Pre Shift Speed Changes

andor_repo/andor.egg-info/PKG-INFO

@@ -1,10 +1,10 @@
-Metadata-Version: 1.0
+Metadata-Version: 2.1
 Name: andor
 Version: 0.0.0
 Summary: UNKNOWN
 Home-page: UNKNOWN
-Author: UNKNOWN
-Author-email: UNKNOWN
 License: UNKNOWN
-Description: UNKNOWN
 Platform: UNKNOWN
+
+UNKNOWN
+

andor_repo/andor/andor_driver.py

@@ -11,13 +11,12 @@ def __init__(self):
         self.cam = atmcd()# atmcd("") was working. Switch back if a problem! Without the "" also appears to be working #load the atmcd library
         # self.reset()
 
-
         (ret) = self.cam.Initialize("/usr/local/etc/andor") #initialise camera # C:\Program Files\Andor SDK
         (ret, iSerialNumber) = self.cam.GetCameraSerialNumber()
 
         (ret) = self.cam.CoolerON()        
         (ret) = self.cam.SetCoolerMode(1)  
-        (ret) = self.cam.SetTemperature(-40) #David added this
+        (ret) = self.cam.SetTemperature(-60) #David added this
         (ret) = self.cam.SetHSSpeed(0,0) #David added this 0
         (ret) = self.cam.SetVSSpeed(4)#.3) #David added this
         (ret) = self.cam.SetVSAmplitude(0) #David added this
@@ -49,7 +48,7 @@ def __init__(self):
         (ret, self.xpixels, self.ypixels) = self.cam.GetDetector()
         self.imageSize = self.xpixels*self.ypixels
         (ret) = self.cam.SetImage(1, 1, 1, self.xpixels, 1, self.ypixels)
-        (ret) = self.cam.SetExposureTime(0.012) # Set exposure time here!
+        (ret) = self.cam.SetExposureTime(0.001) # Set exposure time here! 0.012
         (ret, self.fminExposure, self.fAccumulate, self.fKinetic) = self.cam.GetAcquisitionTimings()
 
         ##############################################################

andor_repo/andor/atmcd.py

@@ -52,9 +52,9 @@ def __init__(self):
       self.dll = cdll.LoadLibrary(dllname)
     elif sys.platform == "win32":
       if platform.architecture()[0] == "64bit" :
-        dllname = "C:\\Program Files\\Andor SDK\\atmcd64d.dll"
+        dllname = "C:\\Program Files\\Andor SOLIS\\atmcd64d.dll"
       else:
-        dllname = "C:\\Program Files\\Andor SDK\\atmcd32d.dll"
+        dllname = "C:\\Program Files\\Andor SOLIS\\atmcd32d.dll"
       self.dll = windll.LoadLibrary(dllname)
     else:
       print("Cannot detect operating system, will now stop")

