mergechannels 0.1.0__tar.gz

mergechannels-0.1.0/.github/workflows/CI.yml

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+# This file is autogenerated by maturin v1.8.2
+# To update, run
+#
+#    maturin generate-ci github
+#
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - mvp
+    tags:
+      - '*'
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  rust_checks_and_python_tests:
+    name: Rust Checks and Python Tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      
+      # Setup Rust toolchain
+      - name: Install Rust stable
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: rustfmt, clippy
+      
+      # Run Rust format check
+      - name: Check Rust formatting
+        run: cargo fmt --all -- --check
+      
+      # Run Clippy
+      - name: Run Clippy
+        run: cargo clippy -- -D warnings
+      
+      # Run Cargo tests
+      - name: Run Cargo tests
+        run: cargo test
+      
+      # # Setup Python for testing
+      # - uses: actions/setup-python@v5
+      #   with:
+      #     python-version: 3.x
+      
+      # Install UV
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+      
+      # Create virtual environment and install the project
+      - name: Create virtual environment and install
+        run: |
+          uv venv .venv --python 3.11
+          source .venv/bin/activate
+          pip install -e .
+      
+      # Run pytest
+      - name: Run pytest
+        run: |
+          source .venv/bin/activate
+          pip install pytest
+          pytest
+
+  linux:
+    needs: rust_checks_and_python_tests
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: x86
+          - runner: ubuntu-22.04
+            target: aarch64
+          - runner: ubuntu-22.04
+            target: armv7
+          - runner: ubuntu-22.04
+            target: s390x
+          - runner: ubuntu-22.04
+            target: ppc64le
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+
+  musllinux:
+    needs: rust_checks_and_python_tests
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: x86
+          - runner: ubuntu-22.04
+            target: aarch64
+          - runner: ubuntu-22.04
+            target: armv7
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
+
+  windows:
+    needs: rust_checks_and_python_tests
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+          - runner: windows-latest
+            target: x86
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+
+  macos:
+    needs: rust_checks_and_python_tests
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-13
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+
+  sdist:
+    needs: rust_checks_and_python_tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
+    needs: [linux, musllinux, windows, macos, sdist]
+    permissions:
+      # Use to sign the release artifacts
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v4
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v2
+        with:
+          subject-path: 'wheels-*/*'
+      - name: Publish to PyPI
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*

mergechannels-0.1.0/.gitignore

@@ -0,0 +1,75 @@
+/target
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.venv/
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+include/
+man/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-selfcheck.json
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+.DS_Store
+
+# Sphinx documentation
+docs/_build/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pyenv
+.python-version
+
+# ignore images
+*.tif*

mergechannels-0.1.0/Cargo.lock

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+# It is not intended for manual editing.
+version = 3
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+ "numpy",
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mergechannels-0.1.0/Cargo.toml

@@ -0,0 +1,15 @@
+[package]
+name = "mergechannels"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "mergechannels"
+crate-type = ["cdylib"]
+
+[dependencies]
+lazy_static = "1.5.0"
+ndarray = "0.16.1"
+numpy = "0.24.0"
+pyo3 = "0.24.1"

mergechannels-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Zachary Swider
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mergechannels-0.1.0/PKG-INFO

@@ -0,0 +1,63 @@
+Metadata-Version: 2.4
+Name: mergechannels
+Version: 0.1.0
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Dist: numpy>=1.24.4
+License-File: LICENSE
+Requires-Python: >=3.8, <3.13
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# mergechannels
+
+This project was originally conceived because I often find myself wanting to apply and blend colormaps to images while working from Python, and for historical reasons many of my favorite colormaps are distributed as [FIJI](https://imagej.net/software/fiji/) lookup tables. I also care about things likes speed and memory usage (e.g., not casting large arrays to floating point dtypes), so I was interested in seeing if I could at least match matplotlib's colormapping performance with my own hand-rolled colorizer in Rust.
+
+There are other great colormapping libraries available (e.g., [microfilm](https://github.com/guiwitz/microfilm), [cmap](https://github.com/pyapp-kit/cmap)) that are more feature-rich than this projecting on your needs, but which don't address the my goals. My hope is that this project can fill and un-met niche and otherwise maintain full compatibility with these and similar libraries.
+
+## Installation
+
+Install pre-compiled binaries from [PyPI](https://pypi.org/project/mergechannels/):
+```bash
+pip install mergechannels
+```
+
+Build from source on your own machine:
+```bash
+pip install git+https://github.com/zacswider/mergechannels.git
+```
+
+## Usage
+*NOTE*: scikit-image is not a dependency of this project, but is used in the examples below to fetch images.
+
+### colorize a single image
+
+```python
+from skimage import data
+import matplotlib.pyplot as plt
+import mergechannels as mc
+
+img = data.camera()
+fig, ax = plt.subplots()
+ax.imshow(mc.apply_colormap(img, 'Orange Hot'))
+```
+
+### apply a different colormap to each channel
+```python
+from skimage import data
+import matplotlib.pyplot as plt
+import mergechannels as mc
+
+cells, nuclei = data.cells3d().max(axis=0)
+cells = to_uint8(cells / cells.max())       <- broken until normalization is handled
+nuclei = to_uint8(nuclei / nuclei.max())    <- broken until normalization is handled
+fig, (a, b, c) = plt.subplots(1, 3)
+a.imshow(cells, cmap='gray')
+b.imshow(nuclei, cmap='gray')
+
+import mergechannels as mc
+c.imshow(mc.merge([cells, nuclei], ['Orange Hot', 'Cyan Hot']))
+```
+
+## Acknowledgements
+This project incorporates a number of colormaps that were hand-crafted by Christophe Leterrier and were originally distributed here under the MIT license: https://github.com/cleterrier/ChrisLUTs