Implemented fluidics interface for syringe pump.

storm_control/fluidics/default_config_syringe.xml

@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<kilroy_configuration num_valves = "3" num_pumps = "1">
+  <valve_commands>
+    <valve_cmd name = "Stop Valve">
+       <valve_pos valve_ID = "1" port_ID = "1"></valve_pos>
+    </valve_cmd>
+    <valve_cmd name = "Flow Hybridization">
+      <valve_pos valve_ID = "1" port_ID = "2"></valve_pos>
+    </valve_cmd>
+    <valve_cmd name = "Flow Wash">
+      <valve_pos valve_ID = "1" port_ID = "3"></valve_pos>
+    </valve_cmd>
+    <valve_cmd name = "Flow STORM Buffer">
+      <valve_pos valve_ID = "1" port_ID = "4"></valve_pos>
+    </valve_cmd>
+    <valve_cmd name = "Set Hyb 1">
+      <valve_pos valve_ID = "2" port_ID = "1"></valve_pos>
+    </valve_cmd>
+    <valve_cmd name = "Set Hyb 2">
+      <valve_pos valve_ID = "2" port_ID = "2"></valve_pos>
+    </valve_cmd>
+    <valve_cmd name = "Set Hyb 3">
+      <valve_pos valve_ID = "2" port_ID = "3"></valve_pos>
+    </valve_cmd>
+    <valve_cmd name = "Set Hyb 4">
+      <valve_pos valve_ID = "2" port_ID = "4"></valve_pos>
+    </valve_cmd>
+  </valve_commands>
+
+  <pump_commands>
+     <pump_cmd name = "Flow 2mL">
+       <pump_config position = "2000" speed = "500"></pump_config>
+     </pump_cmd>
+  </pump_commands>
+
+  <kilroy_protocols>
+     <protocol name = "Extra Wash">
+	<valve duration = "0">Flow Wash</valve>
+        <pump duration = "200">Normal Flow</pump>
+	<pump duration = "0">Stop Flow</pump>
+     </protocol>
+     <protocol name = "Hybridize 1">
+        <pump duration = "0">Normal Flow</pump>
+        <valve duration = "20">Set Hyb 1</valve>
+	<valve duration = "10">Flow Hybridization</valve>
+	<valve duration = "10">Flow Wash</valve>
+	<valve duration = "10">Flow STORM Buffer</valve>
+	<pump duration = "0">Stop Flow</pump>
+     </protocol>
+     <protocol name = "Hybridize 2">
+        <pump duration = "0">Normal Flow</pump>
+        <valve duration = "20">Set Hyb 2</valve>
+	<valve duration = "10">Flow Hybridization</valve>
+	<valve duration = "10">Flow Wash</valve>
+	<valve duration = "10">Flow STORM Buffer</valve>
+	<pump duration = "0">Stop Flow</pump>
+     </protocol>
+   </kilroy_protocols>
+</kilroy_configuration>

storm_control/fluidics/kilroy.py

@@ -16,7 +16,8 @@
 import time
 from PyQt5 import QtCore, QtGui, QtWidgets
 from storm_control.fluidics.valves.valveChain import ValveChain
-from storm_control.fluidics.pumps.pumpControl import PumpControl
+from storm_control.fluidics.pumps.pumpControl import PeristalticPumpControl
+from storm_control.fluidics.pumps.pumpControl import SyringePumpControl
 from storm_control.fluidics.kilroyProtocols import KilroyProtocols
 from storm_control.sc_library.tcpServer import TCPServer
 import storm_control.sc_library.parameters as params
@@ -34,7 +35,12 @@ def __init__(self, parameters):
         self.tcp_port = parameters.get("tcp_port")
         self.pump_com_port = parameters.get("pump_com_port")
         self.pump_ID = parameters.get("pump_ID")
-
+
+        if not parameters.has("pump_type"):
+            self.pump_type = 'peristaltic'
+        else:
+            self.pump_type = parameters.get('pump_type')
+
         if not parameters.has("num_simulated_valves"):
             self.num_simulated_valves = 0
         else:
@@ -70,12 +76,16 @@ def __init__(self, parameters):
                                      verbose = self.verbose)
 
         # Create PumpControl instance
-        self.pumpControl = PumpControl(parameters = parameters)
-
+        if self.pump_type == 'peristaltic':
+            self.pumpControl = PeristalticPumpControl(parameters=parameters)
+        elif self.pump_type == 'syringe':
+            self.pumpControl = SyringePumpControl(parameters=parameters)
+
         # Create KilroyProtocols instance and connect signals
         self.kilroyProtocols = KilroyProtocols(protocol_xml_path = self.protocols_file,
                                                command_xml_path = self.commands_file,
-                                               verbose = self.verbose)
+                                               verbose = self.verbose,
+                                               pumpType = self.pump_type)
 
         self.kilroyProtocols.command_ready_signal.connect(self.sendCommand)
         self.kilroyProtocols.status_change_signal.connect(self.handleProtocolStatusChange)

storm_control/fluidics/kilroyProtocols.py

@@ -8,6 +8,8 @@
 # Jeff Moffitt
 # 2/15/14
 # [email protected]
+#
+# Updated 7/2019 by George Emanuel
 # ----------------------------------------------------------------------------------------
 
 # ----------------------------------------------------------------------------------------
@@ -33,7 +35,8 @@ class KilroyProtocols(QtWidgets.QMainWindow):
     def __init__(self,
                  protocol_xml_path = "default_config.xml",
                  command_xml_path = "default_config.xml",
-                 verbose = False):
+                 verbose = False,
+                 pumpType='peristaltic'):
         super(KilroyProtocols, self).__init__()
 
