added process plugin

example1/resources/diffusion/NODDI.bval

+0 0 2000 2000 1000 1000

example1/resources/diffusion/NODDI.bvec

+0 0 0.021828 -0.015425 -0.70918 -0.2465
+0 0 0.80242 0.22098 -0.00063106 0.1043
+0 0 -0.59636 0.97516 -0.70503 -0.96351

example1/resources/plugins/definitions.py

 import logging
 import os
 
+
+# defined this way, log messages will be formatted correctly
+# and appear with this file-name
 logger = logging.getLogger(__name__)
 
+# path to the root folder of plugin 
+# (bidscoin_example/example1/resources)
+# usefull to retrieve auxiliary files
+plugin_root = os.path.normpath(
+        os.path.join(os.path.dirname(__file__), ".."))
+
+# definition of correct session names and sequences
+# usefull to check the completness and/or correct emplacement
+# of scans
 Series = {
         "ses-LCL": ('localizer',
                     'cmrr_mbep2d_bold_mb2_invertpe', 

example1/resources/plugins/process_plugin.py

+import os
+import shutil
+import logging
+import random
+
+from definitions import checkSeries, plugin_root
+
+logger = logging.getLogger(__name__)
+
+# global variables
+rawfolder = ""
+bidsfolder = ""
+dry_run = False
+
+participants_table = None
+rec_path = ""
+countSeries = {}
+
+
+def InitEP(source: str, destination: str, dry: bool) -> int:
+    global rawfolder
+    global bidsfolder
+    global dry_run
+
+    rawfolder = source
+    bidsfolder = destination
+    dry_run = dry
+
+
+def SubjectEP(scan):
+    scan.sub_values["handiness"] = random.choice([0, 1])
+
+
+def SessionEP(scan):
+    global series
+    global sid
+    sub = scan.subject
+    ses = scan.session
+    path = os.path.join(rawfolder,
+                        sub, ses,
+                        "MRI")
+    series = sorted(os.listdir(path))
+    series = [s.split("-", 1)[1] for s in series]
+    sid = -1
+    checkSeries(path, sub, ses, False)
+    # copytng behevioral data
+    aux_input = os.path.join(rawfolder, sub, ses, "auxiliary")
+    if ses in ("ses-LCL", "ses-HCL"):
+        if not os.path.isdir(aux_input):
+            logger.error("Session {}/{} do not contain auxiliary folder"
+                         .format(sub, ses))
+            return -1
+        for old, new in (("FCsepNBack.tsv", "task-rest_events.tsv"),
+                         ("FCsepNBack.json", "task-rest_events.json"),
+                         ("VAS.tsv", "task-rest_beh.tsv"),
+                         ("VAS.json", "task-rest_beh.json")):
+            source = "{}/{}".format(aux_input, old)
+            if not os.path.isfile(source):
+                logger.error("{}/{}: File {} not found"
+                             .format(sub, ses, source))
+
+
+series = list()
+sid = -1
+Intended = ""
+
+
+def SequenceEP(recording):
+    global series
+    global sid
+    global Intended
+    Intended = ""
+    sid += 1
+    recid = series[sid]
+    if recid != recording.recId():
+        logger.warning("{}: Id mismatch folder {}"
+                       .format(recording.recIdentity(False),
+                               recid))
+    if recid == "cmrr_mbep2d_bold_mb2_invertpe":
+        mod = series[sid + 1]
+        if mod.endswith("cmrr_mbep2d_bold_mb2_task_fat"):
+            Intended = "nBack"
+        elif mod.endswith("cmrr_mbep2d_bold_mb2_task_nfat"):
+            Intended = "nBack"
+        elif mod.endswith("cmrr_mbep2d_bold_mb2_rest"):
+            Intended = "rest"
+        else:
+            Intended = "invalid"
+            logger.warning("{}: Unknown session {}"
+                           .format(recording.recIdentity(),
+                                   mod))
+    elif recid == "gre_field_mapping":
+        if recording.sesId() in ("ses-HCL", "ses-LCL"):
+            Intended = "HCL/LCL"
+        elif recording.sesId() == "ses-STROOP":
+            Intended = "STROOP"
+        else:
+            logger.warning("{}: Unknown session {}"
+                           .format(recording.recIdentity(),
+                                   recording.sesId()))
+            Intended = "invalid"
+    elif recid == "al_mtflash3d_sensArray":
+        det = series[sid + 2]
+        if det.endswith("al_mtflash3d_PDw"):
+            Intended = "PDw"
+        elif det.endswith("al_mtflash3d_T1w"):
+            Intended = "T1w"
+            recording.setAttribute("Intended", "T1w")
+        elif det.endswith("al_mtflash3d_MTw"):
+            Intended = "MTw"
+        else:
+            logger.warning("{}: Unable determine modality"
+                           .format(recording.recIdentity()))
+            Intended = "invalid"
+    elif recid == "al_mtflash3d_sensBody":
+        det = series[sid + 1]
+        if det.endswith("al_mtflash3d_PDw"):
+            Intended = "PDw"
+        elif det.endswith("al_mtflash3d_T1w"):
+            Intended = "T1w"
+        elif det.endswith("al_mtflash3d_MTw"):
+            Intended = "MTw"
+        else:
+            logger.warning("{}: Unable determine modality"
+                           .format(recording.recIdentity()))
+            Intended = "invalid"
+
+
+def RecordingEP(recording):
+    if Intended != "":
+        recording.setAttribute("SeriesDescription", Intended)
+
+
+def SequenceEndEP(outfolder, recording):
+    """
+    Simulates 3D to 4D images conversion
+    """
+    modality = recording.Modality()
+
+    if modality not in ("func", "dwi"):
+        return
+
+    f4D = os.path.join(outfolder, "4D")
+    if not os.path.isfile(f4D + ".nii"):
+        logger.info("{}: Converting {} MRI to 4D"
+                    .format(recording.recIdentity(index=False),
+                            modality))
+        first_file = os.path.join(outfolder, recording.files[0])
+        shutil.copy2(first_file, f4D + ".nii")
+        first_file = os.path.splitext(first_file)[0] + ".json"
+        shutil.copy2(first_file, f4D + ".json")
+
+        # copying fake bval and bvec values
+        # during the bidsifications these files will
+        # be automatically picked up
+        if modality == "dwi":
+            shutil.copy2(os.path.join(plugin_root,
+                                      "diffusion",
+                                      "NODDI.bval"),
+                         os.path.join(outfolder,
+                                      "4D.bval"))
+            shutil.copy2(os.path.join(plugin_root,
+                                      "diffusion",
+                                      "NODDI.bvec"),
+                         os.path.join(outfolder,
+                                      "4D.bvec"))
+        for f_nii in recording.files:
+            f_nii = os.path.join(outfolder, f_nii)
+            f_json = os.path.splitext(f_nii)[0] + ".json"
+            os.remove(f_nii)
+            os.remove(f_json)