Minor tweaks

Author: marcelzwiers

bidscoin/bidsapps/slicereport.py

@@ -4,7 +4,7 @@
 # NB: Set os.environ['DUECREDIT'] values as early as possible to capture all credits
 import os
 import sys
-if __name__ == "__main__" and os.getenv('DUECREDIT_ENABLE','').lower() not in ('1', 'yes', 'true') and len(sys.argv) > 1:    # Ideally the due state (`self.__active=True`) should also be checked (but that's impossible)
+if __name__ == "__main__" and os.getenv('DUECREDIT_ENABLE','').lower() not in ('1', 'yes', 'true') and len(sys.argv) > 1:    # Ideally, the due state (`self.__active=True`) should also be checked (but that's impossible)
     os.environ['DUECREDIT_ENABLE'] = 'yes'
     os.environ['DUECREDIT_FILE']   = os.path.join(sys.argv[1], 'code', 'bidscoin', '.duecredit_slicereport.p')   # NB: argv[1] = bidsfolder
 
@@ -44,6 +44,7 @@
 
 JOBIDS = []         # Collect JOBIDS to synchronize DRMAA jobs
 
+
 def parse_options(options: list) -> str:
     """Check the OPTIONS arguments and return them to a string that can be passed to slicer"""
     for n, option in enumerate(options):
@@ -88,7 +89,7 @@ def slicer_append(inputimage: Path, operations: str, outlineimage: Path, mainopt
     """Run fslmaths, slicer and pngappend (locally or on the cluster) to create a montage of the sliced images"""
 
     # Create a workdir and the shell command
-    workdir  = montage.parent/next(tempfile._get_candidate_names())
+    workdir  = montage.parent/f"work_{next(tempfile._get_candidate_names())}"
     workdir.mkdir()
     inputimg = nib.load(inputimage)
     reorient = ''
@@ -110,6 +111,7 @@ def slicer_append(inputimage: Path, operations: str, outlineimage: Path, mainopt
                f"pngappend {sliceroutput} {montage.name}\n" \
                f"mv {montage.name} {montage.parent}\n" \
                + (f"rm -r {workdir}" if not DEBUG else '')
+    LOGGER.bcdebug(f"Command: {command}")
 
     # Run the command on the HPC cluster or directly in the shell
     if cluster:
@@ -126,12 +128,12 @@ def slicer_append(inputimage: Path, operations: str, outlineimage: Path, mainopt
             jt.joinFiles           = True
             jt.jobName             = 'slicereport'
             jt.outputPath          = f"{os.getenv('HOSTNAME')}:{workdir if DEBUG else tempfile.gettempdir()}/{jt.jobName}.out"
+            LOGGER.bcdebug(f"nativeSpecification: {cluster} -> {jt.nativeSpecification}")
             JOBIDS.append(pbatch.runJob(jt))
             pbatch.deleteJobTemplate(jt)
-            LOGGER.verbose(f"Your '{jt.jobName}' job has been submitted with ID: {JOBIDS[-1]}")
+            LOGGER.info(f"Your '{jt.jobName}' job has been submitted with ID: {JOBIDS[-1]}")
 
     else:
-        LOGGER.bcdebug(f"Command: {command}")
         process = subprocess.run(command, shell=True, capture_output=True, text=True)
         if process.stderr or process.returncode != 0:
             LOGGER.warning(f"{command}\nErrorcode {process.returncode}:\n{process.stdout}\n{process.stderr}")
@@ -241,11 +243,11 @@ def slicereport(bidsfolder: str, pattern: str, outlinepattern: str, outlineimage
                     tsv_writer.writerow([str(session.relative_to(bidsdir))] + len(qcscores) * ['n/a'])
 
             # Search for the (nibabel supported) image(s) to report
-            LOGGER.info(f"Processing images in: {session.relative_to(bidsdir)}")
             images = sorted([match for match in session.glob(pattern) if match.suffixes[0] in valid_exts])
             if not images:
                 LOGGER.warning(f"Could not find images using: {session.relative_to(bidsdir)}/{pattern}")
                 continue
+            LOGGER.info(f"Processing {len(images)} images in: {session.relative_to(bidsdir)}")
             outlineimages = [''] * len(images)
             if outlinepattern:
                 outlinesession = outlinedir/session.relative_to(bidsdir)

bidscoin/cli/_bcoin.py

@@ -44,12 +44,11 @@ def get_parser() -> argparse.ArgumentParser:
                                      description=textwrap.dedent(__doc__),
                                      epilog='examples:\n'
                                             '  bidscoin -l\n'
-                                            '  bidscoin -d data/bidscoin_tutorial\n'
+                                            '  bidscoin -d data/bidscoin\n'
                                             '  bidscoin -t\n'
                                             '  bidscoin -t my_template_bidsmap\n'
                                             '  bidscoin -b my_study_bidsmap\n'
                                             '  bidscoin -i data/my_template_bidsmap.yaml downloads/my_plugin.py\n'
-                                            '  bidscoin -c myproject/bids\n'
                                             '  bidscoin -c myproject/bids format bibtex\n'
                                             '  bidscoin --tracking show\n ')
     parser.add_argument('-l', '--list',        help='List all executables (i.e. the apps, bidsapps and utilities)', action='store_true')

