copy_sigma_files_from_dir — subroutine

---

Module: simple_simple_volinterp

Files: - main/volume/simple_volinterp.f90

Uses: - simple_core_module_api - simple_image - simple_projector

Public symbols: - reproject — function - rotvol — function - rotvol_slim — subroutine

---

Module: simple_simulator

Files: - main/simple_simulator.f90

Uses: - simple_core_module_api - simple_ctf - simple_image

Public symbols: - simimg — subroutine

---

Module: simple_socket_comm

Files: - utils/comm/simple_socket_comm.f90

Public symbols: - simple_socket — type

Private symbols: - accept — subroutine - bind_any — subroutine - c_accept — function - c_bind — function - c_close — function - c_connect — function - c_errno — function - c_htons — function - c_inet_pton — function - c_listen — function - c_read — function - c_send — function - c_setsockopt — function - c_socket — function - close_1 — subroutine - close_2 — subroutine - in_addr — type - listen — subroutine - open — subroutine - read_1 — subroutine - read_2 — subroutine - send_1 — subroutine - set_options — subroutine - sockaddr_in — type - timeval — type

---

Module: simple_sp_project

Files: - main/project/simple_sp_project.f90

Uses: - json_kinds - json_module - simple_ansi_ctrls - simple_cmdline - simple_core_module_api - simple_defs_ori - simple_discrete_stack_io - simple_gui_utils - simple_histogram - simple_image - simple_map_reduce - simple_rec_list - simple_stack_io - simple_starfile

---

Module: simple_srch_sort_loc

Files: - utils/math/simple_srch_sort_loc.f90

Uses: - simple_defs - simple_error

---

Module: simple_srchspace_map

Files: - utils/simple_srchspace_map.f90

Uses: - simple_error - simple_srch_sort_loc

Public symbols: - srchspace_map — type

Private symbols: - get_full2sub_map — function - get_inds_in_full — function - get_sub2full_map — function - kill — subroutine - new_from_distmat — subroutine - new_from_maps — subroutine

---

Module: simple_srchspace_map2D_io

Files: - fileio/simple_srchspace_map2D_io.f90

Uses: - simple_error - simple_fileio - simple_srch_sort_loc - simple_string

Public symbols: - read_srchspace_map2D — subroutine - test_srchspace_map2D_io — subroutine - write_srchspace_map2D — subroutine

---

Module: simple_stack_io

Files: - fileio/simple_stack_io.f90

Uses: - simple_core_module_api - simple_image - simple_imgfile

Private symbols: - close — subroutine - get_image — subroutine - get_ldim — function - get_nptcls — function - open_1 — subroutine - open_2 — subroutine - read — subroutine - read_whole — subroutine - same_stk — function - write — subroutine - write_buffer — subroutine

---

Module: simple_stackops

Files: - utils/simple_stackops.f90

Uses: - simple_core_module_api - simple_image

Public symbols: - acf_stack — subroutine - frameavg_stack — subroutine - make_avg_stack — subroutine - make_pcavec_stack — subroutine - prep_imgfile4movie — subroutine - stats_imgfile — subroutine

Private symbols: - raise_exception — subroutine

---

Module: simple_starfile

Files: - main/star/simple_starfile.f90

Uses: - simple_core_module_api - simple_starfile_wrappers

Private symbols: - calc_part_boundaries — subroutine - complete — subroutine - get_relative_path_here — function - get_relative_path_here — function - get_relative_path_here — function - init — subroutine - write_mics_table — subroutine - write_optics_table — subroutine - write_ptcl2D_table — subroutine - write_ptcl2D_table_parallel — subroutine

---

Module: simple_starfile_tester

Files: - main/star/simple_starfile_tester.f90

Uses: - omp_lib - simple_core_module_api - simple_starfile - simple_starfile_wrappers - simple_test_utils

Public symbols: - run_all_starfile_tests — subroutine

Private symbols: - fill_ptcl_stk — subroutine - make_oris_n — subroutine - setup_tmpdir — subroutine - test_complete_noop_without_tmp — subroutine - test_complete_overwrites_existing — subroutine - test_complete_renames_tmp — subroutine - test_init_creates_no_files — subroutine - test_init_removes_stale_tmp — subroutine - test_verbose_flag_no_content_change — subroutine - test_write_mics_table_all_fields — subroutine - test_write_mics_table_basic — subroutine - test_write_mics_table_empty — subroutine - test_write_mics_table_state_filter — subroutine - test_write_optics_table_all_fields — subroutine - test_write_optics_table_basic — subroutine - test_write_optics_table_empty — subroutine - test_write_optics_table_state_filter — subroutine - test_write_ptcl2D_parallel_basic — subroutine - test_write_ptcl2D_parallel_count — subroutine - test_write_ptcl2D_parallel_empty — subroutine - test_write_ptcl2D_parallel_vs_serial — subroutine - test_write_ptcl2D_table_bad_stkind — subroutine - test_write_ptcl2D_table_basic — subroutine - test_write_ptcl2D_table_indstk_explicit — subroutine - test_write_ptcl2D_table_state_filter — subroutine - test_write_ptcl2D_table_with_mics — subroutine - tmp — function - write_dummy_file — subroutine

---

Module: simple_starfile_wrappers

Files: - main/star/simple_starfile_wrapper.f90

Uses: - simple_core_module_api

Public symbols: - starfile_table_type — type

Private symbols: - C_dealloc_str — subroutine - C_print_pointer — subroutine - C_starfile_table__addObject — subroutine - C_starfile_table__append — subroutine - C_starfile_table__clear — subroutine - C_starfile_table__close_ofile — subroutine - C_starfile_table__delete — subroutine - C_starfile_table__firstobject — function - C_starfile_table__getcomment — subroutine - C_starfile_table__getnames_cnt — subroutine - C_starfile_table__getnames_nr — subroutine - C_starfile_table__getValue_bool — function - C_starfile_table__getValue_double — function - C_starfile_table__getValue_float — function - C_starfile_table__getValue_int — function - C_starfile_table__getValue_string — subroutine - C_starfile_table__hascomment — function - C_starfile_table__hasLabel — function - C_starfile_table__new — function - C_starfile_table__nextobject — function - C_starfile_table__numberofobjects — function - C_starfile_table__open_ofile — subroutine - C_starfile_table__read — subroutine - C_starfile_table__setcomment — subroutine - C_starfile_table__setIsList — subroutine - C_starfile_table__setname — subroutine - C_starfile_table__setValue_bool — subroutine - C_starfile_table__setValue_double — subroutine - C_starfile_table__setValue_float — subroutine - C_starfile_table__setValue_int — subroutine - C_starfile_table__setValue_string — subroutine - C_starfile_table__write_ofile — subroutine - C_starfile_table__write_omem — subroutine - starfile_table__addObject — subroutine - starfile_table__append — subroutine - starfile_table__clear — subroutine - starfile_table__close_ofile — subroutine - starfile_table__delete — subroutine - starfile_table__firstobject — function - starfile_table__getcomment — subroutine - starfile_table__getnames — subroutine - starfile_table__getValue_bool — function - starfile_table__getValue_double — function - starfile_table__getValue_float — function - starfile_table__getValue_int — function - starfile_table__getValue_string — function - starfile_table__hascomment — function - starfile_table__haslabel — function - starfile_table__new — subroutine - starfile_table__nextobject — function - starfile_table__numberofobjects — function - starfile_table__open_ofile — subroutine - starfile_table__read — subroutine - starfile_table__setcomment — subroutine - starfile_table__setIsList — subroutine - starfile_table__setname — subroutine - starfile_table__setValue_bool — subroutine - starfile_table__setValue_double — subroutine - starfile_table__setValue_float — subroutine - starfile_table__setValue_int — subroutine - starfile_table__setValue_string — subroutine - starfile_table__write_ofile — subroutine - starfile_table__write_omem — subroutine

---

Module: simple_starproject

Files: - main/star/simple_starproject.f90

Uses: - cplot2d_wrapper_module - fox_dom - simple_cmdline - simple_core_module_api - simple_refine3d_fnames - simple_rnd - simple_sp_project - simple_starproject_utils

Private symbols: - apply_optics_offset — subroutine - assign_initial_tiltgroups — subroutine - assign_optics — subroutine - assign_xml_tiltinfo — subroutine - check_stk_params — subroutine - cluster_tiltinfo — subroutine - export_cls2D — subroutine - export_iter3D — subroutine - export_manifoldem_ptcls3D — subroutine - export_mics — subroutine - export_opticsgroups — subroutine - export_ptcls2D — subroutine - export_ptcls3D — subroutine - export_stardata — subroutine - export_stream2D — subroutine - get_image_basename — subroutine - import_cls2D — subroutine - import_mics — subroutine - import_ptcls — subroutine - import_ptcls2D — subroutine - import_ptcls3D — subroutine - import_stardata — subroutine - initialise — subroutine - kill — subroutine - plot_opticsgroups — subroutine - populate_opticsmap — subroutine - populate_stkmap — subroutine - propagate_optics2D — subroutine - propagate_optics3D — subroutine - propagate_optics_box — subroutine - read_starheaders — subroutine - set_verbose — subroutine - sort_optics_maxpop — subroutine

---

Module: simple_starproject_stream

Files: - main/star/simple_starproject_stream.f90

Uses: - cplot2d_wrapper_module - fox_dom - simple_cmdline - simple_core_module_api - simple_histogram - simple_parameters - simple_sp_project - simple_starfile_wrappers

Private symbols: - assign_optics — subroutine - assign_optics_single — subroutine - assign_shiftgroups — subroutine - assign_tiltgroups — subroutine - copy_micrographs_optics — subroutine - copy_optics — subroutine - get_relative_path_here — function - get_relative_path_here — function - get_relative_path_here — function - get_relative_path_here — function - h_clust — subroutine - starfile_deinit — subroutine - starfile_init — subroutine - starfile_set_clusters2D_table — subroutine - starfile_set_micrographs_table — subroutine - starfile_set_optics_group_table — subroutine - starfile_set_optics_table — subroutine - starfile_set_particles2D_subtable — subroutine - starfile_set_particles2D_table — subroutine - starfile_set_pick_diameters_table — subroutine - starfile_write_table — subroutine - starpart — type - stream_export_micrographs — subroutine - stream_export_optics — subroutine - stream_export_particles_2D — subroutine - stream_export_pick_diameters — subroutine - stream_export_picking_references — subroutine

---

Module: simple_starproject_tester

Files: - main/star/simple_starproject_tester.f90

Uses: - omp_lib - simple_cmdline - simple_defs - simple_relion - simple_sp_project - simple_starfile - simple_starfile_wrappers - simple_starproject - simple_starproject_utils - simple_string - simple_test_utils

Public symbols: - run_all_starproject_tests — subroutine

Private symbols: - create_directory — subroutine - delete_directory — subroutine - force_openmp_threads — subroutine - make_tiltinfo — function - setup_tmpdir — subroutine - test_large_particle_table_export — subroutine - test_optics_clustering_basic — subroutine - test_particle_export_readback — subroutine - test_relion_allocate_opticsgroups — subroutine - test_relion_epu_tiltgroups — subroutine - test_relion_find_movienames — subroutine - test_relion_single_tiltgroup — subroutine - test_relion_write_corrected_micrographs_star — subroutine - test_relion_write_micrographs_star — subroutine - test_relion_write_particles2D_star — subroutine - test_relion_writer_micrographs — subroutine - test_roundtrip_micrographs — subroutine - test_star_export_micrographs — subroutine - test_star_micrographs_readback — subroutine - test_starfile_append_mode — subroutine - test_starfile_basic_init — subroutine - test_starfile_multiple_tables — subroutine - test_starfile_write_and_readback — subroutine - test_write_omem_parallel_stability — subroutine - test_xml_tiltinfo — subroutine - tmpfile — function - write_textfile — subroutine

---

Module: simple_starproject_utils

Files: - main/star/simple_starproject_utils.f90

Uses: - simple_core_module_api - simple_sp_project

Public symbols: - center_boxes — subroutine - enable_rlnflag — subroutine - enable_splflag — subroutine - enable_splflags — subroutine - find_separators — subroutine - get_rlnflagindex — subroutine - h_clust — subroutine - split_dataline — subroutine

