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

@@ -5,6 +5,7 @@ from qim3d.io import DataLoader
 from qim3d.io.logger import log
 from qim3d.process import layers2d as l2d
 from qim3d.io import load
+import qim3d.viz
 
 # matplotlib.use("Agg")
 import matplotlib.pyplot as plt
@@ -18,6 +19,9 @@ class Session:
         self.base_path = None
         self.explorer = None
         self.file_path = None
+        self.delta = 1
+        self.min_margin = 10
+        self.n_layers = 4
 
 
 class Interface:
@@ -46,6 +50,9 @@ class Interface:
         session = Session()
         session.base_path = args[0]
         session.explorer = args[1]
+        session.delta = args[2]
+        session.min_margin = args[3]
+        session.n_layers = args[4]
 
         # Get the file path from the explorer or base path
         if session.base_path and os.path.isfile(session.base_path):
@@ -72,13 +79,26 @@ class Interface:
         else:
             raise ValueError("Invalid path")
 
+    def set_spinner(self, message):
+        return gr.update(
+            elem_classes="btn btn-spinner",
+            value=f"{message}",
+            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}")
 
             with gr.Row():
                 with gr.Column(scale=1, min_width=320):
-                    gr.Markdown("### File selection")
                     with gr.Row():
                         with gr.Column(scale=99, min_width=128):
                             base_path = gr.Textbox(
@@ -102,36 +122,65 @@ class Interface:
                         elem_classes="h-256 hide-overflow",
                     )
 
-                    # Run button
+                    # TODO Add description for parameters in the interface
+                    with gr.Row():
+                        delta = gr.Slider(
+                            minimum=0.5,
+                            maximum=1.0,
+                            value=1,
+                            step=0.01,
+                            label="Delta value",
+                        )
+                    with gr.Row():
+                        min_margin = gr.Slider(
+                            minimum=1, maximum=50, value=10, step=1, label="Min margin"
+                        )
                     with gr.Row():
-                        btn_run = gr.Button("Run Layers2D", elem_classes="btn btn-run")
+                        n_layers = gr.Slider(
+                            minimum=1,
+                            maximum=8,
+                            value=4,
+                            step=1,
+                            label="Number of layers",
+                        )
+                    with gr.Row():
+                        btn_run = gr.Button(
+                            "Run Layers2D", elem_classes="btn btn-html btn-run"
+                        )
 
-                with gr.Column(scale=4):
+                with gr.Column(scale=2):
                     with gr.Row():
                         input_plot = gr.Plot(
                             show_label=True,
                             label="Source image",
                             visible=True,
-                            elem_classes="plot",
+                            elem_classes="rounded",
                         )
                         output_plot = gr.Plot(
                             show_label=True,
                             label="Detected layers",
                             visible=True,
-                            elem_classes="plot",
+                            elem_classes="rounded",
                         )
             # Session
             session = gr.State([])
             pipeline = Pipeline()
-            inputs = [base_path, explorer]
+            inputs = [base_path, explorer, delta, min_margin, n_layers]
+            spinner_loading = gr.Text("Loading data...", visible=False)
+            spinner_running = gr.Text("Running pipeline...", visible=False)
 
             # fmt: off
             reload_base_path.click(fn=self.update_explorer,inputs=base_path, outputs=explorer)
 
             btn_run.click(
                 fn=self.start_session, inputs=inputs, outputs=session).then(
+                fn=self.set_spinner, inputs=spinner_loading, outputs=btn_run).then(
                 fn=pipeline.load_data, inputs=session, outputs=session).then(
-                fn=pipeline.plot_input_img, inputs=session, outputs=input_plot)
+                fn=self.set_spinner, inputs=spinner_running, outputs=btn_run).then(
+                fn=pipeline.plot_input_img, inputs=session, outputs=input_plot).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
@@ -139,9 +188,9 @@ class Interface:
 
 class Pipeline:
     def __init__(self):
-        self.figsize = (6, 6)
+        self.figsize = (8, 8)
 
-    def plot_input_img(self, session, cmap="viridis"):
+    def plot_input_img(self, session, cmap="Greys_r"):
         plt.close()
         fig, ax = plt.subplots(figsize=self.figsize)
 
@@ -153,6 +202,43 @@ class Pipeline:
 
         return fig
 
+    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())
+
+        data_lines = []
+        for i in range(len(l2d_obj.get_segmentation_lines())):
+            data_lines.append(l2d_obj.get_segmentation_lines()[i])
+
+        # Show how add_line_to_plot works:
+        for line in data_lines:
+            qim3d.viz.layers2d.add_line_to_plot(ax, line)
+
+        # Adjustments
+        ax.axis("off")
+        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 usre data is 2D
+
+        # TODO: Handle "is_inverted" from gradio
+        l2d_obj = l2d.Layers2d()
+        l2d_obj.prepare_update(
+            data=data,
+            is_inverted=False,
+            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(
@@ -165,7 +251,6 @@ class Pipeline:
                 f"Failed to load the image: {error_message}"
             ) from error_message
 
-        print(session.data)
         return session