From 8ddf7f8ab0e16080d7b7409b643527ac942a3375 Mon Sep 17 00:00:00 2001 From: Dan Levitas Date: Tue, 20 Aug 2024 18:39:07 +0000 Subject: [PATCH] [ENH] Add BIDS URI option for IntendedFor mapping --- handler/convert.js | 6 +++++ handler/ezBIDS_core/ezBIDS_core.py | 43 +++++++++++++++++++----------- ui/src/Finalize.vue | 1 + ui/src/SeriesPage.vue | 17 ++++++++++-- ui/src/store/index.ts | 2 ++ 5 files changed, 52 insertions(+), 17 deletions(-) diff --git a/handler/convert.js b/handler/convert.js index 5a67e853..d01b5243 100755 --- a/handler/convert.js +++ b/handler/convert.js @@ -187,6 +187,9 @@ async.forEachOf(info.objects, (o, idx, next_o) => { } path += tokens.join("_"); path += "_" + suffix + ".nii.gz"; //TODO - not sure if this is robust enough.. + if (info.BIDSURI === true) { + path = "bids::" + "sub-" + io._entities.subject + "/" + path + } item.sidecar.IntendedFor.push(path); } } @@ -387,6 +390,9 @@ async.forEachOf(info.objects, (o, idx, next_o) => { } path += tokens.join("_"); path += "_" + suffix + ".nii.gz"; //TODO - not sure if this is robust enough.. + if (info.BIDSURI === true) { + path = "bids::" + "sub-" + io._entities.subject + "/" + path + } item.sidecar.IntendedFor.push(path); } } diff --git a/handler/ezBIDS_core/ezBIDS_core.py b/handler/ezBIDS_core/ezBIDS_core.py index ed0f8135..d3576bbf 100755 --- a/handler/ezBIDS_core/ezBIDS_core.py +++ b/handler/ezBIDS_core/ezBIDS_core.py @@ -473,7 +473,12 @@ def modify_uploaded_dataset_list(uploaded_img_list): config_file = "" exclude_data = False - config_file_list = natsorted([x for x in os.listdir(DATA_DIR) if x.endswith('ezBIDS_template.json')]) + config_file_list = [] + for root, dirs, files in os.walk(DATA_DIR): + for file in files: + if file.endswith('ezBIDS_template.json'): + config_file_list.append(os.path.join(root, file)) + if len(config_file_list): # Ideally only one config file uploaded, but if multiple configurations found, select last one (most recent?) config = True @@ -1392,7 +1397,7 @@ def determine_sub_ses_IDs(dataset_list, bids_compliant): List of dictionaries containing pertinent and unique information about the data, primarily coming from the metadata in the json files. - subjects_information : list + subs_information : list List of dictionaries containing subject identification info, such as PatientID, PatientName, PatientBirthDate, and corresponding session information. @@ -1402,7 +1407,7 @@ def determine_sub_ses_IDs(dataset_list, bids_compliant): """ date_counter = 1 subject_idx_counter = 0 - subjects_information = [] + subs_information = [] participants_info = {} # Determine unique subjects from uploaded dataset for sub in np.unique([x["subject"] for x in dataset_list]): @@ -1550,9 +1555,9 @@ def determine_sub_ses_IDs(dataset_list, bids_compliant): "validationErrors": [] } - subjects_information.append(subject_ids_info) + subs_information.append(subject_ids_info) - return dataset_list, subjects_information, participants_info + return dataset_list, subs_information, participants_info def determine_unique_series(dataset_list, bids_compliant): @@ -1638,7 +1643,7 @@ def determine_unique_series(dataset_list, bids_compliant): return dataset_list, dataset_list_unique_series -def template_configuration(dataset_list_unique_series, subjects_information, config_file): +def template_configuration(dataset_list_unique_series, subs_information, config_file): """ Parameters ---------- @@ -1646,7 +1651,7 @@ def template_configuration(dataset_list_unique_series, subjects_information, con A modified version of dataset_list, where this list contains only the dictionaries of acquisitions with a unique series group ID. - subjects_information : list + subs_information : list List of dictionaries containing subject identification info, such as PatientID, PatientName, PatientBirthDate, and corresponding session information. @@ -1669,13 +1674,16 @@ def template_configuration(dataset_list_unique_series, subjects_information, con A modified version of dataset_list, where this list contains only the dictionaries of acquisitions with a unique series group ID. - subjects_information : list + subs_information : list List of dictionaries containing subject identification info, such as PatientID, PatientName, PatientBirthDate, and corresponding session information. events : dictionary Information pertaining to the events timing files for func/bold data. + + bids_uri : boolean + Specifies whether or not user wants BIDS URI format for IntendedFor metadata mapping """ config_data = open(config_file) @@ -1687,6 +1695,7 @@ def template_configuration(dataset_list_unique_series, subjects_information, con subjects_sessions_info = config_data["subjects"] config_dataset_list_unique_series = config_data["series"] config_dataset_list_objects = config_data["objects"] + bids_uri = config_data["BIDSURI"] # Try to determine subject (and session) mapping from what's in the configuration match_start_index = None @@ -1712,7 +1721,7 @@ def template_configuration(dataset_list_unique_series, subjects_information, con "AcquisitionDateTime" ] - for sub_info in subjects_information: + for sub_info in subs_information: sub = sub_info["subject"] for key in ref_patient_info.keys(): if ref_subject_id in ref_patient_info[key]: @@ -1819,7 +1828,7 @@ def template_configuration(dataset_list_unique_series, subjects_information, con events["sampleValues"] = {} return (readme, dataset_description_dic, participants_column_info, - dataset_list_unique_series, subjects_information, events) + dataset_list_unique_series, subs_information, events, bids_uri) def create_lookup_info(): @@ -3106,15 +3115,15 @@ def check_dwi_b0maps(dataset_list_unique_series): dataset_list = organize_dataset(dataset_list) # Determine subject (and session) information -dataset_list, subjects_information, participants_info = determine_sub_ses_IDs(dataset_list, bids_compliant) +dataset_list, subs_information, participants_info = determine_sub_ses_IDs(dataset_list, bids_compliant) # Make a new list containing the dictionaries of only unique dataset acquisitions dataset_list, dataset_list_unique_series = determine_unique_series(dataset_list, bids_compliant) # If ezBIDS configuration file detected in upload, use that for datatype, suffix, and entity identifications if config is True: - readme, dataset_description_dic, participants_column_info, dataset_list_unique_series, subjects_information, events = \ - template_configuration(dataset_list_unique_series, subjects_information, config_file) + readme, dataset_description_dic, participants_column_info, dataset_list_unique_series, subs_information, events, \ + bids_uri = template_configuration(dataset_list_unique_series, subs_information, config_file) else: # README @@ -3160,6 +3169,9 @@ def check_dwi_b0maps(dataset_list_unique_series): } } + # BIDS URI + bids_uri = False + # Generate lookup information directory to help with datatype and suffix identification (and to some degree, entities) lookup_dic = create_lookup_info() @@ -3212,12 +3224,13 @@ def check_dwi_b0maps(dataset_list_unique_series): EZBIDS = { "readme": readme, "datasetDescription": dataset_description_dic, - "subjects": subjects_information, + "subjects": subs_information, "participantsColumn": participants_column_info, "participantsInfo": participants_info, "series": ui_series_info_list, "objects": objects_list, - "events": events + "events": events, + "BIDSURI": bids_uri } # Write dictionary to ezBIDS_core.json diff --git a/ui/src/Finalize.vue b/ui/src/Finalize.vue index 24e2033f..dae1ae24 100755 --- a/ui/src/Finalize.vue +++ b/ui/src/Finalize.vue @@ -204,6 +204,7 @@ export default defineComponent({ //things that convert.ts uses objects: this.ezbids.objects, //most important thing that convert.ts needs + BIDSURI: this.ezbids.BIDSURI, events: this.ezbids.events, entityMappings, //helps with convert datasetDescription: this.ezbids.datasetDescription, diff --git a/ui/src/SeriesPage.vue b/ui/src/SeriesPage.vue index 852919b3..04ff3cc6 100755 --- a/ui/src/SeriesPage.vue +++ b/ui/src/SeriesPage.vue @@ -48,6 +48,9 @@ The information you specify here will be applied to all subjects that uses matching SeriesDescription. You can also override this information later for each subject.

+ + Use BIDS URI format for IntendedFor metadata mapping (if applicable) +
< Please select a series to view/edit
@@ -308,7 +311,7 @@ import ModalityForm from './components/modalityForm.vue'; import { prettyBytes } from './filters'; -import { Series, IObject } from './store'; +import { Series, IObject, IEzbids } from './store'; import { validateEntities, validate_B0FieldIdentifier_B0FieldSource, metadataAlerts } from './libUnsafe'; import anatYaml from '../src/assets/schema/rules/sidecars/anat.yaml'; @@ -378,6 +381,16 @@ export default defineComponent({ this.showInfo[entity] = !this.showInfo[entity]; }, + BIDSURI($root: IEzbids, b: boolean) { + if (b === true) { + $root.BIDSURI = true; + localStorage.setItem('checkboxState', 'true'); + } else { + $root.BIDSURI = false; + localStorage.setItem('checkboxState', 'false'); + } + }, + validate(s: Series | null) { if (!s) return; @@ -389,7 +402,7 @@ export default defineComponent({ validate_B0FieldIdentifier_B0FieldSource(s); } - /* Alert users to metadata issues, such as missing required fields or + /* Alert users to metadata issues, such as missing required fields or improperly-formmated metadata field values. */ let bidsDatatypeMetadata = {}; diff --git a/ui/src/store/index.ts b/ui/src/store/index.ts index d8efe742..f353c66a 100755 --- a/ui/src/store/index.ts +++ b/ui/src/store/index.ts @@ -314,6 +314,7 @@ const state = { subjects: [] as Subject[], series: [] as Series[], objects: [] as IObject[], + BIDSURI: false, _organized: [] as OrganizedSubject[], //above things are organized into subs/ses/run/object hierarchy for quick access @@ -509,6 +510,7 @@ const store = createStore({ subjects: [], series: [], objects: [], + BIDSURI: false, _organized: [], //above things are organized into subs/ses/run/object hierarchy for quick access