torch-grid-utils 0.0.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- torch_grid_utils-0.0.1/.copier-answers.yml +11 -0
- torch_grid_utils-0.0.1/.github/ISSUE_TEMPLATE.md +15 -0
- torch_grid_utils-0.0.1/.github/TEST_FAIL_TEMPLATE.md +12 -0
- torch_grid_utils-0.0.1/.github/dependabot.yml +10 -0
- torch_grid_utils-0.0.1/.github/workflows/ci.yml +108 -0
- torch_grid_utils-0.0.1/.gitignore +111 -0
- torch_grid_utils-0.0.1/.pre-commit-config.yaml +37 -0
- torch_grid_utils-0.0.1/LICENSE +28 -0
- torch_grid_utils-0.0.1/PKG-INFO +43 -0
- torch_grid_utils-0.0.1/README.md +11 -0
- torch_grid_utils-0.0.1/pyproject.toml +150 -0
- torch_grid_utils-0.0.1/src/torch_grid_utils/__init__.py +13 -0
- torch_grid_utils-0.0.1/src/torch_grid_utils/coordinate_grid.py +61 -0
- torch_grid_utils-0.0.1/src/torch_grid_utils/fftfreq_grid.py +204 -0
- torch_grid_utils-0.0.1/tests/test_coordinate_grid.py +254 -0
- torch_grid_utils-0.0.1/tests/test_fftfreq_grid.py +494 -0
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# Do not edit - changes here will be overwritten by Copier
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_commit: v1
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_src_path: gh:pydev-guide/pyrepo-copier
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author_email: alisterburt@gmail.com
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author_name: Alister Burt
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github_username: alisterburt
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mode: tooling
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module_name: torch_grid_utils
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project_name: torch-grid-utils
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project_short_description: Grids for 2D/3D image manipulations in PyTorch
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* torch-grids version:
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* Python version:
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* Operating System:
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### Description
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Describe what you were trying to get done.
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Tell us what happened, what went wrong, and what you expected to happen.
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### What I Did
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```
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Paste the command(s) you ran and the output.
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If there was a crash, please include the traceback here.
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```
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---
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title: "{{ env.TITLE }}"
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labels: [bug]
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---
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The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
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The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
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with commit: {{ sha }}
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Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
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(This post will be updated if another test fails, as long as this issue remains open.)
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# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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commit-message:
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prefix: "ci(dependabot):"
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name: CI
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on:
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push:
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branches:
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- main
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tags:
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- "v*"
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pull_request:
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workflow_dispatch:
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schedule:
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# run every week (for --pre release tests)
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- cron: "0 0 * * 0"
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# cancel in-progress runs that use the same workflow and branch
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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check-manifest:
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# check-manifest is a tool that checks that all files in version control are
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# included in the sdist (unless explicitly excluded)
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- run: pipx run check-manifest
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test:
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name: ${{ matrix.platform }} (${{ matrix.python-version }})
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runs-on: ${{ matrix.platform }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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platform: [ubuntu-latest, ] # macos-latest, windows-latest]
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steps:
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- uses: actions/checkout@v4
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- name: ๐ Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache-dependency-path: "pyproject.toml"
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cache: "pip"
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- name: Install Dependencies
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run: |
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python -m pip install -U pip
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# if running a cron job, we add the --pre flag to test against pre-releases
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python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || '' }}
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- name: ๐งช Run Tests
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run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
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# If something goes wrong with --pre tests, we can open an issue in the repo
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- name: ๐ Report --pre Failures
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if: failure() && github.event_name == 'schedule'
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uses: JasonEtco/create-an-issue@v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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PLATFORM: ${{ matrix.platform }}
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PYTHON: ${{ matrix.python-version }}
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RUN_ID: ${{ github.run_id }}
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TITLE: "[test-bot] pip install --pre is failing"
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with:
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filename: .github/TEST_FAIL_TEMPLATE.md
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update_existing: true
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- name: Coverage
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uses: codecov/codecov-action@v3
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deploy:
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name: Deploy
