Merge pull request #151 from dartmouth-pbs/fix/emptydir2

FIX,TST: better handling of dicom-only conversion

Author: yarikoptic

heudiconv/convert.py

@@ -236,15 +236,18 @@ def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
 
         prefix, outtypes, item_dicoms = item[:3]
         if not isinstance(outtypes, (list, tuple)):
-            outtypes = [outtypes]
+            outtypes = (outtypes,)
 
         prefix_dirname = op.dirname(prefix + '.ext')
         outname_bids = prefix + '.json'
         bids_outfiles = []
         lgr.info('Converting %s (%d DICOMs) -> %s . '
                  'Converter: %s . Output types: %s',
                  prefix, len(item_dicoms), prefix_dirname, converter, outtypes)
-        if not op.exists(prefix_dirname):
+        # We want to create this dir only if we are converting it to nifti,
+        # or if we're using BIDS
+        dicom_only = outtypes == ('dicom',)
+        if not(dicom_only and bids) and not op.exists(prefix_dirname):
             os.makedirs(prefix_dirname)
 
         for outtype in outtypes:
@@ -254,6 +257,9 @@ def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
 
             seqtype = op.basename(op.dirname(prefix)) if bids else None
 
+            # set empty outname and scaninfo in case we only want dicoms
+            outname = ''
+            scaninfo = ''
             if outtype == 'dicom':
                 convert_dicom(item_dicoms, bids, prefix,
                               outdir, tempdirs, symlink, overwrite)
@@ -299,17 +305,17 @@ def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
                         "multiple files")
         elif not bids_outfiles:
             lgr.debug("No BIDS files were produced, nothing to embed to then")
-        else:
+        elif outname:
             embed_metadata_from_dicoms(bids, item_dicoms, outname, outname_bids,
                                        prov_file, scaninfo, tempdirs, with_prov,
                                        min_meta)
-        if op.exists(scaninfo):
+        if scaninfo and op.exists(scaninfo):
             lgr.info("Post-treating %s file", scaninfo)
             treat_infofile(scaninfo)
 
         # this may not always be the case: ex. fieldmap1, fieldmap2
         # will address after refactor
-        if op.exists(outname):
+        if outname and op.exists(outname):
             set_readonly(outname)
 
     if custom_callable is not None:

tests/data/01-anat-scout/0001.dcm

@@ -1,6 +1,7 @@
 from heudiconv.cli.run import main as runner
 
 import os
+import os.path as op
 from mock import patch
 from six.moves import StringIO
 
@@ -98,7 +99,7 @@ def test_scans_keys_reproin(tmpdir, invocation):
     args += invocation
     runner(args.split())
     # for now check it exists
-    scans_keys = glob(pjoin(tmpdir.strpath, '*/*/*/*/*.tsv'))
+    scans_keys = glob(pjoin(tmpdir.strpath, '*/*/*/*/*/*.tsv'))
     assert(len(scans_keys) == 1)
     with open(scans_keys[0]) as f:
         reader = csv.reader(f, delimiter='\t')
@@ -123,3 +124,23 @@ def test_ls(stdout):
     out = stdout.getvalue()
     assert 'StudySessionInfo(locator=' in out
     assert 'Halchenko/Yarik/950_bids_test4' in out
+
+
+def test_scout_conversion(tmpdir):
+    tmppath = tmpdir.strpath
+    args = (
+        "-b -f reproin --files %s"
+        % (TESTS_DATA_PATH)
+    ).split(' ') + ['-o', tmppath]
+    runner(args)
+
+    assert not op.exists(pjoin(
+        tmppath,
+        'Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/anat'))
+
+    assert op.exists(pjoin(
+        tmppath,
+        'Halchenko/Yarik/950_bids_test4/sourcedata/sub-phantom1sid1/'
+        'ses-localizer/anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz'
+    )
+    )

tests/test_heuristics.py

@@ -6,7 +6,26 @@
 from tinydb import TinyDB, Query
 from subprocess import CalledProcessError
 
-from heudiconv.cli.monitor import monitor, process, run_heudiconv, MASK_NEWDIR
+try:
+    from heudiconv.cli.monitor import (monitor, process, run_heudiconv,
+                                       MASK_NEWDIR)
+
+    Header = namedtuple('header', ['wd', 'mask', 'cookie', 'len'])
+    header = Header(5, MASK_NEWDIR, 5, 5)
+    watch_path = b'WATCHME'
+    filename = b'FILE'
+    type_names = b'TYPE'
+
+    path2 = watch_path + b'/' + filename + b'/subpath'
+
+    my_events = [(header, type_names, watch_path, filename),
+                 (header, type_names, path2, b'')]
+except AttributeError:
+    # Import of inotify fails on mac os x with error
+    # lsym(0x11fbeb780, inotify_init): symbol not found
+    # because inotify doesn't seem to exist on Mac OS X
+    my_events = []
+    pytestmark = pytest.mark.skip(reason='Unable to import inotify')
 
 
 class MockInotifyTree(object):
@@ -26,16 +45,6 @@ def __call__(self):
         return self.time
 
 
-Header = namedtuple('header', ['wd', 'mask', 'cookie', 'len'])
-header = Header(5, MASK_NEWDIR, 5, 5)
-watch_path = b'WATCHME'
-filename = b'FILE'
-type_names = b'TYPE'
-
-path2 = watch_path + b'/' + filename + b'/subpath'
-
-my_events = [(header, type_names, watch_path, filename),
-             (header, type_names, path2, b'')]
 
 @pytest.mark.skip(reason="TODO")
 @patch('inotify.adapters.InotifyTree', MockInotifyTree(my_events))