mergechannels 0.1.0__cp311-cp311-macosx_11_0_arm64.whl → 0.1.2__cp311-cp311-macosx_11_0_arm64.whl

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Files changed (10) hide show
  1. mergechannels/__init__.py +4 -4
  2. mergechannels/__init__.pyi +8 -2
  3. mergechannels/_internal.py +17 -26
  4. mergechannels/mergechannels.cpython-311-darwin.so +0 -0
  5. mergechannels-0.1.2.dist-info/METADATA +115 -0
  6. mergechannels-0.1.2.dist-info/RECORD +11 -0
  7. {mergechannels-0.1.0.dist-info → mergechannels-0.1.2.dist-info}/licenses/LICENSE +1 -1
  8. mergechannels-0.1.0.dist-info/METADATA +0 -63
  9. mergechannels-0.1.0.dist-info/RECORD +0 -11
  10. {mergechannels-0.1.0.dist-info → mergechannels-0.1.2.dist-info}/WHEEL +0 -0
mergechannels/__init__.py CHANGED
@@ -2,12 +2,12 @@
2
2
  from .mergechannels import ( # type: ignore
3
3
  apply_color_map,
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  apply_colors_and_merge_nc,
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- )
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+ )
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6
 
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  from ._internal import merge
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8
 
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  __all__ = [
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- "apply_color_map",
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- "apply_colors_and_merge_nc",
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- "merge",
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+ 'apply_color_map',
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+ 'apply_colors_and_merge_nc',
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+ 'merge',
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  ]
mergechannels/__init__.pyi CHANGED
@@ -9,13 +9,19 @@ def merge(
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  arrs: Sequence[np.ndarray],
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  colors: Sequence[COLORMAPS] = (),
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  blending: Literal[BLENDING_OPTIONS] = 'max',
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+ saturation_limits: tuple[float, float] = (0.2, 99.8),
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  ) -> np.ndarray:
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  ...
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15
 
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- def apply_color_map(arr: np.ndarray, cmap_name: COLORMAPS) -> np.ndarray: ...
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+ def apply_color_map(
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+ arr: np.ndarray,
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+ cmap_name: COLORMAPS,
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+ saturation_limits: tuple[float, float] = (0.2, 99.8),
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+ ) -> np.ndarray: ...
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21
 
17
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  def apply_colors_and_merge_nc(
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  arrs: Sequence[np.ndarray],
19
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  colors: Sequence[COLORMAPS] = (),
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  blending: Literal[BLENDING_OPTIONS] = 'max',
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- ) -> np.ndarray: ...
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+ saturation_limits: Sequence[tuple[float, float]] = (),
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+ ) -> np.ndarray: ...
mergechannels/_internal.py CHANGED
@@ -11,24 +11,16 @@ from ._blending import BLENDING_OPTIONS
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11
 
12
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  def merge(
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  arrs: Sequence[np.ndarray],
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- colors: Sequence[COLORMAPS] = (),
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+ colors: Sequence[COLORMAPS],
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  blending: BLENDING_OPTIONS = 'max',
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  ) -> np.ndarray:
17
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  '''
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  apply cmaps to arrays and blend the colors
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  '''
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+ # region validation
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  n_arrs = len(arrs)
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  n_colors = len(colors)
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- if n_arrs > 0 and n_colors == 0:
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- arr_shapes = [arr.shape for arr in arrs]
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- if not all([len(arr_shape) == 3 for arr_shape in arr_shapes]):
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- raise ValueError(
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- 'Expected a sequence of pre-colorized arrays, '
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- f'got {n_arrs} arrays of shapes {arr_shapes}'
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- )
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- # call merge rgb arrs here
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- return np.zeros((3,3))
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- if not n_arrs == n_colors:
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+ if not n_arrs == n_colors and n_arrs > 0:
32
24
  raise ValueError(
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  'Expected an equal number of arrays to colorize and colormap names to apply. '
34
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  f'Got {n_arrs} arrays and {n_colors} colors'
@@ -38,19 +30,18 @@ def merge(
38
30
  raise ValueError(
39
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  f'Expected every array to have the same shape, got {arr_shapes}'
40
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  )
41
- # call apply and merge rgb arrs here
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- match n_arrs:
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- case 1:
44
- return apply_color_map(arr=arrs[0], cmap_name=colors[0])
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- case _:
46
- return apply_colors_and_merge_nc(arrs, colors, blending)
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-
48
-
49
-
50
-
51
-
52
-
53
-
54
-
55
-
33
+ if not len(arr_shapes[0]) == 2:
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+ raise ValueError(
35
+ f'Expected every array to be 2D, got {arr_shapes[0]}'
36
+ )
37
+ arr_dtypes = [arr.dtype for arr in arrs]
38
+ if not len(set(arr_dtypes)) == 1:
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+ raise ValueError(
40
+ f'Expected every array to have the same dtype, got {arr_dtypes}'
41
+ )
42
+ # endregion
56
43
 
