Moved lsdirs() and is_hidden() from bcoin.py -> __init__.py

bidscoin/__init__.py

@@ -87,3 +87,29 @@ def bidsversion() -> str:
     """
 
     return (schemafolder/'BIDS_VERSION').read_text().strip()
+
+
+def is_hidden(path: Path) -> bool:
+    """
+    Checks if a path is or contains a hidden rootfolder.
+
+    :param path:    The path to be checked
+    :return:        True if a part of the path starts with a '.', otherwise False
+    """
+
+    if any([p.startswith('.') for p in path.parts]):
+        return True
+    else:
+        return False
+
+
+def lsdirs(folder: Path, wildcard: str='*') -> List[Path]:
+    """
+    Gets all directories in a folder, ignores files
+
+    :param folder:      The full pathname of the folder
+    :param wildcard:    Simple (glob.glob) shell-style wildcards. Foldernames starting with a dot are considered hidden and will be skipped. Use '**/wildcard for recursive search'
+    :return:            A list with all directories in the folder
+    """
+
+    return sorted([fname for fname in sorted(folder.glob(wildcard)) if fname.is_dir() and not is_hidden(fname.relative_to(folder))])

bidscoin/bcoin.py

@@ -176,33 +176,6 @@ def run_command(command: str) -> int:
     return process.returncode
 
 
-def is_hidden(path: Path) -> bool:
-    """
-    Checks if a path contains a hidden folder.
-
-    :param path:    The path to be checked.
-    :return:        True if a part of the path starts with a '.', otherwise False.
-    """
-
-    if any([p.name.startswith('.') for p in path.parents]):
-        LOGGER.verbose(f"Path '{path.absolute()}' is hidden")
-        return True
-    else:
-        return False
-
-
-def lsdirs(folder: Path, wildcard: str='*') -> List[Path]:
-    """
-    Gets all directories in a folder, ignores files
-
-    :param folder:      The full pathname of the folder
-    :param wildcard:    Simple (glob.glob) shell-style wildcards. Foldernames starting with a dot are considered hidden and will be skipped. Use '**/wildcard for recursive search'
-    :return:            A list with all directories in the folder
-    """
-
-    return sorted([fname for fname in sorted(folder.glob(wildcard)) if fname.is_dir() and not is_hidden(fname.relative_to(folder))])
-
-
 def list_executables(show: bool=False) -> list:
     """
     :param show:    Print the installed console scripts if True

bidscoin/bids.py

@@ -27,7 +27,7 @@
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[1]))
-from bidscoin import bcoin, schemafolder, heuristicsfolder, bidsmap_template, __version__
+from bidscoin import bcoin, schemafolder, heuristicsfolder, bidsmap_template, is_hidden, lsdirs
 from bidscoin.utilities import dicomsort
 from ruamel.yaml import YAML
 yaml = YAML()
@@ -326,7 +326,7 @@ def unpack(sourcefolder: Path, wildcard: str='', workfolder: Path='') -> Tuple[L
     tarzipfiles = list(sourcefolder.glob(wildcard)) if wildcard else []
 
     # See if we have a flat unsorted (DICOM) data organization, i.e. no directories, but DICOM-files
-    flatDICOM = not bcoin.lsdirs(sourcefolder) and get_dicomfile(sourcefolder).is_file()
+    flatDICOM = not lsdirs(sourcefolder) and get_dicomfile(sourcefolder).is_file()
 
     # Check if we are going to do unpacking and/or sorting
     if tarzipfiles or flatDICOM or (sourcefolder/'DICOMDIR').is_file():
@@ -385,8 +385,6 @@ def is_dicomfile(file: Path) -> bool:
     """
 
     if file.is_file():
-        if file.stem.startswith('.'):
-            LOGGER.verbose(f'File is hidden: {file}')
         with file.open('rb') as dicomfile:
             dicomfile.seek(0x80, 1)
             if dicomfile.read(4) == b'DICM':
@@ -446,8 +444,8 @@ def get_dicomfile(folder: Path, index: int=0) -> Path:
     :return:        The filename of the first dicom-file in the folder.
     """
 
-    if folder.name.startswith('.'):
-        LOGGER.verbose(f'Ignoring hidden folder: {folder}')
+    if is_hidden(folder):
+        LOGGER.verbose(f"Ignoring hidden folder: {folder}")
         return Path()
 
     if (folder/'DICOMDIR').is_file():
@@ -458,8 +456,8 @@ def get_dicomfile(folder: Path, index: int=0) -> Path:
 
     idx = 0
     for file in files:
-        if file.stem.startswith('.'):
-            LOGGER.verbose(f'Ignoring hidden file: {file}')
+        if is_hidden(file):
+            LOGGER.verbose(f"Ignoring hidden file: {file}")
             continue
         if is_dicomfile(file):
             if idx == index:
@@ -478,14 +476,14 @@ def get_parfiles(folder: Path) -> List[Path]:
     :return:        The filenames of the PAR-files in the folder.
     """
 
