diff --git a/.doctrees/api/datman.config.doctree b/.doctrees/api/datman.config.doctree index ea69540b..14fddccb 100644 Binary files a/.doctrees/api/datman.config.doctree and b/.doctrees/api/datman.config.doctree differ diff --git a/.doctrees/api/datman.dashboard.doctree b/.doctrees/api/datman.dashboard.doctree index 276ac6da..2fffd423 100644 Binary files a/.doctrees/api/datman.dashboard.doctree and b/.doctrees/api/datman.dashboard.doctree differ diff --git a/.doctrees/api/datman.exceptions.doctree b/.doctrees/api/datman.exceptions.doctree index ac2011e4..2d9b06b7 100644 Binary files a/.doctrees/api/datman.exceptions.doctree and b/.doctrees/api/datman.exceptions.doctree differ diff --git a/.doctrees/api/datman.exporters.doctree b/.doctrees/api/datman.exporters.doctree index e7147389..b26cb5de 100644 Binary files a/.doctrees/api/datman.exporters.doctree and b/.doctrees/api/datman.exporters.doctree differ diff --git a/.doctrees/api/datman.fs_log_scraper.doctree b/.doctrees/api/datman.fs_log_scraper.doctree index 872ac88c..1b0484bc 100644 Binary files a/.doctrees/api/datman.fs_log_scraper.doctree and b/.doctrees/api/datman.fs_log_scraper.doctree differ diff --git a/.doctrees/api/datman.header_checks.doctree b/.doctrees/api/datman.header_checks.doctree index 0b6e7869..fd461792 100644 Binary files a/.doctrees/api/datman.header_checks.doctree and b/.doctrees/api/datman.header_checks.doctree differ diff --git a/.doctrees/api/datman.metrics.doctree b/.doctrees/api/datman.metrics.doctree index 3c08589b..b8f86218 100644 Binary files a/.doctrees/api/datman.metrics.doctree and b/.doctrees/api/datman.metrics.doctree differ diff --git a/.doctrees/api/datman.scan.doctree b/.doctrees/api/datman.scan.doctree index 708e9e78..3e9a78d1 100644 Binary files a/.doctrees/api/datman.scan.doctree and b/.doctrees/api/datman.scan.doctree differ diff --git a/.doctrees/api/datman.scan_list.doctree b/.doctrees/api/datman.scan_list.doctree index c1d1d756..1e03fd5c 100644 Binary files a/.doctrees/api/datman.scan_list.doctree and b/.doctrees/api/datman.scan_list.doctree differ diff --git a/.doctrees/api/datman.scanid.doctree b/.doctrees/api/datman.scanid.doctree index 63bfe916..bb79e171 100644 Binary files a/.doctrees/api/datman.scanid.doctree and b/.doctrees/api/datman.scanid.doctree differ diff --git a/.doctrees/api/datman.utils.doctree b/.doctrees/api/datman.utils.doctree index edf97d33..8144ebc1 100644 Binary files a/.doctrees/api/datman.utils.doctree and b/.doctrees/api/datman.utils.doctree differ diff --git a/.doctrees/api/datman.xnat.doctree b/.doctrees/api/datman.xnat.doctree index 8f1124fa..e9ecf139 100644 Binary files a/.doctrees/api/datman.xnat.doctree and b/.doctrees/api/datman.xnat.doctree differ diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 34148797..86ca86bd 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/api/datman.config.html b/api/datman.config.html index 7f5b09e5..168274ae 100644 --- a/api/datman.config.html +++ b/api/datman.config.html @@ -112,16 +112,16 @@

These can both be overridden at __init__.py

-class datman.config.TagInfo(export_settings, site_settings=None)[source]
+class datman.config.TagInfo(export_settings, site_settings=None)[source]

Bases: object

-get(tag, field=None)[source]
+get(tag, field=None)[source]
-keys()[source]
+keys()[source]
@@ -135,11 +135,11 @@
-class datman.config.config(filename=None, system=None, study=None)[source]
+class datman.config.config(filename=None, system=None, study=None)[source]

Bases: object

-get_key(key, site=None, ignore_defaults=False, defaults_only=False)[source]
+get_key(key, site=None, ignore_defaults=False, defaults_only=False)[source]

Searches the configuration from most specific settings to least to allow overrides + additional settings to be discovered.

Searches from site (if given) -> study -> local system -> system wide

@@ -153,24 +153,24 @@
-get_path(path_type, study=None)[source]
+get_path(path_type, study=None)[source]

returns the absolute path to a folder type

-get_sites(study=None)[source]
+get_sites(study=None)[source]
-get_study_base(study=None)[source]
+get_study_base(study=None)[source]

Return the base directory for a study

-get_study_tags(study=None)[source]
+get_study_tags(study=None)[source]

Returns a dictionary of study tags mapped to the sites defined for that tag.

If a study has not been set then an exception is raised

@@ -178,7 +178,7 @@
-get_tags(site=None, study=None)[source]
+get_tags(site=None, study=None)[source]

Returns a TagInfo instance.

If you get the tags without a study set or without specifying a site you get the configuration of all defined tags from ‘ExportSettings’ in @@ -192,7 +192,7 @@

-get_xnat_projects(study=None)[source]
+get_xnat_projects(study=None)[source]
@@ -202,12 +202,12 @@
-load_yaml(filename)[source]
+load_yaml(filename)[source]
-map_xnat_archive_to_project(filename)[source]
+map_xnat_archive_to_project(filename)[source]

Maps the XNAT tag (e.g. SPN01) to the project name e.g. SPINS Can either supply a full filename in which case only the first part is considered or just a tag.

@@ -222,7 +222,7 @@
-set_study(study_name)[source]
+set_study(study_name)[source]

This function can take just the study ID for every study except DTI. So where possible, please give it an exact match to a project name or a full session ID.

@@ -252,7 +252,7 @@
-datman.config.study_required(wrapper=None, enabled=None, adapter=None, proxy=<class 'FunctionWrapper'>)[source]
+datman.config.study_required(wrapper=None, enabled=None, adapter=None, proxy=<class 'FunctionWrapper'>)[source]
diff --git a/api/datman.dashboard.html b/api/datman.dashboard.html index 5ba6ba64..f6f118b0 100644 --- a/api/datman.dashboard.html +++ b/api/datman.dashboard.html @@ -106,27 +106,27 @@

datman.dashboard module

-datman.dashboard.add_scan(name, tag=None, series=None, description=None, source_id=None)[source]
+datman.dashboard.add_scan(name, tag=None, series=None, description=None, source_id=None)[source]
-datman.dashboard.add_session(name, date=None)[source]
+datman.dashboard.add_session(name, date=None)[source]
-datman.dashboard.add_subject(name)[source]
+datman.dashboard.add_subject(name)[source]
-datman.dashboard.dashboard_required(f)[source]
+datman.dashboard.dashboard_required(f)[source]
-datman.dashboard.filename_required(f)[source]
+datman.dashboard.filename_required(f)[source]

This decorator checks that the wrapped function has received a datman style file name as either a string or as a datman.scanid.Identifier instance with kwargs tag, series, and description set.

@@ -136,22 +136,22 @@
-datman.dashboard.get_bids_scan(name)[source]
+datman.dashboard.get_bids_scan(name)[source]
-datman.dashboard.get_bids_subject(bids_name, bids_session, study=None)[source]
+datman.dashboard.get_bids_subject(bids_name, bids_session, study=None)[source]
-datman.dashboard.get_default_user()[source]
+datman.dashboard.get_default_user()[source]
-datman.dashboard.get_project(name=None, tag=None, site=None, create=False)[source]
+datman.dashboard.get_project(name=None, tag=None, site=None, create=False)[source]

Return a study from the dashboard database that either matches the study name (e.g. ‘SPINS’) or matches a study tag (e.g. ‘SPN01’) + an optional site code to help locate the correct study when the same code @@ -160,17 +160,17 @@

-datman.dashboard.get_scan(name, tag=None, series=None, description=None, source_id=None, create=False)[source]
+datman.dashboard.get_scan(name, tag=None, series=None, description=None, source_id=None, create=False)[source]
-datman.dashboard.get_session(name, create=False, date=None)[source]
+datman.dashboard.get_session(name, create=False, date=None)[source]
-datman.dashboard.get_study_subjects(study, site=None, phantoms=False)[source]
+datman.dashboard.get_study_subjects(study, site=None, phantoms=False)[source]

Pulls a list of subjects from the dashboard from a specified study

Parameters
@@ -188,12 +188,12 @@
-datman.dashboard.get_subject(name, create=False)[source]
+datman.dashboard.get_subject(name, create=False)[source]
-datman.dashboard.release_db(f)[source]
+datman.dashboard.release_db(f)[source]

This decorator ensures that transactions are ended after exit.

