clabtoolkit 0.3.2a1__tar.gz → 0.3.3__tar.gz

clabtoolkit-0.3.3/MANIFEST.in

@@ -0,0 +1,22 @@
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+include pyproject.toml
+
+# Include package source code
+recursive-include clabtoolkit *.py
+recursive-include clabtoolkit/config *.json
+
+# Include documentation
+recursive-include docs *.rst *.py *.bat *.png
+recursive-include docs Makefile
+include docs/make.bat
+
+# EXCLUDE tests data completely  
+prune tests
+
+# Exclude unwanted files (only those that exist)
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

{clabtoolkit-0.3.2a1 → clabtoolkit-0.3.3}/PKG-INFO

@@ -1,12 +1,10 @@
 Metadata-Version: 2.4
 Name: clabtoolkit
-Version: 0.3.2a1
+Version: 0.3.3
 Summary: A comprehensive toolkit for neuroimaging data processing and analysis
-Home-page: https://github.com/connectomicslab/clabtoolkit
-Author: Yasser Alemán-Gómez
 Author-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
 Maintainer-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
-License: Apache-2.0
+License-Expression: Apache-2.0
 Project-URL: Homepage, https://github.com/connectomicslab/clabtoolkit
 Project-URL: Repository, https://github.com/connectomicslab/clabtoolkit
 Project-URL: Documentation, https://clabtoolkit.readthedocs.io
@@ -15,7 +13,6 @@ Keywords: neuroimaging,image-processing,bids,freesurfer,connectivity
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
@@ -25,38 +22,42 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Image Processing
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.rst
 Requires-Dist: nibabel>=5.3.2
 Requires-Dist: numpy>=1.23.5
-Requires-Dist: pandas>=2.2.3
+Requires-Dist: pandas>=2.3.1
 Requires-Dist: pydicom>=3.0.1
-Requires-Dist: rich>=13.9.4
-Requires-Dist: scipy>=1.14.1
-Requires-Dist: setuptools>=68.0.0
-Requires-Dist: scikit-image>=0.22.0
+Requires-Dist: rich>=14.1.0
+Requires-Dist: scipy>=1.16.0
+Requires-Dist: setuptools>=80.9.0
+Requires-Dist: scikit-image>=0.25.2
+Requires-Dist: h5py>=3.14.0
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: pyvista>=0.45.3
+Requires-Dist: nilearn>=0.12.0
+Requires-Dist: joblib>=1.5.1
 Provides-Extra: dev
-Requires-Dist: pytest>=7.0.0; extra == "dev"
-Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
-Requires-Dist: black>=23.0.0; extra == "dev"
-Requires-Dist: ruff>=0.1.0; extra == "dev"
-Requires-Dist: mypy>=1.5.0; extra == "dev"
-Requires-Dist: pre-commit>=3.0.0; extra == "dev"
-Requires-Dist: tox>=4.0.0; extra == "dev"
+Requires-Dist: pytest>=8.4.1; extra == "dev"
+Requires-Dist: pytest-cov>=6.2.1; extra == "dev"
+Requires-Dist: black>=25.1.0; extra == "dev"
+Requires-Dist: ruff>=0.12.5; extra == "dev"
+Requires-Dist: mypy>=1.17.0; extra == "dev"
+Requires-Dist: pre-commit>=4.2.0; extra == "dev"
+Requires-Dist: tox>=4.28.1; extra == "dev"
+Requires-Dist: termcolor>=3.1.0; extra == "dev"
+Requires-Dist: tabulate>=0.9.0; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: sphinx>=7.0.0; extra == "docs"
-Requires-Dist: sphinx-rtd-theme>=1.3.0; extra == "docs"
-Requires-Dist: myst-parser>=2.0.0; extra == "docs"
+Requires-Dist: sphinx>=8.2.3; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=3.0.2; extra == "docs"
+Requires-Dist: myst-parser>=4.0.1; extra == "docs"
 Provides-Extra: test
-Requires-Dist: pytest>=7.0.0; extra == "test"
-Requires-Dist: pytest-cov>=4.0.0; extra == "test"
-Requires-Dist: pytest-xdist>=3.0.0; extra == "test"
-Dynamic: author
-Dynamic: home-page
+Requires-Dist: pytest>=8.4.1; extra == "test"
+Requires-Dist: pytest-cov>=6.2.1; extra == "test"
+Requires-Dist: pytest-xdist>=3.8.0; extra == "test"
 Dynamic: license-file
-Dynamic: requires-python
 
 ========================
 Connectomics Lab Toolkit

{clabtoolkit-0.3.2a1 → clabtoolkit-0.3.3}/clabtoolkit/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Yasser Alemán-Gómez"""
 __email__ = "yasseraleman@protonmail.com"
-__version__ = "0.3.1"
+__version__ = "0.3.3"

{clabtoolkit-0.3.2a1 → clabtoolkit-0.3.3}/clabtoolkit/bidstools.py

@@ -28,49 +28,11 @@ from rich.panel import Panel
 from . import misctools as cltmisc
 
