RM: reproin - Remove (ancient) DBIC specific craft

ReproIn was developed "as deployed" and it hardcoded many
remappings etc relevant now only to some older studies etc.
In this commit all of those are removed.

I did leave/added some as examples on how protocols2fix could
be specified.

Also Matteo has moved on, so removed him from Ack

Author: yarikoptic

heudiconv/heuristics/reproin.py

@@ -148,150 +148,55 @@
 # NOTE: even if filename has number that is 0-padded, internally no padding
 # is done
 fix_accession2run = {
-    'A000005': ['^1-'],
-    'A000035': ['^8-', '^9-'],
-    'A000067': ['^9-'],
-    'A000072': ['^5-'],
-    'A000081': ['^5-'],
-    'A000082': ['^5-'],
-    'A000088': ['^9-'],
-    'A000090': ['^5-'],
-    'A000127': ['^21-'],
-    'A000130': ['^15-'],
-    'A000137': ['^9-', '^11-'],
-    'A000297': ['^12-'],
-    'A000326': ['^15-'],
-    'A000376': ['^15-'],
-    'A000384': ['^8-', '^11-'],
-    'A000467': ['^15-'],
-    'A000490': ['^15-'],
-    'A000511': ['^15-'],
-    'A000797': ['^[1-7]-'],
+    # e.g.:
+    # 'A000035': ['^8-', '^9-'],
 }
 
