mergechannels 0.1.0__cp311-cp311-macosx_11_0_arm64.whl → 0.1.1__cp311-cp311-macosx_11_0_arm64.whl

mergechannels/__init__.pyi

@@ -9,13 +9,19 @@ def merge(
 	arrs: Sequence[np.ndarray],
 	colors: Sequence[COLORMAPS] = (),
 	blending: Literal[BLENDING_OPTIONS] = 'max',
+    saturation_limits: tuple[float, float] = (0.2, 99.8),
 ) -> np.ndarray:
     ...
 
-def apply_color_map(arr: np.ndarray, cmap_name: COLORMAPS) -> np.ndarray: ...
+def apply_color_map(
+    arr: np.ndarray,
+    cmap_name: COLORMAPS,
+    saturation_limits: tuple[float, float] = (0.2, 99.8),
+) -> np.ndarray: ...
 
 def apply_colors_and_merge_nc(
     arrs: Sequence[np.ndarray],
     colors: Sequence[COLORMAPS] = (),
     blending: Literal[BLENDING_OPTIONS] = 'max',
+    saturation_limits: Sequence[tuple[float, float]] = (),
 ) -> np.ndarray: ...

mergechannels/_internal.py

@@ -11,24 +11,16 @@ from ._blending import BLENDING_OPTIONS
 
 def merge(
 	arrs: Sequence[np.ndarray],
-	colors: Sequence[COLORMAPS] = (),
+	colors: Sequence[COLORMAPS],
 	blending: BLENDING_OPTIONS = 'max',
 ) -> np.ndarray:
 	'''
 	apply cmaps to arrays and blend the colors
 	'''
+	# region validation
 	n_arrs = len(arrs)
 	n_colors = len(colors)
-	if n_arrs > 0 and n_colors == 0:
-		arr_shapes = [arr.shape for arr in arrs]
-		if not all([len(arr_shape) == 3 for arr_shape in arr_shapes]):
-			raise ValueError(
-				'Expected a sequence of pre-colorized arrays, '
-				f'got {n_arrs} arrays of shapes {arr_shapes}'
-			)
-		# call merge rgb arrs here
-		return np.zeros((3,3))
-	if not n_arrs == n_colors:
+	if not n_arrs == n_colors and n_arrs > 0:
 		raise ValueError(
 			'Expected an equal number of arrays to colorize and colormap names to apply. '
 			f'Got {n_arrs} arrays and {n_colors} colors'
@@ -38,7 +30,17 @@ def merge(
 		raise ValueError(
 			f'Expected every array to have the same shape, got {arr_shapes}'
 		)
-	# call apply and merge rgb arrs here
+	if not len(arr_shapes[0]) == 2:
+		raise ValueError(
+			f'Expected every array to be 2D, got {arr_shapes[0]}'
+		)
+	arr_dtypes = [arr.dtype for arr in arrs]
+	if not len(set(arr_dtypes)) == 1:
+		raise ValueError(
+			f'Expected every array to have the same dtype, got {arr_dtypes}'
+		)
+	# endregion
+	
 	match n_arrs:
 		case 1:
 			return apply_color_map(arr=arrs[0], cmap_name=colors[0])

