diff --git a/example1/resources/diffusion/NODDI.bval b/example1/resources/diffusion/NODDI.bval
new file mode 100644
index 0000000000000000000000000000000000000000..b2e286ce85d8f6d04ed86d64b1d9ecb8f0064d7e
--- /dev/null
+++ b/example1/resources/diffusion/NODDI.bval
@@ -0,0 +1 @@
+0 0 2000 2000 1000 1000
diff --git a/example1/resources/diffusion/NODDI.bvec b/example1/resources/diffusion/NODDI.bvec
new file mode 100644
index 0000000000000000000000000000000000000000..22f1e8093c8d5d491252e2f30b4cf473ce4fea25
--- /dev/null
+++ b/example1/resources/diffusion/NODDI.bvec
@@ -0,0 +1,3 @@
+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
diff --git a/example1/resources/plugins/definitions.py b/example1/resources/plugins/definitions.py
index 385f752491acc982a8bb5a7d3e7567513e06a65a..7b30193ed84785ac7fe46965a59801ec641e0e7c 100644
--- a/example1/resources/plugins/definitions.py
+++ b/example1/resources/plugins/definitions.py
@@ -1,8 +1,20 @@
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',
diff --git a/example1/resources/plugins/process_plugin.py b/example1/resources/plugins/process_plugin.py
new file mode 100644
index 0000000000000000000000000000000000000000..207bec01c7a25e828e9fb01431a9983b86588041
--- /dev/null
+++ b/example1/resources/plugins/process_plugin.py
@@ -0,0 +1,171 @@
+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)