bidscoin/utilities/bidsparticipants.py

@@ -34,10 +34,7 @@ def bidsparticipants(sourcefolder: str, bidsfolder: str, bidsmap: str='bidsmap.y
         raise SystemExit(f"\n[ERROR] Exiting the program because your bidsfolder argument '{bidsfolder}' was not found")
 
     # Start logging
-    if dryrun:
-        console = bcoin.setup_logging()
-    else:
-        console = bcoin.setup_logging(bidsfolder/'code'/'bidscoin'/'bidsparticipants.log')
+    console = bcoin.setup_logging(Path() if dryrun else bidsfolder/'code'/'bidscoin'/'bidsparticipants.log')
     LOGGER.info('')
     LOGGER.info(f"-------------- START bidsparticipants {__version__} ------------")
     LOGGER.info(f">>> bidsparticipants sourcefolder={rawfolder} bidsfolder={bidsfolder} bidsmap={bidsmap}")
@@ -73,7 +70,7 @@ def bidsparticipants(sourcefolder: str, bidsfolder: str, bidsmap: str='bidsmap.y
         LOGGER.info(f"------------------- Subject {n}/{len(subjects)} -------------------")
         personals = {}
         subject   = rawfolder/subject.name.replace('sub-', subprefix.replace('*',''))     # TODO: This assumes e.g. that the subject-ids in the rawfolder did not contain BIDS-invalid characters (such as '_')
-        sessions  = lsdirs(subject, ('' if sesprefix=='*' else sesprefix) + '*')
+        sessions  = lsdirs(subject, ('' if sesprefix == '*' else sesprefix) + '*')
         if not subject.is_dir():
             LOGGER.error(f"Could not find source-folder: {subject}")
             continue

docs/utilities.rst

@@ -51,12 +51,11 @@ The bidscoin command-line utility serves as a central starting point to test and
 
     examples:
       bidscoin -l
-      bidscoin -d data/bidscoin_tutorial
+      bidscoin -d data/bidscoin
       bidscoin -t
       bidscoin -t my_template_bidsmap
       bidscoin -b my_study_bidsmap
       bidscoin -i data/my_template_bidsmap.yaml downloads/my_plugin.py
-      bidscoin -c myproject/bids
       bidscoin -c myproject/bids format bibtex
       bidscoin --tracking show
 

tests/conftest.py

@@ -8,9 +8,10 @@
     import sys
     sys.path.append(str(Path(__file__).parents[2]))
 from bidscoin.utilities import dicomsort
+from bidscoin import bcoin
 
 Path('./.duecredit.p').unlink(missing_ok=True)
-
+bcoin.setup_logging()
 
 @pytest.fixture(scope='session')
 def raw_dicomdir(tmp_path_factory):

tests/test_bcoin.py

@@ -3,7 +3,6 @@
 from bidscoin import bcoin
 from pathlib import Path
 
-bcoin.setup_logging()
 
 assert bidscoin.schemafolder.is_dir()
 assert bidscoin.templatefolder.is_dir()

tests/test_bids.py

@@ -10,8 +10,6 @@
 from bidscoin import bcoin, bids, bidsmap_template, bidscoinroot
 from bidscoin.bids import BidsMap, RunItem, DataSource, Plugin, Meta
 
-bcoin.setup_logging()
-
 
 @pytest.fixture(scope='module')
 def dcm_file():

tests/test_bidsmapper.py

@@ -2,8 +2,6 @@
 import re
 from bidscoin import bcoin, bidsmapper, bidsmap_template
 
-bcoin.setup_logging()
-
 
 @pytest.mark.parametrize('subprefix', ['Doe', 'Doe^', '*'])
 @pytest.mark.parametrize('sesprefix', ['0', '*'])

tests/test_fixmeta.py

@@ -1,11 +1,8 @@
 import json
 import shutil
 from pathlib import Path
-from bidscoin import bcoin
 from bidscoin.bidsapps.fixmeta import fixmeta
 
-bcoin.setup_logging()
-
 
 def test_fixmeta(tmp_path, test_data):
 

tests/test_heuristics.py

@@ -1,9 +1,7 @@
 import jsonschema
 import json
 import yaml
-from bidscoin import bcoin, bidscoinroot
-
-bcoin.setup_logging()
+from bidscoin import bidscoinroot
 
 
 def test_jsonschema_validate_bidsmaps():