Fix LDI laser engine errors caused by IlluminationController

software/control/celesta.py

@@ -10,6 +10,10 @@
 from squid.abc import LightSource
 from control.microscope import LightSourceType, IntensityControlMode, ShutterControlMode
 
+import squid.logging
+
+log = squid.logging.get_logger(__name__)
+
 
 def lumencor_httpcommand(command="GET IP", ip="192.168.201.200"):
     """
@@ -43,9 +47,9 @@ def __init__(self, **kwds):
             self.n_lasers = self.get_number_lasers()
             self.live = True
         except:
-            print(traceback.format_exc())
+            log.error(traceback.format_exc())
             self.live = False
-            print("Failed to connect to Lumencor Laser at ip:", ip)
+            log.error("Failed to connect to Lumencor Laser at ip:", ip)
 
         if self.live:
             [self.pmin, self.pmax] = self.get_intensity_range()
@@ -89,17 +93,14 @@ def get_color(self, laser_id):
         """Returns the color of the current laser"""
         self.message = lumencor_httpcommand(command="GET CHMAP", ip=self.ip)
         colors = self.message["message"].split(" ")[2:]
-        print(colors)
+        log.info(colors)
         return colors[int(laser_id)]
 
     def get_IP(self):
         self.message = lumencor_httpcommand(command="GET IP", ip=self.ip)
         return self.message
 
     def get_shutter_control_mode(self):
-        """
-        Return True/False the lasers can be controlled with TTL.
-        """
         self.message = lumencor_httpcommand(command="GET TTLENABLE", ip=self.ip)
         response = self.message["message"]
         if response[-1] == "1":
@@ -108,63 +109,45 @@ def get_shutter_control_mode(self):
             return ShutterControlMode.Software
 
     def set_shutter_control_mode(self, mode):
-        """
-        Turn on/off external TTL control mode.
-        """
         if mode == ShutterControlMode.TTL:
             ttl_enable = "1"
         else:
             ttl_enable = "0"
         self.message = lumencor_httpcommand(command="SET TTLENABLE " + ttl_enable, ip=self.ip)
 
     def get_shutter_state(self, laser_id):
-        """
-        Return True/False the laser is on/off.
-        """
         self.message = lumencor_httpcommand(command="GET CH " + str(laser_id), ip=self.ip)
         response = self.message["message"]
         self.on = response[-1] == "1"
         return self.on
 
     def get_intensity_range(self):
-        """
-        Return [minimum power, maximum power].
-        """
         max_int = 1000  # default
         self.message = lumencor_httpcommand(command="GET MAXINT", ip=self.ip)
         if self.message["message"][0] == "A":
             max_int = float(self.message["message"].split(" ")[-1])
         return [0, max_int]
 
     def get_intensity(self, laser_id):
-        """
-        Return the current laser power.
-        """
         self.message = lumencor_httpcommand(command="GET CHINT " + str(laser_id), ip=self.ip)
-        # print(command = 'GET CHINT '+str(laser_id), ip=self.ip)
+        log.debug(command = 'GET CHINT '+str(laser_id), ip=self.ip)
         response = self.message["message"]
         power = float(response.split(" ")[-1])
-        return power
+        intensity = power / self.pmax * 100
+        return intensity
 
     def set_shutter_state(self, laser_id, on):
-        """
-        Turn the laser on/off.
-        """
         if on:
             self.message = lumencor_httpcommand(command="SET CH " + str(laser_id) + " 1", ip=self.ip)
             self.on = True
         else:
             self.message = lumencor_httpcommand(command="SET CH " + str(laser_id) + " 0", ip=self.ip)
             self.on = False
-        print("Turning On/Off", self.on, self.message)
+        log.info("Turning On/Off", self.on, self.message)
 
-    def set_intensity(self, laser_id, power_in_mw):
-        """
-        power_in_mw - The desired laser power in mW.
-        """
-        print("Setting Power", power_in_mw, self.message)
-        if power_in_mw > self.pmax:
-            power_in_mw = self.pmax
+    def set_intensity(self, laser_id, intensity):
+        log.info("Setting intensity to ", intensity)
+        power_in_mw = self.pmax * intensity / 100
         self.message = lumencor_httpcommand(
             command="SET CHINT " + str(laser_id) + " " + str(int(power_in_mw)), ip=self.ip
         )
@@ -173,18 +156,12 @@ def set_intensity(self, laser_id, power_in_mw):
         return False
 
     def shut_down(self):
-        """
-        Turn the laser off.
-        """
         if self.live:
             for i in range(self.n_lasers):
                 self.set_intensity(i, 0)
                 self.set_shutter_state(i, False)
 
     def get_status(self):
-        """
-        Get the status
-        """
         return self.live
 
