clabtoolkit 0.4.0__tar.gz → 0.4.2__tar.gz

clabtoolkit-0.4.2/HISTORY.rst

@@ -0,0 +1,35 @@
+=======
+History
+=======
+
+0.4.1 (2026-02-19)
+------------------
+
+* Major refactoring of Parcellation class with improved attribute handling
+* Enhanced color table loading and export with multiple format support
+* Added region adjacency computation to Parcellation
+* Improved BIDS file entity extraction with parallel processing
+* Added DiffusionScheme class for gradient visualization
+* Enhanced Connectome class initialization and metrics computation
+* Added derivatives inventory functionality
+* Improved surface tools with PyVista fallback support
+* Added usage examples notebooks
+* Multiple bug fixes in mask handling, color processing, and data type conversion
+* Improved documentation and code organization
+
+0.3.4 (2025-01-09)
+------------------
+
+* Enhanced documentation and ReadTheDocs configuration
+* Moved region growing method to imagetools module  
+* Improved Sphinx autodoc configuration for better API documentation
+* Multiple improvements to surface visualization and plotting functionality
+* Added new morphometry and connectivity analysis tools
+* Enhanced BIDS dataset handling and entity management
+* Improved surface mesh operations and color mapping
+* Added network analysis tools and visualization capabilities
+
+0.3.1 (2025-05-22)
+------------------
+
+* Fourth release on PyPI. 

{clabtoolkit-0.4.0 → clabtoolkit-0.4.2}/MANIFEST.in

@@ -14,6 +14,9 @@ recursive-include docs *.rst *.py *.bat *.png
 recursive-include docs Makefile
 include docs/make.bat
 
+# Include usage examples
+recursive-include usage_examples *.ipynb *.py *.md
+
 # EXCLUDE tests data completely  
 prune tests
 

{clabtoolkit-0.4.0 → clabtoolkit-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clabtoolkit
-Version: 0.4.0
+Version: 0.4.2
 Summary: A comprehensive toolkit for neuroimaging data processing and analysis
 Author-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
 Maintainer-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>

{clabtoolkit-0.4.0 → clabtoolkit-0.4.2}/clabtoolkit/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Yasser Alemán-Gómez"""
 __email__ = "yasseraleman@protonmail.com"
-__version__ = "0.4.0"
+__version__ = "0.4.1"

{clabtoolkit-0.4.0 → clabtoolkit-0.4.2}/clabtoolkit/bidstools.py

@@ -23,6 +23,8 @@ from rich.progress import (
 )
 from rich.console import Console
 from rich.panel import Panel
+import concurrent.futures
+
 
 # Importing the clabtoolkit modules
 from . import misctools as cltmisc
@@ -777,29 +779,29 @@ def get_all_entities(root_dir: str) -> Tuple[Dict[str, Set[str]], List[str]]:
     # Leave only the files that are BIDs files
     bids_files = cltmisc.filter_by_substring(bids_files, bids_folders)
 
-    # Initialize a set to store all unique entities
-    all_entities = []
-    all_suffixes = []
-    for file in bids_files:
-
+    def process_file(file):
         filename = os.path.basename(file)
         ent_dict = str2entity(filename)
 
-        # Remove suffix and extension from the entity dictionary
+        suffix = None
         if "suffix" in ent_dict:
-            suffix = ent_dict["suffix"]
-            all_suffixes.append(suffix)
-            del ent_dict["suffix"]
+            suffix = ent_dict.pop("suffix")
+
+        ent_dict.pop("extension", None)
+        ent_dict.pop("run", None)
 
-        if "extension" in ent_dict:
-            del ent_dict["extension"]
+        return list(ent_dict.keys()), suffix
 
-        if "run" in ent_dict:
-            del ent_dict["run"]
+    all_entities = []
+    all_suffixes = []
 
-        file_ent_keys = list(ent_dict.keys())
+    with concurrent.futures.ThreadPoolExecutor() as executor:
+        results = executor.map(process_file, bids_files)
 
-        all_entities.extend(file_ent_keys)
+    for entity_keys, suffix in results:
+        all_entities.extend(entity_keys)
+        if suffix is not None:
+            all_suffixes.append(suffix)
 
     # Unique entities
     all_entities = sorted(set(all_entities))
@@ -952,14 +954,12 @@ def entities4table(
 def entities_to_table(
     filepath: str,
     entities_to_extract: Optional[Union[str, List[str], Dict[str, str]]] = None,
+    include_suffix: bool = False,
 ) -> pd.DataFrame:
     """
     Creates a DataFrame with BIDS entities extracted from a filename.
 
-    This function parses BIDS-compliant filenames to extract specified entities
-    (such as subject, session, task) and organizes them into a DataFrame with
-    appropriate column names. It supports special handling for certain entities
-    like atlas and description fields.
+    ...
 
     Parameters
     ----------
@@ -971,42 +971,27 @@ def entities_to_table(
         - If list: Multiple entity names to extract
         - If dict: Keys are entity names, values are custom column names
         - If None: Returns a single column with the full filename
+    include_suffix : bool, default=True
+        If True, adds a 'Type' column containing the BIDS suffix
+        (e.g., 'bold', 'T1w', 'dwi') extracted from the filename.
 
