Improvements to create_overlay_data (#39)

* add option to reset overlay data, plus some fixes

* add tests for create_overlay_data

* Update reamde

Author: almarklein

README.md

@@ -106,10 +106,10 @@ up the slicer (and which must be present in the layout) are:
 
 **method `VolumeSlicer.create_overlay_data(mask, color=None)`**
 
-Given a 3D mask array and an index, create an object that
-can be used as output for `slicer.overlay_data`. The color
-can be a hex color or an rgb/rgba tuple. Alternatively, color
-can be a list of such colors, defining a colormap.
+Given a 3D mask array, create an object that can be used as
+output for `slicer.overlay_data`. Set mask to `None` to clear the mask.
+The color can be a hex color or an rgb/rgba tuple. Alternatively,
+color can be a list of such colors, defining a colormap.
 
 **property `VolumeSlicer.axis`** (`int`): The axis to slice.
 

dash_slicer/slicer.py

@@ -289,15 +289,19 @@ def overlay_data(self):
         return self._overlay_data
 
     def create_overlay_data(self, mask, color=None):
-        """Given a 3D mask array and an index, create an object that
-        can be used as output for `slicer.overlay_data`. The color
-        can be a hex color or an rgb/rgba tuple. Alternatively, color
-        can be a list of such colors, defining a colormap.
+        """Given a 3D mask array, create an object that can be used as
+        output for `slicer.overlay_data`. Set mask to `None` to clear the mask.
+        The color can be a hex color or an rgb/rgba tuple. Alternatively,
+        color can be a list of such colors, defining a colormap.
         """
         # Check the mask
-        if mask.dtype not in (np.bool, np.uint8):
+        if mask is None:
+            return [None for index in range(self.nslices)]  # A reset
+        elif not isinstance(mask, np.ndarray):
+            raise TypeError("Mask must be an ndarray or None.")
+        elif mask.dtype not in (np.bool, np.uint8):
             raise ValueError(f"Mask must have bool or uint8 dtype, not {mask.dtype}.")
-        if mask.shape != self._volume.shape:
+        elif mask.shape != self._volume.shape:
             raise ValueError(
                 f"Overlay must has shape {mask.shape}, but expected {self._volume.shape}"
             )
@@ -306,6 +310,8 @@ def create_overlay_data(self, mask, color=None):
         # Create a colormap (list) from the given color(s)
         if color is None:
             colormap = discrete_colors[3:]
+        elif isinstance(color, str):
+            colormap = [color]
         elif isinstance(color, (tuple, list)) and all(
             isinstance(x, (int, float)) for x in color
         ):

tests/test_slicer.py

@@ -63,3 +63,43 @@ def test_scene_id_and_context_id():
 
     # Context id's must be unique
     assert s1._context_id != s2._context_id and s1._context_id != s3._context_id
+
+
+def test_create_overlay_data():
+
+    app = dash.Dash()
+    vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
+    s = VolumeSlicer(app, vol)
+
+    # Bool overlay
+    overlay = s.create_overlay_data(vol > 10)
+    assert isinstance(overlay, list) and len(overlay) == s.nslices
+    assert all(isinstance(x, str) for x in overlay)
+
+    # Bool overlay - with color
+    overlay = s.create_overlay_data(vol > 10, "#ff0000")
+    assert isinstance(overlay, list) and len(overlay) == s.nslices
+    assert all(isinstance(x, str) for x in overlay)
+
+    # Uint8 overlay - with colormap
+    overlay = s.create_overlay_data(vol.astype(np.uint8), ["#ff0000", "#00ff00"])
+    assert isinstance(overlay, list) and len(overlay) == s.nslices
+    assert all(isinstance(x, str) for x in overlay)
+
+    # Reset
+    overlay = s.create_overlay_data(None)
+    assert isinstance(overlay, list) and len(overlay) == s.nslices
+    assert all(x is None for x in overlay)
+
+    # Reset by zero mask
+    overlay = s.create_overlay_data(vol > 300)
+    assert isinstance(overlay, list) and len(overlay) == s.nslices
+    assert all(x is None for x in overlay)
+
+    # Wrong
+    with raises(TypeError):
+        s.create_overlay_data("not a valid mask")
+    with raises(ValueError):
+        s.create_overlay_data(vol.astype(np.float32))  # wrong dtype
+    with raises(ValueError):
+        s.create_overlay_data(vol[:-1])  # wrong shape