---

Module: simple_stat

Files: - utils/math/simple_stat.f90

Uses: - simple_defs - simple_error - simple_is_check_assert - simple_srch_sort_loc - simple_type_defs

---

Module: simple_strategy2D

Files: - main/strategies/search/simple_strategy2D.f90

Uses: - simple_builder - simple_oris - simple_parameters - simple_strategy2d_srch

Public symbols: - strategy2D — type - strategy2D_per_ptcl — type

Private symbols: - generic_kill — subroutine - generic_new — subroutine - generic_srch — subroutine

---

Module: simple_strategy2D_alloc

Files: - main/strategies/search/simple_strategy2D_alloc.f90

Uses: - simple_eul_prob_tab_utils - simple_pftc_srch_api

Public symbols: - clean_strategy2D — subroutine - prep_strategy2D_batch — subroutine - prep_strategy2D_glob — subroutine - prep_strategy2D_thread — subroutine - set_strategy2D_stoch_bound — subroutine

---

Module: simple_strategy2D_eval

Files: - main/strategies/search/simple_strategy2D_eval.f90

Uses: - simple_builder - simple_core_module_api - simple_oris - simple_parameters - simple_strategy2d - simple_strategy2d_srch

Public symbols: - strategy2D_eval — type

Private symbols: - kill_eval — subroutine - new_eval — subroutine - srch_eval — subroutine

---

Module: simple_strategy2D_greedy

Files: - main/strategies/search/simple_strategy2D_greedy.f90

Uses: - simple_builder - simple_oris - simple_parameters - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_srch

Public symbols: - strategy2D_greedy — type

Private symbols: - kill_greedy — subroutine - new_greedy — subroutine - srch_greedy — subroutine

---

Module: simple_strategy2D_greedy_smpl

Files: - main/strategies/search/simple_strategy2D_greedy_smpl.f90

Uses: - simple_builder - simple_eul_prob_tab_utils - simple_oris - simple_parameters - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_srch

Public symbols: - strategy2D_greedy_smpl — type

Private symbols: - kill_greedy_smpl — subroutine - new_greedy_smpl — subroutine - srch_greedy_smpl — subroutine

---

Module: simple_strategy2D_inpl

Files: - main/strategies/search/simple_strategy2D_inpl.f90

Uses: - simple_builder - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_srch

Public symbols: - strategy2D_inpl — type

Private symbols: - kill_inpl — subroutine - new_inpl — subroutine - srch_inpl — subroutine

---

Module: simple_strategy2D_inpl_smpl

Files: - main/strategies/search/simple_strategy2D_inpl_smpl.f90

Uses: - simple_builder - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_srch - simple_type_defs

Public symbols: - strategy2D_inpl_smpl — type

Private symbols: - kill_inpl_smpl — subroutine - new_inpl_smpl — subroutine - srch_inpl_smpl — subroutine

---

Module: simple_strategy2D_matcher

Files: - main/strategies/search/simple_strategy2D_matcher.f90

Uses: - simple_binoris_io - simple_builder - simple_classaverager - simple_convergence - simple_core_module_api - simple_decay_funs - simple_eul_prob_tab2d - simple_imgarr_utils - simple_matcher_pftc_prep - simple_matcher_ptcl_batch - simple_matcher_smpl_and_lplims - simple_pftc_srch_api - simple_progress - simple_qsys_funs - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_greedy - simple_strategy2d_greedy_smpl - simple_strategy2d_inpl - simple_strategy2d_inpl_smpl - simple_strategy2d_prob - simple_strategy2d_snhc - simple_strategy2d_snhc_smpl - simple_strategy2d_snhc_smpl_many - simple_strategy2d_srch - simple_strategy2d_tseries - simple_syslib

Public symbols: - cluster2D_exec — subroutine - reset_sgd_stream_dispatch_count — subroutine - set_b_p_ptrs2D — subroutine

Private symbols: - allocate_strategy_for_particle — subroutine - build_batch_particles_local — subroutine - cleanup_search_state — subroutine - cluster2D_ctrl — type - compute_neigh_frac — subroutine - display — subroutine - ensure_even_odd_partition — subroutine - finalize_restoration_and_convergence — subroutine - init_ctrl — subroutine - maybe_write_bench — subroutine - prepare_alignment_references — subroutine - prepare_batches — subroutine - prepare_class_averages_and_restoration — subroutine - report_stream_batch — subroutine - restore_class_averages_for_batch — subroutine - sample_particles_for_update — subroutine - write_orientations — subroutine

---

Module: simple_strategy2D_prob

Files: - main/strategies/search/simple_strategy2D_prob.f90

Uses: - simple_builder - simple_eul_prob_tab_utils - simple_oris - simple_parameters - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_srch

Public symbols: - strategy2D_prob — type

Private symbols: - kill_prob — subroutine - new_prob — subroutine - srch_prob — subroutine

---

Module: simple_strategy2D_snhc

Files: - main/strategies/search/simple_strategy2D_snhc.f90

Uses: - simple_builder - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_srch

Public symbols: - strategy2D_snhc — type

Private symbols: - kill_snhc — subroutine - new_snhc — subroutine - srch_snhc — subroutine

---

Module: simple_strategy2D_snhc_smpl

Files: - main/strategies/search/simple_strategy2D_snhc_smpl.f90

Uses: - simple_builder - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_srch - simple_type_defs

Public symbols: - strategy2D_snhc_smpl — type

Private symbols: - kill_snhc_smpl — subroutine - new_snhc_smpl — subroutine - srch_snhc_smpl — subroutine

---

Module: simple_strategy2D_snhc_smpl_many

Files: - main/strategies/search/simple_strategy2D_snhc_smpl_many.f90

Uses: - simple_builder - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_srch - simple_type_defs

Public symbols: - strategy2D_snhc_smpl_many — type

Private symbols: - kill_snhc_smpl_many — subroutine - new_snhc_smpl_many — subroutine - srch_snhc_smpl_many — subroutine

---

Module: simple_strategy2D_srch

Files: - main/strategies/search/simple_strategy2D_srch.f90

Uses: - simple_builder - simple_core_module_api - simple_eul_prob_tab2d - simple_pftc_shsrch_grad - simple_pftc_srch_api - simple_strategy2d_alloc

Private symbols: - assign_ori — subroutine - inpl_srch — subroutine - inpl_srch_first — subroutine - inpl_srch_peaks — subroutine - kill — subroutine - new — subroutine - prep4srch — subroutine - store_solution — subroutine

---

Module: simple_strategy2D_tseries

Files: - main/strategies/search/simple_strategy2D_tseries.f90

Uses: - simple_builder - simple_pftc_srch_api - simple_strategy2d - simple_strategy2d_alloc - simple_strategy2d_srch

Public symbols: - strategy2D_tseries — type

Private symbols: - kill_tseries — subroutine - new_tseries — subroutine - per_ref_srch — subroutine - srch_tseries — subroutine

---

Module: simple_strategy2D_utils

Files: - main/strategies/search/simple_strategy2D_utils.f90

Uses: - simple_builder - simple_clustering_utils - simple_cmdline - simple_histogram - simple_image_bin - simple_image_msk - simple_parameters - simple_pftc_shsrch_grad - simple_pftc_srch_api - simple_pspecs - simple_segmentation - simple_sp_project

Public symbols: - align_and_score_cavg_clusters — function - calc_cavg_offset — subroutine - calc_cavg_pairwise_algninfo — function - calc_cavg_sigstats_components — subroutine - calc_cluster_cavgs_dmat — function - calc_match_cavgs_dmat — function - flag_non_junk_cavgs — subroutine - id_junk — subroutine - id_junk_and_prep_cavgs4clust — subroutine - prep_cavgs4clust — subroutine - test_strategy2D_utils — subroutine - write_aligned_cavgs — subroutine

Private symbols: - align_clusters2medoids — function - calc_cc_and_res_dmats — subroutine - calc_cc_and_res_dmats_ref — subroutine - calc_scores — subroutine - calc_sigstats_dmats — subroutine - calc_sigstats_dmats_ref — subroutine - cavg_sigstats_matrices — type - identify_good_bad_clusters — subroutine - kill_cavg_sigstats_matrices — subroutine - match_imgs — function - match_imgs2ref — function - rank_clusters — subroutine - rtsq_imgs — subroutine

---

Module: simple_strategy3D

Files: - main/strategies/search/simple_strategy3D.f90

Uses: - simple_builder - simple_oris - simple_parameters - simple_strategy3d_srch

Public symbols: - strategy3D — type

Private symbols: - generic_kill — subroutine - generic_new — subroutine - generic_oris_assign — subroutine - generic_srch — subroutine

---

Module: simple_strategy3D_alloc

Files: - main/strategies/search/simple_strategy3D_alloc.f90

Uses: - simple_builder - simple_eul_prob_tab_utils - simple_pftc_srch_api

Public symbols: - clean_strategy3D — subroutine - prep_strategy3D — subroutine - prep_strategy3D_thread — subroutine

---

Module: simple_strategy3D_eval

Files: - main/strategies/search/simple_strategy3D_eval.f90

Uses: - simple_builder - simple_core_module_api - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_srch - simple_strategy3d_utils

Public symbols: - strategy3D_eval — type

Private symbols: - kill_eval — subroutine - new_eval — subroutine - oris_assign_eval — subroutine - srch_eval — subroutine

---

Module: simple_strategy3D_greedy

Files: - main/strategies/search/simple_strategy3D_greedy.f90

Uses: - simple_builder - simple_core_module_api - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils

Public symbols: - strategy3D_greedy — type

Private symbols: - kill_greedy — subroutine - new_greedy — subroutine - oris_assign_greedy — subroutine - srch_greedy — subroutine

---

Module: simple_strategy3D_greedy_inpl

Files: - main/strategies/search/simple_strategy3D_greedy_inpl.f90

Uses: - simple_builder - simple_core_module_api - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils

Public symbols: - strategy3D_greedy_inpl — type

Private symbols: - kill_greedy_inpl — subroutine - new_greedy_inpl — subroutine - oris_assign_greedy_inpl — subroutine - srch_greedy_inpl — subroutine

---

Module: simple_strategy3D_greedy_smpl

Files: - main/strategies/search/simple_strategy3D_greedy_smpl.f90

Uses: - simple_builder - simple_core_module_api - simple_eul_prob_tab_utils - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils - simple_type_defs

Public symbols: - strategy3D_greedy_smpl — type

Private symbols: - kill_greedy_smpl — subroutine - new_greedy_smpl — subroutine - oris_assign_greedy_smpl — subroutine - srch_greedy_smpl — subroutine

---

Module: simple_strategy3D_greedy_sub

Files: - main/strategies/search/simple_strategy3D_greedy_sub.f90

Uses: - simple_builder - simple_core_module_api - simple_eul_prob_tab_utils - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils - simple_type_defs

Public symbols: - strategy3D_greedy_sub — type

Private symbols: - kill_greedy_sub — subroutine - new_greedy_sub — subroutine - oris_assign_greedy_sub — subroutine - srch_greedy_sub — subroutine

---

Module: simple_strategy3D_matcher

Files: - main/strategies/search/simple_strategy3D_matcher.f90

Uses: - simple_binoris_io - simple_builder - simple_euclid_sigma2 - simple_eul_prob_tab - simple_matcher_2dprep - simple_matcher_3drec - simple_matcher_ptcl_batch - simple_matcher_refvol_utils - simple_matcher_smpl_and_lplims - simple_pftc_srch_api - simple_qsys_funs - simple_refine3d_fnames - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_eval - simple_strategy3d_greedy - simple_strategy3d_greedy_inpl - simple_strategy3d_greedy_smpl - simple_strategy3d_greedy_sub - simple_strategy3d_prob - simple_strategy3d_shc - simple_strategy3d_shc_smpl - simple_strategy3d_snhc_smpl - simple_strategy3d_srch - simple_syslib