Read operations on the database open a transaction. This transaction isnt terminated until a rollback or commit happens or until the @@ -204,7 +204,7 @@

-datman.dashboard.scanid_required(f)[source]
+datman.dashboard.scanid_required(f)[source]

This decorator checks that the wrapped function’s first argument is an instance of datman.scanid.Identifier and attempts to convert it if not.

A DashboardException will be raised if an Identifier isn’t found or can’t @@ -213,7 +213,7 @@

-datman.dashboard.set_study_status(name, is_open)[source]
+datman.dashboard.set_study_status(name, is_open)[source]
diff --git a/api/datman.exceptions.html b/api/datman.exceptions.html index 314df411..eff7aa68 100644 --- a/api/datman.exceptions.html +++ b/api/datman.exceptions.html @@ -107,64 +107,64 @@

Defines the exceptions used by datman sub-modules

-exception datman.exceptions.ConfigException[source]
+exception datman.exceptions.ConfigException[source]

Bases: Exception

-exception datman.exceptions.DashboardException[source]
+exception datman.exceptions.DashboardException[source]

Bases: Exception

Default exception for dashboard errors

-exception datman.exceptions.ExportException[source]
+exception datman.exceptions.ExportException[source]

Bases: Exception

-exception datman.exceptions.ExporterException[source]
+exception datman.exceptions.ExporterException[source]

Bases: Exception

Default exception for errors exporting data from raw.

-exception datman.exceptions.InputException[source]
+exception datman.exceptions.InputException[source]

Bases: Exception

-exception datman.exceptions.MetadataException[source]
+exception datman.exceptions.MetadataException[source]

Bases: Exception

-exception datman.exceptions.ParseException[source]
+exception datman.exceptions.ParseException[source]

Bases: Exception

For participant ID parsing issues.

-exception datman.exceptions.QCException[source]
+exception datman.exceptions.QCException[source]

Bases: Exception

-exception datman.exceptions.UndefinedSetting[source]
+exception datman.exceptions.UndefinedSetting[source]

Bases: Exception

-exception datman.exceptions.XnatException[source]
+exception datman.exceptions.XnatException[source]

Bases: Exception

Default exception for XNAT errors

diff --git a/api/datman.exporters.html b/api/datman.exporters.html index d8cd2c76..d37a112a 100644 --- a/api/datman.exporters.html +++ b/api/datman.exporters.html @@ -114,17 +114,17 @@ unique key that can be referenced in config files (e.g. ‘nii’).

-class datman.exporters.BidsExporter(config, session, experiment, bids_opts=None, **kwargs)[source]
+class datman.exporters.BidsExporter(config, session, experiment, bids_opts=None, **kwargs)[source]

Bases: datman.exporters.SessionExporter

An exporter that runs dcm2bids.

-add_repeat_num()[source]
+add_repeat_num()[source]
-export(raw_data_dir, **kwargs)[source]
+export(raw_data_dir, **kwargs)[source]

Exports raw data to the current Exporter’s format.

Parameters
@@ -136,12 +136,12 @@
-get_sidecars()[source]
+get_sidecars()[source]
-needs_raw_data()[source]
+needs_raw_data()[source]

Whether raw data must be downloaded for the Exporter.

Returns
@@ -159,7 +159,7 @@
-outputs_exist()[source]
+outputs_exist()[source]

Whether outputs have already been generated for this Exporter.

Returns
@@ -180,12 +180,12 @@
-class datman.exporters.DBExporter(config, session, experiment, **kwargs)[source]
+class datman.exporters.DBExporter(config, session, experiment, **kwargs)[source]

Bases: datman.exporters.SessionExporter

Add a datman-style session and its contents to datman’s QC dashboard.

-add_tech_notes(session)[source]
+add_tech_notes(session)[source]

Add the path to a scan session’s tech notes to the database.

Parameters
@@ -197,12 +197,12 @@
-errors_outdated(scan, fname)[source]
+errors_outdated(scan, fname)[source]
-export(*args, **kwargs)[source]
+export(*args, **kwargs)[source]

Exports raw data to the current Exporter’s format.

Parameters
@@ -214,7 +214,7 @@
-get_bids_name(dm_name, session)[source]
+get_bids_name(dm_name, session)[source]

Get BIDS style scan name from a datman style nifti.

Returns
@@ -232,13 +232,13 @@
-classmethod get_output_dir(session)[source]
+classmethod get_output_dir(session)[source]

Retrieve the exporter’s output dir without needing an instance.

-make_scan(file_stem)[source]
+make_scan(file_stem)[source]

Add a single scan to datman’s QC dashboard.

Parameters
@@ -249,7 +249,7 @@
-make_session()[source]
+make_session()[source]

Add the current session to datman’s QC database.

Returns
@@ -282,7 +282,7 @@
-needs_raw_data()[source]
+needs_raw_data()[source]

Whether raw data must be downloaded for the Exporter.

Returns
@@ -300,7 +300,7 @@
-outputs_exist()[source]
+outputs_exist()[source]

Whether outputs have already been generated for this Exporter.

Returns
@@ -321,12 +321,12 @@
-class datman.exporters.DcmExporter(output_dir, fname_root, echo_dict=None, dry_run=False, **kwargs)[source]
+class datman.exporters.DcmExporter(output_dir, fname_root, echo_dict=None, dry_run=False, **kwargs)[source]

Bases: datman.exporters.SeriesExporter

Export a single dicom from a scan.

-export(raw_data_dir, **kwargs)[source]
+export(raw_data_dir, **kwargs)[source]

Exports raw data to the current Exporter’s format.

Parameters
@@ -350,12 +350,12 @@
-class datman.exporters.Exporter[source]
+class datman.exporters.Exporter[source]

Bases: abc.ABC

An abstract base class for all Exporters.

-abstract export(raw_data_dir, **kwargs)[source]
+abstract export(raw_data_dir, **kwargs)[source]

Exports raw data to the current Exporter’s format.

Parameters
@@ -367,13 +367,13 @@
-classmethod get_output_dir(session)[source]
+classmethod get_output_dir(session)[source]

Retrieve the exporter’s output dir without needing an instance.

-make_output_dir()[source]
+make_output_dir()[source]

Creates the directory where the Exporter’s outputs will be stored.

Returns
@@ -387,7 +387,7 @@
-abstract needs_raw_data()[source]
+abstract needs_raw_data()[source]

Whether raw data must be downloaded for the Exporter.

Returns
@@ -405,7 +405,7 @@
-abstract outputs_exist()[source]
+abstract outputs_exist()[source]

Whether outputs have already been generated for this Exporter.

Returns
@@ -426,12 +426,12 @@
-class datman.exporters.NiiExporter(output_dir, fname_root, echo_dict=None, dry_run=False, **kwargs)[source]
+class datman.exporters.NiiExporter(output_dir, fname_root, echo_dict=None, dry_run=False, **kwargs)[source]

Bases: datman.exporters.SeriesExporter

Export a series to nifti format with datman-style names.

-export(raw_data_dir, **kwargs)[source]
+export(raw_data_dir, **kwargs)[source]

Exports raw data to the current Exporter’s format.

Parameters
@@ -448,7 +448,7 @@
-move_file(gen_file)[source]
+move_file(gen_file)[source]

Move the temp outputs of dcm2niix to the intended output directory.

Parameters
@@ -460,7 +460,7 @@
-report_issues(stem, messages)[source]
+report_issues(stem, messages)[source]

Write an error log if dcm2niix had errors during conversion.

Parameters
@@ -482,12 +482,12 @@
-class datman.exporters.NiiLinkExporter(config, session, experiment, **kwargs)[source]
+class datman.exporters.NiiLinkExporter(config, session, experiment, **kwargs)[source]

Bases: datman.exporters.SessionExporter

Populates a study’s nii folder with symlinks pointing to the bids dir.

-belongs_to_session(nifti_path)[source]
+belongs_to_session(nifti_path)[source]

Check if a nifti belongs to this repeat or another for this session.