 
-# Loading the JSON file containing the BIDs configuration file. It includes the entities and suffixes
-# of the BIDs dataset.
-def load_bids_json(bids_json: str = None):
-    """
-    Load the JSON file containing the BIDs configuration file.
-
-    Parameters:
-    ----------
-    bids_json : str
-        JSON file containing the BIDs configuration.
-
-    Returns:
-    --------
-    config_dict : dict
-        Dictionary containing the default .
-
-    """
-
-    # Get the absolute of this file
-    if bids_json is None:
-        cwd = os.path.dirname(os.path.abspath(__file__))
-        bids_json = os.path.join(cwd, "config", "bids.json")
-    else:
-        if not os.path.isfile(bids_json):
-            raise ValueError(
-                "Please, provide a valid JSON file containing the BIDs configuration dictionary."
-            )
-    try:
-        with open(bids_json) as f:
-            config_dict = json.load(f)
-    except FileNotFoundError:
-        raise FileNotFoundError(f"Default configuration file not found at: {bids_json}")
-    except json.JSONDecodeError:
-        raise ValueError(f"Error parsing the default configuration file: {bids_json}")
-
-    return config_dict
-
-
 ####################################################################################################
 ####################################################################################################
 ############                                                                            ############
 ############                                                                            ############
-############           Methods dedicated to work with BIDs naming conventions           ############
+############     Section 1: Methods dedicated to work with BIDs naming conventions      ############
 ############                                                                            ############
 ############                                                                            ############
 ####################################################################################################
@@ -462,7 +424,7 @@ def recursively_replace_entity_value(
     """
     This method replaces the values of certain entities in all the files and folders of a BIDs dataset.
 
-    Parameters:
+    Parameters
     ----------
     root_dir: str
         Root directory of the BIDs dataset
@@ -1158,6 +1120,10 @@ def entities_to_table(
             temp = os.path.splitext(filename)[0]
             result_df.insert(0, "Participant", temp)
 
+    # Declaring all the columns as string type
+    for col in result_df.columns:
+        result_df[col] = result_df[col].astype(str)
+
     return result_df
 
 
@@ -1165,13 +1131,11 @@ def entities_to_table(
 ####################################################################################################
 ############                                                                            ############
 ############                                                                            ############
-############           Methods dedicated to work with BIDs file organization            ############
+############     Section 2: Methods dedicated to work with BIDs file organization       ############
 ############                                                                            ############
 ############                                                                            ############
 ####################################################################################################
 ####################################################################################################
-
-
 def get_subjects(bids_dir: str) -> list:
     """
     Get a list of all subjects in the BIDs directory.
@@ -1762,8 +1726,6 @@ def get_bids_database_table(
 
 
 ####################################################################################################
-
-
 def get_derivatives_folders(
     deriv_dir: str,
 ) -> list:
@@ -1826,7 +1788,7 @@ def is_bids_filename(filename: str) -> bool:
     Args:
         filename (str): The filename to validate.
 
-    Returns:
+    Returns
         bool: True if valid BIDS filename, False otherwise.
     """
     # Remove extension if present
@@ -1858,7 +1820,7 @@ def get_individual_files_and_folders(
     """
     This function detects all the files or folders inside a folder and its subfolders containing the strings supplied by the variable cad4query.
 
-    Parameters:
+    Parameters
     ----------
     input_folder : str
         Path to the input folder.
@@ -1866,12 +1828,12 @@ def get_individual_files_and_folders(
     cad4query : str, list, or dict
         String or list of strings to filter the files and folders. If a dictionary is provided, it should contain key-value pairs where the key is the string before '-' and the value is the string after '-'.
 
-    Returns:
+    Returns
     -------
     list
         List of files or folders that match the query.
 
-    Raises:
+    Raises
     ------
     ValueError
         If the input folder does not exist.
@@ -1879,7 +1841,7 @@ def get_individual_files_and_folders(
     TypeError
         If the input folder is not a string.
 
-    Examples:
+    Examples
     --------
     >>> input_folder = "/path/to/input/folder"
     >>> cad4query = "sub-01"
@@ -1945,15 +1907,19 @@ def generate_bids_tree(
     ----------
     bids_root : str
         Path to the BIDS root directory.
+
     max_depth : int, optional
         Maximum depth to traverse. If None (default), traverses entire directory
         structure without depth limitation.
+
     show_hidden : bool, optional
         Whether to show hidden files and folders (starting with '.').
         Default is False.
+
     exclude_patterns : set of str, optional
         Set of file/folder name patterns to exclude from the tree. If None,
         defaults to {'.git', '__pycache__', '.DS_Store', 'Thumbs.db'}.
+
     save_to_file : str, optional
         Path to save the tree output as a text file. If None, only returns
         the string without saving.
@@ -1968,11 +1934,14 @@ def generate_bids_tree(
     ------
     FileNotFoundError
         If the specified bids_root path does not exist.
+
     NotADirectoryError
         If the specified bids_root path is not a directory.
+
     PermissionError
         If there are insufficient permissions to read certain directories.
         Individual permission errors are handled gracefully and noted in output.
+
     OSError
         If there are file system related errors during tree generation or
         file saving operations.
@@ -2094,6 +2063,7 @@ def generate_bids_tree(
     return tree_output
 
