updated NeuralNetworks

src/yass/yass_gui.py

@@ -18,7 +18,7 @@ class plot_widget:
     def __init__(self,  window):
         self.window = window
 
-	# voltage window
+		# voltage window
         self.fig2 = Figure(figsize=(6,3))
         self.a2 = self.fig2.add_subplot(111)
         self.a2.set_yticks([])
@@ -28,7 +28,7 @@ def __init__(self,  window):
         self.canvas2.get_tk_widget().place(x = 225, y = 300)#, relwidth = , relheight = 1)
         self.canvas2.draw()
 
-	# geometry window
+		# geometry window
         self.fig1 = Figure(figsize=(3.0,3))
         self.a = self.fig1.add_subplot(111)
         self.a.set_ylabel("um", fontsize=8)
@@ -69,6 +69,7 @@ def set_filename_denoise(self):
         self.nn_denoise_box.delete(0, 'end')
         self.nn_denoise_box.insert(0, self.nn_denoise_txt)
 
+
     def refresh(self):
 
 		# yaml can't save tuples, so we save them as strings
@@ -83,26 +84,28 @@ def refresh(self):
 
         self.config_params['neuralnetwork']['denoise']['filter_sizes'] = \
 			 str(self.config_params['neuralnetwork']['denoise']['filter_sizes'])
-
-		# update entries from screen
+
+
+		# update single entries from screen
         self.root_dir = self.root_dir_box.get()
-        #self.config_params['data']['root_folder']+self.config_params['data']['recordings']
-        #self.data_root + self.config_params['data']['recordings']
 
         self.sample_rate = float(self.sample_rate_box.get())
-        self.config_params['recordings']['sampling_rate'] = self.sample_rate
+        self.config_params['recordings']['sampling_rate'] = int(self.sample_rate)
 
         self.n_chan = int(self.n_chan_box.get())
         self.config_params['recordings']['n_channels'] = self.n_chan
 
         self.radius = float(self.radius_box.get())
         self.config_params['recordings']['spatial_radius'] = self.radius
 
-	# redraw everything
-	# plot geometry file
+        self.spike_size_ms = float(self.spike_size_ms_box.get())
+        self.config_params['recordings']['spike_size_ms'] = self.spike_size_ms
+
+		# redraw everything
+		# plot geometry file
         self.window.filemenu.plot.plot_geom()
 
-	# load snipit of data and visualize
+		# load snipit of data and visualize
         self.window.filemenu.plot.plot_voltage()
 
         with open(self.fname_config[:-5]+"_modified.yaml", 'w') as f:
@@ -118,6 +121,7 @@ def refresh(self):
 		# Replace the target string
         filedata = filedata.replace("'[", "[")
         filedata = filedata.replace("]'", "]")
+        filedata = filedata.replace("null", "")
 
 		# Write the file out again
         with open(self.fname_config[:-5]+"_modified.yaml", 'w') as file: 
@@ -160,12 +164,7 @@ def refresh_button(self, txt, x, y):
 	#self.filename_loaded = txt
         button_refresh = Button(self.window,text=txt,command=lambda:self.refresh())
         button_refresh.place(x=x, y=y)
-
-	# reread all text data into
-
-	# reload everything
-        # self.load_config()
-
+
 
     def display_train_run_button(self, label_txt, txt, x, y):
 	#self.filename_loaded = txt
@@ -176,9 +175,14 @@ def display_train_run_button(self, label_txt, txt, x, y):
         dirname=Entry(self.window)
         dirname.insert(0,txt)
         dirname.place(x=x+95,y=y)
+
 
     def run(self):
+
+		# first save the file
+        self.refresh()
 
+		# run yass
         cmd = "yass sort "+ self.fname_config[:-5]+"_modified.yaml"
 
         returned_value = os.system(cmd)  # returns the exit code in unix
@@ -213,11 +217,11 @@ def display_metadata_and_buttons(self):
 
         if self.config_params['data']['root_folder']=='./':
             self.data_root = os.path.split(self.fname_config)[0]+'/'
+            self.config_params['data']['root_folder'] = self.data_root
         else:
             self.data_root = self.config_params['data']['root_folder']
 