         # Initialize internal attributes
@@ -47,6 +50,7 @@ def __init__(self,
         self.status = [-1, -1] # Protocol ID, command ID within protocol
         self.issued_command = []
         self.received_message = None
+        self.pumpType = pumpType
 
         print("----------------------------------------------------------------------")
 
@@ -59,7 +63,8 @@ def __init__(self,
 
         # Create instance of PumpCommands class
         self.pumpCommands = PumpCommands(xml_file_path = self.command_xml_path,
-                                         verbose = self.verbose)
+                                         verbose = self.verbose,
+                                         pumpType = pumpType)
 
         # Connect pump commands issue signal
         self.pumpCommands.change_command_signal.connect(self.issuePumpCommand)

storm_control/fluidics/pumps/gilson_mp3.py

@@ -50,6 +50,9 @@ def __init__(self,
         self.startFlow(self.speed, self.direction)
         self.identification = self.getIdentification()
 
+    def pumpType(self):
+        return 'peristaltic'
+
     def getIdentification(self):
         return self.sendImmediate(self.pump_ID, "%")
 

storm_control/fluidics/pumps/hamilton_psd6.py

@@ -0,0 +1,147 @@
+#!/usr/bin/python
+# ----------------------------------------------------------------------------------------
+# The basic I/O class for a Hamilton syringe pump
+# ----------------------------------------------------------------------------------------
+# George Emanuel
+# 6/28/19
+# ----------------------------------------------------------------------------------------
+
+import serial
+
+acknowledge = '\x06'
+start = '\x0A'
+stop = '\x0D'
+
+
+# ----------------------------------------------------------------------------------------
+# HamiltonPSD6 Syringe Pump Class Definition
+# ----------------------------------------------------------------------------------------
+class APump():
+    def __init__(self, parameters=False):
+
+        print('Initializing pump')
+
+        # Define attributes
+        self.com_port = parameters.get("pump_com_port", "COM3")
+        self.pump_ID = parameters.get("pump_ID", 30)
+        self.verbose = parameters.get("verbose", True)
+        self.simulate = parameters.get("simulate_pump", True)
+        self.serial_verbose = parameters.get("serial_verbose", False)
+        self.flip_flow_direction = parameters.get("flip_flow_direction", False)
+
+        # Create serial port
+        self.serial = serial.Serial(
+            port=self.com_port, baudrate=9600, timeout=0.1)
+
+        # enable h commands
+        self.sendString('/1h30001R\r')
+
+        # TODO Confirm that this initialization only pushes to waste
+        self.sendString('/1OZ1R\r')
+
+        # Define initial pump status
+        self.flow_status = "Stopped"
+        self.speed = 1000
+        self.direction = "Forward"
+
+        self.disconnect()
+        self.setSpeed(self.speed)
+        self.identification = 'HamiltonSyringe'
+
+    def pumpType(self):
+        return 'syringe'
+
+    def getIdentification(self):
+        return self.sendImmediate(self.pump_ID, "%")
+
+    def getPumpPosition(self):
+        return int(self.sendString('/1?R\r').decode()
+                   .split('`')[1].split('\x03')[0])
+
+    def getValvePosition(self):
+        positionDict = {
+            0: 'Moving',
+            1: 'Input',
+            2: 'Output',
+            3: 'Wash',
+            4: 'Return',
+            5: 'Bypass',
+            6: 'Extra'
+        }
+        return positionDict[int(self.sendString('/1?23000\r').decode()
+                                .split('`')[1].split('\x03')[0])]
+
+    def getStatus(self):
+        return (self.getPumpPosition(), self.getValvePosition())
+
+        message = self.readDisplay()
+
+        if self.flip_flow_direction:
+            direction = {" ": "Not Running", "-": "Forward", "+": "Reverse"}. \
+                get(message[0], "Unknown")
+        else:
+            direction = {" ": "Not Running", "+": "Forward", "-": "Reverse"}. \
+                get(message[0], "Unknown")
+
+        status = "Stopped" if direction == "Not Running" else "Flowing"
+
+        control = {"K": "Keypad", "R": "Remote"}.get(message[-1], "Unknown")
+
+        auto_start = "Disabled"
+
+        speed = float(message[1:len(message) - 1])
+
+        return (status, self.getPumpPosition(), direction, control, auto_start, "No Error")
+
+    def close(self):
+        pass
+
+    def setValvePosition(self, valvePosition):
+        # valve position is either 'input' or 'output'
+        if valvePosition == 'Input':
+            self.sendString('/1IR\r')
+        elif valvePosition == 'Output':
+            self.sendString('/1OR\r')
+
+    def setSyringePosition(self, position, valvePosition=None, speed=500,
+                           emptyFirst=False):
+        commandString = '/1'
+
+        if emptyFirst:
+            commandString += 'OV5000A0'
+
+        if valvePosition is not None:
+            if valvePosition == 'Input':
+                commandString += 'I'
+            else:
+                commandString += 'O'
+
+        commandString += 'V' + str(int(speed))
+        commandString += 'A' + str(int(position))
+
+        self.sendString(commandString + 'R\r')
+
+    def emptySyringe(self):
+        self.sendString('/1OV5000A0R\r')
+
+    def stopSyringe(self):
+        self.sendString('/1TR\r')
+
+    def resetSyringe(self):
+        self.sendString('/1OZ1R\r')
+
+    def setSpeed(self, speed):
+        if 2 <= speed <= 5800:
+            self.sendString('/1V%iR\r' % speed)
+
+    def stopFlow(self):
+        self.setSpeed(0.0)
+        return True
+
+    def disconnect(self):
+        pass
+        #self.sendAndAcknowledge('\xff')
+
+    def sendString(self, string):
+        self.serial.write(string.encode())
+        return self.serial.readline()