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needs: test
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if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
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runs-on: ubuntu-latest
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permissions:
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# IMPORTANT: this permission is mandatory for trusted publishing on PyPi
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# see https://docs.pypi.org/trusted-publishers/
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id-token: write
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# This permission allows writing releases
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contents: write
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: ๐ Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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- name: ๐ท Build
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run: |
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python -m pip install build
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python -m build
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- name: ๐ข Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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- uses: softprops/action-gh-release@v1
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with:
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generate_release_notes: true
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files: './dist/*'
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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lib/
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lib64/
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parts/
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var/
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wheels/
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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# Unit test / coverage reports
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# Translations
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# Jupyter Notebook
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# ruff
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# enable pre-commit.ci at https://pre-commit.ci/
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# it adds:
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# 1. auto fixing pull requests
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# 2. auto updating the pre-commit configuration
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ci:
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autoupdate_schedule: monthly
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autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
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autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
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repos:
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- repo: https://github.com/abravalheri/validate-pyproject
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rev: v0.16
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hooks:
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- id: validate-pyproject
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- repo: https://github.com/crate-ci/typos
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rev: v1.20.9
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hooks:
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args: [--force-exclude] # omitting --write-changes
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rev: v0.4.1
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hooks:
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args: [--fix] # may also add '--unsafe-fixes'
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rev: v1.9.0
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- id: mypy
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files: "^src/"
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# # you have to add the things you want to type check against here
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# additional_dependencies:
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# - numpy
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BSD 3-Clause License
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Copyright (c) 2023, Alister Burt
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Metadata-Version: 2.3
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Name: torch-grid-utils
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Version: 0.0.1
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Summary: Grid utilities for 2D/3D image manipulations in PyTorch
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Project-URL: homepage, https://github.com/alisterburt/torch-grids
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Project-URL: repository, https://github.com/alisterburt/torch-grids
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Author-email: Alister Burt <alisterburt@gmail.com>
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License: BSD-3-Clause
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License-File: LICENSE
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Classifier: Development Status :: 3 - Alpha
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Classifier: License :: OSI Approved :: BSD License
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Typing :: Typed
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Requires-Dist: ipython; extra == 'dev'
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Requires-Dist: mypy; extra == 'dev'
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Requires-Dist: pdbpp; extra == 'dev'
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Requires-Dist: pre-commit; extra == 'dev'
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Requires-Dist: rich; extra == 'dev'
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Requires-Dist: ruff; extra == 'dev'
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Provides-Extra: test
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Requires-Dist: pytest; extra == 'test'
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Requires-Dist: pytest-cov; extra == 'test'
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Description-Content-Type: text/markdown
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# torch-grid-utils
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[](https://github.com/alisterburt/torch-grids/raw/main/LICENSE)
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[](https://pypi.org/project/torch-grids)
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[](https://python.org)
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[](https://github.com/alisterburt/torch-grids/actions/workflows/ci.yml)
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[](https://codecov.io/gh/alisterburt/torch-grids)
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*torch-grid-utils* provides grids for 2D/3D image manipulations in PyTorch.
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# torch-grid-utils
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[](https://github.com/alisterburt/torch-grids/raw/main/LICENSE)
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[](https://pypi.org/project/torch-grids)
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[](https://python.org)
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[](https://github.com/alisterburt/torch-grids/actions/workflows/ci.yml)
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[](https://codecov.io/gh/alisterburt/torch-grids)
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*torch-grid-utils* provides grids for 2D/3D image manipulations in PyTorch.