Parameters
@@ -509,7 +509,7 @@
-clear_errors(dm_file)[source]
+clear_errors(dm_file)[source]

Remove an error file from a previous BIDs export issue.

Parameters
@@ -520,7 +520,7 @@
-export(*args, **kwargs)[source]
+export(*args, **kwargs)[source]

Exports raw data to the current Exporter’s format.

Parameters
@@ -537,7 +537,7 @@
-get_bids_niftis()[source]
+get_bids_niftis()[source]

Get all nifti files from a BIDS session.

Returns
@@ -555,7 +555,7 @@
-get_dm_names()[source]
+get_dm_names()[source]

Get the datman-style scan names for an entire XNAT experiment.

Returns
@@ -573,18 +573,18 @@
-get_error_file(dm_file)[source]
+get_error_file(dm_file)[source]
-classmethod get_output_dir(session)[source]
+classmethod get_output_dir(session)[source]

Retrieve the exporter’s output dir without needing an instance.

-get_series_num(side_car)[source]
+get_series_num(side_car)[source]

Find the correct series number for a scan.

Most JSON side car files have the correct series number already. However, series that are split during nifti conversion (e.g. @@ -607,7 +607,7 @@

-make_datman_name(bids_path, scan_tag)[source]
+make_datman_name(bids_path, scan_tag)[source]

Create a Datman-style file name for a bids file.

Parameters
@@ -628,7 +628,7 @@
+make_link(dm_file, bids_file)[source]

Create a symlink in the datman style that points to a bids file.

Parameters
@@ -643,7 +643,7 @@
-match_dm_to_bids(dm_names, bids_names)[source]
+match_dm_to_bids(dm_names, bids_names)[source]

Match each datman file name to its BIDS equivalent.

Parameters
@@ -671,7 +671,7 @@
-needs_raw_data()[source]
+needs_raw_data()[source]

Whether raw data must be downloaded for the Exporter.

Returns
@@ -689,7 +689,7 @@
-outputs_exist()[source]
+outputs_exist()[source]

Whether outputs have already been generated for this Exporter.

Returns
@@ -703,7 +703,7 @@
-report_errors(dm_file)[source]
+report_errors(dm_file)[source]

Create an error file to report probable BIDS conversion issues.

Parameters
@@ -721,7 +721,7 @@
-class datman.exporters.SeriesExporter(output_dir, fname_root, echo_dict=None, dry_run=False, **kwargs)[source]
+class datman.exporters.SeriesExporter(output_dir, fname_root, echo_dict=None, dry_run=False, **kwargs)[source]

Bases: datman.exporters.Exporter

A base class for exporters that take a single series as input.

@@ -731,7 +731,7 @@
-needs_raw_data()[source]
+needs_raw_data()[source]

Whether raw data must be downloaded for the Exporter.

Returns
@@ -749,7 +749,7 @@
-outputs_exist()[source]
+outputs_exist()[source]

Whether outputs have already been generated for this Exporter.

Returns
@@ -765,7 +765,7 @@
-class datman.exporters.SessionExporter(config, session, experiment, dry_run=False, **kwargs)[source]
+class datman.exporters.SessionExporter(config, session, experiment, dry_run=False, **kwargs)[source]

Bases: datman.exporters.Exporter

A base class for exporters that take an entire session as input.

Subclasses should override __init__ (without changing basic input args) @@ -776,12 +776,12 @@

-class datman.exporters.SharedExporter(config, session, experiment, bids_opts=None, **kwargs)[source]
+class datman.exporters.SharedExporter(config, session, experiment, bids_opts=None, **kwargs)[source]

Bases: datman.exporters.SessionExporter

Export an XNAT ‘shared’ experiment.

-export(*args, **kwargs)[source]
+export(*args, **kwargs)[source]

Exports raw data to the current Exporter’s format.

Parameters
@@ -798,7 +798,7 @@
-find_bids_files(name_map=None)[source]
+find_bids_files(name_map=None)[source]

Find all bids files that have been created for the source session.

Parameters
@@ -820,7 +820,7 @@
-find_dm_files(dir_type, name_map=None)[source]
+find_dm_files(dir_type, name_map=None)[source]

Find datman-style source files in all listed directory types.

Parameters
@@ -847,7 +847,7 @@
-find_resource_files(name_map=None)[source]
+find_resource_files(name_map=None)[source]

Find all source session resources files.

Parameters
@@ -869,7 +869,7 @@
-find_source_session(config, experiment)[source]
+find_source_session(config, experiment)[source]

Find the original data on the filesystem.

Parameters
@@ -895,13 +895,13 @@
-classmethod get_output_dir(session)[source]
+classmethod get_output_dir(session)[source]

Retrieve the exporter’s output dir without needing an instance.

-make_name_map(dm_dirs, use_bids=False)[source]
+make_name_map(dm_dirs, use_bids=False)[source]

Create a dictionary of source files to their ‘shared’ alias.

Parameters
@@ -928,7 +928,7 @@
-needs_raw_data()[source]
+needs_raw_data()[source]

Whether raw data must be downloaded for the Exporter.

Returns
@@ -946,7 +946,7 @@
-outputs_exist()[source]
+outputs_exist()[source]

Whether outputs have already been generated for this Exporter.

Returns
@@ -967,7 +967,7 @@
-datman.exporters.get_exporter(key, scope='series')[source]
+datman.exporters.get_exporter(key, scope='series')[source]

Find an exporter class for a given key identifier.

Parameters
diff --git a/api/datman.fs_log_scraper.html b/api/datman.fs_log_scraper.html index a9bc6cf2..b98acddb 100644 --- a/api/datman.fs_log_scraper.html +++ b/api/datman.fs_log_scraper.html @@ -110,63 +110,63 @@

The FSLog class aggregates/parses the most useful details from the log files.

-class datman.fs_log_scraper.FSLog(freesurfer_folder)[source]
+class datman.fs_log_scraper.FSLog(freesurfer_folder)[source]

Bases: object

-static get_args(cmd_args)[source]
+static get_args(cmd_args)[source]
-get_date(date_str)[source]
+get_date(date_str)[source]
-get_kernel(log_uname)[source]
+get_kernel(log_uname)[source]
-static get_niftis(cmd_args)[source]
+static get_niftis(cmd_args)[source]
-get_subject(subject_field)[source]
+get_subject(subject_field)[source]
-parse_recon_done(recon_done)[source]
+parse_recon_done(recon_done)[source]
-read_log(path)[source]
+read_log(path)[source]
-datman.fs_log_scraper.check_diff(log_field, standards_field)[source]
+datman.fs_log_scraper.check_diff(log_field, standards_field)[source]
-datman.fs_log_scraper.choose_standard_sub(subject_logs)[source]
+datman.fs_log_scraper.choose_standard_sub(subject_logs)[source]
-datman.fs_log_scraper.make_standards(standard_log)[source]
+datman.fs_log_scraper.make_standards(standard_log)[source]
-datman.fs_log_scraper.scrape_logs(fs_output_folders, standards=None, col_headers=False)[source]
+datman.fs_log_scraper.scrape_logs(fs_output_folders, standards=None, col_headers=False)[source]

Takes a list of paths to freesurfer output folders and generates a list of log lines containing differences relative to a ‘standard’ subject.

A field will be left empty if no differences are found

@@ -174,7 +174,7 @@
-datman.fs_log_scraper.verify_standards(standards_dict, expected_keys)[source]
+datman.fs_log_scraper.verify_standards(standards_dict, expected_keys)[source]
diff --git a/api/datman.header_checks.html b/api/datman.header_checks.html index 42337f60..ddf146ec 100644 --- a/api/datman.header_checks.html +++ b/api/datman.header_checks.html @@ -108,47 +108,47 @@ files.