mergechannels-0.1.1.dist-info/METADATA

@@ -0,0 +1,112 @@
+Metadata-Version: 2.4
+Name: mergechannels
+Version: 0.1.1
+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
+License-File: LICENSE
+License: MIT
+Requires-Python: >=3.8, <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](https://img.shields.io/pypi/v/mergechannels)
+
+# 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, not creating multiple whole arrays just to add them together), so I was interested in seeing if I could at least match matplotlib's colormapping performance with my own hand-rolled colorizer in Rust.
+
+
+
+## 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 mergechannels as mc
+
+img = data.camera()
+colorized = mc.apply_color_map(img, 'Red/Green')
+fig, axes = plt.subplots(1, 2, figsize=(6, 3), dpi=150)
+for ax in axes: ax.axis('off')
+(a, b) = axes
+a.imshow(img, cmap='gray')
+b.imshow(colorized)
+plt.show()
+print(colorized.shape, colorized.dtype)
+>> (512, 512, 3) uint8
+```
+![colorize a single image](assets/readme_images/camera_red-green.png)
+
+
+### 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)     # normalize your own arrays, mergechannels doesn't currently handle this
+nuclei = to_uint8(nuclei)   # normalize your own arrays, mergechannels doesn't currently handle this
+
+fig, axes = plt.subplots(2, 2, figsize=(6, 6), dpi=150)
+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(
+    mc.merge(
+        [cells, nuclei],
+        ['I Blue', 'I Forest'],
+        blending='min',     # use minimum blending with inverted colormaps
+    ),
+)
+fig.tight_layout()
+plt.show()
+```
+![apply a different colormap to each channel](assets/readme_images/cells_multicolor.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.
+- Add support for any numerical dtype
+- Add support for 3D images
+- Add option to return any colormap as a matplotlib colormap
+- 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
+
+## Acknowledgements
+
+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.dist-info/RECORD

@@ -0,0 +1,11 @@
+mergechannels-0.1.1.dist-info/METADATA,sha256=SBF12qNSkvavAvXpnM0ej--oF_wZFwGaKqJo7aC5d8U,4520
+mergechannels-0.1.1.dist-info/WHEEL,sha256=wsVBlw9xyAuHecZeOYqJ_tA7emUKfXYOn-_180uZRi4,104
+mergechannels-0.1.1.dist-info/licenses/LICENSE,sha256=R5es2fadg5bQoUJCJlcU36nDOAG6Te2XtsfysfTT_xY,1070
+mergechannels/_internal.py,sha256=61RV6adhxkdqevanP06lpmONweppc6z5j8HTNkZq3uo,1267
+mergechannels/__init__.pyi,sha256=yKPkFwpgY2pMlEXj6LvwLr7f9t0bcGnu5i9eMSeSlWo,710
+mergechannels/__init__.py,sha256=Tj-1QoMYkvDi-Bew6N2kbKrOhtgo4kq61_vmnHacp3o,224
+mergechannels/_luts.py,sha256=DxwCMBnAAJc1ZX-D4cq8HabW-sLuBQpUqOWMWXqt_84,1035
+mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
+mergechannels/mergechannels.cpython-311-darwin.so,sha256=uKy-VrPCwnX-QPaVHSiIaPIhomKSfuo02_a4x8pJJIs,726208
+mergechannels-0.1.1.dist-info/RECORD,,

mergechannels-0.1.0.dist-info/METADATA

@@ -1,63 +0,0 @@
-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

mergechannels-0.1.0.dist-info/RECORD

@@ -1,11 +0,0 @@
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-mergechannels-0.1.0.dist-info/licenses/LICENSE,sha256=R5es2fadg5bQoUJCJlcU36nDOAG6Te2XtsfysfTT_xY,1070
-mergechannels/_internal.py,sha256=UrR1K-JYbg8BS7wbmtxcOLWnWuoxmKJztlWT3TQ-Pyk,1300
-mergechannels/__init__.pyi,sha256=Z4dmA6TQydClHHVU_wje6X4CD0xh8l_b9D2imN4pLzI,524
-mergechannels/__init__.py,sha256=Tj-1QoMYkvDi-Bew6N2kbKrOhtgo4kq61_vmnHacp3o,224
-mergechannels/_luts.py,sha256=DxwCMBnAAJc1ZX-D4cq8HabW-sLuBQpUqOWMWXqt_84,1035
-mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
-mergechannels/mergechannels.cpython-311-darwin.so,sha256=GKUfHavebuAc_qSI3Kayol7aT8y2rP625kWw9fLq_ZY,711560
-mergechannels-0.1.0.dist-info/RECORD,,