image2image-reg 0.1.10__tar.gz

image2image_reg-0.1.10/.github/ISSUE_TEMPLATE.md

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+* image2image-reg version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

image2image_reg-0.1.10/.github/TEST_FAIL_TEMPLATE.md

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+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

image2image_reg-0.1.10/.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

image2image_reg-0.1.10/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * 0" # every week (for --pre release tests)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-manifest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+    uses: pyapp-kit/workflows/.github/workflows/test-pyrepo.yml@v2
+    secrets: inherit
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      pip-install-pre-release: ${{ github.event_name == 'schedule' }}
+      report-failures: ${{ github.event_name == 'schedule' }}
+      extras: 'test'
+      # changing this to "artifact" prevents uploading to codecov here,
+      # instead it uploads an artifact with the coverage data
+      coverage-upload: artifact
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12"]#, "3.13"]
+        include:
+          - python-version: "3.9"
+            os: ubuntu-latest
+          - python-version: "3.9"
+            os: macos-13
+          - python-version: "3.11"
+            os: macos-latest
+          - python-version: "3.12"
+            os: macos-latest
+
+
+  # now add another job to combine and upload the coverage
+  upload_coverage:
+    if: always()
+    needs: [test]
+    uses: pyapp-kit/workflows/.github/workflows/upload-coverage.yml@v2
+    secrets:
+      codecov_token: ${{ secrets.CODECOV_TOKEN }}
+
+  deploy_test:
+    name: Deploy to PyPI (test)
+    needs: [check-manifest, test]
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          pip install -U pip build twine
+          python -m build
+          twine check dist/*
+
+      - name: Build and publish
+        run: twine upload --repository testpypi dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+
+  deploy:
+    name: Deploy
+    needs: [check-manifest, test, deploy_test]
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          git tag
+          pip install -U pip build twine
+          python -m build
+          twine check dist/*
+          ls -lh dist
+
+      - name: Build and publish
+        run: twine upload dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

image2image_reg-0.1.10/.pre-commit-config.yaml

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+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+default_install_hook_types: [pre-commit, commit-msg]
+
+repos:
+#  -   repo: https://github.com/pre-commit/pre-commit-hooks
+#      rev: v4.4.0
+#      hooks:
+#      - id: no-commit-to-branch
+#        args: ['--branch', 'master', "--branch", "main"]
+
+  -   repo: https://github.com/MarcoGorelli/absolufy-imports
+      rev: v0.3.1
+      hooks:
+      -   id: absolufy-imports
+          exclude: _vendor|vendored
+
+  -   repo: https://github.com/hadialqattan/pycln
+      rev: v2.1.3
+      hooks:
+      - id: pycln
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.1
+    hooks:
+      - id: validate-pyproject
+
+  -   repo: https://github.com/psf/black
+      rev: 23.1.0
+      hooks:
+      - id: black
+        pass_filenames: true
+
+  -   repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.252
+      hooks:
+        - id: ruff
+          args: [--fix]
+
+#  - repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.0.1
+#    hooks:
+#      - id: mypy
+#        files: "^src/"
+#        # # you have to add the things you want to type check against here
+#        # additional_dependencies:
+#        #   - numpy

image2image_reg-0.1.10/LICENSE

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+BSD License
+
+Copyright (c) 2023, Lukasz G. Migas
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

image2image_reg-0.1.10/MANIFEST.in

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+# Things to always exclude
+global-exclude .git*
+global-exclude .ipynb_checkpoints
+global-exclude *.py[co]
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+# Top-level config
+include MANIFEST.in
+include LICENSE
+recursive-include tests *
+recursive-include src *.typed
+
+# Always include
+global-include *.pyx
+global-include *.c

image2image_reg-0.1.10/Makefile

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+.PHONY: pre watch dist settings-schema untrack
+
+# note: much faster to run mypy as daemon,
+# dmypy run -- ...
+# https://mypy.readthedocs.io/en/stable/mypy_daemon.html
+typecheck:
+	tox -e mypy
+
+check-manifest:
+	pip install -U check-manifest
+	check-manifest
+
+dist: check-manifest
+	pip install -U build
+	python -m build
+
+pre:
+	pre-commit run -a
+
+# If the first argument is "watch"...
+ifeq (watch,$(firstword $(MAKECMDGOALS)))
+  # use the rest as arguments for "watch"
+  WATCH_ARGS := $(wordlist 2,$(words $(MAKECMDGOALS)),$(MAKECMDGOALS))
+  # ...and turn them into do-nothing targets
+  $(eval $(WATCH_ARGS):;@:)
+endif
+
+
+.PHONY: untrack
+untrack:
+	git rm -r --cached .
+	git add .
+	git commit -m ".gitignore fix"

