mergechannels 0.4.0__cp312-cp312-musllinux_1_2_x86_64.whl → 0.5.1__cp312-cp312-musllinux_1_2_x86_64.whl

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Files changed (11) hide show
  1. mergechannels/__init__.py +5 -0
  2. mergechannels/__init__.pyi +47 -17
  3. mergechannels/_internal.py +74 -9
  4. mergechannels/_luts.py +147 -149
  5. mergechannels/mergechannels.cpython-312-x86_64-linux-musl.so +0 -0
  6. mergechannels-0.5.1.dist-info/METADATA +397 -0
  7. mergechannels-0.5.1.dist-info/RECORD +12 -0
  8. {mergechannels-0.4.0.dist-info → mergechannels-0.5.1.dist-info}/WHEEL +1 -1
  9. mergechannels-0.4.0.dist-info/METADATA +0 -146
  10. mergechannels-0.4.0.dist-info/RECORD +0 -12
  11. {mergechannels-0.4.0.dist-info → mergechannels-0.5.1.dist-info}/licenses/LICENSE +0 -0
mergechannels/__init__.py CHANGED
@@ -4,6 +4,10 @@ from .mergechannels import ( # type: ignore
4
4
  dispatch_multi_channel,
5
5
  )
6
6
  from ._internal import merge, apply_color_map
7
+ from ._luts import COLORMAPS as _COLORMAPS
8
+ from typing import Literal # noqa: F401
9
+
10
+ COLORMAPS = _COLORMAPS
7
11
 
8
12
 
9
13
  __all__ = [
@@ -11,4 +15,5 @@ __all__ = [
11
15
  'dispatch_multi_channel',
12
16
  'merge',
13
17
  'apply_color_map',
18
+ 'COLORMAPS',
14
19
  ]
mergechannels/__init__.pyi CHANGED
@@ -1,39 +1,69 @@
1
-
2
- from typing import Literal, Sequence
1
+ from __future__ import annotations
2
+ from typing import TYPE_CHECKING, Literal, Sequence, Union
3
3
  import numpy as np
4
4
 
5
- from python.mergechannels._blending import BLENDING_OPTIONS
6
- from python.mergechannels._luts import COLORMAPS
5
+ from mergechannels._blending import BLENDING_OPTIONS
6
+ from mergechannels._luts import COLORMAPS
7
+
8
+ if TYPE_CHECKING:
9
+ from matplotlib.colors import Colormap as MatplotlibColormap
10
+ from cmap import Colormap as CmapColormap
11
+ from nptyping import (
12
+ NDArray,
13
+ Shape,
14
+ UInt8,
15
+ )
16
+
7
17
 
18
+ Number = Union[int, float]
8
19
 
9
20
  def apply_color_map(
10
- arr: np.ndarray,
11
- color: COLORMAPS,
12
- percentiles: tuple[float, float] | None = None,
13
- saturation_limits: tuple[float, float] | None = None,
21
+ arr: np.ndarray,
22
+ color: Union[
23
+ COLORMAPS,
24
+ NDArray[Shape['3, 255'], UInt8],
25
+ MatplotlibColormap,
26
+ CmapColormap,
27
+ ],
28
+ percentiles: tuple[Number, Number] | None = None,
29
+ saturation_limits: tuple[Number, Number] | None = None,
14
30
  ) -> np.ndarray:
15
31
  ...
16
32
 
17
33
  def merge(
18
- arrs: Sequence[np.ndarray],
19
- colors: Sequence[COLORMAPS],
20
- blending: BLENDING_OPTIONS = 'max',
21
- percentiles: tuple[float, float] | Sequence[tuple[float, float]] | None = None,
22
- saturation_limits: tuple[float, float] | Sequence[tuple[float, float]] | None = None,
34
+ arrs: Sequence[np.ndarray],
35
+ colors: Sequence[COLORMAPS],
36
+ blending: BLENDING_OPTIONS = 'max',
37
+ percentiles: Sequence[tuple[float, float]] | None = None,
38
+ saturation_limits: Sequence[tuple[float, float]] | None = None,
23
39
  ) -> np.ndarray:
24
40
  ...
25
41
 
26
42
  def dispatch_single_channel(
27
43
  array_reference: np.ndarray,
28
- cmap_name: str,
29
- limits: tuple[float, float],
44
+ cmap_name: Union[COLORMAPS, None],
45
+ cmap_values: Union[
46
+ NDArray[Shape['3, 255'], UInt8],
47
+ MatplotlibColormap,
48
+ CmapColormap,
49
+ None,
50
+ ],
51
+ limits: tuple[Number, Number] | None = None,
30
52
  ) -> np.ndarray:
31
53
  ...
32
54
 
33
55
  def dispatch_multi_channel(
34
56
  array_references: Sequence[np.ndarray],
35
- cmap_names: Sequence[str],
57
+ cmap_names: Sequence[Union[COLORMAPS, None]],
58
+ cmap_values: Sequence[
59
+ Union[
60
+ NDArray[Shape['3, 255'], UInt8],
61
+ MatplotlibColormap,
62
+ CmapColormap,
63
+ None,
64
+ ]
65
+ ],
36
66
  blending: Literal[BLENDING_OPTIONS],
37
- limits: Sequence[tuple[float, float]],
67
+ limits: Sequence[tuple[Number, Number]] | None = None,
38
68
  ) -> np.ndarray:
39
69
  ...
mergechannels/_internal.py CHANGED
@@ -1,6 +1,9 @@
1
+ from __future__ import annotations
1
2
  from typing import (
3
+ TYPE_CHECKING,
2
4
  Sequence,
3
5
  Union,
6
+ Tuple,
4
7
  )
5
8
 
6
9
  import numpy as np
@@ -12,9 +15,67 @@ from mergechannels import (
12
15
  from ._luts import COLORMAPS
13
16
  from ._blending import BLENDING_OPTIONS
14
17
 
18
+ if TYPE_CHECKING:
19
+ from matplotlib.colors import Colormap as MatplotlibColormap
20
+ from cmap import Colormap as CmapColormap
21
+ from nptyping import (
22
+ NDArray,
23
+ Shape,
24
+ UInt8,
25
+ )
26
+
27
+ def _parse_cmap_arguments(
28
+ color: Union[
29
+ COLORMAPS,
30
+ NDArray[Shape['3, 255'], UInt8],
31
+ MatplotlibColormap,
32
+ CmapColormap,
33
+ ],
34
+ ) -> Tuple[Union[COLORMAPS, None], Union[NDArray[Shape['3, 256'], UInt8], None]]:
35
+ '''
36
+ Parse the color argument and return the corresponding cmap name and cmap values
37
+
38
+ Args:
39
+ color: a user-specified argument which may be the name of mergechannels colormap, a ndarray
40
+ lookup table, and matplotlib colormap, or a cmap colormap.