Public symbols: - refine3D_exec — subroutine

Private symbols: - build_batch_particles_local — subroutine - choose_and_run_strategy — subroutine - ensure_even_odd_partition — subroutine - init_ctrl — subroutine - maybe_write_orientations — subroutine - prepare_particles_batches — subroutine - prepare_refs_sigmas_and_pftc — subroutine - print_flags — subroutine - refine3D_ctrl — type - sample_particles_for_update — subroutine - strategy3D_per_ptcl — type

---

Module: simple_strategy3D_prob

Files: - main/strategies/search/simple_strategy3D_prob.f90

Uses: - simple_builder - simple_core_module_api - simple_eul_prob_tab_utils - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils

Public symbols: - strategy3D_prob — type

Private symbols: - assign_state_fixed — subroutine - kill_prob — subroutine - new_prob — subroutine - oris_assign_prob — subroutine - srch_prob — subroutine

---

Module: simple_strategy3D_shc

Files: - main/strategies/search/simple_strategy3D_shc.f90

Uses: - simple_builder - simple_core_module_api - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils

Public symbols: - strategy3D_shc — type

Private symbols: - kill_shc — subroutine - new_shc — subroutine - oris_assign_shc — subroutine - srch_shc — subroutine

---

Module: simple_strategy3D_shc_smpl

Files: - main/strategies/search/simple_strategy3D_shc_smpl.f90

Uses: - simple_builder - simple_core_module_api - simple_eul_prob_tab_utils - simple_oris - simple_parameters - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils - simple_type_defs

Public symbols: - strategy3D_shc_smpl — type

Private symbols: - kill_shc_smpl — subroutine - new_shc_smpl — subroutine - oris_assign_shc_smpl — subroutine - srch_shc_smpl — subroutine

---

Module: simple_strategy3D_snhc_smpl

Files: - main/strategies/search/simple_strategy3D_snhc_smpl.f90

Uses: - simple_builder - simple_decay_funs - simple_eul_prob_tab_utils - simple_oris - simple_parameters - simple_pftc_srch_api - simple_strategy3d - simple_strategy3d_alloc - simple_strategy3d_srch - simple_strategy3d_utils - simple_type_defs

Public symbols: - strategy3D_snhc_smpl — type

Private symbols: - kill_snhc_smpl — subroutine - new_snhc_smpl — subroutine - oris_assign_snhc_smpl — subroutine - srch_snhc_smpl — subroutine

---

Module: simple_strategy3D_srch

Files: - main/strategies/search/simple_strategy3D_srch.f90

Uses: - simple_builder - simple_core_module_api - simple_eul_prob_tab - simple_parameters - simple_pftc_shsrch_grad - simple_strategy3d_alloc

Private symbols: - inpl_srch — subroutine - inpl_srch_first — subroutine - inpl_srch_peaks — subroutine - kill — subroutine - new — subroutine - prep4prob — subroutine - prep4srch — subroutine - store_solution — subroutine

---

Module: simple_strategy3D_utils

Files: - main/strategies/search/simple_strategy3D_utils.f90

Uses: - simple_core_module_api - simple_strategy3d_alloc - simple_strategy3d_srch

Public symbols: - assign_ori — subroutine - extract_peak_ori — subroutine - extract_peak_oris — subroutine

---

Module: simple_stream2D_state

Files: - main/stream/simple_stream2D_state.f90

Uses: - json_module - simple_cmdline - simple_core_module_api - simple_qsys_env - simple_sp_project - simple_starproject - simple_stream_chunk

---

Module: simple_stream_abinitio2D_chunks

Files: - main/stream/simple_stream_abinitio2D_chunks.f90

Uses: - simple_stream_api

Public symbols: - analyze_first_available_chunk — subroutine - exec_stream_abinitio2D_chunks — subroutine - flag_converged_chunks — subroutine - generate_chunk_projects — subroutine - init_one_chunk — subroutine - stream_abinitio2D_chunks — type

---

Module: simple_stream_api

Files: - main/apis/simple_stream_api.f90

Uses: - json_kinds - json_module - simple_class_frcs - simple_cmdline - simple_commander_base - simple_core_module_api - simple_defs_environment - simple_euclid_sigma2 - simple_gui_utils - simple_guistats - simple_image - simple_nice - simple_parameters - simple_progress - simple_projfile_utils - simple_qsys_env - simple_qsys_funs - simple_rec_list - simple_sp_project - simple_stack_io - simple_starproject_stream - simple_stream2d_state - simple_stream_chunk - simple_stream_chunk2d_utils - simple_stream_cluster2d_utils - simple_stream_communicator - simple_stream_utils - simple_stream_watcher

---

Module: simple_stream_chunk

Files: - main/stream/simple_stream_chunk.f90

Uses: - simple_cmdline - simple_core_module_api - simple_defs_environment - simple_euclid_sigma2 - simple_image - simple_parameters - simple_qsys_env - simple_qsys_funs - simple_rec_list - simple_sp_project

Private symbols: - analyze2D — subroutine - assign — subroutine - average_into — subroutine - calc_sigma2 — subroutine - copy — subroutine - debug_print — subroutine - display_iter — subroutine - gen_final_cavgs — subroutine - generate — subroutine - get_projfile_fname — function - init_chunk — subroutine - is_available — function - kill — subroutine - print_info — subroutine - read — subroutine - remove_folder — subroutine - split_sigmas_into — subroutine - terminate_chunk — subroutine - to_analyze2D — function

---

Module: simple_stream_chunk2D_utils

Files: - main/stream/simple_stream_chunk2D_utils.f90

Uses: - simple_cmdline - simple_core_module_api - simple_defs_environment - simple_gui_utils - simple_parameters - simple_rec_list - simple_sp_project - simple_stream2d_state - simple_stream_chunk - simple_stream_cluster2d_utils

Public symbols: - analyze2D_new_chunks — subroutine - init_chunk_clustering — subroutine - memoize_chunks — subroutine - update_chunks — subroutine

Private symbols: - set_chunk_dimensions — subroutine

---

Module: simple_stream_cluster2D_utils

Files: - main/stream/simple_stream_cluster2D_utils.f90

Uses: - json_kinds - json_module - simple_class_frcs - simple_cmdline - simple_commanders_cluster2d - simple_core_module_api - simple_euclid_sigma2 - simple_image - simple_parameters - simple_qsys_funs - simple_rec_list - simple_sp_project - simple_stack_io - simple_starproject - simple_starproject_stream - simple_stream2d_state

Public symbols: - cleanup_root_folder — subroutine - consolidate_sigmas — subroutine - setup_downscaling — subroutine - terminate_chunks — subroutine - terminate_stream2D — subroutine - tidy_2Dstream_iter — subroutine - update_user_params2D — subroutine - write_project_stream2D — subroutine - write_repick_refs — subroutine

Private symbols: - apply_snapshot_selection — subroutine - debug_print — subroutine - get_latest_optics_map — subroutine - get_latest_optics_map — subroutine - rank_cavgs — subroutine - rescale_cavgs — subroutine - rescale_refs — subroutine - set_dimensions — subroutine - set_resolution_limits — subroutine - set_snapshot_time — subroutine - write_raw_project — subroutine

---

Module: simple_stream_communicator

Files: - utils/comm/simple_stream_communicator.f90

Uses: - json_kinds - json_module - simple_core_module_api - simple_fileio - unix

Public symbols: - stream_http_communicator — type

Private symbols: - add_to_json_1 — subroutine - add_to_json_2 — subroutine - add_to_json_3 — subroutine - add_to_json_4 — subroutine - add_to_json_5 — subroutine - background_heartbeat — subroutine - create — subroutine - curl_request — subroutine - destroy_arg — subroutine - evaluate_checksum — function - get_json_arg_1 — subroutine - get_json_arg_2 — subroutine - get_json_arg_3 — subroutine - get_json_arg_4 — subroutine - get_json_arg_5 — subroutine - join_background_heartbeat — subroutine - remove_from_json_if_present — subroutine - send_heartbeat — subroutine - send_jobstats — subroutine - term — subroutine - update_json_1 — subroutine - update_json_2 — subroutine - update_json_3 — subroutine - update_json_4 — subroutine

---

Module: simple_stream_p00_master

Files: - main/stream/simple_stream_p00_master.f90

Uses: - simple_forked_process - simple_gui_assembler - simple_gui_metadata_api - simple_gui_metadata_utils - simple_http_post - simple_memory_monitor - simple_stream_api - simple_stream_p01_preprocess_new - simple_stream_p02_assign_optics_new - simple_stream_p03_initial_analysis - simple_stream_p04_refpick_extract_new - simple_stream_p05_sieve_cavgs_new - simple_stream_p06_pool2d_new - simple_stream_state - simple_syslib - unix

Public symbols: - stream_p00_master — type

Private symbols: - append_pending — subroutine - assign_optics_fork — type - close_child_pipe_fds — subroutine - close_fd_silent — subroutine - close_pipe_except_fd — subroutine - exec_stream_p00_master — subroutine - init_cline_assign_optics — subroutine - init_cline_opening2D — subroutine - init_cline_particle_sieving — subroutine - init_cline_pool2D — subroutine - init_cline_preprocess — subroutine - init_cline_reference_picking — subroutine - init_ipc_pipe — subroutine - init_metadata_assign_optics — subroutine - init_metadata_opening2D — subroutine - init_metadata_particle_sieving — subroutine - init_metadata_pool2D — subroutine - init_metadata_preprocess — subroutine - init_metadata_reference_picking — subroutine - initial_analysis_fork — type - kill_ipc_pipe — subroutine - log_master_memory_state — subroutine - metadata_listener — subroutine - particle_sieving_fork — type - pool2D_fork — type - preprocess_fork — type - reference_picking_fork — type - safe_destroy_json_ptr — subroutine - send_framed_to_pipe — subroutine - send_update_to_stage_pipes — subroutine - sigint_handler — subroutine - sigterm_handler — subroutine - trim_pending_capacity — subroutine - try_extract_framed_message — subroutine - try_read_from_fd — subroutine - xassign_optics — subroutine - xinitial_analysis — subroutine - xparticle_sieving — subroutine - xpool2D — subroutine - xpreprocess — subroutine - xreference_picking — subroutine

---

Module: simple_stream_p01_preprocess_new

Files: - main/stream/simple_stream_p01_preprocess_new.f90

Uses: - simple_gui_metadata_api - simple_gui_metadata_utils - simple_histogram - simple_image - simple_motion_correct_utils - simple_motion_gain_analysis - simple_motion_gain_helpers - simple_stream_api - simple_stream_state - unix

Public symbols: - stream_p01_preprocess — type

Private symbols: - auto_detect_gain_flip — subroutine - create_movies_set_project — subroutine - exec_stream_p01_preprocess — subroutine - generate_gain_from_movies — subroutine - import_previous_projects — subroutine - mics_window_stats — subroutine - send_to_preprocess_in_pipe — subroutine - set_stat_thresholds — subroutine - sigterm_handler — subroutine - test_stat_thresholds — subroutine - update_projects_list — subroutine - write_mic_star_and_field — subroutine

---

Module: simple_stream_p02_assign_optics_new

Files: - main/stream/simple_stream_p02_assign_optics_new.f90

Uses: - simple_gui_metadata_api - simple_stream_api - simple_stream_state - unix

Public symbols: - stream_p02_assign_optics — type

Private symbols: - exec_stream_p02_assign_optics — subroutine - send_to_assign_optics_in_pipe — subroutine - sigterm_handler — subroutine - wait_for_stream_folder — subroutine

---

Module: simple_stream_p03_initial_analysis

Files: - main/stream/simple_stream_p03_initial_analysis.f90

Uses: - simple_abinitio_utils - simple_cavg_quality_analysis - simple_cavg_quality_model - simple_cavg_quality_types - simple_commanders_abinitio - simple_commanders_abinitio2d - simple_commanders_cavgs - simple_commanders_denoise - simple_commanders_mkcavgs - simple_commanders_pick - simple_commanders_reproject - simple_commanders_sieve - simple_defs - simple_fileio - simple_gui_metadata_api - simple_image_msk - simple_imgarr_utils - simple_mini_stream_utils - simple_procimgstk - simple_projfile_utils - simple_qsys_env - simple_stream_api - simple_stream_state - unix

