2024-01-02 per grace,rreplace json output with csv file

.gitignore

@@ -1,2 +1,3 @@
 gradio_cached_examples
-.env
+flagged
+.env

app.py

@@ -5,6 +5,8 @@ import uuid
 import shutil
 import tempfile
 import pydicom
+import datetime
+import pandas as pd
 import SimpleITK as sitk
 from huggingface_hub import snapshot_download
 
@@ -38,6 +40,7 @@ def imread(file_list):
 
 def main_func(input_file_list):
     with tempfile.TemporaryDirectory() as tempdir:
+        print('start time:',datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S'))
         image_file = os.path.join(tempdir,f"image.nii.gz")
         first_file = input_file_list[0].name
         if first_file.endswith(".dcm"):
@@ -63,22 +66,23 @@ def main_func(input_file_list):
         inference(image_file,tempdir,weight_file)
 
         mask_file = os.path.join(tempdir,"lungqia-0.nii.gz")
-        json_file = os.path.join(tempdir,"export-0.json")
+        csv_file = os.path.join(tempdir,"export-0.csv")
         my_uid = uuid.uuid4().hex
         output_pdf_file = os.path.join('/tmp',f'{my_uid}.pdf')
-        output_json_file = os.path.join('/tmp',f'{my_uid}.json')
+        output_csv_file = os.path.join('/tmp',f'{my_uid}.csv')
 
-        inst = NiftiVisualizer("NA",image_file,mask_file,json_file,tempdir)
+        inst = NiftiVisualizer("NA",image_file,mask_file,csv_file,tempdir)
         tmp_pdf_file = inst.gen_pdf()
         assert(os.path.exists(tmp_pdf_file))
 
-        with open(json_file,'r') as f:
-            output_json = json.loads(f.read())
+        output_df = pd.read_csv(csv_file)
 
         shutil.copy(tmp_pdf_file,output_pdf_file)
-        shutil.copy(json_file,output_json_file)
-
-        return output_pdf_file, output_json, output_pdf_file, output_json_file
+        shutil.copy(csv_file,output_csv_file)
+        
+        print('uid:',os.path.basename(output_csv_file))
+        print('end time:',datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S'))
+        return output_pdf_file, output_df, output_pdf_file, output_csv_file
 
 with gr.Blocks() as demo:
     with gr.Column():
@@ -95,12 +99,12 @@ with gr.Blocks() as demo:
             btn = gr.Button("process")
         with gr.Column():
             pdf = PDF(label="Upload a PDF", interactive=True)
-            gr_json = gr.Json()
+            gr_df = gr.Dataframe()
             download_button_pdf = gr.DownloadButton("Download report pdf", visible=True)
-            download_button_json = gr.DownloadButton("Download report json", visible=True)
+            download_button_csv = gr.DownloadButton("Download report csv", visible=True)
     btn.click(fn=main_func, 
         inputs=[in_file],
-        outputs=[pdf,gr_json,download_button_pdf,download_button_json],
+        outputs=[pdf,gr_df,download_button_pdf,download_button_csv],
     )#example=[example_nifti_path],cache_examples=True