Merge branch 'master' into fix/ref

Author: yarikoptic

heudiconv/cli/run.py

@@ -56,7 +56,7 @@ def process_extra_commands(outdir, args):
     args : Namespace
         arguments
     """
-    if args.command == 'treat-json':
+    if args.command == 'treat-jsons':
         for f in args.files:
             treat_infofile(f)
     elif args.command == 'ls':
@@ -174,7 +174,8 @@ def get_parser():
                         help='Do not catch exceptions and show exception '
                         'traceback')
     parser.add_argument('--command',
-                        choices=('treat-json', 'ls', 'populate-templates'),
+                        choices=('ls', 'populate-templates',
+                                 'treat-jsons', 'sanitize-jsons'),
                         help='custom actions to be performed on provided '
                         'files instead of regular operation.')
     parser.add_argument('-g', '--grouping', default='studyUID',

heudiconv/convert.py

@@ -375,6 +375,7 @@ def convert_dicom(item_dicoms, bids, prefix,
 
 def nipype_convert(item_dicoms, prefix, with_prov, bids, tmpdir):
     """ """
+    import nipype
     if with_prov:
         from nipype import config
         config.enable_provenance()
@@ -387,6 +388,11 @@ def nipype_convert(item_dicoms, prefix, with_prov, bids, tmpdir):
     convertnode.base_dir = tmpdir
     convertnode.inputs.source_names = item_dicoms
     convertnode.inputs.out_filename = op.basename(op.dirname(prefix))
+    if nipype.__version__.split('.')[0] == '0':
+        # deprecated since 1.0, might be needed(?) before
+        convertnode.inputs.terminal_output = 'allatonce'
+    else:
+        convertnode.terminal_output = 'allatonce'
     convertnode.inputs.bids_format = bids
     eg = convertnode.run()
 

tests/test_heuristics.py

@@ -10,6 +10,7 @@
 import re
 
 import pytest
+from .utils import HEURISTICS_PATH, TESTS_DATA_PATH
 
 import logging
 lgr = logging.getLogger(__name__)
@@ -23,22 +24,25 @@
 # this will fail if not in project's root directory
 def test_smoke_converall(tmpdir):
     runner(
-        ("-f heuristics/convertall.py -c dcm2niix -o %s -b --datalad "
-         "-s fmap_acq-3mm -d tests/data/{subject}/*" % tmpdir).split(' ')
+        ("-f %s/convertall.py -c dcm2niix -o %s -b --datalad "
+         "-s fmap_acq-3mm -d %s/{subject}/*"
+         % (HEURISTICS_PATH, tmpdir, TESTS_DATA_PATH)
+        ).split(' ')
     )
 
 
 @pytest.mark.parametrize('heuristic', ['dbic_bids', 'convertall'])
 @pytest.mark.parametrize(
     'invocation', [
-        "--files tests/data",    # our new way with automated groupping
-        "-d tests/data/{subject}/* -s 01-fmap_acq-3mm" # "old" way specifying subject
+        "--files %s" % TESTS_DATA_PATH,    # our new way with automated groupping
+        "-d %s/{subject}/* -s 01-fmap_acq-3mm" % TESTS_DATA_PATH # "old" way specifying subject
         # should produce the same results
     ])
 @pytest.mark.skipif(Dataset is None, reason="no datalad")
 def test_dbic_bids_largely_smoke(tmpdir, heuristic, invocation):
     is_bids = True if heuristic == 'dbic_bids' else False
-    arg = "--random-seed 1 -f heuristics/%s.py -c dcm2niix -o %s" % (heuristic, tmpdir)
+    arg = "--random-seed 1 -f %s/%s.py -c dcm2niix -o %s" \
+          % (HEURISTICS_PATH, heuristic, tmpdir)
     if is_bids:
         arg += " -b"
     arg += " --datalad "
@@ -47,7 +51,7 @@ def test_dbic_bids_largely_smoke(tmpdir, heuristic, invocation):
     ).split(' ')
 
