mergechannels 0.1.1__tar.gz → 0.2.0__tar.gz

{mergechannels-0.1.1 → mergechannels-0.2.0}/.gitattributes

@@ -4,4 +4,4 @@
 *.jpeg filter=lfs diff=lfs merge=lfs -text
 *.gif filter=lfs diff=lfs merge=lfs -text
 *.tif filter=lfs diff=lfs merge=lfs -text
-*.tiff filter=lfs diff=lfs merge=lfs -text
+*.tiff filter=lfs diff=lfs merge=lfs -text

{mergechannels-0.1.1 → mergechannels-0.2.0}/.github/workflows/CI.yml

@@ -8,8 +8,7 @@ name: CI
 on:
   push:
     branches:
-      - main
-      - mvp
+      - '*'
     tags:
       - '*'
   pull_request:
@@ -24,50 +23,73 @@ jobs:
     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
+        with:
+          enable-cache: true
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run pre-commit
+        shell: bash -l {0}
+        run: uv run pre-commit run --all-files
+
+  tox_tests:
+    name: Tox Tests (${{ matrix.python-version }}) # Add python version to name for clarity
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+      fail-fast: true # Optional: prevent other matrix jobs from cancelling if one fails
+    steps:
+      - uses: actions/checkout@v4
+
+      # Set up the specific Python version for this matrix job
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install UV using the official action, enabling caching
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          # Enable uv's cache for faster subsequent runs
+          enable-cache: true
+
+      # Install tox and tox-uv using uv tool install
+      # This installs them into an isolated environment managed by uv
+      - name: Install Tox with tox-uv plugin using UV
+        run: uv tool install tox --with tox-uv
+
+      # Run Tox using uvx
+      # uvx ensures that the 'tox' command installed via 'uv tool install' is used
+      - name: Run Tox tests via uvx
         run: |
-          source .venv/bin/activate
-          pip install pytest
-          pytest
+          PY_VERSION=$(echo ${{ matrix.python-version }} | tr -d '.')
+          uvx tox -e py$PY_VERSION
 
-  linux:
-    needs: rust_checks_and_python_tests
+
+  build:
+    needs: [rust_checks_and_python_tests, tox_tests]
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -104,6 +126,7 @@ jobs:
 
   musllinux:
     needs: rust_checks_and_python_tests
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -136,6 +159,7 @@ jobs:
 
   windows:
     needs: rust_checks_and_python_tests
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -164,6 +188,7 @@ jobs:
 
   macos:
     needs: rust_checks_and_python_tests
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
@@ -191,6 +216,7 @@ jobs:
 
   sdist:
     needs: rust_checks_and_python_tests
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -209,7 +235,7 @@ jobs:
     name: Release
     runs-on: ubuntu-latest
     if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
-    needs: [linux, musllinux, windows, macos, sdist]
+    needs: [build, musllinux, windows, macos, sdist]
     permissions:
       # Use to sign the release artifacts
       id-token: write

{mergechannels-0.1.1 → mergechannels-0.2.0}/.gitignore

@@ -72,4 +72,8 @@ docs/_build/
 .python-version
 
 # ignore images
-*.tif*
+*.tif*
+
+# ignore notebooks
+*.ipynb
+*.ju.py

mergechannels-0.2.0/.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.3
+    hooks:
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]

{mergechannels-0.1.1 → mergechannels-0.2.0}/Cargo.lock

@@ -59,12 +59,13 @@ dependencies = [
 
 [[package]]
 name = "mergechannels"
-version = "0.1.1"
+version = "0.2.0"
 dependencies = [
  "lazy_static",
  "ndarray",
  "numpy",
  "pyo3",
+ "smallvec",
 ]
 
 [[package]]
@@ -239,6 +240,12 @@ version = "2.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "357703d41365b4b27c590e3ed91eabb1b663f07c4c084095e60cbed4362dff0d"
 
