mergechannels 0.1.1__cp310-cp310-win_amd64.whl → 0.2.0__cp310-cp310-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of mergechannels might be problematic. Click here for more details.

Files changed (9) hide show
  1. mergechannels/__init__.py +7 -7
  2. mergechannels/__init__.pyi +20 -17
  3. mergechannels/_internal.py +27 -20
  4. mergechannels/mergechannels.cp310-win_amd64.pyd +0 -0
  5. {mergechannels-0.1.1.dist-info → mergechannels-0.2.0.dist-info}/METADATA +59 -26
  6. mergechannels-0.2.0.dist-info/RECORD +11 -0
  7. {mergechannels-0.1.1.dist-info → mergechannels-0.2.0.dist-info}/WHEEL +1 -1
  8. {mergechannels-0.1.1.dist-info → mergechannels-0.2.0.dist-info}/licenses/LICENSE +1 -1
  9. mergechannels-0.1.1.dist-info/RECORD +0 -11
mergechannels/__init__.py CHANGED
@@ -1,13 +1,13 @@
1
1
  # Import Rust functions
2
2
  from .mergechannels import ( # type: ignore
3
- apply_color_map,
4
- apply_colors_and_merge_nc,
5
- )
6
-
3
+ dispatch_single_channel,
4
+ dispatch_multi_channel,
5
+ )
7
6
  from ._internal import merge
8
7
 
8
+
9
9
  __all__ = [
10
- "apply_color_map",
11
- "apply_colors_and_merge_nc",
12
- "merge",
10
+ 'dispatch_single_channel',
11
+ 'dispatch_multi_channel',
12
+ 'merge',
13
13
  ]
mergechannels/__init__.pyi CHANGED
@@ -1,27 +1,30 @@
1
- from typing import Sequence, Literal
2
1
 
2
+ from typing import Literal, Sequence
3
3
  import numpy as np
4
4
 
5
- from ._luts import COLORMAPS
6
- from ._blending import BLENDING_OPTIONS
5
+ from python.mergechannels._blending import BLENDING_OPTIONS
6
+ from python.mergechannels._luts import COLORMAPS
7
+
7
8
 
8
9
  def merge(
9
- arrs: Sequence[np.ndarray],
10
- colors: Sequence[COLORMAPS] = (),
11
- blending: Literal[BLENDING_OPTIONS] = 'max',
10
+ arrs: np.ndarray | Sequence[np.ndarray],
11
+ colors: Sequence[COLORMAPS] = (),
12
+ blending: Literal[BLENDING_OPTIONS] = 'max',
12
13
  saturation_limits: tuple[float, float] = (0.2, 99.8),
13
14
  ) -> np.ndarray:
14
15
  ...
15
16
 
16
- def apply_color_map(
17
- arr: np.ndarray,
18
- cmap_name: COLORMAPS,
19
- saturation_limits: tuple[float, float] = (0.2, 99.8),
20
- ) -> np.ndarray: ...
17
+ def dispatch_single_channel(
18
+ array_reference: np.ndarray,
19
+ cmap_name: str,
20
+ limits: tuple[float, float],
21
+ ) -> np.ndarray:
22
+ ...
21
23
 
22
- def apply_colors_and_merge_nc(
23
- arrs: Sequence[np.ndarray],
24
- colors: Sequence[COLORMAPS] = (),
25
- blending: Literal[BLENDING_OPTIONS] = 'max',
26
- saturation_limits: Sequence[tuple[float, float]] = (),
27
- ) -> np.ndarray: ...
24
+ def dispatch_multi_channel(
25
+ array_references: Sequence[np.ndarray],
26
+ cmap_names: Sequence[str],
27
+ blending: Literal[BLENDING_OPTIONS],
28
+ limits: Sequence[tuple[float, float]],
29
+ ) -> np.ndarray:
30
+ ...
mergechannels/_internal.py CHANGED
@@ -3,8 +3,8 @@ from typing import Sequence
3
3
  import numpy as np
4
4
 