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# https://peps.python.org/pep-0517/
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[build-system]
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requires = ["hatchling", "hatch-vcs"]
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build-backend = "hatchling.build"
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# https://hatch.pypa.io/latest/config/metadata/
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[tool.hatch.version]
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source = "vcs"
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# read more about configuring hatch at:
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# https://hatch.pypa.io/latest/config/build/
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[tool.hatch.build.targets.wheel]
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only-include = ["src"]
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sources = ["src"]
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# https://peps.python.org/pep-0621/
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[project]
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name = "torch-grid-utils"
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dynamic = ["version"]
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description = "Grid utilities for 2D/3D image manipulations in PyTorch"
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readme = "README.md"
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requires-python = ">=3.10"
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license = { text = "BSD-3-Clause" }
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authors = [{ name = "Alister Burt", email = "alisterburt@gmail.com" }]
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# https://pypi.org/classifiers/
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classifiers = [
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"Development Status :: 3 - Alpha",
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"License :: OSI Approved :: BSD License",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Typing :: Typed",
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]
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# add your package dependencies here
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dependencies = [
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"torch",
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"numpy",
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"einops",
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]
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# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
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# "extras" (e.g. for `pip install .[test]`)
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[project.optional-dependencies]
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# add dependencies used for testing here
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test = ["pytest", "pytest-cov"]
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# add anything else you like to have in your dev environment here
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dev = [
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"ipython",
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"mypy",
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"pdbpp", # https://github.com/pdbpp/pdbpp
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"pre-commit",
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"rich", # https://github.com/Textualize/rich
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"ruff",
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]
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[project.urls]
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homepage = "https://github.com/alisterburt/torch-grids"
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repository = "https://github.com/alisterburt/torch-grids"
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# Entry points
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# https://peps.python.org/pep-0621/#entry-points
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# same as console_scripts entry point
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# [project.scripts]
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# torch-grid-utils-cli = "torch_grid_utils:main_cli"
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# [project.entry-points."some.group"]
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# tomatoes = "torch_grid_utils:main_tomatoes"
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# https://docs.astral.sh/ruff
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[tool.ruff]
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line-length = 88
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target-version = "py38"
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src = ["src"]
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# https://docs.astral.sh/ruff/rules
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[tool.ruff.lint]
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pydocstyle = { convention = "numpy" }
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select = [
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"E", # style errors
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"W", # style warnings
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"F", # flakes
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"D", # pydocstyle
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"D417", # Missing argument descriptions in Docstrings
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"I", # isort
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"UP", # pyupgrade
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"C4", # flake8-comprehensions
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"B", # flake8-bugbear
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"A001", # flake8-builtins
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"RUF", # ruff-specific rules
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"TCH", # flake8-type-checking
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"TID", # flake8-tidy-imports
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]
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ignore = [
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"D401", # First line should be in imperative mood (remove to opt in)
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]
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[tool.ruff.lint.per-file-ignores]
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"tests/*.py" = ["D", "S"]
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# https://docs.astral.sh/ruff/formatter/
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[tool.ruff.format]
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docstring-code-format = true
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skip-magic-trailing-comma = false # default is false
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# https://mypy.readthedocs.io/en/stable/config_file.html
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[tool.mypy]
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files = "src/**/"
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strict = true
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disallow_any_generics = false
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disallow_subclassing_any = false
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show_error_codes = true
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pretty = true
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# # module specific overrides
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# [[tool.mypy.overrides]]
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# module = ["numpy.*",]
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# ignore_errors = true
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# https://docs.pytest.org/
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[tool.pytest.ini_options]
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minversion = "7.0"
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testpaths = ["tests"]
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filterwarnings = ["error"]
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# https://coverage.readthedocs.io/
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[tool.coverage.report]
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show_missing = true
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exclude_lines = [
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"pragma: no cover",
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"if TYPE_CHECKING:",
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"@overload",
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"except ImportError",
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"\\.\\.\\.",
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"raise NotImplementedError()",
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"pass",
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]
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[tool.coverage.run]
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source = ["torch_grids"]
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+
|
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# https://github.com/mgedmin/check-manifest#configuration
|
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|
+
# add files that you want check-manifest to explicitly ignore here
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# (files that are in the repo but shouldn't go in the package)
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[tool.check-manifest]
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ignore = [
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".pre-commit-config.yaml",
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".ruff_cache/**/*",
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"tests/**/*",
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]
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@@ -0,0 +1,13 @@
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"""Grids for 2D/3D image manipulations in PyTorch"""
|
|
2
|
+
|
|
3
|
+
from importlib.metadata import PackageNotFoundError, version
|
|
4
|
+
|
|
5
|
+
try:
|
|
6
|
+
__version__ = version("torch-grid-utils")
|
|
7
|
+
except PackageNotFoundError:
|
|
8
|
+
__version__ = "uninstalled"
|
|
9
|
+
__author__ = "Alister Burt"
|
|
10
|
+
__email__ = "alisterburt@gmail.com"
|
|
11
|
+
|
|
12
|
+
from .fftfreq_grid import fftfreq_grid
|
|
13
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from .coordinate_grid import coordinate_grid
|
|
@@ -0,0 +1,61 @@
|
|
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|
+
from typing import Sequence
|
|
2
|
+
|
|
3
|
+
import einops
|
|
4
|
+
import numpy as np
|
|
5
|
+
import torch
|
|
6
|
+
|
|
7
|
+
|
|
8
|
+
def coordinate_grid(
|
|
9
|
+
image_shape: Sequence[int],
|
|
10
|
+
center: torch.Tensor | tuple[float, ...] | None = False,
|
|
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|
+
norm: bool = False,
|
|
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|
+
device: torch.device | None = None,
|
|
13
|
+
) -> torch.FloatTensor:
|
|
14
|
+
"""Get a dense grid of array coordinates from grid dimensions.