+[[package]]
+name = "smallvec"
+version = "1.15.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8917285742e9f3e1683f0a9c4e6b57960b7314d0b08d30d1ecd426713ee2eee9"
+
 [[package]]
 name = "syn"
 version = "2.0.98"

{mergechannels-0.1.1 → mergechannels-0.2.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "mergechannels"
-version = "0.1.1"
+version = "0.2.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -13,3 +13,4 @@ lazy_static = "1.5.0"
 ndarray = "0.16.1"
 numpy = "0.24.0"
 pyo3 = "0.24.1"
+smallvec = "1.15.0"

{mergechannels-0.1.1 → mergechannels-0.2.0}/LICENSE

@@ -18,4 +18,4 @@ 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.
+SOFTWARE.

{mergechannels-0.1.1 → mergechannels-0.2.0}/PKG-INFO

@@ -1,24 +1,28 @@
 Metadata-Version: 2.4
 Name: mergechannels
-Version: 0.1.1
+Version: 0.2.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: numpy>=1.24.4
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: numpy>1.25.0
+Provides-Extra: nvim
 License-File: LICENSE
+Summary: Apply and merge colormaps
+Author-email: Zac Swider <zac.swider@gmail.com>
 License: MIT
-Requires-Python: >=3.8, <3.13
+Requires-Python: >=3.9, <=3.13
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 
 [![CI](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml/badge.svg)](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml)
-![License](https://img.shields.io/badge/license-MIT-blue.svg)
+![PyPI - License](https://img.shields.io/pypi/l/mergechannels)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergechannels)
 ![PyPI](https://img.shields.io/pypi/v/mergechannels)
 
 # mergechannels
@@ -59,7 +63,7 @@ plt.show()
 print(colorized.shape, colorized.dtype)
 >> (512, 512, 3) uint8
 ```
-![colorize a single image](assets/readme_images/camera_red-green.png)
+![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png)
 
 
 ### apply a different colormap to each channel
@@ -69,38 +73,66 @@ import matplotlib.pyplot as plt
 import mergechannels as mc
 
 cells, nuclei = data.cells3d().max(axis=0)
-cells = to_uint8(cells)     # normalize your own arrays, mergechannels doesn't currently handle this
-nuclei = to_uint8(nuclei)   # normalize your own arrays, mergechannels doesn't currently handle this
+assert cells.dtype == 'uint16' and nuclei.dtype == 'uint16'
+fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
+for ax in axes.ravel(): ax.axis('off')
+(a, b) = axes.ravel()
+a.imshow(mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot']))
+b.imshow(mc.merge([cells, nuclei],['I Blue', 'I Forest'], blending='min'))
+fig.tight_layout()
+plt.show()
+```
+![max and min multicolor blending](https://raw.githubusercontent.com/zacswider/README_Images/main/overlay_normal_and_inverted.png)
+
+### apply a colormap to a whole stack
+```python
+from skimage import data
+from matplotlib import pyplot as plt
+import mergechannels as mc
+
+volume = data.cells3d()
+cells = volume[:, 0]
+nuclei = volume[:, 1]
+merged = mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot'])
+plt.imshow(merged[24]); plt.show()
+```
+![colorize a whole stack of images](https://raw.githubusercontent.com/zacswider/README_Images/main/merged_stacks.png)
 
-fig, axes = plt.subplots(2, 2, figsize=(6, 6), dpi=150)
+### adjust the saturation limits when applying colormaps
+``` python
+from skimage import data
+import matplotlib.pyplot as plt
+import mergechannels as mc
+
+cells, nuclei = data.cells3d().max(axis=0)
+channels = [cells, nuclei]
+colormaps = ['I Blue', 'I Forest']
+fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
 for ax in axes.ravel(): ax.axis('off')
-(a, b, c, d) = axes.ravel()
-a.imshow(cells, cmap='gray')
-b.imshow(nuclei, cmap='gray')
-c.imshow(
+(a, b) = axes.ravel()
+a.imshow(mc.merge(channels, colormaps, blending='min'))
+b.imshow(
     mc.merge(
-        [cells, nuclei],
-        ['Orange Hot', 'Cyan Hot'],  # maximum blending is the default
-    ),
-)
-d.imshow(
-    mc.merge(
-        [cells, nuclei],
-        ['I Blue', 'I Forest'],
-        blending='min',     # use minimum blending with inverted colormaps
+        channels,
+        colormaps,
+        blending='min',
+        saturation_limits=(
+            0.01,  # bottom 1% of pixels set to black point
+            0.97,  # top 3% of pixels set to white point
+        ),
     ),
 )
 fig.tight_layout()
 plt.show()
 ```
-![apply a different colormap to each channel](assets/readme_images/cells_multicolor.png)
+![adjust saturation limits](https://raw.githubusercontent.com/zacswider/README_Images/main/adjust_sat_lims.png)
 
