Merge pull request #142 from mgxd/fix/ref

fix: various fixes left over from refactor

Author: yarikoptic

.gitignore

@@ -2,3 +2,4 @@
 .cache/
 .coverage
 *.egg-info/
+.idea/

Dockerfile

@@ -5,7 +5,7 @@
 # pull request on our GitHub repository:
 #     https://github.com/kaczmarj/neurodocker
 #
-# Timestamp: 2017-12-26 18:41:41
+# Timestamp: 2018-02-02 16:32:55
 
 FROM debian:stretch
 
@@ -40,15 +40,15 @@ RUN apt-get update -qq \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 #------------------------
-# Install dcm2niix v1.0.20171017
+# Install dcm2niix v1.0.20171215
 #------------------------
 WORKDIR /tmp
 RUN deps='cmake g++ gcc git make pigz zlib1g-dev' \
     && apt-get update -qq && apt-get install -yq --no-install-recommends $deps \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
     && mkdir dcm2niix \
-    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20171017 | tar xz -C dcm2niix --strip-components 1 \
+    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20171215 | tar xz -C dcm2niix --strip-components 1 \
     && mkdir dcm2niix/build && cd dcm2niix/build \
     && cmake .. && make \
     && make install \
@@ -127,7 +127,7 @@ RUN echo '{ \
     \n    [ \
     \n      "dcm2niix", \
     \n      { \
-    \n        "version": "v1.0.20171017" \
+    \n        "version": "v1.0.20171215" \
     \n      } \
     \n    ], \
     \n    [ \
@@ -159,6 +159,6 @@ RUN echo '{ \
     \n      "/neurodocker/startup.sh heudiconv" \
     \n    ] \
     \n  ], \
-    \n  "generation_timestamp": "2017-12-26 18:41:41", \
+    \n  "generation_timestamp": "2018-02-02 16:32:55", \
     \n  "neurodocker_version": "0.3.2" \
     \n}' > /neurodocker/neurodocker_specs.json

heudiconv/bids.py

@@ -123,8 +123,7 @@ def tuneup_bids_json_files(json_files):
             # Let's hope no word 'Date' comes within a study name or smth like
             # that
             raise ValueError("There must be no dates in .json sidecar")
-        #json.dump(json_, open(jsonfile, 'w'), indent=2)
-        save_json(jsonfile, json_, indent=2) # ensure this does same as above
+        save_json(jsonfile, json_, indent=2)
 
     # Load the beast
     seqtype = op.basename(op.dirname(jsonfile))
@@ -163,7 +162,7 @@ def add_participant_record(studydir, subject, age, sex):
     participant_id = 'sub-%s' % subject
 
     if not create_file_if_missing(participants_tsv,
-            '\t'.join(['participant_id', 'age', 'sex', 'group']) + '\n'):
+           '\t'.join(['participant_id', 'age', 'sex', 'group']) + '\n'):
         # check if may be subject record already exists
         with open(participants_tsv) as f:
             f.readline()

heudiconv/cli/run.py

@@ -7,8 +7,9 @@
 from ..parser import get_study_sessions
 from ..utils import load_heuristic, anonymize_sid, treat_infofile, SeqInfo
 from ..convert import prep_conversion
+from ..bids import populate_bids_templates, tuneup_bids_json_files
+from ..queue import queue_conversion
 
-from ..bids import (populate_bids_templates, tuneup_bids_json_files)
 import inspect
 import logging
 lgr = logging.getLogger(__name__)
@@ -37,7 +38,7 @@ def _pdb_excepthook(type, value, tb):
             # print()
             pdb.post_mortem(tb)
         else:
-            lgr.warn(
+            lgr.warning(
               "We cannot setup exception hook since not in interactive mode")
 