|
|
15
|
+
|
|
16
|
+
For input `image_shape` of `(d, h, w)`, this function produces a
|
|
17
|
+
`(d, h, w, 3)` grid of coordinates. Coordinate order matches the order of
|
|
18
|
+
dimensions in `image_shape`.
|
|
19
|
+
|
|
20
|
+
Parameters
|
|
21
|
+
----------
|
|
22
|
+
image_shape: Sequence[int]
|
|
23
|
+
Shape of the image for which coordinates should be returned.
|
|
24
|
+
center: torch.Tensor | tuple[float, ...] | None
|
|
25
|
+
Array of center points relative to which coordinates will be calculated.
|
|
26
|
+
If `None`, default to the array origin `[0, ...]` of zero in all dimensions.
|
|
27
|
+
norm: bool
|
|
28
|
+
Whether to compute the Euclidean norm of the coordinate grid.
|
|
29
|
+
device: torch.device
|
|
30
|
+
PyTorch device on which to put the coordinate grid.
|
|
31
|
+
|
|
32
|
+
Returns
|
|
33
|
+
-------
|
|
34
|
+
grid: torch.LongTensor
|
|
35
|
+
`(*image_shape, image_ndim)` array of coordinates if `norm` is `False`
|
|
36
|
+
else `(*image_shape, )`.
|
|
37
|
+
"""
|
|
38
|
+
grid = torch.tensor(
|
|
39
|
+
np.indices(image_shape),
|
|
40
|
+
device=device,
|
|
41
|
+
dtype=torch.float32
|
|
42
|
+
) # (coordinates, *image_shape)
|
|
43
|
+
grid = einops.rearrange(grid, 'coords ... -> ... coords')
|
|
44
|
+
ndim = len(image_shape)
|
|
45
|
+
if center is not None:
|
|
46
|
+
center = torch.as_tensor(center, dtype=grid.dtype, device=grid.device)
|
|
47
|
+
center = torch.atleast_1d(center)
|
|
48
|
+
center, ps = einops.pack([center], pattern='* coords')
|
|
49
|
+
ones = ' '.join('1' * ndim)
|
|
50
|
+
axis_ids = ' '.join(_unique_characters(ndim))
|
|
51
|
+
center = einops.rearrange(center, f"b coords -> b {ones} coords")
|
|
52
|
+
grid = grid - center
|
|
53
|
+
[grid] = einops.unpack(grid, packed_shapes=ps, pattern=f'* {axis_ids} coords')
|
|
54
|
+
if norm is True:
|
|
55
|
+
grid = einops.reduce(grid ** 2, '... coords -> ...', reduction='sum') ** 0.5
|
|
56
|
+
return grid
|
|
57
|
+
|
|
58
|
+
|
|
59
|
+
def _unique_characters(n: int) -> str:
|
|
60
|
+
chars = "abcdefghijklmnopqrstuvwxyz"
|
|
61
|
+
return chars[:n]
|