-datman.header_checks.check_bvals(series_path, standard_path)[source]
+datman.header_checks.check_bvals(series_path, standard_path)[source]
-datman.header_checks.compare_headers(series, standard, ignore=None, tolerance=None)[source]
+datman.header_checks.compare_headers(series, standard, ignore=None, tolerance=None)[source]
-datman.header_checks.construct_diffs(series_json, standard_json, ignored_fields=None, tolerances=None, dti=False)[source]
+datman.header_checks.construct_diffs(series_json, standard_json, ignored_fields=None, tolerances=None, dti=False)[source]
-datman.header_checks.find_bvals(json_path)[source]
+datman.header_checks.find_bvals(json_path)[source]
-datman.header_checks.handle_diff(value, expected, tolerance=None)[source]
+datman.header_checks.handle_diff(value, expected, tolerance=None)[source]
-datman.header_checks.parse_file(file_path)[source]
+datman.header_checks.parse_file(file_path)[source]
-datman.header_checks.read_json(json_file)[source]
+datman.header_checks.read_json(json_file)[source]
-datman.header_checks.remove_fields(json_contents, fields)[source]
+datman.header_checks.remove_fields(json_contents, fields)[source]
-datman.header_checks.write_diff_log(diffs, output_path)[source]
+datman.header_checks.write_diff_log(diffs, output_path)[source]
diff --git a/api/datman.metrics.html b/api/datman.metrics.html index c798deaa..87e2dab1 100644 --- a/api/datman.metrics.html +++ b/api/datman.metrics.html @@ -107,11 +107,11 @@

Classes and functions for generating QC metrics.

-class datman.metrics.ABCDPHAMetrics(input_nii, output_dir)[source]
+class datman.metrics.ABCDPHAMetrics(input_nii, output_dir)[source]

Bases: datman.metrics.Metric

-generate()[source]
+generate()[source]
@@ -123,11 +123,11 @@
-class datman.metrics.AnatMetrics(input_nii, output_dir)[source]
+class datman.metrics.AnatMetrics(input_nii, output_dir)[source]

Bases: datman.metrics.Metric

-generate(img_gap=5, width=1600)[source]
+generate(img_gap=5, width=1600)[source]
@@ -139,11 +139,11 @@
-class datman.metrics.AnatPHAMetrics(input_nii, output_dir)[source]
+class datman.metrics.AnatPHAMetrics(input_nii, output_dir)[source]

Bases: datman.metrics.Metric

-generate()[source]
+generate()[source]
@@ -155,11 +155,11 @@
-class datman.metrics.DTIMetrics(nii_input, output_dir, bval=None, bvec=None)[source]
+class datman.metrics.DTIMetrics(nii_input, output_dir, bval=None, bvec=None)[source]

Bases: datman.metrics.MetricDTI

-generate(img_gap=2, width=1600)[source]
+generate(img_gap=2, width=1600)[source]
@@ -171,11 +171,11 @@
-class datman.metrics.DTIPHAMetrics(nii_input, output_dir, bval=None, bvec=None)[source]
+class datman.metrics.DTIPHAMetrics(nii_input, output_dir, bval=None, bvec=None)[source]

Bases: datman.metrics.MetricDTI

-generate()[source]
+generate()[source]
@@ -187,11 +187,11 @@
-class datman.metrics.FMRIMetrics(input_nii, output_dir)[source]
+class datman.metrics.FMRIMetrics(input_nii, output_dir)[source]

Bases: datman.metrics.Metric

-generate(img_gap=2, width=1600)[source]
+generate(img_gap=2, width=1600)[source]
@@ -203,11 +203,11 @@
-class datman.metrics.FMRIPHAMetrics(input_nii, output_dir)[source]
+class datman.metrics.FMRIPHAMetrics(input_nii, output_dir)[source]

Bases: datman.metrics.Metric

-generate()[source]
+generate()[source]
@@ -219,16 +219,16 @@
-class datman.metrics.IgnoreMetrics(input_nii, output_dir)[source]
+class datman.metrics.IgnoreMetrics(input_nii, output_dir)[source]

Bases: datman.metrics.Metric

-exists()[source]
+exists()[source]
-generate()[source]
+generate()[source]
@@ -238,43 +238,43 @@
-write_manifest(overwrite=False)[source]
+write_manifest(overwrite=False)[source]
-class datman.metrics.Metric(input_nii, output_dir)[source]
+class datman.metrics.Metric(input_nii, output_dir)[source]

Bases: abc.ABC

-command_succeeded(command_name)[source]
+command_succeeded(command_name)[source]
-exists()[source]
+exists()[source]
-abstract generate()[source]
+abstract generate()[source]
-classmethod get_requirements()[source]
+classmethod get_requirements()[source]
-classmethod is_runnable()[source]
+classmethod is_runnable()[source]
-make_image(output, img_gap=2, width=1600, nii_input=None)[source]
+make_image(output, img_gap=2, width=1600, nii_input=None)[source]

Uses FSL’s slicer function to generate a png from a nifti file.

Parameters
@@ -293,12 +293,12 @@
-make_manifest()[source]
+make_manifest()[source]
-make_montage(output)[source]
+make_montage(output)[source]

Uses FSL’s slicer function to generate a montage of three slices.

Parameters
@@ -314,12 +314,12 @@
-abstract outputs()[source]
+abstract outputs()[source]
-read_manifest()[source]
+read_manifest()[source]
@@ -329,7 +329,7 @@
-run(command, output)[source]
+run(command, output)[source]

Run a command if outputs are still needed.

Parameters
@@ -347,29 +347,29 @@
-set_outputs()[source]
+set_outputs()[source]
-write_manifest(overwrite=False)[source]
+write_manifest(overwrite=False)[source]
-class datman.metrics.MetricDTI(nii_input, output_dir, bval=None, bvec=None)[source]
+class datman.metrics.MetricDTI(nii_input, output_dir, bval=None, bvec=None)[source]

Bases: datman.metrics.Metric

-class datman.metrics.QAPHAMetrics(nii_input, output_dir, bval=None, bvec=None)[source]
+class datman.metrics.QAPHAMetrics(nii_input, output_dir, bval=None, bvec=None)[source]

Bases: datman.metrics.MetricDTI

-generate()[source]
+generate()[source]
@@ -379,14 +379,14 @@
-update_expected_outputs()[source]
+update_expected_outputs()[source]
-class datman.metrics.QCOutput(order: int = - 1, title: str = None, caption: str = None)[source]
+class datman.metrics.QCOutput(order: int = - 1, title: str = None, caption: str = None)[source]

Bases: object

@@ -407,7 +407,7 @@
-datman.metrics.get_handlers(subject)[source]
+datman.metrics.get_handlers(subject)[source]

Returns the set of QC functions to use for a subject.

Parameters
diff --git a/api/datman.scan.html b/api/datman.scan.html index 7708b90e..3ce812ed 100644 --- a/api/datman.scan.html +++ b/api/datman.scan.html @@ -111,7 +111,7 @@ become out of date if this is not true.

-class datman.scan.DatmanNamed(ident)[source]
+class datman.scan.DatmanNamed(ident)[source]

Bases: object

A parent class for all classes that will obey the datman naming scheme

@@ -123,7 +123,7 @@
-class datman.scan.Scan(subject_id, config, bids_root=None)[source]
+class datman.scan.Scan(subject_id, config, bids_root=None)[source]

Bases: datman.scan.DatmanNamed

Holds all information for a single scan (session).

@@ -142,17 +142,17 @@ datman naming convention

-find_files(file_stem, format='nii')[source]
+find_files(file_stem, format='nii')[source]
-get_resource_dir(session)[source]
+get_resource_dir(session)[source]
-get_tagged_nii(tag)[source]
+get_tagged_nii(tag)[source]
@@ -164,7 +164,7 @@
-class datman.scan.Series(path)[source]
+class datman.scan.Series(path)[source]

Bases: datman.scan.DatmanNamed

Holds all information about a series file of any format (e.g. nifti).

diff --git a/api/datman.scan_list.html b/api/datman.scan_list.html index f3aab9ed..67889bbf 100644 --- a/api/datman.scan_list.html +++ b/api/datman.scan_list.html @@ -131,18 +131,18 @@
-class datman.scan_list.ScanEntryABC(scan_path)[source]
+class datman.scan_list.ScanEntryABC(scan_path)[source]

Bases: object

-abstract get_target_name()[source]
+abstract get_target_name()[source]
-datman.scan_list.generate_scan_list(scan_entry_class, zip_files, dest_dir)[source]
+datman.scan_list.generate_scan_list(scan_entry_class, zip_files, dest_dir)[source]

Use this function to generate a scans.csv file of the expected format.

scan_entry_class: A subclass of ScanEntryABC that will be used to

generate each entry in scans.csv

@@ -154,22 +154,22 @@
-datman.scan_list.get_scan_list_contents(scans_csv)[source]
+datman.scan_list.get_scan_list_contents(scans_csv)[source]
-datman.scan_list.make_new_entries(processed_scans, zip_files, EntryClass)[source]
+datman.scan_list.make_new_entries(processed_scans, zip_files, EntryClass)[source]
-datman.scan_list.start_new_scan_list(output)[source]
+datman.scan_list.start_new_scan_list(output)[source]
-datman.scan_list.update_scans_csv(output, new_entries)[source]
+datman.scan_list.update_scans_csv(output, new_entries)[source]
diff --git a/api/datman.scanid.html b/api/datman.scanid.html index 12a775ff..e48828a3 100644 --- a/api/datman.scanid.html +++ b/api/datman.scanid.html @@ -115,25 +115,25 @@
-class datman.scanid.BIDSFile(subject, session, suffix, task=None, acq=None, ce=None, dir=None, rec=None, run=None, echo=None, mod=None)[source]
+class datman.scanid.BIDSFile(subject, session, suffix, task=None, acq=None, ce=None, dir=None, rec=None, run=None, echo=None, mod=None)[source]

Bases: object

-class datman.scanid.DatmanIdentifier(identifier, settings=None)[source]
+class datman.scanid.DatmanIdentifier(identifier, settings=None)[source]

Bases: datman.scanid.Identifier

Parses a datman-style ID into fields.