Public symbols: - stream_p03_initial_analysis — type

Private symbols: - balance_classes — subroutine - cleanup_previous — subroutine - duplicate_balanced_stack — subroutine - exec_stream_p03_initial_analysis — subroutine - micimporter — subroutine - reestimate_box_size_from_selected_cavgs — subroutine - restart_cleanup_allocatables — subroutine - run_abinitio2D — subroutine - run_abinitio3D_and_reproject — subroutine - run_cavg_quality_selection — subroutine - run_cavg_size_selection — subroutine - run_cls_split — subroutine - run_extract — subroutine - run_make_cavgs — subroutine - run_reextract — subroutine - run_sieve_ptcls — subroutine - send_available_cavgs2D — subroutine - send_cavg2D_meta — subroutine - send_meta — subroutine - send_meta2D — subroutine - send_micrograph_meta — subroutine - send_pickref_meta — subroutine - send_selected_pickrefs — subroutine - send_to_initial_analysis_in_pipe — subroutine - sigterm_handler — subroutine - update_os_out_stk — subroutine - write_quality_stack — subroutine

---

Module: simple_stream_p04_refpick_extract_new

Files: - main/stream/simple_stream_p04_refpick_extract_new.f90

Uses: - simple_commanders_pick - simple_gui_metadata_api - simple_stream_api - simple_stream_state - simple_timer - unix

Public symbols: - stream_p04_refpick_extract — type

Private symbols: - create_individual_project — subroutine - exec_stream_pick_extract — subroutine - import_previous_mics — subroutine - send_cavg2D_meta — subroutine - send_meta — subroutine - send_micrograph_meta — subroutine - send_pickrefs — subroutine - send_to_refpick_in_pipe — subroutine - sigterm_handler — subroutine - update_projects_list — subroutine - validate_ptcl2D_star_inputs — subroutine - write_micrographs_starfile — subroutine - write_project — subroutine

---

Module: simple_stream_p05_sieve_cavgs_new

Files: - main/stream/simple_stream_p05_sieve_cavgs_new.f90

Uses: - simple_fileio - simple_gui_metadata_api - simple_ptcl_sieve - simple_stream_api - simple_stream_pool2d_utils - simple_stream_state - unix

Public symbols: - stream_p05_sieve_cavgs — type

Private symbols: - exec_stream_p05_sieve_cavgs — subroutine - send_cavg2D_meta — subroutine - send_cavgs2D_batch — subroutine - send_meta — subroutine - send_to_sieve_cavgs_in_pipe — subroutine - sigterm_handler — subroutine

---

Module: simple_stream_p06_pool2D_new

Files: - main/stream/simple_stream_p06_pool2D_new.f90

Uses: - simple_gui_metadata_api - simple_gui_metadata_utils - simple_stream2d_state - simple_stream_api - simple_stream_pool2d_utils - simple_stream_state - unix

Public symbols: - stream_p06_pool2D — type

Private symbols: - cleanup4restart — subroutine - exec_stream_p06_pool2D — subroutine - import_sets_into_pool — subroutine - send_cavg2D_meta — subroutine - send_cavgs2D — subroutine - send_meta — subroutine - send_meta_snapshot2D — subroutine - send_to_pool2D_in_pipe — subroutine - sigterm_handler — subroutine - unpause_pool — subroutine

---

Module: simple_stream_pool2D_utils

Files: - main/stream/simple_stream_pool2D_utils.f90

Uses: - simple_classaverager - simple_euclid_sigma2 - simple_procimgstk - simple_ran_tabu - simple_stream_api

Public symbols: - generate_pool_stats — subroutine - get_pool_ptr — subroutine - init_pool_clustering — subroutine - iterate_pool — subroutine - set_lpthres_type — subroutine - set_pool_resolution_limits — subroutine - update_match_class_states — subroutine - update_mskdiam — subroutine - update_pool — subroutine - update_pool_aln_params — subroutine - update_pool_status — subroutine

Private symbols: - biased_stack_sampling — subroutine - generate_pool_jpeg — subroutine - set_iteration_time — subroutine - set_pool_dimensions — subroutine - uniform_stack_sampling — subroutine - update_match_class_states_in_pool — subroutine - update_pool_dims — subroutine - update_pool_for_gui — subroutine

---

Module: simple_stream_state

Files: - main/stream/simple_stream_state.f90

---

Module: simple_stream_utils

Files: - main/stream/simple_stream_utils.f90

Uses: - json_kinds - json_module - simple_cmdline - simple_core_module_api - simple_default_clines - simple_gui_utils - simple_image - simple_image_msk - simple_parameters - simple_qsys_env - simple_rec_list - simple_sp_project - simple_stack_io - simple_stream_communicator

Public symbols: - create_stream_project — subroutine - get_latest_optics_map_id — function - import_new_projects — subroutine - init_stream_qenv — subroutine - process_selected_refs — subroutine - process_selected_refs_2 — subroutine - stream_datestr — function - terminate_stream — subroutine - update_user_params — subroutine - wait_for_folder — subroutine - wait_for_folder2 — subroutine

---

Module: simple_stream_watcher

Files: - main/stream/simple_stream_watcher.f90

Uses: - simple_core_module_api - simple_progress

---

Module: simple_string

Files: - utils/simple_string.f90

Uses: - simple_defs - simple_defs_string - simple_error

---

Module: simple_string_tester

Files: - utils/simple_string_tester.f90

Uses: - simple_defs - simple_string - simple_test_utils

Public symbols: - run_all_string_tests — subroutine

Private symbols: - test_append_operator — subroutine - test_assign_and_ctor — subroutine - test_default_and_kill — subroutine - test_ends_with — subroutine - test_equality_operators — subroutine - test_has_substr — subroutine - test_is_blank_and_is_allocated — subroutine - test_numeric_conversion — subroutine - test_readfile — subroutine - test_readline_empty_line — subroutine - test_readline_eof_behavior — subroutine - test_readline_long_line — subroutine - test_readline_multiple_lines — subroutine - test_readline_writeline — subroutine - test_strlen — subroutine - test_substr_ind — subroutine - test_substr_remove — subroutine - test_substr_replace — subroutine - test_to_char — subroutine - test_to_fnv1a_hash64 — subroutine - test_writeline_unallocated — subroutine

---

Module: simple_string_utils

Files: - utils/simple_string_utils.f90

Uses: - simple_defs - simple_defs_string - simple_error - simple_string

---

Module: simple_sym

Files: - main/simple_sym.f90

Uses: - simple_ori - simple_ori_api - simple_oris

---

Module: simple_symanalyzer

Files: - main/simple_symanalyzer.f90

Uses: - simple_core_module_api - simple_image - simple_parameters - simple_projector - simple_simple_volinterp - simple_volpft_symsrch

Public symbols: - print_subgroups — subroutine - symmetrize_map — subroutine - symmetry_tester — subroutine

Private symbols: - eval_point_groups — subroutine - find_symaxis — subroutine - symaverage — subroutine

---

Module: simple_syslib

Files: - fileio/simple_syslib.f90

Uses: - iso_c_binding - simple_defs - simple_defs_fname - simple_error - simple_string - simple_string_utils

Public symbols: - del_file — subroutine - exec_cmdline — subroutine - find_next_int_dir_prefix — function - fsync — function - get_absolute_pathname — function - get_current_rss_bytes — function - get_peak_rss_bytes — function - get_sysinfo — function - isdir — function - list_dirs — function - makedir — function - memory_monitor_report_c — function - memory_monitor_start_c — function - memory_monitor_stop_c — function - mkdir — function - print_slurm_env — subroutine - raise_sys_error — subroutine - redirect_stdout_stderr — subroutine - regexp_match — function - removedir — function - restore_stdout_stderr — subroutine - rmdir — function - safe_flush — subroutine - simple_abspath — function - simple_chdir — subroutine - simple_chmod — function - simple_file_stat — subroutine - simple_getcwd — subroutine - simple_getenv — function - simple_list_dirs — function - simple_list_files — subroutine - simple_list_files_regexp — subroutine - simple_mkdir — subroutine - simple_redirect_output_c — function - simple_rename — subroutine - simple_restore_output_c — function - simple_rmdir — subroutine - simple_rmfile — subroutine - simple_touch — subroutine - sscanf — function - symlink — function - syslib_c2fortran_string — subroutine - syslib_symlink — subroutine - touch — function - unlink — function - wait_pid — function

---

Module: simple_syslib_tester

Files: - fileio/simple_syslib_tester.f90

Uses: - simple_defs - simple_string - simple_syslib - simple_test_utils

Public symbols: - run_all_syslib_tests — subroutine

Private symbols: - setup_test_env — subroutine - teardown_test_env — subroutine - test_exec_cmdline — subroutine - test_find_next_int_dir_prefix — subroutine - test_get_current_rss_bytes — subroutine - test_get_peak_rss_bytes — subroutine - test_get_process_id — subroutine - test_getenv_wrapper — subroutine - test_is_file_open — subroutine - test_is_io_and_is_open — subroutine - test_print_slurm_env_smoke — subroutine - test_simple_abspath — subroutine - test_simple_file_stat — subroutine - test_simple_getcwd_and_chdir — subroutine - test_simple_list_dirs — subroutine - test_simple_list_files — subroutine - test_simple_list_files_regexp — subroutine - test_simple_mkdir_dir_exists_rmdir — subroutine - test_simple_rename_and_del_file — subroutine - test_simple_rmfile — subroutine - test_simple_touch_and_file_exists — subroutine - test_syslib_c2fortran_string — subroutine - test_syslib_symlink — subroutine

---

Module: simple_tent_smooth

Files: - utils/filter/simple_tent_smooth.f90

Public symbols: - box_filter_1d — subroutine - box_filter_x — subroutine - box_filter_y — subroutine - box_filter_z — subroutine - tent_smooth_3d — subroutine

---

Module: simple_test_exec_api

Files: - main/apis/simple_test_exec_api.f90

Uses: - iso_fortran_env - simple_cmdline - simple_core_module_api - simple_exec_helpers - simple_jiffys - simple_test_exec_class - simple_test_exec_fft - simple_test_exec_geometry - simple_test_exec_highlevel - simple_test_exec_io - simple_test_exec_masks - simple_test_exec_network - simple_test_exec_numerics - simple_test_exec_optimize - simple_test_exec_parallel - simple_test_exec_single - simple_test_exec_stats - simple_test_exec_utils - simple_ui - simple_ui_program

---

Module: simple_test_exec_class

Files: - main/exec/simple_test_exec_class.f90

Uses: - simple_cmdline - simple_commanders_test_class

Public symbols: - exec_test_class_commander — subroutine

---

Module: simple_test_exec_fft

Files: - main/exec/simple_test_exec_fft.f90

Uses: - simple_cmdline - simple_commanders_test_fft

Public symbols: - exec_test_fft_commander — subroutine

---

Module: simple_test_exec_geometry

Files: - main/exec/simple_test_exec_geometry.f90

Uses: - simple_cmdline - simple_commanders_test_geometry

Public symbols: - exec_test_geometry_commander — subroutine

---

Module: simple_test_exec_highlevel

Files: - main/exec/simple_test_exec_highlevel.f90

Uses: - simple_cmdline - simple_commanders_test_highlevel

Public symbols: - exec_test_highlevel_commander — subroutine

---

Module: simple_test_exec_io

Files: - main/exec/simple_test_exec_io.f90

Uses: - simple_cmdline - simple_commanders_test_io

Public symbols: - exec_test_io_commander — subroutine

---

Module: simple_test_exec_masks

Files: - main/exec/simple_test_exec_masks.f90

Uses: - simple_cmdline - simple_commanders_test_masks

Public symbols: - exec_test_masks_commander — subroutine

---

Module: simple_test_exec_network

Files: - main/exec/simple_test_exec_network.f90

Uses: - simple_cmdline - simple_commanders_test_network

Public symbols: - exec_test_network_commander — subroutine

---

Module: simple_test_exec_numerics

Files: - main/exec/simple_test_exec_numerics.f90

Uses: - simple_cmdline - simple_commanders_test_numerics

Public symbols: - exec_test_numerics_commander — subroutine

---

Module: simple_test_exec_optimize

Files: - main/exec/simple_test_exec_optimize.f90

Uses: - simple_cmdline - simple_commanders_test_optimize

Public symbols: - exec_test_optimize_commander — subroutine

---

Module: simple_test_exec_parallel

Files: - main/exec/simple_test_exec_parallel.f90

Uses: - simple_cmdline - simple_commanders_test_parallel

Public symbols: - exec_test_parallel_commander — subroutine

---

Module: simple_test_exec_single

Files: - main/exec/simple_test_exec_single.f90

Uses: - simple_cmdline - simple_commanders_test_single

Public symbols: - exec_test_single_commander — subroutine

---

Module: simple_test_exec_stats

Files: - main/exec/simple_test_exec_stats.f90

Uses: - simple_cmdline - simple_commanders_test_stats

Public symbols: - exec_test_stats_commander — subroutine

---

Module: simple_test_exec_utils

Files: - main/exec/simple_test_exec_utils.f90

Uses: - simple_cmdline - simple_commanders_test_utils

Public symbols: - exec_test_utils_commander — subroutine

---

Module: simple_test_ui_class

Files: - main/ui/simple_test/simple_test_ui_class.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_class_programs — subroutine - new_strategy2D — subroutine - new_ui_hash_test — subroutine - new_units — subroutine

