Merge pull request #207 from arnaudbore/add_feature_intended_for

Upgrade feature Intended for

dcm2bids/acquisition.py

@@ -26,8 +26,8 @@ def __init__(
         participant,
         dataType,
         modalityLabel,
-        indexSidecar=None,
         customLabels="",
+        id=None,
         srcSidecar=None,
         sidecarChanges=None,
         intendedFor=None,
@@ -38,8 +38,8 @@ def __init__(
 
         self._modalityLabel = ""
         self._customLabels = ""
+        self._id = ""
         self._intendedFor = None
-        self._indexSidecar = None
 
         self.participant = participant
         self.dataType = dataType
@@ -57,6 +57,11 @@ def __init__(
         else:
             self.intendedFor = intendedFor
 
+        if id is None:
+            self.id = None
+        else:
+            self.id = id
+
         self.dstFile = ''
 
     def __eq__(self, other):
@@ -79,6 +84,18 @@ def modalityLabel(self, modalityLabel):
         """ Prepend '_' if necessary"""
         self._modalityLabel = self.prepend(modalityLabel)
 
+    @property
+    def id(self):
+        """
+        Returns:
+            A string '_<id>'
+        """
+        return self._id
+
+    @id.setter
+    def id(self, value):
+        self._id = value
+
     @property
     def customLabels(self):
         """
@@ -191,23 +208,7 @@ def intendedFor(self, value):
         else:
             self._intendedFor = [value]
 
-    @property
-    def indexSidecar(self):
-        """
-        Returns:
-            A int '_<indexSidecar>'
-        """
-        return self._indexSidecar
-
-    @indexSidecar.setter
-    def indexSidecar(self, value):
-        """
-        Returns:
-            A int '_<indexSidecar>'
-        """
-        self._indexSidecar = value
-
-    def dstSidecarData(self, descriptions, intendedForList):
+    def dstSidecarData(self, intendedForList):
         """
         """
         data = self.srcSidecar.origData
@@ -218,12 +219,14 @@ def dstSidecarData(self, descriptions, intendedForList):
             intendedValue = []
 
             for index in self.intendedFor:
-                intendedValue = intendedValue + intendedForList[index]
-
-            if len(intendedValue) == 1:
-                data["IntendedFor"] = intendedValue[0]
-            else:
-                data["IntendedFor"] = intendedValue
+                if index in intendedForList:
+                    intendedValue = intendedValue + [intendedForList[index]]
+                else:
+                    logging.warning(f"No id found for IntendedFor value '{index}'.")
+                    logging.warning(f"No sidecar changes for field IntendedFor will be made for json file {self.dstFile}.json with this id.")
+                    logging.warning("Check: https://unfmontreal.github.io/Dcm2Bids/docs/how-to/create-config-file/#id-and-intendedFor.\n")
+
+            data["IntendedFor"] = [item for sublist in intendedValue for item in sublist]
 
         # sidecarChanges
         for key, value in self.sidecarChanges.items():

dcm2bids/cli/dcm2bids.py

@@ -8,10 +8,10 @@
 import argparse
 
 from dcm2bids.dcm2bids_gen import Dcm2BidsGen
-from dcm2bids.utils.tools import check_latest
 from dcm2bids.utils.utils import DEFAULT
 from dcm2bids.version import __version__
 
+
 def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.doc,
                                 formatter_class=argparse.RawTextHelpFormatter)
@@ -71,9 +71,6 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    check_latest()
-    check_latest("dcm2niix")
-
     app = Dcm2BidsGen(**vars(args))
     return app.run()
 

dcm2bids/dcm2bids_gen.py

@@ -4,7 +4,6 @@
 Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
 """
 
-import argparse
 import logging
 import os
 from pathlib import Path
@@ -22,6 +21,7 @@
 from dcm2bids.utils.tools import check_latest, dcm2niix_version
 from dcm2bids.version import __version__
 
+
 class Dcm2BidsGen(object):
     """ Object to handle dcm2bids execution steps
 
@@ -75,7 +75,6 @@ def __init__(
         self.logger.info("BIDS directory: %s", os.path.realpath(output_dir))
         self.logger.info("Validate BIDS: %s", self.bids_validate)
 