image2image_reg-0.1.10/PKG-INFO

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+Metadata-Version: 2.4
+Name: image2image-reg
+Version: 0.1.10
+Summary: Whole slide image registration using elastix.
+Author-email: "Lukasz G. Migas" <lukas.migas@yahoo.com>
+License: BSD 3-Clause License
+Project-URL: homepage, https://github.com/vandeplaslab/image2image-reg
+Project-URL: repository, https://github.com/vandeplaslab/image2image-reg
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydantic>=2
+Requires-Dist: numpy
+Requires-Dist: itk-elastix
+Requires-Dist: opencv-python
+Requires-Dist: SimpleITK
+Requires-Dist: scikit-image
+Requires-Dist: click-groups
+Requires-Dist: mpire
+Requires-Dist: colour-science>=0.4.1
+Requires-Dist: tabulate
+Requires-Dist: loguru
+Requires-Dist: image2image-io
+Provides-Extra: valis
+Requires-Dist: valis-wsi; extra == "valis"
+Requires-Dist: opencv-contrib-python; extra == "valis"
+Requires-Dist: fastcluster; extra == "valis"
+Requires-Dist: scikit-learn; extra == "valis"
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pdbpp; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: rich; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: image2image-reg[test]; extra == "dev"
+Dynamic: license-file
+
+# image2image-reg
+
+[![License](https://img.shields.io/pypi/l/image2image-reg.svg?color=green)](https://github.com/vandeplaslab/image2image-reg/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/image2image-reg.svg?color=green)](https://pypi.org/project/image2image-reg)
+[![Python Version](https://img.shields.io/pypi/pyversions/image2image-reg.svg?color=green)](https://python.org)
+[![CI](https://github.com/vandeplaslab/image2image-reg/actions/workflows/ci.yml/badge.svg)](https://github.com/vandeplaslab/image2image-reg/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/vandeplaslab/image2image-reg/branch/main/graph/badge.svg)](https://codecov.io/gh/vandeplaslab/image2image-reg)
+
+Whole slide image registration using elastix and/or Valis-WSI.
+
+## Overview
+
+`image2image-reg` is a library for whole-slide image registration. It provides a command-line interface for performing
+registration, transformation and evaluation of whole-slide image registrations. The library is inspired by `wsireg` and
+`valis`. In fact, the registration workflow is a complete rewrite of the `wsireg` library to provide more flexibility
+and control over the registration process.
+
+## Differences from `wsireg`
+
+- [DONE] Registrations are organized into `projects`. Project is a collection of configuration, logs, visualisations and images.
+This should provide a more structured way of organizing your images and not cluttering the working directory.
+- [WIP] Registrations can be initialized with `affine` matrix (to get a good starting point) - this will allow for faster
+registration and hopefully better results.
+- [WIP] Registrations can be focused on specific region of interest (mask) - while it's possible to do this in `wsireg`,
+it's not as straightforward as it should be.
+- [DONE] Better support for point and GeoJSON data.
+- [DONE] Better CLI interface - more structured and easier to use.
+- [DONE] Better logging - more informative and easier to debug.
+- [DONE] Reusable registrations - since all registration data is contained within the project, it's much easier to re-run
+certain tasks (such as export images) without having to re-run the registration process.
+
+## Planned features:
+
+- [WIP] Better support for `Valis` registrations.
+- [WIP] Better support for masks.
+- Add better measures and means of testing effectiveness of registration.
+- Add better multi-processing support.
+- Add 3D module for elastiX registrations.
+
+## Getting started
+
+The library provides a command-line interface which can be invoked:
+
+```bash
+i2reg --help
+```
+
+Will generate output like this:
+
+```bash
+Usage: i2reg [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]...
+
+  Launch registration app.
+
+Options:
+  --version      Show the version and exit.
+  --dev          Flat to indicate that CLI should run in development mode and catch all errors.
+  --no_color     Flag to disable colored logs (essential when logging to file).
+  -q, --quiet    Minimal output - only errors and exceptions will be shown.
+  --debug        Maximum output - all messages will be shown.
+  -v, --verbose  Verbose output. This is additive flag so `-vvv` will print `INFO` messages and -vvvv will print
+                 `DEBUG` information.
+  --log FILE     Write logs to file (specify log path).
+  -h, --help     Show this message and exit.
+
+Project:
+  new             Create a new project.
+  about           Print information about the registration...
+  validate        Validate project configuration.
+  add-image       Add images to the project.
+  add-path        Specify the registration path between the...
+  add-attachment  Add attachment image to registered modality.
+  add-points      Add attachment points (csv/tsv/txt) to...
+  add-shape       Add attachment shape (GeoJSON) to...
+  add-merge       Specify how (if) images should be merged.
+
+Execute:
+  preprocess  Preprocess images.
+  register    Register images.
+  clear       Clear project data...
+  export      Export images.
+
+Valis:
+  valis-init      Initialize Valis configuration file.
+  valis-register  Register images using the Valis algorithm.
+
+Utility:
+  merge    Export images.
+  convert  Convert images to pyramidal OME-TIFF.
+```
+
+## Contributing
+
+Contributions are always welcome. Please feel free to submit PRs with new features, bug fixes, or documentation improvements.
+
+```bash
+git clone https://github.com/vandeplaslab/image2image-reg.git
+
+pip install -e .[dev]
+```