---

Module: simple_test_ui_fft

Files: - main/ui/simple_test/simple_test_ui_fft.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_fft_programs — subroutine - new_corrs2weights_test — subroutine - new_eval_polarftcc — subroutine - new_ft_expanded — subroutine - new_gencorrs_fft — subroutine - new_order_corr — subroutine - new_phasecorr — subroutine - new_rank_weights — subroutine - new_rotate_ref — subroutine

---

Module: simple_test_ui_geometry

Files: - main/ui/simple_test/simple_test_ui_geometry.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_geometry_programs — subroutine - new_angres — subroutine - new_ori_test — subroutine - new_oris_test — subroutine - new_sym_test — subroutine - new_uniform_euler — subroutine - new_uniform_rot — subroutine

---

Module: simple_test_ui_highlevel

Files: - main/ui/simple_test/simple_test_ui_highlevel.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_highlevel_programs — subroutine - new_mini_stream — subroutine - new_pcg_recon — subroutine - new_ptcls_ppca_subproject_distr — subroutine - new_reproject — subroutine - new_simulate_particles — subroutine - new_simulated_workflow — subroutine - new_subproject_distr — subroutine - print_test_highlevel_programs — subroutine

---

Module: simple_test_ui_io

Files: - main/ui/simple_test/simple_test_ui_io.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_io_programs — subroutine - new_imgfile — subroutine - new_inside_write — subroutine - new_io — subroutine - new_io_parallel — subroutine - new_mrc2jpeg — subroutine - new_mrc_validate — subroutine - new_stack_io — subroutine - new_star_export — subroutine - new_starfile_test — subroutine - print_test_io_programs — subroutine

---

Module: simple_test_ui_masks

Files: - main/ui/simple_test/simple_test_ui_masks.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_masks_programs — subroutine - new_bounds_from_mask3D_test — subroutine - new_graphene_mask — subroutine - new_image_bin — subroutine - new_mask — subroutine - new_msk_routines — subroutine - new_nano_mask — subroutine - new_otsu_test — subroutine - new_ptcl_center — subroutine

---

Module: simple_test_ui_network

Files: - main/ui/simple_test/simple_test_ui_network.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_network_programs — subroutine - new_socket_client — subroutine - new_socket_comm_distr — subroutine - new_socket_io — subroutine - new_socket_server — subroutine

---

Module: simple_test_ui_numerics

Files: - main/ui/simple_test/simple_test_ui_numerics.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_numerics_programs — subroutine - new_eigh_test — subroutine - new_kbinterpol_fast — subroutine - new_maxnloc_test — subroutine - new_neigh — subroutine

---

Module: simple_test_ui_optimize

Files: - main/ui/simple_test/simple_test_ui_optimize.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_optimize_programs — subroutine - new_lbfgsb — subroutine - new_lbfgsb_cosine — subroutine - new_lplims — subroutine - new_lpstages_test — subroutine - new_opt_lp — subroutine

---

Module: simple_test_ui_parallel

Files: - main/ui/simple_test/simple_test_ui_parallel.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_parallel_programs — subroutine - new_coarrays — subroutine - new_openacc — subroutine - new_openmp — subroutine - new_simd — subroutine

---

Module: simple_test_ui_single

Files: - main/ui/simple_test/simple_test_ui_single.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_single_programs — subroutine - new_atoms_stats — subroutine - new_detect_atoms — subroutine - new_simulate_nanoparticle — subroutine - new_single_workflow — subroutine

---

Module: simple_test_ui_stats

Files: - main/ui/simple_test/simple_test_ui_stats.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_stats_programs — subroutine - new_class_sample_test — subroutine - new_clustering — subroutine - new_ctf_test — subroutine - new_eo_diff — subroutine - new_extr_frac — subroutine - new_multinomal_test — subroutine - new_pca_all — subroutine - new_pca_imgvar — subroutine - new_sp_project — subroutine

---

Module: simple_test_ui_utils

Files: - main/ui/simple_test/simple_test_ui_utils.f90

Uses: - simple_ui_modules

Public symbols: - construct_test_utils_programs — subroutine - new_ansi_colors — subroutine - new_binoris_io_test — subroutine - new_binoris_test — subroutine - new_cif2mrc — subroutine - new_cif2pdb — subroutine - new_cmdline — subroutine - new_install — subroutine - new_nice — subroutine - new_pdb2mrc — subroutine - new_peak_thres_fdr — subroutine - new_serialize — subroutine - new_stringmatch — subroutine

---

Module: simple_test_utils

Files: - utils/simple_test_utils.f90

Uses: - simple_defs - simple_string

Public symbols: - assert_char — subroutine - assert_double — subroutine - assert_false — subroutine - assert_int — subroutine - assert_real — subroutine - assert_string_eq — subroutine - assert_true — subroutine - report_summary — subroutine

---

Module: simple_testfuns

Files: - utils/math/simple_testfuns.f90

Uses: - simple_core_module_api

Public symbols: - get_testfun — subroutine - testfun — function - testfun1 — function - testfun10 — function - testfun11 — function - testfun12 — function - testfun13 — function - testfun14 — function - testfun15 — function - testfun16 — function - testfun17 — function - testfun18 — function - testfun19 — function - testfun2 — function - testfun20 — function - testfun21 — function - testfun22 — function - testfun23 — function - testfun24 — function - testfun25 — function - testfun26 — function - testfun27 — function - testfun28 — function - testfun29 — function - testfun3 — function - testfun30 — function - testfun31 — function - testfun32 — function - testfun4 — function - testfun5 — function - testfun6 — function - testfun7 — function - testfun8 — function - testfun9 — function

---

Module: simple_tifflib

Files: - fileio/simple_tifflib.f90

Uses: - iso_c_binding

Public symbols: - TIFFAllocateStripBuffer — function - TIFFClose — subroutine - TIFFCurrentDirectory — function - TIFFfree — function - TIFFGetField — function - TIFFGetVersion — function - TIFFIsTiled — function - TIFFLastDirectory — function - TIFFmalloc — function - TIFFMuteWarnings — subroutine - TIFFNumberOfStrips — function - TIFFOpen — function - TIFFPrintInfo — subroutine - TIFFReadDirectory — function - TIFFReadEncodedStrip — function - TIFFReadRawStrip — function - TIFFSetDirectory — function - TIFFStripSize — function - TIFFUnMuteWarnings — subroutine

---

Module: simple_timer

Files: - utils/simple_timer.f90

Uses: - ifport - simple_defs - simple_error - simple_is_check_assert - simple_string_utils

Public symbols: - cast_time_char — function - now — subroutine - reset_timer — subroutine - timer_loop_end — subroutine - timer_loop_start — subroutine - timer_profile_break — subroutine - timer_profile_report — subroutine - timer_profile_setup — subroutine - timer_profile_start — subroutine - tocprint — subroutine

---

Module: simple_timer_omp

Files: - utils/simple_timer_omp.f90

Uses: - simple_defs

Public symbols: - now_omp — subroutine - reset_timer_omp — subroutine

---

Module: simple_trajectory_chunker

Files: - main/nano/simple_trajectory_chunker.f90

Uses: - simple_core_module_api - simple_flex_analysis_strategy - simple_srch_sort_loc

Public symbols: - make_trajectory_chunk_plan — subroutine - select_trajectory_chunk_plan — subroutine - trajectory_chunk — type - trajectory_chunk_plan — type - trajectory_chunks_to_parts — subroutine - write_trajectory_chunks_csv — subroutine

Private symbols: - kill_trajectory_chunk_plan — subroutine - make_boundary_bands — subroutine - prepare_weighted_features — subroutine

---

Module: simple_tseries_graphene_subtr

Files: - main/nano/simple_tseries_graphene_subtr.f90

Uses: - simple_atoms - simple_pftc_srch_api

Public symbols: - calc_peaks — subroutine - init_graphene_subtr — subroutine - kill_graphene_subtr — subroutine - remove_lattices — subroutine

Private symbols: - calc_3bands_mask — function - interp_peak — subroutine - obscure_peak — subroutine - range_convention — subroutine - remove_lattice — subroutine

---

Module: simple_type_defs

Files: - defs/simple_type_defs.f90

Uses: - simple_defs - simple_string

---

Module: simple_ui

Files: - main/ui/simple_ui.f90

Uses: - json_file_module - json_kinds - json_module - simple_ansi_ctrls - simple_core_module_api - simple_linked_list - simple_ui_hash - simple_ui_param - simple_ui_params_common - simple_ui_program - simple_ui_simple_group - simple_ui_single_group - simple_ui_stream_group - simple_ui_test_group

Public symbols: - get_prg_ptr — subroutine - get_test_prg_ptr — subroutine - list_simple_prgs_in_ui — subroutine - list_simple_test_prgs_in_ui — subroutine - list_single_prgs_in_ui — subroutine - list_stream_prgs_in_ui — subroutine - make_test_ui — subroutine - make_ui — subroutine - print_stream_ui_json — subroutine - print_ui_json — subroutine - validate_ui_json — subroutine - validate_ui_presentation — subroutine - write_ui_json — subroutine

Private symbols: - print_registered_programs — subroutine - validate_category_metadata — subroutine - validate_input_list — subroutine

---

Module: simple_ui_abinitio3D

Files: - main/ui/simple/simple_ui_abinitio3D.f90

Uses: - simple_ui_modules

Public symbols: - construct_abinitio3D_programs — subroutine - new_abinitio3D — subroutine - new_abinitio3D_cavgs — subroutine - new_estimate_lpstages — subroutine - new_noisevol — subroutine

---

Module: simple_ui_cavgproc

Files: - main/ui/simple/simple_ui_cavgproc.f90

Uses: - simple_ui_modules

Public symbols: - construct_cavgproc_programs — subroutine - new_cluster_cavgs — subroutine - new_cluster_cavgs_selection — subroutine - new_cluster_stack — subroutine - new_match_cavgs — subroutine - new_match_stacks — subroutine - new_model_cavgs_rejection — subroutine - new_select_clusters — subroutine

---

Module: simple_ui_cluster2D

Files: - main/ui/simple/simple_ui_cluster2D.f90

Uses: - simple_ui_modules

Public symbols: - construct_cluster2D_programs — subroutine - new_abinitio2D — subroutine - new_abinitio2D_chunks — subroutine - new_bootstrap_cavgs — subroutine - new_make_cavgs — subroutine - new_map_cavgs_selection — subroutine - new_sample_classes — subroutine - new_unbootstrap_cavgs — subroutine - new_write_classes — subroutine

---

Module: simple_ui_denoise

Files: - main/ui/simple/simple_ui_denoise.f90

Uses: - simple_ui_modules

Public symbols: - construct_denoise_programs — subroutine - new_cls_split — subroutine - new_denoise_project — subroutine - new_flex_analysis — subroutine - new_icm2D — subroutine - new_icm3D — subroutine - new_map_params_from_den — subroutine - new_ppca_denoise — subroutine - new_ppca_denoise_classes — subroutine - new_ppca_volvar — subroutine