     Returns
     -------
     pd.DataFrame
         DataFrame containing the extracted entities as columns.
+        If include_suffix is True, a 'Type' column is appended at the end.
         If the file is not BIDS-compliant, returns an empty DataFrame.
 
     Examples
     --------
-    >>> # Extract subject and session from a BIDS file
     >>> df = entities_to_table(
     ...     '/data/sub-01/ses-pre/sub-01_ses-pre_task-rest_bold.nii.gz',
-    ...     ['sub', 'ses']
-    ... )
-    >>> print(df)
-        Participant Session
-    0          01     pre
-
-    >>> # Extract entities with custom column names
-    >>> df = entities_to_table(
-    ...     '/data/sub-01/anat/sub-01_T1w.nii.gz',
-    ...     {'sub': 'SubjectID'}
-    ... )
-    >>> print(df)
-        SubjectID
-    0        01
-
-    >>> # Extract atlas with special handling
-    >>> df = entities_to_table(
-    ...     '/data/sub-01/atlas-chimera123_desc-parcellation.nii.gz',
-    ...     ['atlas', 'desc']
+    ...     ['sub', 'ses'],
+    ...     include_suffix=True
     ... )
     >>> print(df)
-        Atlas ChimeraCode Description
-    0   chimera        123 parcellation
-
+        Participant Session  Type
+    0          01     pre  bold
     """
     # Type checking
     if filepath is None or not isinstance(filepath, str):
@@ -1019,7 +1004,6 @@ def entities_to_table(
         with open(default_config_path, "r") as f:
             config_data = json.load(f)
 
-        # Merge raw and derivatives entities
         if (
             "bids_entities" in config_data
             and "raw_entities" in config_data["bids_entities"]
@@ -1042,63 +1026,49 @@ def entities_to_table(
             f"Error parsing the default configuration file: {default_config_path}"
         )
 
-    # Extract file directory and name
     file_directory = os.path.dirname(filepath)
-    filename = os.path.basename(filepath)
+    filename = cltmisc.get_real_basename(filepath)
+    filename = filename.split(".")[0]
 
-    # Create an empty DataFrame
     result_df = pd.DataFrame()
 
-    # Only process if the file follows BIDS naming convention
     if is_bids_filename(filename):
 
-        # Parse entities from the filename
         entities_dict = str2entity(filename)
 
-        # Remove the 'extension' key if it exists
         if "extension" in entities_dict:
             entities_dict.pop("extension")
-        # Remove the 'suffix' key if it exists
-        if "suffix" in entities_dict:
-            entities_dict.pop("suffix")
+
+        # Extract suffix before removing it
+        suffix = entities_dict.pop("suffix", "")
 
         if entities_to_extract is not None:
-            # Convert string input to list
             if isinstance(entities_to_extract, str):
                 entities_to_extract = [entities_to_extract]
 
-            # Convert list to dictionary for unified processing
             if isinstance(entities_to_extract, list):
-                # Create dict with entity names as both keys and values
                 entities_to_extract = {entity: "" for entity in entities_to_extract}
         else:
             entities_to_extract = {entity: "" for entity in entities_dict.keys()}
 
-        # Initialize DataFrame with one empty row
         if result_df.empty:
             result_df = pd.DataFrame([{}])
 
-        # Process entities in reverse order to maintain column order
         entity_keys = list(entities_to_extract.keys())
         for entity in reversed(entity_keys):
-            # Get entity value from filename or empty string if not found
             value = entities_dict.get(entity, "")
 
             if entity in ent_out_dict.keys():
-                # If entity is in the mapping dictionary, use its value
                 var_name = ent_out_dict[entity]
                 if entity == "atlas":
-                    # Special handling for atlas
                     if "chimera" in value:
                         result_df.insert(0, "ChimeraCode", value.replace("chimera", ""))
                         result_df.insert(0, "Atlas", "chimera")
-
                     else:
                         result_df.insert(0, "ChimeraCode", "")
                         result_df.insert(0, "Atlas", value)
 
                 elif entity == "desc":
-                    # Special handling for description
                     result_df.insert(0, "Description", value)
                     if "grow" in value:
                         result_df.insert(0, "GrowIntoWM", value.replace("grow", ""))
@@ -1106,21 +1076,24 @@ def entities_to_table(
                 else:
                     result_df.insert(0, var_name, value)
             else:
-
                 result_df.insert(0, entity.capitalize(), value)
 
+        # Append Type column at the end if requested
+        if include_suffix:
+            result_df["Type"] = suffix
+
     else:
-        # If no entities specified, use full filename as Participant
         if result_df.empty:
             result_df = pd.DataFrame([{}])
 
         if "Participant" not in result_df.columns:
-            # If 'Participant' column doesn't exist, create it
-            # Remove the extension from the filename in case it exists
             temp = os.path.splitext(filename)[0]
             result_df.insert(0, "Participant", temp)
 
-    # Declaring all the columns as string type
+        # No suffix available for non-BIDS files
+        if include_suffix:
+            result_df["Type"] = ""
+
     for col in result_df.columns:
         result_df[col] = result_df[col].astype(str)
 
@@ -1792,6 +1765,7 @@ def is_bids_filename(filename: str) -> bool:
         bool: True if valid BIDS filename, False otherwise.
     """
     # Remove extension if present
+    filename = cltmisc.get_real_basename(filename)
     base_filename = filename.split(".")[0]
 
     parts = base_filename.split("_")