-# dictionary containing fixes, keys are md5sum of study_description from
-# dicoms, in the form of PI-Experimenter^protocolname
-# values are list of tuples in the form (regex_pattern, substitution)
+# A dictionary containing fixes/remapping for sequence names per study.
+# Keys are md5sum of study_description from DICOMs, in the form of PI-Experimenter^protocolname
+# You can use `heudiconv -f reproin --command ls --files  PATH
+# to list the "study hash".
+# Values are list of tuples in the form (regex_pattern, substitution).
+# If the  key is an empty string`''''`, it would apply to any study.
 protocols2fix = {
-    # QA
-    '43b67d9139e8c7274578b7451ab21123':
-        [
-         # ('anat-scout.*', 'anat-scout_ses-{date}'),
-         # do not change it so we retain _ses-{date}
-         # ('anat-scout.*', 'anat-scout'),
-         ('BOLD_p2_s4_3\.5mm', 'func_task-rest_acq-p2-s4-3.5mm'),
-         ('BOLD_p2_s4',        'func_task-rest_acq-p2-s4'),
-         ('BOLD_p2_noprescannormalize', 'func-bold_task-rest_acq-p2noprescannormalize'),
-         ('BOLD_p2',                    'func-bold_task-rest_acq-p2'),
-         ('BOLD_', 'func_task-rest'),
-         ('DTI_30_p2_s4_3\.5mm', 'dwi_acq-DTI-30-p2-s4-3.5mm'),
-         ('DTI_30_p2_s4',        'dwi_acq-DTI-30-p2-s4'),
-         ('DTI_30_p2',           'dwi_acq-DTI-30-p2'),
-         ('_p2_s4_3\.5mm', '_acq-p2-s4-3.5mm'),
-         ('_p2_s4',        '_acq-p2-s4'),
-         ('_p2', '_acq-p2'),
-        ],
-    '9d148e2a05f782273f6343507733309d':
-        [('anat_', 'anat-'),
-         ('run-life[0-9]', 'run+_task-life'),
-         ('scout_run\+', 'scout'),
-         ('T2w', 'T2w_run+'),
-         # substitutions for old protocol names
-         ('AAHead_Scout_32ch-head-coil', 'anat-scout'),
-         ('MPRAGE', 'anat-T1w_acq-MPRAGE_run+'),
-         ('gre_field_mapping_2mm', 'fmap_run+_acq-2mm'),
-         ('gre_field_mapping_3mm', 'fmap_run+_acq-3mm'),
-         ('epi_bold_sms_p2_s4_2mm_life1_748',
-            'func_run+_task-life_acq-2mm748'),
-         ('epi_bold_sms_p2_s4_2mm_life2_692',
-            'func_run+_task-life_acq-2mm692'),
-         ('epi_bold_sms_p2_s4_2mm_life3_754',
-            'func_run+_task-life_acq-2mm754'),
-         ('epi_bold_sms_p2_s4_2mm_life4_824',
-            'func_run+_task-life_acq-2mm824'),
-         ('epi_bold_p2_3mm_nofs_life1_374',
-            'func_run+_task-life_acq-3mmnofs374'),
-         ('epi_bold_p2_3mm_nofs_life2_346',
-          'func_run+_task-life_acq-3mmnofs346'),
-         ('epi_bold_p2_3mm_nofs_life3_377',
-          'func_run+_task-life_acq-3mmnofs377'),
-         ('epi_bold_p2_3mm_nofs_life4_412',
-          'func_run+_task-life_acq-3mmnofs412'),
-         ('t2_space_sag_p4_iso', 'anat-T2w_run+'),
-         ('gre_field_mapping_2.4mm', 'fmap_run+_acq-2.4mm'),
-         ('rest_p2_sms4_2.4mm_64sl_1000tr_32te_600dyn',
-            'func_run+_task-rest_acq-2.4mm64sl1000tr32te600dyn'),
-         ('DTI_30', 'dwi_run+_acq-30'),
-         ('t1_space_sag_p2_iso', 'anat-T1w_acq-060mm_run+')],
-    '76b36c80231b0afaf509e2d52046e964':
-        [('fmap_run\+_2mm', 'fmap_run+_acq-2mm')],
-    'c6d8fbccc72990bee61d28e73b2618a4':
-        [('run=', 'run+')],
-    'a751cc977f1e354fcafcb0ea2de123bd':
-        [
-          ('_unlabeled', '_task-unlabeled'),
-          ('_mSense', '_acq-mSense'),
-          ('_p1_sms4_2.5mm', '_acq-p1-sms4-2.5mm'),
-          ('_p1_sms4_3mm', '_acq-p1-sms4-3mm'),
-        ],
-    'd160113cf5ea8c5d0cbbbe14ef625e76':
-        [
-          ('_run0', '_run-0'),
-        ],
-    '1bd62e10672fe0b435a9aa8d75b45425':
-        [
-            # need to add incrementing session -- study should have 2
-            # and no need for run+ for the scout!
-            ('scout(_run\+)?$', 'scout_ses+'),
-        ],
-    'da218a66de902adb3ad9407d514e3639':
-        [
-            # those sequences renamed later to include DTI- in their acq-
-            # so fot consistency
-            ('hardi_64',  'dwi_acq-DTI-hardi64'),
-            ('acq-hardi', 'acq-DTI-hardi'),
-        ],
-    'ed20c1ad4a0861b2b65768e159258eec':
-        [
-            ('fmap_acq-discorr-dti-', 'fmap_acq-dwi_dir-'),
-            ('_test', ''),
-        ],
-    '1996f745c30c1df1d3851844e56d294f':
-        [
-            ('fmap_acq-discorr-dti-', 'fmap_acq-dwi_dir-'),
-        ],
-    # '022969bfde39c2940c114edf1db3fabc':
-    #    [  # should be applied only for ses-03!
-    #        ('_acq-MPRAGE_ses-02', '_acq-MPRAGE_ses-03'),
-    #    ],
-    # to be used only once for one interrupted accession but we cannot
-    # fix per accession yet
-    #    '23763823d2b9b4b09dafcadc8e8edf21':
-    #        [
-    #            ('anat-T1w_acq-MPRAGE', 'anat-T1w_acq-MPRAGE_run-06'),
-    #            ('anat_T2w', 'anat_T2w_run-06'),
-    #            ('fmap_acq-3mm', 'fmap_acq-3mm_run-06'),
-    #        ],
+    # e.g., QA:
+    # '43b67d9139e8c7274578b7451ab21123':
+    #     [
+    #      ('BOLD_p2_s4_3\.5mm', 'func_task-rest_acq-p2-s4-3.5mm'),
+    #      ('BOLD_', 'func_task-rest'),
+    #      ('_p2_s4',        '_acq-p2-s4'),
+    #      ('_p2', '_acq-p2'),
+    #     ],
+    # '':  # for any study example with regexes used
+    #     [
+    #         ('AAHead_Scout_.*', 'anat-scout'),
+    #         ('^dti_.*', 'dwi'),
+    #         ('^.*_distortion_corr.*_([ap]+)_([12])', r'fmap-epi_dir-\1_run-\2'),
+    #         ('^(.+)_ap.*_r(0[0-9])', r'func_task-\1_run-\2'),
+    #         ('^t1w_.*', 'anat-T1w'),
+    #         # problematic case -- multiple identically named pepolar fieldmap runs
+    #         # I guess we will just sacrifice ability to detect canceled runs here.
+    #         # And we cannot just use _run+ since it would increment independently
+    #         # for ap and then for pa.  We will rely on having ap preceding pa.
+    #         # Added  _acq-mb8  so they match the one in funcs
+    #         ('func_task-discorr_acq-ap', r'fmap-epi_dir-ap_acq-mb8_run+'),
+    #         ('func_task-discorr_acq-pa', r'fmap-epi_dir-pa_acq-mb8_run='),
+    # ]
 }
-# there was also screw up in the locator specification
-# so we need to fix in both
-# protocols2fix['67ae5e641ea9d487b6fdf56fb91aeb93'] = protocols2fix['022969bfde39c2940c114edf1db3fabc']
 