The datman convention is detailed here

-get_xnat_experiment_id()[source]
+get_xnat_experiment_id()[source]
-get_xnat_subject_id()[source]
+get_xnat_subject_id()[source]
@@ -165,60 +165,60 @@
-class datman.scanid.Identifier[source]
+class datman.scanid.Identifier[source]

Bases: abc.ABC

-get_bids_name()[source]
+get_bids_name()[source]
-get_full_subjectid()[source]
+get_full_subjectid()[source]
-get_full_subjectid_with_timepoint()[source]
+get_full_subjectid_with_timepoint()[source]
-get_full_subjectid_with_timepoint_session()[source]
+get_full_subjectid_with_timepoint_session()[source]
-abstract get_xnat_experiment_id()[source]
+abstract get_xnat_experiment_id()[source]
-abstract get_xnat_subject_id()[source]
+abstract get_xnat_subject_id()[source]
-match(identifier)[source]
+match(identifier)[source]
-class datman.scanid.KCNIIdentifier(identifier, settings=None)[source]
+class datman.scanid.KCNIIdentifier(identifier, settings=None)[source]

Bases: datman.scanid.Identifier

Parses a KCNI style ID into datman-style fields.

The KCNI convention is detailed here.

-get_xnat_experiment_id()[source]
+get_xnat_experiment_id()[source]
-get_xnat_subject_id()[source]
+get_xnat_subject_id()[source]
@@ -245,7 +245,7 @@
-datman.scanid.get_field(match, field, settings=None)[source]
+datman.scanid.get_field(match, field, settings=None)[source]

Find the value of an ID field, allowing for user specified changes.

Parameters
@@ -273,7 +273,7 @@
-datman.scanid.get_kcni_identifier(identifier, settings=None)[source]
+datman.scanid.get_kcni_identifier(identifier, settings=None)[source]

Get a KCNIIdentifier from a valid string or an identifier.

Parameters
@@ -303,39 +303,39 @@
-datman.scanid.get_session_num(ident)[source]
+datman.scanid.get_session_num(ident)[source]

For those times when you always want a numeric session (including for phantoms who are technically always session ‘1’)

-datman.scanid.get_subid(current_subid, settings=None)[source]
+datman.scanid.get_subid(current_subid, settings=None)[source]
-datman.scanid.is_phantom(identifier)[source]
+datman.scanid.is_phantom(identifier)[source]
-datman.scanid.is_scanid(identifier)[source]
+datman.scanid.is_scanid(identifier)[source]
-datman.scanid.is_scanid_with_session(identifier)[source]
+datman.scanid.is_scanid_with_session(identifier)[source]
-datman.scanid.make_filename(ident, tag, series, description, ext=None)[source]
+datman.scanid.make_filename(ident, tag, series, description, ext=None)[source]
-datman.scanid.parse(identifier, settings=None)[source]
+datman.scanid.parse(identifier, settings=None)[source]

Parse a subject ID matching a supported naming convention.

The ‘settings’ flag can be used to exclude any IDs that do not match the specified convention, or to translate certain ID fields to maintain @@ -397,12 +397,12 @@

-datman.scanid.parse_bids_filename(path)[source]
+datman.scanid.parse_bids_filename(path)[source]
-datman.scanid.parse_filename(path)[source]
+datman.scanid.parse_filename(path)[source]

Parse a datman style file name.

Parameters
diff --git a/api/datman.utils.html b/api/datman.utils.html index ce340897..1444dfe8 100644 --- a/api/datman.utils.html +++ b/api/datman.utils.html @@ -107,13 +107,13 @@

A collection of utilities for generally munging imaging data.

-class datman.utils.XNATConnection(xnat_url, user_name, password)[source]
+class datman.utils.XNATConnection(xnat_url, user_name, password)[source]

Bases: object

-class datman.utils.cd(path)[source]
+class datman.utils.cd(path)[source]

Bases: object

A context manager for changing directory. Since best practices dictate returning to the original directory, saves the original directory and @@ -124,7 +124,7 @@

-datman.utils.check_dependency_configured(program_name, shell_cmd=None, env_vars=None)[source]
+datman.utils.check_dependency_configured(program_name, shell_cmd=None, env_vars=None)[source]
<program_name> Name to add to the exception message if the program is

not correctly configured.

@@ -140,12 +140,12 @@
-datman.utils.check_returncode(returncode)[source]
+datman.utils.check_returncode(returncode)[source]
-datman.utils.define_folder(path)[source]
+datman.utils.define_folder(path)[source]

Sets a variable to be the path to a folder. Also, if the folder does not exist, this makes it so, unless we lack the permissions to do so, which leads to a graceful exit.

@@ -153,18 +153,15 @@
-datman.utils.filter_niftis(candidates)[source]
+datman.utils.filter_niftis(candidates)[source]

Takes a list and returns all items that contain the extensions ‘.nii’ or ‘.nii.gz’.

-datman.utils.find_tech_notes(folder)[source]
-

Find any technotes located within a folder.

-

If only one PDF is found it is assumed to be the tech notes. If multiple -are found, unless one contains the string ‘TechNotes’, the first pdf is -guessed to be the tech notes.

+datman.utils.find_tech_notes(folder)[source] +

Find any technotes located within a given folder.

Parameters

folder (str) – A full path to a folder to search.

@@ -184,7 +181,7 @@
-datman.utils.get_all_headers_in_folder(path, recurse=False)[source]
+datman.utils.get_all_headers_in_folder(path, recurse=False)[source]

Get DICOM headers for all files in the given path.

Returns a dictionary mapping path->headers for all files (headers == None for files that are not dicoms).

@@ -192,7 +189,7 @@
-datman.utils.get_archive_headers(path, stop_after_first=False)[source]
+datman.utils.get_archive_headers(path, stop_after_first=False)[source]

Get dicom headers from a scan archive.

Path can be a path to a tarball or zip of dicom folders, or a folder. It is assumed that this archive contains the dicoms from a single exam, organized @@ -206,7 +203,7 @@

-datman.utils.get_extension(path)[source]
+datman.utils.get_extension(path)[source]

Get the filename extension on this path.

This is a slightly more sophisticated version of os.path.splitext in that this will correctly return the extension for ‘.tar.gz’ files, for example. @@ -215,7 +212,7 @@

-datman.utils.get_files_with_tag(parentdir, tag, fuzzy=False)[source]
+datman.utils.get_files_with_tag(parentdir, tag, fuzzy=False)[source]

Returns a list of files that have the specified tag.

Filenames must conform to the datman naming convention (see scanid.parse_filename) in order to be considered.

@@ -225,13 +222,13 @@
-datman.utils.get_folder_headers(path, stop_after_first=False)[source]
+datman.utils.get_folder_headers(path, stop_after_first=False)[source]

Generate a dictionary of subfolders and dicom headers.

-datman.utils.get_loaded_modules()[source]
+datman.utils.get_loaded_modules()[source]

Returns a space separated list of loaded modules

These are modules loaded by the environment-modules system. This function just looks in the LOADEDMODULES environment variable for the list.

