Re-Refactoring of IO helper functions (bidscoin.plugins -> bidscoin.utilities)

Author: marcelzwiers

bidscoin/bids.py

@@ -19,17 +19,15 @@
 from fnmatch import fnmatch
 from pathlib import Path
 from typing import Union, Any, Iterable, NewType
-from pydicom import config
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[1]))
-from bidscoin import bcoin, schemafolder, templatefolder, lsdirs, is_hidden, __version__, DEBUG
+from bidscoin import bcoin, schemafolder, templatefolder, is_hidden, __version__
 from bidscoin.plugins import EventsParser
 from ruamel.yaml import YAML
 yaml = YAML()
 yaml.representer.ignore_aliases = lambda *data: True    # Expand aliases (https://stackoverflow.com/questions/58091449/disabling-alias-for-yaml-file-in-python)
-config.INVALID_KEY_BEHAVIOR = 'IGNORE'
 
 # Define custom data types (replace with proper classes or TypeAlias of Python >= 3.10)
 Plugin     = NewType('Plugin',     dict[str, Any])

bidscoin/bidscoiner.py

@@ -21,7 +21,7 @@
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[1]))
 from bidscoin import bcoin, bids, lsdirs, bidsversion, trackusage, __version__, DEBUG
-from bidscoin.plugins import unpack
+from bidscoin.utilities import unpack
 
 
 def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force: bool=False, bidsmap: str='bidsmap.yaml', cluster: str='') -> None:

bidscoin/bidsmapper.py

@@ -20,7 +20,7 @@
     sys.path.append(str(Path(__file__).parents[1]))
 from bidscoin import bcoin, lsdirs, trackusage, check_version, __version__
 from bidscoin.bids import BidsMap
-from bidscoin.plugins import unpack
+from bidscoin.utilities import unpack
 
 _, uptodate, versionmessage = check_version()
 

bidscoin/plugins/__init__.py

@@ -14,9 +14,9 @@
 from typing import Union
 from pathlib import Path
 from bidscoin import bids, run_command, lsdirs, due, Doi
-from bidscoin.utilities import physio
+from bidscoin.utilities import physio, is_dicomfile, is_parfile, get_dicomfield, get_parfield, get_dicomfile, get_parfiles
 from bidscoin.bids import BidsMap, DataFormat, Plugin, Plugins
-from bidscoin.plugins import PluginInterface, is_dicomfile, is_parfile, get_dicomfield, get_parfield, get_dicomfile, get_parfiles
+from bidscoin.plugins import PluginInterface
 try:
     from nibabel.testing import data_path
 except ImportError:
@@ -92,7 +92,6 @@ def has_support(self, file: Path, dataformat: Union[DataFormat, str]='') -> str:
 
         return ''
 
-
     def get_attribute(self, dataformat: Union[DataFormat, str], sourcefile: Path, attribute: str, options) -> Union[str, int]:
         """
         This plugin supports reading attributes from DICOM and PAR dataformats
@@ -109,7 +108,6 @@ def get_attribute(self, dataformat: Union[DataFormat, str], sourcefile: Path, at
         if dataformat == 'PAR':
             return get_parfield(attribute, sourcefile)
 
-
     def bidsmapper(self, session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap, template: BidsMap) -> None:
         """
         The goal of this plugin function is to identify all the different runs in the session and update the
@@ -190,7 +188,6 @@ def bidsmapper(self, session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap,
             else:
                 LOGGER.bcdebug(f"Existing/duplicate sample: {run.datasource}")
 
-
     @due.dcite(Doi('10.1016/j.jneumeth.2016.03.001'), description='dcm2niix: DICOM to NIfTI converter', tags=['reference-implementation'])
     def bidscoiner(self, session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[None, dict]:
         """
@@ -206,9 +203,8 @@ def bidscoiner(self, session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[No
         """
 
         # Get the subject identifiers and the BIDS root folder from the bidsses folder
-        subid      = bidsses.name if bidsses.name.startswith('sub-') else bidsses.parent.name
-        sesid      = bidsses.name if bidsses.name.startswith('ses-') else ''
-        bidsfolder = bidsses.parent.parent if sesid else bidsses.parent
+        subid = bidsses.name if bidsses.name.startswith('sub-') else bidsses.parent.name
+        sesid = bidsses.name if bidsses.name.startswith('ses-') else ''
 
         # Get started and see what dataformat we have
         options          = Plugin(bidsmap.plugins['dcm2niix2bids'])
@@ -222,13 +218,10 @@ def bidscoiner(self, session: Path, bidsmap: BidsMap, bidsses: Path) -> Union[No
 
         # Make a list of all the data sources/runs
         sources: list[Path] = []
-        manufacturer = 'UNKNOWN'
         if dataformat == 'DICOM':
-            sources      = lsdirs(session, '**/*')
-            manufacturer = datasource.attributes('Manufacturer')
+            sources = lsdirs(session, '**/*')
         elif dataformat == 'PAR':
-            sources      = get_parfiles(session)
-            manufacturer = 'Philips Medical Systems'
+            sources = get_parfiles(session)
         else:
             LOGGER.error(f"Unsupported dataformat '{dataformat}'")
 

bidscoin/plugins/dcm2niix2bids.py

@@ -62,7 +62,6 @@ def test(self, options: Plugin=OPTIONS) -> int:
 
         return 0
 
-
     def has_support(self, file: Path, dataformat: Union[DataFormat, str]='') -> str:
         """
         This plugin function assesses whether a sourcefile is of a supported dataformat
@@ -81,7 +80,6 @@ def has_support(self, file: Path, dataformat: Union[DataFormat, str]='') -> str:
 
         return ''
 
-
     def get_attribute(self, dataformat: Union[DataFormat, str], sourcefile: Path, attribute: str, options: Plugin) -> Union[str, int, float, list]:
         """
         This plugin supports reading attributes from DICOM and PAR dataformats
@@ -107,7 +105,6 @@ def get_attribute(self, dataformat: Union[DataFormat, str], sourcefile: Path, at
 
         return value
 
-
     def bidscoiner(self, session: Path, bidsmap: BidsMap, bidsses: Path) -> None:
         """
         The bidscoiner plugin to convert the session Nibabel source-files into BIDS-valid NIfTI-files in the

bidscoin/plugins/nibabel2bids.py

@@ -12,7 +12,8 @@
 from pathlib import Path
 from bidscoin import run_command, is_hidden, bids, due, Doi
 from bidscoin.bids import BidsMap, DataFormat, Plugin
-from bidscoin.plugins import PluginInterface, is_dicomfile, get_twixfield, get_sparfield, get_p7field
+from bidscoin.plugins import PluginInterface
+from bidscoin.utilities import is_dicomfile, get_twixfield, get_sparfield, get_p7field
 
 LOGGER = logging.getLogger(__name__)
 
@@ -45,7 +46,6 @@ def test(self, options: Plugin=OPTIONS) -> int:
         # Test the spec2nii installation
         return run_command(f"{options.get('command',OPTIONS['command'])} -v")
 
-
     def has_support(self, file: Path, dataformat: Union[DataFormat, str]='') -> str:
         """
         This plugin function assesses whether a sourcefile is of a supported dataformat
@@ -68,7 +68,6 @@ def has_support(self, file: Path, dataformat: Union[DataFormat, str]='') -> str:
 
         return ''
 
-
     def get_attribute(self, dataformat: Union[DataFormat, str], sourcefile: Path, attribute: str, options: Plugin) -> str:
         """
         This plugin function reads attributes from the supported sourcefile