New Layered Surface Segmentation

All documentation is here https://www.notion.so/qim-dtu/layered_surface_segmentation-704a14494e4a437a9f3311e06eea8e69

qim3d/gui/layers2d.py

@@ -27,7 +27,7 @@ from .interface import BaseInterface
 # from qim3d.processing import layers2d as l2d
 from qim3d.processing import overlay_rgb_images, segment_layers, get_lines
 from qim3d.io import load
-from qim3d.viz.layers2d import image_with_lines, image_with_overlay
+from qim3d.viz.layers2d import image_with_lines
 
 #TODO figure out how not update anything and go through processing when there are no data loaded
 # So user could play with the widgets but it doesnt throw error
@@ -453,8 +453,8 @@ class Interface(BaseInterface):
                 if self.is_transposed(slicing_axis, segmenting_axis):
                     seg = np.rot90(seg, k = 3)
                 # slice = 255 * (slice/np.max(slice))
-                return image_with_overlay(np.repeat(slice[..., None], 3, -1), seg, alpha) 
-                # return overlay_rgb_images(np.repeat(slice[..., None], 3, -1), seg, alpha)
+                # return image_with_overlay(np.repeat(slice[..., None], 3, -1), seg, alpha) 
+                return overlay_rgb_images(slice, seg, alpha)
             else:
                 lines = get_lines(seg)
                 if self.is_transposed(slicing_axis, segmenting_axis):