Layered Surface Segmentation Feature

In this branch, the feature for demostrating Layered Surface Segmentation based on the slgbuilder package, is implemented. The feature is divided into a functional file, visualisation file and a gui file, all named Layers2d.

qim3d/gui/layers2d.py

@@ -23,9 +23,11 @@ class Session:
         self.min_margin = 10
         self.n_layers = 4
         self.is_inverted = False
-        
+
+        self.l2d_obj = None
+
         #TODO: Add here the slice positions
-        #TODO: Add here the l2d_obj ? 
+
 
 class Interface:
     def __init__(self):
@@ -68,14 +70,23 @@ class Interface:
 
         return session
 
-    def update_session_slices(self, session, x_pos, y_pos, z_pos):
-        #TODO: Add here the update of the slices
-        return session
+    #TODO: Add here the update of the slices
+    # def update_session_slices(self, session, x_pos, y_pos, z_pos):
+    #     return session
     
-    def update_session_parameters(self, session, delta, min_margin, n_layers, is_inverted):
+    def update_session_delta(self, session, delta):
         session.delta = delta
+        return session
+    
+    def update_session_min_margin(self, session, min_margin):
         session.min_margin = min_margin
+        return session
+    
+    def update_session_n_layers(self, session, n_layers):
         session.n_layers = n_layers
+        return session
+    
+    def update_session_is_inverted(self, session, is_inverted):
         session.is_inverted = is_inverted
         return session
     
@@ -95,6 +106,14 @@ class Interface:
         else:
             raise ValueError("Invalid path")
 
+    def set_relaunch_button(self):
+        # Sets the button to relaunch
+        return gr.update(
+            elem_classes="btn btn-run",
+            value=f"Relaunch",
+            interactive=True,
+        )
+
     def set_spinner(self, message):
         # spinner icon/shows the user something is happeing
         return gr.update(
@@ -103,13 +122,6 @@ class Interface:
             interactive=False,
         )
 
-    def set_relaunch_button(self):
-        return gr.update(
-            elem_classes="btn btn-run",
-            value=f"Relaunch",
-            interactive=True,
-        )
-
     def create_interface(self):
         with gr.Blocks(css=self.css_path) as gradio_interface:
             gr.Markdown(f"# {self.title}")
@@ -191,12 +203,15 @@ class Interface:
                             visible=True,
                             elem_classes="rounded",
                         )
-            # Session
+            
             session = gr.State([])
+            
             pipeline = Pipeline()
+            
             inputs = [base_path, explorer, delta, min_margin, n_layers, is_inverted]
             spinner_loading = gr.Text("Loading data...", visible=False)
             spinner_running = gr.Text("Running pipeline...", visible=False)
+            spinner_updating = gr.Text("Updating layers...", visible=False)
 
             # fmt: off
             reload_base_path.click(fn=self.update_explorer,inputs=base_path, outputs=explorer)
@@ -213,9 +228,35 @@ class Interface:
             
             #TODO: Add here the update of the slices
             
-            #TODO: Add here the update of the parameters
+            delta.change(
+                fn=self.update_session_delta, inputs=[session, delta], outputs=session, show_progress=False).success(
+                fn=self.set_spinner, inputs=spinner_updating, outputs=btn_run).then(
+                fn=pipeline.process_l2d, inputs=session, outputs=session).then(
+                fn=pipeline.plot_l2d_output, inputs=session, outputs=output_plot).then(
+                fn=self.set_relaunch_button, inputs=[], outputs=btn_run)
+            
+            min_margin.change(
+                fn=self.update_session_min_margin, inputs=[session, min_margin], outputs=session, show_progress=False).success(
+                fn=self.set_spinner, inputs=spinner_updating, outputs=btn_run).then(
+                fn=pipeline.process_l2d, inputs=session, outputs=session).then(
+                fn=pipeline.plot_l2d_output, inputs=session, outputs=output_plot).then(
+                fn=self.set_relaunch_button, inputs=[], outputs=btn_run)
+            
+            n_layers.change(
+                fn=self.update_session_n_layers, inputs=[session, n_layers], outputs=session, show_progress=False).success(
+                fn=self.set_spinner, inputs=spinner_updating, outputs=btn_run).then(
+                fn=pipeline.process_l2d, inputs=session, outputs=session).then(
+                fn=pipeline.plot_l2d_output, inputs=session, outputs=output_plot).then(
+                fn=self.set_relaunch_button, inputs=[], outputs=btn_run)
             
+            is_inverted.change(
+                fn=self.update_session_is_inverted, inputs=[session, is_inverted], outputs=session, show_progress=False).success(
+                fn=self.set_spinner, inputs=spinner_updating, outputs=btn_run).then(
+                fn=pipeline.process_l2d, inputs=session, outputs=session).then(
+                fn=pipeline.plot_l2d_output, inputs=session, outputs=output_plot).then(
+                fn=self.set_relaunch_button, inputs=[], outputs=btn_run)            
             # fmt: on
+            
         return gradio_interface
 
 
@@ -223,7 +264,44 @@ class Pipeline:
     def __init__(self):
         self.figsize = (8, 8)
 
+    def load_data(self, session):
+        try:
+            session.data = load(
+                session.file_path,
+                virtual_stack=session.virtual_stack,
+                dataset_name=session.dataset_name,
+            )
+        except Exception as error_message:
+            raise ValueError(
+                f"Failed to load the image: {error_message}"
+            ) from error_message
+
+        return session
+
+    def process_l2d(self, session):
+        data = session.data
+        # TODO Add here some checks to be user data is 2D
+
+        if session.l2d_obj is None:
+            l2d_obj = l2d.Layers2d()
+        else:
+            l2d_obj = session.l2d_obj
+            
+        l2d_obj.prepare_update(
+            data=data,
+            is_inverted=session.is_inverted,
+            delta=session.delta,
+            min_margin=session.min_margin,
+            n_layers=session.n_layers,
+        )
+        l2d_obj.update()
+
+        session.l2d_obj = l2d_obj
+
+        return session
+    
     def plot_input_img(self, session, cmap="Greys_r"):
+        
         plt.close()
         fig, ax = plt.subplots(figsize=self.figsize)
 
@@ -237,7 +315,7 @@ class Pipeline:
 
     def plot_l2d_output(self, session):
         l2d_obj = session.l2d_obj
-        fig, ax = qim3d.viz.layers2d.create_plot_of_2d_array(l2d_obj.get_data())
+        fig, ax = qim3d.viz.layers2d.create_plot_of_2d_array(l2d_obj.get_data_not_inverted())
 
         data_lines = []
         for i in range(len(l2d_obj.get_segmentation_lines())):
@@ -252,38 +330,7 @@ class Pipeline:
         fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
 
         return fig
-
-    def process_l2d(self, session):
-        data = session.data
-        # TODO Add here some checks to be user data is 2D
-
-        l2d_obj = l2d.Layers2d()
-        l2d_obj.prepare_update(
-            data=data,
-            is_inverted=session.is_inverted,
-            delta=session.delta,
-            min_margin=session.min_margin,
-            n_layers=session.n_layers,
-        )
-        l2d_obj.update()
-
-        session.l2d_obj = l2d_obj
-
-        return session
-
-    def load_data(self, session):
-        try:
-            session.data = load(
-                session.file_path,
-                virtual_stack=session.virtual_stack,
-                dataset_name=session.dataset_name,
-            )
-        except Exception as error_message:
-            raise ValueError(
-                f"Failed to load the image: {error_message}"
-            ) from error_message
-
-        return session
+    
 
 def run_interface(host = "0.0.0.0"):
     gradio_interface = Interface().create_interface()