41
+
42
+ Returns:
43
+ A tuple specifying the corresponding mergechannels colormap name (or None if N/A), and an
44
+ array of the lookup table (or None if N/A)
45
+ '''
46
+ if isinstance(color, str):
47
+ return color, None
48
+ else:
49
+ try: # try to convert from a matplotlib colormap
50
+ if not color._isinit: # type: ignore
51
+ color._init() # type: ignore
52
+ cmap_values = (color._lut[:color.N, :3] * 255).astype('uint8') # type: ignore
53
+ except AttributeError: # try to convert from a cmaps ColorMap
54
+ try:
55
+ cmap_values = (np.asarray(color.lut()[:, :3]) * 255).astype('uint8') # type: ignore
56
+ except AttributeError: # must be a list of lists or an array castable to u8 (256, 3)
57
+ cmap_values = np.asarray(color).astype('uint8') # type: ignore
58
+
59
+ if not (
60
+ isinstance(cmap_values, np.ndarray)
61
+ and cmap_values.shape == (256, 3)
62
+ and cmap_values.dtype == np.uint8
63
+ ):
64
+ raise ValueError(
65
+ 'Expected a matplotlib colormap, a cmaps colormap, or an object directly castable to '
66
+ f'an 8-bit array of shape (256, 3), got {type(cmap_values)}: {color}'
67
+ )
68
+ return None, cmap_values
69
+
70
+
15
71
  def apply_color_map(
16
72
  arr: np.ndarray,
17
- color: COLORMAPS,
73
+ color: Union[
74
+ COLORMAPS,
75
+ NDArray[Shape['3, 255'], UInt8],
76
+ MatplotlibColormap,
77
+ CmapColormap,
78
+ ],
18
79
  percentiles: Union[tuple[float, float], None] = None,
19
80
  saturation_limits: Union[tuple[float, float], None] = None,
20
81
  ) -> np.ndarray:
@@ -27,23 +88,26 @@ def apply_color_map(
27
88
  low, high = np.percentile(arr, percentiles)
28
89
  saturation_limits = (low, high)
29
90
 
91
+ cmap_name, cmap_values = _parse_cmap_arguments(color)
92
+
30
93
  return dispatch_single_channel(
31
94
  array_reference=arr,
32
- cmap_name=color,
95
+ cmap_name=cmap_name,
96
+ cmap_values=cmap_values,
33
97
  limits=saturation_limits,
34
98
  )
35
99
 
36
-
37
100
  def merge(
38
- arrs: Sequence[np.ndarray],
39
- colors: Sequence[COLORMAPS],
40
- blending: BLENDING_OPTIONS = 'max',
41
- percentiles: Union[Sequence[tuple[float, float]], None] = None,
42
- saturation_limits: Union[Sequence[tuple[float, float]], None] = None,
101
+ arrs: Sequence[np.ndarray],
102
+ colors: Sequence[COLORMAPS],
103
+ blending: BLENDING_OPTIONS = 'max',
104
+ percentiles: Sequence[tuple[float, float]] | None = None,
105
+ saturation_limits: Sequence[tuple[float, float]] | None = None,
43
106
  ) -> np.ndarray:
44
107
  '''
45
108
  apply cmaps to arrays and blend the colors
46
109
  '''
110
+ cmap_names, cmap_values = zip(*[_parse_cmap_arguments(color) for color in colors])
47
111
  if saturation_limits is None:
48
112
  if percentiles is None:
49
113
  percentiles = [(1.1, 99.9)] * len(arrs)
@@ -53,7 +117,8 @@ def merge(
53
117
  )
54
118
  return dispatch_multi_channel(
55
119
  array_references=arrs,
56
- cmap_names=colors,
120
+ cmap_names=cmap_names,
121
+ cmap_values=cmap_values,
57
122
  blending=blending,
58
123
  limits=saturation_limits, # type: ignore
59
124
  )
mergechannels/_luts.py CHANGED
@@ -1,177 +1,175 @@
1
1
  from typing import Literal
2
2
 
3
3
  COLORMAPS = Literal[
4
- 'Circus Ink Purple',
5
- 'Spectrum Parabolic Ramp',
6
- 'Pop cherry',
7
- 'Circus Green',
8
- 'Rainbow RGB',
9
- 'Parabolic RGB',
4
+ '16_colors',
5
+ '3-3-2 RGB',
6
+ '3color-BMR',
7
+ '3color-CGY',
10
8
  '3color-RMB',
11
- 'Pop magenta inverted',
12
- 'Red Hot',
13
- 'Duo Cyan',
14
- 'Yellow',
15
- 'Grays g=0.25 inverted',
16
- 'betterRed',
17
- 'Grays g=1.75',
18
- 'blue_orange_icb',
19
- 'Pop green',
20
- 'mpl-inferno',
21
- 'I Blue',
9
+ '3color-YGC',
10
+ '5_ramps',
11
+ '6_shades',
12
+ 'BOP blue',
13
+ 'BOP orange',
22
14
  'BOP purple',
23
- 'Duo Yellow',
24
- 'Phase Ink Mint-Cherry',
25
- 'betterOrange',
26
15
  'Blue',
27
- '6_shades',
28
- 'Ink Cyan',
29
- 'OIMB3',
30
- 'Quartetto MYGB Blue',
31
- 'Ink Green',
32
- 'Red/Green',
33
- 'Turbo',
16
+ 'Circus Cherry',
17
+ 'Circus Cyan',
18
+ 'Circus Green',
34
19
  'Circus Ink Black',
20
+ 'Circus Ink Cherry',
21
+ 'Circus Ink Cyan',
22
+ 'Circus Ink Green',
23
+ 'Circus Ink Mint',
24
+ 'Circus Ink Purple',
25
+ 'Circus Ink Yellow',
26
+ 'Circus Mint',
27
+ 'Circus Purple',
28
+ 'Circus Yellow',
29
+ 'Cyan',
30
+ 'Cyan Hot',
31
+ 'Duo Cherry',
32
+ 'Duo Cyan',
35
33
  'Duo Green',
36
- 'mpl-viridis',
37
- 'Grays g=0.25',
38
- 'Quartetto RYGB Blue',
39
- 'smart',
40
- 'Thermal',
41
- 'OIMB2',
42
- 'Pop blue inverted',
43
34
  'Duo Intense Cherry',
44
- 'Phase Bold Green-Magenta',
45
- 'Quartetto MYGB Magenta',
46
- 'Pop purple inverted',
47
- 'glow',
48
- 'OPF orange',
49
- 'Pop cyan inverted',
50
- 'physics',
51
- 'Phase Ink Yellow-Cyan',
52
- 'Circus Ink Mint',
53
- 'Ink Wash Purple',
54
- 'OIMB1',
55
- 'betterCyan',
56
- 'mpl-magma',
35
+ 'Duo Intense Cyan',
57
36
  'Duo Intense Green',
58
- 'edges',
59
- 'Quartetto MYGB Green',
60
- 'Ink Wash Cherry',
61
- 'OPF purple',
62
- 'Ink Wash Cyan',
37
+ 'Duo Intense Mint',
63
38
  'Duo Intense Purple',
64
- 'I Yellow',
65
- '16_colors',
66
- 'Circus Cyan',
67
- 'Pop lavender inverted',
68
- 'sepia',
69
- 'Duo Intense Cyan',
39
+ 'Duo Intense Yellow',
40
+ 'Duo Mint',
41
+ 'Duo Purple',
42
+ 'Duo Yellow',
43
+ 'Fire',
44
+ 'Grays',
45
+ 'Grays g=0.25',
46
+ 'Grays g=0.25 inverted',
47
+ 'Grays g=0.50',
48
+ 'Grays g=0.50 inverted',
49
+ 'Grays g=0.75',
50
+ 'Grays g=0.75 inverted',
70
51
  'Grays g=1.00 inverted',
71
- 'ICA2',
72
- 'Quartetto RYGB Green',
73
- 'Ink Wash Green',
74
- 'Pop blue',
75
- 'Quartetto RYGB Red',
76
- 'I Forest',
77
- 'ICA3',
78
- 'Circus Yellow',
79
- 'Pop mint',
80
- 'BOP orange',
52
+ 'Grays g=1.25',
81
53
  'Grays g=1.25 inverted',
82
- 'I Red',
83
- '3color-CGY',
54
+ 'Grays g=1.50',
55
+ 'Grays g=1.50 inverted',
56
+ 'Grays g=1.75',
57
+ 'Grays g=1.75 inverted',
58
+ 'Grays g=2.00',
59
+ 'Grays g=2.00 inverted',
60
+ 'Green',
61
+ 'Green Fire Blue',
62
+ 'HiLo',
63
+ 'I Blue',
64
+ 'I Bordeaux',
65
+ 'I Cyan',
66
+ 'I Forest',
84
67
