clabtoolkit 0.2.0__tar.gz → 0.3.2a1__tar.gz

{clabtoolkit-0.2.0 → clabtoolkit-0.3.2a1}/CONTRIBUTING.rst

@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
+3. The pull request should work for Python >3.10, and for PyPy. Check
    https://travis-ci.com/yasseraleman/clabtoolkit/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

clabtoolkit-0.3.2a1/HISTORY.rst

@@ -0,0 +1,8 @@
+=======
+History
+=======
+
+0.3.1 (2025-05-22)
+------------------
+
+* Fourth release on PyPI. 

{clabtoolkit-0.2.0 → clabtoolkit-0.3.2a1}/MANIFEST.in

@@ -7,5 +7,10 @@ include README.rst
 recursive-include tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
+recursive-include clabtoolkit/config *
+
+exclude clabtoolkit/clabtoolkit/test3.py
+exclude clabtoolkit/clabtoolkit/test_2.py
+exclude clabtoolkit/clabtoolkit/test_file.py
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

clabtoolkit-0.3.2a1/PKG-INFO

@@ -0,0 +1,211 @@
+Metadata-Version: 2.4
+Name: clabtoolkit
+Version: 0.3.2a1
+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
+Project-URL: Homepage, https://github.com/connectomicslab/clabtoolkit
+Project-URL: Repository, https://github.com/connectomicslab/clabtoolkit
+Project-URL: Documentation, https://clabtoolkit.readthedocs.io
+Project-URL: Bug Tracker, https://github.com/connectomicslab/clabtoolkit/issues
+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
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+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
+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: 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
+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"
+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"
+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
+Dynamic: license-file
+Dynamic: requires-python
+
+========================
+Connectomics Lab Toolkit
+========================
+
+
+.. image:: https://img.shields.io/pypi/v/clabtoolkit.svg
+        :target: https://pypi.python.org/pypi/clabtoolkit
+
+.. image:: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml/badge.svg
+        :target: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml
+
+.. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest
+        :target: https://clabtoolkit.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/pyversions/clabtoolkit.svg
+        :target: https://pypi.python.org/pypi/clabtoolkit
+
+.. image:: https://codecov.io/gh/connectomicslab/clabtoolkit/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/connectomicslab/clabtoolkit
+
+
+A comprehensive Python toolkit for neuroimaging data processing and analysis, specifically designed for working with brain connectivity data, BIDS datasets, and various neuroimaging formats.
+
+* **Free software**: Apache Software License 2.0
+* **Documentation**: https://clabtoolkit.readthedocs.io
+* **Source Code**: https://github.com/connectomicslab/clabtoolkit
+* **Python versions**: 3.9+
+
+Installation
+------------
+
+Install from PyPI::
+
+    pip install clabtoolkit
+
+For development installation::
+
+    git clone https://github.com/connectomicslab/clabtoolkit.git
+    cd clabtoolkit
+    pip install -e .[dev]
+
+Features
+--------
+
+**BIDS Tools** (``clabtoolkit.bidstools``)
+    * BIDS dataset validation and manipulation
+    * Entity extraction from BIDS filenames
+    * Conversion between BIDS formats
+    * Metadata handling for neuroimaging datasets
+
+**Connectivity Tools** (``clabtoolkit.connectivitytools``)
+    * Brain connectivity matrix analysis
+    * Network-based statistics
+    * Graph theory metrics computation
+    * Connectivity visualization utilities
+
+**FreeSurfer Tools** (``clabtoolkit.freesurfertools``)
+    * FreeSurfer output parsing and processing
+    * Surface-based analysis utilities
+    * Cortical thickness and morphometry tools
+    * Integration with FreeSurfer workflows
+
+**Image Processing Tools** (``clabtoolkit.imagetools``)
+    * Neuroimaging data I/O operations
+    * Image registration and transformation
+    * Quality control and preprocessing utilities
+    * Multi-modal image processing
+
+**Parcellation Tools** (``clabtoolkit.parcellationtools``)
+    * Brain parcellation scheme handling
+    * Region-of-interest (ROI) extraction
+    * Atlas-based analysis tools
+    * Custom parcellation creation
+
+**Surface Tools** (``clabtoolkit.surfacetools``)
+    * Surface mesh processing and analysis
+    * Cortical surface manipulation
+    * Surface-based statistics
+    * Visualization of surface data
+
+**DWI Tools** (``clabtoolkit.dwitools``)
+    * Diffusion-weighted imaging analysis
+    * Tractography processing utilities
+    * DTI and advanced diffusion modeling
+    * White matter analysis tools
+
+**Quality Control Tools** (``clabtoolkit.qcqatools``)
+    * Automated quality assessment
+    * Image artifact detection
+    * Quality metrics computation
+    * Reporting and visualization
+
+**Visualization Tools** (``clabtoolkit.visualizationtools``)
+    * Brain visualization utilities
+    * Interactive plotting capabilities
+    * Publication-ready figures
+    * Multi-modal data visualization
+
+Quick Start
+-----------
+
+.. code-block:: python
+
+    import clabtoolkit.bidstools as bids
+    import clabtoolkit.connectivitytools as conn
+    
+    # Load BIDS configuration
+    config = bids.load_bids_json()
+    
+    # Extract entities from BIDS filename
+    entities = bids.str2entity("sub-01_ses-M00_T1w.nii.gz")
+    print(entities)  # {'sub': '01', 'ses': 'M00', 'suffix': 'T1w', 'extension': 'nii.gz'}
+    
+    # Process connectivity data
+    # conn_matrix = conn.load_connectivity_matrix("path/to/connectivity.mat")
+
+Contributing
+------------
+
+Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.
+
+1. Fork the repository
+2. Create your feature branch (``git checkout -b feature/amazing-feature``)
+3. Commit your changes (``git commit -m 'Add some amazing feature'``)
+4. Push to the branch (``git push origin feature/amazing-feature``)
+5. Open a Pull Request
+
+Testing
+-------
+
+Run tests with::
+
+    pytest
+
+Run tests with coverage::
+
+    pytest --cov=clabtoolkit
+
+Changelog
+---------
+
+See `HISTORY.rst <HISTORY.rst>`_ for a detailed changelog.
+
+Credits
+-------
+
+This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