     sys.excepthook = _pdb_excepthook
@@ -116,15 +117,15 @@ def get_parser():
     parser.add_argument('--version', action='version', version=__version__)
     group = parser.add_mutually_exclusive_group()
     group.add_argument('-d', '--dicom_dir_template', dest='dicom_dir_template',
-                        help='location of dicomdir that can be indexed with '
-                        'subject id {subject} and session {session}. Tarballs '
-                        '(can be compressed) are supported in addition to '
-                        'directory. All matching tarballs for a subject are '
-                        'extracted and their content processed in a single pass')
+                       help='location of dicomdir that can be indexed with '
+                       'subject id {subject} and session {session}. Tarballs '
+                       '(can be compressed) are supported in addition to '
+                       'directory. All matching tarballs for a subject are '
+                       'extracted and their content processed in a single pass')
     group.add_argument('--files', nargs='*',
-                        help='Files (tarballs, dicoms) or directories '
-                        'containing files to process. Cannot be provided if '
-                        'using --dicom_dir_template or --subjects')
+                       help='Files (tarballs, dicoms) or directories '
+                       'containing files to process. Cannot be provided if '
+                       'using --dicom_dir_template or --subjects')
     parser.add_argument('-s', '--subjects', dest='subjs', type=str, nargs='*',
                         help='list of subjects - required for dicom template. '
                         'If not provided, DICOMS would first be "sorted" and '

heudiconv/convert.py

@@ -2,6 +2,7 @@
 import os.path as op
 import logging
 import shutil
+import sys
 
 from .utils import (
     read_config,
@@ -68,6 +69,7 @@ def conversion_info(subject, outdir, info, filegroup, ses):
                 try:
                     files = filegroup[item]
                 except KeyError:
+                    PY3 = sys.version_info[0] >= 3
                     files = filegroup[(str if PY3 else unicode)(item)]
                 outprefix = template.format(**parameters)
                 convert_info.append((op.join(outpath, outprefix),
@@ -266,8 +268,8 @@ def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
                     tmpdir = tempdirs('dcm2niix')
 
                     # run conversion through nipype
-                    res = nipype_convert(item_dicoms, prefix, with_prov, bids,
-                                         tmpdir)
+                    res, prov_file = nipype_convert(item_dicoms, prefix, with_prov,
+                                                    bids, tmpdir)
 
                     bids_outfiles = save_converted_files(res, item_dicoms, bids,
                                                          outtype, prefix,
@@ -281,13 +283,7 @@ def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
                     # Fix up and unify BIDS files
                     tuneup_bids_json_files(bids_outfiles)
 
-                    prov_file = prefix + '_prov.ttl' if with_prov else None
                     if prov_file:
-                        safe_copyfile(op.join(convertnode.base_dir,
-                                              convertnode.name,
-                                             'provenance.ttl'),
-                                      prov_file,
-                                      overwrite=overwrite)
                         prov_files.append(prov_file)
 
                     tempdirs.rmtree(tmpdir)
@@ -330,8 +326,17 @@ def convert_dicom(item_dicoms, bids, prefix,
         DICOMs to save
     bids : bool
         Save to BIDS format
-    sourcedir : string
-        Path to BIDS output
+    prefix : string
+        Conversion outname
+    outdir : string
+        Output directory
+    tempdirs : TempDirs instance
+        Object to handle temporary directories created
+        TODO: remove
+    symlink : bool
+        Create softlink to DICOMs - if False, create hardlink instead.
+    overwrite : bool
+        If True, allows overwriting of previous conversion
 
     Returns
     -------
@@ -389,7 +394,17 @@ def nipype_convert(item_dicoms, prefix, with_prov, bids, tmpdir):
     else:
         convertnode.terminal_output = 'allatonce'
     convertnode.inputs.bids_format = bids
-    return convertnode.run()
+    eg = convertnode.run()
+
+    # prov information
+    prov_file = prefix + '_prov.ttl' if with_prov else None
+    if prov_file:
+        safe_copyfile(op.join(convertnode.base_dir,
+                              convertnode.name,
+                              'provenance.ttl'),
+                      prov_file)
+
+    return eg, prov_file
 
 
 def save_converted_files(res, item_dicoms, bids, outtype, prefix, outname_bids, overwrite):

heudiconv/queue.py

@@ -11,7 +11,7 @@ def queue_conversion(progname, queue, outdir, heuristic, dicoms, sid,
 
         # Rework this...
         convertcmd = ' '.join(['python', progname,
-                               '-o', study_outdir,
+                               '-o', outdir,
                                '-f', heuristic,
                                '-s', sid,
                                '--anon-cmd', anon_cmd,