mergechannels 0.1.1__cp39-cp39-musllinux_1_2_i686.whl → 0.2.0__cp39-cp39-musllinux_1_2_i686.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",
-	"merge",
+	'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:
@@ -40,19 +41,25 @@ def merge(
 			f'Expected every array to have the same dtype, got {arr_dtypes}'
 		)
 	# endregion
-	
-	match n_arrs:
-		case 1:
-			return apply_color_map(arr=arrs[0], cmap_name=colors[0])
-		case _:
-			return apply_colors_and_merge_nc(arrs, colors, blending)
-
-
-
-
-
-
-
-
-
-
+	if n_arrs == 1:
+		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:
+		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-0.1.1.dist-info → mergechannels-0.2.0.dist-info}/METADATA

@@ -1,24 +1,28 @@
 Metadata-Version: 2.4
 Name: mergechannels
-Version: 0.1.1
+Version: 0.2.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: numpy>=1.24.4
+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: >=3.8, <3.13
+Requires-Python: >=3.9, <=3.13
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 
 [![CI](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml/badge.svg)](https://github.com/zacswider/mergechannels/actions/workflows/CI.yml)
-![License](https://img.shields.io/badge/license-MIT-blue.svg)
+![PyPI - License](https://img.shields.io/pypi/l/mergechannels)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergechannels)
 ![PyPI](https://img.shields.io/pypi/v/mergechannels)
 
 # mergechannels
@@ -59,7 +63,7 @@ plt.show()
 print(colorized.shape, colorized.dtype)
 >> (512, 512, 3) uint8
 ```
-![colorize a single image](assets/readme_images/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
@@ -69,38 +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)
+
+### 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)
 
-fig, axes = plt.subplots(2, 2, figsize=(6, 6), dpi=150)
+### 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(
+(a, b) = axes.ravel()
+a.imshow(mc.merge(channels, colormaps, blending='min'))
+b.imshow(
     mc.merge(
-        [cells, nuclei],
-        ['Orange Hot', 'Cyan Hot'],  # maximum blending is the default
-    ),
-)
-d.imshow(
-    mc.merge(
-        [cells, nuclei],
-        ['I Blue', 'I Forest'],
-        blending='min',     # use minimum blending with inverted colormaps
+        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()
 ```
-![apply a different colormap to each channel](assets/readme_images/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
@@ -110,3 +142,4 @@ mergechannels is currently incredibly simple. It can apply one or more colormaps
 There are other great colormapping libraries available (e.g., [microfilm](https://github.com/guiwitz/microfilm), [cmap](https://github.com/pyapp-kit/cmap)) that are more feature-rich than this one, but which don't address my goals. My hope is that this project can fill an un-met niche and otherwise maintain full compatibility with these and similar libraries.
 
 This project incorporates a number of colormaps that were hand-crafted by Christophe Leterrier and were originally distributed here under the MIT license: https://github.com/cleterrier/ChrisLUTs
+

mergechannels-0.2.0.dist-info/RECORD

@@ -0,0 +1,12 @@
+mergechannels-0.2.0.dist-info/METADATA,sha256=t-okrnqyvIiZxuLqTlubmCkXCxKz9U43u7bhSIEiNBc,5725
+mergechannels-0.2.0.dist-info/WHEEL,sha256=HOrEN-3-tneoNRHquHb_WYiy9XtSpRH9mZcmVJb6weM,103
+mergechannels-0.2.0.dist-info/licenses/LICENSE,sha256=csvD60rgtSorbYEM3f8867qNyPCzmIXyFNj8h01Bd6c,1071
+mergechannels.libs/libgcc_s-b5472b99.so.1,sha256=wh8CpjXz9IccAyeERcB7YDEx7NH2jF-PykwOyYNeRRI,453841
+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=DxwCMBnAAJc1ZX-D4cq8HabW-sLuBQpUqOWMWXqt_84,1035
+mergechannels/mergechannels.cpython-39-i386-linux-gnu.so,sha256=72ChShcrMk59HJM2URMmpIOpdImPcm5idVL9y8VtV5Q,850505
+mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mergechannels-0.2.0.dist-info/RECORD,,

{mergechannels-0.1.1.dist-info → mergechannels-0.2.0.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_i686

{mergechannels-0.1.1.dist-info → mergechannels-0.2.0.dist-info}/licenses/LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

mergechannels-0.1.1.dist-info/RECORD

@@ -1,12 +0,0 @@
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-mergechannels-0.1.1.dist-info/WHEEL,sha256=PiAdvggALNinEet8GZKOoSW3q3OQH9VgCVJ24Bi5sfk,103
-mergechannels-0.1.1.dist-info/licenses/LICENSE,sha256=R5es2fadg5bQoUJCJlcU36nDOAG6Te2XtsfysfTT_xY,1070
-mergechannels.libs/libgcc_s-b5472b99.so.1,sha256=wh8CpjXz9IccAyeERcB7YDEx7NH2jF-PykwOyYNeRRI,453841
-mergechannels/_luts.py,sha256=DxwCMBnAAJc1ZX-D4cq8HabW-sLuBQpUqOWMWXqt_84,1035
-mergechannels/_internal.py,sha256=61RV6adhxkdqevanP06lpmONweppc6z5j8HTNkZq3uo,1267
-mergechannels/__init__.pyi,sha256=yKPkFwpgY2pMlEXj6LvwLr7f9t0bcGnu5i9eMSeSlWo,710
-mergechannels/__init__.py,sha256=Tj-1QoMYkvDi-Bew6N2kbKrOhtgo4kq61_vmnHacp3o,224
-mergechannels/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mergechannels/_blending.py,sha256=mE5Cr9wvVJRcwfymg_UUZUjdIKx2mldfLU8QJT95bVM,84
-mergechannels/mergechannels.cpython-39-i386-linux-gnu.so,sha256=nrL7npB16ITLIEMrD2zCshqEAoTpyNthj-a8HxDf5DQ,788993
-mergechannels-0.1.1.dist-info/RECORD,,