includes fixes from downstairs

ArduinoWidgets.py

@@ -52,6 +52,9 @@ def __init__(self, parent):
         # signals
         self.Signals = Signals()
 
+        self.stopped = False
+        self.reprogram = False
+
         self.initUI()
 
     def initUI(self):
@@ -60,6 +63,12 @@ def initUI(self):
         self.FormLayout.setVerticalSpacing(10)
         self.FormLayout.setLabelAlignment(QtCore.Qt.AlignRight)
 
+        # reprogram
+        self.reprogramCheckBox = QtWidgets.QCheckBox("reupload sketch")
+        self.reprogramCheckBox.setChecked(False)
+        self.reprogramCheckBox.stateChanged.connect(self.reprogramCheckBox_changed)
+        self.FormLayout.addRow(self.reprogramCheckBox)
+
         # get com ports and ini selector
         # com_ports = self.get_com_ports()
         # TODO is this UI element required? Yes if you want to run multiple box from one computer
@@ -137,9 +146,11 @@ def initUI(self):
 
     # FUTURE TODO implement baud rate selector
 
-    # def reset_board(self):
-    #     # TODO implement - necessary?
-    #     pass
+    def reprogramCheckBox_changed(self):
+        if self.reprogramCheckBox.checkState() == 2:
+            self.reprogram = True
+        else:
+            self.reprogram = False
 
     def send(self,command):
         """ sends string command interface to arduino, interface compatible """
@@ -277,7 +288,10 @@ def Run(self,folder):
             self.log_task(folder)
 
         # upload
-        self.upload()
+        if self.reprogram:
+            self.upload()
+        else:
+            print(" --- resetting arduino only --- reusing previous sketch --- ")
 
         # connect to serial port
         self.connection = self.connect()
@@ -303,7 +317,7 @@ def Run(self,folder):
         # everybody that needs to do sth when new data arrives listens to that signal
 
         def read_from_port(ser):
-            while True:
+            while not self.stopped:
                 try:
                     line = ser.readline().decode('utf-8').strip()
                     if line is not '': # filtering out empty reads
@@ -317,10 +331,15 @@ def read_from_port(ser):
                     # FIXME CHECK if this will also fail on failed reads!
                     break
 
-        thread = threading.Thread(target=read_from_port, args=(self.connection, ))
-        thread.start() # apparently this line is not passed, thread hangs here? if yes,then why multithreading at all???
+        self.thread = threading.Thread(target=read_from_port, args=(self.connection, ))
+        self.thread.start() # apparently this line is not passed, thread hangs here? if yes,then why multithreading at all???
 
     def closeEvent(self, event):
+
+        # take care of ending the threads
+        self.stopped = True
+        self.thread.join()
+
         # overwrite logged arduino vars file
         if self.parent().logging:
             try:

HardwareWidgets.py

@@ -56,25 +56,18 @@ def Run(self,folder):
         animal = self.parent().animal
         task = self.parent().task
         task_config = self.parent().task_config['Bonsai']
-        # task_folder = os.path.join(self.parent().profile['tasks_folder'], task)
         task_folder = Path(self.parent().profile['tasks_folder']).joinpath(task)
-
-        # fname = animal+'.raw' # FIXME there is a thing with _ and 0 appended, check this
-
         out_path = folder.joinpath('bonsai_') # this needs to be fixed in bonsai
-
-
+
         # constructing the bonsai exe string
         parameters = "-p:save_path=\""+str(out_path)+"\""
 
         # TODO add bonsai com_port passing, check if multiple can be passed with colon separation
         # parameters = "-p:save_path=\""+str(out_path)+"\""
 
         bonsai_exe = Path(self.parent().profiles['General']['bonsai_cmd'])
-
-        # bonsai_workflow = os.path.join(task_folder,'Bonsai',task_config['workflow_fname'])
         bonsai_workflow = task_folder.joinpath('Bonsai',task_config['workflow_fname'])
-        bonsai_workflow = "\""+bonsai_workflow+"\""
+
 
         command = ' '.join([str(bonsai_exe),str(bonsai_workflow),"--start",parameters,"&"])
 
@@ -87,6 +80,10 @@ def Run(self,folder):
 
     pass
 
+    def closeEvent(self, event):
+        # stub
+        self.close()
+
 """
  __        ______        ___       _______   ______  _______  __       __
 |  |      /  __  \      /   \     |       \ /      ||   ____||  |     |  |
@@ -118,6 +115,8 @@ def __init__(self, parent):
 
         self.Buffer = sp.zeros((100,2))
 
+        self.stopped = False
+
         self.LoadCellMonitor = LoadCellMonitor(self)
         self.init_udp_server()
         self.initUI()
@@ -198,7 +197,7 @@ def Run(self, folder):
         # exception and then I let it pass w/o doing anything. Verify if necessary
 
         def udp_reader():
-            while True:
+            while not self.stopped:
                 try:
                     # read data and publish it via a qt signal
                     # raw_read = sock.recv(12) # replace chunk size stuff with 1 int 2 floats or whatever you get from bonsai
@@ -279,7 +278,8 @@ def closeEvent(self, event):
         # if serial connection is open, close it
         if hasattr(self,'arduino_2nd_ser'):
             self.arduino_2nd_ser.close()
-        self.LoadCellMonitor.close()
+
+        self.stopped = True
         # self.th_read.join()
         self.close()
 
@@ -368,6 +368,11 @@ def on_lc_data(self,x,y):
         self.LineFB_pp.setData(y=self.lc_data[:,0])
         self.LineLR_pp.setData(y=self.lc_data[:,1])
 
+
+    def closeEvent(self, event):
+        # stub
+        self.close()
+
 """ copy paste working script from the computer downstairs """
 # ###
 # import sys, os

TaskControl.py

@@ -35,8 +35,8 @@ def onLastClosed(self):
 
 if __name__ == "__main__":
     import argparse
-    # profiles_fpath = 'profiles_fphot.ini' # the fiber photometry computer downstairs in the viv
-    profiles_fpath = 'profiles_ccu.ini' # my ccu desktop in the open lab
+    profiles_fpath = 'profiles_fphot.ini' # the fiber photometry computer downstairs in the viv
+    # profiles_fpath = 'profiles_ccu.ini' # my ccu desktop in the open lab
 
     # argparsing
     parser = argparse.ArgumentParser(description=' xXx Unified TaskControl xXx ')

Tasks/dummy_dev/Arduino/platformio.ini

@@ -1,7 +1,7 @@
-[env:megaatmega2560]
-platform = atmelavr
-board = megaatmega2560
-framework = arduino
-upload_port = /dev/ttyACM0
-src_filter = +<main.cpp>
-
+[env:megaatmega2560]
+platform = atmelavr
+board = megaatmega2560
+framework = arduino
+upload_port = COM8
+src_filter = +<main.cpp>
+