UC2-REST 0.2.0.17__tar.gz → 0.2.0.18__tar.gz

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UC2-REST
-Version: 0.2.0.17
+Version: 0.2.0.18
 Summary: This pacage will help you to drive the ESP32-driven microscopy control modules from UC2
 Home-page: https://github.com/openUC2/UC2-REST
 Author: Benedict Diederich

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/UC2_REST.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UC2-REST
-Version: 0.2.0.17
+Version: 0.2.0.18
 Summary: This pacage will help you to drive the ESP32-driven microscopy control modules from UC2
 Home-page: https://github.com/openUC2/UC2-REST
 Author: Benedict Diederich

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/uc2rest/UC2Client.py

@@ -160,6 +160,7 @@ class UC2Client(object):
             # FIXME: this is not working
             url = f"http://{self.host}:{self.port}{path}"
             try:
+                if timeout==0: timeout=.2
                 r = requests.post(url, json=payload, headers=self.headers,  timeout=timeout)
                 returnMessage = r.json()
                 returnMessage["success"] = r.status_code==200
@@ -172,7 +173,7 @@ class UC2Client(object):
         elif self.is_serial or self.isPyScript:
             if timeout <=0:
                 getReturn = False
-            return self.serial.post_json(path, payload, getReturn=getReturn, nResponses=nResponses)
+            return self.serial.post_json(path, payload, getReturn=getReturn, timeout=timeout, nResponses=nResponses)
         else:
             self.logger.error("No ESP32 device is connected - check IP or Serial port!")
             return None

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/uc2rest/__version__.py

@@ -6,7 +6,7 @@ __version__.py
 
 __title__ = 'UC2-REST'
 __description__ = 'This pacage will help you to drive the ESP32-driven microscopy control modules from UC2'
-__version__ = "v0.2.0.17"
+__version__ = "v0.2.0.18"
 __author__ = 'Benedict Diederich'
 __author_email__ = 'benedictdied@gmail.com'
 __license__ = 'GPL v3'

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/uc2rest/home.py

@@ -78,7 +78,7 @@ class Home(object):
                 {
                  "stepperid": axis,
                  "timeout":timeout*1000,
-                 "speed":speed,
+                 "speed":direction*abs(speed),
                  "direction":direction,
                  "endposrelease":endposrelease, 
                  "endstoppolarity":endstoppolarity

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/uc2rest/laser.py

@@ -46,7 +46,7 @@ class Laser(object):
 
         }
         #self._parent.logger.debug("Setting Laser "+str(channel)+", value: "+str(value))
-        r = self._parent.post_json(path, payload, getReturn=is_blocking)
+        r = self._parent.post_json(path, payload, getReturn=is_blocking, timeout=.5)
         return r
 
     def set_laserpin(self, laserid=1, laserpin=0):
@@ -61,33 +61,3 @@ class Laser(object):
         r = self._parent.post_json(path, payload)
         return r
 
-    def get_laserpins(self):
-        path = '/laser_get'
-        
-        r = self._parent.get_json(path)
-        
-        if type(r) is dict:
-            # cast laser pins
-            if "LASER1pin" in r: r["LASER1pin"] = int(r["LASER1pin"])
-            else: r["LASER1pin"] = 0
-            if r.__contains__("LASER2pin"): r["LASER2pin"] = int(r["LASER2pin"])
-            else: r["LASER2pin"] = 0
-            if r.__contains__("LASER3pin"): r["LASER3pin"] = int(r["LASER3pin"])
-            else: r["LASER3pin"] = 0
-        else:
-            r={}
-            r["LASER1pin"] = 0
-            r["LASER2pin"] = 0
-            r["LASER3pin"] = 0
-        
-        return r
-    
-    def get_laserpin(self, laserid=1):
-        path = '/laser_get'
-        
-        payload = {
-            "task": path,
-        }
-        
-        r = self._parent.post_json(path, payload,timeout=2)
-        return r["LASER"+str(laserid)+"pin"]

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/uc2rest/motor.py

@@ -48,14 +48,17 @@ class Motor(object):
         self.stepSizeZ =  1
         self.stepSizeA =  1
 
