fix: revert to explicit relative imports, use heudiconv executable for queue submissions

Author: mgxd

heudiconv/__init__.py

@@ -1,7 +1,7 @@
 # set logger handler
 import logging
 import os
-from heudiconv.info import (__version__, __packagename__)
+from .info import (__version__, __packagename__)
 
 # Rudimentary logging support.
 lgr = logging.getLogger(__name__)

heudiconv/bids.py

@@ -11,10 +11,10 @@
 from random import sample
 from glob import glob
 
-from heudiconv.external.pydicom import dcm
+from .external.pydicom import dcm
 
-from heudiconv.parser import find_files
-from heudiconv.utils import (
+from .parser import find_files
+from .utils import (
     load_json,
     save_json,
     create_file_if_missing,

heudiconv/cli/run.py

@@ -5,12 +5,12 @@
 from argparse import ArgumentParser
 import sys
 
-from heudiconv import __version__, __packagename__
-from heudiconv.parser import get_study_sessions
-from heudiconv.utils import load_heuristic, anonymize_sid, treat_infofile, SeqInfo
-from heudiconv.convert import prep_conversion
-from heudiconv.bids import populate_bids_templates, tuneup_bids_json_files
-from heudiconv.queue import queue_conversion
+from .. import __version__, __packagename__
+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
 
 import inspect
 import logging
@@ -84,11 +84,11 @@ def process_extra_commands(outdir, args):
     elif args.command == 'sanitize-jsons':
         tuneup_bids_json_files(args.files)
     elif args.command == 'heuristics':
-        from heudiconv.utils import get_known_heuristics_with_descriptions
+        from .utils import get_known_heuristics_with_descriptions
         for name_desc in get_known_heuristics_with_descriptions().items():
             print("- %s: %s" % name_desc)
     elif args.command == 'heuristic-info':
-        from heudiconv.utils import get_heuristic_description, get_known_heuristic_names
+        from .utils import get_heuristic_description, get_known_heuristic_names
         if not args.heuristic:
             raise ValueError("Specify heuristic using -f. Known are: %s"
                              % ', '.join(get_known_heuristic_names()))
@@ -284,15 +284,6 @@ def process_args(args):
             continue
 
         if args.queue:
-            # if seqinfo and not dicoms:
-            #     # flatten them all and provide into batching, which again
-            #     # would group them... heh
-            #     dicoms = sum(seqinfo.values(), [])
-            #     raise NotImplementedError(
-            #         "we already grouped them so need to add a switch to avoid "
-            #         "any grouping, so no outdir prefix doubled etc")
-
-            pyscript = op.abspath(inspect.getfile(inspect.currentframe()))
 
             studyid = sid
             if session:
@@ -302,8 +293,7 @@ def process_args(args):
             # remove any separators
             studyid = studyid.replace(op.sep, '_')
 
-            queue_conversion(pyscript,
-                             args.queue,
+            queue_conversion(args.queue,
                              studyid,
                              args.queue_args)
             continue

heudiconv/convert.py

@@ -4,7 +4,7 @@
 import shutil
 import sys
 
-from heudiconv.utils import (
+from .utils import (
     read_config,
     load_json,
     save_json,
@@ -18,15 +18,15 @@
     assure_no_file_exists,
     file_md5sum
 )
-from heudiconv.bids import (
+from .bids import (
     convert_sid_bids,
     populate_bids_templates,
     save_scans_key,
     tuneup_bids_json_files,
     add_participant_record,
     BIDSError
 )
-from heudiconv.dicoms import (
+from .dicoms import (
     group_dicoms_into_seqinfos,
     embed_metadata_from_dicoms,
     compress_dicoms

heudiconv/dicoms.py

@@ -5,8 +5,8 @@
 from collections import OrderedDict
 import tarfile
 
-from heudiconv.external.pydicom import dcm
-from heudiconv.utils import SeqInfo, load_json, set_readonly
+from .external.pydicom import dcm
+from .utils import SeqInfo, load_json, set_readonly
 
 lgr = logging.getLogger(__name__)
 
