Fixed count

app.py

@@ -21,31 +21,33 @@ service_account_json = {
     "universe_domain": "googleapis.com"
 }
 
+
 def set_min_dense_1(max_dense_0):
     global scaled_thresh1
     print("max_dense_0", max_dense_0)
-    scaled_thresh1 = int(max_dense_0) * max_val/255
-    dense_0 = np.where(textured_cxr<scaled_thresh1, textured_cxr, 0)
-    dense_1 = np.where(((textured_cxr<scaled_thresh2) & (textured_cxr>=scaled_thresh1)), textured_cxr, 0)
+    scaled_thresh1 = int(max_dense_0) * max_val / 255
+    dense_0 = np.where(textured_cxr < scaled_thresh1, textured_cxr, 0)
+    dense_1 = np.where(((textured_cxr < scaled_thresh2) & (textured_cxr >= scaled_thresh1)), textured_cxr, 0)
     return max_dense_0, dense_0, dense_1
 
+
 def set_min_dense_2(max_dense_1):
     global scaled_thresh2
     print("max_dense_1", max_dense_1)
-    scaled_thresh2 = int(max_dense_1) * max_val/255
-    dense_1 = np.where(((textured_cxr<scaled_thresh2) & (textured_cxr>=scaled_thresh1)), textured_cxr, 0)
-    dense_2 = np.where(((textured_cxr<scaled_thresh3) & (textured_cxr>=scaled_thresh2)), textured_cxr, 0)
+    scaled_thresh2 = int(max_dense_1) * max_val / 255
+    dense_1 = np.where(((textured_cxr < scaled_thresh2) & (textured_cxr >= scaled_thresh1)), textured_cxr, 0)
+    dense_2 = np.where(((textured_cxr < scaled_thresh3) & (textured_cxr >= scaled_thresh2)), textured_cxr, 0)
     return max_dense_1, dense_1, dense_2
 
+
 def set_min_dense_3(max_dense_2):
     global scaled_thresh3
     print("max_dense_2", max_dense_2)
-    scaled_thresh3 = int(max_dense_2) * max_val/255
-    dense_2 = np.where(((textured_cxr<scaled_thresh3) & (textured_cxr>=scaled_thresh2)), textured_cxr, 0)
-    dense_3 = np.where(((textured_cxr<255) & (textured_cxr>=scaled_thresh3)), textured_cxr, 0)
+    scaled_thresh3 = int(max_dense_2) * max_val / 255
+    dense_2 = np.where(((textured_cxr < scaled_thresh3) & (textured_cxr >= scaled_thresh2)), textured_cxr, 0)
+    dense_3 = np.where(((textured_cxr < 255) & (textured_cxr >= scaled_thresh3)), textured_cxr, 0)
     return max_dense_2, dense_2, dense_3
 
-
 def authenticate_gcs():
     return storage.Client.from_service_account_info(service_account_json)
 
@@ -57,7 +59,6 @@ def download_csv_from_gcs(filename):
     csv_content = blob.download_as_text()
     return csv_content
 
-
 def read_csv_from_gcs(user):
     filename = f"density_{user}.csv"
     try:
@@ -69,14 +70,12 @@ def read_csv_from_gcs(user):
         print("Error reading CSV from GCS:", e)
         return []
 
-
 def upload_csv_to_gcs(csv_content, filename):
     client = authenticate_gcs()
     bucket = client.get_bucket(GCS_BUCKET_NAME)
     blob = bucket.blob(os.path.join(GCS_FOLDER_PATH, filename))
     blob.upload_from_string(csv_content)
 
-
 def new__cxr(max_dense_0, max_dense_1, max_dense_2):
     global textured_cxr, lung_noised, max_val, cxr, mask, scaled_thresh1, scaled_thresh2, scaled_thresh3, image_id, index, count
     index += 1
@@ -84,22 +83,21 @@ def new__cxr(max_dense_0, max_dense_1, max_dense_2):
         index = 1
         image_id += 1
 
