Update use of napari api (#184)

brainglobe · Jul 11, 2024 · 52ff499 · 52ff499
1 parent 4dbc1e6
commit 52ff499
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Showing 5 changed files with 4 additions and 19 deletions.
diff --git a/brainglobe_segmentation/layout/gui_constants.py b/brainglobe_segmentation/layout/gui_constants.py
@@ -18,7 +18,6 @@
 
 POINT_SIZE = 100
 SPLINE_SIZE = 50
-NUM_COLORS = 10
 BRUSH_SIZE = 250
 SPLINE_POINTS_DEFAULT = 1000
 SPLINE_SMOOTHING_DEFAULT = 0.1

diff --git a/brainglobe_segmentation/regions/layers.py b/brainglobe_segmentation/regions/layers.py
@@ -11,7 +11,6 @@ def add_new_label_layer(
     base_image,
     name="region",
     selected_label=1,
-    num_colors=10,
     brush_size=30,
 ):
     """
@@ -22,28 +21,24 @@ def add_new_label_layer(
     referencing)
     :param str name: Name of the new labels layer
     :param int selected_label: Label ID to be preselected
-    :param int num_colors: How many colors (labels)
     :param int brush_size: Default size of the label brush
     :return label_layer: napari labels layer
     """
     labels = np.empty_like(base_image)
-    label_layer = viewer.add_labels(labels, num_colors=num_colors, name=name)
+    label_layer = viewer.add_labels(labels, name=name)
     label_layer.n_dimensional = True
     label_layer.selected_label = selected_label
     label_layer.brush_size = brush_size
     return label_layer
 
 
-def add_new_region_layer(
-    viewer, label_layers, image_like, brush_size, num_colors
-):
+def add_new_region_layer(viewer, label_layers, image_like, brush_size):
     num = len(label_layers)
     new_label_layer = add_new_label_layer(
         viewer,
         image_like,
         name=f"region_{num}",
         brush_size=brush_size,
-        num_colors=num_colors,
     )
     new_label_layer.mode = "PAINT"
     label_layers.append(new_label_layer)
@@ -53,23 +48,19 @@ def add_existing_label_layers(
     viewer,
     label_file,
     selected_label=1,
-    num_colors=10,
     brush_size=30,
 ):
     """
     Loads an existing image as a napari labels layer
     :param viewer: Napari viewer instance
     :param label_file: Filename of the image to be loaded
     :param int selected_label: Label ID to be preselected
-    :param int num_colors: How many colors (labels)
     :param int brush_size: Default size of the label brush
     :return label_layer: napari labels layer
     """
     label_file = Path(label_file)
     labels = tifffile.imread(label_file)
-    label_layer = viewer.add_labels(
-        labels, num_colors=num_colors, name=label_file.stem
-    )
+    label_layer = viewer.add_labels(labels, name=label_file.stem)
     label_layer.selected_label = selected_label
     label_layer.brush_size = brush_size
     return label_layer

diff --git a/brainglobe_segmentation/segmentation_panels/regions.py b/brainglobe_segmentation/segmentation_panels/regions.py
@@ -7,7 +7,6 @@
     CALCULATE_VOLUMES_DEFAULT,
     COLUMN_WIDTH,
     IMAGE_FILE_EXT,
-    NUM_COLORS,
     SAVE_DEFAULT,
     SEGM_METHODS_PANEL_ALIGN,
     SUMMARIZE_VOLUMES_DEFAULT,
@@ -34,7 +33,6 @@ def __init__(
         save_default=SAVE_DEFAULT,
         brush_size=BRUSH_SIZE,
         image_file_extension=IMAGE_FILE_EXT,
-        num_colors=NUM_COLORS,
     ):
         super(RegionSeg, self).__init__()
         self.parent = parent
@@ -46,7 +44,6 @@ def __init__(
         # Brushes / ...
         self.brush_size_default = BRUSH_SIZE  # Keep track of default
         self.brush_size = brush_size  # Initialise
-        self.num_colors = num_colors
 
         # File formats
         self.image_file_extension = image_file_extension
@@ -168,7 +165,6 @@ def add_new_region(self):
             self.parent.label_layers,
             self.parent.base_layer.data,
             self.brush_size,
-            self.num_colors,
         )
 
     def add_region_from_existing_layer(self, override=False):

diff --git a/brainglobe_segmentation/tracks/analysis.py b/brainglobe_segmentation/tracks/analysis.py
@@ -45,7 +45,7 @@ def track_analysis(
             viewer.add_points(
                 spline,
                 size=napari_spline_size,
-                edge_color="cyan",
+                border_color="cyan",
                 face_color="cyan",
                 blending="additive",
                 opacity=0.7,

diff --git a/tests/tests/test_integration/test_gui/test_gui.py b/tests/tests/test_integration/test_gui/test_gui.py
@@ -75,7 +75,6 @@ def check_defaults(widget):
     assert widget.track_seg.spline_size == int(50 / widget.mean_voxel_size)
     assert widget.track_seg.track_file_extension == ".points"
     assert widget.region_seg.image_file_extension == ".tiff"
-    assert widget.region_seg.num_colors == 10
     assert widget.region_seg.brush_size == int(250 / widget.mean_voxel_size)
     assert widget.track_seg.spline_points_default == 1000
     assert widget.track_seg.spline_smoothing_default == 0.1