5
5
  from mergechannels import (
6
- apply_color_map,
7
- apply_colors_and_merge_nc,
6
+ dispatch_single_channel,
7
+ dispatch_multi_channel,
8
8
  )
9
9
  from ._luts import COLORMAPS
10
10
  from ._blending import BLENDING_OPTIONS
@@ -13,6 +13,7 @@ def merge(
13
13
  arrs: Sequence[np.ndarray],
14
14
  colors: Sequence[COLORMAPS],
15
15
  blending: BLENDING_OPTIONS = 'max',
16
+ saturation_limits: tuple[float, float] = (0.011, 0.999),
16
17
  ) -> np.ndarray:
17
18
  '''
18
19
  apply cmaps to arrays and blend the colors
@@ -30,9 +31,9 @@ def merge(
30
31
  raise ValueError(
31
32
  f'Expected every array to have the same shape, got {arr_shapes}'
32
33
  )
33
- if not len(arr_shapes[0]) == 2:
34
+ if len(arr_shapes[0]) not in (2, 3):
34
35
  raise ValueError(
35
- f'Expected every array to be 2D, got {arr_shapes[0]}'
36
+ f'Expected every array to be 2D or 3D, got {arr_shapes[0]}'
36
37
  )
37
38
  arr_dtypes = [arr.dtype for arr in arrs]
38
39
  if not len(set(arr_dtypes)) == 1:
@@ -40,19 +41,25 @@ def merge(
40
41
  f'Expected every array to have the same dtype, got {arr_dtypes}'
41
42
  )
42
43
  # endregion
43
-
44
- match n_arrs:
45
- case 1:
46
- return apply_color_map(arr=arrs[0], cmap_name=colors[0])
47
- case _:
48
- return apply_colors_and_merge_nc(arrs, colors, blending)
49
-
50
-
51
-
52
-
53
-
54
-
55
-
56
-
57
-
58
-
44
+ if n_arrs == 1:
45
+ if arrs[0].dtype == 'uint8':
46
+ limits = (0, 255)
47
+ else:
48
+ low, high = np.percentile(arrs[0], np.array(saturation_limits) * 100)
49
+ limits = (low, high)
50
+ return dispatch_single_channel(
51
+ array_reference=arrs[0],
52
+ cmap_name=colors[0],
53
+ limits=limits,
54
+ )
55
+ else:
56
+ if all(arr.dtype == 'uint8' for arr in arrs):
57
+ limits = (0, 255)
58
+ else:
59
+ limits = tuple(np.percentile(arr, np.array(saturation_limits) * 100) for arr in arrs)
60
+ return dispatch_multi_channel(
61
+ array_references=arrs,
62
+ cmap_names=colors,
63
+ blending=blending,
64
+ limits=limits, # type: ignore
65
+ )
{mergechannels-0.1.1.dist-info → mergechannels-0.2.0.dist-info}/METADATA RENAMED
@@ -1,24 +1,28 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: mergechannels
3
- Version: 0.1.1
3
+ Version: 0.2.0
4
4
  Classifier: Programming Language :: Rust
5
5
  Classifier: Programming Language :: Python :: Implementation :: CPython
6
6
  Classifier: Programming Language :: Python :: Implementation :: PyPy
7
7
  Classifier: License :: OSI Approved :: MIT License
8
8
  Classifier: Programming Language :: Python :: 3
9
- Classifier: Programming Language :: Python :: 3.8
10
9
  Classifier: Programming Language :: Python :: 3.9
11
10
  Classifier: Programming Language :: Python :: 3.10
12
11
  Classifier: Programming Language :: Python :: 3.11
13
12
  Classifier: Programming Language :: Python :: 3.12
14
- Requires-Dist: numpy>=1.24.4
13
+ Classifier: Programming Language :: Python :: 3.13
14
+ Requires-Dist: numpy>1.25.0
15
+ Provides-Extra: nvim
15
16
  License-File: LICENSE
17
+ Summary: Apply and merge colormaps
18
+ Author-email: Zac Swider <zac.swider@gmail.com>
16
19
  License: MIT
17
- Requires-Python: >=3.8, <3.13
20
+ Requires-Python: >=3.9, <=3.13
18
21
  Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
19
22
 
20
23
  [![CI](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml/badge.svg)](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml)
21
- ![License](https://img.shields.io/badge/license-MIT-blue.svg)
24
+ ![PyPI - License](https://img.shields.io/pypi/l/mergechannels)
25
+ ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergechannels)
22
26
  ![PyPI](https://img.shields.io/pypi/v/mergechannels)
23
27
 
