Update app.py

Adjust the slice orientation by transposing and flipping the slice data.
Add options to visualize different views (axial, coronal, sagittal).

app.py

@@ -10,16 +10,20 @@ plt.switch_backend('Agg')
 
 def load_nrrd(file_path):
     data, _ = nrrd.read(file_path.name)
-    num_slices = data.shape[2]
-    return data, num_slices
+    return data
 
-def visualize_slice(file_path, slice_index):
-    data, num_slices = load_nrrd(file_path)
+def visualize_slice(file_path, slice_index, view_axis):
+    data = load_nrrd(file_path)
     
     # Ensure the slice index is within the range of available slices
-    slice_index = min(max(0, slice_index), num_slices - 1)
+    slice_index = min(max(0, slice_index), data.shape[view_axis] - 1)
     
-    slice_image = data[:, :, slice_index]
+    if view_axis == 0:  # Axial
+        slice_image = np.flipud(np.rot90(data[slice_index, :, :], k=1))
+    elif view_axis == 1:  # Coronal
+        slice_image = np.flipud(np.rot90(data[:, slice_index, :], k=1))
+    elif view_axis == 2:  # Sagittal
+        slice_image = np.flipud(np.rot90(data[:, :, slice_index], k=1))
 
     # Plot the slice
     fig, ax = plt.subplots()
@@ -35,20 +39,22 @@ def visualize_slice(file_path, slice_index):
     
     return pil_img
 
-def update_slider(file_path):
-    _, num_slices = load_nrrd(file_path)
-    return gr.update(maximum=num_slices-1, value=0)
+def update_slider(file_path, view_axis):
+    data = load_nrrd(file_path)
+    return gr.update(maximum=data.shape[view_axis] - 1, value=0)
 
 with gr.Blocks() as app:
     gr.Markdown("## NRRD Slice Visualizer")
     gr.Markdown("Upload an NRRD file and use the slider to select and visualize slices.")
     
     file_input = gr.File(label="Upload NRRD File")
+    view_axis_selector = gr.Radio(choices=[0, 1, 2], value=2, label="View Axis", info="0: Axial, 1: Coronal, 2: Sagittal")
     slider = gr.Slider(minimum=0, maximum=1, step=1, value=0, label="Slice Selector")
     image_output = gr.Image(type="pil", label="Selected Slice")
     
-    file_input.change(fn=update_slider, inputs=file_input, outputs=slider)
-    file_input.change(fn=visualize_slice, inputs=[file_input, slider], outputs=image_output)
-    slider.change(fn=visualize_slice, inputs=[file_input, slider], outputs=image_output)
+    file_input.change(fn=update_slider, inputs=[file_input, view_axis_selector], outputs=slider)
+    file_input.change(fn=visualize_slice, inputs=[file_input, slider, view_axis_selector], outputs=image_output)
+    view_axis_selector.change(fn=update_slider, inputs=[file_input, view_axis_selector], outputs=slider)
+    slider.change(fn=visualize_slice, inputs=[file_input, slider, view_axis_selector], outputs=image_output)
 
 app.launch()