-    # Read CSV data from GCS
-    csv_data = read_csv_from_gcs(user)
+    count += 1
 
-    # Write count, thresh1, thresh2, thresh3 to CSV file on GCS
-    current_count = count  # Store the current count
-    if current_count <= 30:
-        fieldnames = ['count', 'thresh_1', 'thresh_2', 'thresh_3']
+    csv_data = read_csv_from_gcs(user)
+    # write count, thresh1, thresh2, thresh3 to csv file
+    if count <= 30:
         csv_content = ""
         for row in csv_data:
             csv_content += ",".join(row) + "\n"
-        csv_content += f"{current_count},{max_dense_0},{max_dense_1},{max_dense_2}\n"
+        csv_content += f"{count},{max_dense_0},{max_dense_1},{max_dense_2}\n"
         filename = f"density_{user}.csv"
         upload_csv_to_gcs(csv_content, filename)
 
-    count += 1
-    if count > 30:
+
+
+    if (count > 30):
         empty_image = np.zeros((256, 256), dtype=np.uint8)
         label1.update(visible=False)
         count = 1
@@ -110,7 +108,7 @@ def new__cxr(max_dense_0, max_dense_1, max_dense_2):
             csv_content += ",".join(row) + "\n"
         fieldnames = ['count', 'thresh_1', 'thresh_2', 'thresh_3']
         csv_content += ",".join(fieldnames) + "\n"
-        csv_content += f"{current_count},{max_dense_0},{max_dense_1},{max_dense_2}\n"
+        csv_content += f"{count},{max_dense_0},{max_dense_1},{max_dense_2}\n"
         filename = f"density_{user}.csv"
         upload_csv_to_gcs(csv_content, filename)
         return empty_image, empty_image, empty_image, empty_image, empty_image, empty_image, empty_image, 30
@@ -130,14 +128,14 @@ def new__cxr(max_dense_0, max_dense_1, max_dense_2):
     thresh1 = 50
     thresh2 = 100
     thresh3 = 150
-    scaled_thresh1 = thresh1 * max_val/255
-    scaled_thresh2 = thresh2 * max_val/255
-    scaled_thresh3 = thresh3 * max_val/255
-    dense_0 = np.where(textured_cxr<scaled_thresh1, textured_cxr, 0)
-    dense_1 = np.where(((textured_cxr<scaled_thresh2) & (textured_cxr>=scaled_thresh1)), textured_cxr, 0)
-    dense_2 = np.where(((textured_cxr<scaled_thresh3) & (textured_cxr>=scaled_thresh2)), textured_cxr, 0)
-    dense_3 = np.where(((textured_cxr<255) & (textured_cxr>=scaled_thresh3)), textured_cxr, 0)
-    return cxr, textured_cxr, lung_noised, dense_0, dense_1, dense_2, dense_3, count
+    scaled_thresh1 = thresh1 * max_val / 255
+    scaled_thresh2 = thresh2 * max_val / 255
+    scaled_thresh3 = thresh3 * max_val / 255
+    dense_0 = np.where(textured_cxr < scaled_thresh1, textured_cxr, 0)
+    dense_1 = np.where(((textured_cxr < scaled_thresh2) & (textured_cxr >= scaled_thresh1)), textured_cxr, 0)
+    dense_2 = np.where(((textured_cxr < scaled_thresh3) & (textured_cxr >= scaled_thresh2)), textured_cxr, 0)
+    dense_3 = np.where(((textured_cxr < 255) & (textured_cxr >= scaled_thresh3)), textured_cxr, 0)
+    return cxr, textured_cxr, lung_noised, lung_noised, dense_0, dense_1, dense_2, dense_3, count
 
 
 def create_csv():
@@ -159,13 +157,14 @@ def create_csv():
 def check_auth(username, password):
     global user, fresh_start
     user = username
-    if(user == 'gk' and password == 'upmc2009'):
+    if (user == 'gk' and password == 'upmc2009'):
         create_csv()
         return True
-    elif(user == 'veytel' and password == 'pittsburgh'):
+    elif (user == 'veytel' and password == 'pittsburgh'):
         create_csv()
         return True
 
