Added new file tracker monitor.py

app.py

@@ -15,7 +15,7 @@
 from dash.exceptions import PreventUpdate
 
 from utils import (parse_jsonstring, segmentation_generic,
-                   image_with_contour, image_string_to_PILImage)
+                   image_with_contour, image_without_contour, image_string_to_PILImage)
 from dash_canvas.components import image_upload_zone
 
 import subprocess
@@ -60,14 +60,17 @@
                         image_upload_zone('upload-image'),
 
                 ]),
-                dcc.Tab(
-                    label='Ground Truth Image',
-                    value='ground-truth-tab',
-                    children=[
-                        html.Img(id='ground-truth',
-                                 src='assets/Snailcpy_GT.jpg',
-                                 width='100%'),
-                    ]),
+                #dcc.Tab(
+                   # label='Ground Truth Image',
+                    #value='ground-truth-tab',
+                    #children=[
+                     #  dcc.Graph(
+                      # id='ground-truth',
+                       #figure=image_with_contour('assets/Snailcpy_GT.jpg',
+                        #                            img > 0, shape=(height, width))
+                       #)
+
+                    #]),
                 dcc.Tab(
                     label='Segmentation result',
                     value='segmentation-result-tab',
@@ -76,7 +79,12 @@
                         id='segmentation',
                         figure=image_with_contour(np.ones_like(img),
                                     img > 0, shape=(height, width))
-                        )
+                        ),
+                      # dcc.Graph(
+                       #id='ground-truth2',
+                       #figure=image_with_contour('assets/Snailcpy_GT.jpg',
+                        #                            img > 0, shape=(height, width))
+                       #)
                     ]),
                 dcc.Tab(
                      label='How to use this app',
@@ -113,6 +121,7 @@
             id='algorithm',
             options=[
                     {'label': 'Watershed', 'value': 'watershed'},
+                    {'label': 'GeneticSearch', 'value': 'genetic_search'},
                     {'label': 'Random Walker', 'value': 'random_walker'},
                     {'label': 'Random Forest', 'value': 'random_forest'}
                 ],
@@ -126,12 +135,14 @@
             [Input('canvas', 'json_data')],
             [State('canvas', 'image_content'),
             State('algorithm', 'value')])
-def update_figure_upload(string, image, algorithm):
+#create button to read current directory, if mask file exists in current dir, read it and display results
+def update_figure_upload(string, image, algorithm): 
     print("update figure")
     if string:
         if image is None:
             im = img
             image = img
+        # if seg exists calculate mask
         else:
             #print("Before PILImage")
             im = image_string_to_PILImage(image)
@@ -144,42 +155,32 @@ def update_figure_upload(string, image, algorithm):
         #skimage.io.imsave("medial.png", img_as_uint(imgSk))
 
         io.imsave("Snail_GT.jpg", mask)
-        file_copy("Snail_GT.jpg", "assets/Snailcpy_GT.jpg")
 
-        #file_copy function can be removed, the code below can be called----
-        #shutil.copyfile("Snail_GT.jpg", "assets/Snailcopy1_GT.jpg") 
-
-
-        #import subprocess
         if mask.sum() > 0:
-        	#ERRORS- 
-        		#CommandNotFound Error Message: Your shell has not been properly configured to use 'conda activate'
-        		#FileNotFound: python: can't open file 'GeneticSearch.py': [Errno 2] No such file or directory
 
-            #command1 = subprocess.Popen(['python GeneticSearch.py', './assets/Snail.jpg', './assets/Snail_GT.jpg'])
-            #command1 = subprocess.Popen(['bash -c "conda activate root; python GeneticSearch.py"', './assets/Snail_resize.jpg', './assets/Snail_GT.jpg'], shell=True)
-            #subprocess.Popen(['conda run -n env; python GeneticSearch.py', './assets/Snail_resize.jpg', './assets/Snail_GT.jpg'], shell=True)
             seg = segmentation_generic(im, mask, mode=algorithm)
+
         else:
         	seg = np.zeros(shape)
 
         return image_with_contour(im, seg, shape=shape)
     else:
         raise PreventUpdate
 
+
 #This function can be removed and shutil.copfile() can be used in the update_figure_upload function
 def file_copy(src, dest):
 	#Copy the source to destination
 	shutil.copyfile(src, dest) #Update dest filename after each segmentation
 	return
-
+    
 @app.callback(Output('canvas', 'image_content'),
             [Input('upload-image', 'contents')])
 def update_canvas_upload(image_string):
     # The line below causes NoneType Error
     if image_string is None:
         raise PreventUpdate
-    else:
+    else:        
         print("uploading", image_string[:100])
         return image_string
 
@@ -192,6 +193,7 @@ def change_focus(string):
     return 'segmentation-canvas-tab'
 
 
+
 if __name__ == '__main__':
     app.run_server(debug=True)
 

monitor.py

@@ -0,0 +1,32 @@
+# Monitoring files for changes
+# pip install watchdog
+
+import time
+from watchdog.observers import Observer
+from watchdog.events import FileSystemEventHandler
+
+class MyHandler(FileSystemEventHandler):
+	def on_modified(self, event):
+		print("{event.src_path} has been modified")
+
+event_handler = MyHandler()
+observer = Observer()
+observer.schedule(event_handler, path = '.', recursive=False)
+observer.start()
+
+try:
+	while True:
+		time.sleep(1)
+except KeyboardInterrupt:
+	observer.stop()
+observer.join()
+
+# watchdog in javascript?
+
+# When you run this program and make any changes to any file in current directory,
+# the on_modified function from MyHandler class gets called with the event.
+# In the MyHandler class you can define your own functions to handle the events. 
+# In the path, you can specify the files/directories you want to monitor. 
+# To stop this program, use Ctrl + C
+
+# Monitor a filesystem and react when a change occurs, so that I can check for the segmentation mask in the directory