mergechannels 0.1.2__cp39-cp39-musllinux_1_2_aarch64.whl → 0.3.0__cp39-cp39-musllinux_1_2_aarch64.whl

mergechannels/__init__.py

@@ -1,13 +1,13 @@
 # Import Rust functions
 from .mergechannels import (  # type: ignore
-	apply_color_map,
-	apply_colors_and_merge_nc,
+	dispatch_single_channel,
+	dispatch_multi_channel,
 )
-
 from ._internal import merge
 
+
 __all__ = [
-	'apply_color_map',
-	'apply_colors_and_merge_nc',
+	'dispatch_single_channel',
+	'dispatch_multi_channel',
 	'merge',
 ]

mergechannels/__init__.pyi

@@ -1,27 +1,30 @@
-from typing import Sequence, Literal
 
+from typing import Literal, Sequence
 import numpy as np
 
-from ._luts import COLORMAPS
-from ._blending import BLENDING_OPTIONS
+from python.mergechannels._blending import BLENDING_OPTIONS
+from python.mergechannels._luts import COLORMAPS
+
 
 def merge(
-	arrs: Sequence[np.ndarray],
-	colors: Sequence[COLORMAPS] = (),
-	blending: Literal[BLENDING_OPTIONS] = 'max',
+    arrs: np.ndarray | Sequence[np.ndarray],
+    colors: Sequence[COLORMAPS] = (),
+    blending: Literal[BLENDING_OPTIONS] = 'max',
     saturation_limits: tuple[float, float] = (0.2, 99.8),
 ) -> np.ndarray:
     ...
 
-def apply_color_map(
-    arr: np.ndarray,
-    cmap_name: COLORMAPS,
-    saturation_limits: tuple[float, float] = (0.2, 99.8),
-) -> np.ndarray: ...
+def dispatch_single_channel(
+    array_reference: np.ndarray,
+    cmap_name: str,
+    limits: tuple[float, float],
+) -> np.ndarray:
+    ...
 
-def apply_colors_and_merge_nc(
-    arrs: Sequence[np.ndarray],
-    colors: Sequence[COLORMAPS] = (),
-    blending: Literal[BLENDING_OPTIONS] = 'max',
-    saturation_limits: Sequence[tuple[float, float]] = (),
-) -> np.ndarray: ...
+def dispatch_multi_channel(
+    array_references: Sequence[np.ndarray],
+    cmap_names: Sequence[str],
+    blending: Literal[BLENDING_OPTIONS],
+    limits: Sequence[tuple[float, float]],
+) -> np.ndarray:
+    ...

mergechannels/_internal.py

@@ -3,8 +3,8 @@ from typing import Sequence
 import numpy as np
 
 from mergechannels import (
-	apply_color_map,
-	apply_colors_and_merge_nc,
+	dispatch_single_channel,
+	dispatch_multi_channel,
 )
 from ._luts import COLORMAPS
 from ._blending import BLENDING_OPTIONS
@@ -13,6 +13,7 @@ def merge(
 	arrs: Sequence[np.ndarray],
 	colors: Sequence[COLORMAPS],
 	blending: BLENDING_OPTIONS = 'max',
+    saturation_limits: tuple[float, float] = (0.011, 0.999),
 ) -> np.ndarray:
 	'''
 	apply cmaps to arrays and blend the colors
@@ -30,9 +31,9 @@ def merge(
 		raise ValueError(
 			f'Expected every array to have the same shape, got {arr_shapes}'
 		)
-	if not len(arr_shapes[0]) == 2:
+	if len(arr_shapes[0]) not in (2, 3):
 		raise ValueError(
-			f'Expected every array to be 2D, got {arr_shapes[0]}'
+			f'Expected every array to be 2D or 3D, got {arr_shapes[0]}'
 		)
 	arr_dtypes = [arr.dtype for arr in arrs]
 	if not len(set(arr_dtypes)) == 1:
@@ -40,8 +41,25 @@ def merge(
 			f'Expected every array to have the same dtype, got {arr_dtypes}'
 		)
 	# endregion
-
 	if n_arrs == 1:
-		return apply_color_map(arr=arrs[0], cmap_name=colors[0])
+		if arrs[0].dtype == 'uint8':
+			limits = (0, 255)
+		else:
+			low, high = np.percentile(arrs[0], np.array(saturation_limits) * 100)
+			limits = (low, high)
+		return dispatch_single_channel(
+			array_reference=arrs[0],
+			cmap_name=colors[0],
+			limits=limits,
+		)
 	else:
-		return apply_colors_and_merge_nc(arrs, colors, blending)
+		if all(arr.dtype == 'uint8' for arr in arrs):
+			limits = (0, 255)
+		else:
+			limits = tuple(np.percentile(arr, np.array(saturation_limits) * 100) for arr in arrs)
+		return dispatch_multi_channel(
+			array_references=arrs,
+			cmap_names=colors,
+			blending=blending,
+			limits=limits,  # type: ignore
+		)