image2image_reg-0.1.10/README.md

@@ -0,0 +1,100 @@
+# image2image-reg
+
+[![License](https://img.shields.io/pypi/l/image2image-reg.svg?color=green)](https://github.com/vandeplaslab/image2image-reg/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/image2image-reg.svg?color=green)](https://pypi.org/project/image2image-reg)
+[![Python Version](https://img.shields.io/pypi/pyversions/image2image-reg.svg?color=green)](https://python.org)
+[![CI](https://github.com/vandeplaslab/image2image-reg/actions/workflows/ci.yml/badge.svg)](https://github.com/vandeplaslab/image2image-reg/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/vandeplaslab/image2image-reg/branch/main/graph/badge.svg)](https://codecov.io/gh/vandeplaslab/image2image-reg)
+
+Whole slide image registration using elastix and/or Valis-WSI.
+
+## Overview
+
+`image2image-reg` is a library for whole-slide image registration. It provides a command-line interface for performing
+registration, transformation and evaluation of whole-slide image registrations. The library is inspired by `wsireg` and
+`valis`. In fact, the registration workflow is a complete rewrite of the `wsireg` library to provide more flexibility
+and control over the registration process.
+
+## Differences from `wsireg`
+
+- [DONE] Registrations are organized into `projects`. Project is a collection of configuration, logs, visualisations and images.
+This should provide a more structured way of organizing your images and not cluttering the working directory.
+- [WIP] Registrations can be initialized with `affine` matrix (to get a good starting point) - this will allow for faster
+registration and hopefully better results.
+- [WIP] Registrations can be focused on specific region of interest (mask) - while it's possible to do this in `wsireg`,
+it's not as straightforward as it should be.
+- [DONE] Better support for point and GeoJSON data.
+- [DONE] Better CLI interface - more structured and easier to use.
+- [DONE] Better logging - more informative and easier to debug.
+- [DONE] Reusable registrations - since all registration data is contained within the project, it's much easier to re-run
+certain tasks (such as export images) without having to re-run the registration process.
+
+## Planned features:
+
+- [WIP] Better support for `Valis` registrations.
+- [WIP] Better support for masks.
+- Add better measures and means of testing effectiveness of registration.
+- Add better multi-processing support.
+- Add 3D module for elastiX registrations.
+
+## Getting started
+
+The library provides a command-line interface which can be invoked:
+
+```bash
+i2reg --help
+```
+
+Will generate output like this:
+
+```bash
+Usage: i2reg [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]...
+
+  Launch registration app.
+
+Options:
+  --version      Show the version and exit.
+  --dev          Flat to indicate that CLI should run in development mode and catch all errors.
+  --no_color     Flag to disable colored logs (essential when logging to file).
+  -q, --quiet    Minimal output - only errors and exceptions will be shown.
+  --debug        Maximum output - all messages will be shown.
+  -v, --verbose  Verbose output. This is additive flag so `-vvv` will print `INFO` messages and -vvvv will print
+                 `DEBUG` information.
+  --log FILE     Write logs to file (specify log path).
+  -h, --help     Show this message and exit.
+
+Project:
+  new             Create a new project.
+  about           Print information about the registration...
+  validate        Validate project configuration.
+  add-image       Add images to the project.
+  add-path        Specify the registration path between the...
+  add-attachment  Add attachment image to registered modality.
+  add-points      Add attachment points (csv/tsv/txt) to...
+  add-shape       Add attachment shape (GeoJSON) to...
+  add-merge       Specify how (if) images should be merged.
+
+Execute:
+  preprocess  Preprocess images.
+  register    Register images.
+  clear       Clear project data...
+  export      Export images.
+
+Valis:
+  valis-init      Initialize Valis configuration file.
+  valis-register  Register images using the Valis algorithm.
+
+Utility:
+  merge    Export images.
+  convert  Convert images to pyramidal OME-TIFF.
+```
+
+## Contributing
+
+Contributions are always welcome. Please feel free to submit PRs with new features, bug fixes, or documentation improvements.
+
+```bash
+git clone https://github.com/vandeplaslab/image2image-reg.git
+
+pip install -e .[dev]
+```