@@ -239,17 +236,17 @@
-datman.utils.get_relative_source(source, target)[source]
+datman.utils.get_relative_source(source, target)[source]
-datman.utils.get_resources(open_zipfile)[source]
+datman.utils.get_resources(open_zipfile)[source]
-datman.utils.get_subject_metadata(config=None, study=None, allow_partial=False)[source]
+datman.utils.get_subject_metadata(config=None, study=None, allow_partial=False)[source]

Returns all QC’d session IDs mapped to any blacklisted scans they have

This will collect and organize all checklist and blacklist data for a study. Sessions that do not have a completed checklist entry will have @@ -282,67 +279,67 @@

-datman.utils.get_tarfile_headers(path, stop_after_first=False)[source]
+datman.utils.get_tarfile_headers(path, stop_after_first=False)[source]

Get headers for dicom files within a tarball

-datman.utils.get_xnat_credentials(config, xnat_cred)[source]
+datman.utils.get_xnat_credentials(config, xnat_cred)[source]
-datman.utils.get_zipfile_headers(path, stop_after_first=False)[source]
+datman.utils.get_zipfile_headers(path, stop_after_first=False)[source]

Get headers for a dicom file within a zipfile

-datman.utils.has_permissions(path)[source]
+datman.utils.has_permissions(path)[source]

Checks for write access to submitted path.

-datman.utils.is_dicom(fileobj)[source]
+datman.utils.is_dicom(fileobj)[source]
-datman.utils.is_named_like_a_dicom(path)[source]
+datman.utils.is_named_like_a_dicom(path)[source]
-datman.utils.locate_metadata(filename, study=None, subject=None, config=None, path=None)[source]
+datman.utils.locate_metadata(filename, study=None, subject=None, config=None, path=None)[source]
-datman.utils.make_temp_directory(suffix='', prefix='tmp', path=None)[source]
+datman.utils.make_temp_directory(suffix='', prefix='tmp', path=None)[source]
-datman.utils.make_zip(source_dir, dest_zip)[source]
+datman.utils.make_zip(source_dir, dest_zip)[source]
-datman.utils.makedirs(path)[source]
+datman.utils.makedirs(path)[source]

Make the directory (including parent directories) if they don’t exist

-datman.utils.nifti_basename(fpath)[source]
+datman.utils.nifti_basename(fpath)[source]

return basename without extension (either .nii.gz or .nii)

-datman.utils.read_blacklist(study=None, scan=None, subject=None, config=None, path=None, bids_ses=None, use_bids=False)[source]
+datman.utils.read_blacklist(study=None, scan=None, subject=None, config=None, path=None, bids_ses=None, use_bids=False)[source]

This function is used to look up blacklisted scans. If the dashboard is found it ONLY checks the dashboard database. Otherwise it expects a datman style ‘blacklist’ file on the filesystem.

@@ -380,7 +377,7 @@
-datman.utils.read_checklist(study=None, subject=None, config=None, path=None, bids_id=None, bids_ses=None, use_bids=False)[source]
+datman.utils.read_checklist(study=None, subject=None, config=None, path=None, bids_id=None, bids_ses=None, use_bids=False)[source]

This function is used to look-up QC checklist entries. If the dashboard is found it will ONLY check the dashboard database, otherwise it expects a datman style ‘checklist’ file on the filesystem.

@@ -413,22 +410,22 @@
-datman.utils.read_credentials(cred_file)[source]
+datman.utils.read_credentials(cred_file)[source]
-datman.utils.read_json(path)[source]
+datman.utils.read_json(path)[source]
-datman.utils.remove_empty_files(path)[source]
+datman.utils.remove_empty_files(path)[source]
-datman.utils.run(cmd, dryrun=False, specialquote=True, verbose=True)[source]
+datman.utils.run(cmd, dryrun=False, specialquote=True, verbose=True)[source]

Runs the command in default shell, returning STDOUT and a return code. The return code uses the python convention of 0 for success, non-zero for failure

@@ -436,13 +433,13 @@
-datman.utils.run_dummy_q(list_of_names)[source]
+datman.utils.run_dummy_q(list_of_names)[source]

This holds the script until all of the queued items are done.

-datman.utils.split_path(path)[source]
+datman.utils.split_path(path)[source]

Splits a path into all the component parts, returns a list

>>> split_path('a/b/c/d.txt')
 ['a', 'b', 'c', 'd.txt']
@@ -452,14 +449,14 @@
 
 

 

-datman.utils.splitext(path)[source]

+datman.utils.splitext(path)[source]
 
Function that will remove extension, including specially-defined extensions
 that fool os.path.splitext

 

 
 

 

-datman.utils.submit_job(cmd, job_name, log_dir, system='other', cpu_cores=1, walltime='2:00:00', dryrun=False, partition=None, argslist='', workdir='/tmp')[source]

+datman.utils.submit_job(cmd, job_name, log_dir, system='other', cpu_cores=1, walltime='2:00:00', dryrun=False, partition=None, argslist='', workdir='/tmp')[source]
 
submits a job or joblist the queue depending on the system

 

 
Parameters

@@ -481,12 +478,12 @@
 
 

 

-datman.utils.update_blacklist(entries, study=None, config=None, path=None)[source]

+datman.utils.update_blacklist(entries, study=None, config=None, path=None)[source]
 

 
 

 

-datman.utils.update_checklist(entries, study=None, config=None, path=None)[source]

+datman.utils.update_checklist(entries, study=None, config=None, path=None)[source]
 
Add or update QC checklist entries.

 
This will preferentially update the dashboard database (ignoring any
 ‘checklist.csv’ files) unless the dashboard is not installed or a specific
@@ -513,7 +510,7 @@
 
 

 

-datman.utils.validate_subject_id(subject_id, config)[source]

+datman.utils.validate_subject_id(subject_id, config)[source]
 
Ensures subject ID correctness based on configuration settings.

 

 
This checks that a given ID:
    
@@ -551,12 +548,12 @@
 
 
    
 
    
-datman.utils.write_json(path, contents)[source]
    
+datman.utils.write_json(path, contents)[source]
 
    
 
 
    
 
    
-datman.utils.write_metadata(lines, path, retry=3)[source]
    
+datman.utils.write_metadata(lines, path, retry=3)[source]
 
    Repeatedly attempts to write lines to <path>. The destination file
 will be overwritten with <lines> so any contents you wish to preserve
 should be contained within the list.
    
diff --git a/api/datman.xnat.html b/api/datman.xnat.html
index d8e75be5..e1a90910 100644
--- a/api/datman.xnat.html
+++ b/api/datman.xnat.html
@@ -107,11 +107,11 @@
 
    Module to interact with the xnat server
    
 
    
 
    
-class datman.xnat.XNATExperiment(project, subject_name, experiment_json)[source]
    
+class datman.xnat.XNATExperiment(project, subject_name, experiment_json)[source]
 
    Bases: datman.xnat.XNATObject
    
 
    
 
    
-assign_scan_names(config, ident)[source]
    
+assign_scan_names(config, ident)[source]
 
    Assign a datman style name to each scan in this experiment.
    
 
    This will populate the XnatScan.names and XnatScan.tags fields
 for any scan that matches the study’s export configuration.
    
@@ -129,7 +129,7 @@
 
 
    
 
    
-download(xnat, dest_folder, zip_name=None)[source]
    
+download(xnat, dest_folder, zip_name=None)[source]
 
    Download a zip file containing all data for this session. Returns the
 path to the new file if download is successful, raises an exception if
 not
    
@@ -148,7 +148,7 @@
 
 
    
 
    
-get_autorun_ids(xnat)[source]
    
+get_autorun_ids(xnat)[source]
 
    Find the ID(s) of the ‘autorun.xml’ workflow
    
 
    XNAT has this obnoxious, on-by-default and seemingly impossible to
 disable, ‘workflow’ called AutoRun.xml. It appears to do nothing other
@@ -178,13 +178,13 @@
 
 
    
 
    
-get_resources(xnat_connection)[source]
    
+get_resources(xnat_connection)[source]
 
    Returns a list of all resource URIs from this session.
    
 
    
 
 
    
 
    
-is_shared()[source]
    
+is_shared()[source]
 
    Detect if the experiment is shared from another XNAT Project.
    
 
    Shared sessions have identical metadata to their source sessions,
 the only way to tell a link apart from source data is to look for a
@@ -195,17 +195,17 @@
 
 
    
 
    
-class datman.xnat.XNATObject[source]
    
+class datman.xnat.XNATObject[source]
 
    Bases: abc.ABC
    
 
    
 
 
    
 
    
-class datman.xnat.XNATScan(experiment, scan_json)[source]
    
+class datman.xnat.XNATScan(experiment, scan_json)[source]
 
    Bases: datman.xnat.XNATObject
    
 
    
 
    
-download(xnat_conn, output_dir)[source]
    
+download(xnat_conn, output_dir)[source]
 
    Download all dicoms for this series.
    
