Metadata-Version: 2.4
Name: mia_processes
Version: 2.7.0
Summary: mia_processes
Home-page: http://populse.github.io/mia_processes
Author: Populse team
Author-email: Populse team <populse-support@univ-grenoble-alpes.fr>
License: CeCILL-B
Project-URL: homepage, http://populse.github.io/mia_processes/
Project-URL: repository, https://github.com/populse/mia_processes
Platform: OS Independent
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: boto
Requires-Dist: cmp
Requires-Dist: cfflib
Requires-Dist: dipy
Requires-Dist: nibabel
Requires-Dist: nilearn
Requires-Dist: nipy
Requires-Dist: nipype
Requires-Dist: nitime
Requires-Dist: nitransforms
Requires-Dist: niworkflows
Requires-Dist: numpy
Requires-Dist: openpyxl
Requires-Dist: paramiko
Requires-Dist: populse-db<3.0.0,>=2.5.0
Requires-Dist: populse_mia<3.0.0,>=2.5.0
Requires-Dist: pyxnat
Requires-Dist: reportlab
Requires-Dist: scipy
Requires-Dist: statsmodels
Requires-Dist: templateflow
Requires-Dist: torch
Requires-Dist: vtk
Provides-Extra: doc
Requires-Dist: sphinx>=1.0; extra == "doc"
Dynamic: author
Dynamic: home-page
Dynamic: license-file
Dynamic: platform

<p align="center" >
	<img src="https://github.com/populse/mia_processes/blob/master/mia_processes/sources_images/Logo_mia_processes_1537x1025.jpg" alt="mia_processes logo" height="300" width="450">
    <br />
    <sub style="font-size: 8px;">This image was generated with ChatGPT from a text description.</sub>
</p>

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[![](https://img.shields.io/badge/license-CeCILL-blue.svg)](https://github.com/populse/mia_processes/blob/master/LICENSE)
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# Documentation

[The documentation is available in mia_processes's website](https://populse.github.io/mia_processes).

# Installation

* A compatible version of [Python](https://www.python.org/) (>= 3.5) and [pip](https://packaging.python.org/guides/tool-recommendations/) must be installed.

* Depending on the Python setup and OS, the `python3` command may be used as the default Python command.

    Try:
        `python -V`

    If it returns `Python 3.x.x`, replace all the `python3` commands below by `python`.

    If not installed, install it ...

 * Make sure to have pip installed.

    Try:
        `pip -V`

    If it returns a path including `/python3.x/`, replace all the `pip3` commands below by `pip`.

    If not installed, install it ...

* From PyPI

  * [Install the latest version of mia_processes and its dependencies from the Python Packaging Index](https://docs.python.org/3/installing/index.html):

        pip3 install mia_processes # depending of the setup, it could be necessary to add --user option

* From source, for Linux distributions.

  * Install a Version Control System, for example [git](https://git-scm.com/book/en/v2/Getting-Started-About-Version-Control). Depending of your distribution, [package management system](https://en.wikipedia.org/wiki/Package_manager) can be different:

        sudo apt-get install git # Debian like
        sudo dnf install git # Fedora 22 and later
        # etc.

  * Clone the source codes.

    * Get source codes from Github. Replace [mia_processes_install_dir] with a directory of your choice:

          git clone https://github.com/populse/mia_processes.git [mia_processes_install_dir]

    * Or download the zip file (mia_processes-master.zip) of the project ([green button "Clone or download"](https://github.com/populse/mia_processes)), then extract the data in the directory of your choice ([mia_processes_install_dir]):

          unzip mia_processes-master.zip -d [mia_processes_install_dir]  # In this case [mia_processes_install_dir] becomes [mia_processes_install_dir]/mia_processes-master

  * Install the Python module distribution:

        cd [mia_processes_install_dir]
        python3 setup.py install # depending of the setup, it could be necessary to add --user option

  * Remove the [mia_processes_install_dir] directory:

        cd ..
        rm -r [mia_install_dir]

* The populse project uses Git Large File Storage (LFS). In developer mode (without installing the source codes), after cloning the source codes, it is advisable to retrieve the large files with Git LFS:

    * If Git LFS is not already installed on your system, you need to install it first.

        * Ex. on Fedora:

              sudo dnf install git-lfs

    * Initialize Git LFS

        * On a reposirory:

              git lfs install

    * Retrieve Files with Git LFS

        * On a repository:

              git lfs pull

# Third-party softwares

Many mia_processes bricks (atomic processes) use third-party softwares. To use these bricks, the corresponding [third-party softwares must be installed](https://populse.github.io/populse_mia/html/installation/3rd-party_installations.html).


# Requirements

In order to get all the bricks and pipelines proposed by mia_processes some third libraries are required:
* boto
* cmp
* cfflib
* dipy
* nibabel
* nilearn
* nipy
* nipype
* nitime
* nitransforms
* numpy
* openpyxl
* paramiko
* populse-db >= 2.5.0, < 3.0.0
* populse_mia >= 2.5.0, < 3.0.0
* pyxnat
* reportlab
* scipy
* statsmodels
* templateflow
* torch
* vtk

# License

* The whole populse project is open source.
* Mia_processes is precisely released under the CeCILL software license.
* All license details can be found [here](http://cecill.info/licences/Licence_CeCILL_V2.1-en.html), or refer to the license file [here](https://github.com/populse/mia_processes/blob/master/LICENSE).

# Support and Communication

In case of a problem or to ask a question about how to do something in mia_processes, please [open an issue](https://github.com/populse/mia_processes/issues).

The developer team can even be contacted using populse-support@univ-grenoble-alpes.fr.