+
 def change_vis():
     global count
     if count >= 30:
@@ -173,15 +172,16 @@ def change_vis():
     else:
         return gr.Label.update(visible=False), gr.Button.update(visible=True)
 
+
 with gr.Blocks() as demo:
     count = 1
     image_id = 1
     index = 1
     executable_path = os.path.dirname(os.path.realpath(__file__))
     cxr_dir = os.path.join(executable_path, "Images/cxr")
-    mask_dir =  os.path.join(executable_path, "Images/mask")
-    textured_cxr_dir =  os.path.join(executable_path, "Images/textured_cxr")
-    lung_noised_dir =  os.path.join(executable_path, "Images/lung_noised")
+    mask_dir = os.path.join(executable_path, "Images/mask")
+    textured_cxr_dir = os.path.join(executable_path, "Images/textured_cxr")
+    lung_noised_dir = os.path.join(executable_path, "Images/lung_noised")
     cxr_file = "cxr" + str(image_id) + "_cxr.png"
     mask_file = "cxr" + str(image_id) + "_mask.png"
     textured_cxr_file = "cxr" + str(image_id) + "_textured_" + str(index) + ".png"
@@ -195,19 +195,23 @@ with gr.Blocks() as demo:
     mask = cv.imread(mask_path, cv.IMREAD_GRAYSCALE)
     textured_cxr = cv.imread(textured_cxr_path, cv.IMREAD_GRAYSCALE)
     lung_noised = cv.imread(lung_noised_path, cv.IMREAD_GRAYSCALE)
-    max_val = np.percentile(cxr, 97) # To optimize later
+    max_val = np.percentile(cxr, 97)  # To optimize later
     thresh1 = 50
     thresh2 = 100
     thresh3 = 150
-    scaled_thresh1 = thresh1 * max_val/255
-    scaled_thresh2 = thresh2 * max_val/255
-    scaled_thresh3 = thresh3 * max_val/255
-    dense_0 = np.where(textured_cxr<scaled_thresh1, textured_cxr, 0)
-    dense_1 = np.where(((textured_cxr<scaled_thresh2) & (textured_cxr>=scaled_thresh1)), textured_cxr, 0)
-    dense_2 = np.where(((textured_cxr<scaled_thresh3) & (textured_cxr>=scaled_thresh2)), textured_cxr, 0)
-    dense_3 = np.where(((textured_cxr<255) & (textured_cxr>=scaled_thresh3)), textured_cxr, 0)
+    scaled_thresh1 = thresh1 * max_val / 255
+    scaled_thresh2 = thresh2 * max_val / 255
+    scaled_thresh3 = thresh3 * max_val / 255
+    dense_0 = np.where(textured_cxr < scaled_thresh1, textured_cxr, 0)
+    dense_1 = np.where(((textured_cxr < scaled_thresh2) & (textured_cxr >= scaled_thresh1)), textured_cxr, 0)
+    dense_2 = np.where(((textured_cxr < scaled_thresh3) & (textured_cxr >= scaled_thresh2)), textured_cxr, 0)
+    dense_3 = np.where(((textured_cxr < 255) & (textured_cxr >= scaled_thresh3)), textured_cxr, 0)
     # open csv in append mode
-    with gr.Row():     
+    # add title
+    with gr.Row():
+        label_title = gr.Label("VeyTel Density Mapper", visible=True)
+
+    with gr.Row():
         with gr.Column():
             im1 = gr.Image(cxr, label="Original CXR")
         with gr.Column():
@@ -216,23 +220,24 @@ with gr.Blocks() as demo:
             im3 = gr.Image(lung_noised, label="Synthetic CXR")
         with gr.Column():
             label1 = gr.Label("Completed! Please close window", visible=False)
-            
+
     with gr.Row():
         with gr.Column():
             dense0 = gr.Image(dense_0, label="Dense 0")
             with gr.Row():
                 min_dense_0 = gr.Textbox(value='0', label="Min")
-                max_dense_0 = gr.Slider(0, 255, value=50, step = 1, label="Max")
+                max_dense_0 = gr.Slider(0, 255, value=50, step=1, label="Max")
 