 
+####################################################################################################
 def generate_bids_tree_with_stats(bids_root: str, **kwargs) -> str:
     """
     Generate a BIDS tree with additional statistics.
@@ -2102,6 +2072,7 @@ def generate_bids_tree_with_stats(bids_root: str, **kwargs) -> str:
     ----------
     bids_root : str
         Path to the BIDS root directory.
+
     **kwargs
         Additional keyword arguments passed to generate_bids_tree().
         See generate_bids_tree() documentation for available parameters.
@@ -2115,10 +2086,13 @@ def generate_bids_tree_with_stats(bids_root: str, **kwargs) -> str:
     ------
     FileNotFoundError
         If the specified bids_root path does not exist.
+
     NotADirectoryError
         If the specified bids_root path is not a directory.
+
     PermissionError
         If there are insufficient permissions to read directories.
+
     OSError
         If there are file system related errors.
 
@@ -2164,6 +2138,7 @@ def generate_bids_tree_with_stats(bids_root: str, **kwargs) -> str:
     return tree + stats
 
 
+####################################################################################################
 def validate_bids_structure(bids_root: str) -> List[str]:
     """
     Basic validation of BIDS structure and return warnings.
@@ -2233,3 +2208,53 @@ def validate_bids_structure(bids_root: str) -> List[str]:
         warnings.append("Derivatives directory found")
 
     return warnings
+
+
+####################################################################################################
+####################################################################################################
+############                                                                            ############
+############                                                                            ############
+############           Section 3: Useful methods for BIDs file organization             ############
+############                                                                            ############
+############                                                                            ############
+####################################################################################################
+####################################################################################################
+
+
+# Loading the JSON file containing the BIDs configuration file. It includes the entities and suffixes
+# of the BIDs dataset.
+####################################################################################################
+def load_bids_json(bids_json: str = None):
+    """
+    Load the JSON file containing the BIDs configuration file.
+
+    Parameters
+    ----------
+    bids_json : str
+        JSON file containing the BIDs configuration.
+
+    Returns
+    --------
+    config_dict : dict
+        Dictionary containing the default .
+
+    """
+
+    # Get the absolute of this file
+    if bids_json is None:
+        cwd = os.path.dirname(os.path.abspath(__file__))
+        bids_json = os.path.join(cwd, "config", "bids.json")
+    else:
+        if not os.path.isfile(bids_json):
+            raise ValueError(
+                "Please, provide a valid JSON file containing the BIDs configuration dictionary."
+            )
+    try:
+        with open(bids_json) as f:
+            config_dict = json.load(f)
+    except FileNotFoundError:
+        raise FileNotFoundError(f"Default configuration file not found at: {bids_json}")
+    except json.JSONDecodeError:
+        raise ValueError(f"Error parsing the default configuration file: {bids_json}")
+
+    return config_dict

{clabtoolkit-0.3.2a1 → clabtoolkit-0.3.3}/clabtoolkit/config/config.json

@@ -1,9 +1,9 @@
 {
     "metrics_units": {
         "thickness": "mm",
-        "area": "cm²",
-        "volume": "cm³",
-        "curv": "mm⁻¹",
+        "area": "cm2",
+        "volume": "cm3",
+        "curv": "mm-1",
         "sulc": "au",
         "lgi": "au",
         "euler": "au",
@@ -12,21 +12,21 @@
         "fold_opening": "mm",
         "sulcal_length": "mm",
         "fa": "au",
-        "md": "mm²/s",
+        "md": "mm2/s",
         "cs": "au",
         "cp": "au",
         "cl": "au",
-        "trace": "mm²/s",
-        "ad": "mm²/s",
-        "rd": "mm²/s",
+        "trace": "mm2/s",
+        "ad": "mm2/s",
+        "rd": "mm2/s",
         "fwfa": "au",
-        "fwmd": "mm²/s",
+        "fwmd": "mm2/s",
         "fwvf": "au",
         "gfa": "au",
         "rtop": "au",
         "rtpp": "au",
         "rtap": "au",
-        "msd": "mm²/s",
+        "msd": "mm2/s",
         "icvf": "au",
         "ecvf": "au",
         "isovf": "au",
@@ -44,8 +44,8 @@
         "axon_diameter": "μm",
         "mvf": "au",
         "charm_fraction": "au",
-        "charm_dpar": "mm²/s",
-        "charm_dperp": "mm²/s",
+        "charm_dpar": "mm2/s",
+        "charm_dperp": "mm^2/s",
         "wmti_fraction_restricted": "au",
         "wmti_fraction_hindered": "au",
         "wmti_fraction_free": "au",