Merge pull request #119 from mgxd/fix/qol

MAINT: general housekeeping

Author: mgxd

heudiconv/bids.py

@@ -14,8 +14,14 @@
 import dcmstack as ds
 
 from .parser import find_files
-from .utils import (load_json, save_json, create_file_if_missing,
-                    json_dumps_pretty, set_readonly, is_readonly)
+from .utils import (
+    load_json,
+    save_json,
+    create_file_if_missing,
+    json_dumps_pretty,
+    set_readonly,
+    is_readonly,
+)
 
 lgr = logging.getLogger(__name__)
 

heudiconv/cli/run.py

@@ -5,7 +5,7 @@
 
 from .. import __version__, __packagename__
 from ..parser import get_study_sessions
-from ..utils import (load_heuristic, anonymize_sid, treat_infofile, SeqInfo)
+from ..utils import load_heuristic, anonymize_sid, treat_infofile, SeqInfo
 from ..convert import prep_conversion
 
 import inspect

heudiconv/convert.py

@@ -3,13 +3,30 @@
 import logging
 import shutil
 
-from .utils import (read_config, load_json, save_json, write_config, TempDirs,
-                    safe_copyfile, treat_infofile, set_readonly,
-                    clear_temp_dicoms)
-from .bids import (convert_sid_bids, populate_bids_templates, save_scans_key,
-                   tuneup_bids_json_files, add_participant_record)
-from .dicoms import (group_dicoms_into_seqinfos, embed_metadata_from_dicoms,
-                     compress_dicoms)
+from .utils import (
+    read_config,
+    load_json,
+    save_json,
+    write_config,
+    TempDirs,
+    safe_copyfile,
+    treat_infofile,
+    set_readonly,
+    clear_temp_dicoms,
+    seqinfo_fields,
+)
+from .bids import (
+    convert_sid_bids,
+    populate_bids_templates,
+    save_scans_key,
+    tuneup_bids_json_files,
+    add_participant_record,
+)
+from .dicoms import (
+    group_dicoms_into_seqinfos,
+    embed_metadata_from_dicoms,
+    compress_dicoms
+)
 
 lgr = logging.getLogger(__name__)
 
@@ -115,6 +132,7 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
         filegroup = {si.series_id: x for si, x in seqinfo.items()}
         dicominfo_file = op.join(idir, 'dicominfo%s.tsv' % ses_suffix)
         with open(dicominfo_file, 'wt') as fp:
+            fp.write('\t'.join([val for val in seqinfo_fields]) + '\n')
             for seq in seqinfo_list:
                 fp.write('\t'.join([str(val) for val in seq]) + '\n')
         lgr.debug("Calling out to %s.infodict", heuristic)

heudiconv/dicoms.py

@@ -85,7 +85,10 @@ def group_dicoms_into_seqinfos(files, file_filter, dcmfilter, grouping):
                 if studyUID is None:
                     studyUID = file_studyUID
                 elif not per_accession_number:
-                    assert studyUID == file_studyUID
+                    assert studyUID == file_studyUID, (
+                    "Conflicting study identifiers found [{}, {}].".format(
+                    studyUID, file_studyUID
+                    ))
         except AttributeError as exc:
             lgr.warning('Ignoring %s since not quite a "normal" DICOM: %s',
                         filename, exc)

heudiconv/external/dlad.py

@@ -2,7 +2,7 @@
 import os.path as op
 import logging
 
-from ..utils import (create_file_if_missing, mark_sensitive)
+from ..utils import create_file_if_missing, mark_sensitive
 
 lgr = logging.getLogger(__name__)
 

heudiconv/parser.py

@@ -10,8 +10,14 @@
 from tempfile import mkdtemp
 
 from .dicoms import group_dicoms_into_seqinfos
-from .utils import (docstring_parameter, StudySessionInfo, load_json,
-                    save_json, create_file_if_missing, json_dumps_pretty)
+from .utils import (
+    docstring_parameter,
+    StudySessionInfo,
+    load_json,
+    save_json,
+    create_file_if_missing,
+    json_dumps_pretty,
+)
 
 lgr = logging.getLogger(__name__)
 

heudiconv/utils.py

@@ -14,31 +14,31 @@
 from collections import namedtuple
 from glob import glob
 
-SeqInfo = namedtuple(
-    'SeqInfo',
-    ['total_files_till_now',  # 0
-     'example_dcm_file',      # 1
-     'series_id',             # 2
-     'unspecified1',          # 3
-     'unspecified2',          # 4
-     'unspecified3',          # 5
-     'dim1', 'dim2', 'dim3', 'dim4', # 6, 7, 8, 9
-     'TR', 'TE',              # 10, 11
-     'protocol_name',         # 12
-     'is_motion_corrected',   # 13
-     'is_derived',            # 14
-     'patient_id',            # 15
-     'study_description',     # 16
-     'referring_physician_name', # 17
-     'series_description',    # 18
-     'sequence_name',         # 19
-     'image_type',            # 20
-     'accession_number',      # 21
-     'patient_age',           # 22
-     'patient_sex',           # 23
-     'date'                   # 24
-     ]
-)
+seqinfo_fields = [
+    'total_files_till_now',  # 0
+    'example_dcm_file',      # 1
+    'series_id',             # 2
+    'dcm_dir_name',          # 3
+    'unspecified2',          # 4
+    'unspecified3',          # 5
+    'dim1', 'dim2', 'dim3', 'dim4', # 6, 7, 8, 9
+    'TR', 'TE',              # 10, 11
+    'protocol_name',         # 12
+    'is_motion_corrected',   # 13
+    'is_derived',            # 14
+    'patient_id',            # 15
+    'study_description',     # 16
+    'referring_physician_name', # 17
+    'series_description',    # 18
+    'sequence_name',         # 19
+    'image_type',            # 20
+    'accession_number',      # 21
+    'patient_age',           # 22
+    'patient_sex',           # 23
+    'date'                   # 24
+ ]
+
+SeqInfo = namedtuple('SeqInfo', seqinfo_fields)
 
 StudySessionInfo = namedtuple(
     'StudySessionInfo',