 

software/control/core/core.py

@@ -522,9 +522,6 @@ def __init__(
 
         self.enable_channel_auto_filter_switching = True
 
-        if USE_LDI_SERIAL_CONTROL:
-            self.ldi = self.microscope.ldi
-
         if SUPPORT_SCIMICROSCOPY_LED_ARRAY:
             # to do: add error handling
             self.led_array = serial_peripherals.SciMicroscopyLEDArray(

software/control/gui_hcs.py

@@ -21,7 +21,7 @@
 import squid.config
 import squid.stage.utils
 import control.microscope
-from control.microscope import LightSourceType, IntensityControlMode, ShutterControlMode
+from control.microscope import LightSourceType, IntensityControlMode, ShutterControlMode, IlluminationController
 
 log = squid.logging.get_logger(__name__)
 
@@ -371,7 +371,7 @@ def loadHardwareObjects(self):
         if USE_LDI_SERIAL_CONTROL:
             try:
                 self.ldi = serial_peripherals.LDI()
-                self.illuminationController = control.microscope.IlluminationController(
+                self.illuminationController = IlluminationController(
                     self.microcontroller, self.ldi.intensity_mode, self.ldi.shutter_mode, LightSourceType.LDI, self.ldi
                 )
             except Exception:
@@ -383,7 +383,7 @@ def loadHardwareObjects(self):
                 import control.celesta
 
                 self.celesta = control.celesta.CELESTA()
-                self.illuminationController = control.microscope.IlluminationController(
+                self.illuminationController = IlluminationController(
                     self.microcontroller,
                     IntensityControlMode.Software,
                     ShutterControlMode.TTL,

software/control/microscope.py

@@ -213,7 +213,6 @@ def __init__(
         self.channel_mappings_software = {}
         self.is_on = {}
         self.intensity_settings = {}
-        self.pmin, self.pmax = 0, 1000
         self.current_channel = None
 
         if self.light_source_type is not None:
@@ -224,7 +223,6 @@ def configure_light_source(self):
         self.set_intensity_control_mode(self.intensity_control_mode)
         self.set_shutter_control_mode(self.shutter_control_mode)
         self.channel_mappings_software = self.light_source.channel_mappings
-        self.get_intensity_range()
         for ch in self.channel_mappings_software:
             self.intensity_settings[ch] = self.get_intensity(ch)
             self.is_on[ch] = self.light_source.get_shutter_state(self.channel_mappings_software[ch])
@@ -249,14 +247,9 @@ def get_shutter_control_mode(self):
             self.shutter_control_mode = mode
             return mode
 
-    def get_intensity_range(self, channel=None):
-        if self.intensity_control_mode == IntensityControlMode.Software:
-            [self.pmin, self.pmax] = self.light_source.get_intensity_range()
-
     def get_intensity(self, channel):
         if self.intensity_control_mode == IntensityControlMode.Software:
-            power = self.light_source.get_intensity(self.channel_mappings_software[channel])
-            intensity = power / self.pmax * 100
+            intensity = self.light_source.get_intensity(self.channel_mappings_software[channel])
             self.intensity_settings[channel] = intensity
             return intensity  # 0 - 100
 
@@ -267,7 +260,6 @@ def turn_on_illumination(self, channel=None):
         if self.shutter_control_mode == ShutterControlMode.Software:
             self.light_source.set_shutter_state(self.channel_mappings_software[channel], on=True)
         elif self.shutter_control_mode == ShutterControlMode.TTL:
-            print("TTL!!")
             # self.microcontroller.set_illumination(self.channel_mappings_TTL[channel], self.intensity_settings[channel])
             self.microcontroller.turn_on_illumination()
 
