Refactoring + deepcopy bugfixes

bidscoin/bcoin.py

@@ -498,11 +498,11 @@ def test_bidsmap(bidsmapfile: str):
     return bidsmap.validate(1)
 
 
-def test_bidscoin(bidsmapfile: Path, options: dict=None, testplugins: bool=True, testgui: bool=True, testtemplate: bool=True) -> int:
+def test_bidscoin(bidsmapfile, options: dict=None, testplugins: bool=True, testgui: bool=True, testtemplate: bool=True) -> int:
     """
     Performs a bidscoin installation test
 
-    :param bidsmapfile: The bidsmap or the full pathname/basename of the bidsmap yaml-file
+    :param bidsmapfile: The full pathname/basename of the bidsmap yaml-file or the bidsmap object itself
     :param options:     The bidscoin options. If empty, the default options are used
     :return:            0 if the test was successful, otherwise 1
     """
@@ -568,16 +568,15 @@ def test_bidscoin(bidsmapfile: Path, options: dict=None, testplugins: bool=True,
     list_executables(True)
 
     # Test the plugins
-    options = bidsmap['Options'] if not options and bidsmap else {}
-    if not options.get('plugins'):
+    if not bidsmap.plugins:
         LOGGER.warning('No plugins found in the bidsmap (BIDScoin will likely not do anything)')
     if testplugins:
 
         # Show an overview of the plugins and show the test results
         list_plugins(True)
         for plugin in pluginfolder.glob('*.py'):
             if plugin.stem != '__init__':
-                errorcode = test_plugin(plugin.stem, options['plugins'].get(plugin.stem,{}) if options else {})
+                errorcode = test_plugin(plugin.stem, bidsmap.plugins.get(plugin.stem, {}))
                 success   = not errorcode and success
                 if errorcode:
                     LOGGER.warning(f"Failed test: {plugin.stem}")
@@ -705,9 +704,9 @@ def main():
         settracking(value=args.tracking)
         reportcredits(args=args.credits)
 
-    except Exception:
+    except Exception as error:
         trackusage('bidscoin_exception')
-        raise
+        raise error
 
 
 if __name__ == "__main__":

bidscoin/bidsapps/deface.py

@@ -167,9 +167,9 @@ def main():
     try:
         deface(**vars(args))
 
-    except Exception:
+    except Exception as error:
         trackusage('deface_exception')
-        raise
+        raise error
 
 
 if __name__ == '__main__':

bidscoin/bidsapps/echocombine.py

@@ -213,9 +213,9 @@ def main():
     try:
         echocombine(**vars(args))
 
-    except Exception:
+    except Exception as error:
         trackusage('echocombine_exception')
-        raise
+        raise error
 
 
 if __name__ == '__main__':

bidscoin/bidsapps/fixmeta.py

@@ -53,9 +53,9 @@ def fixmeta(bidsfolder: str, pattern: str, metadata: dict, participant: list, bi
     LOGGER.info(f"Command: fixmeta {' '.join(sys.argv[1:])}")
 
     # Load the bidsmap data (-> plugins)
-    bidsmap, _ = bids.BidsMap(Path(bidsmap or 'bidsmap.yaml'), bidsdir/'code'/'bidscoin', checks=(False, False, False))
-    if not bidsmap:
-        bidsmap, _ = bids.BidsMap(bidsmap_template, checks=(False, False, False))
+    bidsmap = bids.BidsMap(Path(bidsmap or 'bidsmap.yaml'), bidsdir/'code'/'bidscoin', checks=(False, False, False))
+    if not bidsmap.filepath:
+        bidsmap = bids.BidsMap(bidsmap_template, checks=(False, False, False))
     plugins  = bidsmap.plugins
     provdata = bids.bidsprov(bidsdir)
 
@@ -117,9 +117,9 @@ def main():
     try:
         fixmeta(**vars(args))
 
