use skimage for intensity resc., accept float im

microfilm/colorify.py

@@ -5,6 +5,7 @@
 import matplotlib
 from matplotlib.colors import ListedColormap
 from skimage.color import hsv2rgb
+from skimage.exposure import rescale_intensity
 
 def cmaps_def(cmap_name, num_colors=256, flip_map=False):
     """
@@ -229,30 +230,18 @@ def rescale_image(image, rescale_type='min_max', limits=None):
         
     """
 
-    if not np.issubdtype(image.dtype, np.unsignedinteger):
-        raise Exception(f"Image should be unsigned integer but yours is {image.dtype}")   
-
-    max_of_dtype = np.iinfo(image.dtype).max
-    image = image.astype(np.float64)
-
-    if not np.any(image > 0):#blank image
-        image_rescaled = image
-    elif image.min() == image.max():#all pixels have same value
-        image_rescaled = np.ones_like(image)
-    elif rescale_type == 'min_max':
-        min_val = np.min(image)#np.min(image[image>0])
-        image_rescaled = (image-min_val)/(image.max()-min_val)
-        image_rescaled[image_rescaled<0] = 0
+    if image.min() == image.max():#all pixels have same value
+        image_rescaled = np.ones(image.shape, dtype=np.float64)
+    if rescale_type == 'min_max':
+        image_rescaled = rescale_intensity(image, in_range='image', out_range=(0,1))
     elif rescale_type == 'dtype':
-        image_rescaled = image / max_of_dtype
+        image_rescaled = rescale_intensity(image, in_range='dtype', out_range=(0,1))
     elif rescale_type == 'zero_max':
-        image_rescaled = image / image.max()
+        image_rescaled = rescale_intensity(image, in_range=(0, image.max()), out_range=(0,1))
     elif rescale_type == 'limits':
         if limits is None:
             raise Exception(f"You need to provide explicit intensity limits of the form [min, max]")
-        image_rescaled = (image - limits[0]) / (limits[1] - limits[0])
-        image_rescaled[image_rescaled<0] = 0
-        image_rescaled[image_rescaled>1] = 1
+        image_rescaled = rescale_intensity(image, in_range=(limits[0], limits[1]), out_range=(0,1))
 
     return image_rescaled