mergechannels/_luts.py

@@ -1,81 +1,177 @@
 from typing import Literal
 
 COLORMAPS = Literal[
+	'Circus Ink Purple',
+	'Spectrum Parabolic Ramp',
+	'Pop cherry',
+	'Circus Green',
 	'Rainbow RGB',
+	'Parabolic RGB',
 	'3color-RMB',
+	'Pop magenta inverted',
 	'Red Hot',
+	'Duo Cyan',
 	'Yellow',
+	'Grays g=0.25 inverted',
 	'betterRed',
+	'Grays g=1.75',
 	'blue_orange_icb',
+	'Pop green',
 	'mpl-inferno',
 	'I Blue',
 	'BOP purple',
+	'Duo Yellow',
+	'Phase Ink Mint-Cherry',
 	'betterOrange',
 	'Blue',
 	'6_shades',
+	'Ink Cyan',
 	'OIMB3',
+	'Quartetto MYGB Blue',
+	'Ink Green',
 	'Red/Green',
 	'Turbo',
+	'Circus Ink Black',
+	'Duo Green',
 	'mpl-viridis',
+	'Grays g=0.25',
+	'Quartetto RYGB Blue',
 	'smart',
 	'Thermal',
 	'OIMB2',
+	'Pop blue inverted',
+	'Duo Intense Cherry',
+	'Phase Bold Green-Magenta',
+	'Quartetto MYGB Magenta',
+	'Pop purple inverted',
 	'glow',
 	'OPF orange',
+	'Pop cyan inverted',
 	'physics',
+	'Phase Ink Yellow-Cyan',
+	'Circus Ink Mint',
+	'Ink Wash Purple',
 	'OIMB1',
 	'betterCyan',
 	'mpl-magma',
+	'Duo Intense Green',
 	'edges',
+	'Quartetto MYGB Green',
+	'Ink Wash Cherry',
 	'OPF purple',
+	'Ink Wash Cyan',
+	'Duo Intense Purple',
 	'I Yellow',
 	'16_colors',
+	'Circus Cyan',
+	'Pop lavender inverted',
 	'sepia',
+	'Duo Intense Cyan',
+	'Grays g=1.00 inverted',
 	'ICA2',
+	'Quartetto RYGB Green',
+	'Ink Wash Green',
+	'Pop blue',
+	'Quartetto RYGB Red',
 	'I Forest',
 	'ICA3',
+	'Circus Yellow',
+	'Pop mint',
 	'BOP orange',
+	'Grays g=1.25 inverted',
 	'I Red',
 	'3color-CGY',
 	'I Green',
 	'Fire',
 	'Magenta Hot',
+	'Grays g=0.50',
 	'Orange Hot',
+	'Circus Ink Cherry',
+	'Pop purple',
+	'Ink Yellow',
 	'unionjack',
+	'Ink Wash Yellow',
 	'I Cyan',
 	'Cyan Hot',
+	'Pop mint inverted',
 	'I Magenta',
 	'Grays',
+	'Phase Green-Magenta',
 	'Cyan',
+	'Grays g=0.75',
+	'Phase Bold Ink Mint-Cherry',
+	'Grays g=1.75 inverted',
 	'phase',
 	'gem',
+	'Pop cherry inverted',
+	'Pop red',
+	'Circus Cherry',
 	'OPF fresh',
+	'Circus Ink Cyan',
 	'betterGreen',
+	'Phase Ink Green-Magenta',
 	'3color-BMR',
+	'Ink Wash Black',
+	'Pop red inverted',
+	'Duo Purple',
 	'betterBlue',
+	'Phase Bold Ink Yellow-Cyan',
+	'Quartetto RYGB Yellow',
 	'Magenta',
+	'Duo Mint',
 	'Red',
+	'Grays g=1.25',
 	'I Bordeaux',
+	'Grays g=1.50 inverted',
+	'Green Hot',
 	'glasbey',
 	'glasbey_on_dark',
 	'mpl-plasma',
+	'Ink Cherry',
+	'Ink Mint',
+	'Circus Ink Yellow',
+	'Pop cyan',
+	'Pop green inverted',
+	'Ink Purple',
 	'3color-YGC',
+	'Pop yellow',
+	'Quartetto MYGB Yellow',
+	'Duo Cherry',
 	'Green',
+	'Grays g=0.50 inverted',
+	'Circus Ink Green',
 	'ICA',
+	'Phase Mint-Cherry',
+	'Ink Black',
 	'Yellow Hot',
+	'Phase Bold Yellow-Cyan',
 	'thallium',
+	'Pop yellow inverted',
 	'Spectrum',
 	'royal',
 	'glasbey_inverted',
 	'betterYellow',
+	'Circus Purple',
+	'Grays g=2.00',
 	'HiLo',
 	'cool',
 	'Green Fire Blue',
+	'Ink Wash Mint',
+	'Grays g=0.75 inverted',
 	'BOP blue',
 	'thal',
 	'Ice',
+	'Circus Mint',
+	'Grays g=1.50',
+	'Duo Intense Mint',
 	'brgbcmyw',
+	'Phase Yellow-Cyan',
 	'I Purple',
+	'Duo Intense Yellow',
+	'Phase Bold Ink Green-Magenta',
+	'Pop magenta',
 	'3-3-2 RGB',
+	'Grays g=2.00 inverted',
 	'5_ramps',
+	'Phase Bold Mint-Cherry',
 ]

