Refactor toggle label

Author: constantinpape

examples/image_series_annotator_app.py

@@ -11,7 +11,7 @@
 
 from magicgui import magicgui
 from micro_sam.segment_from_prompts import segment_from_points
-from micro_sam.sam_annotator.util import create_prompt_menu, prompt_layer_to_points
+from micro_sam.sam_annotator.util import create_prompt_menu, prompt_layer_to_points, toggle_label
 from napari import Viewer
 
 
@@ -64,15 +64,8 @@ def image_series_annotator(image_paths, embedding_save_path, output_folder):
 
     # toggle the points between positive / negative
     @v.bind_key("t")
-    def toggle_label(event=None):
-        # get the currently selected label
-        current_properties = prompts.current_properties
-        current_label = current_properties["label"][0]
-        new_label = "negative" if current_label == "positive" else "positive"
-        current_properties["label"] = np.array([new_label])
-        prompts.current_properties = current_properties
-        prompts.refresh()
-        prompts.refresh_colors()
+    def _toggle_label(event=None):
+        toggle_label(prompts)
 
     # bind the segmentation to a key 's'
     @v.bind_key("s")

examples/sam_annotator_2d.py

@@ -13,10 +13,11 @@ def livecell_annotator():
 
 def main():
     # 2d annotator for livecell data
-    # livecell_annotator()
+    livecell_annotator()
 
+    # TODO
     # 2d annotator for cell tracking challenge hela data
-    hela_2d_annotator()
+    # hela_2d_annotator()
 
 
 if __name__ == "__main__":

micro_sam/sam_annotator/annotator_2d.py

@@ -8,7 +8,9 @@
 from ..visualization import project_embeddings_for_visualization
 from ..segment_instances import segment_from_embeddings
 from ..segment_from_prompts import segment_from_points
-from .util import commit_segmentation_widget, create_prompt_menu, prompt_layer_to_points, LABEL_COLOR_CYCLE
+from .util import (
+    commit_segmentation_widget, create_prompt_menu, prompt_layer_to_points, toggle_label, LABEL_COLOR_CYCLE
+)
 
 
 @magicgui(call_button="Segment Object [S]")
@@ -96,15 +98,8 @@ def _commit(v):
         commit_segmentation_widget(v)
 
     @v.bind_key("t")
-    def toggle_label(event=None):
-        # get the currently selected label
-        current_properties = prompts.current_properties
-        current_label = current_properties["label"][0]
-        new_label = "negative" if current_label == "positive" else "positive"
-        current_properties["label"] = np.array([new_label])
-        prompts.current_properties = current_properties
-        prompts.refresh()
-        prompts.refresh_colors()
+    def _toggle_label(event=None):
+        toggle_label(prompts)
 
     @v.bind_key("Shift-C")
     def clear_prompts(v):

micro_sam/sam_annotator/annotator_3d.py

@@ -10,7 +10,8 @@
 from ..visualization import project_embeddings_for_visualization
 from .util import (
     commit_segmentation_widget, create_prompt_menu,
-    prompt_layer_to_points, segment_slices_with_prompts, LABEL_COLOR_CYCLE
+    prompt_layer_to_points, segment_slices_with_prompts,
+    toggle_label, LABEL_COLOR_CYCLE
 )
 
 
@@ -228,15 +229,8 @@ def _commit(v):
         commit_segmentation_widget(v)
 
     @v.bind_key("t")
-    def toggle_label(event=None):
-        # get the currently selected label
-        current_properties = prompts.current_properties
-        current_label = current_properties["label"][0]
-        new_label = "negative" if current_label == "positive" else "positive"
-        current_properties["label"] = np.array([new_label])
-        prompts.current_properties = current_properties
-        prompts.refresh()
-        prompts.refresh_colors()
+    def _toggle_label(event=None):
+        toggle_label(prompts)
 
     @v.bind_key("Shift-C")
     def clear_prompts(v):

micro_sam/sam_annotator/annotator_tracking.py

@@ -12,7 +12,8 @@
 from .. import util
 from ..segment_from_prompts import segment_from_mask, segment_from_points
 from .util import (
-    create_prompt_menu, prompt_layer_to_points, prompt_layer_to_state, segment_slices_with_prompts, LABEL_COLOR_CYCLE
+    create_prompt_menu, prompt_layer_to_points, prompt_layer_to_state,
+    segment_slices_with_prompts, toggle_label, LABEL_COLOR_CYCLE
 )
 from ..visualization import project_embeddings_for_visualization
 
@@ -58,7 +59,7 @@ def _shift_object(mask, motion_model):
     return mask_shifted
 
 
-# TODO handle divison annotations + division classifier
+# TODO division classifier
 def _track_from_prompts(
     prompt_layer, seg, predictor, slices, image_embeddings,
     stop_upper, threshold, projection,
@@ -223,7 +224,11 @@ def annotator_tracking(raw, embedding_path=None, show_embeddings=False):
     prompts = v.add_points(
         data=[[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]],  # FIXME workaround
         name="prompts",
-        properties={"label": labels, "state": state_labels},
+        properties={
+            "label": labels,
+            "state": state_labels,
+            # "track_id": [1, 1],
+        },
         edge_color="label",
         edge_color_cycle=LABEL_COLOR_CYCLE,
         symbol="o",
@@ -264,15 +269,8 @@ def _track_object(v):
         track_objet_widget(v)
 
     @v.bind_key("t")
-    def toggle_label(event=None):
-        # get the currently selected label
-        current_properties = prompts.current_properties
-        current_label = current_properties["label"][0]
-        new_label = "negative" if current_label == "positive" else "positive"
-        current_properties["label"] = np.array([new_label])
-        prompts.current_properties = current_properties
-        prompts.refresh()
-        prompts.refresh_colors()
+    def _toggle_label(event=None):
+        toggle_label(prompts)
 
     @v.bind_key("Shift-C")
     def clear_prompts(v):

micro_sam/sam_annotator/util.py

@@ -139,3 +139,14 @@ def _update_progress():
         _update_progress()
 
     return seg, slices, stop_lower, stop_upper
+
+
+def toggle_label(prompts):
+    # get the currently selected label
+    current_properties = prompts.current_properties
+    current_label = current_properties["label"][0]
+    new_label = "negative" if current_label == "positive" else "positive"
+    current_properties["label"] = np.array([new_label])
+    prompts.current_properties = current_properties
+    prompts.refresh()
+    prompts.refresh_colors()