 
 ## Roadmap
-mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D 8-bit images and that's it.
+mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D and 3D 8-bit or 16-bit images and that's it.
 - Add support for any numerical dtype
-- Add support for 3D images
 - Add option to return any colormap as a matplotlib colormap
+- Add option to pass external colormaps to mergechannels
 - Add support for directly passing matplotlib colormaps instead of colormap names
 - Parallelize colormap application on large images (if it's helpful)
 - Add option to overlay binary or instance masks onto colorized images
@@ -110,3 +142,4 @@ mergechannels is currently incredibly simple. It can apply one or more colormaps
 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 one, but which don't address my goals. My hope is that this project can fill an un-met niche and otherwise maintain full compatibility with these and similar libraries.
 
 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
+

{mergechannels-0.1.1 → mergechannels-0.2.0}/README.md

@@ -1,5 +1,6 @@
 [![CI](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml/badge.svg)](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml)
-![License](https://img.shields.io/badge/license-MIT-blue.svg)
+![PyPI - License](https://img.shields.io/pypi/l/mergechannels)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergechannels)
 ![PyPI](https://img.shields.io/pypi/v/mergechannels)
 
 # mergechannels
@@ -40,7 +41,7 @@ plt.show()
 print(colorized.shape, colorized.dtype)
 >> (512, 512, 3) uint8
 ```
-![colorize a single image](assets/readme_images/camera_red-green.png)
+![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png)
 
 
 ### apply a different colormap to each channel
@@ -50,38 +51,66 @@ import matplotlib.pyplot as plt
 import mergechannels as mc
 
 cells, nuclei = data.cells3d().max(axis=0)
-cells = to_uint8(cells)     # normalize your own arrays, mergechannels doesn't currently handle this
-nuclei = to_uint8(nuclei)   # normalize your own arrays, mergechannels doesn't currently handle this
+assert cells.dtype == 'uint16' and nuclei.dtype == 'uint16'
+fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
+for ax in axes.ravel(): ax.axis('off')
+(a, b) = axes.ravel()
+a.imshow(mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot']))
+b.imshow(mc.merge([cells, nuclei],['I Blue', 'I Forest'], blending='min'))
+fig.tight_layout()
+plt.show()
+```
+![max and min multicolor blending](https://raw.githubusercontent.com/zacswider/README_Images/main/overlay_normal_and_inverted.png)
+
+### apply a colormap to a whole stack
+```python
+from skimage import data
+from matplotlib import pyplot as plt
+import mergechannels as mc
+
+volume = data.cells3d()
+cells = volume[:, 0]
+nuclei = volume[:, 1]
+merged = mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot'])
+plt.imshow(merged[24]); plt.show()
+```
+![colorize a whole stack of images](https://raw.githubusercontent.com/zacswider/README_Images/main/merged_stacks.png)
+
+### adjust the saturation limits when applying colormaps
+``` python
+from skimage import data
+import matplotlib.pyplot as plt
+import mergechannels as mc
 
-fig, axes = plt.subplots(2, 2, figsize=(6, 6), dpi=150)
+cells, nuclei = data.cells3d().max(axis=0)
+channels = [cells, nuclei]
+colormaps = ['I Blue', 'I Forest']
+fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
 for ax in axes.ravel(): ax.axis('off')
-(a, b, c, d) = axes.ravel()
-a.imshow(cells, cmap='gray')
-b.imshow(nuclei, cmap='gray')
-c.imshow(
-    mc.merge(
-        [cells, nuclei],
-        ['Orange Hot', 'Cyan Hot'],  # maximum blending is the default
-    ),
-)
-d.imshow(
+(a, b) = axes.ravel()
+a.imshow(mc.merge(channels, colormaps, blending='min'))
+b.imshow(
     mc.merge(
-        [cells, nuclei],
-        ['I Blue', 'I Forest'],
-        blending='min',     # use minimum blending with inverted colormaps
+        channels,
+        colormaps,
+        blending='min',
+        saturation_limits=(
+            0.01,  # bottom 1% of pixels set to black point
+            0.97,  # top 3% of pixels set to white point
+        ),
     ),
 )
 fig.tight_layout()
 plt.show()
 ```
-![apply a different colormap to each channel](assets/readme_images/cells_multicolor.png)
+![adjust saturation limits](https://raw.githubusercontent.com/zacswider/README_Images/main/adjust_sat_lims.png)
 
