clabtoolkit 0.0.1__tar.gz

clabtoolkit-0.0.1/AUTHORS.rst

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+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Yasser Alemán-Gómez <yasseraleman@protonmail.com>
+
+Contributors
+------------
+
+None yet. Why not be the first?

clabtoolkit-0.0.1/CONTRIBUTING.rst

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+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/yasseraleman/clabtoolkit/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Connectomics Lab Toolkit could always use more documentation, whether as part of the
+official Connectomics Lab Toolkit docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/yasseraleman/clabtoolkit/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `clabtoolkit` for local development.
+
+1. Fork the `clabtoolkit` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/clabtoolkit.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv clabtoolkit
+    $ cd clabtoolkit/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 clabtoolkit tests
+    $ python setup.py test or pytest
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+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
+   https://travis-ci.com/yasseraleman/clabtoolkit/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+
+    $ python -m unittest tests.test_clabtoolkit
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.

clabtoolkit-0.0.1/HISTORY.rst

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+=======
+History
+=======
+
+0.0.1 (2024-03-06)
+------------------
+
+* First release on PyPI.

clabtoolkit-0.0.1/LICENSE

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+Apache Software License 2.0
+
+Copyright (c) 2024, Yasser Alemán-Gómez
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+

clabtoolkit-0.0.1/MANIFEST.in

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+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

clabtoolkit-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: clabtoolkit
+Version: 0.0.1
+Summary: This package contains a set of useful tools for image processing
+Home-page: https://github.com/connectomicslab/clabtoolkit
+Author: Yasser Alemán-Gómez
+Author-email: yasseraleman@protonmail.com
+License: Apache Software License 2.0
+Keywords: clabtoolkit
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Requires-Python: >=3.6
+License-File: LICENSE
+License-File: AUTHORS.rst
+
+========================
+Connectomics Lab Toolkit
+========================
+
+
+.. image:: https://img.shields.io/pypi/v/clabtoolkit.svg
+        :target: https://pypi.python.org/pypi/clabtoolkit
+
+.. image:: https://img.shields.io/travis/yasseraleman/clabtoolkit.svg
+        :target: https://travis-ci.com/yasseraleman/clabtoolkit
+
+.. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest
+        :target: https://clabtoolkit.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+
+
+
+This package contains a set of useful tools for image processing
+
+
+* Free software: Apache Software License 2.0
+* Documentation: https://clabtoolkit.readthedocs.io.
+
+
+Features
+--------
+
+* TODO
+
+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
+
+
+=======
+History
+=======
+
+0.0.1 (2024-03-06)
+------------------
+
+* First release on PyPI.

clabtoolkit-0.0.1/README.rst

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+========================
+Connectomics Lab Toolkit
+========================
+
+
+.. image:: https://img.shields.io/pypi/v/clabtoolkit.svg
+        :target: https://pypi.python.org/pypi/clabtoolkit
+
+.. image:: https://img.shields.io/travis/yasseraleman/clabtoolkit.svg
+        :target: https://travis-ci.com/yasseraleman/clabtoolkit
+
+.. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest
+        :target: https://clabtoolkit.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+
+
+
+This package contains a set of useful tools for image processing
+
+
+* Free software: Apache Software License 2.0
+* Documentation: https://clabtoolkit.readthedocs.io.
+
+
+Features
+--------
+
+* TODO
+
+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-0.0.1/clabtoolkit/__init__.py

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+"""Top-level package for Connectomics Lab Toolkit."""
+
+__author__ = """Yasser Alemán-Gómez"""
+__email__ = 'yasseraleman@protonmail.com'
+__version__ = '0.0.1'

