mergechannels 0.1.2__tar.gz → 0.3.0__tar.gz

{mergechannels-0.1.2 → mergechannels-0.3.0}/Cargo.lock

@@ -1,6 +1,6 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 3
+version = 4
 
 [[package]]
 name = "autocfg"
@@ -59,12 +59,13 @@ dependencies = [
 
 [[package]]
 name = "mergechannels"
-version = "0.1.2"
+version = "0.3.0"
 dependencies = [
  "lazy_static",
  "ndarray",
  "numpy",
  "pyo3",
+ "smallvec",
 ]
 
 [[package]]
@@ -239,6 +240,12 @@ version = "2.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "357703d41365b4b27c590e3ed91eabb1b663f07c4c084095e60cbed4362dff0d"
 
+[[package]]
+name = "smallvec"
+version = "1.15.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8917285742e9f3e1683f0a9c4e6b57960b7314d0b08d30d1ecd426713ee2eee9"
+
 [[package]]
 name = "syn"
 version = "2.0.98"

{mergechannels-0.1.2 → mergechannels-0.3.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "mergechannels"
-version = "0.1.2"
+version = "0.3.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -13,3 +13,4 @@ lazy_static = "1.5.0"
 ndarray = "0.16.1"
 numpy = "0.24.0"
 pyo3 = "0.24.1"
+smallvec = "1.15.0"

{mergechannels-0.1.2 → mergechannels-0.3.0}/PKG-INFO

@@ -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-0.1.2 → mergechannels-0.3.0}/README.md

@@ -41,8 +41,7 @@ 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
@@ -52,38 +51,66 @@ 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/assets/christ_luts/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Christophe Leterrier
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+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.

mergechannels-0.3.0/assets/converted/Circus Cherry.txt

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