-    except Exception:
+    except Exception as error:
         trackusage('fixmeta_exception')
-        raise
+        raise error
 
 
 if __name__ == '__main__':

bidscoin/bidsapps/medeface.py

@@ -215,9 +215,9 @@ def main():
     try:
         medeface(**vars(args))
 
-    except Exception:
+    except Exception as error:
         trackusage('medeface_exception')
-        raise
+        raise error
 
 
 if __name__ == '__main__':

bidscoin/bidsapps/skullstrip.py

@@ -245,9 +245,9 @@ def main():
     try:
         skullstrip(**vars(args))
 
-    except Exception:
+    except Exception as error:
         trackusage('skullstrip_exception')
-        raise
+        raise error
 
 
 if __name__ == '__main__':

bidscoin/bidsapps/slicereport.py

@@ -50,7 +50,7 @@ def parse_options(options: list) -> str:
     for n, option in enumerate(options):
         if options[n-1] == 'l': continue                  # Skip checking the LUT string
         if not (option in ('L','l','i','e','t','n','u','s','c') or option.replace('.','').replace('-','').isdecimal()):
-            print(f"Invalid OPTIONS: {' '.join(options)}"); sys.exit(2)
+            raise SystemExit(f"[ERROR] Invalid OPTIONS: {' '.join(options)}")
         if option.isalpha():
             options[n] = '-' + options[n]
 
@@ -68,18 +68,18 @@ def parse_outputs(outputargs: list, name: str) -> tuple:
     isnumber = lambda arg: arg.replace('.','').replace('-','').isdecimal()
     for n, outputarg in enumerate(outputargs):
         if not (outputarg in ('x', 'y', 'z', 'a', 'A', 'S', 'LF') or isnumber(outputarg)):
-            print(f"Invalid {name}: '{outputarg}' in '{' '.join(outputargs)}'"); sys.exit(2)
+            raise SystemExit(f"[ERROR] Invalid {name}: '{outputarg}' in '{' '.join(outputargs)}'")
         if outputarg.isalpha() and outputarg != 'LF':
             slices += f"{'' if n==0 else '-' if outputargs[n-1]=='LF' else '+'} slice_tmp{n}.png "
             if outputarg == 'a':
                 outputs += f"-{outputarg} slice_tmp{n}.png "
             elif outputarg in ('x', 'y', 'z', 'A'):
                 if not isnumber(outputargs[n+1]):
-                    print(f"Invalid {name}: '{outputargs[n+1]}' in '{' '.join(outputargs)}'"); sys.exit(2)
+                    raise SystemExit(f"[ERROR] Invalid {name}: '{outputargs[n+1]}' in '{' '.join(outputargs)}'")
                 outputs += f"-{outputarg} {outputargs[n+1]} slice_tmp{n}.png "
             elif outputarg == 'S':
                 if not (isnumber(outputargs[n+1]) and isnumber(outputargs[n+2])):
-                    print(f"Invalid {name}: {outputarg} >> '{' '.join(outputargs)}'"); sys.exit(2)
+                    raise SystemExit(f"[ERROR] Invalid {name}: {outputarg} >> '{' '.join(outputargs)}'")
                 outputs += f"-{outputarg} {outputargs[n+1]} {outputargs[n+2]} slice_tmp{n}.png "
 
     return outputs, slices
@@ -135,7 +135,7 @@ def slicer_append(inputimage: Path, operations: str, outlineimage: Path, mainopt
         if process.stderr or process.returncode != 0:
             LOGGER.warning(f"{command}\nErrorcode {process.returncode}:\n{process.stdout}\n{process.stderr}")
         if process.returncode != 0:
-            sys.exit(process.returncode)
+            raise SystemExit(process.returncode)
 
 
 def slicereport(bidsfolder: str, pattern: str, outlinepattern: str, outlineimage: str, participant: list, reportfolder: str, xlinkfolder: str, qcscores: list, cluster: str, operations: str, suboperations: str, options: list, outputs: list, suboptions: list, suboutputs: list):
@@ -330,9 +330,9 @@ def main():
     try:
         slicereport(**vars(args))
 
