Implement simple converter func, releaving dependency on skimage (#15)

* Implement simple converter func, releaving dependency on skimage

* enable py39

Author: almarklein

.github/workflows/ci.yml

@@ -24,9 +24,9 @@ jobs:
           - name: Linux py38
             os: ubuntu-latest
             pyversion: '3.8'
-          # - name: Linux py39
-          #   os: ubuntu-latest
-          #   pyversion: '3.9'
+          - name: Linux py39
+            os: ubuntu-latest
+            pyversion: '3.9'
           - name: MacOS py38
             os: macos-latest
             pyversion: '3.8'

dash_slicer/utils.py

@@ -3,12 +3,24 @@
 
 import numpy as np
 import PIL.Image
-import skimage
+
+
+def img_as_ubyte(img):
+    """Quick-n-dirty conversion function.
+    We'll have explicit contrast limits eventually.
+    """
+    if img.dtype == np.uint8:
+        return img
+    else:
+        img = img.astype(np.float32)
+        mi, ma = img.min(), img.max()
+        img = (img - mi) * (255 / (ma - mi)) + 0.5
+        return img.astype(np.uint8)
 
 
 def img_array_to_uri(img_array, new_size=None):
     """Convert the given image (numpy array) into a base64-encoded PNG."""
-    img_array = skimage.util.img_as_ubyte(img_array)
+    img_array = img_as_ubyte(img_array)
     # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
     # from plotly.express._imshow import _array_to_b64str
     # return _array_to_b64str(img_array)

requirements.txt

@@ -3,4 +3,3 @@ numpy
 plotly
 dash
 dash_core_components
-scikit-image

tests/test_utils.py

@@ -1,9 +1,31 @@
-from dash_slicer.utils import img_array_to_uri, get_thumbnail_size, shape3d_to_size2d
+from dash_slicer.utils import (
+    img_as_ubyte,
+    img_array_to_uri,
+    get_thumbnail_size,
+    shape3d_to_size2d,
+)
 
 import numpy as np
 from pytest import raises
 
 
+def test_img_as_ubyte():
+
+    im = np.zeros((100, 100), np.float32)
+    im[0, 0] = 100
+
+    # Anything but uint8 is stretched to min-max
+    im2 = img_as_ubyte(im)
+    assert im2.dtype == np.uint8
+    assert im2.min() == 0 and im2.max() == 255
+
+    # Uint- stays where it is
+    im2[0, 0] = 100
+    im3 = img_as_ubyte(im2)
+    assert im3.dtype == np.uint8
+    assert im3.min() == 0 and im3.max() == 100
+
+
 def test_img_array_to_uri():
 
     im = np.random.uniform(0, 255, (100, 100)).astype(np.uint8)