Update app.py

app.py

@@ -1,3 +1,5 @@
+%%writefile app.py
+
 import streamlit as st
 from streamlit_drawable_canvas import st_canvas
 from streamlit_image_coordinates import streamlit_image_coordinates
@@ -18,9 +20,45 @@ import nibabel as nib
 import tempfile
 
 print('script run')
+#further improvement
+#decorator singletion or use cache data class
+# https://docs.streamlit.io/develop/api-reference/caching-and-state/st.experimental_singleton
+# https://docs.streamlit.io/develop/concepts/architecture/caching
+def download_idc_data():
+  #download IDC data cases
+  client = index.IDCClient()
+  #define serieUIDs to download
+  serieUIDs_list = ["1.3.6.1.4.1.14519.5.2.1.8421.4008.125612661111422710051062993644",
+                    "1.3.6.1.4.1.14519.5.2.1.3344.4008.552105302448832783460360105045",
+                    "1.3.6.1.4.1.14519.5.2.1.3344.4008.217290429362492484143666931850",
+                    "1.3.6.1.4.1.14519.5.2.1.3344.4008.315023636447426194723399171147",
+                    "1.3.6.1.4.1.14519.5.2.1.3344.4008.307374355712319704057189924161"]
+
+  #download series and convert to .nii.gz
+  samples_root_dir = "/content/SegVolIDCTest/model/asset/idc_samples"
+  if not os.path.exists(samples_root_dir) : os.mkdir(samples_root_dir)
+  for idx, serieUID_ddl in enumerate(serieUIDs_list):
+    sample_dcm_dir = os.path.join(samples_root_dir, f"ddl_series{idx}_dcm")
+    sample_nii_dir = os.path.join(samples_root_dir, f"ddl_series{idx}_nii")
+    for dir in [sample_dcm_dir, sample_nii_dir]:
+      if os.path.exists(dir):
+        shutil.rmtree(dir)
+      os.makedirs(dir)
+    client.download_from_selection(seriesInstanceUID=\
+       serieUID_ddl, \
+       downloadDir=sample_dcm_dir)
+    subprocess.call(["dcm2niix", "-o", sample_nii_dir, "-z", "y",
+                   "-f", "IDC_%i", "-g", "y", sample_dcm_dir])
+  return glob.glob(os.path.join(samples_root_dir, "*nii/*.nii.gz"))
 
 #############################################
 st.session_state.option = None
+
+if 'idc_data' not in st.session_state:
+  case_list = download_idc_data()
+  st.session_state.idc_data = True
+else:
+  case_list = glob.glob("/content/SegVolIDCTest/model/asset/idc_samples/*nii/*.nii.gz")
 # init session_state
 if 'option' not in  st.session_state:
     st.session_state.option = None
@@ -61,36 +99,11 @@ if 'running' not in st.session_state:
 if 'transparency' not in st.session_state:
     st.session_state.transparency = 0.25
 
-#download IDC data cases
-client = index.IDCClient()
-#define serieUIDs to download
-serieUIDs_list = ["1.3.6.1.4.1.14519.5.2.1.8421.4008.125612661111422710051062993644",
-                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.552105302448832783460360105045",
-                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.217290429362492484143666931850",
-                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.315023636447426194723399171147",
-                  "1.3.6.1.4.1.14519.5.2.1.3344.4008.307374355712319704057189924161"]
-
-#download series and convert to .nii.gz
-samples_root_dir = "model/asset/idc_samples"
-if os.path.exists(samples_root_dir): shutil.rmtree(samples_root_dir)
-os.mkdir(samples_root_dir)
-for idx, serieUID_ddl in enumerate(serieUIDs_list):
-  sample_dcm_dir = os.path.join(samples_root_dir, f"ddl_series{idx}_dcm")
-  sample_nii_dir = os.path.join(samples_root_dir, f"ddl_series{idx}_nii")
-  for dir in [sample_dcm_dir, sample_nii_dir]:
-    if os.path.exists(dir): shutil.rmtree(dir)
-    os.mkdir(dir)
-  client.download_from_selection(seriesInstanceUID=\
-     serieUID_ddl, \
-     downloadDir=sample_dcm_dir)
-  subprocess.call(["dcm2niix", "-o", sample_nii_dir, "-z", "y",
-                 "-f", "IDC_%i", "-g", "y", sample_dcm_dir])
-case_list = glob.glob(os.path.join(samples_root_dir, "*nii/*.nii.gz"))
 # case_list = [
-#     'model/asset/FLARE22_Tr_0002_0000.nii.gz',
-#     'model/asset/FLARE22_Tr_0005_0000.nii.gz',
-#     'model/asset/FLARE22_Tr_0034_0000.nii.gz',
-#     'model/asset/FLARE22_Tr_0045_0000.nii.gz'
+#     '/content/SegVolIDCTest/model/asset/FLARE22_Tr_0002_0000.nii.gz',
+#     '/content/SegVolIDCTest/model/asset/FLARE22_Tr_0005_0000.nii.gz',
+#     '/content/SegVolIDCTest/model/asset/FLARE22_Tr_0034_0000.nii.gz',
+#     '/content/SegVolIDCTest/model/asset/FLARE22_Tr_0045_0000.nii.gz'
 # ]
 