  'I Green',
85
- 'Fire',
68
+ 'I Magenta',
69
+ 'I Purple',
70
+ 'I Red',
71
+ 'I Yellow',
72
+ 'ICA',
73
+ 'ICA2',
74
+ 'ICA3',
75
+ 'Ice',
76
+ 'Ink Black',
77
+ 'Ink Cherry',
78
+ 'Ink Cyan',
79
+ 'Ink Green',
80
+ 'Ink Mint',
81
+ 'Ink Purple',
82
+ 'Ink Wash Black',
83
+ 'Ink Wash Cherry',
84
+ 'Ink Wash Cyan',
85
+ 'Ink Wash Green',
86
+ 'Ink Wash Mint',
87
+ 'Ink Wash Purple',
88
+ 'Ink Wash Yellow',
89
+ 'Ink Yellow',
90
+ 'Magenta',
86
91
  'Magenta Hot',
87
- 'Grays g=0.50',
92
+ 'OIMB1',
93
+ 'OIMB2',
94
+ 'OIMB3',
95
+ 'OPF fresh',
96
+ 'OPF orange',
97
+ 'OPF purple',
88
98
  'Orange Hot',
89
- 'Circus Ink Cherry',
90
- 'Pop purple',
91
- 'Ink Yellow',
92
- 'unionjack',
93
- 'Ink Wash Yellow',
94
- 'I Cyan',
95
- 'Cyan Hot',
96
- 'Pop mint inverted',
97
- 'I Magenta',
98
- 'Grays',
99
- 'Phase Green-Magenta',
100
- 'Cyan',
101
- 'Grays g=0.75',
99
+ 'Parabolic RGB',
100
+ 'Phase Bold Green-Magenta',
101
+ 'Phase Bold Ink Green-Magenta',
102
102
  'Phase Bold Ink Mint-Cherry',
103
- 'Grays g=1.75 inverted',
104
- 'phase',
105
- 'gem',
103
+ 'Phase Bold Ink Yellow-Cyan',
104
+ 'Phase Bold Mint-Cherry',
105
+ 'Phase Bold Yellow-Cyan',
106
+ 'Phase Green-Magenta',
107
+ 'Phase Ink Green-Magenta',
108
+ 'Phase Ink Mint-Cherry',
109
+ 'Phase Ink Yellow-Cyan',
110
+ 'Phase Mint-Cherry',
111
+ 'Phase Yellow-Cyan',
112
+ 'Pop blue',
113
+ 'Pop blue inverted',
114
+ 'Pop cherry',
106
115
  'Pop cherry inverted',
116
+ 'Pop cyan',
117
+ 'Pop cyan inverted',
118
+ 'Pop green',
119
+ 'Pop green inverted',
120
+ 'Pop lavender inverted',
121
+ 'Pop magenta',
122
+ 'Pop magenta inverted',
123
+ 'Pop mint',
124
+ 'Pop mint inverted',
125
+ 'Pop purple',
126
+ 'Pop purple inverted',
107
127
  'Pop red',
108
- 'Circus Cherry',
109
- 'OPF fresh',
110
- 'Circus Ink Cyan',
111
- 'betterGreen',
112
- 'Phase Ink Green-Magenta',
113
- '3color-BMR',
114
- 'Ink Wash Black',
115
128
  'Pop red inverted',
116
- 'Duo Purple',
117
- 'betterBlue',
118
- 'Phase Bold Ink Yellow-Cyan',
129
+ 'Pop yellow',
130
+ 'Pop yellow inverted',
131
+ 'Quartetto MYGB Blue',
132
+ 'Quartetto MYGB Green',
133
+ 'Quartetto MYGB Magenta',
134
+ 'Quartetto MYGB Yellow',
135
+ 'Quartetto RYGB Blue',
136
+ 'Quartetto RYGB Green',
137
+ 'Quartetto RYGB Red',
119
138
  'Quartetto RYGB Yellow',
120
- 'Magenta',
121
- 'Duo Mint',
139
+ 'Rainbow RGB',
122
140
  'Red',
123
- 'Grays g=1.25',
124
- 'I Bordeaux',
125
- 'Grays g=1.50 inverted',
126
- 'Green Hot',
141
+ 'Red Hot',
142
+ 'Red/Green',
143
+ 'Spectrum',
144
+ 'Thermal',
145
+ 'Turbo',
146
+ 'Yellow',
147
+ 'Yellow Hot',
148
+ 'betterBlue',
149
+ 'betterCyan',
150
+ 'betterGreen',
151
+ 'betterOrange',
152
+ 'betterRed',
153
+ 'betterYellow',
154
+ 'blue_orange_icb',
155
+ 'brgbcmyw',
156
+ 'cool',
157
+ 'edges',
158
+ 'gem',
127
159
  'glasbey',
160
+ 'glasbey_inverted',
128
161
  'glasbey_on_dark',
162
+ 'glow',
163
+ 'mpl-inferno',
164
+ 'mpl-magma',
129
165
  'mpl-plasma',
130
- 'Ink Cherry',
131
- 'Ink Mint',
132
- 'Circus Ink Yellow',
133
- 'Pop cyan',
134
- 'Pop green inverted',
135
- 'Ink Purple',
136
- '3color-YGC',
137
- 'Pop yellow',
138
- 'Quartetto MYGB Yellow',
139
- 'Duo Cherry',
140
- 'Green',
141
- 'Grays g=0.50 inverted',
142
- 'Circus Ink Green',
143
- 'ICA',
144
- 'Phase Mint-Cherry',
145
- 'Ink Black',
146
- 'Yellow Hot',
147
- 'Phase Bold Yellow-Cyan',
148
- 'thallium',
149
- 'Pop yellow inverted',
150
- 'Spectrum',
166
+ 'mpl-viridis',
167
+ 'phase',
168
+ 'physics',
151
169
  'royal',
152
- 'glasbey_inverted',
153
- 'betterYellow',
154
- 'Circus Purple',
155
- 'Grays g=2.00',
156
- 'HiLo',
157
- 'cool',
158
- 'Green Fire Blue',
159
- 'Ink Wash Mint',
160
- 'Grays g=0.75 inverted',
161
- 'BOP blue',
170
+ 'sepia',
171
+ 'smart',
162
172
  'thal',
163
- 'Ice',
164
- 'Circus Mint',
165
- 'Grays g=1.50',
166
- 'Duo Intense Mint',
167
- 'brgbcmyw',
168
- 'Phase Yellow-Cyan',
169
- 'I Purple',
170
- 'Duo Intense Yellow',
171
- 'Phase Bold Ink Green-Magenta',
172
- 'Pop magenta',
173
- '3-3-2 RGB',
174
- 'Grays g=2.00 inverted',
175
- '5_ramps',
176
- 'Phase Bold Mint-Cherry',
173
+ 'thallium',
174
+ 'unionjack',
177
175
  ]
mergechannels-0.5.1.dist-info/METADATA ADDED
@@ -0,0 +1,397 @@
1
+ Metadata-Version: 2.4
2
+ Name: mergechannels
3
+ Version: 0.5.1
4
+ Classifier: Programming Language :: Rust
5
+ Classifier: Programming Language :: Python :: Implementation :: CPython
6
+ Classifier: Programming Language :: Python :: Implementation :: PyPy
7
+ Classifier: License :: OSI Approved :: MIT License
8
+ Classifier: Programming Language :: Python :: 3
9
+ Classifier: Programming Language :: Python :: 3.9
10
+ Classifier: Programming Language :: Python :: 3.10
11
+ Classifier: Programming Language :: Python :: 3.11
12
+ Classifier: Programming Language :: Python :: 3.12
13
+ Classifier: Programming Language :: Python :: 3.13
14
+ Requires-Dist: numpy>1.25.0
15
+ Requires-Dist: nptyping==2.5.0 ; extra == 'types'
16
+ Provides-Extra: types
17
+ License-File: LICENSE
18
+ Summary: Apply and merge colormaps
19
+ Author-email: Zac Swider <zac.swider@gmail.com>
20
+ License: MIT
21
+ Requires-Python: >=3.9, <=3.13
22
+ Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
23
+
24
+ [![CI](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml/badge.svg)](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml)
25
+ ![PyPI - License](https://img.shields.io/pypi/l/mergechannels)
26
+ ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergechannels)
27
+ ![PyPI](https://img.shields.io/pypi/v/mergechannels)
28
+
29
+ # mergechannels
30
+
31
+ This project was originally conceived because I often find myself wanting to apply and blend colormaps to images while working from Python, and 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, so I was interested in seeing if I could at least match matplotlib's colormapping performance with my own hand-rolled colorizer in Rust.
32
+
33
