Merge pull request #29 from haesleinhuepf/fix_rgb

Fix rgb

Author: haesleinhuepf

docs/demo.ipynb

@@ -1,4 +1,4 @@
-__version__ = "0.6.4"
+__version__ = "0.7.0"
 
 from ._static_view import jupyter_displayable_output, insight
 from ._utilities import merge_rgb

docs/images/biapol.png

@@ -4,7 +4,7 @@
 
 class ImageWidget(Canvas):
     def __init__(self, image, zoom_factor:float=1.0, zoom_spline_order:int=0, colormap:str=None, display_min:float=None, display_max:float=None):
-        if not ((len(image.shape) == 2) or (len(image.shape) == 3 and image.shape[-1] == 3)):
+        if not ((len(image.shape) == 2) or (len(image.shape) in [3, 4] and image.shape[-1] == 3)):
             raise NotImplementedError("Only 2D images are supported" + str(image.shape))
         height = image.shape[0] * zoom_factor
         width = image.shape[1] * zoom_factor
@@ -43,7 +43,7 @@ def _update_image(self):
             self.put_image_data(_img_to_rgb(zoomed, colormap=self.colormap, display_min=self.display_min, display_max=self.display_max), 0, 0)
 
     def _zoom(self, data):
-        if len(data.shape) == 3:
+        if len(data.shape) > 2 and data.shape[-1] == 3:
             # handle RGB images
             return np.asarray([self._zoom(data[:,:,i]) for i in range(data.shape[2])]).swapaxes(0, 2).swapaxes(1, 0)
 
@@ -72,7 +72,7 @@ def _img_to_rgb(image,
                 display_max=None):
     from ._colormaps import _labels_lut, create_colormap
 
-    if len(image.shape) == 3 and image.shape[2] == 3:
+    if len(image.shape) > 2 and image.shape[-1] == 3:
         return image
 
     if image.dtype == bool:

docs/rgb_images.ipynb

@@ -23,7 +23,7 @@ def __init__(self,
         if slice_number is None:
             slice_number = int(image.shape[axis] / 2)
 
-        if len(self.image.shape) == 3 and self.image.shape[-1] != 3:
+        if len(self.image.shape) > 2: # and self.image.shape[-1] != 3:
             sliced_image = np.take(image, slice_number, axis=axis)
         else:
             sliced_image = image
@@ -49,6 +49,11 @@ def configuration_updated(event=None):
             if len(self.image.shape) == 3 and self.image.shape[-1] != 3:
                 self.slice_slider.layout.display = None
                 self.view.data = np.take(self.image, self.slice_slider.value, axis=axis)
+            elif len(self.image.shape) == 4 and self.image.shape[-1] == 3:
+                self.slice_slider.layout.display = None
+                self.view.data = np.take(self.image, self.slice_slider.value, axis=axis)
+            elif len(self.image.shape) == 4:
+                raise NotImplementedError("Only 2D and 3D images are supported" + str(image.shape))
             else:
                 self.view.data = self.image
                 self.slice_slider.layout.display = 'none'

stackview/__init__.py

@@ -199,6 +199,14 @@ def _imshow(image, title: str = None, labels: bool = False, min_display_intensit
     """
     import numpy as np
 
+    if len(image.shape) == 3 and image.shape[2] == 3: # RGB image
+        import matplotlib.pyplot as plt
+        plt.imshow(image, vmin=min_display_intensity, vmax=max_display_intensity,
+                   interpolation='nearest', alpha=alpha)
+        if not continue_drawing:
+            plt.show()
+        return
+
     if len(image.shape) == 3:
         image = np.asarray(image).max(axis=0)
 

stackview/_image_widget.py

@@ -90,11 +90,15 @@ def switch(images,
 
     if toggleable:
         def display_(buttons, images, colormap, display_min, display_max):
-            display_image = np.zeros([images[0].shape[0], images[0].shape[1], 3])
+            display_image = np.zeros(list(images[0].shape) + [3])
             for button, image, colormap_, display_min_, display_max_ in zip(buttons, images, colormap,
                                                                              display_min, display_max):
                 if button.value:
-                    display_image_to_add = _img_to_rgb(image, display_min=display_min_, display_max=display_max_, colormap=colormap_)
+                    if len(image.shape) == 3 and image.shape[-1] != 3:
+                        display_image_to_add = np.asarray([_img_to_rgb(i, display_min=display_min_, display_max=display_max_, colormap=colormap_) for i in image])
+                    else:
+                        display_image_to_add = _img_to_rgb(image, display_min=display_min_, display_max=display_max_, colormap=colormap_)
+                        
                     if display_image is None:
                         display_image = display_image_to_add
                     else: