add custom-rules for dicom2specs

.datalad/config

@@ -11,3 +11,6 @@
 [datalad "procedures.repack-studyspec"]
 	call-format = "bash {script} {args}"
 	help = "helper to convert valid-json into studyspec.json format"
+
+[datalad "procedures.add_customrules"]
+		help = "add hirni's custom_rules.py script to dataset"

custom_rules/custom_rules.py

@@ -0,0 +1,118 @@
+"""custom rules for dicom2spec for sfb_cuetarget study"""
+
+
+class MyDICOM2SpecRules(object):
+
+    def __init__(self, dicommetadata):
+        """
+
+        Parameter
+        ----------
+        dicommetadata: list of dict
+            dicom metadata as extracted by datalad; one dict per image series
+        """
+        self._dicom_series = dicommetadata
+
+    def __call__(self, subject=None, anon_subject=None, session=None):
+        """
+
+        Parameters
+        ----------
+
+        Returns
+        -------
+        list of tuple (dict, bool)
+        """
+        spec_dicts = []
+
+        # check whether any "active task" present in thte current series_dict
+        # we can use that to infer the session as 1 or 4 based on that
+        if session == None and any(s['SeriesDescription'].startswith("fMRI_task") for s in self._dicom_series):
+            session = "004"
+        else:
+            session = "001"
+
+        # print("session == ")
+        # print(session)
+        # print("\n")
+
+        for dicom_dict in self._dicom_series:
+            spec_dicts.append((self._rules(dicom_dict,
+                                           subject=subject,
+                                           anon_subject=anon_subject,
+                                           session=session),
+                               self.series_is_valid(dicom_dict)
+                               )
+                              )
+        return spec_dicts
+
+    def _rules(self, series_dict, subject=None, anon_subject=None,
+               session=None):
+
+        # use this to figure out which fields you have available in the dict.
+        # print('\n-----------------------\n')
+        # print('\nnext series dict:\n')
+        # print(series_dict)
+
+        # figure out modality:
+        task = None
+        modality = None
+        comment = ''
+        run = None
+        aquisition = None
+        if series_dict['SeriesDescription'].startswith("t1"):
+            modality = 'T1w'
+            aquisition = 'mprage'
+        if series_dict['SeriesDescription'].startswith("gre_field_mapping"):
+            modality = 'fieldmap'
+        if series_dict['SeriesDescription'].startswith("IR-EPI"):
+            # c.f. https://www.ncbi.nlm.nih.gov/pubmed/14635150
+            modality = 'T1w'
+            aquisition = 'mprage'
+        if series_dict['SeriesDescription'].startswith("DTI"):
+            modality = 'dwi'
+        if series_dict['SeriesDescription'].startswith("fMRI_task"):
+            modality = 'bold'
+            task = 'active'
+            # number afterwards indicates run number (range: 1 to 4)
+            run = series_dict['SeriesDescription'][len("fMRI_task")]
+        if series_dict['SeriesDescription'].startswith("fMRI_withouttask"):
+            modality = 'bold'
+            task = 'passive'
+            # number afterwards indicates run number (range: 1 to 4)
+            run = series_dict['SeriesDescription'][len("fMRI_withouttask")]
+        if series_dict['SeriesDescription'].startswith("fMRI_resting"):
+            modality = 'bold'
+            task = 'rest'
+        # for any single-band reference image, overwrite to `sbref` instead of bold
+        if series_dict['SeriesDescription'].endswith("SBRef"):
+            modality = 'sbref'
+
+        if series_dict['SeriesDescription'].startswith("AAHead_Scout"):
+            comment = "Localizer - will be ignored for BIDS"
+
+
+        return {'description': series_dict['SeriesDescription']
+                if "SeriesDescription" in series_dict else '',
+                'comment': comment,
+                'subject': series_dict['PatientID'] if not subject else subject,
+                'anon-subject': anon_subject if anon_subject else None,
+                'bids-session': session if session else None,
+                'bids-modality' : modality,
+                'bids-task': task,
+                'bids-run': run,
+                'bids-acquisition': acquisition
+                }
+
+    def series_is_valid(self, series_dict):
+        # For all series which this returns `false`, the hirni-spec2bids will
+        # skip the conversion to niftis.
+
+        # Skip all localizers
+        valid = not series_dict['SeriesDescription'].startswith("AAHead_Scout")
+        # skip DTI for now
+        valid = valid and not series_dict['SeriesDescription'].startswith("DTI")
+        return valid
+
+
+__datalad_hirni_rules = MyDICOM2SpecRules

procedures/add_customrules.py

@@ -0,0 +1,22 @@
+"""Procedure to configure custom rules for dicom2spec"""
+
+import sys
+import os.path as op
+
+from datalad.distribution.dataset import require_dataset
+
+ds = require_dataset(
+    sys.argv[1],
+    check_installed=True,
+    purpose='adding custom rule')
+
+# grab config
+cfg = ds.config
+
+# TODO: what to do when a rules is already present? abort? overwrite?
+cfg.add('datalad.hirni.dicom2spec.rules',
+        # we assume that hirni_addons have been installed into `sourcedata/code/.`
+        op.join("code","hirni_addons", "custom_rules", "custom_rules.py"),
+        where='dataset')
+
+ds.save(message="add custom_rules.py to dataset configuration")