update

tigerhx/guitool.py

@@ -166,7 +166,8 @@ def init_app(application_path):
 
     default_models = ['cine4d_v0001_xyz_mms12.onnx',
                     'cine4d_v0002_xyz_mms12acdc.onnx',
-                    'cine4d_v0003_xy_mms12acdc.onnx']
+                    'cine4d_v0003_xy_mms12acdc.onnx',
+                    'cine4d_v0004_xy_retrain.onnx']
 
     for m0 in default_models:
         model_file = join(model_path, m0)

tigerhx/tigercinegui.py

@@ -28,6 +28,7 @@
 root = None
 progress_bar = None
 display_type_combo = None
+colormap_combo = None
 data = None  # Ensure data is globally accessible
 fig, ax = None, None
 canvas = None
@@ -90,17 +91,23 @@ def process_files_multithreaded(files, slice_select, model_ff):
         LVM = LVM.astype(int)
         Seg = emp.astype(int)
 
-        dict = {'input': img_ori, 
-                 'LV': LV , 'LVM': LVM, 'RV': RV ,
-                  'Seg': Seg, 'Seg_AHA': Seg_AHA, 'voxel_size': np.array(voxel_size)}
+        mask = np.max(Seg, axis=(2, 3))
+        xx, yy = np.nonzero(mask)
+        x0, x1 = max(0, xx.min() - 10), min(mask.shape[0], xx.max() + 10)
+        y0, y1 = max(0, yy.min() - 10), min(mask.shape[1], yy.max() + 10)
+
+        dict = {'input': img_ori, 'Seg': Seg, 'SegAHA': Seg_AHA,
+                'input_crop': img_ori[x0:x1, y0:y1], 'Seg_crop': Seg[x0:x1, y0:y1],
+                'SegAHA_crop': Seg_AHA[x0:x1, y0:y1],
+                'LV': LV, 'LVM': LVM, 'RV': RV,
+                'voxel_size': np.array(voxel_size)}
 
         dict['model'] = basename(model_ff)
         savemat(f'./output/{name}_pred_{onnx_version}.mat', dict, do_compression=True)
         log_message(log_box, f'{num + 1}/{len(files)}: {basename(file)} finished ......')
         root.after(0, update_mat_listbox)
 
-
-    #root.after(0, lambda: progress_bar.pack_forget())
+    # root.after(0, lambda: progress_bar.pack_forget())
     log_message(log_box, f'All job finished.........')
     progress_bar['value'] = 0
     root.update_idletasks()  # Ensure the GUI updates
@@ -128,7 +135,7 @@ def on_mat_select(event):
                     log_message(log_box, f"'{selected_type}' not found in {selected_mat}")
 
                 if 'model' in data:
-                    model_name = data['model'][0] #from .mat file , the string stored into a cell array
+                    model_name = data['model'][0]  # from .mat file, the string stored into a cell array
                     log_message(log_box, f"Predicted using {model_name}")
             except Exception as e:
                 log_message(log_box, f"An error occurred: {e}")
@@ -144,6 +151,11 @@ def on_display_type_change(event):
                 update_time_slider(seg)  # Adapt the range of the time points
     except:
         log_message(log_box, f"Select a result file....")
+
+def on_colormap_change(event):
+    if seg is not None:
+        show_montage(seg)  # Redraw the figure with the selected colormap
+
 def show_montage(emp, time_frame=0):
     global fig, ax, canvas, im
     plt.close('all')  # Close all previous figures
@@ -198,10 +210,17 @@ def show_montage(emp, time_frame=0):
     # Resize the mosaic to 400x600
     mosaic_resized = resize(padded_mosaic, (600, 400), anti_aliasing=True)
 
+    colormap = colormap_combo.get()  # Get the selected colormap
+    if colormap == 'gray':
+        cmap = 'gray'
+    elif colormap == 'vivid':
+        cmap = 'viridis'  # Replace 'vivid' with an actual matplotlib colormap, like 'viridis'
+
     if im is None:
-        im = ax.imshow(mosaic_resized)
+        im = ax.imshow(mosaic_resized, cmap=cmap)
     else:
         im.set_data(mosaic_resized)
+        im.set_cmap(cmap)
         im.set_clim(vmin=emp.min(), vmax=emp.max())
 
     canvas = FigureCanvasTkAgg(fig, master=canvas_frame)
@@ -304,20 +323,47 @@ def list_and_log_sample_files(sample_dir):
 display_type_label.pack(side=tk.LEFT)
 
 # Create a combo box for selecting display type
-display_types = ['Seg', 'Seg_AHA', 'input', 'LV', 'LVM', 'RV']
-display_type_combo = ttk.Combobox(display_type_frame, values=display_types, width=10)
+display_types = ['input', 'Seg', 'SegAHA',
+                 'input_crop', 'Seg_crop', 'SegAHA_crop',
+                 'LV', 'LVM', 'RV']
+display_type_combo = ttk.Combobox(display_type_frame, values=display_types, width=16)
 display_type_combo.pack(side=tk.LEFT, padx=5)
 display_type_combo.current(0)  # Set default display type to 'Seg'
 display_type_combo.bind("<<ComboboxSelected>>", on_display_type_change)
 
-refresh_button = tk.Button(display_type_frame, text="Refresh Preds", command=update_mat_listbox)
-refresh_button.pack(side=tk.LEFT, padx=5)
+# Create a label for the colormap combo box
+colormap_label = tk.Label(display_type_frame, text="Colormap")
+colormap_label.pack(side=tk.LEFT, padx=5)
+
+# Create a combo box for selecting colormap
+colormap_combo = ttk.Combobox(display_type_frame, values=['gray', 'vivid'], width=10)
+colormap_combo.pack(side=tk.LEFT, padx=5)
+colormap_combo.current(0)  # Set default colormap to 'gray'
+colormap_combo.bind("<<ComboboxSelected>>", on_colormap_change)
 
 # Create a listbox for the .mat files
-mat_listbox = tk.Listbox(listbox_frame, width=40, height=10)
-mat_listbox.pack(side=tk.TOP, fill=tk.BOTH, expand=True)
+#mat_listbox = tk.Listbox(listbox_frame, width=40, height=10)
+#mat_listbox.pack(side=tk.TOP, fill=tk.BOTH, expand=True)
+#mat_listbox.bind('<<ListboxSelect>>', on_mat_select)
+
+
+
+# Create a frame for the listbox and display type combo box
+listbox_frame = tk.Frame(frame)
+listbox_frame.pack(padx=10, pady=10, fill=tk.BOTH, expand=True)
+
+# Create a scrollbar for the listbox
+listbox_scrollbar = tk.Scrollbar(listbox_frame, orient=tk.VERTICAL)
+listbox_scrollbar.pack(side=tk.RIGHT, fill=tk.Y)
+
+# Create a listbox for the .mat files
+mat_listbox = tk.Listbox(listbox_frame, width=40, height=10, yscrollcommand=listbox_scrollbar.set)
+mat_listbox.pack(side=tk.LEFT, fill=tk.BOTH, expand=True)
 mat_listbox.bind('<<ListboxSelect>>', on_mat_select)
 
+# Configure the scrollbar to work with the listbox
+listbox_scrollbar.config(command=mat_listbox.yview)
+
 # Create a progress bar
 progress_bar = ttk.Progressbar(frame, mode='determinate')
 progress_bar.pack(side=tk.TOP, fill=tk.BOTH)
@@ -346,4 +392,3 @@ def list_and_log_sample_files(sample_dir):
 
 # Run the application
 root.mainloop()
-