{mergechannels-0.1.2.dist-info → mergechannels-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mergechannels
-Version: 0.1.2
+Version: 0.3.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -12,7 +12,10 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: numpy>1.25.0
+Provides-Extra: nvim
 License-File: LICENSE
+Summary: Apply and merge colormaps
+Author-email: Zac Swider <zac.swider@gmail.com>
 License: MIT
 Requires-Python: >=3.9, <=3.13
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
@@ -60,8 +63,7 @@ plt.show()
 print(colorized.shape, colorized.dtype)
 >> (512, 512, 3) uint8
 ```
-![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png
-)
+![colorize a single image](https://raw.githubusercontent.com/zacswider/README_Images/main/camera_red-green.png)
 
 
 ### apply a different colormap to each channel
@@ -71,38 +73,66 @@ import matplotlib.pyplot as plt
 import mergechannels as mc
 
 cells, nuclei = data.cells3d().max(axis=0)
-cells = to_uint8(cells)     # normalize your own arrays, mergechannels doesn't currently handle this
-nuclei = to_uint8(nuclei)   # normalize your own arrays, mergechannels doesn't currently handle this
+assert cells.dtype == 'uint16' and nuclei.dtype == 'uint16'
+fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
+for ax in axes.ravel(): ax.axis('off')
+(a, b) = axes.ravel()
+a.imshow(mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot']))
+b.imshow(mc.merge([cells, nuclei],['I Blue', 'I Forest'], blending='min'))
+fig.tight_layout()
+plt.show()
+```
+![max and min multicolor blending](https://raw.githubusercontent.com/zacswider/README_Images/main/overlay_normal_and_inverted.png)
 
-fig, axes = plt.subplots(2, 2, figsize=(6, 6), dpi=150)
+### apply a colormap to a whole stack
+```python
+from skimage import data
+from matplotlib import pyplot as plt
+import mergechannels as mc
+
+volume = data.cells3d()
+cells = volume[:, 0]
+nuclei = volume[:, 1]
+merged = mc.merge([cells, nuclei],['Orange Hot', 'Cyan Hot'])
+plt.imshow(merged[24]); plt.show()
+```
+![colorize a whole stack of images](https://raw.githubusercontent.com/zacswider/README_Images/main/merged_stacks.png)
+
+### adjust the saturation limits when applying colormaps
+``` python
+from skimage import data
+import matplotlib.pyplot as plt
+import mergechannels as mc
+
+cells, nuclei = data.cells3d().max(axis=0)
+channels = [cells, nuclei]
+colormaps = ['I Blue', 'I Forest']
+fig, axes = plt.subplots(1, 2, figsize=(3, 6), dpi=300)
 for ax in axes.ravel(): ax.axis('off')
-(a, b, c, d) = axes.ravel()
-a.imshow(cells, cmap='gray')
-b.imshow(nuclei, cmap='gray')
-c.imshow(
-    mc.merge(
-        [cells, nuclei],
-        ['Orange Hot', 'Cyan Hot'],  # maximum blending is the default
-    ),
-)
-d.imshow(
+(a, b) = axes.ravel()
+a.imshow(mc.merge(channels, colormaps, blending='min'))
+b.imshow(
     mc.merge(
-        [cells, nuclei],
-        ['I Blue', 'I Forest'],
-        blending='min',     # use minimum blending with inverted colormaps
+        channels,
+        colormaps,
+        blending='min',
+        saturation_limits=(
+            0.01,  # bottom 1% of pixels set to black point
+            0.97,  # top 3% of pixels set to white point
+        ),
     ),
 )
 fig.tight_layout()
 plt.show()
 ```
-![max and min multicolor blending](https://raw.githubusercontent.com/zacswider/README_Images/main/cells_multicolor.png)
+![adjust saturation limits](https://raw.githubusercontent.com/zacswider/README_Images/main/adjust_sat_lims.png)
 
