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‎CONTRIBUTING.md

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# Contributing
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This page includes some guidelines to enable you to contribute to the project.
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## Found a bug?
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If you find a bug in the source code or in using the theme, you can
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open an issue on GitHub.
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Even better, you can submit a pull request with a fix.
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## Submission guidelines
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### Submitting an issue
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Before you submit an issue, please search the issue tracker, maybe an issue
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for your problem already exists and the discussion might inform you of workarounds
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readily available.
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We want to fix all the issues as soon as possible, but before fixing a bug we
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need to reproduce and confirm it. In order to reproduce bugs we will need as
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much information as possible, and preferably a sample demonstrating the issue.
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### Submitting a pull request (PR)
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If you wish to contribute to the code base, please open a pull request by
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following GitHub's guidelines.
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## Development Conventions
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`atlalign` uses:
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- Black for formatting code
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- Flake8 for linting code
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- PyDocStyle for checking docstrings
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‎LICENSE.md

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GNU LESSER GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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This version of the GNU Lesser General Public License incorporates
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the terms and conditions of version 3 of the GNU General Public
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License, supplemented by the additional permissions listed below.
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0. Additional Definitions.
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As used herein, "this License" refers to version 3 of the GNU Lesser
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General Public License, and the "GNU GPL" refers to version 3 of the GNU
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General Public License.
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"The Library" refers to a covered work governed by this License,
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other than an Application or a Combined Work as defined below.
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An "Application" is any work that makes use of an interface provided
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Defining a subclass of a class defined by the Library is deemed a mode
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A "Combined Work" is a work produced by combining or linking an
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Application with the Library. The particular version of the Library
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with which the Combined Work was made is also called the "Linked
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Version".
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The "Minimal Corresponding Source" for a Combined Work means the
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Corresponding Source for the Combined Work, excluding any source code
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The "Corresponding Application Code" for a Combined Work means the
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and utility programs needed for reproducing the Combined Work from the
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You may convey a covered work under sections 3 and 4 of this License
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2. Conveying Modified Versions.
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If you modify a copy of the Library, and, in your modifications, a
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b) Give prominent notice with the combined library that part of it
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6. Revised Versions of the GNU Lesser General Public License.
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Each version is given a distinguishing version number. If the
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Library.

‎README.md

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# Atlas Alignment
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### Overview
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This project implements multiple alignment algorithms - including deep learning.
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### Official documentation
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All details related to installation and logic are described in the official documentation. Once
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deployed a link will be added. Until then one can generate it locally following the instructions
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below.
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### Normal installation
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Make sure the `pip` version is at least `19.1`.
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```bash
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pip install --upgrade pip
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pip --version # make sure >= 19.1
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```
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Then one can move on to installing the actual `atlalign` package:
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```
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pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign[tf]
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```
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The extras entry `[tf]` represents TensorFlow and can be dropped if it is already installed.
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### Development installation + docs
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As described above, make sure to get the most recent `pip`.
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```
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git clone https://github.com/BlueBrain/atlas_alignment
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cd atlas_alignment
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pip install -e .[dev,docs,tf]
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```
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Assuming the user ran the above it should be possible to generate the docs
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```
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cd docs
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make clean && make html
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```

‎atlalign/__init__.py

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"""Image registration package.
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Release markers:
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X.Y
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X.Y.Z for bug fixes
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"""
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"""
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The package atlalign is a tool for registration of 2D images.
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Copyright (C) 2021 EPFL/Blue Brain Project
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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"""
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__version__ = "0.5"

‎atlalign/allen/__init__.py

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"""Collection of modules related to using Allen Brain database and API."""
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"""
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The package atlalign is a tool for registration of 2D images.
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Copyright (C) 2021 EPFL/Blue Brain Project
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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"""
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# variables
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from atlalign.allen.utils import CACHE_FOLDER, get_image # noqa
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# functions
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from atlalign.allen.sync import ( # noqa
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corners_rs9,
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download_dataset,
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get_reference_image,
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pir_to_xy_API,
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pir_to_xy_local,
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pir_to_xy_local_coronal,
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warp_rs9,
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xy_to_pir_API,
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)

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