         with gr.Column():
             dense1 = gr.Image(dense_1, label="Dense 1")
             with gr.Row():
                 min_dense_1 = gr.Textbox(value='50', label="Min")
-                max_dense_1 = gr.Slider(0, 255, value=100, step = 1, label="Max")
-                max_dense_0.change(set_min_dense_1, inputs=max_dense_0, outputs=[min_dense_1, dense0, dense1]).then(set_min_dense_1, inputs=max_dense_0, outputs=[min_dense_1, dense0, dense1])
+                max_dense_1 = gr.Slider(0, 255, value=100, step=1, label="Max")
+                max_dense_0.change(set_min_dense_1, inputs=max_dense_0, outputs=[min_dense_1, dense0, dense1]).then(
+                    set_min_dense_1, inputs=max_dense_0, outputs=[min_dense_1, dense0, dense1])
 
         with gr.Column():
-            progress_log =  gr.Slider(1, 30, value=1, step = 1, label="progress")
+            progress_log = gr.Slider(1, 30, value=1, step=1, label="progress")
             button1 = gr.Button(value="Save & continue", visible=True)
 
     with gr.Row():
@@ -240,24 +245,27 @@ with gr.Blocks() as demo:
             dense2 = gr.Image(dense_2, label="Dense 2")
             with gr.Row():
                 min_dense_2 = gr.Textbox(value='100', label="Min")
-                max_dense_2 = gr.Slider(0, 255, value=150, step = 1, label="Max")
-                max_dense_1.change(set_min_dense_2, inputs=max_dense_1, outputs=[min_dense_2, dense1, dense2]).then(set_min_dense_2, inputs=max_dense_1, outputs=[min_dense_2, dense1, dense2])
+                max_dense_2 = gr.Slider(0, 255, value=150, step=1, label="Max")
+                max_dense_1.change(set_min_dense_2, inputs=max_dense_1, outputs=[min_dense_2, dense1, dense2]).then(
+                    set_min_dense_2, inputs=max_dense_1, outputs=[min_dense_2, dense1, dense2])
 
         with gr.Column():
             dense3 = gr.Image(dense_3, label="Dense 3")
             with gr.Row():
                 min_dense_3 = gr.Textbox(value='150', label="Min")
                 max_dense_3 = gr.Textbox(value='255', label="Max")
-                max_dense_2.change(set_min_dense_3, inputs=max_dense_2, outputs=[min_dense_3, dense2, dense3]).then(set_min_dense_3, inputs=max_dense_2, outputs=[min_dense_3, dense2, dense3])
+                max_dense_2.change(set_min_dense_3, inputs=max_dense_2, outputs=[min_dense_3, dense2, dense3]).then(
+                    set_min_dense_3, inputs=max_dense_2, outputs=[min_dense_3, dense2, dense3])
 
-        with gr.Column(): # adding additional for better visualization
+        with gr.Column():  # adding additional for better visualization
             im3_1 = gr.Image(lung_noised, label="Synthetic CXR")
 
-    button1.click(new__cxr, inputs = [max_dense_0, max_dense_1, max_dense_2], outputs = [im1, im2, im3, im3_1, dense0, dense1, dense2, dense3, progress_log])
-    button1.click(change_vis,outputs=[label1, button1])    
+    button1.click(new__cxr, inputs=[max_dense_0, max_dense_1, max_dense_2],
+                  outputs=[im1, im2, im3, im3_1, dense0, dense1, dense2, dense3, progress_log])
+    button1.click(change_vis, outputs=[label1, button1])
+
 if __name__ == "__main__":
     demo.launch(auth=check_auth)
 
 
 
-