---

Module: simple_ui_descriptor_types

Files: - main/ui/simple_ui_descriptor_types.f90

Uses: - simple_string

Public symbols: - ui_choices — function

Private symbols: - ui_choice — type

---

Module: simple_ui_dock

Files: - main/ui/simple/simple_ui_dock.f90

Uses: - simple_ui_modules

Public symbols: - construct_dock_programs — subroutine - new_dock_volpair — subroutine - new_volanalyze — subroutine - new_volcluster — subroutine

---

Module: simple_ui_filter

Files: - main/ui/simple/simple_ui_filter.f90

Uses: - simple_ui_modules

Public symbols: - construct_filter_programs — subroutine - new_filter — subroutine - new_nu_filt3D — subroutine - new_uniform_filter2D — subroutine - new_uniform_filter3D — subroutine

---

Module: simple_ui_hash

Files: - main/ui/simple_ui_hash.f90

Uses: - simple_string - simple_ui_program - simple_vrefhash

Public symbols: - test_ui_hash — subroutine - ui_hash — type

Private symbols: - get_ref_ui_param_char — subroutine - get_ref_ui_param_str — subroutine - get_ref_ui_program_char — subroutine - get_ref_ui_program_str — subroutine - set_ref_ui_param_char — subroutine - set_ref_ui_param_str — subroutine - set_ref_ui_program_char — subroutine - set_ref_ui_program_str — subroutine

---

Module: simple_ui_image

Files: - main/ui/simple/simple_ui_image.f90

Uses: - simple_ui_modules

Public symbols: - construct_image_programs — subroutine - new_binarize — subroutine - new_convert — subroutine - new_ctf_correct — subroutine - new_ctfops — subroutine - new_normalize — subroutine - new_scale — subroutine - new_stack — subroutine - new_stackops — subroutine

---

Module: simple_ui_mask

Files: - main/ui/simple/simple_ui_mask.f90

Uses: - simple_ui_modules

Public symbols: - construct_mask_programs — subroutine - new_auto_spher_mask — subroutine - new_automask2D — subroutine - new_mask — subroutine

---

Module: simple_ui_modules

Files: - main/ui/simple_ui_modules.f90

Uses: - simple_ansi_ctrls - simple_core_module_api - simple_ui_descriptor_types - simple_ui_hash - simple_ui_params_common - simple_ui_program - simple_ui_utils - simple_ui_visibility

---

Module: simple_ui_ori

Files: - main/ui/simple/simple_ui_ori.f90

Uses: - simple_ui_modules

Public symbols: - construct_ori_programs — subroutine - new_make_oris — subroutine - new_oriops — subroutine - new_oristats — subroutine - new_vizoris — subroutine

---

Module: simple_ui_other

Files: - main/ui/simple/simple_ui_other.f90

Uses: - simple_ui_modules

Public symbols: - construct_other_programs — subroutine - new_cif2pdb — subroutine - new_fractionate_movies — subroutine - new_split_ — subroutine - new_split_stack — subroutine

---

Module: simple_ui_param

Files: - main/ui/simple_ui_param.f90

Uses: - simple_error - simple_string - simple_string_utils - simple_ui_descriptor_types

Public symbols: - finalize — subroutine - infer_units — function - normalize_numeric_example — function - set_choices — subroutine - set_generated_default — subroutine - set_param_1 — subroutine - set_param_2 — subroutine - set_placeholder — subroutine - standardize_placeholder — function

---

Module: simple_ui_params_common

Files: - main/ui/simple_ui_params_common.f90

Uses: - simple_core_module_api - simple_ui_descriptor_types - simple_ui_param

Public symbols: - set_ui_params — subroutine

---

Module: simple_ui_preproc

Files: - main/ui/simple/simple_ui_preproc.f90

Uses: - simple_ui_modules

Public symbols: - construct_preproc_programs — subroutine - new_assign_optics_groups — subroutine - new_ctf_estimate — subroutine - new_extract — subroutine - new_gen_pspecs_and_thumbs — subroutine - new_motion_correct — subroutine - new_particle_sieving — subroutine - new_pick — subroutine - new_preprocess — subroutine - new_reextract — subroutine

---

Module: simple_ui_print

Files: - main/ui/simple/simple_ui_print.f90

Uses: - simple_ui_modules

Public symbols: - construct_print_programs — subroutine - new_info_image — subroutine - new_info_stktab — subroutine - new_print_dose_weights — subroutine - new_print_fsc — subroutine - new_print_magic_boxes — subroutine

---

Module: simple_ui_program

Files: - main/ui/simple_ui_program.f90

Uses: - json_module - simple_ansi_ctrls - simple_core_module_api - simple_linked_list - simple_ui_default_values - simple_ui_descriptor_types - simple_ui_param - simple_ui_visibility

Public symbols: - add_input_num — subroutine - add_input_param — subroutine - add_input_str — subroutine - add_program_groups_json — subroutine - add_program_input_json — subroutine - add_program_requirements_json — subroutine - add_requirement — subroutine - append_input — subroutine - append_required_keys_from_list — subroutine - apply_generated_default — subroutine - bind_input — subroutine - cardinality_text — function - category_descriptor — type - create_json_entry — subroutine - create_section_from_list — subroutine - find_input_text — subroutine - get_category — function - get_display_name — function - get_executable — function - get_name — function - get_required_keys — function - group_label — function - input_text_for_key — function - kill — subroutine - new — subroutine - print_cmdline — subroutine - print_help — subroutine - print_param_hash — subroutine - print_param_list — subroutine - print_requirement_groups — subroutine - print_requirement_inputs — subroutine - print_ui — subroutine - register_group — subroutine - set_category — subroutine - ui_activation — type - ui_activation_equals_any — function - ui_cli_param_choices — function - ui_cli_param_summary — function - ui_input_group — type - ui_program — type - ui_program_input — type - ui_requirement_group — type - write2json — subroutine

---

Module: simple_ui_project

Files: - main/ui/simple/simple_ui_project.f90

Uses: - simple_ui_modules

Public symbols: - construct_project_programs — subroutine - new_export_manifoldem_starproject — subroutine - new_export_relion — subroutine - new_export_starproject — subroutine - new_extract_subproj — subroutine - new_import_boxes — subroutine - new_import_cavgs — subroutine - new_import_movies — subroutine - new_import_particles — subroutine - new_import_starproject — subroutine - new_merge_projects — subroutine - new_new_project — subroutine - new_print_project_field — subroutine - new_print_project_info — subroutine - new_prune_project — subroutine - new_ptcl3D_state_consensus — subroutine - new_reimport_particles — subroutine - new_replace_project_field — subroutine - new_selection — subroutine - new_update_project — subroutine - new_validate_projfile — subroutine - new_write_mic_filetab — subroutine - new_zero_project_shifts — subroutine

---

Module: simple_ui_refine3D

Files: - main/ui/simple/simple_ui_refine3D.f90

Uses: - simple_ui_modules

Public symbols: - construct_refine3D_programs — subroutine - new_automask — subroutine - new_bootstrap_rec3D — subroutine - new_postprocess — subroutine - new_reconstruct3D — subroutine - new_refine3D — subroutine - new_refine3D_auto — subroutine - new_refine3D_multi — subroutine

---

Module: simple_ui_res

Files: - main/ui/simple/simple_ui_res.f90

Uses: - simple_ui_modules

Public symbols: - construct_res_programs — subroutine - new_fsc — subroutine - new_fsc_area_score — subroutine

---

Module: simple_ui_sim

Files: - main/ui/simple/simple_ui_sim.f90

Uses: - simple_ui_modules

Public symbols: - construct_sim_programs — subroutine - new_cif2mrc — subroutine - new_pdb2mrc — subroutine - new_simulate_movie — subroutine - new_simulate_noise — subroutine - new_simulate_particles — subroutine

---

Module: simple_ui_simple_group

Files: - main/ui/simple_ui_simple_group.f90

Uses: - simple_ui_abinitio3d - simple_ui_cavgproc - simple_ui_cluster2d - simple_ui_denoise - simple_ui_dock - simple_ui_filter - simple_ui_hash - simple_ui_image - simple_ui_mask - simple_ui_ori - simple_ui_other - simple_ui_preproc - simple_ui_print - simple_ui_project - simple_ui_refine3d - simple_ui_res - simple_ui_sim - simple_ui_sym - simple_ui_validate - simple_ui_volume

Public symbols: - add_simple_programs — subroutine

---

Module: simple_ui_single_group

Files: - main/ui/simple_ui_single_group.f90

Uses: - simple_ui_hash - single_ui_atom - single_ui_map - single_ui_nano2d - single_ui_nano3d - single_ui_trajectory - single_ui_tseries - single_ui_validate

Public symbols: - add_single_programs — subroutine

---

Module: simple_ui_stream

Files: - main/ui/simple/simple_ui_stream.f90

Uses: - simple_ui_modules

Public symbols: - construct_stream_programs — subroutine - new_abinitio2D_stream — subroutine - new_assign_optics — subroutine - new_gen_pickrefs — subroutine - new_master — subroutine - new_pick_extract — subroutine - new_preproc — subroutine - new_sieve_cavgs — subroutine

---

Module: simple_ui_stream_group

Files: - main/ui/simple_ui_stream_group.f90

Uses: - simple_ui_hash - simple_ui_stream

Public symbols: - add_stream_programs — subroutine

---

Module: simple_ui_sym

Files: - main/ui/simple/simple_ui_sym.f90

Uses: - simple_ui_modules

Public symbols: - construct_symmetry_programs — subroutine - new_symaxis_search — subroutine - new_symmetrize_map — subroutine - new_symmetry_test — subroutine

---

Module: simple_ui_test_group

Files: - main/ui/simple_ui_test_group.f90

Uses: - simple_test_ui_class - simple_test_ui_fft - simple_test_ui_geometry - simple_test_ui_highlevel - simple_test_ui_io - simple_test_ui_masks - simple_test_ui_network - simple_test_ui_numerics - simple_test_ui_optimize - simple_test_ui_parallel - simple_test_ui_single - simple_test_ui_stats - simple_test_ui_utils - simple_ui_hash

Public symbols: - add_test_programs — subroutine

---

Module: simple_ui_utils

Files: - main/ui/simple_ui_utils.f90

Uses: - simple_error - simple_ui_hash - simple_ui_program

Public symbols: - add_ui_program — subroutine

---

Module: simple_ui_validate

Files: - main/ui/simple/simple_ui_validation.f90

Uses: - simple_ui_modules

Public symbols: - construct_validate_programs — subroutine - new_check_refpick — subroutine - new_mini_stream — subroutine - new_model_validate — subroutine

---

Module: simple_ui_visibility

Files: - main/ui/simple_ui_visibility.f90

Public symbols: - ui_visibility_name — function

---

Module: simple_ui_volume

Files: - main/ui/simple/simple_ui_volume.f90

Uses: - simple_ui_modules

Public symbols: - construct_volume_programs — subroutine - new_center — subroutine - new_reconstruct3D_pcg — subroutine - new_reproject — subroutine - new_volops — subroutine

---

Module: simple_vol_pproc_policy

Files: - main/volume/simple_vol_pproc_policy.f90

Uses: - simple_core_module_api - simple_parameters

Public symbols: - plan_state_postprocess — subroutine - state_mask_is_compatible — subroutine - vol_pproc_plan — type

---

Module: simple_volanalyzer

Files: - main/volume/simple_volanalyzer.f90

Uses: - simple_core_module_api - simple_dock_vols - simple_image - simple_ori - simple_parameters - simple_simple_volinterp

Public symbols: - calc_volpair_corrmat — subroutine - dock_compare_volumes — subroutine - init_volanalyzer — subroutine

---

Module: simple_volcluster

Files: - main/volume/simple_volcluster.f90

Uses: - simple_core_module_api - simple_image - simple_parameters

Public symbols: - calc_volcluster_dmat — function - read_volcluster_volumes — subroutine - write_volcluster_report — subroutine