+ The current goal of this library is to be a simple, fast, and memory-efficient way to apply and blend colormaps to images. The api should be intuitive, flexible, and simple. If this is not the case in your hands, please open an issue.
34
+
35
+
36
+ ## Installation
37
+
38
+ Install pre-compiled binaries from [PyPI](https://pypi.org/project/mergechannels/):
39
+ ```bash
40
+ pip install mergechannels
41
+ ```
42
+
43
+ Build from source on your own machine:
44
+ ```bash
45
+ pip install git+https://github.com/zacswider/mergechannels.git
46
+ ```
47
+
48
+ ## Usage
49
+ *NOTE*: `skimage`, `matplotlib`, and `cmap` are not dependencies of this project, but are used in the examples below to fetch data/colormaps, and display images.
50
+
51
+
52
+ ### apply a different colormap to each channel
53
+ The primary entrypoint for merging multiple channels is with `mergechannels.merge`. This function expects a sequence of arrays, a sequence of colormaps, a blending approach, and optionally a sequence of pre-determined saturation limits. The arrays is expected to be either u8 or u16 and 2 or 3D.
54
+
55
+ ```python
56
+ from skimage import data
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+ import matplotlib.pyplot as plt
58
+ import mergechannels as mc
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+
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+ cells, nuclei = data.cells3d().max(axis=0)
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+
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+ fig, axes = plt.subplots(1, 3)
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+ for ax in axes: ax.axis('off')
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+ a, b, c = axes
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+ a.imshow(cells, cmap='gray')
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+ b.imshow(nuclei, cmap='gray')
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+ c.imshow(mc.merge([cells, nuclei], ['Orange Hot', 'Cyan Hot']))
68
+ ```
69
+ ![simple channel blending](https://raw.githubusercontent.com/zacswider/README_Images/main/simple_channel_merge.png)
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+
71
+ #### What constitutes a colormap?
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+ Colormaps can be the literal name of one of the FIJI colormaps compiled into the mergechannels binary (see a list as the bottom of the page), a matplotlib colormap, or a [cmap](https://pypi.org/project/cmap/) colormap. The example below creates a similar blending as above, but by explicitly passing pre-generated colormaps (one from the matplotlib library, one from the cmap library). These can also be combined with string literals.
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+
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+ ```python
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+ import cmap
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+ import matplotlib.pyplot as plt
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+ from skimage import data
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+ import mergechannels as mc
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+
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+ cells, nuclei = data.cells3d().max(axis=0)
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+ blue = cmap.Colormap('seaborn:mako')
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+ copper = plt.get_cmap('copper')
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+
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+ fig, axes = plt.subplots(1, 3)
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+ for ax in axes: ax.axis('off')
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+ a, b, c = axes
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+ a.imshow(mc.apply_color_map(nuclei, blue))
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+ b.imshow(mc.apply_color_map(cells, copper))
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+ c.imshow(mc.merge([nuclei, cells], [blue, copper]))
90
+ ```
91
+ ![channel blending with external cmaps](https://raw.githubusercontent.com/zacswider/README_Images/main/external_cmaps.png)
92
+
93
+ #### What are my blending options?
94
+ The `blending` argument to `mergechannels.merge` can be one of the following:
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+ - `'max'`: the maximum RGB value of each pixel is used. This is the default (and intuitive) behavior.
96
+ - `'min'`: the minimum RGB value of each pixel is used. This is useful when combining inverted colormaps.
97
+ - `'mean'`: the mean RGB value of each pixel is used. This is typically most useful when combinding fluorescence with brightfield, but can often require re-scaling the images after blending.
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+ - `'sum'`: the sum of the RGB values of each pixel is used (saturating). Results in high saturation images but can often be overwhelming and difficult to interpret.
99
+
100
+ The default and intuitive behavior is the use `'max'` blending, but oftentimes minimum blending is desired when combining inverted colormaps.
101
+ ```python
102
+ from skimage import data
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+ import matplotlib.pyplot as plt
104
+ import mergechannels as mc
105
+
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+ cells, nuclei = data.cells3d().max(axis=0)
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+ fig, axes = plt.subplots(1, 3, dpi=200)
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+ for ax in axes: ax.axis('off')
109
+ a, b, c = axes
110
+ a.imshow(cells, cmap='gray')
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+ b.imshow(nuclei, cmap='gray')
112
+ c.imshow(mc.merge([cells, nuclei],['I Blue', 'I Forest'], blending='min'))
113
+ ```
114
+ ![minimum blending with inverted colormaps](https://raw.githubusercontent.com/zacswider/README_Images/main/inverted_blending.png)
115
+
116
+ #### How can I control display brightness?
