Merge pull request #215 from DominikaZ/fix-nonexistent-jsonfiles

Add only existing jsonfiles to jsonfiles and make it set

bidscoin/plugins/dcm2niix2bids.py

@@ -266,7 +266,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
         bidsname   = bids.get_bidsname(subid, sesid, run, not bidsignore, runtime=True)
         bidsignore = bidsignore or bids.check_ignore(bidsname+'.json', bidsmap['Options']['bidscoin']['bidsignore'], 'file')
         bidsname   = bids.increment_runindex(outfolder, bidsname, run, scans_table)
-        jsonfiles  = [(outfolder/bidsname).with_suffix('.json')]     # List -> Collect the associated json-files (for updating them later) -- possibly > 1
+        jsonfiles  = set()  # Set -> Collect the associated json-files (for updating them later) -- possibly > 1
 
         # Check if the bidsname is valid
         bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.json').as_posix()
@@ -293,6 +293,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
             try:
                 physiodata = physio.readphysio(sourcefile)
                 physio.physio2tsv(physiodata, outfolder/bidsname)
+                jsonfiles.update(outfolder.glob(f"{bidsname}.json"))  # add existing created json files: bidsname.json
             except Exception as physioerror:
                 LOGGER.error(f"Could not read/convert physiological file: {sourcefile}\n{physioerror}")
                 continue
@@ -308,6 +309,8 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
             if bcoin.run_command(command):
                 if not list(outfolder.glob(f"{bidsname}.*nii*")): continue
 
+            jsonfiles.update(outfolder.glob(f"{bidsname}.json"))  # add existing created json files: bidsname.json
+
             # Handle the ABCD GE pepolar sequence
             extrafile = list(outfolder.glob(f"{bidsname}a.nii*"))
             if extrafile:
@@ -320,7 +323,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
                     LOGGER.verbose(f"Renaming GE reversed polarity image: {extrafile[0]} -> {invfile}")
                     extrafile[0].replace(invfile)
                     extrafile[0].with_suffix('').with_suffix('.json').replace(invfile.with_suffix('').with_suffix('.json'))
-                    jsonfiles.append(invfile.with_suffix('').with_suffix('.json'))
+                    jsonfiles.add(invfile.with_suffix('').with_suffix('.json'))
                 else:
                     LOGGER.warning(f"Unexpected variants of {outfolder/bidsname}* were produced by dcm2niix. Possibly this can be remedied by using the dcm2niix -i option (to ignore derived, localizer and 2D images) or by clearing the BIDS folder before running bidscoiner")
 
@@ -335,8 +338,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
             # Rename all files that got additional postfixes from dcm2niix. See: https://github.com/rordenlab/dcm2niix/blob/master/FILENAMING.md
             dcm2niixpostfixes = ('_c', '_i', '_Eq', '_real', '_imaginary', '_MoCo', '_t', '_Tilt', '_e', '_ph', '_ADC', '_fieldmaphz')      #_c%d, _e%d and _ph (and any combination of these in that order) are for multi-coil data, multi-echo data and phase data
             dcm2niixfiles     = sorted(set([dcm2niixfile for dcm2niixpostfix in dcm2niixpostfixes for dcm2niixfile in outfolder.glob(f"{bidsname}*{dcm2niixpostfix}*.nii*")]))
-            if not jsonfiles[0].is_file() and dcm2niixfiles:                                                    # Possibly renamed by dcm2niix, e.g. with multi-echo data (but not always for the first echo)
-                jsonfiles.pop(0)
+
             for dcm2niixfile in dcm2niixfiles:
 
                 # Strip each dcm2niix postfix and assign it to bids entities in a newly constructed bidsname
@@ -431,12 +433,12 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
                     if oldjsonfile in jsonfiles:
                         jsonfiles.remove(oldjsonfile)
                     if newjsonfile not in jsonfiles:
-                        jsonfiles.append(newjsonfile)
+                        jsonfiles.add(newjsonfile)
                 for oldfile in outfolder.glob(dcm2niixfile.with_suffix('').stem + '.*'):
                     oldfile.replace(newjsonfile.with_suffix(''.join(oldfile.suffixes)))
 
         # Loop over all the newly produced json sidecar-files and adapt the data (NB: assumes every NIfTI-file comes with a json-file)
-        for jsonfile in sorted(set(jsonfiles)):
+        for jsonfile in sorted(jsonfiles):
 
             # Load / copy over the source meta-data
             metadata = bids.updatemetadata(sourcefile, jsonfile, run['meta'], options['meta'], datasource)