Merge branch 'automatic-objects-colormap' into 'main'

Automatic objects colormap

See merge request !130

qim3d/processing/operations.py

@@ -91,6 +91,9 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i
     import skimage
     import scipy
 
+    if len(np.unique(bin_vol)) > 2:
+        raise ValueError("bin_vol has to be binary volume - it must contain max 2 unique values.")
+
     # Compute distance transform of binary volume
     distance = scipy.ndimage.distance_transform_edt(bin_vol)
 

qim3d/viz/colormaps.py

@@ -86,11 +86,17 @@ def objects(
         ```
         ![colormap objects](assets/screenshots/viz-colormaps-objects.gif)
 
+    Tip:
+        It can be easily used when calling visualization functions as
+        ```python
+        qim3d.viz.slices(segmented_volume, cmap = 'objects')
+        ```
+        which automatically detects number of unique classes 
+        and creates the colormap object with defualt arguments.
+
     Tip:
         The `min_dist` parameter can be used to control the distance between neighboring colors.
         ![colormap objects mind_dist](assets/screenshots/viz-colormaps-min_dist.gif)
-
-
     """
     from skimage import color
 

qim3d/viz/explore.py

@@ -19,7 +19,6 @@ import seaborn as sns
 
 import qim3d
 
-
 def slices(
     vol: np.ndarray,
     axis: int = 0,
@@ -33,7 +32,7 @@ def slices(
     img_width: int = 2,
     show: bool = False,
     show_position: bool = True,
-    interpolation: Optional[str] = "none",
+    interpolation: Optional[str] = None,
     img_size=None,
     cbar: bool = False,
     cbar_style: str = "small",
@@ -85,6 +84,11 @@ def slices(
         img_height = img_size
         img_width = img_size
 
+    # If we pass python None to the imshow function, it will set to 
+    # default value 'antialiased'
+    if interpolation is None:
+        interpolation = 'none'
+
     # Numpy array or Torch tensor input
     if not isinstance(vol, (np.ndarray, da.core.Array)):
         raise ValueError("Data type not supported")
@@ -107,6 +111,19 @@ def slices(
             f"Invalid value for 'axis'. It should be an integer between 0 and {vol.ndim - 1}."
         )
 
+    if type(cmap) == matplotlib.colors.LinearSegmentedColormap or cmap == 'objects':
+        num_labels = len(np.unique(vol))
+
+        if cmap == 'objects':
+            cmap = qim3d.viz.colormaps.objects(num_labels)
+        # If vmin and vmax are not set like this, then in case the 
+        # number of objects changes on new slice, objects might change 
+        # colors. So when using a slider, the same object suddently 
+        # changes color (flickers), which is confusing and annoying.
+        vmin = 0
+        vmax = num_labels
+
+
     # Get total number of slices in the specified dimension
     n_total = vol.shape[axis]
 
@@ -152,9 +169,10 @@ def slices(
         vol = vol.compute()
 
     if cbar:
-        # In this case, we want the vrange to be constant across the slices, which makes them all comparable to a single cbar.
-        new_vmin = vmin if vmin else np.min(vol)
-        new_vmax = vmax if vmax else np.max(vol)
+        # In this case, we want the vrange to be constant across the 
+        # slices, which makes them all comparable to a single cbar.
+        new_vmin = vmin if vmin is not None else np.min(vol)
+        new_vmax = vmax if vmax is not None else np.max(vol)
 
     # Run through each ax of the grid
     for i, ax_row in enumerate(axs):
@@ -164,8 +182,9 @@ def slices(
                 slice_img = vol.take(slice_idxs[slice_idx], axis=axis)
 
                 if not cbar:
-                    # If vmin is higher than the highest value in the image ValueError is raised
-                    # We don't want to override the values because next slices might be okay
+                    # If vmin is higher than the highest value in the 
+                    # image ValueError is raised. We don't want to 
+                    # override the values because next slices might be okay
                     new_vmin = (
                         None
                         if (isinstance(vmin, (float, int)) and vmin > np.max(slice_img))
@@ -277,7 +296,7 @@ def slicer(
     img_height: int = 3,
     img_width: int = 3,
     show_position: bool = False,
-    interpolation: Optional[str] = "none",
+    interpolation: Optional[str] = None,
     img_size=None,
     cbar: bool = False,
     **imshow_kwargs,