117
+ If desired, pre-determined saturation limits can be passed to `apply_color_map` to clip the images values to a range that best represents the contents of the image. These can be explicit pixel values passed with the `saturation_limits` argument, or as percentile values passed with the `percentiles` argument. If the latter, the percentile values will be used to calculate the saturation limits based on the distribution of pixel values in the images (this is sometimes referred to as "autoscaling). The default behavior is to calculate use the 1.1th percentile value as the dark point and the 99.9th percentile as the bright point.
118
+
119
+ ```python
120
+ from skimage import data
121
+ import matplotlib.pyplot as plt
122
+ import mergechannels as mc
123
+
124
+ cells, nuclei = data.cells3d().max(axis=0)
125
+ channels = [cells, nuclei]
126
+ colormaps = ['I Blue', 'I Forest']
127
+ fig, axes = plt.subplots(1, 3, dpi=300)
128
+ for ax in axes: ax.axis('off')
129
+ (a, b, c) = axes
130
+ a.imshow(mc.merge(channels, colormaps, blending='min')) # use the default autoscaling
131
+ b.imshow(
132
+ mc.merge(
133
+ channels,
134
+ colormaps,
135
+ blending='min',
136
+ saturation_limits=[
137
+ (1000, 20_000), # pre-determined dark and light points for ch1
138
+ (1000, 50_000), # pre-determined dark and light points for ch2
139
+ ],
140
+ ),
141
+ )
142
+ c.imshow(
143
+ mc.merge(
144
+ channels,
145
+ colormaps,
146
+ blending='min',
147
+ percentiles=[(
148
+ 1, # bottom 1% of pixels set to black point
149
+ 97, # top 3% of pixels set to white point
150
+ )]*len(channels), # apply this to all channels
151
+ ),
152
+ )
153
+ ```
154
+ ![adjust the brightness with explicit of percentile based approaches](https://raw.githubusercontent.com/zacswider/README_Images/main/brightness_adjust.png)
155
+
156
+
157
+ NOTE: if you are already working with appropriately scaled u8 images, you will see ~10X performance improvements (relative to the mergechannels and matplotlib naive default implementations) by passing `saturation_limits=(0, 255)` as this significantly reduces the amount of arithmetic done per pixel.
158
+
159
+
160
+ ### apply a colormap to a whole stack
161
+ ```python
162
+ from skimage import data
163
+ from matplotlib import pyplot as plt
164
+ import mergechannels as mc
165
+
166
+ volume = data.cells3d()
167
+ cells = volume[:, 0]
168
+ nuclei = volume[:, 1]
169
+ merged = mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot'])
170
+ plt.imshow(merged[24]); plt.show()
171
+ ```
172
+ ![colorize a whole stack of images](https://raw.githubusercontent.com/zacswider/README_Images/main/merged_stacks.png)
173
+
174
+
175
+ ### colorize a single image
176
+ The primary entrypoint to applying a colormap to a single image is with `apply_color_map`. this function takes an array, a colormap, and an optional percentiles argument. The arrays is expected to be either u8 or u16 and 2 or 3D.
177
+
178
+ ```python
179
+ from skimage import data
180
+ import matplotlib.pyplot as plt
181
+ import mergechannels as mc
182
+
183
+ img = data.camera()
184
+ colorized = mc.apply_color_map(img, 'Red/Green')
185
+
186
+ fig, axes = plt.subplots(1, 2)
187
+ for ax in axes: ax.axis('off')
188
+ (a, b) = axes
189
+ a.imshow(img, cmap='gray')
190
+ b.imshow(colorized)
191
+ plt.show()
192
+ print(colorized.shape, colorized.dtype)
193
+ >> (512, 512, 3) uint8
194
+ ```
195
+ ![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png)
196
+
197
+ Similar to `mergechannels.merge`, `apply_color_map` will also accept colormaps directly from `matplotlib` and `cmap`, explicit saturation limits, or perctile values for autoscaling.
198
+
199
+ ## Roadmap
200
+ mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2/3D 8/16-bit images and that's it.
201
+ - ~~Add support to u8 and u16 images~~
202
+ - Add support for any numerical dtype
203
+ - Add option to return any colormap as a matplotlib colormap
204
+ - ~~Add option to pass external colormaps to mergechannels~~
205
+ - Parallelize colormap application on large images (if it's helpful)
206
+ - Add option to overlay binary or instance masks onto colorized images
207
+
208
+ ## Acknowledgements
209
+
210
+ 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.
211
+
212
+ This project incorporates a number of colormaps that were hand-crafted by Christophe Leterrier and James Manton which were originally distributed [here](https://github.com/cleterrier/ChrisLUTs) and [here](https://sites.imagej.net/JDM_LUTs/) respectively.
213
+
214
+ ## Colormaps
215
+ ### FIJI built-in LUTs
216
+
217
+ <p>16_colors: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_16_colors.png" style="vertical-align: middle"></p>
218
+ <p>3-3-2 RGB: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_3-3-2 RGB.png" style="vertical-align: middle"></p>
219
+ <p>5_ramps: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_5_ramps.png" style="vertical-align: middle"></p>
220
+ <p>6_shades: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_6_shades.png" style="vertical-align: middle"></p>
221
+ <p>Blue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Blue.png" style="vertical-align: middle"></p>
222
+ <p>Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Cyan.png" style="vertical-align: middle"></p>
223
+ <p>Cyan Hot: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Cyan Hot.png" style="vertical-align: middle"></p>
224
+ <p>Fire: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Fire.png" style="vertical-align: middle"></p>
225
+ <p>Grays: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Grays.png" style="vertical-align: middle"></p>
226
+ <p>Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Green.png" style="vertical-align: middle"></p>
227
+ <p>Green Fire Blue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Green Fire Blue.png" style="vertical-align: middle"></p>
228
+ <p>HiLo: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_HiLo.png" style="vertical-align: middle"></p>
229
+ <p>ICA: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_ICA.png" style="vertical-align: middle"></p>
230
+ <p>ICA2: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_ICA2.png" style="vertical-align: middle"></p>
231
+ <p>ICA3: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_ICA3.png" style="vertical-align: middle"></p>
232
+ <p>Ice: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Ice.png" style="vertical-align: middle"></p>
233
+ <p>Magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Magenta.png" style="vertical-align: middle"></p>
234
+ <p>Magenta Hot: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Magenta Hot.png" style="vertical-align: middle"></p>
235
+ <p>Orange Hot: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Orange Hot.png" style="vertical-align: middle"></p>
236
+ <p>Rainbow RGB: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Rainbow RGB.png" style="vertical-align: middle"></p>
237
+ <p>Red: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Red.png" style="vertical-align: middle"></p>
238
+ <p>Red Hot: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Red Hot.png" style="vertical-align: middle"></p>
239
+ <p>Red/Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Red%25Green.png" style="vertical-align: middle"></p>
240
+ <p>Spectrum: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Spectrum.png" style="vertical-align: middle"></p>
241
+ <p>Thermal: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Thermal.png" style="vertical-align: middle"></p>
242
+ <p>Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Yellow.png" style="vertical-align: middle"></p>
243
+ <p>Yellow Hot: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_Yellow Hot.png" style="vertical-align: middle"></p>
244
+ <p>blue_orange_icb: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_blue_orange_icb.png" style="vertical-align: middle"></p>
245
+ <p>brgbcmyw: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_brgbcmyw.png" style="vertical-align: middle"></p>
246
+ <p>cool: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_cool.png" style="vertical-align: middle"></p>
247
+ <p>edges: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_edges.png" style="vertical-align: middle"></p>