Private symbols: - kill_volumes — subroutine

---

Module: simple_volpft_corrcalc

Files: - main/volume/simple_volpft_corrcalc.f90

Uses: - simple_core_module_api - simple_projector

Public symbols: - volpft_corrcalc — type

Private symbols: - corr_1 — function - corr_2 — function - corr_mag — function - extract_ref — subroutine - extract_target_1 — subroutine - extract_target_2 — subroutine - get_kfromto — function - get_nspace — function - get_nspace_nonred — function - kill — subroutine - new — subroutine

---

Module: simple_volpft_symsrch

Files: - main/volume/simple_volpft_symsrch.f90

Uses: - simple_core_module_api - simple_opt_factory - simple_opt_spec - simple_optimizer - simple_parameters - simple_projector - simple_volpft_corrcalc

Public symbols: - volpft_srch4symaxis — subroutine - volpft_symsrch_init — subroutine

Private symbols: - volpft_symsrch_costfun — function - volpft_symsrch_kill — subroutine - volpft_symsrch_scorefun — function

---

Module: simple_vrefhash

Files: - utils/structs/simple_vrefhash.f90

Uses: - simple_error - simple_string - simple_string_utils

Public symbols: - vrefhash — type - vrefhash_bucket — type - vrefhash_node — type

Private symbols: - clear — subroutine - del_char — subroutine - del_str — subroutine - destroy — subroutine - finalize_node — subroutine - find_node — subroutine - get_ref_char — subroutine - get_ref_str — subroutine - init — subroutine - keys — function - keys_sorted — function - set_ref_char — subroutine - set_ref_str — subroutine

---

Module: simple_vrefhash_tester

Files: - utils/structs/simple_vrefhash_tester.f90

Uses: - simple_string - simple_test_utils - simple_vrefhash

Public symbols: - run_all_vrefhash_tests — subroutine

Private symbols: - inc — subroutine - my_cfg — type - my_obj — type - test_collision_sanity_many_keys — subroutine - test_delete — subroutine - test_init_clear_destroy_and_count — subroutine - test_keys_returns_all_keys — subroutine - test_keys_sorted_returns_sorted_keys — subroutine - test_missing_key_get_ref_returns_null — subroutine - test_reference_semantics_updates_visible — subroutine - test_replace_pointer_on_same_key — subroutine - test_set_get_has_key_with_char_and_string_keys — subroutine - test_store_multiple_dynamic_types — subroutine

---

Module: simple_winfuns

Files: - main/interp/simple_winfuns.f90

Uses: - simple_defs

Public symbols: - winfuns — type

Private symbols: - ifun — function - wfun — function

---

Module: single_commanders_experimental

Files: - main/commanders/single/single_commanders_experimental.f90

Uses: - simple_commanders_api - simple_commanders_reproject - simple_matcher_2dprep - simple_matcher_ptcl_io - simple_opt_mask - single_commanders_nano3d

Public symbols: - commander_cavgseoproc_nano — type - commander_cavgsproc_nano — type - commander_ptclsproc_nano — type - commander_trajectory_make_projavgs — type - commander_tsegmaps_core_finder — type - commander_validate_cavgs_vs_model — type - exec_cavgseoproc_nano — subroutine - exec_cavgsproc_nano — subroutine - exec_ptclsproc_nano — subroutine - exec_trajectory_make_projavgs — subroutine - exec_tsegmaps_core_finder — subroutine - exec_validate_cavgs_vs_model — subroutine

---

Module: single_commanders_nano2D

Files: - main/commanders/single/single_commanders_nano2D.f90

Uses: - simple_commanders_api - simple_commanders_cluster2d - simple_commanders_imgproc - simple_commanders_mkcavgs - simple_commanders_sim

Public symbols: - commander_analysis2D_nano — type - commander_center2D_nano — type - commander_cluster2D_nano — type - exec_analysis2D_nano — subroutine - exec_center2D_nano — subroutine - exec_cluster2D_nano — subroutine

---

Module: single_commanders_nano3D

Files: - main/commanders/single/single_commanders_nano3D.f90

Uses: - simple_abinitio_utils - simple_commanders_abinitio - simple_commanders_api - simple_commanders_atoms - simple_commanders_cluster2d - simple_commanders_ori - simple_commanders_rec - simple_commanders_refine3d - simple_commanders_reproject - simple_flex_analysis_strategy - simple_nanoparticle - simple_refine3d_fnames - simple_trajectory_chunker

Public symbols: - commander_abinitio3D_nano — type - commander_autorefine3D_nano — type - commander_refine3D_nano — type - commander_trajectory_reconstruct3D_distr — type - exec_abinitio3D_nano — subroutine - exec_autorefine3D_nano — subroutine - exec_commander_trajectory_reconstruct3D_distr — subroutine - exec_refine3D_nano — subroutine

---

Module: single_commanders_trajectory

Files: - main/commanders/single/single_commanders_trajectory.f90

Uses: - simple_commanders_api - simple_commanders_imgops - simple_tseries_graphene_subtr - single_tseries_tracker

Public symbols: - commander_extract_substk — type - commander_graphene_subtr — type - commander_import_trajectory — type - commander_track_particles — type - commander_track_particles_distr — type - commander_trajectory_backgr_subtr — type - commander_trajectory_denoise — type - commander_trajectory_swap_stack — type - exec_extract_substk — subroutine - exec_graphene_subtr — subroutine - exec_import_trajectory — subroutine - exec_track_particles — subroutine - exec_track_particles_distr — subroutine - exec_trajectory_backgr_subtr — subroutine - exec_trajectory_denoise — subroutine - exec_trajectory_swap_stack — subroutine

---

Module: single_commanders_tseries

Files: - main/commanders/single/single_commanders_tseries.f90

Uses: - simple_bspline_smoother - simple_commanders_api - simple_denoise_movies - simple_imgarr_utils - simple_motion_correct_iter - single_tseries_extractor

Public symbols: - commander_tseries_extractor — type - commander_tseries_import — type - commander_tseries_make_pickavg — type - commander_tseries_motion_correct — type - commander_tseries_motion_correct_distr — type - commander_tseries_prep4tracking — type - downscale_frames — subroutine - exec_tseries_extractor — subroutine - exec_tseries_import — subroutine - exec_tseries_make_pickavg — subroutine - exec_tseries_motion_correct — subroutine - exec_tseries_motion_correct_distr — subroutine - exec_tseries_prep4tracking — subroutine - find_outliers — subroutine

---

Module: single_exec_api

Files: - main/apis/single_exec_api.f90

Uses: - iso_fortran_env - simple_cmdline - simple_core_module_api - simple_exec_helpers - simple_jiffys - simple_ui - simple_ui_program - single_exec_atom - single_exec_map - single_exec_nano2d - single_exec_nano3d - single_exec_trajectory - single_exec_tseries - single_exec_validate

---

Module: single_exec_atom

Files: - main/exec/single_exec_atom.f90

Uses: - simple_cmdline - simple_commanders_atoms - simple_commanders_sim

Public symbols: - exec_atom_commander — subroutine

---

Module: single_exec_map

Files: - main/exec/single_exec_map.f90

Uses: - simple_cmdline - simple_commanders_atoms - single_commanders_experimental

Public symbols: - exec_map_commander — subroutine

---

Module: single_exec_nano2D

Files: - main/exec/single_exec_nano2D.f90

Uses: - simple_cmdline - simple_commanders_imgproc - single_commanders_nano2d

Public symbols: - exec_nano2D_commander — subroutine

---

Module: single_exec_nano3D

Files: - main/exec/single_exec_nano3D.f90

Uses: - simple_cmdline - simple_exec_helpers - simple_string - single_commanders_nano3d

Public symbols: - exec_nano3D_commander — subroutine

---

Module: single_exec_trajectory

Files: - main/exec/single_exec_trajectory.f90

Uses: - simple_cmdline - single_commanders_experimental - single_commanders_nano3d - single_commanders_trajectory

Public symbols: - exec_trajectory_commander — subroutine

---

Module: single_exec_tseries

Files: - main/exec/single_exec_tseries.f90

Uses: - simple_cmdline - single_commanders_trajectory - single_commanders_tseries

Public symbols: - exec_tseries_commander — subroutine

---

Module: single_exec_validate

Files: - main/exec/single_exec_validate.f90

Uses: - simple_cmdline - single_commanders_experimental

Public symbols: - exec_validate_commander — subroutine

---

Module: single_tseries_extractor

Files: - main/nano/single_tseries_extractor.f90

Uses: - simple_core_module_api - simple_image - simple_parameters - simple_sp_project - simple_stack_io

Public symbols: - extract_trajectory — subroutine - init_trajectory_extractor — subroutine - kill_trajectory_extractor — subroutine

Private symbols: - build_mapping — subroutine - identify_neighbours — subroutine - update_background_pspec — subroutine

---

Module: single_tseries_tracker

Files: - main/nano/single_tseries_tracker.f90

Uses: - simple_bspline_smoother - simple_core_module_api - simple_image - simple_image_bin - simple_motion_align_nano - simple_parameters - simple_segmentation

Public symbols: - init_tracker — subroutine - kill_tracker — subroutine - track_particle — subroutine

Private symbols: - center_reference — function - cleanup_centering_images — subroutine - identify_neighbours — subroutine - update_background_pspec — subroutine - write_tester_dump — subroutine - write_trajectory — subroutine

---

Module: single_ui_atom

Files: - main/ui/single/single_ui_atom.f90

Uses: - simple_ui_modules

Public symbols: - construct_single_atom_programs — subroutine - new_atoms_register — subroutine - new_atoms_rmsd — subroutine - new_atoms_stats — subroutine - new_core_atoms_analysis — subroutine - new_crys_score — subroutine - new_detect_atoms — subroutine - new_simulate_nanoparticle — subroutine

---

Module: single_ui_map

Files: - main/ui/single/single_ui_map.f90

Uses: - simple_ui_modules

Public symbols: - construct_single_map_programs — subroutine - new_conv_atom_denoise — subroutine - new_tsegmaps_core_finder — subroutine

---

Module: single_ui_nano2D

Files: - main/ui/single/single_ui_nano2D.f90

Uses: - simple_ui_modules

Public symbols: - construct_single_nano2D_programs — subroutine - new_analysis2D_nano — subroutine - new_center2D_nano — subroutine - new_cluster2D_nano — subroutine - new_estimate_diam — subroutine

---

Module: single_ui_nano3D

Files: - main/ui/single/single_ui_nano3D.f90

Uses: - simple_ui_modules

Public symbols: - construct_single_nano3D_programs — subroutine - new_abinitio3D_nano — subroutine - new_autorefine3D_nano — subroutine - new_refine3D_nano — subroutine

---

Module: single_ui_trajectory

Files: - main/ui/single/single_ui_trajectory.f90

Uses: - simple_ui_modules

Public symbols: - construct_single_trajectory_programs — subroutine - new_extract_substk — subroutine - new_graphene_subtr — subroutine - new_import_trajectory — subroutine - new_trajectory_denoise — subroutine - new_trajectory_make_projavgs — subroutine - new_trajectory_reconstruct3D — subroutine - new_trajectory_swap_stack — subroutine

---

Module: single_ui_tseries

Files: - main/ui/single/single_ui_tseries.f90

Uses: - simple_ui_modules

Public symbols: - construct_single_tseries_programs — subroutine - new_track_particles — subroutine - new_tseries_extractor — subroutine - new_tseries_import — subroutine - new_tseries_make_pickavg — subroutine - new_tseries_motion_correct — subroutine - new_tseries_prep4tracking — subroutine

---

Module: single_ui_validate

Files: - main/ui/single/single_ui_validate.f90

Uses: - simple_ui_modules

Public symbols: - construct_single_validate_programs — subroutine - new_cavgseoproc_nano — subroutine - new_cavgsproc_nano — subroutine - new_ptclsproc_nano — subroutine - new_validate_cavgs_vs_model — subroutine