clabtoolkit-0.3.2a1/README.rst

@@ -0,0 +1,151 @@
+========================
+Connectomics Lab Toolkit
+========================
+
+
+.. image:: https://img.shields.io/pypi/v/clabtoolkit.svg
+        :target: https://pypi.python.org/pypi/clabtoolkit
+
+.. image:: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml/badge.svg
+        :target: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml
+
+.. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest
+        :target: https://clabtoolkit.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/pyversions/clabtoolkit.svg
+        :target: https://pypi.python.org/pypi/clabtoolkit
+
+.. image:: https://codecov.io/gh/connectomicslab/clabtoolkit/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/connectomicslab/clabtoolkit
+
+
+A comprehensive Python toolkit for neuroimaging data processing and analysis, specifically designed for working with brain connectivity data, BIDS datasets, and various neuroimaging formats.
+
+* **Free software**: Apache Software License 2.0
+* **Documentation**: https://clabtoolkit.readthedocs.io
+* **Source Code**: https://github.com/connectomicslab/clabtoolkit
+* **Python versions**: 3.9+
+
+Installation
+------------
+
+Install from PyPI::
+
+    pip install clabtoolkit
+
+For development installation::
+
+    git clone https://github.com/connectomicslab/clabtoolkit.git
+    cd clabtoolkit
+    pip install -e .[dev]
+
+Features
+--------
+
+**BIDS Tools** (``clabtoolkit.bidstools``)
+    * BIDS dataset validation and manipulation
+    * Entity extraction from BIDS filenames
+    * Conversion between BIDS formats
+    * Metadata handling for neuroimaging datasets
+
+**Connectivity Tools** (``clabtoolkit.connectivitytools``)
+    * Brain connectivity matrix analysis
+    * Network-based statistics
+    * Graph theory metrics computation
+    * Connectivity visualization utilities
+
+**FreeSurfer Tools** (``clabtoolkit.freesurfertools``)
+    * FreeSurfer output parsing and processing
+    * Surface-based analysis utilities
+    * Cortical thickness and morphometry tools
+    * Integration with FreeSurfer workflows
+
+**Image Processing Tools** (``clabtoolkit.imagetools``)
+    * Neuroimaging data I/O operations
+    * Image registration and transformation
+    * Quality control and preprocessing utilities
+    * Multi-modal image processing
+
+**Parcellation Tools** (``clabtoolkit.parcellationtools``)
+    * Brain parcellation scheme handling
+    * Region-of-interest (ROI) extraction
+    * Atlas-based analysis tools
+    * Custom parcellation creation
+
+**Surface Tools** (``clabtoolkit.surfacetools``)
+    * Surface mesh processing and analysis
+    * Cortical surface manipulation
+    * Surface-based statistics
+    * Visualization of surface data
+
+**DWI Tools** (``clabtoolkit.dwitools``)
+    * Diffusion-weighted imaging analysis
+    * Tractography processing utilities
+    * DTI and advanced diffusion modeling
+    * White matter analysis tools
+
+**Quality Control Tools** (``clabtoolkit.qcqatools``)
+    * Automated quality assessment
+    * Image artifact detection
+    * Quality metrics computation
+    * Reporting and visualization
+
+**Visualization Tools** (``clabtoolkit.visualizationtools``)
+    * Brain visualization utilities
+    * Interactive plotting capabilities
+    * Publication-ready figures
+    * Multi-modal data visualization
+
+Quick Start
+-----------
+
+.. code-block:: python
+
+    import clabtoolkit.bidstools as bids
+    import clabtoolkit.connectivitytools as conn
+    
+    # Load BIDS configuration
+    config = bids.load_bids_json()
+    
+    # Extract entities from BIDS filename
+    entities = bids.str2entity("sub-01_ses-M00_T1w.nii.gz")
+    print(entities)  # {'sub': '01', 'ses': 'M00', 'suffix': 'T1w', 'extension': 'nii.gz'}
+    
+    # Process connectivity data
+    # conn_matrix = conn.load_connectivity_matrix("path/to/connectivity.mat")
+
+Contributing
+------------
+
+Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.
+
+1. Fork the repository
+2. Create your feature branch (``git checkout -b feature/amazing-feature``)
+3. Commit your changes (``git commit -m 'Add some amazing feature'``)
+4. Push to the branch (``git push origin feature/amazing-feature``)
+5. Open a Pull Request
+
+Testing
+-------
+
+Run tests with::
+
+    pytest
+
+Run tests with coverage::
+
+    pytest --cov=clabtoolkit
+
+Changelog
+---------
+
+See `HISTORY.rst <HISTORY.rst>`_ for a detailed changelog.
+
+Credits
+-------
+
+This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

{clabtoolkit-0.2.0 → clabtoolkit-0.3.2a1}/clabtoolkit/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Yasser Alemán-Gómez"""
 __email__ = "yasseraleman@protonmail.com"
-__version__ = "0.2.0"
+__version__ = "0.3.1"