248
+ <p>gem: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_gem.png" style="vertical-align: middle"></p>
249
+ <p>glasbey: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_glasbey.png" style="vertical-align: middle"></p>
250
+ <p>glasbey_inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_glasbey_inverted.png" style="vertical-align: middle"></p>
251
+ <p>glasbey_on_dark: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_glasbey_on_dark.png" style="vertical-align: middle"></p>
252
+ <p>glow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_glow.png" style="vertical-align: middle"></p>
253
+ <p>mpl-inferno: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_mpl-inferno.png" style="vertical-align: middle"></p>
254
+ <p>mpl-magma: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_mpl-magma.png" style="vertical-align: middle"></p>
255
+ <p>mpl-plasma: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_mpl-plasma.png" style="vertical-align: middle"></p>
256
+ <p>mpl-viridis: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_mpl-viridis.png" style="vertical-align: middle"></p>
257
+ <p>phase: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_phase.png" style="vertical-align: middle"></p>
258
+ <p>physics: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_physics.png" style="vertical-align: middle"></p>
259
+ <p>royal: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_royal.png" style="vertical-align: middle"></p>
260
+ <p>sepia: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_sepia.png" style="vertical-align: middle"></p>
261
+ <p>smart: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_smart.png" style="vertical-align: middle"></p>
262
+ <p>thal: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_thal.png" style="vertical-align: middle"></p>
263
+ <p>thallium: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_thallium.png" style="vertical-align: middle"></p>
264
+ <p>unionjack: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/builtin_luts_unionjack.png" style="vertical-align: middle"></p>
265
+
266
+ ### [My custom LUTs](https://github.com/zacswider/LUTs)
267
+
268
+ <p>OIMB1: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_OIMB1.png" style="vertical-align: middle"></p>
269
+ <p>OIMB2: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_OIMB2.png" style="vertical-align: middle"></p>
270
+ <p>OIMB3: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_OIMB3.png" style="vertical-align: middle"></p>
271
+ <p>betterBlue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_betterBlue.png" style="vertical-align: middle"></p>
272
+ <p>betterCyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_betterCyan.png" style="vertical-align: middle"></p>
273
+ <p>betterGreen: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_betterGreen.png" style="vertical-align: middle"></p>
274
+ <p>betterOrange: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_betterOrange.png" style="vertical-align: middle"></p>
275
+ <p>betterRed: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_betterRed.png" style="vertical-align: middle"></p>
276
+ <p>betterYellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/zac_luts_betterYellow.png" style="vertical-align: middle"></p>
277
+
278
+ ### [Christophe Leterrier's LUTs](https://github.com/cleterrier/ChrisLUTs)
279
+
280
+ <p>3color-BMR: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_3color-BMR.png" style="vertical-align: middle"></p>
281
+ <p>3color-CGY: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_3color-CGY.png" style="vertical-align: middle"></p>
282
+ <p>3color-RMB: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_3color-RMB.png" style="vertical-align: middle"></p>
283
+ <p>3color-YGC: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_3color-YGC.png" style="vertical-align: middle"></p>
284
+ <p>BOP blue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_BOP blue.png" style="vertical-align: middle"></p>
285
+ <p>BOP orange: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_BOP orange.png" style="vertical-align: middle"></p>
286
+ <p>BOP purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_BOP purple.png" style="vertical-align: middle"></p>
287
+ <p>I Blue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Blue.png" style="vertical-align: middle"></p>
288
+ <p>I Bordeaux: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Bordeaux.png" style="vertical-align: middle"></p>
289
+ <p>I Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Cyan.png" style="vertical-align: middle"></p>
290
+ <p>I Forest: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Forest.png" style="vertical-align: middle"></p>
291
+ <p>I Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Green.png" style="vertical-align: middle"></p>
292
+ <p>I Magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Magenta.png" style="vertical-align: middle"></p>
293
+ <p>I Purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Purple.png" style="vertical-align: middle"></p>
294
+ <p>I Red: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Red.png" style="vertical-align: middle"></p>
295
+ <p>I Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_I Yellow.png" style="vertical-align: middle"></p>
296
+ <p>OPF fresh: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_OPF fresh.png" style="vertical-align: middle"></p>
297
+ <p>OPF orange: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_OPF orange.png" style="vertical-align: middle"></p>
298
+ <p>OPF purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_OPF purple.png" style="vertical-align: middle"></p>
299
+ <p>Turbo: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/christ_luts_Turbo.png" style="vertical-align: middle"></p>
300
+
301
+ ### [James Manton's LUTs](https://sites.imagej.net/JDM_LUTs/)
302
+
303
+ <p>Circus Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Cherry.png" style="vertical-align: middle"></p>
304
+ <p>Circus Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Cyan.png" style="vertical-align: middle"></p>
305
+ <p>Circus Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Green.png" style="vertical-align: middle"></p>
306
+ <p>Circus Ink Black: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Ink Black.png" style="vertical-align: middle"></p>
307
+ <p>Circus Ink Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Ink Cherry.png" style="vertical-align: middle"></p>
308
+ <p>Circus Ink Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Ink Cyan.png" style="vertical-align: middle"></p>
309
+ <p>Circus Ink Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Ink Green.png" style="vertical-align: middle"></p>
310
+ <p>Circus Ink Mint: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Ink Mint.png" style="vertical-align: middle"></p>
311
+ <p>Circus Ink Purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Ink Purple.png" style="vertical-align: middle"></p>
312
+ <p>Circus Ink Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Ink Yellow.png" style="vertical-align: middle"></p>
313
+ <p>Circus Mint: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Mint.png" style="vertical-align: middle"></p>
314
+ <p>Circus Purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Purple.png" style="vertical-align: middle"></p>
315
+ <p>Circus Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Circus Yellow.png" style="vertical-align: middle"></p>
316
+ <p>Duo Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Cherry.png" style="vertical-align: middle"></p>
317
+ <p>Duo Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Cyan.png" style="vertical-align: middle"></p>
318
+ <p>Duo Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Green.png" style="vertical-align: middle"></p>
319
+ <p>Duo Intense Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Intense Cherry.png" style="vertical-align: middle"></p>
320
+ <p>Duo Intense Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Intense Cyan.png" style="vertical-align: middle"></p>
321
+ <p>Duo Intense Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Intense Green.png" style="vertical-align: middle"></p>
322