+        self.DEFAULT_ACCELERATION = 10000
+
         self.motorAxisOrder = [0,1,2,3] # motor axis is 1,2,3,0 => X,Y,Z,T # FIXME: Hardcoded
 
         # register a callback function for the motor status on the serial loop
-        self._parent.serial.register_callback(self._callback_motor_status, pattern="steppers")
+        if hasattr(self._parent, "serial"):
+            self._parent.serial.register_callback(self._callback_motor_status, pattern="steppers")
 
         # move motor to wake them up #FIXME: Should not be necessary!
-        self.move_stepper(steps=(1,1,1,1), speed=(1000,1000,1000,1000), is_absolute=(False,False,False,False))
-        self.move_stepper(steps=(-1,-1,-1,-1), speed=(1000,1000,1000,1000), is_absolute=(False,False,False,False))
+        #self.move_stepper(steps=(1,1,1,1), speed=(1000,1000,1000,1000), is_absolute=(False,False,False,False))
+        #self.move_stepper(steps=(-1,-1,-1,-1), speed=(1000,1000,1000,1000), is_absolute=(False,False,False,False))
 
     def _callback_motor_status(self, data):
         ''' cast the json in the form:
@@ -77,7 +80,46 @@ class Motor(object):
         except Exception as e:
             print("Error in _callback_motor_status: ", e)
 
+    def setTrigger(self, axis="X", pin=1, offset=0, period=1):
+        # {"task": "/motor_act", "setTrig": {"steppers": [{"stepperid": 1, "trigPin": 1, "trigOff":0, "trigPer":1}]}}
+        if type(axis) is not int:
+            axis = self.xyztTo1230(axis)
+        path = "/motor_act"
+        payload = {
+            "task": path,
+            "setTrig":{
+                "steppers": [
+                {
+                 "stepperid": axis,
+                 "trigPin": pin,
+                 "trigOff": offset,
+                 "trigPer": period
+                 }]
+            }}
+        r = self._parent.post_json(path, payload)
+        return r
+
+    # {"task": "/motor_act", "stagescan": {"nStepsLine": 100, "dStepsLine": 1, "nTriggerLine": 1, "nStepsPixel": 100, "dStepsPixel": 1, "nTriggerPixel": 1, "delayTimeStep": 10, "stopped": 0, "nFrames": 5}}"}}
+    def startStageScanning(self, nStepsLine=100, dStepsLine=1, nTriggerLine=1, nStepsPixel=100, dStepsPixel=1, nTriggerPixel=1, delayTimeStep=10, nFrames=5):
+        path = "/motor_act"
+        payload = {
+            "task": path,
+            "stagescan":{
+                "nStepsLine": nStepsLine,
+                "dStepsLine": dStepsLine,
+                "nTriggerLine": nTriggerLine,
+                "nStepsPixel": nStepsPixel,
+                "dStepsPixel": dStepsPixel,
+                "nTriggerPixel": nTriggerPixel,
+                "delayTimeStep": delayTimeStep,
+                "stopped": 0,
+                "nFrames": nFrames
+            }}
+        r = self._parent.post_json(path, payload)
+        return r
 
+    def stopStageScanning(self):
+        self.startStageScanning(stopped=1)
 
     def setIsCoreXY(self, isCoreXY = False):
         self.isCoreXY = isCoreXY
@@ -164,7 +206,7 @@ class Motor(object):
             # have to move only one motor to move in XY direction
            return self.move_xyza(steps=(0,steps[0], steps[1], 0), speed=(0,speed[0],speed[1],0), is_blocking=is_blocking, is_absolute=is_absolute, is_enabled=is_enabled, timeout=timeout)
         else:
-            if len(speed)!= 2:
+            if type(speed)==int or len(speed)!= 2:
                 speed = (speed,speed)
 
             if len(acceleration)!= 2:
@@ -339,10 +381,12 @@ class Motor(object):
                              "position": int(steps[iMotor]),
                              "speed": int(speed[iMotor]),
                              "isabs": isAbsoluteArray[iMotor],
-                             "isaccel":0,
+                             "isaccel":1,
                              "isen": is_enabled}
                 if acceleration[iMotor] is not None:
                     motorProp["accel"] = int(acceleration[iMotor])
+                else:
+                    motorProp["accel"] = self.DEFAULT_ACCELERATION
                 motorPropList.append(motorProp)
 
         path = "/motor_act"
@@ -478,7 +522,7 @@ class Motor(object):
         r = self._parent.post_json(path, payload)
         return r
 