 
 ## Roadmap
-mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D 8-bit images and that's it.
+mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D and 3D 8-bit or 16-bit images and that's it.
 - Add support for any numerical dtype
-- Add support for 3D images
 - Add option to return any colormap as a matplotlib colormap
+- Add option to pass external colormaps to mergechannels
 - Add support for directly passing matplotlib colormaps instead of colormap names
 - Parallelize colormap application on large images (if it's helpful)
 - Add option to overlay binary or instance masks onto colorized images
@@ -90,4 +119,4 @@ mergechannels is currently incredibly simple. It can apply one or more colormaps
 
 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 one, but which don't address my goals. My hope is that this project can fill an un-met niche and otherwise maintain full compatibility with these and similar libraries.
 
-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
+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

{mergechannels-0.1.1 → mergechannels-0.2.0}/assets/builtin_luts/phase.lut

@@ -254,4 +254,3 @@
 248   4   4
 252   0   0
 252   0   0
-

{mergechannels-0.1.1 → mergechannels-0.2.0}/assets/christ_luts/Turbo.lut

@@ -254,4 +254,4 @@ Index	Red	Green	Blue
 252	133	7	2
 253	129	6	2
 254	126	5	2
-255	122	4	3
+255	122	4	3

{mergechannels-0.1.1 → mergechannels-0.2.0}/pyproject.toml

@@ -4,22 +4,37 @@ build-backend = "maturin"
 
 [project]
 name = "mergechannels"
+description = "Apply and merge colormaps"
+readme = "README.md"
+authors = [{ name = "Zac Swider", email = "zac.swider@gmail.com" }]
 license = { text = "MIT" }
-requires-python = ">=3.8, <3.13"
+requires-python = ">=3.9, <=3.13"
 classifiers = [
     "Programming Language :: Rust",
     "Programming Language :: Python :: Implementation :: CPython",
     "Programming Language :: Python :: Implementation :: PyPy",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 dynamic = ["version"]
-dependencies = ["numpy>=1.24.4"]
+dependencies = ["numpy>1.25.0"]
+
+[project.optional-dependencies]
+nvim = []
 [tool.maturin]
 features = ["pyo3/extension-module"]
 python-source = "python"
+
+[dependency-groups]
+dev = [
+    "matplotlib>=3.7.5",
+    "pre-commit>=3.5.0",
+    "pynvim>=0.5.2",
+    "pytest-benchmark>=4.0.0",
+    "pytest>=8.3.5",
+]