44
+ if n_arrs == 1:
45
+ return apply_color_map(arr=arrs[0], cmap_name=colors[0])
46
+ else:
47
+ return apply_colors_and_merge_nc(arrs, colors, blending)
mergechannels-0.1.2.dist-info/METADATA ADDED
@@ -0,0 +1,115 @@
1
+ Metadata-Version: 2.4
2
+ Name: mergechannels
3
+ Version: 0.1.2
4
+ Classifier: Programming Language :: Rust
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+ Classifier: Programming Language :: Python :: Implementation :: CPython
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+ Classifier: Programming Language :: Python :: Implementation :: PyPy
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Programming Language :: Python :: 3
9
+ Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
11
+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
14
+ Requires-Dist: numpy>1.25.0
15
+ License-File: LICENSE
16
+ License: MIT
17
+ Requires-Python: >=3.9, <=3.13
18
+ Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
19
+
20
+ [![CI](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml/badge.svg)](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml)
21
+ ![PyPI - License](https://img.shields.io/pypi/l/mergechannels)
22
+ ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergechannels)
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+ ![PyPI](https://img.shields.io/pypi/v/mergechannels)
24
+
25
+ # mergechannels
26
+
27
+ 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.
28
+
29
+
30
+
31
+ ## Installation
32
+
33
+ Install pre-compiled binaries from [PyPI](https://pypi.org/project/mergechannels/):
34
+ ```bash
35
+ pip install mergechannels
36
+ ```
37
+
38
+ Build from source on your own machine:
39
+ ```bash
40
+ pip install git+https://github.com/zacswider/mergechannels.git
41
+ ```
42
+
43
+ ## Usage
44
+ *NOTE*: scikit-image is not a dependency of this project, but is used in the examples below to fetch images.
45
+
46
+ ### colorize a single image
47
+
48
+ ```python
49
+ from skimage import data
50
+ import mergechannels as mc
51
+
52
+ img = data.camera()
53
+ colorized = mc.apply_color_map(img, 'Red/Green')
54
+ fig, axes = plt.subplots(1, 2, figsize=(6, 3), dpi=150)
55
+ for ax in axes: ax.axis('off')
56
+ (a, b) = axes
57
+ a.imshow(img, cmap='gray')
58
+ b.imshow(colorized)
59
+ plt.show()
60
+ print(colorized.shape, colorized.dtype)
61
+ >> (512, 512, 3) uint8
62
+ ```
63
+ ![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png
64
+ )
65
+
66
+
67
+ ### apply a different colormap to each channel
68
+ ```python
69
+ from skimage import data
70
+ import matplotlib.pyplot as plt
71
+ import mergechannels as mc
72
+
73
+ cells, nuclei = data.cells3d().max(axis=0)
74
+ cells = to_uint8(cells) # normalize your own arrays, mergechannels doesn't currently handle this
75
+ nuclei = to_uint8(nuclei) # normalize your own arrays, mergechannels doesn't currently handle this
76
+
77
+ fig, axes = plt.subplots(2, 2, figsize=(6, 6), dpi=150)
78
+ for ax in axes.ravel(): ax.axis('off')
79
+ (a, b, c, d) = axes.ravel()
80
+ a.imshow(cells, cmap='gray')
81
+ b.imshow(nuclei, cmap='gray')
82
+ c.imshow(
83
+ mc.merge(
84
+ [cells, nuclei],
85
+ ['Orange Hot', 'Cyan Hot'], # maximum blending is the default
86
+ ),
87
+ )
88
+ d.imshow(
89
+ mc.merge(
90
+ [cells, nuclei],
91
+ ['I Blue', 'I Forest'],
92
+ blending='min', # use minimum blending with inverted colormaps
93
+ ),
94
+ )
95
+ fig.tight_layout()
96
+ plt.show()
97
+ ```
98
+ ![max and min multicolor blending](https://raw.githubusercontent.com/zacswider/README_Images/main/cells_multicolor.png)
99
+
100
+
101
+ ## Roadmap
102
+ mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D 8-bit images and that's it.
103
+ - Add support for any numerical dtype
104
+ - Add support for 3D images
105
+ - Add option to return any colormap as a matplotlib colormap
106
+ - Add support for directly passing matplotlib colormaps instead of colormap names
107
+ - Parallelize colormap application on large images (if it's helpful)
108
+ - Add option to overlay binary or instance masks onto colorized images
109
+
110
+ ## Acknowledgements
111
+
112
+ 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.
113
+
114
+ 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
115
+
mergechannels-0.1.2.dist-info/RECORD ADDED
@@ -0,0 +1,11 @@
1
+ mergechannels-0.1.2.dist-info/METADATA,sha256=fdx3XuAlrCeScx655leoDJJEMtrZQ2-K2tX--JalIAI,4676
2