-    def get_position(self, axis=None, timeout=1):
+    def get_position(self, axis=None, timeout=.2):
         # pulls all current positions from the stepper controller
         path = "/motor_get"
         payload = {
@@ -489,7 +533,7 @@ class Motor(object):
         _physicalStepSizes = np.array((self.stepSizeA, self.stepSizeX, self.stepSizeY, self.stepSizeZ))
 
         # this may be an asynchronous call.. #FIXME!
-        r = self._parent.post_json(path, payload, getReturn = True, nResponses=1)
+        r = self._parent.post_json(path, payload, getReturn = True, nResponses=1, timeout=timeout)
         if "motor" in r:
             for index, istepper in enumerate(r["motor"]["steppers"]):
                 _position[istepper["stepperid"]]=istepper["position"]*_physicalStepSizes[self.motorAxisOrder[index]]

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/uc2rest/mserial.py

@@ -9,7 +9,7 @@ class Serial:
     def __init__(self, port, baudrate=115200, timeout=5,
                  identity="UC2_Feather", parent=None, DEBUG=False):
 
-        self.ser = None
+        self.serialdevice = None
         self.serialport = port
         self.baudrate = baudrate
         self.timeout = timeout
@@ -42,7 +42,7 @@ class Serial:
 
         # initialize serial connection
         self.thread = None
-        self.ser = self.openDevice(port, baudrate)
+        self.serialdevice= self.openDevice(port, baudrate)
 
     def breakCurrentCommunication(self):
         self.resetLastCommand = True
@@ -66,7 +66,7 @@ class Serial:
     def openDevice(self, port=None, baud_rate=115200):
         try: # try to close an eventually open serial connection
             if str(type(self.ser)) != "<class 'uc2rest.mserial.MockSerial'>":
-                self.ser.close()
+                self.serialdevice.close()
         except: pass
 
         try:
@@ -104,6 +104,12 @@ class Serial:
         return ser
 
     def findCorrectSerialDevice(self):
+        '''
+        This function tries to find the correct serial device from the list of available ports
+        It also checks if the firmware is correct by sending a command and checking for the correct response
+        It may be that - depending on the OS - the response may be corrupted
+        If this is the case try to hard-code the COM port into the config JSON file
+        '''
         _available_ports = serial.tools.list_ports.comports(include_links=False)
         ports_to_check = ["COM", "/dev/tt", "/dev/a", "/dev/cu.SLA", "/dev/cu.wchusb"]
         descriptions_to_check = ["CH340", "CP2102"]
@@ -148,7 +154,7 @@ class Serial:
         ser.write(json.dumps(payload).encode('utf-8'))
         ser.write(b'\n')
         # iterate a few times in case the debug mode on the ESP32 is turned on and it sends additional lines
-        for i in range(100):
+        for i in range(500):
             # if we just want to send but not even wait for a response
             mReadline = ser.readline()
             if self.DEBUG: self._logger.debug("[checkFirmware]: "+str(mReadline))
@@ -173,9 +179,9 @@ class Serial:
             # Check if the last command went through successfully
             #if not self.command_queue.empty() and not reading_json:
             #    currentIdentifier, command = self.command_queue.get()
-                
+
             # device not ready yet
-            if self.ser is None:
+            if self.serialdevice is None:
                 self.is_connected = False
                 continue
             else:
@@ -183,11 +189,9 @@ class Serial:
 
             # if we just want to send but not even wait for a response
             try:
-                mReadline = self.ser.readline()
+                mReadline = self.serialdevice.readline()
             except Exception as e:
                 self._logger.error("Failed to read the line in serial: "+str(e))
-                self.is_connected = False
-                break
             try:
                 line = mReadline.decode('utf-8').strip()
                 if self.DEBUG and line!="": self._logger.debug("[ProcessLines]:"+str(line))
@@ -212,7 +216,7 @@ class Serial:
 
                 except Exception as e:
                     self._logger.error("Failed to load the json from serial %s" % buffer)
-                    self._logger.error("Error: %s", e)
+                    self._logger.error("Error: %s" % str(e))
                     json_response = {}
 
                 with self.lock:
@@ -235,7 +239,7 @@ class Serial:
         message = json.dumps(message)
         return self.sendMessage(message, nResponses=0, timeout=timeout)
 