 # list containing StudyInstanceUID to skip -- hopefully doesn't happen too often
 dicoms2skip = [
-    '1.3.12.2.1107.5.2.43.66112.30000016110117002435700000001',
-    '1.3.12.2.1107.5.2.43.66112.30000016102813152550600000004',  # double scout
+    # e.g.
+    # '1.3.12.2.1107.5.2.43.66112.30000016110117002435700000001',
 ]
 
 DEFAULT_FIELDS = {
     # Let it just be in each json file extracted
-    # 'Manufacturer': "Siemens",
-    # 'ManufacturersModelName': "Prisma",
     "Acknowledgements":
         "We thank Terry Sacket and the rest of the DBIC (Dartmouth Brain Imaging "
         "Center) personnel for assistance in data collection, and "
-        "Yaroslav Halchenko and Matteo Visconti for preparing BIDS dataset. "
-        "TODO: more",
+        "Yaroslav O. Halchenko for preparing BIDS dataset. "
+        "TODO: adjust to your case.",
 }
 
 
@@ -311,38 +216,10 @@ def filter_dicom(dcmdata):
 
 def filter_files(fn):
     """Return True if a file should be kept, else False.
-    We're using it to filter out files that do not start with a number."""
 
-    # do not check for these accession numbers because they haven't been
-    # recopied with the initial number
-    donotfilter = ['A000012', 'A000013', 'A000020', 'A000041']
-
-    split = os.path.split(fn)
-    split2 = os.path.split(split[0])
-    sequence_dir = split2[1]
-    split3 = os.path.split(split2[0])
-    accession_number = split3[1]
+    ATM reproin does not do any filtering. Override if you need to add some
+    """
     return True
-    if accession_number == 'A000043':
-        # crazy one that got copied for some runs but not for others,
-        # so we are going to discard those that got copied and let heudiconv
-        # figure out the rest
-        return False if re.match('^[0-9]+-', sequence_dir) else True
-    elif accession_number == 'unknown':
-        # this one had some stuff without study description, filter stuff before
-        # collecting info, so it doesn't crash completely
-        return False if re.match('^[34][07-9]-sn', sequence_dir) else True
-    elif accession_number in donotfilter:
-        return True
-    elif accession_number.startswith('phantom-'):
-        # Accessions on phantoms, e.g. in dartmouth-phantoms/bids_test4-20161014
-        return True
-    elif accession_number.startswith('heudiconvdcm'):
-        # we were given some tarball with dicoms which was extracted so we
-        # better obey
-        return True
-    else:
-        return True if re.match('^[0-9]+-', sequence_dir) else False
 
 
 def create_key(subdir, file_suffix, outtype=('nii.gz', 'dicom'),