 
 ## Roadmap
-mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D 8-bit images and that's it.
+mergechannels is currently incredibly simple. It can apply one or more colormaps to one or more 2D and 3D 8-bit or 16-bit images and that's it.
 - Add support for any numerical dtype
-- Add support for 3D images
 - Add option to return any colormap as a matplotlib colormap
+- Add option to pass external colormaps to mergechannels
 - Add support for directly passing matplotlib colormaps instead of colormap names
 - Parallelize colormap application on large images (if it's helpful)
 - Add option to overlay binary or instance masks onto colorized images

mergechannels-0.3.0.dist-info/RECORD

@@ -0,0 +1,12 @@
+mergechannels-0.3.0.dist-info/METADATA,sha256=5KI3P3u9O0prtayGxavf_PooNdXYHHnyLp_fjrgW1Pw,5725
+mergechannels-0.3.0.dist-info/WHEEL,sha256=q7wQuuLF3Wf37kPvdOw6GyhvyvSy97yv-4o7K0-XKZc,106
+mergechannels-0.3.0.dist-info/licenses/LICENSE,sha256=csvD60rgtSorbYEM3f8867qNyPCzmIXyFNj8h01Bd6c,1071
+mergechannels.libs/libgcc_s-e52197c3.so.1,sha256=vkPW1Auw6CH9Bjk7frmX3hry_1H9c0tRI0Ncyg71WUI,724137
+mergechannels/__init__.py,sha256=TTNiDGOOJ6_-yR-qvX_nXph646Sz6-MEORc8ItksCRE,232
+mergechannels/__init__.pyi,sha256=tiDx6v14J0cedFdk6fzVRRyA21b4Z8eB_rtSTUjI804,749
+mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
+mergechannels/_internal.py,sha256=ZcdBUFEq8k2Ve_ASOZLTuPBaFEEPqadc9LqAGmBqOas,1773
+mergechannels/_luts.py,sha256=RswhkrCGAFtDthmVHt-Kk7lxROwS-kdsQy1EboyUUc8,3009
+mergechannels/mergechannels.cpython-39-aarch64-linux-gnu.so,sha256=RE0NnmgLsYC5mJ6VoGYiPkOtE1QMDyHAthBrrlegg8M,1116993
+mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mergechannels-0.3.0.dist-info/RECORD,,

{mergechannels-0.1.2.dist-info → mergechannels-0.3.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: maturin (1.8.3)
+Generator: maturin (1.8.6)
 Root-Is-Purelib: false
 Tag: cp39-cp39-musllinux_1_2_aarch64

mergechannels-0.1.2.dist-info/RECORD

@@ -1,12 +0,0 @@
-mergechannels-0.1.2.dist-info/METADATA,sha256=fdx3XuAlrCeScx655leoDJJEMtrZQ2-K2tX--JalIAI,4676
-mergechannels-0.1.2.dist-info/WHEEL,sha256=fSQ1RLO65S2ujgMQXIb-QvyD1St9n5vbyy6LJmLKNTk,106
-mergechannels-0.1.2.dist-info/licenses/LICENSE,sha256=csvD60rgtSorbYEM3f8867qNyPCzmIXyFNj8h01Bd6c,1071
-mergechannels.libs/libgcc_s-e52197c3.so.1,sha256=vkPW1Auw6CH9Bjk7frmX3hry_1H9c0tRI0Ncyg71WUI,724137
-mergechannels/_luts.py,sha256=DxwCMBnAAJc1ZX-D4cq8HabW-sLuBQpUqOWMWXqt_84,1035
-mergechannels/_internal.py,sha256=Abzeacre5CQOcWn9WDIVuxFdEjTLIudEWQn8EsiH3oE,1243
-mergechannels/__init__.pyi,sha256=lSMX8eip_zkzoJPJKvxvAhOsewwagoAhS9H5gXJ2Da8,711
-mergechannels/__init__.py,sha256=jy8Qd3TOQ0mm-K64snjOqjdDQiSJ3gWjOjGZrliYy6k,222
-mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
-mergechannels/mergechannels.cpython-39-aarch64-linux-gnu.so,sha256=MYGbZhRZ0iCJf8FM9wceddReuHZUT8m-EmoKxQjjppo,920313
-mergechannels-0.1.2.dist-info/RECORD,,