     # Test some safeguards
-    if invocation == '--files tests/data':
+    if invocation == "--files %s" % TESTS_DATA_PATH:
         # Multiple subjects must not be specified -- only a single one could
         # be overridden from the command line
         with pytest.raises(ValueError):
@@ -87,10 +91,10 @@ def test_dbic_bids_largely_smoke(tmpdir, heuristic, invocation):
 
 @pytest.mark.parametrize(
     'invocation', [
-        "--files tests/data",    # our new way with automated groupping
+        "--files %s" % TESTS_DATA_PATH,    # our new way with automated groupping
     ])
 def test_scans_keys_dbic_bids(tmpdir, invocation):
-    args = "-f heuristics/dbic_bids.py -c dcm2niix -o %s -b " % tmpdir
+    args = "-f %s/dbic_bids.py -c dcm2niix -o %s -b " % (HEURISTICS_PATH, tmpdir)
     args += invocation
     runner(args.split())
     # for now check it exists
@@ -111,7 +115,10 @@ def test_scans_keys_dbic_bids(tmpdir, invocation):
 
 @patch('sys.stdout', new_callable=StringIO)
 def test_ls(stdout):
-    args = "-f heuristics/dbic_bids.py --command ls --files tests/data".split(' ')
+    args = (
+            "-f %s/dbic_bids.py --command ls --files %s"
+            % (HEURISTICS_PATH, TESTS_DATA_PATH)
+    ).split(' ')
     runner(args)
     out = stdout.getvalue()
     assert 'StudySessionInfo(locator=' in out

tests/test_main.py

@@ -13,6 +13,7 @@
                             find_subj_ses)
 from heudiconv.external.dlad import MIN_VERSION, add_to_datalad
 
+from .utils import TESTS_DATA_PATH
 import csv
 import os
 import pytest
@@ -58,7 +59,17 @@ def test_populate_bids_templates(tmpdir):
     for f in "README", "dataset_description.json", "CHANGES":
         # Just test that we have created them and they all have stuff TODO
         assert "TODO" in tmpdir.join(f).read()
-    assert "something" in tmpdir.join('dataset_description.json').read()
+    description_file = tmpdir.join('dataset_description.json')
+    assert "something" in description_file.read()
+
+    # it should also be available as a command
+    os.unlink(str(description_file))
+    runner([
+        '--command', 'populate-templates', '-f', 'heuristics/convertall.py',
+        '--files', str(tmpdir)
+    ])
+    assert "something" not in description_file.read()
+    assert "TODO" in description_file.read()
 
 
 def test_add_participant_record(tmpdir):
@@ -154,9 +165,11 @@ def test_json_dumps_pretty():
 
 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',
+         ('%s/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm'
+          % TESTS_DATA_PATH,
          ('nii.gz', 'dicom'),
-         ['tests/data/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm'])
+         ['%s/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm'
+          % TESTS_DATA_PATH])
     ]
     outname_bids_file = '/a/path/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/fmap/sub-phantom1sid1_acq-3mm_phasediff.json'
 

tests/utils.py

@@ -1,12 +1,12 @@
 import os.path as op
 import heudiconv
 
+HEURISTICS_PATH = op.join(op.dirname(op.dirname(__file__)), 'heuristics')
+TESTS_DATA_PATH = op.join(op.dirname(__file__), 'data')
+
 
 def gen_heudiconv_args(datadir, outdir, subject, heuristic_file, xargs=None):
-    heuristic = op.realpath(op.join(op.dirname(heudiconv.__file__),
-                                    '..',
-                                    'heuristics',
-                                    heuristic_file))
+    heuristic = op.realpath(op.join(HEURISTICS_PATH, heuristic_file))
     args = ["-d", op.join(datadir, 'sourcedata/{subject}/*/*/*.tgz'),
             "-c", "dcm2niix",
             "-o", outdir,