@@ -55,10 +55,10 @@ def group_dicoms_into_seqinfos(files, file_filter, dcmfilter, grouping):
         lgr.info('Filtering out {0} dicoms based on their filename'.format(
             nfl_before-nfl_after))
     for fidx, filename in enumerate(files):
-        from heudiconv.external.dcmstack import ds
+        import nibabel.nicom.dicomwrappers as dw
         # TODO after getting a regression test check if the same behavior
         #      with stop_before_pixels=True
-        mw = ds.wrapper_from_data(dcm.read_file(filename, force=True))
+        mw = dw.wrapper_from_data(dcm.read_file(filename, force=True))
 
         for sig in ('iop', 'ICE_Dims', 'SequenceName'):
             try:
@@ -385,7 +385,7 @@ def embed_nifti(dcmfiles, niftifile, infofile, bids_info, min_meta):
     import re
 
     if not min_meta:
-        import dcmstack as ds
+        from .external.dcmstack import ds
         stack = ds.parse_and_stack(dcmfiles, force=True).values()
         if len(stack) > 1:
             raise ValueError('Found multiple series')

heudiconv/external/dcmstack.py

@@ -2,12 +2,12 @@
 
 from __future__ import absolute_import
 
-from heudiconv.external.pydicom import dcm  # to assure that we have it one way or another
+from .pydicom import dcm  # to assure that we have it one way or another
 
 try:
     import dcmstack as ds
 except ImportError as e:
-    from heudiconv import lgr
+    from .. import lgr
     # looks different between py2 and 3 so we go for very rudimentary matching
     e_str = str(e)
     # there were changes from how

heudiconv/parser.py

@@ -9,8 +9,8 @@
 import tarfile
 from tempfile import mkdtemp
 
-from heudiconv.dicoms import group_dicoms_into_seqinfos
-from heudiconv.utils import (
+from .dicoms import group_dicoms_into_seqinfos
+from .utils import (
     docstring_parameter,
     StudySessionInfo,
 )

heudiconv/queue.py

@@ -1,20 +1,19 @@
 import subprocess
 import sys
 import os
-
 import logging
 
+from .utils import which
+
 lgr = logging.getLogger(__name__)
 
-def queue_conversion(pyscript, queue, studyid, queue_args=None):
+def queue_conversion(queue, studyid, queue_args=None):
     """
     Write out conversion arguments to file and submit to a job scheduler.
     Parses `sys.argv` for heudiconv arguments.
 
     Parameters
     ----------
-    pyscript: file
-        path to `heudiconv` script
     queue: string
         batch scheduler to use
     studyid: string
@@ -34,9 +33,8 @@ def queue_conversion(pyscript, queue, studyid, queue_args=None):
 
     args = clean_args(sys.argv[1:])
     # make arguments executable
-    args.insert(0, pyscript)
-    pypath = sys.executable or "python"
-    args.insert(0, pypath)
+    heudiconv_exec = which("heudiconv") or "heudiconv"
+    args.insert(0, heudiconv_exec)
     convertcmd = " ".join(args)
 
     # will overwrite across subjects

heudiconv/tests/test_queue.py

@@ -3,10 +3,9 @@
 import subprocess
 
 from heudiconv.cli.run import main as runner
-from heudiconv.queue import clean_args
+from heudiconv.queue import clean_args, which
 from .utils import TESTS_DATA_PATH
 import pytest
-from nipype.utils.filemanip import which
 
 @pytest.mark.skipif(which("sbatch"), reason="skip a real slurm call")
 @pytest.mark.parametrize(

heudiconv/utils.py

@@ -12,6 +12,9 @@
 from pathlib import Path
 from collections import namedtuple
 from glob import glob
+from subprocess import check_output
+
+from nipype.utils.filemanip import which
 
 import logging
 lgr = logging.getLogger(__name__)
@@ -103,18 +106,17 @@ def dec(obj):
 
 
 def anonymize_sid(sid, anon_sid_cmd):
-    import sys
-    from subprocess import check_output
-    
+
     cmd = [anon_sid_cmd, sid]
     shell_return = check_output(cmd)
 
-    ### Handle subprocess returning a bytes literal string to a python3 interpreter
-    if all([sys.version_info[0] > 2, isinstance(shell_return, bytes), isinstance(sid, str)]):
+    if all([sys.version_info[0] > 2,
+            isinstance(shell_return, bytes),
+            isinstance(sid, str)]):
         anon_sid = shell_return.decode()
     else:
         anon_sid = shell_return
-    
+
     return anon_sid.strip()