 
    This will download all files in the series, and if successful,
 set the download_dir attribute to the destination folder.
    
@@ -229,50 +229,50 @@
 
 
    
 
    
-is_derived()[source]
    
+is_derived()[source]
 
    
 
 
    
 
    
-is_multiecho()[source]
    
+is_multiecho()[source]
 
    
 
 
    
 
    
-is_usable(strict=False)[source]
    
+is_usable(strict=False)[source]
 
    
 
 
    
 
    
-raw_dicoms_exist()[source]
    
+raw_dicoms_exist()[source]
 
    
 
 
    
 
    
-set_datman_name(base_name, tags)[source]
    
+set_datman_name(base_name, tags)[source]
 
    
 
 
    
 
    
-set_tag(tag_map)[source]
    
+set_tag(tag_map)[source]
 
    
 
 
    
 
 
    
 
    
-class datman.xnat.XNATSubject(subject_json)[source]
    
+class datman.xnat.XNATSubject(subject_json)[source]
 
    Bases: datman.xnat.XNATObject
    
 
    
 
 
    
 
    
-datman.xnat.get_auth(username=None, file_path=None)[source]
    
+datman.xnat.get_auth(username=None, file_path=None)[source]
 
    
 
 
    
 
    
-datman.xnat.get_connection(config, site=None, url=None, auth=None, server_cache=None)[source]
    
+datman.xnat.get_connection(config, site=None, url=None, auth=None, server_cache=None)[source]
 
    Create (or retrieve) a connection to an XNAT server
    
 
    
 
    Parameters
    
@@ -307,19 +307,19 @@
 
 
    
 
    
-datman.xnat.get_port_str(config=None, port=None)[source]
    
+datman.xnat.get_port_str(config=None, port=None)[source]
 
    Returns a port string of the format :portnum
    
 
    Will raise KeyError if port is None and config file doesn’t define XnatPort
    
 
    
 
 
    
 
    
-datman.xnat.get_server(config=None, url=None, port=None)[source]
    
+datman.xnat.get_server(config=None, url=None, port=None)[source]
 
    
 
 
    
 
    
-class datman.xnat.xnat(server, username, password)[source]
    
+class datman.xnat.xnat(server, username, password)[source]
 
    Bases: object
    
 
    
 
    
@@ -328,19 +328,19 @@
 
 
    
 
    
-create_resource_folder(study, session, experiment, label)[source]
    
+create_resource_folder(study, session, experiment, label)[source]
    
 
    Creates a resource subfolder and returns the xnat identifier.
    
 
    
 
 
    
 
    
-delete_resource(project, session, experiment, resource_group_id, resource_id, retries=3)[source]
    
+delete_resource(project, session, experiment, resource_group_id, resource_id, retries=3)[source]
 
    Delete a resource file from xnat
    
 
    
 
 
    
 
    
-dismiss_autorun(experiment)[source]
    
+dismiss_autorun(experiment)[source]
 
    Mark the AutoRun.xml pipeline as finished.
    
 
    AutoRun.xml gets stuck as ‘Queued’ and can cause failures at renaming
 and deletion. This marks the pipeline as ‘Complete’ to prevent it from
@@ -355,7 +355,7 @@
 
 
    
 
    
-find_project(subject_id, projects=None)[source]
    
+find_project(subject_id, projects=None)[source]
 
    Find the project a subject belongs to.
    
 
    
 
    Parameters
    
@@ -381,7 +381,7 @@
 
 
    
 
    
-find_subject(project, exper_id)[source]
    
+find_subject(project, exper_id)[source]
 
    Find the parent subject ID for an experiment.
    
 
    
 
    Parameters
    
@@ -407,7 +407,7 @@
 
 
    
 
    
-get_dicom(project, session, experiment, scan, filename=None, retries=3)[source]
    
+get_dicom(project, session, experiment, scan, filename=None, retries=3)[source]
 
    Downloads a dicom file from xnat to filename
 If filename is not specified creates a temporary file
 and returns the path to that, user needs to be responsible
@@ -416,7 +416,7 @@
 
 
    
 
    
-get_experiment(project, subject_id, exper_id, create=False)[source]
    
+get_experiment(project, subject_id, exper_id, create=False)[source]
 
    Get an experiment from the XNAT server.
    
 
    
 
    Parameters
    
@@ -447,7 +447,7 @@
 
 
    
 
    
-get_experiment_ids(project, subject='')[source]
    
+get_experiment_ids(project, subject='')[source]
 
    Retrieve all experiment IDs belonging to an XNAT subject.
    
 
    
 
    Parameters
    
@@ -471,7 +471,7 @@
 
 
    
 
    
-get_projects(project='')[source]
    
+get_projects(project='')[source]
 
    Query the XNAT server for project metadata.
    
 
    
 
    Parameters
    
@@ -500,7 +500,7 @@
 
 
    
 
    
-get_resource(project, session, experiment, resource_group_id, resource_id, filename=None, retries=3, zipped=True)[source]
    
+get_resource(project, session, experiment, resource_group_id, resource_id, filename=None, retries=3, zipped=True)[source]
 
    Download a single resource from xnat to filename
 If filename is not specified creates a temporary file and
 returns the path to that, user needs to be responsible for
@@ -509,7 +509,7 @@
 
 
    
 
    
-get_resource_archive(project, session, experiment, resource_id, filename=None, retries=3)[source]
    
+get_resource_archive(project, session, experiment, resource_id, filename=None, retries=3)[source]
 
    Download a resource archive from xnat to filename
 If filename is not specified creates a temporary file and
 returns the path to that, user needs to be responsible format
@@ -518,20 +518,20 @@
 
 
    
 
    
-get_resource_ids(study, session, experiment, folderName=None, create=True)[source]
    
+get_resource_ids(study, session, experiment, folderName=None, create=True)[source]
 
    Return a list of resource id’s (subfolders) from an experiment
    
 
    
 
 
    
 
    
-get_resource_list(study, session, experiment, resource_id)[source]
    
+get_resource_list(study, session, experiment, resource_id)[source]
 
    The list of non-dicom resources associated with an experiment
 returns a list of dicts, mostly interested in ID and name
    
 
    
 
 
    
 
    
-get_scan(project, subject_id, exper_id, scan_id)[source]
    
+get_scan(project, subject_id, exper_id, scan_id)[source]
 
    Get a scan from the XNAT server.
    
 
    
 
    Parameters
    
@@ -561,7 +561,7 @@
 
 
    
 
    
-get_scan_ids(project, subject, experiment)[source]
    
+get_scan_ids(project, subject, experiment)[source]
 
    Retrieve all scan IDs for an XNAT experiment.
    
 
    
 
    Parameters
    
@@ -585,7 +585,7 @@
 
 
    
 
    
-get_subject(project, subject_id, create=False)[source]
    
+get_subject(project, subject_id, create=False)[source]
 
    Get a subject from the XNAT server.
    
 
    
 
    Parameters
    
@@ -615,7 +615,7 @@
 
 
    
 
    
-get_subject_ids(project)[source]
    
+get_subject_ids(project)[source]
 
    Retrieve the IDs for all subjects within an XNAT project.
    
 
    
 
    Parameters
    
@@ -640,7 +640,7 @@
 
 
    
 
    
-make_experiment(project, subject, experiment)[source]
    
+make_experiment(project, subject, experiment)[source]
 
    Make a new (empty) experiment on the XNAT server.
    
 
    
 
    Parameters
    
@@ -658,7 +658,7 @@
 
 
    
 
    
-make_subject(project, subject)[source]
    
+make_subject(project, subject)[source]
 
    Make a new (empty) subject on the XNAT server.
    
 
    
 
    Parameters
    
@@ -675,20 +675,20 @@
 
 
    
 
    
-open_session()[source]
    
+open_session()[source]
 
    Open a session with the XNAT server.
    
