Data explorer

First operational version of the Data Explorer.

Allows browsing files and operation selection

qim3d/gui/data_explorer.py

@@ -69,12 +69,7 @@ class Interface:
             interactive=True,
         )
 
-    def make_pipeline(self, session):
-        print(session.operations)
-        return session
-
     def show_results(self, operations):
-        print(operations)
         update_list = []
         for operation in self.operations:
             if operation in operations:
@@ -145,7 +140,6 @@ class Interface:
 
             # Visualization and results
             with gr.Row(elem_classes="mt-64"):
-
                 # Text box with data summary
                 with gr.Column(visible=False) as result_data_summary:
                     data_summary = gr.Text(
@@ -195,8 +189,9 @@ class Interface:
                     hist_plot = gr.Plot(label="Volume intensity histogram")
 
             ### Gradio objects lists
-            pipeline = Pipeline()
+
             session = gr.State([])
+            pipeline = Pipeline()
 
             # Results
             results = [
@@ -239,15 +234,15 @@ class Interface:
             btn_run.click(
                 fn=self.set_spinner, inputs=[], outputs=btn_run).success(
                 fn=self.start_session, inputs=inputs, outputs=session).success(
-                fn=self.make_pipeline, inputs=session, outputs=session).success(
-                fn=pipeline.process_input, inputs=session, outputs=session).success(
-                fn=pipeline.show_summary_str, inputs=session, outputs=data_summary).success(
-                fn=pipeline.create_zslice_fig, inputs=session, outputs=zslice_plot).success(
-                fn=pipeline.create_yslice_fig, inputs=session, outputs=yslice_plot).success(
-                fn=pipeline.create_xslice_fig, inputs=session, outputs=xslice_plot).success(
-                fn=pipeline.create_projections_figs, inputs=session, outputs=projection_outputs).success(
-                fn=pipeline.show_summary_str, inputs=session, outputs=data_summary).success(
-                fn=pipeline.plot_vol_histogram, inputs=session, outputs=hist_plot).success(
+                fn=pipeline.run_pipeline, inputs=session, outputs=outputs).success(
+                # fn=pipeline.process_input, inputs=session, outputs=session).success(
+                # fn=pipeline.show_summary_str, inputs=session, outputs=data_summary).success(
+                # fn=pipeline.create_zslice_fig, inputs=session, outputs=zslice_plot).success(
+                # fn=pipeline.create_yslice_fig, inputs=session, outputs=yslice_plot).success(
+                # fn=pipeline.create_xslice_fig, inputs=session, outputs=xslice_plot).success(
+                # fn=pipeline.create_projections_figs, inputs=session, outputs=projection_outputs).success(
+                # fn=pipeline.show_summary_str, inputs=session, outputs=data_summary).success(
+                # fn=pipeline.plot_vol_histogram, inputs=session, outputs=hist_plot).success(
                 fn=self.show_results, inputs=operations, outputs=results).success(
                 fn=self.set_relaunch_button, inputs=[], outputs=btn_run)
 
@@ -273,6 +268,7 @@ class Interface:
         session = Session()
         session.root_path = os.path.expanduser("~")
         session.interface = "gradio"
+        session.all_operations = Interface().operations
         session.operations = args[0]
         session.base_path = args[1]
         session.explorer = args[2]
@@ -436,19 +432,61 @@ class Pipeline:
         self.figsize = 8  # Used for matplotlig figure size
         self.display_saturation_percentile = 99
         self.verbose = False
+        self.session = None
+
+    def run_pipeline(self, session):
+        self.session = session
+        outputs = []
+        print(session.all_operations)
+        for operation in session.all_operations:
+            if operation in session.operations:
+                outputs.append(self.run_operation(operation))
+
+            else:
+                print(f"Skipping {operation}")
+                outputs.append(None)
+
+        return outputs
+
+    def run_operation(self, operation):
+        print(f"Running {operation}")
 
-    def process_input(self, session):
+        if operation == "Data summary":
+            return "Hello from Pipeline!"
+
+        elif operation == "Z Slicer":
+            return None
+
+        elif operation == "Y Slicer":
+            return None
+
+        elif operation == "X Slicer":
+            return None
+
+        elif operation == "Z max projection":
+            return None
+
+        elif operation == "Z min projection":
+            return None
+
+        elif operation == "Intensity histogram":
+            return None
+
+        else:
+            raise ValueError("Unknown operation")
+
+    def process_input(self):
         # Get info from Tiff file
-        session.get_data_info()
-        session.create_summary_dict()
+        self.session.get_data_info()
+        self.session.create_summary_dict()
 
         # Memory map data as a virtual stack
 
         try:
-            session.vol = load(
-                session.file_path,
-                virtual_stack=session.virtual_stack,
-                dataset_name=session.dataset_name,
+            self.session.vol = load(
+                self.session.file_path,
+                virtual_stack=self.session.virtual_stack,
+                dataset_name=self.session.dataset_name,
             )
         except:
             return session