Merge pull request #15 from LorenzLamm/rainbow_distances

readd all-storing option and fix issue
CellArchLab · Sep 19, 2024 · fc75799 · fc75799
2 parents fe91737 + 37bef19
commit fc75799
Showing 1 changed file with 27 additions and 20 deletions.
diff --git a/src/lasso_3d/_widget.py b/src/lasso_3d/_widget.py
@@ -55,7 +55,12 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self._layer_selection_widget_connected_components = magicgui(
             self._connected_components,
             mask_layer={"choices": self._get_valid_image_layers},
-            remove_small_objects_size={"value": 100},
+            remove_small_objects_size={
+                "value": 100,
+                "widget_type": "SpinBox",
+                "min": 0,
+                "max": 100000,
+            },
             call_button="Connected Components",
         )
         self.connected_components_box.addWidget(
@@ -87,20 +92,20 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         )
         self.store_tomogram_box.addWidget(self.store_tomogram_widget.native)
 
-        # self.store_all_components_box = QHBoxLayout()
-        # self.store_all_components_widget = magicgui(
-        #     self._store_all_components,
-        #     image_layer={"choices": self._get_valid_image_layers},
-        #     foldername={
-        #         "widget_type": "FileEdit",
-        #         "mode": "d",
-        #         "label": "Folder Path",
-        #     },
-        #     call_button="Store All Components",
-        # )
-        # self.store_all_components_box.addWidget(
-        #     self.store_all_components_widget.native
-        # )
+        self.store_all_components_box = QHBoxLayout()
+        self.store_all_components_widget = magicgui(
+            self._store_all_components,
+            image_layer={"choices": self._get_valid_image_layers},
+            foldername={
+                "widget_type": "FileEdit",
+                "mode": "d",
+                "label": "Folder Path",
+            },
+            call_button="Store All Components",
+        )
+        self.store_all_components_box.addWidget(
+            self.store_all_components_widget.native
+        )
 
         self.color_distances_box = QHBoxLayout()
         color_point = QPushButton("Points")
@@ -126,7 +131,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.layout().addLayout(self.connected_components_box)
         self.layout().addLayout(self.display_connected_components_box)
         self.layout().addLayout(self.store_tomogram_box)
-        # self.layout().addLayout(self.store_all_components_box)
+        self.layout().addLayout(self.store_all_components_box)
         self.layout().addLayout(self.color_distances_box)
 
         viewer.layers.events.inserted.connect(self._on_layer_change)
@@ -154,9 +159,9 @@ def _on_layer_change(self, event):
         self.store_tomogram_widget.image_layer.choices = (
             self._get_valid_labels_layers(None)
         )
-        # self.store_all_components_widget.image_layer.choices = (
-        #     self._get_valid_labels_layers(None)
-        # )
+        self.store_all_components_widget.image_layer.choices = (
+            self._get_valid_labels_layers(None)
+        )
         self.color_distances_widget.image_layer.choices = (
             self._get_valid_labels_layers(None)
         )
@@ -443,13 +448,15 @@ def _store_all_components(
         image_layer: napari.layers.Image,
         foldername: str,
     ):
+        print("Storing all components")
         if image_layer is None:
             return
         out_data = image_layer.data
         for i in range(1, np.max(out_data) + 1):
+            print("Storing component", i)
             out_data_i = (out_data == i) * 1.0
             out_data_i = np.transpose(out_data_i, (2, 1, 0))
-            store_tomogram(foldername + f"/component_{i}.mrc", out_data_i)
+            store_tomogram(str(foldername) + f"/component_{i}.mrc", out_data_i)
 
     def _get_valid_points_layers(
         self, combo_box