-    def post_json(self, path, payload, getReturn=True, nResponses=1, timeout=1):
+    def post_json(self, path, payload, getReturn=True, nResponses=1, timeout=100):
         """Make an HTTP POST request and return the JSON response"""
         if payload is None:
             payload = {}
@@ -290,16 +294,14 @@ class Serial:
         try:
             json_command = json.dumps(command)+"\n"
             with self.lock:
-                t0 = time.time()
-                self.ser.flush()
+                self.serialdevice.flush()
                 self._logger.debug("[SendMessage]: "+str(json_command))
-                self.ser.write(json_command.encode('utf-8') )
-                self._logger.debug("[SendMessage] took: "+str(time.time()-t0))
+                self.serialdevice.write(json_command.encode('utf-8') )
         except Exception as e:
             if self.DEBUG: self._logger.error(e)
             return "Failed to Send"
         self.commands[identifier]=command
-        if nResponses <= 0 or not self.is_connected or not type(self.ser.BAUDRATES) is tuple:
+        if nResponses <= 0 or not self.is_connected or not type(self.serialdevice.BAUDRATES) is tuple:
             return identifier
         while self.running:
             time.sleep(0.002)
@@ -320,7 +322,7 @@ class Serial:
     def stop(self):
         self.running = False
         self.thread.join()
-        self.ser.close()
+        self.serialdevice.close()
 
     def closeSerial(self):
         self.stop()
@@ -329,7 +331,7 @@ class Serial:
     def reconnect(self):
         self.running = False
         try:
-            self.ser.close()
+            self.serialdevice.close()
         except:
             pass
         self.serialdevice = self.openDevice(port = self.serialport, baud_rate = self.baudrate)
@@ -388,6 +390,9 @@ class MockSerial:
         self.manufacturer = "UC2Mock"
         self.BAUDRATES = -1
 
+    def flush(self):
+        pass
+
     def isOpen(self):
         return self.is_open
 

{UC2-REST-0.2.0.17 → UC2-REST-0.2.0.18}/uc2rest/temperature.py

@@ -1,8 +1,8 @@
 class Temperature(object):
-    
+
     def __init__(self, parent):
         self._parent = parent
-        
+
     '''
     ##############################################################################################################################
     Temperature Controllers
@@ -12,9 +12,9 @@ class Temperature(object):
     def stop_heating(self):
         r = self.set_temperature(active=0)
         return r
-    
-    def set_temperature(self, active=1, Kp=1000, Ki=0.1, Kd=0.1, target=37, timeout=600000, updaterate=1000):
-        # {"task": "/heat_act", "active":1, "Kp":1000, "Ki":0.1, "Kd":0.1, "target":37, "timeout":600000, "updaterate":1000}
+
+    def set_temperature(self, active=1, Kp=1000, Ki=0.1, Kd=0.1, target=37, timeout=600000000, updaterate=1000):
+        # {"task": "/heat_act", "active":1, "Kp":1000, "Ki":0.1, "Kd":0.1, "target":37, "timeout":60000000, "updaterate":1000}
         path = "/heat_act"
         payload = {
             "task": path,
@@ -28,19 +28,19 @@ class Temperature(object):
             }
         r = self._parent.post_json(path, payload, getReturn=False)
         return r
-    
+
     def get_temperature(self, timeout=0.5):
         path = "/heat_get"
         r = self._parent.get_json(path, timeout=timeout)
         try:
             r = r["heat"]
         except:
-            r = 9999
+            r = -273.15
         return r
 
 
 if __name__ == "__main__":
-    
+
     #%%
     import uc2rest
     import time
@@ -52,5 +52,3 @@ if __name__ == "__main__":
         time.sleep(1)
     ESP32.temperature.stop_heating()
     ESP32.close()
-
-