+ <p>Duo Intense Mint: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Intense Mint.png" style="vertical-align: middle"></p>
323
+ <p>Duo Intense Purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Intense Purple.png" style="vertical-align: middle"></p>
324
+ <p>Duo Intense Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Intense Yellow.png" style="vertical-align: middle"></p>
325
+ <p>Duo Mint: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Mint.png" style="vertical-align: middle"></p>
326
+ <p>Duo Purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Purple.png" style="vertical-align: middle"></p>
327
+ <p>Duo Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Duo Yellow.png" style="vertical-align: middle"></p>
328
+ <p>Grays g=0.25: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=0.25.png" style="vertical-align: middle"></p>
329
+ <p>Grays g=0.25 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=0.25 inverted.png" style="vertical-align: middle"></p>
330
+ <p>Grays g=0.50: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=0.50.png" style="vertical-align: middle"></p>
331
+ <p>Grays g=0.50 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=0.50 inverted.png" style="vertical-align: middle"></p>
332
+ <p>Grays g=0.75: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=0.75.png" style="vertical-align: middle"></p>
333
+ <p>Grays g=0.75 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=0.75 inverted.png" style="vertical-align: middle"></p>
334
+ <p>Grays g=1.00 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=1.00 inverted.png" style="vertical-align: middle"></p>
335
+ <p>Grays g=1.25: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=1.25.png" style="vertical-align: middle"></p>
336
+ <p>Grays g=1.25 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=1.25 inverted.png" style="vertical-align: middle"></p>
337
+ <p>Grays g=1.50: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=1.50.png" style="vertical-align: middle"></p>
338
+ <p>Grays g=1.50 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=1.50 inverted.png" style="vertical-align: middle"></p>
339
+ <p>Grays g=1.75: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=1.75.png" style="vertical-align: middle"></p>
340
+ <p>Grays g=1.75 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=1.75 inverted.png" style="vertical-align: middle"></p>
341
+ <p>Grays g=2.00: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=2.00.png" style="vertical-align: middle"></p>
342
+ <p>Grays g=2.00 inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Grays g=2.00 inverted.png" style="vertical-align: middle"></p>
343
+ <p>Ink Black: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Black.png" style="vertical-align: middle"></p>
344
+ <p>Ink Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Cherry.png" style="vertical-align: middle"></p>
345
+ <p>Ink Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Cyan.png" style="vertical-align: middle"></p>
346
+ <p>Ink Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Green.png" style="vertical-align: middle"></p>
347
+ <p>Ink Mint: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Mint.png" style="vertical-align: middle"></p>
348
+ <p>Ink Purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Purple.png" style="vertical-align: middle"></p>
349
+ <p>Ink Wash Black: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Wash Black.png" style="vertical-align: middle"></p>
350
+ <p>Ink Wash Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Wash Cherry.png" style="vertical-align: middle"></p>
351
+ <p>Ink Wash Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Wash Cyan.png" style="vertical-align: middle"></p>
352
+ <p>Ink Wash Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Wash Green.png" style="vertical-align: middle"></p>
353
+ <p>Ink Wash Mint: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Wash Mint.png" style="vertical-align: middle"></p>
354
+ <p>Ink Wash Purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Wash Purple.png" style="vertical-align: middle"></p>
355
+ <p>Ink Wash Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Wash Yellow.png" style="vertical-align: middle"></p>
356
+ <p>Ink Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Ink Yellow.png" style="vertical-align: middle"></p>
357
+ <p>Parabolic RGB: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Parabolic RGB.png" style="vertical-align: middle"></p>
358
+ <p>Phase Bold Green-Magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Bold Green-Magenta.png" style="vertical-align: middle"></p>
359
+ <p>Phase Bold Ink Green-Magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Bold Ink Green-Magenta.png" style="vertical-align: middle"></p>
360
+ <p>Phase Bold Ink Mint-Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Bold Ink Mint-Cherry.png" style="vertical-align: middle"></p>
361
+ <p>Phase Bold Ink Yellow-Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Bold Ink Yellow-Cyan.png" style="vertical-align: middle"></p>
362
+ <p>Phase Bold Mint-Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Bold Mint-Cherry.png" style="vertical-align: middle"></p>
363
+ <p>Phase Bold Yellow-Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Bold Yellow-Cyan.png" style="vertical-align: middle"></p>
364
+ <p>Phase Green-Magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Green-Magenta.png" style="vertical-align: middle"></p>
365
+ <p>Phase Ink Green-Magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Ink Green-Magenta.png" style="vertical-align: middle"></p>
366
+ <p>Phase Ink Mint-Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Ink Mint-Cherry.png" style="vertical-align: middle"></p>
367
+ <p>Phase Ink Yellow-Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Ink Yellow-Cyan.png" style="vertical-align: middle"></p>
368
+ <p>Phase Mint-Cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Mint-Cherry.png" style="vertical-align: middle"></p>
369
+ <p>Phase Yellow-Cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Phase Yellow-Cyan.png" style="vertical-align: middle"></p>
370
+ <p>Pop blue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop blue.png" style="vertical-align: middle"></p>
371
+ <p>Pop blue inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop blue inverted.png" style="vertical-align: middle"></p>
372
+ <p>Pop cherry: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop cherry.png" style="vertical-align: middle"></p>
373
+ <p>Pop cherry inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop cherry inverted.png" style="vertical-align: middle"></p>
374
+ <p>Pop cyan: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop cyan.png" style="vertical-align: middle"></p>
375
+ <p>Pop cyan inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop cyan inverted.png" style="vertical-align: middle"></p>
376
+ <p>Pop green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop green.png" style="vertical-align: middle"></p>
377
+ <p>Pop green inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop green inverted.png" style="vertical-align: middle"></p>
378
+ <p>Pop lavender inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop lavender inverted.png" style="vertical-align: middle"></p>
379
+ <p>Pop magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop magenta.png" style="vertical-align: middle"></p>
380
+ <p>Pop magenta inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop magenta inverted.png" style="vertical-align: middle"></p>
381
+ <p>Pop mint: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop mint.png" style="vertical-align: middle"></p>
382
+ <p>Pop mint inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop mint inverted.png" style="vertical-align: middle"></p>
383
+ <p>Pop purple: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop purple.png" style="vertical-align: middle"></p>
384
+ <p>Pop purple inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop purple inverted.png" style="vertical-align: middle"></p>
385
+ <p>Pop red: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop red.png" style="vertical-align: middle"></p>
386
+ <p>Pop red inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop red inverted.png" style="vertical-align: middle"></p>
