Add flag for ezBIDS (#336)

* Added flag for ezbids conversion

This will ensure that AcqusitionDate and AcqusitionTime are
included in the sidecar jsons.

* bump version create new release/tag

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -175,6 +175,7 @@ def __init__(
         file_format="%p_%i_%t_%s",
         silent=False,
         tempdir_location=None,
+        ezbids=False
     ):
         """
         This class is a simple wrapper for dcm2niix and contains methods to do the following in order:
@@ -215,6 +216,7 @@ def __init__(
         self.blood_json = None
         self.blood_tsv = None
         self.telemetry_data = {}
+        self.ezbids=ezbids
         self.dcm2niix_path = self.check_for_dcm2niix()
         if not self.dcm2niix_path:
             logger.error(
@@ -589,6 +591,7 @@ def run_dcm2niix(self):
                             check_for_missing,
                             dicom_header,
                             dicom2bids_json=metadata_dictionaries["dicom2bids"],
+                            ezbids=self.ezbids,
                             **self.additional_arguments,
                         )
 
@@ -1162,6 +1165,13 @@ def cli():
         "This information helps to improve PET2BIDS and provides an indicator of real world "
         "usage crucial for obtaining funding.",
     )
+    parser.add_argument(
+        "--ezbids",
+        action="store_true",
+        default=False,
+        help="Add fields to json output that are useful for ezBIDS or other conversion software. This will de-anonymize"
+             " pet2bids output and add AcquisitionDate an AcquisitionTime into the output json."
+    )
     return parser
 
 
@@ -1328,6 +1338,7 @@ def main():
             additional_arguments=cli_args.kwargs,
             tempdir_location=cli_args.tempdir,
             silent=cli_args.silent,
+            ezbids=cli_args.ezbids,
         )
 
         if cli_args.trc:

pypet2bids/pypet2bids/update_json_pet_file.py

@@ -149,6 +149,7 @@ def update_json_with_dicom_value(
     dicom_header,
     dicom2bids_json=None,
     silent=True,
+    ezbids=False,
     **additional_arguments,
 ):
     """
@@ -160,6 +161,9 @@ def update_json_with_dicom_value(
     :param missing_values: dictionary output from check_json indicating missing fields and/or values
     :param dicom_header: the dicom or dicoms that may contain information not picked up by dcm2niix
     :param dicom2bids_json: a json file that maps dicom header entities to their corresponding BIDS entities
+    :param silent: run silently without error, status, or warning messages
+    :param ezbids: boolean to supply additional data that ezbids or other software requires, defaults to false. When
+    true the sidecar json will be updated with AcquisitionDate, AcquisitionTime, and AcquisitionDateTime
     :return: a dictionary of successfully updated (written to the json file) fields and values
     """
 
@@ -297,6 +301,20 @@ def update_json_with_dicom_value(
     # remove scandate if it exists
     json_updater.remove("ScanDate")
 
+    # lastly if ezbids is true update the sidecar with acquisition data
+    if ezbids:
+        acquisition_date = parser.parse(dicom_header.get("AcquisitionDate", ""))
+        acquisition_time = parser.parse(dicom_header.get("AcquisitionTime", ""))
+        if acquisition_time and acquisition_date:
+            acquisition_datetime = datetime.datetime.combine(acquisition_date.date(), acquisition_time.time())
+        else:
+            acquisition_datetime = "0000-00-00T00:00:00"
+        json_updater.update(
+            {"AcquisitionDate": f"{acquisition_date.date()}",
+             "AcquisitionTime": f"{acquisition_time.time()}",
+             "AcquisitionDateTime": f"{acquisition_datetime.isoformat()}"
+             })
+
     # after updating raise warnings to user if values in json don't match values in dicom headers, only warn!
     updated_values = json.load(open(path_to_json, "r"))
     for key, value in paired_fields.items():

pypet2bids/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.3.17"
+version = "1.4.0"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <[email protected]>"]
 license = "MIT"