-
     @property
     def dicomDirs(self):
         """List of DICOMs directories"""
@@ -133,7 +132,7 @@ def run(self):
 
         self.logger.info("moving acquisitions into BIDS folder")
 
-        intendedForList = [[] for i in range(len(parser.descriptions))]
+        intendedForList = {}
         for acq in parser.acquisitions:
             acq.setDstFile()
             intendedForList = self.move(acq, intendedForList)
@@ -147,12 +146,11 @@ def run(self):
             except:
                 self.logger.info("The bids-validator does not seem to work properly. "
                                  "The bids-validator may not been installed on your computer. "
-                                 f"Please check: https://github.com/bids-standard/bids-validator#quickstart.")
+                                 "Please check: https://github.com/bids-standard/bids-validator#quickstart.")
 
     def move(self, acquisition, intendedForList):
         """Move an acquisition to BIDS format"""
         for srcFile in glob(acquisition.srcRoot + ".*"):
-
             ext = Path(srcFile).suffixes
             ext = [curr_ext for curr_ext in ext if curr_ext in ['.nii', '.gz',
                                                                 '.json',
@@ -173,8 +171,15 @@ def move(self, acquisition, intendedForList):
                     self.logger.info("Use --clobber option to overwrite")
                     continue
 
+            # Populate intendedFor
+            if '.nii' in ext:
+                if acquisition.id in intendedForList:
+                    intendedForList[acquisition.id].append(acquisition.dstIntendedFor + "".join(ext))
+                else:
+                    intendedForList[acquisition.id] = [acquisition.dstIntendedFor + "".join(ext)]
+
             # it's an anat nifti file and the user using a deface script
-            if (self.config.get("defaceTpl") and acquisition.dataType == "func" and ".nii" in ext):
+            if (self.config.get("defaceTpl") and acquisition.dataType == "anat" and ".nii" in ext):
                 try:
                     os.remove(dstFile)
                 except FileNotFoundError:
@@ -185,20 +190,13 @@ def move(self, acquisition, intendedForList):
                 cmd = [w.replace('dstFile', dstFile) for w in defaceTpl]
                 run_shell_command(cmd)
 
-                intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + "".join(ext))
-
             elif ".json" in ext:
-                data = acquisition.dstSidecarData(self.config["descriptions"],
-                                                  intendedForList)
+                data = acquisition.dstSidecarData(intendedForList)
                 save_json(dstFile, data)
                 os.remove(srcFile)
 
             # just move
             else:
                 os.rename(srcFile, dstFile)
 
-            intendedFile = acquisition.dstIntendedFor + ".nii.gz"
-            if intendedFile not in intendedForList[acquisition.indexSidecar]:
-                intendedForList[acquisition.indexSidecar].append(intendedFile)
-
-        return intendedForList
+        return intendedForList

dcm2bids/participant.py

@@ -5,7 +5,6 @@
 from os.path import join as opj
 
 from dcm2bids.utils.utils import DEFAULT
-from dcm2bids.version import __version__
 
 
 class Participant(object):
@@ -92,4 +91,4 @@ def hasSession(self):
         Returns:
             Boolean
         """
-        return self.session.strip() != DEFAULT.session
+        return self.session.strip() != DEFAULT.session

dcm2bids/sidecar.py

@@ -226,7 +226,6 @@ def build_acquisitions(self, participant):
                 desc = valid_descriptions[0]
                 acq = Acquisition(participant,
                                   srcSidecar=sidecar, **desc)
-                acq.indexSidecar = self.descriptions.index(desc)
                 acq.setDstFile()
 
                 if acq.intendedFor != [None]:
@@ -245,7 +244,6 @@ def build_acquisitions(self, participant):
                 self.logger.warning("Several Pairing  <-  %s", sidecarName)
                 for desc in valid_descriptions:
                     acq = Acquisition(participant,
-                                      indexSidecar=self.descriptions.index(desc),
                                       **desc)
                     self.logger.warning("    ->  %s", acq.suffix)
 

dcm2bids/utils/utils.py

@@ -14,6 +14,7 @@ class DEFAULT(object):
     doc = "Documentation at https://unfmontreal.github.io/Dcm2Bids/"
 
     link_bids_validator = "https://github.com/bids-standard/bids-validator#quickstart"
+    link_doc_intended_for = "https://unfmontreal.github.io/Dcm2Bids/docs/tutorial/first-steps/#populating-the-config-file"
 