387
+ <p>Pop yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop yellow.png" style="vertical-align: middle"></p>
388
+ <p>Pop yellow inverted: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Pop yellow inverted.png" style="vertical-align: middle"></p>
389
+ <p>Quartetto MYGB Blue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto MYGB Blue.png" style="vertical-align: middle"></p>
390
+ <p>Quartetto MYGB Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto MYGB Green.png" style="vertical-align: middle"></p>
391
+ <p>Quartetto MYGB Magenta: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto MYGB Magenta.png" style="vertical-align: middle"></p>
392
+ <p>Quartetto MYGB Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto MYGB Yellow.png" style="vertical-align: middle"></p>
393
+ <p>Quartetto RYGB Blue: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto RYGB Blue.png" style="vertical-align: middle"></p>
394
+ <p>Quartetto RYGB Green: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto RYGB Green.png" style="vertical-align: middle"></p>
395
+ <p>Quartetto RYGB Red: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto RYGB Red.png" style="vertical-align: middle"></p>
396
+ <p>Quartetto RYGB Yellow: <img src="https://raw.githubusercontent.com/zacswider/README_Images/main/jdm_luts_Quartetto RYGB Yellow.png" style="vertical-align: middle"></p>
397
+
mergechannels-0.5.1.dist-info/RECORD ADDED
@@ -0,0 +1,12 @@
1
+ mergechannels-0.5.1.dist-info/METADATA,sha256=-VwHNevVPYYI3iuLZ9ko69Dr7b8kqJ980DOjVTiOQvU,36764
2
+ mergechannels-0.5.1.dist-info/WHEEL,sha256=C0UEYGfmbwV7RUquuUeO4xByZw-_EeUrnedPz08oKg4,107
3
+ mergechannels-0.5.1.dist-info/licenses/LICENSE,sha256=csvD60rgtSorbYEM3f8867qNyPCzmIXyFNj8h01Bd6c,1071
4
+ mergechannels.libs/libgcc_s-1e52349c.so.1,sha256=Ani0u_W_tB8ESsFePO4D2mn2lrgWLhyFdw6RETxBTYM,437537
5
+ mergechannels/__init__.py,sha256=RpIHde1-y_FgqPaFQFhVoqurnZDbOQgOT4b5I3ejYrI,391
6
+ mergechannels/__init__.pyi,sha256=_fyJhcixWLF7vDjCGnQyncOB1H2ykP-khAThzwvTaEk,1777
7
+ mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
8
+ mergechannels/_internal.py,sha256=5jic4Zy4pATDKvZxP4Hr4j4McdiYFwaI1XDtfMDBVwA,3498
9
+ mergechannels/_luts.py,sha256=gFcSIjbLqRS33UvrOryYRKAU5i8EGLjgQbXMJYpiy48,2967
10
+ mergechannels/mergechannels.cpython-312-x86_64-linux-musl.so,sha256=66nNEAt9cwJrYYSXSaC6nLci7VakEUHfTvlWEfUUmFk,1022777
11
+ mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
12
+ mergechannels-0.5.1.dist-info/RECORD,,
{mergechannels-0.4.0.dist-info → mergechannels-0.5.1.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
1
1
  Wheel-Version: 1.0
2
- Generator: maturin (1.8.6)
2
+ Generator: maturin (1.9.1)
3
3
  Root-Is-Purelib: false
4
4
  Tag: cp312-cp312-musllinux_1_2_x86_64
mergechannels-0.4.0.dist-info/METADATA DELETED
@@ -1,146 +0,0 @@
1
- Metadata-Version: 2.4
2
- Name: mergechannels
3
- Version: 0.4.0
4
- Classifier: Programming Language :: Rust
5
- Classifier: Programming Language :: Python :: Implementation :: CPython
6
- Classifier: Programming Language :: Python :: Implementation :: PyPy
7
- Classifier: License :: OSI Approved :: MIT License
8
- Classifier: Programming Language :: Python :: 3
9
- Classifier: Programming Language :: Python :: 3.9
10
- Classifier: Programming Language :: Python :: 3.10
11
- Classifier: Programming Language :: Python :: 3.11
12
- Classifier: Programming Language :: Python :: 3.12
13
- Classifier: Programming Language :: Python :: 3.13
14
- Requires-Dist: numpy>1.25.0
15
- Provides-Extra: nvim
16
- License-File: LICENSE
17
- Summary: Apply and merge colormaps
18
- Author-email: Zac Swider <zac.swider@gmail.com>
19
- License: MIT
20
- Requires-Python: >=3.9, <=3.13
21
- Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
22
-
23
- [![CI](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml/badge.svg)](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml)
24
- ![PyPI - License](https://img.shields.io/pypi/l/mergechannels)
25
- ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergechannels)
26
- ![PyPI](https://img.shields.io/pypi/v/mergechannels)
27
-
28
- # mergechannels
29
-
30
- 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.
31
-
32
-
33
-
34
- ## Installation
35
-
36
- Install pre-compiled binaries from [PyPI](https://pypi.org/project/mergechannels/):
37
- ```bash
38
- pip install mergechannels
39
- ```
40
-
41
- Build from source on your own machine:
42
- ```bash
43
- pip install git+https://github.com/zacswider/mergechannels.git
44
- ```
45
-
46
- ## Usage
47
- *NOTE*: scikit-image is not a dependency of this project, but is used in the examples below to fetch images.
48
-
49
- ### colorize a single image
50
-
51
- ```python
52
- from skimage import data
53
- import matplotlib.pyplot as plt
54
- import mergechannels as mc
55
-
56
- img = data.camera()
57
- colorized = mc.apply_color_map(img, 'Red/Green')
58
- fig, axes = plt.subplots(1, 2, figsize=(6, 3), dpi=150)
59
- for ax in axes: ax.axis('off')
60
- (a, b) = axes
61
- a.imshow(img, cmap='gray')
62
- b.imshow(colorized)
63
- plt.show()
64
- print(colorized.shape, colorized.dtype)
65
- >> (512, 512, 3) uint8
66
- ```
67
- ![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png)
68
-
69
-
70
- ### apply a different colormap to each channel
71
- ```python
72
- from skimage import data
73
- import matplotlib.pyplot as plt
74
- import mergechannels as mc
75
-
76
- cells, nuclei = data.cells3d().max(axis=0)
77
- assert cells.dtype == 'uint16' and nuclei.dtype == 'uint16'
78
- fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
79
- for ax in axes.ravel(): ax.axis('off')
80
- (a, b) = axes.ravel()
81
- a.imshow(mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot']))
82
- b.imshow(mc.merge([cells, nuclei],['I Blue', 'I Forest'], blending='min'))
83
- fig.tight_layout()
84
- plt.show()
85
- ```
86
- ![max and min multicolor blending](https://raw.githubusercontent.com/zacswider/README_Images/main/overlay_normal_and_inverted.png)
87
-
88
- ### apply a colormap to a whole stack
89
- ```python
90
- from skimage import data
91
- from matplotlib import pyplot as plt
92
- import mergechannels as mc
93
-
94
- volume = data.cells3d()
95
- cells = volume[:, 0]
96
- nuclei = volume[:, 1]
97
- merged = mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot'])
98
- plt.imshow(merged[24]); plt.show()
99
- ```
100
- ![colorize a whole stack of images](https://raw.githubusercontent.com/zacswider/README_Images/main/merged_stacks.png)
101
-
102
- ### adjust the saturation limits when applying colormaps
103
- ``` python
104
- from skimage import data
105
- import matplotlib.pyplot as plt
106
- import mergechannels as mc
107
-
108
- cells, nuclei = data.cells3d().max(axis=0)
109
- channels = [cells, nuclei]
110
- colormaps = ['I Blue', 'I Forest']
111
- fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
112
- for ax in axes.ravel(): ax.axis('off')
113
- (a, b) = axes.ravel()
114
- a.imshow(mc.merge(channels, colormaps, blending='min'))
115
- b.imshow(
116
- mc.merge(
117
- channels,
118
- colormaps,
119
- blending='min',
120
- percentiles=[(
121
- 1, # bottom 1% of pixels set to black point
122
- 97, # top 3% of pixels set to white point
123
- )]*len(channels),
124
- ),
125
- )
126
- fig.tight_layout()
127
- plt.show()
128
- ```
129
- ![adjust saturation limits](https://raw.githubusercontent.com/zacswider/README_Images/main/adjust_sat_lims.png)
130
-
131
-
132
- ## Roadmap
133
- 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.
134
- - Add support for any numerical dtype
135
- - Add option to return any colormap as a matplotlib colormap
136
- - Add option to pass external colormaps to mergechannels
137
- - Add support for directly passing matplotlib colormaps instead of colormap names
138
- - Parallelize colormap application on large images (if it's helpful)
139
- - Add option to overlay binary or instance masks onto colorized images
140
-
141
- ## Acknowledgements
142
-
143
- 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.
144
-
145
- 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
146
-
mergechannels-0.4.0.dist-info/RECORD DELETED
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