-    except Exception:
+    except Exception as error:
         trackusage('slicereport_exception')
-        raise
+        raise error
 
 
 if __name__ == '__main__':

bidscoin/bidscoiner.py

@@ -44,8 +44,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
     bidscoinfolder = bidsfolder/'code'/'bidscoin'
     bidscoinfolder.mkdir(parents=True, exist_ok=True)
     if not rawfolder.is_dir():
-        print(f"Rawfolder '{rawfolder}' not found")
-        return
+        raise SystemExit(f"\n[ERROR] Exiting the program because your sourcefolder argument '{sourcefolder}' was not found")
 
     # Start logging
     bcoin.setup_logging(bidscoinfolder/'bidscoiner.log')
@@ -81,7 +80,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
 
     # Create a README file if it does not exist
     readme_file = bidsfolder/'README'
-    if not (readme_file.is_file() or next(bidsfolder.glob('README.*'))):
+    if not (readme_file.is_file() or next(bidsfolder.glob('README.*'), None)):
         LOGGER.info(f"Creating a template README file (adjust it to your needs): {readme_file}")
         try:
             urllib.request.urlretrieve('https://raw.githubusercontent.com/bids-standard/bids-starter-kit/main/templates/README.MD', readme_file)
@@ -150,7 +149,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
 
                 # Check if we should skip the session-folder
                 datasource = bids.get_datasource(subject, bidsmap.plugins)
-                subid,_    = datasource.subid_sesid(bidsmap[datasource.dataformat]['subject'], bidsmap[datasource.dataformat]['session'])
+                subid,_    = datasource.subid_sesid(bidsmap.dataformat(datasource.dataformat).subject, bidsmap.dataformat(datasource.dataformat).session)
                 if (bidsfolder/subid).is_dir() and not force:
                     LOGGER.info(f">>> Skipping already processed subject: {bidsfolder/subid} (you can use the -f option to overrule)")
                     continue
@@ -263,15 +262,15 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
                     if not datasource.dataformat:
                         LOGGER.info(f">>> No datasources found in '{sesfolder}'")
                         continue
-                    subid        = bidsmap[datasource.dataformat]['subject']
-                    sesid        = bidsmap[datasource.dataformat]['session']
+                    subid        = bidsmap.dataformat(datasource.dataformat).subject
+                    sesid        = bidsmap.dataformat(datasource.dataformat).session
                     subid, sesid = datasource.subid_sesid(subid, sesid or '')
                     bidssession  = bidsfolder/subid/sesid       # TODO: Support DICOMDIR with multiple subjects (as in PYDICOMDIR)
                     if not force and bidssession.is_dir():
                         datatypes = set()
-                        for dataformat in dataformats:
-                            for datatype in lsdirs(bidssession):                               # See what datatypes we already have in the bids session-folder
-                                if list(datatype.iterdir()) and bidsmap[dataformat].get(datatype.name): # See if we are going to add data for this datatype
+                        for datatype in [dtype for dtype in lsdirs(bidssession) if next(dtype.iterdir())]:  # See what non-empty datatypes we already have in the bids session-folder
+                            for dataformat in bidsmap.dataformats:
+                                if datatype.name in dataformat.datatypes:                                   # See if we are going to add data for this datatype
                                     datatypes.add(datatype.name)
                         if datatypes:
                             LOGGER.info(f">>> Skipping processed session: {bidssession} already has {datatypes} data (you can carefully use the -f option to overrule)")
@@ -320,9 +319,9 @@ def main():
     try:
         bidscoiner(**vars(args))
 
-    except Exception:
+    except Exception as error:
         trackusage('bidscoiner_exception')
-        raise
+        raise error
 
 
 if __name__ == "__main__":