-        #print ("SELF data root: ", self.data_root)
-
+
 	# display root directory
         #text_ = self.config_params['data']['root_folder']+self.config_params['data']['recordings']
         text_ = self.data_root+self.config_params['data']['recordings']
@@ -238,19 +242,25 @@ def display_metadata_and_buttons(self):
         text_= self.config_params['recordings']['spatial_radius']
         self.radius_box = self.display_single("Neighbour dist ", text_,  70, 120)
         self.radius = float(text_)
+
+	# load radius of local chans:
+        text_= self.config_params['recordings']['spike_size_ms']
+        self.spike_size_ms_box = self.display_single("Spk width ", text_,  70, 150)
+        self.spike_size_ms = float(text_)
+
 
 	# Refresh button
         #text_ = config_params['neuralnetwork']['detect']['filename']
         self.refresh_button("Update config", 500, 30)
 
 	# display NN detect
         text_ = self.config_params['neuralnetwork']['detect']['filename']
-        self.nn_detect_button("NN detect", text_, 0, 160)
+        self.nn_detect_button("NN detect", text_, 0, 180)
         self.nn_detect = text_
 
 	# display NN denoise
         text_ = self.config_params['neuralnetwork']['denoise']['filename']
-        self.nn_denoise_button("NN detect", text_, 0, 190)
+        self.nn_denoise_button("NN detect", text_, 0, 210)
         self.nn_denoise = text_
 
 	# run YASS button
@@ -282,30 +292,27 @@ def plot_geom(self):
 
         self.a.set_title("Geometry (partial)\n(centre chan + neigbhours)", fontsize=8)    
 
-	# load geometry file
+		# load geometry file
         geom_file = self.data_root + self.config_params['data']['geometry']
-        print (geom_file)
+        #print (geom_file)
         geom = np.loadtxt(geom_file)
         #print ("Geom: ", geom)
 
         self.a.scatter(geom[:,0],geom[:,1],s=10, color='black')
 
-	#find nearest chan to middle:
+		#find nearest chan to middle:
         middle_chan_x = np.mean(geom[:,0])
         middle_chan_y = np.mean(geom[:,1])
         mid_chan_id = self.closest_node([middle_chan_x, middle_chan_y], geom)
 
         self.a.scatter(geom[mid_chan_id,0],geom[mid_chan_id,1],s=150,color='red')
 
-	# find chans within radius
+		# find chans within radius
         local_chans_id = self.chans_within_radius(geom[mid_chan_id], geom, self.radius)
 
         self.a.scatter(geom[local_chans_id,0],geom[local_chans_id,1],s=50, color='blue')
 
-	# zoom on on arrays to show middle chan + neighbour chans as example
-        #print (np.min(geom[local_chans_id,0]), np.min(geom[local_chans_id,1]))
-        #print (np.max(geom[local_chans_id,0]), np.max(geom[local_chans_id,1]))
-
+		# zoom on on arrays to show middle chan + neighbour chans as example
         spacer = 60
         if np.min(geom[local_chans_id,0])>0:
             min_ = np.min(geom[local_chans_id,0])-spacer
@@ -375,7 +382,7 @@ def plot_voltage(self):
             start_ch=0
 
         x = np.arange(end-start)/float(self.sampling_rate)
-        print (x.shape, end-start)
+        #print (x.shape, end-start)
         for c in range(start_ch,min(start_ch+10, start_ch+self.n_channels)):
             self.a2.plot(x, rawdata2D[start:end,c]+c*100,c='black')
 
@@ -394,7 +401,7 @@ def parse_yaml(self, filename):
 	    # scalar values to Python the dictionary format
             self.config_params = yaml.load(f, Loader=yaml.FullLoader)
 
-        print (self.config_params)
+        #print (self.config_params)
         # laod meta data
         self.window.filemenu.plot.display_metadata_and_buttons()
 
@@ -405,22 +412,3 @@ def parse_yaml(self, filename):
         self.window.filemenu.plot.plot_voltage()
 
 
-# root = Tk()
-# root.title('YASS')
-# root.geometry("800x600") #You want the size of the app to be 500x500
-# root.resizable(0, 0) 
-
-# # initialize plotting widget
-# plot = plot_widget(root)
-
-# # initialize menu widget
-# menubar = Menu(root)
-
-# # add menu items
-# root.filemenu = Menu(menubar, tearoff=0)
-# root.filemenu.plot = plot
-# root.filemenu.add_command(label="Open", command=plot.load_config)
-# menubar.add_cascade(label="File", menu=root.filemenu)
-
-# root.config(menu=menubar)
-# root.mainloop()