24
28
  # mergechannels
@@ -59,7 +63,7 @@ plt.show()
59
63
  print(colorized.shape, colorized.dtype)
60
64
  >> (512, 512, 3) uint8
61
65
  ```
62
- ![colorize a single image](assets/readme_images/camera_red-green.png)
66
+ ![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png)
63
67
 
64
68
 
65
69
  ### apply a different colormap to each channel
@@ -69,38 +73,66 @@ import matplotlib.pyplot as plt
69
73
  import mergechannels as mc
70
74
 
71
75
  cells, nuclei = data.cells3d().max(axis=0)
72
- cells = to_uint8(cells) # normalize your own arrays, mergechannels doesn't currently handle this
73
- nuclei = to_uint8(nuclei) # normalize your own arrays, mergechannels doesn't currently handle this
76
+ assert cells.dtype == 'uint16' and nuclei.dtype == 'uint16'
77
+ fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
78
+ for ax in axes.ravel(): ax.axis('off')
79
+ (a, b) = axes.ravel()
80
+ a.imshow(mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot']))
81
+ b.imshow(mc.merge([cells, nuclei],['I Blue', 'I Forest'], blending='min'))
82
+ fig.tight_layout()
83
+ plt.show()
84
+ ```
85
+ ![max and min multicolor blending](https://raw.githubusercontent.com/zacswider/README_Images/main/overlay_normal_and_inverted.png)
86
+
87
+ ### apply a colormap to a whole stack
88
+ ```python
89
+ from skimage import data
90
+ from matplotlib import pyplot as plt
91
+ import mergechannels as mc
92
+
93
+ volume = data.cells3d()
94
+ cells = volume[:, 0]
95
+ nuclei = volume[:, 1]
96
+ merged = mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot'])
97
+ plt.imshow(merged[24]); plt.show()
98
+ ```
99
+ ![colorize a whole stack of images](https://raw.githubusercontent.com/zacswider/README_Images/main/merged_stacks.png)
74
100
 
75
- fig, axes = plt.subplots(2, 2, figsize=(6, 6), dpi=150)
101
+ ### adjust the saturation limits when applying colormaps
102
+ ``` python
103
+ from skimage import data
104
+ import matplotlib.pyplot as plt
105
+ import mergechannels as mc
106
+
107
+ cells, nuclei = data.cells3d().max(axis=0)
108
+ channels = [cells, nuclei]
109
+ colormaps = ['I Blue', 'I Forest']
110
+ fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
76
111
  for ax in axes.ravel(): ax.axis('off')
77
- (a, b, c, d) = axes.ravel()
78
- a.imshow(cells, cmap='gray')
79
- b.imshow(nuclei, cmap='gray')
80
- c.imshow(
112
+ (a, b) = axes.ravel()
113
+ a.imshow(mc.merge(channels, colormaps, blending='min'))
114
+ b.imshow(
81
115
  mc.merge(
82
- [cells, nuclei],
83
- ['Orange Hot', 'Cyan Hot'], # maximum blending is the default
84
- ),
85
- )
86
- d.imshow(
87
- mc.merge(
88
- [cells, nuclei],
89
- ['I Blue', 'I Forest'],
90
- blending='min', # use minimum blending with inverted colormaps
116
+ channels,
117
+ colormaps,
118
+ blending='min',
119
+ saturation_limits=(
120
+ 0.01, # bottom 1% of pixels set to black point
121
+ 0.97, # top 3% of pixels set to white point
122
+ ),
91
123
  ),
92
124
  )
93
125
  fig.tight_layout()
94
126
  plt.show()
95
127
  ```
96
- ![apply a different colormap to each channel](assets/readme_images/cells_multicolor.png)
128
+ ![adjust saturation limits](https://raw.githubusercontent.com/zacswider/README_Images/main/adjust_sat_lims.png)
97
129
 
98
130
 
99
131
  ## Roadmap
100
- mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D 8-bit images and that's it.
132
+ 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.
101
133
  - Add support for any numerical dtype
102
- - Add support for 3D images
103
134
  - Add option to return any colormap as a matplotlib colormap
135
+ - Add option to pass external colormaps to mergechannels
104
136
  - Add support for directly passing matplotlib colormaps instead of colormap names
105
137
  - Parallelize colormap application on large images (if it's helpful)
106
138
  - Add option to overlay binary or instance masks onto colorized images
@@ -109,4 +141,5 @@ mergechannels is currently incredibly simple. It can apply one or more colormaps
109
141
 