---

Module: subroutine

Files: - main/class/simple_classaverager.f90 - main/class/simple_classaverager_core.f90 - main/class/simple_classaverager_restore.f90 - main/image/simple_image.f90 - main/image/simple_image_access.f90 - main/image/simple_image_arith.f90 - main/image/simple_image_calc.f90 - main/image/simple_image_core.f90 - main/image/simple_image_ctf.f90 - main/image/simple_image_fft.f90 - main/image/simple_image_filt.f90 - main/image/simple_image_freq_anal.f90 - main/image/simple_image_geom.f90 - main/image/simple_image_io.f90 - main/image/simple_image_norm.f90 - main/image/simple_image_ops.f90 - main/image/simple_image_polar.f90 - main/image/simple_image_seg.f90 - main/image/simple_image_vis.f90 - main/nu_filt/simple_nu_filter.f90 - main/nu_filt/simple_nu_filter_apply.f90 - main/nu_filt/simple_nu_filter_bank.f90 - main/nu_filt/simple_nu_filter_extend.f90 - main/nu_filt/simple_nu_filter_potts.f90 - main/nu_filt/simple_nu_filter_state.f90 - main/nu_filt/simple_nu_filter_stats.f90 - main/ori/simple_oris.f90 - main/ori/simple_oris_dists.f90 - main/ori/simple_oris_getters.f90 - main/ori/simple_oris_io.f90 - main/ori/simple_oris_life.f90 - main/ori/simple_oris_neig.f90 - main/ori/simple_oris_reshape.f90 - main/ori/simple_oris_sampling.f90 - main/ori/simple_oris_setters.f90 - main/ori/simple_oris_stats.f90 - main/ori/simple_oris_transform.f90 - main/params/simple_parameters.f90 - main/params/simple_parameters_core.f90 - main/params/simple_parameters_parse.f90 - main/params/simple_parameters_phases.f90 - main/pftc/simple_polarft_access.f90 - main/pftc/simple_polarft_calc.f90 - main/pftc/simple_polarft_core.f90 - main/pftc/simple_polarft_corr.f90 - main/pftc/simple_polarft_ctf.f90 - main/pftc/simple_polarft_geom.f90 - main/pftc/simple_polarft_memo.f90 - main/pftc/simple_polarft_ops_io.f90 - main/project/simple_sp_project.f90 - main/project/simple_sp_project_cls.f90 - main/project/simple_sp_project_core.f90 - main/project/simple_sp_project_io.f90 - main/project/simple_sp_project_mic.f90 - main/project/simple_sp_project_optics.f90 - main/project/simple_sp_project_out.f90 - main/project/simple_sp_project_ptcl.f90 - main/project/simple_sp_project_stk.f90 - main/simple_abinitio_controller.f90 - main/simple_abinitio_utils.f90

Uses: - simple_commanders_euclid - simple_ctf - simple_euclid_sigma2 - simple_gpu_utils - simple_gridding - simple_imgarr_utils - simple_jpg - simple_linalg - simple_map_reduce - simple_matcher_ptcl_io - simple_math - simple_math_ctf - simple_math_ft - simple_memoize_ft_maps - simple_parameters - simple_projector - simple_projector_pft_batch - simple_ran_tabu - simple_sp_project - simple_tent_smooth

Public symbols: - add_edge — subroutine - add_fsc — subroutine - add_oriplot — subroutine - append_and_thin_nu_highres_candidate — subroutine - apply_dose_weighing — subroutine - assert_polarize_pdim — subroutine - cache_nu_extension_frontier_dmats — subroutine - cache_nu_highres_extension_frontier_after_selection — subroutine - calc_class_center_shift — subroutine - calc_final_rec — subroutine - calc_lplim_final_stage — function - calc_rec — subroutine - calculate_histogram — subroutine - calculate_indices — subroutine - calculate_optics_plot — subroutine - calculate_plot — subroutine - cavger_update_sums — subroutine - check_file_formats — subroutine - check_vol — subroutine - clear_polar_memo — subroutine - collect_nu_base_label_voxels — subroutine - compact_nu_highres_dmat_bank_for_capacity — subroutine - dealloc_cavgs — subroutine - double_check_file_formats — subroutine - dt_1d — subroutine - ensure_phase_shift_fields — subroutine - exec_refine3D — subroutine - fill_nu_frontier_dmat_from_bank — subroutine - gen_c1 — subroutine - gen_euclid_crvec — subroutine - gen_euclid_residual_grad — subroutine - gen_hybrid_grad_for_rot_8_local — subroutine - gen_many2many_euclids_cufft_kernel — subroutine - gen_ortho_reprojs4viz — subroutine - generate_random_volumes — subroutine - get_projections — subroutine - init_gridcorr_mats — subroutine - inject_refine3D_volume — subroutine - loc_var_masked — subroutine - log_nu_aux_replacement_margin_stats — subroutine - log_nu_objective_smoothing_bank — subroutine - memo_ptcls_alloc_error — subroutine - memoize_polar_point — subroutine - mkfnames — subroutine - normalize_input_volumes — subroutine - normalized_masked_value — subroutine - open_pft_or_ctf2_array_for_write — subroutine - pack_nu_dmat_to_mask_vector — subroutine - prep_class_command_lines — subroutine - prep_final_rec_cline — subroutine - prepare_nu_smooth_norm — subroutine - print_states — subroutine - prune_nu_highres_extension_bank — subroutine - randomize_states — subroutine - read_cavgs — subroutine - read_masks — subroutine - register_stage_volume — subroutine - require_valid_stats_mask — subroutine - reset_mats — subroutine - set_action — subroutine - set_boxcoords — subroutine - set_face_indices — subroutine - set_indstk_from_range — subroutine - set_ldim_box_from_stk — subroutine - set_lplims_from_frcs — subroutine - set_lplims_from_input — subroutine - set_symmetry_class_vars — subroutine - shift_stack_slice2D — subroutine - sort_oris — function - strip_refine3D_planning_keys — subroutine - symmetrize — subroutine - write_abinitio_lowpass_snapshot — subroutine - write_final_rec_outputs — subroutine

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Module: unix

Files: - extlibs/unix/src/unix.f90

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Module: unix_dirent

Files: - extlibs/unix/src/unix_dirent.F90

Public symbols: - c_closedir — function - c_opendir — function - c_readdir — function

Private symbols: - c_dirent — type - c_dirent — type

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Module: unix_errno

Files: - extlibs/unix/src/unix_errno.F90

Public symbols: - c_errno — function

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Module: unix_fcntl

Files: - extlibs/unix/src/unix_fcntl.F90

Public symbols: - c_fcntl — function - c_open — function

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Module: unix_inet

Files: - extlibs/unix/src/unix_inet.F90

Public symbols: - c_htonl — function - c_htons — function - c_inet_addr — function

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Module: unix_ioctl

Files: - extlibs/unix/src/unix_ioctl.F90

Public symbols: - c_ioctl — function

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Module: unix_ipc

Files: - extlibs/unix/src/unix_ipc.F90

Public symbols: - c_ftok — function

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Module: unix_mqueue

Files: - extlibs/unix/src/unix_mqueue.F90

Public symbols: - c_mq_close — function - c_mq_getattr — function - c_mq_open — function - c_mq_receive — function - c_mq_send — function - c_mq_setattr — function - c_mq_timedreceive — function - c_mq_timedsend — function - c_mq_unlink — function

Private symbols: - c_mq_attr — type

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Module: unix_msg

Files: - extlibs/unix/src/unix_msg.F90

Public symbols: - c_msgctl — function - c_msgget — function - c_msgrcv — function - c_msgsnd — function

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Module: unix_netdb

Files: - extlibs/unix/src/unix_netdb.F90

Public symbols: - c_freeaddrinfo — subroutine - c_gai_strerror — function - c_getaddrinfo — function

Private symbols: - c_addrinfo — type - c_addrinfo — type - c_in_addr — type - c_sockaddr — type - c_sockaddr — type - c_sockaddr_in — type - c_sockaddr_in — type

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Module: unix_pthread

Files: - extlibs/unix/src/unix_pthread.F90

Public symbols: - c_pthread_cancel — function - c_pthread_create — function - c_pthread_detach — function - c_pthread_exit — subroutine - c_pthread_join — function - c_pthread_mutex_destroy — function - c_pthread_mutex_init — function - c_pthread_mutex_lock — function - c_pthread_mutex_trylock — function - c_pthread_mutex_unlock — function - c_pthread_setcancelstate — function - c_pthread_setcanceltype — function - c_pthread_t — type

Private symbols: - c_pthread_mutex_t — type

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Module: unix_regex

Files: - extlibs/unix/src/unix_regex.F90

Public symbols: - c_regcomp — function - c_regerror — function - c_regexec — function - c_regfree — subroutine

Private symbols: - c_regex_t — type - c_regex_t — type - c_regmatch_t — type

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Module: unix_semaphore

Files: - extlibs/unix/src/unix_semaphore.F90

Public symbols: - c_sem_close — function - c_sem_destroy — function - c_sem_getvalue — function - c_sem_init — function - c_sem_open — function - c_sem_post — function - c_sem_timedwait — function - c_sem_trywait — function - c_sem_unlink — function - c_sem_wait — function

Private symbols: - c_sem_t — type

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Module: unix_signal

Files: - extlibs/unix/src/unix_signal.F90

Public symbols: - c_kill — function - c_signal — function

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Module: unix_socket

Files: - extlibs/unix/src/unix_socket.F90

Public symbols: - c_accept — function - c_bind — function - c_connect — function - c_listen — function - c_send — function - c_setsockopt — function - c_socket — function

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Module: unix_stat

Files: - extlibs/unix/src/unix_stat.F90

Public symbols: - c_fstat — function - c_lstat — function - c_mkdir — function - c_mkfifo — function - c_stat — function - c_umask — function

Private symbols: - c_stat_type — type - c_stat_type — type - c_stat_type — type

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Module: unix_stdio

Files: - extlibs/unix/src/unix_stdio.F90

Public symbols: - c_fclose — function - c_fdopen — function - c_fflush — function - c_fgetc — function - c_fgets — function - c_fopen — function - c_fprintf — function - c_fputs — function - c_fread — function - c_fwrite — function - c_getchar — function - c_getline — function - c_pclose — function - c_perror — subroutine - c_popen — function - c_putchar — function - c_scanf — function - c_setbuf — subroutine - c_setvbuf — function

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Module: unix_stdlib

Files: - extlibs/unix/src/unix_stdlib.F90

Public symbols: - c_exit — subroutine - c_free — subroutine

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Module: unix_string

Files: - extlibs/unix/src/unix_string.F90

Public symbols: - c_memcpy — function - c_memset — function - c_strerror — function - c_strlen — function

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Module: unix_syslog

Files: - extlibs/unix/src/unix_syslog.F90

Public symbols: - c_closelog — subroutine - c_openlog — subroutine - c_syslog — subroutine

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Module: unix_termios

Files: - extlibs/unix/src/unix_termios.F90

Public symbols: - c_cfgetispeed — function - c_cfgetospeed — function - c_cfmakeraw — subroutine - c_cfsetispeed — function - c_cfsetospeed — function - c_cfsetspeed — function - c_tcdrain — function - c_tcflow — function - c_tcflush — function - c_tcgetattr — function - c_tcsendbreak — function - c_tcsetattr — function

Private symbols: - c_termios — type - c_termios — type

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Module: unix_time

Files: - extlibs/unix/src/unix_time.F90

Public symbols: - c_asctime — function - c_clock_gettime — function - c_ctime — function - c_gettimeofday — function - c_gmtime — function - c_gmtime_r — function - c_localtime — function - c_localtime_r — function - c_mktime — function - c_strftime — function - c_time — function - c_timegm — function

Private symbols: - c_timespec — type - c_timeval — type - c_timezone — type - c_tm — type

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Module: unix_types

Files: - extlibs/unix/src/unix_types.F90

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Module: unix_unistd

Files: - extlibs/unix/src/unix_unistd.F90

Public symbols: - c_chdir — function - c_close — function - c_dup — function - c_dup2 — function - c_execl — function - c_fork — function - c_getpid — function - c_pipe — function - c_read — function - c_setsid — function - c_unlink — function - c_usleep — function - c_write — function

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Module: unix_utsname

Files: - extlibs/unix/src/unix_utsname.F90

Public symbols: - c_uname — function

Private symbols: - c_utsname — type - c_utsname — type

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Module: unix_wait

Files: - extlibs/unix/src/unix_wait.F90

Public symbols: - c_wait — function - c_waitpid — function

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