@@ -290,8 +282,7 @@ def set_current_channel(self, channel):
     def set_intensity(self, channel, intensity):
         if self.intensity_control_mode == IntensityControlMode.Software:
             if intensity != self.intensity_settings[channel]:
-                power = intensity / 100 * self.pmax
-                self.light_source.set_intensity(self.channel_mappings_software[channel], power)
+                self.light_source.set_intensity(self.channel_mappings_software[channel], intensity)
                 self.intensity_settings[channel] = intensity
         self.microcontroller.set_illumination(self.channel_mappings_TTL[channel], intensity)
 

software/control/serial_peripherals.py

@@ -3,6 +3,8 @@
 import time
 from typing import Tuple, Optional
 import struct
+from control.microscope import LightSourceType, IntensityControlMode, ShutterControlMode
+from control._def import *
 from squid.abc import LightSource
 
 import squid.logging
@@ -430,6 +432,7 @@ def __init__(self, SN="00000001"):
             735: 730,
             750: 730,
         }
+        self.active_channel = None
 
     def initialize(self):
         self.serial_connection.write_and_check("run!\r", "ok")
@@ -459,33 +462,48 @@ def set_intensity(self, channel, intensity):
         intensity = "{:.2f}".format(intensity)
         self.log.debug("set:" + channel + "=" + intensity + "\r")
         self.serial_connection.write_and_check("set:" + channel + "=" + intensity + "\r", "ok")
-        self.log.debug("active channel: " + str(self.active_channel))
 
     def get_intensity(self, channel):
-        return 0  # To be implemented
-
-    def get_intensity_range(self):
-        return [0, 100]
-
-    def set_shutter_state(self, channel, state):
+        try:
+            response = self.serial_connection.write_and_read("set?\r")
+            pairs = response.replace('SET:', '').split(',')
+            intensities = {}
+            for pair in pairs:
+                channel, value = pair.split('=')
+                intensities[int(channel)] = int(value)
+            return intensity[channel]
+        except:
+            return None
+
+    def set_shutter_state(self, channel, on):
         channel = str(channel)
-        state = str(state)
+        state = str(on)
+        if self.active_channel is not None and channel != self.active_channel:
+            self.set_active_channel_shutter(False)
         self.serial_connection.write_and_check("shutter:" + channel + "=" + state + "\r", "ok")
+        if on:
+            self.active_channel = channel
 
     def get_shutter_state(self, channel):
-        self.serial_connection.write_and_check("shutter?\r", "")
-        return 0  # To be implemented
-
-    def set_active_channel(self, channel):
-        self.active_channel = channel
-        self.log.debug("[set active channel to " + str(channel) + "]")
+        try:
+            response = self.serial_connection.write_and_read("shutter?" + channel + "\r")
+            state = response.split('=')[1]
+            return 1 if state == 'OPEN' else 0
+        except:
+            return None
 
     def set_active_channel_shutter(self, state):
         channel = str(self.active_channel)
         state = str(state)
         self.log.debug("shutter:" + channel + "=" + state + "\r")
         self.serial_connection.write_and_check("shutter:" + channel + "=" + state + "\r", "ok")
 
+    def shut_down(self):
+        for ch in list(set(self.channel_mappings.values())):
+            self.set_intensity(ch, 0)
+            self.set_shutter_state(ch, False)
+        self.serial_connection.close()
+
 
 class LDI_Simulation(LightSource):
     """Wrapper for communicating with LDI over serial"""
@@ -539,25 +557,21 @@ def set_intensity(self, channel, intensity):
     def get_intensity(self, channel):
         return 0
 
-    def get_intensity_range(self):
-        return [0, 100]
-
-    def set_shutter_state(self, channel, state):
+    def set_shutter_state(self, channel, on):
         channel = str(channel)
-        state = str(state)
+        state = str(on)
 
     def get_shutter_state(self, channel):
         return 0
 
-    def set_active_channel(self, channel):
-        self.active_channel = channel
-        self.log.debug("[set active channel to " + str(channel) + "]")
-
     def set_active_channel_shutter(self, state):
         channel = str(self.active_channel)
         state = str(state)
         self.log.debug("shutter:" + channel + "=" + state + "\r")
 
+    def shut_down(self):
+        pass
+
 
 class SciMicroscopyLEDArray:
     """Wrapper for communicating with SciMicroscopy over serial"""

software/squid/abc.py

@@ -106,16 +106,6 @@ def get_intensity(self, channel) -> float:
         """
         pass
 
-    @abstractmethod
-    def get_intensity_range(self) -> Tuple[float, float]:
-        """
-        Get the valid intensity range.
-
-        Returns:
-            Tuple[float, float]: (minimum intensity, maximum intensity)
-        """
-        pass
-
     @abstractmethod
     def shut_down(self):
         """Safely shut down the light source."""