110
142
  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.
111
143
 
112
- 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
144
+ 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
145
+
mergechannels-0.2.0.dist-info/RECORD ADDED
@@ -0,0 +1,11 @@
1
+ mergechannels-0.2.0.dist-info/METADATA,sha256=k5x2tptazozlFMop2CjUJSMhfRV561HKMOYjFQq1xrw,5847
2
+ mergechannels-0.2.0.dist-info/WHEEL,sha256=tvMehAuwYswG9dMmwHb6RW7O-9AAAcnneXQ2akCAgrw,96
3
+ mergechannels-0.2.0.dist-info/licenses/LICENSE,sha256=13XDkLAzpvwoVSoi1BksE9O_nNxoO9WVFRcF1HPMvJo,1092
4
+ mergechannels/__init__.py,sha256=xbqeTJbcgfawYB0ZngDmCtLFCjlSNNz7DbgyFHqKELI,245
5
+ mergechannels/__init__.pyi,sha256=Zg7q86czacOLaWtUp11le88DPm3Qc50VdNH-SpQh3L8,779
6
+ mergechannels/_blending.py,sha256=fyw9IV1QzSR_RKCJtI-q67ylnBv9PrA4ofX-uvXXJaY,87
7
+ mergechannels/_internal.py,sha256=IBM21aiaderimszSQ85x0cC8xkvw-xKuJaPo73x8udY,1838
8
+ mergechannels/_luts.py,sha256=QtQPO-6P-x0vjGaizsEOgth0miX0vIcZEHVaVzlumBY,1116
9
+ mergechannels/mergechannels.cp310-win_amd64.pyd,sha256=FHRphWI3I7JQzYVRHY7_nxrsUS1SaAPvgr4014F3Yj4,507392
10
+ mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
11
+ mergechannels-0.2.0.dist-info/RECORD,,
{mergechannels-0.1.1.dist-info → mergechannels-0.2.0.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
1
1
  Wheel-Version: 1.0
2
- Generator: maturin (1.8.3)
2
+ Generator: maturin (1.8.6)
3
3
  Root-Is-Purelib: false
4
4
  Tag: cp310-cp310-win_amd64
{mergechannels-0.1.1.dist-info → mergechannels-0.2.0.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-0.1.1.dist-info/RECORD DELETED
@@ -1,11 +0,0 @@
1
- mergechannels-0.1.1.dist-info/METADATA,sha256=O_22ND9cZ3QI3ciFGZAFKM-uekER4eiuh5qtk01FKFI,4612
2
- mergechannels-0.1.1.dist-info/WHEEL,sha256=77DqkvxB4HqZitBRK_M49NRS207JKb0MotMEjnxEWQ8,96
3
- mergechannels-0.1.1.dist-info/licenses/LICENSE,sha256=qBDSUScUj9TtHM9cTe1mi7luamcrO--X01yLnx1iS5Q,1090
4
- mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
5
- mergechannels/_blending.py,sha256=fyw9IV1QzSR_RKCJtI-q67ylnBv9PrA4ofX-uvXXJaY,87
6
- mergechannels/_internal.py,sha256=iX5LY9_ac03ugzcnT7UV54kezPlI-ADD8ah3Y1LNiNU,1325
7
- mergechannels/_luts.py,sha256=QtQPO-6P-x0vjGaizsEOgth0miX0vIcZEHVaVzlumBY,1116
8
- mergechannels/__init__.py,sha256=nmEYzwQvfD9BydS564upIiIyFA15wKhUGtAqe3RH490,237
9
- mergechannels/__init__.pyi,sha256=cekSFzU1_uFnCdxnOQCa_RGs8eNu_hsnTCbHwK_bZFM,736
10
- mergechannels/mergechannels.cp310-win_amd64.pyd,sha256=MADOJ5ZIWCGWUIadYAqxej2na7ihtdQO8mkiyKbITK4,449536
11
- mergechannels-0.1.1.dist-info/RECORD,,