-    if folder.name.startswith('.'):
-        LOGGER.verbose(f'Ignoring hidden folder: {folder}')
+    if is_hidden(folder):
+        LOGGER.verbose(f"Ignoring hidden folder: {folder}")
         return []
 
     parfiles = []
     for file in sorted(folder.iterdir()):
-        if file.stem.startswith('.'):
-            LOGGER.verbose(f'Ignoring hidden file: {file}')
+        if is_hidden(file):
+            LOGGER.verbose(f"Ignoring hidden file: {file}")
             continue
         if is_parfile(file):
             parfiles.append(file)
@@ -498,8 +496,8 @@ def get_datasource(session: Path, plugins: dict, recurse: int=2) -> DataSource:
 
     datasource = DataSource()
     for item in sorted(session.iterdir()):
-        if item.stem.startswith('.'):
-            LOGGER.verbose(f'Ignoring hidden datasource: {item}')
+        if is_hidden(item):
+            LOGGER.verbose(f"Ignoring hidden data-source: {item}")
             continue
         if item.is_dir() and recurse:
             datasource = get_datasource(item, plugins, recurse-1)
@@ -901,10 +899,10 @@ def load_bidsmap(yamlfile: Path, folder: Path=Path(), plugins:Union[tuple,list]=
         bidsmapversion = bidsmap['Options']['version']
     else:
         bidsmapversion = 'Unknown'
-    if bidsmapversion.rsplit('.', 1)[0] != __version__.rsplit('.', 1)[0] and any(checks):
-        LOGGER.warning(f'BIDScoiner version conflict: {yamlfile} was created with version {bidsmapversion}, but this is version {__version__}')
-    elif bidsmapversion != __version__ and any(checks):
-        LOGGER.info(f'BIDScoiner version difference: {yamlfile} was created with version {bidsmapversion}, but this is version {__version__}. This is normally ok but check the https://bidscoin.readthedocs.io/en/latest/CHANGELOG.html')
+    if bidsmapversion.rsplit('.', 1)[0] != bidscoinversion.rsplit('.', 1)[0] and any(checks):
+        LOGGER.warning(f'BIDScoiner version conflict: {yamlfile} was created with version {bidsmapversion}, but this is version {bidscoinversion}')
+    elif bidsmapversion != bidscoinversion and any(checks):
+        LOGGER.info(f'BIDScoiner version difference: {yamlfile} was created with version {bidsmapversion}, but this is version {bidscoinversion}. This is normally ok but check the https://bidscoin.readthedocs.io/en/latest/CHANGELOG.html')
 
     # Make sure we get a proper plugin options and dataformat sections (use plugin default bidsmappings when a template bidsmap is loaded)
     if not bidsmap['Options'].get('plugins'):

bidscoin/bidsapps/deface.py

@@ -14,7 +14,7 @@
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[2]))
-from bidscoin import bcoin, bids
+from bidscoin import bcoin, bids, lsdirs
 
 
 def deface(bidsdir: str, pattern: str, subjects: list, force: bool, output: str, cluster: bool, nativespec: str, kwargs: dict):
@@ -45,7 +45,7 @@ def deface(bidsdir: str, pattern: str, subjects: list, force: bool, output: str,
 
     # Get the list of subjects
     if not subjects:
-        subjects = bcoin.lsdirs(bidsdir, 'sub-*')
+        subjects = lsdirs(bidsdir, 'sub-*')
         if not subjects:
             LOGGER.warning(f"No subjects found in: {bidsdir/'sub-*'}")
     else:
@@ -70,7 +70,7 @@ def deface(bidsdir: str, pattern: str, subjects: list, force: bool, output: str,
             for n, subject in enumerate(tqdm(subjects, unit='subject', leave=False), 1):
 
                 subid    = subject.name
-                sessions = bcoin.lsdirs(subject, 'ses-*')
+                sessions = lsdirs(subject, 'ses-*')
                 if not sessions:
                     sessions = [subject]
                 for session in sessions:

bidscoin/bidsapps/echocombine.py

@@ -12,7 +12,7 @@
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[2]))
-from bidscoin import bcoin, bids
+from bidscoin import bcoin, bids, lsdirs
 
 unknowndatatype = 'extra_data'
 
@@ -44,7 +44,7 @@ def echocombine(bidsdir: str, pattern: str, subjects: list, output: str, algorit
 