+ mergechannels-0.1.2.dist-info/WHEEL,sha256=wsVBlw9xyAuHecZeOYqJ_tA7emUKfXYOn-_180uZRi4,104
3
+ mergechannels-0.1.2.dist-info/licenses/LICENSE,sha256=csvD60rgtSorbYEM3f8867qNyPCzmIXyFNj8h01Bd6c,1071
4
+ mergechannels/_internal.py,sha256=Abzeacre5CQOcWn9WDIVuxFdEjTLIudEWQn8EsiH3oE,1243
5
+ mergechannels/__init__.pyi,sha256=lSMX8eip_zkzoJPJKvxvAhOsewwagoAhS9H5gXJ2Da8,711
6
+ mergechannels/__init__.py,sha256=jy8Qd3TOQ0mm-K64snjOqjdDQiSJ3gWjOjGZrliYy6k,222
7
+ mergechannels/_luts.py,sha256=DxwCMBnAAJc1ZX-D4cq8HabW-sLuBQpUqOWMWXqt_84,1035
8
+ mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
9
+ mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
10
+ mergechannels/mergechannels.cpython-311-darwin.so,sha256=smcFKCmpG-5u5ODm8ZGm_Bz11lYxFyuNPkeujYslAg0,726064
11
+ mergechannels-0.1.2.dist-info/RECORD,,
{mergechannels-0.1.0.dist-info → mergechannels-0.1.2.dist-info}/licenses/LICENSE RENAMED
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
18
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
19
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
20
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
- SOFTWARE.
21
+ SOFTWARE.
mergechannels-0.1.0.dist-info/METADATA DELETED
@@ -1,63 +0,0 @@
1
- Metadata-Version: 2.4
2
- Name: mergechannels
3
- Version: 0.1.0
4
- Classifier: Programming Language :: Rust
5
- Classifier: Programming Language :: Python :: Implementation :: CPython
6
- Classifier: Programming Language :: Python :: Implementation :: PyPy
7
- Requires-Dist: numpy>=1.24.4
8
- License-File: LICENSE
9
- Requires-Python: >=3.8, <3.13
10
- Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
11
-
12
- # mergechannels
13
-
14
- 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.
15
-
16
- 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.
17
-
18
- ## Installation
19
-
20
- Install pre-compiled binaries from [PyPI](https://pypi.org/project/mergechannels/):
21
- ```bash
22
- pip install mergechannels
23
- ```
24
-
25
- Build from source on your own machine:
26
- ```bash
27
- pip install git+https://github.com/zacswider/mergechannels.git
28
- ```
29
-
30
- ## Usage
31
- *NOTE*: scikit-image is not a dependency of this project, but is used in the examples below to fetch images.
32
-
33
- ### colorize a single image
34
-
35
- ```python
36
- from skimage import data
37
- import matplotlib.pyplot as plt
38
- import mergechannels as mc
39
-
40
- img = data.camera()
41
- fig, ax = plt.subplots()
42
- ax.imshow(mc.apply_colormap(img, 'Orange Hot'))
43
- ```
44
-
45
- ### apply a different colormap to each channel
46
- ```python
47
- from skimage import data
48
- import matplotlib.pyplot as plt
49
- import mergechannels as mc
50
-
51
- cells, nuclei = data.cells3d().max(axis=0)
52
- cells = to_uint8(cells / cells.max()) <- broken until normalization is handled
53
- nuclei = to_uint8(nuclei / nuclei.max()) <- broken until normalization is handled
54
- fig, (a, b, c) = plt.subplots(1, 3)
55
- a.imshow(cells, cmap='gray')
56
- b.imshow(nuclei, cmap='gray')
57
-
58
- import mergechannels as mc
59
- c.imshow(mc.merge([cells, nuclei], ['Orange Hot', 'Cyan Hot']))
60
- ```
61
-
62
- ## Acknowledgements
63
- 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 DELETED
@@ -1,11 +0,0 @@
1
- mergechannels-0.1.0.dist-info/METADATA,sha256=tK_250ZwpjXLerJFVfX5GcLBgbLRcwCGpExsDb9ebtg,2677
2
- mergechannels-0.1.0.dist-info/WHEEL,sha256=wsVBlw9xyAuHecZeOYqJ_tA7emUKfXYOn-_180uZRi4,104
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- mergechannels-0.1.0.dist-info/licenses/LICENSE,sha256=R5es2fadg5bQoUJCJlcU36nDOAG6Te2XtsfysfTT_xY,1070
4
- mergechannels/_internal.py,sha256=UrR1K-JYbg8BS7wbmtxcOLWnWuoxmKJztlWT3TQ-Pyk,1300
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- mergechannels/__init__.pyi,sha256=Z4dmA6TQydClHHVU_wje6X4CD0xh8l_b9D2imN4pLzI,524
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- mergechannels/__init__.py,sha256=Tj-1QoMYkvDi-Bew6N2kbKrOhtgo4kq61_vmnHacp3o,224
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- mergechannels/_luts.py,sha256=DxwCMBnAAJc1ZX-D4cq8HabW-sLuBQpUqOWMWXqt_84,1035
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- mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
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- mergechannels/mergechannels.cpython-311-darwin.so,sha256=GKUfHavebuAc_qSI3Kayol7aT8y2rP625kWw9fLq_ZY,711560
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- mergechannels-0.1.0.dist-info/RECORD,,