 
    
 
 
    
 
    
-put_dicoms(project, subject, experiment, filename, retries=3)[source]
    
+put_dicoms(project, subject, experiment, filename, retries=3)[source]
 
    Upload an archive of dicoms to XNAT
 filename: archive to upload
    
 
    
 
 
    
 
    
-put_resource(project, subject, experiment, filename, data, folder, retries=3)[source]
    
+put_resource(project, subject, experiment, filename, data, folder, retries=3)[source]
 
    POST a resource file to the xnat server
    
 
    
 
    Parameters
    
@@ -703,7 +703,7 @@
 
 
    
 
    
-rename_experiment(project, subject, old_name, new_name)[source]
    
+rename_experiment(project, subject, old_name, new_name)[source]
 
    Change an experiment’s name on XNAT.
    
 
    
 
    Parameters
    
@@ -731,7 +731,7 @@
 
 
    
 
    
-rename_subject(project, old_name, new_name, rename_exp=False)[source]
    
+rename_subject(project, old_name, new_name, rename_exp=False)[source]
 
    Change a subjects’s name on XNAT.
    
 
    
 
    Parameters
    
diff --git a/searchindex.js b/searchindex.js
index c4bd1082..41c89d13 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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14,url:[14,17],us:[0,3,5,7,9,11,12,13,14,16,17,18,19,20,22],use_bid:[6,13],user:[12,14,17,18,20,22],user_nam:13,usernam:[14,17,20,22],usesredcap:17,usual:17,ut1:[12,17],ut2:[12,17],util:[1,2,8,20],uto:[12,17],v:20,valid:[6,10,12,14],validate_subject_id:13,valu:[0,3,8,10,12,13,17,18,19],variabl:[3,13,14,15,17,20,22],variou:17,vector:[0,19],verbos:13,veri:16,verifi:13,verify_standard:7,versa:17,version:[13,15,16,22],versu:14,vice:17,visual:9,voxel:[0,19],wa:[0,3,6,13,14,17,18,19],wai:[11,14,17,20],wait:4,walltim:13,want:[12,13,20],warn:10,we:[0,13,16,19],weight:[0,19],welcom:16,well:[4,22],were:[13,17],what:[0,16,17,19],whatev:[17,18],when:[0,4,11,12,13,14,16,17,18,19],whenev:[6,16],where:[3,6,10,11,13,14,17],whether:[6,13,14,17],which:[0,3,6,13,17,18,19],who:[12,13,17,20],whole:[0,19],why:18,wide:[3,14],width:9,wish:13,within:[4,12,13,14,17,18,20],without:[0,3,6,13,16,19,20],work:[4,6,13,17,22],workdir:13,workflow:14,would:17,wrap:4,wrapper:3,write:[0,6,9,13,16,17,19],write_diff_log:8,write_json:13,write_manifest:9,write_metadata:13,wrong:[11,18],www:[0,19],x:13,xml:14,xnat:[0,1,2,3,5,6,19,20,22],xnat_conn:14,xnat_connect:14,xnat_cr:13,xnat_fetch_sess:[17,19],xnat_pass:[17,20,22],xnat_url:13,xnat_us:[17,20,22],xnatarch:17,xnatconnect:13,xnatconvent:17,xnatcredenti:17,xnatexcept:[5,14],xnatexperi:[6,14],xnatlogin:17,xnatobject:14,xnatport:[14,17],xnatscan:14,xnatserv:17,xnatsourc:[17,22],xnatsourcearch:17,xnatsourcecredenti:17,xnatsubject:14,xxx:17,yaml:[3,17],yet:13,yml:[17,20],you:[0,3,12,13,16,17,18,19,20],your:[0,16,17,19,20],yrk:17,z0:12,z:12,zero:13,zip:[11,13,14,17,18,22],zip_fil:11,zip_nam:14,zipfil:[0,13,14,19]},titles:["Introduction","Library API (application program interface)","datman package","datman.config module","datman.dashboard module","datman.exceptions module","datman.exporters module","datman.fs_log_scraper module","datman.header_checks module","datman.metrics module","datman.scan module","datman.scan_list module","datman.scanid module","datman.utils module","datman.xnat module","What\u2019s new?","Contributing to Datman","Configuration Files","Other important files","datman","Installation","<no title>","Script 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\ No newline at end of file
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3,5,7,9,11,12,13,14,16,17,18,19,20,22],use_bid:[6,13],user:[12,14,17,18,20,22],user_nam:13,usernam:[14,17,20,22],usesredcap:17,usual:17,ut1:[12,17],ut2:[12,17],util:[1,2,8,20],uto:[12,17],v:20,valid:[6,10,12,14],validate_subject_id:13,valu:[0,3,8,10,12,13,17,18,19],variabl:[3,13,14,15,17,20,22],variou:17,vector:[0,19],verbos:13,veri:16,verifi:13,verify_standard:7,versa:17,version:[13,15,16,22],versu:14,vice:17,visual:9,voxel:[0,19],wa:[0,3,6,13,14,17,18,19],wai:[11,14,17,20],wait:4,walltim:13,want:[12,13,20],warn:10,we:[0,13,16,19],weight:[0,19],welcom:16,well:[4,22],were:[13,17],what:[0,16,17,19],whatev:[17,18],when:[0,4,11,12,13,14,16,17,18,19],whenev:[6,16],where:[3,6,10,11,13,14,17],whether:[6,13,14,17],which:[0,3,6,13,17,18,19],who:[12,13,17,20],whole:[0,19],why:18,wide:[3,14],width:9,wish:13,within:[4,12,13,14,17,18,20],without:[0,3,6,13,16,19,20],work:[4,6,13,17,22],workdir:13,workflow:14,would:17,wrap:4,wrapper:3,write:[0,6,9,13,16,17,19],write_diff_log:8,write_json:13,write_manifest:9,write_metadata:13,wrong:[11,18],www:[0,19],x:13,xml:14,xnat:[0,1,2,3,5,6,19,20,22],xnat_conn:14,xnat_connect:14,xnat_cr:13,xnat_fetch_sess:[17,19],xnat_pass:[17,20,22],xnat_url:13,xnat_us:[17,20,22],xnatarch:17,xnatconnect:13,xnatconvent:17,xnatcredenti:17,xnatexcept:[5,14],xnatexperi:[6,14],xnatlogin:17,xnatobject:14,xnatport:[14,17],xnatscan:14,xnatserv:17,xnatsourc:[17,22],xnatsourcearch:17,xnatsourcecredenti:17,xnatsubject:14,xxx:17,yaml:[3,17],yet:13,yml:[17,20],you:[0,3,12,13,16,17,18,19,20],your:[0,16,17,19,20],yrk:17,z0:12,z:12,zero:13,zip:[11,13,14,17,18,22],zip_fil:11,zip_nam:14,zipfil:[0,13,14,19]},titles:["Introduction","Library API (application program interface)","datman package","datman.config module","datman.dashboard module","datman.exceptions module","datman.exporters module","datman.fs_log_scraper module","datman.header_checks module","datman.metrics module","datman.scan module","datman.scan_list module","datman.scanid module","datman.utils module","datman.xnat module","What\u2019s new?","Contributing to Datman","Configuration Files","Other important files","datman","Installation","<no title>","Script Overview"],titleterms:{"export":6,"import":18,"new":15,api:1,applic:1,blacklist:[17,18],checklist:18,config:3,configur:17,contain:20,contribut:16,control:[0,19],csv:18,dashboard:4,datman:[0,2,3,4,5,6,7,8,9,10,11,12,13,14,16,19],dcm2bid:18,dm_blacklist_rm:22,dm_link:22,dm_link_shared_id:22,dm_parse_fac:22,dm_qc_report:22,dm_redcap_scan_complet:22,dm_sftp:22,dm_task_fil:22,dm_xnat_extract:22,dm_xnat_upload:22,docker:20,exampl:[17,18],except:5,exportinfo:17,exportset:17,extern:18,file:[17,18],fs_log_scrap:7,ftp:17,glossari:17,gold:17,header_check:8,idmap:17,indic:19,instal:20,interfac:1,introduct:[0,19],json:18,librari:1,link:18,log:17,metadata:17,metric:9,modul:[3,4,5,6,7,8,9,10,11,12,13,14],option:17,other:18,overrid:17,overview:[0,19,22],packag:2,path:17,pattern:17,program:1,project:17,qualiti:[0,19],redcap:17,requir:17,s:15,scan:[10,18],scan_list:11,scanid:12,script:22,set:17,site:17,standard:17,studi:17,submodul:2,systemset:17,tabl:19,task:17,util:13,what:15,xnat:[14,17],xnat_fetch_sess:22}})
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