     # Get the list of subjects
     if not subjects:
-        subjects = bcoin.lsdirs(bidsdir, 'sub-*')
+        subjects = lsdirs(bidsdir, 'sub-*')
         if not subjects:
             LOGGER.warning(f"No subjects found in: {bidsdir/'sub-*'}")
     else:
@@ -56,7 +56,7 @@ def echocombine(bidsdir: str, pattern: str, subjects: list, output: str, algorit
         for n, subject in enumerate(tqdm(subjects, unit='subject', leave=False), 1):
 
             subid    = subject.name
-            sessions = bcoin.lsdirs(subject, 'ses-*')
+            sessions = lsdirs(subject, 'ses-*')
             if not sessions:
                 sessions = [subject]
             for session in sessions:

bidscoin/bidsapps/medeface.py

@@ -17,7 +17,7 @@
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[2]))
-from bidscoin import bcoin, bids
+from bidscoin import bcoin, bids, lsdirs
 
 
 def medeface(bidsdir: str, pattern: str, maskpattern: str, subjects: list, force: bool, output: str, cluster: bool, nativespec: str, kwargs: dict):
@@ -51,7 +51,7 @@ def medeface(bidsdir: str, pattern: str, maskpattern: str, subjects: list, force
 
     # Get the list of subjects
     if not subjects:
-        subjects = bcoin.lsdirs(bidsdir, 'sub-*')
+        subjects = lsdirs(bidsdir, 'sub-*')
         if not subjects:
             LOGGER.warning(f"No subjects found in: {bidsdir/'sub-*'}")
     else:
@@ -76,7 +76,7 @@ def medeface(bidsdir: str, pattern: str, maskpattern: str, subjects: list, force
         for n, subject in enumerate(subjects, 1):
 
             subid    = subject.name
-            sessions = bcoin.lsdirs(subject, 'ses-*')
+            sessions = lsdirs(subject, 'ses-*')
             if not sessions:
                 sessions = [subject]
             for session in sessions:
@@ -128,7 +128,7 @@ def medeface(bidsdir: str, pattern: str, maskpattern: str, subjects: list, force
         for n, subject in enumerate(tqdm(subjects, unit='subject', leave=False), 1):
 
             subid    = subject.name
-            sessions = bcoin.lsdirs(subject, 'ses-*')
+            sessions = lsdirs(subject, 'ses-*')
             if not sessions:
                 sessions = [subject]
             for session in sessions:

bidscoin/bidsapps/skullstrip.py

@@ -13,7 +13,7 @@
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[2]))
-from bidscoin import bcoin, bids
+from bidscoin import bcoin, bids, lsdirs
 
 
 def skullstrip(bidsdir: str, pattern: str, subjects: list, masked: str, output: list, force: bool, args: str, cluster: bool):
@@ -56,7 +56,7 @@ def skullstrip(bidsdir: str, pattern: str, subjects: list, masked: str, output:
 
     # Get the list of subjects
     if not subjects:
-        subjects = bcoin.lsdirs(bidsdir, 'sub-*')
+        subjects = lsdirs(bidsdir, 'sub-*')
         if not subjects:
             LOGGER.warning(f"No subjects found in: {bidsdir/'sub-*'}")
     else:
@@ -68,7 +68,7 @@ def skullstrip(bidsdir: str, pattern: str, subjects: list, masked: str, output:
         for n, subject in enumerate(tqdm(subjects, unit='subject', leave=False), 1):
 
             subid    = subject.name
-            sessions = bcoin.lsdirs(subject, 'ses-*')
+            sessions = lsdirs(subject, 'ses-*')
             if not sessions:
                 sessions = [subject]
             for session in sessions:

bidscoin/bidsapps/slicereport.py

@@ -12,7 +12,7 @@
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[2]))
-from bidscoin import bcoin, bids, bidsversion, __version__
+from bidscoin import bcoin, bids, lsdirs, bidsversion, __version__
 
 html_head = """<!DOCTYPE html>
 <html lang="en">
@@ -159,7 +159,7 @@ def slicereport(bidsdir: str, pattern: str, outlinepattern: str, outlineimage: s
 
     # Get the list of subjects
     if not subjects:
-        subjects = bcoin.lsdirs(bidsdir, 'sub-*')
+        subjects = lsdirs(bidsdir, 'sub-*')
         if not subjects:
             print(f"No subjects found in: {bidsdir/'sub-*'}"); return
     else:
@@ -185,7 +185,7 @@ def slicereport(bidsdir: str, pattern: str, outlinepattern: str, outlineimage: s
 