     # cli dcm2bids
     cliSession = ""

docs/how-to/create-config-file.md

@@ -17,6 +17,7 @@
       }
     },
     {
+      "id": "task-rest",
       "dataType": "func",
       "modalityLabel": "bold",
       "customLabels": "task-rest",
@@ -28,12 +29,13 @@
     {
       "dataType": "fmap",
       "modalityLabel": "fmap",
-      "intendedFor": 1,
+      "intendedFor": "task_rest",
       "criteria": {
         "ProtocolName": "*field_mapping*"
       }
     },
     {
+      "id": "id_task_learning",
       "dataType": "func",
       "modalityLabel": "bold",
       "customLabels": "task-learning",
@@ -50,7 +52,7 @@
       "criteria": {
         "SeriesDescription": "fmap_task-learning"
       },
-      "IntendedFor": 2,
+      "IntendedFor": "id_task_learning",
       "sidecarChanges": {
         "TaskName": "learning"
       }
@@ -146,15 +148,14 @@ WARNING:dcm2bids.structure:✅ Filename was reordered according to BIDS entity t
 
 Optional field to change or add information in a sidecar.
 
-## intendedFor
+## id and intendedFor
 
-Optional field to add an `IntendedFor` entry in the sidecar of a fieldmap. Just
-put the index or a list of indices of the description(s) that's intended for.
+Optional field to add an `IntendedFor` entry in the sidecar of a fieldmap. 
+You will need to set an id to the corresponding description and put the same id in the `IntendedFor` field.
 
-Python index begins at `0` so in the example, **`1`** means it is intended for
-`task-rest_bold` and **`2`** is intended for `task-learning` which will be
-renamed to only `learning` because of the
-`"sidecarChanges": { "TaskName": "learning" }` field.
+Fo example, **`task_rest`** means it is intended for `task-rest_bold` 
+and **`id_task_learning`** is intended for `task-learning` which will be
+renamed to only `learning` because of the `"sidecarChanges": { "TaskName": "learning" }` field.
 
 ## Multiple config files
 

docs/tutorial/first-steps.md

@@ -671,7 +671,7 @@ good unique identifier.
 === "Command"
 
     ```sh
-    cat code/dcm2bids_config.json
+    cat tmp_dcm2bids/helper/004_In_DCM2NIIX_regression_test_20180918114023.json
     ```
 
 === "Output"
@@ -807,11 +807,11 @@ task name:
       "modalityLabel": "bold",
       "customLabels": "task-rest",
       "criteria": {
-        "SeriesDescription": "Axial EPI-FMRI (Interleaved I to S)*",
-        "sidecarChanges": {
+        "SeriesDescription": "Axial EPI-FMRI (Interleaved I to S)*"
+      },
+      "sidecarChanges": {
         "TaskName": "rest"
       }
-      }
     }
   ]
 }
@@ -887,6 +887,7 @@ file with the appropriate info.
 {
   "descriptions": [
     {
+      "id": "id_task-rest",
       "dataType": "func",
       "modalityLabel": "bold",
       "customLabels": "task-rest",
@@ -904,7 +905,7 @@ file with the appropriate info.
       "criteria": {
         "SeriesDescription": "EPI PE=AP*"
       },
-      "intendedFor": 0
+      "intendedFor": "id_task-rest"
     },
     {
       "dataType": "fmap",
@@ -913,7 +914,7 @@ file with the appropriate info.
       "criteria": {
         "SeriesDescription": "EPI PE=PA*"
       },
-      "intendedFor": 0
+      "intendedFor": "id_task-rest"
     }
   ]
 }