Extract function to get row info and add test

Author: mvdoc

bin/heudiconv

@@ -23,6 +23,8 @@ __version__ = '0.2'
 import argparse
 from glob import glob
 import csv
+import dicom as dcm
+import dcmstack as ds
 import inspect
 import json
 import os
@@ -944,27 +946,31 @@ def convert(items, symlink=True, converter=None,
     shutil.rmtree(tmpdir)
 
 
+def get_formatted_scans_key_row(item, outname_bids_files):
+    dcm_fn = item[-1][0]
+    mw = ds.wrapper_from_data(dcm.read_file(dcm_fn, stop_before_pixels=True))
+    # we need to store filenames and acquisition times
+    # parse date and time and get it into isoformat
+    date = mw.dcm_data.AcquisitionDate
+    time = mw.dcm_data.AcquisitionTime.split('.')[0]
+    td = time + date
+    acq_time = datetime.strptime(td, '%H%M%S%Y%m%d').isoformat()
+    # add random string
+    randstr = ''.join(map(chr, sample(k=8, population=range(33, 127))))
+    row = [acq_time, mw.dcm_data.PerformingPhysicianName, randstr]
+    return row
+
+
 def save_scans_key(items, outname_bids_files):
-    import dicom as dcm
-    import dcmstack as ds
     header = ['filename', 'acq_time', 'operator', 'randstr']
     rows = []
+    import pdb; pdb.set_trace()
     for item, outname_bids_file in zip(items, outname_bids_files):
-        dcm_fn = item[-1][0]
-        mw = ds.wrapper_from_data(dcm.read_file(dcm_fn, force=True))
-        # we need to store filenames and acquisition times
-        # parse date and time and get it into isoformat
-        date = mw.dcm_data.AcquisitionDate
-        time = mw.dcm_data.AcquisitionTime.split('.')[0]
-        td = time + date
-        acq_time = datetime.strptime(td, '%H%M%S%Y%m%d').isoformat()
         # get filenames
         f_name = '/'.join(outname_bids_file.split('/')[-2:])
         f_name = f_name.replace('json', 'nii.gz')
-        # store it
-        randstr = ''.join(map(chr, sample(k=8, population=range(33, 127))))
         rows.append(
-            (f_name, acq_time, mw.dcm_data.PerformingPhysicianName, randstr)
+            [f_name] + get_formatted_scans_key_row(item, outname_bids_file)
         )
     # where should we store it?
     output_dir = dirname(dirname(outname_bids_file))

tests/test_main.py

@@ -97,10 +97,29 @@ def test_prepare_for_datalad(tmpdir):
         assert not ds.repo.is_under_annex(f)
     assert not ds.repo.is_under_annex('.gitattributes')
 
+
 def test_json_dumps_pretty():
     pretty = heudiconv.json_dumps_pretty
     assert pretty({}) == "{}"
     assert pretty({"a": -1, "b": "123", "c": [1, 2, 3], "d": ["1.0", "2.0"]}) \
         == '{\n  "a": -1,\n  "b": "123",\n  "c": [1, 2, 3],\n  "d": ["1.0", "2.0"]\n}'
     assert pretty({'a': ["0.3", "-1.9128906358217845e-12", "0.2"]}) \
         == '{\n  "a": ["0.3", "-1.9128906358217845e-12", "0.2"]\n}'
+
+
+def test_get_formatted_scans_key_row():
+    item = [
+        ('tests/data/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm',
+         ('nii.gz', 'dicom'),
+         ['tests/data/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm'])
+    ]
+    outname_bids_file = '/a/path/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/fmap/sub-phantom1sid1_acq-3mm_phasediff.json'
+
+    row = heudiconv.get_formatted_scans_key_row(item, outname_bids_file)
+    assert(len(row) == 3)
+    assert(row[0] == '2016-10-14T09:26:34')
+    assert(row[1] == '')
+    randstr1 = row[2]
+    row = heudiconv.get_formatted_scans_key_row(item, outname_bids_file)
+    randstr2 = row[2]
+    assert(randstr1 != randstr2)