     # Loop over the subject/session-directories
     for subject in subjects:
-        sessions = bcoin.lsdirs(subject, 'ses-*')
+        sessions = lsdirs(subject, 'ses-*')
         if not sessions:
             sessions = [subject]
         for session in sessions:

bidscoin/bidscoiner.py

@@ -15,7 +15,7 @@
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[1]))
-from bidscoin import bcoin, bids, bidsversion, __version__
+from bidscoin import bcoin, bids, lsdirs, bidsversion, __version__
 
 
 def bidscoiner(rawfolder: str, bidsfolder: str, subjects: list=(), force: bool=False, bidsmapfile: str='bidsmap.yaml') -> None:
@@ -125,7 +125,7 @@ def bidscoiner(rawfolder: str, bidsfolder: str, subjects: list=(), force: bool=F
     subprefix = bidsmap['Options']['bidscoin']['subprefix'].replace('*','')
     sesprefix = bidsmap['Options']['bidscoin']['sesprefix'].replace('*','')
     if not subjects:
-        subjects = bcoin.lsdirs(rawfolder, (subprefix if subprefix!='*' else '') + '*')
+        subjects = lsdirs(rawfolder, (subprefix if subprefix!='*' else '') + '*')
         if not subjects:
             LOGGER.warning(f"No subjects found in: {rawfolder/subprefix}*")
     else:
@@ -140,7 +140,7 @@ def bidscoiner(rawfolder: str, bidsfolder: str, subjects: list=(), force: bool=F
                 LOGGER.error(f"The '{subject}' subject folder does not exist")
                 continue
 
-            sessions = bcoin.lsdirs(subject, (sesprefix if sesprefix!='*' else '') + '*')
+            sessions = lsdirs(subject, (sesprefix if sesprefix!='*' else '') + '*')
             if not sessions or (subject/'DICOMDIR').is_file():
                 sessions = [subject]
             for session in sessions:
@@ -161,7 +161,7 @@ def bidscoiner(rawfolder: str, bidsfolder: str, subjects: list=(), force: bool=F
                     if not force and bidssession.is_dir():
                         datatypes = []
                         for dataformat in dataformats:
-                            for datatype in bcoin.lsdirs(bidssession):                               # See what datatypes we already have in the bids session-folder
+                            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
                                     datatypes.append(datatype.name)
                         if datatypes:

bidscoin/bidsmapper.py

@@ -13,7 +13,7 @@
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[1]))
-from bidscoin import bcoin, bids, check_version, __version__
+from bidscoin import bcoin, bids, lsdirs, check_version, __version__
 
 _, uptodate, versionmessage = check_version()
 
@@ -103,13 +103,13 @@ def bidsmapper(rawfolder: str, bidsfolder: str, bidsmapfile: str, templatefile:
         return {}
 
     # Loop over all subjects and sessions and built up the bidsmap entries
-    subjects = bcoin.lsdirs(rawfolder, ('' if subprefix=='*' else subprefix) + '*')
+    subjects = lsdirs(rawfolder, ('' if subprefix=='*' else subprefix) + '*')
     if not subjects:
         LOGGER.warning(f'No subjects found in: {rawfolder/subprefix}*')
     with logging_redirect_tqdm():
         for n, subject in enumerate(tqdm(subjects, unit='subject', leave=False), 1):
 
-            sessions = bcoin.lsdirs(subject, ('' if sesprefix=='*' else sesprefix) + '*')
+            sessions = lsdirs(subject, ('' if sesprefix=='*' else sesprefix) + '*')
             if not sessions or (subject/'DICOMDIR').is_file():
                 sessions = [subject]
             for session in sessions:

bidscoin/plugins/dcm2niix2bids.py

@@ -13,7 +13,7 @@
 from bids_validator import BIDSValidator
 from typing import Union
 from pathlib import Path
-from bidscoin import bcoin, bids
+from bidscoin import bcoin, bids, lsdirs
 from bidscoin.utilities import physio
 try:
     from nibabel.testing import data_path
@@ -120,7 +120,7 @@ def bidsmapper_plugin(session: Path, bidsmap_new: dict, bidsmap_old: dict, templ
     # Collect the different DICOM/PAR source files for all runs in the session
     sourcefiles = []
     if dataformat == 'DICOM':
-        for sourcedir in bcoin.lsdirs(session, '**/*'):
+        for sourcedir in lsdirs(session, '**/*'):
             for n in range(1):      # Option: Use range(2) to scan two files and catch e.g. magnitude1/2 fieldmap files that are stored in one Series folder (but bidscoiner sees only the first file anyhow and it makes bidsmapper 2x slower :-()
                 sourcefile = bids.get_dicomfile(sourcedir, n)
                 if sourcefile.name and is_sourcefile(sourcefile):
@@ -198,7 +198,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
     manufacturer = 'UNKNOWN'
     sources      = []
     if dataformat == 'DICOM':
-        sources      = bcoin.lsdirs(session, '**/*')
+        sources      = lsdirs(session, '**/*')
         manufacturer = datasource.attributes('Manufacturer')
     elif dataformat == 'PAR':
         sources      = bids.get_parfiles(session)