clabtoolkit-0.0.1/clabtoolkit/bidstools.py

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+import os
+import shutil
+import clabtoolkit as clt
+
+
+# This function copies the BIDs folder and its derivatives for e given subjects to a new location
+def _copy_bids_folder(
+    bids_dir: str, out_dir: str, fold2copy: list = ["anat"], subjs2copy: str = None, deriv_dir: str = None,
+include_derivatives: bool = False):
+    """
+    Copy full bids folders
+    @params:
+        bids_dir     - Required  : BIDs dataset directory:
+        out_dir      - Required  : Output directory:
+        fold2copy    - Optional  : List of folders to copy: default = ['anat']
+        subjs2copy   - Optional  : List of subjects to copy: 
+        deriv_dir    - Optional  : Derivatives directory: default = None
+        include_derivatives - Optional  : Include derivatives folder: default = False
+    """
+
+    # Listing the subject ids inside the dicom folder
+    if subjs2copy is None:
+        my_list = os.listdir(bids_dir)
+        subj_ids = []
+        for it in my_list:
+            if "sub-" in it:
+                subj_ids.append(it)
+        subj_ids.sort()
+    else:
+        subj_ids = subjs2copy
+    
+    # Selecting the derivatives folder
+    if include_derivatives:
+        if deriv_dir is None:
+            deriv_dir = os.path.join(bids_dir, "derivatives")
+    
+        if not os.path.isdir(deriv_dir):
+            # Lunch a warning message if the derivatives folder does not exist
+            print("WARNING: The derivatives folder does not exist.")
+            print("WARNING: The derivatives folder will not be copied.")
+            include_derivatives = False
+
+        # Selecting all the derivatives folders
+        der_pipe_folders = []
+        directories = os.listdir(deriv_dir)
+        der_pipe_folders = []
+        for directory in directories:
+            pipe_dir = os.path.join(deriv_dir, directory)
+            if not directory.startswith(".") and os.path.isdir(pipe_dir):
+                der_pipe_folders.append(pipe_dir)
+
+    # Failed sessions and derivatives
+    fail_sess = []
+    fail_deriv = []
+
+    # Loop around all the subjects
+    nsubj = len(subj_ids)
+    for i, subj_id in enumerate(subj_ids):  # Loop along the IDs
+        subj_dir = os.path.join(bids_dir, subj_id)
+        out_subj_dir = os.path.join(out_dir, subj_id)
+
+        clt._printprogressbar(
+            i + 1,
+            nsubj,
+            "Processing subject "
+            + subj_id
+            + ": "
+            + "("
+            + str(i + 1)
+            + "/"
+            + str(nsubj)
+            + ")",
+        )
+
+        # Loop along all the sessions inside the subject directory
+        for ses_id in os.listdir(subj_dir):  # Loop along the session
+            ses_dir = os.path.join(subj_dir, ses_id)
+            out_ses_dir = os.path.join(out_subj_dir, ses_id)
+
+            # print('Copying SubjectId: ' + subjId + ' ======>  Session: ' +  sesId)
+
+            if fold2copy[0] == "all":
+                directories = os.listdir(ses_dir)
+                fold2copy = []
+                for directory in directories:
+                    if not directory.startswith(".") and os.path.isdir(os.path.join(ses_dir, directory)):
+                        print(directory)
+                        fold2copy.append(directory)
+
+            for fc in fold2copy:
+                # Copying the anat folder
+                if os.path.isdir(ses_dir):
+                    fold_to_copy = os.path.join(ses_dir, fc)
+
+                    try:
+                        # Creating destination directory using make directory
+                        dest_dir = os.path.join(out_ses_dir, fc)
+                        os.makedirs(dest_dir, exist_ok=True)
+
+                        shutil.copytree(fold_to_copy, dest_dir, dirs_exist_ok=True)
+
+                    except:
+                        fail_sess.append(fold_to_copy)
+
+            if include_derivatives:
+                # Copying the derivatives folder
+
+                for pipe_dir in der_pipe_folders:
+                    if os.path.isdir(pipe_dir):
+
+                        out_pipe_dir = os.path.join(out_dir, "derivatives", os.path.basename(pipe_dir))
+
+                        pipe_indiv_subj_in = os.path.join(pipe_dir, subj_id, ses_id)
+                        pipe_indiv_subj_out = os.path.join(out_pipe_dir, subj_id, ses_id)
+
+                        if os.path.isdir(pipe_indiv_subj_in):
+                            try:
+                                # Creating destination directory using make directory
+                                os.makedirs(pipe_indiv_subj_out, exist_ok=True)
+
+                                # Copying the folder
+                                shutil.copytree(pipe_indiv_subj_in, pipe_indiv_subj_out, dirs_exist_ok=True)
+
+                            except:
+                                fail_deriv.append(pipe_indiv_subj_in)
+    
+    # Print the failed sessions and derivatives
+    print(" ")
+    if fail_sess:
+        print("THE PROCESS FAILED COPYING THE FOLLOWING SESSIONS:")
+        for i in fail_sess:
+            print(i)
+    print(" ")
+
+    if fail_deriv:
+        print("THE PROCESS FAILED COPYING THE FOLLOWING DERIVATIVES:")
+        for i in fail_deriv:
+            print(i)
+    print(" ")
+    
+    print("End of copying the files.")