Update yaml files - pin napari < 0.5 (#694)

* Update environment_cpu.yaml

* Update environment_gpu.yaml

Author: anwai98

environment_cpu.yaml

@@ -4,10 +4,10 @@ channels:
     - conda-forge
 dependencies:
     - cpuonly
-    - nifty=1.2.1=*_4
+    - nifty =1.2.1=*_4
     - imagecodecs
     - magicgui
-    - napari
+    - napari <0.5
     - pip
     - pooch
     - pyqt

environment_gpu.yaml

@@ -5,9 +5,9 @@ channels:
     - conda-forge
 dependencies:
     - imagecodecs
-    - nifty=1.2.1=*_4
+    - nifty =1.2.1=*_4
     - magicgui
-    - napari
+    - napari <0.5
     - pip
     - pooch
     - pyqt

micro_sam/sam_annotator/_annotator.py

@@ -29,15 +29,15 @@ def _create_layers(self):
         self._point_prompt_layer = self._viewer.add_points(
             name="point_prompts",
             property_choices={"label": self._point_labels},
-            border_color="label",
-            border_color_cycle=vutil.LABEL_COLOR_CYCLE,
+            edge_color="label",
+            edge_color_cycle=vutil.LABEL_COLOR_CYCLE,
             symbol="o",
             face_color="transparent",
-            border_width=0.5,
+            edge_width=0.5,
             size=12,
             ndim=self._ndim,
         )
-        self._point_prompt_layer.border_color_mode = "cycle"
+        self._point_prompt_layer.edge_color_mode = "cycle"
 
         # Add the shape layer for box and other shape prompts.
         self._viewer.add_shapes(

micro_sam/sam_annotator/annotator_tracking.py

@@ -109,16 +109,16 @@ def _create_layers(self):
                 "state": self._track_state_labels,
                 "track_id": ["1"],  # we use string to avoid pandas warning
             },
-            border_color="label",
-            border_color_cycle=vutil.LABEL_COLOR_CYCLE,
+            edge_color="label",
+            edge_color_cycle=vutil.LABEL_COLOR_CYCLE,
             symbol="o",
             face_color="state",
             face_color_cycle=STATE_COLOR_CYCLE,
-            border_width=0.4,
+            edge_width=0.4,
             size=12,
             ndim=self._ndim,
         )
-        self._point_prompt_layer.border_color_mode = "cycle"
+        self._point_prompt_layer.edge_color_mode = "cycle"
         self._point_prompt_layer.face_color_mode = "cycle"
 
         # Using the box layer to set divisions currently doesn't work.
@@ -132,9 +132,9 @@ def _create_layers(self):
             edge_color="green",
             property_choices={"track_id": ["1"]},
             # property_choces={"track_id": ["1"], "state": self._track_state_labels},
-            # border_color_cycle=STATE_COLOR_CYCLE,
+            # edge_color_cycle=STATE_COLOR_CYCLE,
         )
-        # self._box_prompt_layer.border_color_mode = "cycle"
+        # self._box_prompt_layer.edge_color_mode = "cycle"
 
         # Add the label layers for the current object, the automatic segmentation and the committed segmentation.
         dummy_data = np.zeros(self._shape, dtype="uint32")

test/test_prompt_generators.py

@@ -34,15 +34,15 @@ def _debug(self, mask, coordinates=None, labels=None, box=None, deformed_mask=No
                 data=coordinates,
                 name="prompts",
                 properties={"label": labels},
-                border_color="label",
-                border_color_cycle=["#00FF00", "#FF0000"],
+                edge_color="label",
+                edge_color_cycle=["#00FF00", "#FF0000"],
                 symbol="o",
                 face_color="transparent",
-                border_width=0.5,
+                edge_width=0.5,
                 size=5,
                 ndim=2
             )  # this function helps to view the (colored) background/foreground points
-            prompts.border_color_mode = "cycle"
+            prompts.edge_color_mode = "cycle"
 
         if deformed_mask is not None:
             v.add_labels(deformed_mask.astype("uint8"), name="deformed mask / prediction")