 #############################################
@@ -219,7 +232,7 @@ else:
             top, bottom = st.select_slider(
                 'Top and bottom of box',
                 options=range(0, 325),
-                value=(0, 324), 
+                value=(0, 324),
                 disabled=st.session_state.running
             )
             st.session_state.rectangle_3Dbox[0] = top
@@ -230,19 +243,19 @@ else:
         st.session_state.transparency = st.slider('Mask opacity', 0.0, 1.0, 0.25, disabled=st.session_state.running)
 
     with col_image1:
-        
+
         image_z_array = image_3D[selected_index_z]
 
         preds_z_array = None
         if st.session_state.preds_3D is not None:
             preds_z_array = st.session_state.preds_3D[selected_index_z]
-            
+
         image_z = make_fig(image_z_array, preds_z_array, st.session_state.points, selected_index_z, 'xy')
-        
-        
+
+
         if st.session_state.use_point_prompt:
             value_xy = streamlit_image_coordinates(image_z, width=325)
-            
+
             if value_xy is not None:
                 point_ax_xy = (selected_index_z, value_xy['y'], value_xy['x'])
                 if len(st.session_state.points) >= 3:
@@ -282,16 +295,16 @@ else:
 
     with col_image2:
         image_y_array = image_3D[:, selected_index_y, :]
-        
+
         preds_y_array = None
         if st.session_state.preds_3D is not None:
             preds_y_array = st.session_state.preds_3D[:, selected_index_y, :]
-        
+
         image_y = make_fig(image_y_array, preds_y_array, st.session_state.points, selected_index_y, 'xz')
-        
+
         if st.session_state.use_point_prompt:
             value_yz = streamlit_image_coordinates(image_y, width=325)
-            
+
             if value_yz is not None:
                 point_ax_xz = (value_yz['y'], selected_index_y, value_yz['x'])
                 if len(st.session_state.points) >= 3:
@@ -332,8 +345,8 @@ with col2:
         original_shape = st.session_state.data_item['ori_shape']
         pred_array = st.session_state.preds_3D_ori
         original_array = np.zeros(original_shape)
-        original_array[foreground_start_coord[0]:foreground_end_coord[0], 
-                    foreground_start_coord[1]:foreground_end_coord[1], 
+        original_array[foreground_start_coord[0]:foreground_end_coord[0],
+                    foreground_start_coord[1]:foreground_end_coord[1],
                     foreground_start_coord[2]:foreground_end_coord[2]] = pred_array
 
         original_array = original_array.transpose(2, 1, 0)
@@ -356,8 +369,8 @@ with col3:
     if st.button(run_button_name, type="primary", use_container_width=True,
             disabled=(
                 st.session_state.data_item is None or
-                (st.session_state.text_prompt is None and len(st.session_state.points) == 0 and st.session_state.use_box_prompt is False) or 
-                st.session_state.irregular_box or 
+                (st.session_state.text_prompt is None and len(st.session_state.points) == 0 and st.session_state.use_box_prompt is False) or
+                st.session_state.irregular_box or
                 st.session_state.running
                 )):
         st.session_state.running = True