flir_repo/driver_spyder.py

@@ -0,0 +1,234 @@
+
+import math
+import logging
+import asyncio
+import asyncserial
+import os
+import matplotlib.pyplot as plt
+import keyboard
+import time
+import PySpin
+import sys
+import time
+import numpy as np
+from PIL import Image
+import os
+os.environ["KMP_DUPLICATE_LIB_OK"]="TRUE"
+
+GAIN_VALUE = 23.8 #in dB, 0-40;
+#GAMMA_VALUE = 0.5 #0.25-1
+
+# MOT_OFFSET_HEIGHT = 0 #These corrections are for a MOT that is not at the center of the frame
+# MOT_OFFSET_WIDTH  = 0
+#OFFSET = 964 #52 #652 #This will be the pixel width and height of the roi
+IMAGE_HEIGHT = 964 #964 #OFFSET #964 pixels default
+IMAGE_WIDTH  = 1288 #1288 #OFFSET #1288 pixels default
+# HEIGHT_OFFSET = round((964+1-IMAGE_HEIGHT-MOT_OFFSET_HEIGHT)/2)#(964-IMAGE_HEIGHT)/2) # Y, to keep in middle of sensor
+# WIDTH_OFFSET = round((1288+1-IMAGE_WIDTH-MOT_OFFSET_WIDTH)/2)#(1288-IMAGE_WIDTH)/2) # X, to keep in middle of sensor
+
+global continue_recording
+continue_recording = True
+
+CHOSEN_TRIGGER = 2
+
+logger = logging.getLogger(__name__)
+
+
+class UnexpectedResponse(Exception):
+    pass
+
+# Set camera serial numbers
+serial_1 = '20343286'
+
+# Get system
+system = PySpin.System.GetInstance()
+
+# Get camera list
+cam_list = system.GetCameras()
+
+# Get cameras by serial
+cam_1 = cam_list.GetBySerial(serial_1)
+
+###################### init #################################
+
+# Initialize cameras
+cam_1.Init()
+
+# Set acquisition mode to acquire a single frame, this ensures acquired images are sync'd since camera 2 and 3 are setup to be triggered
+cam_1.AcquisitionMode.SetValue(PySpin.AcquisitionMode_Continuous)     
+cam_1.ExposureAuto.SetValue(PySpin.ExposureAuto_Off)
+cam_1.ExposureMode.SetValue(PySpin.ExposureMode_Timed) #Timed or TriggerWidth (must comment out trigger parameters other that Line)
+cam_1.ExposureTime.SetValue(1000)
+cam_1.GainAuto.SetValue(PySpin.GainAuto_Off)
+cam_1.Gain.SetValue(GAIN_VALUE)
+
+#cam_1.Gamma.SetValue(GAMMA_VALUE)                       #always fails?
+#cam_1.AdcBitDepth.SetValue(PySpin.AdcBitDepth_Bit16)    #always fails?
+
+cam_1.PixelFormat.SetValue(PySpin.PixelFormat_Mono16)
+cam_1.Width.SetValue(IMAGE_WIDTH)
+cam_1.Height.SetValue(IMAGE_HEIGHT)
+# cam_1.OffsetX.SetValue(WIDTH_OFFSET)
+# cam_1.OffsetY.SetValue(HEIGHT_OFFSET)
+
+#This takes an image quickly. The first image is always corrupt for whatever reason. This picture is not saved.
+cam_1.TriggerMode.SetValue(PySpin.TriggerMode_Off)
+cam_1.BeginAcquisition()
+cam_1.EndAcquisition()
+
+cam_1.TriggerSource.SetValue(PySpin.TriggerSource_Line0)
+cam_1.TriggerSelector.SetValue(PySpin.TriggerSelector_FrameStart)
+cam_1.TriggerActivation.SetValue(PySpin.TriggerActivation_RisingEdge)
+
+cam_1=cam_1
+
+print("FLIR driver initialization successful...")
+
+#################### await_trigger ###################################
+
+cam_1.ExposureTime.SetValue(int(4000)) # microseconds
+cam_1.TriggerMode.SetValue(PySpin.TriggerMode_Off)
+cam_1.TriggerMode.SetValue(PySpin.TriggerMode_On)
+cam_1.BeginAcquisition()
+
+#################### convert_images ###################################
+images=[]
+
+image = cam_1.GetNextImage()
+print("Picture Successfully taken at: ",time.strftime("%d %b %Y %H:%M:%S", time.localtime()))
+images.append(np.array(image.GetData(),dtype="uint16").reshape((image.GetHeight(),image.GetWidth()))) #convert PySpin ImagePtr into numpy array 
+image.Release()
+
+cam_1.EndAcquisition()
+
+#################### save_image ###################################
+
+image = Image.fromarray(images[0])
+
+# Save images
+msec = str(time.time())[11:14]
+filename = 'H%s_M%d_S%g_MS' % (int(time.strftime("%H", time.localtime())), int(time.strftime("%M", time.localtime())),int(time.strftime("%S", time.localtime())))
+filename = filename+msec
+##########################Save locally############################################
+pre1 = time.time()
+if os.path.isfile(r"S:\flir_images\Image_"+filename+".png") == True:
+    image.save(r"S:\flir_images\Image_"+filename+"(2).png")
+    post1=time.time()-pre1
+    print("Saved image "+filename+"(2).png locally in",post1*1000, "millisecond")
+else:
+    image.save(r"S:\flir_images\Image_"+filename+".png")
+    post1=time.time()-pre1
+    print("Saved image "+filename+".png locally in",post1*1000, "millisecond")
+        ##########################Save locally############################################   
+
+        #########################Save to datadepot############################################
+        # pre2 = time.time()
+        # if os.path.isfile(r"N:\data\flir_images\Image_"+filename+".png") == True:
+            # image.save(r"N:\data\flir_images\Image_"+filename+"(2).png")
+            # post2=time.time()-pre2
+            # print("Saved image "+filename+"(2).png to datadepot in",post2*1000, "millisecond")
+        # else:
+            # image.save(r"N:\data\flir_images\Image_"+filename+".png")
+            # post2=time.time()-pre2
+            # print("Saved image "+filename+".png to datadepot in",post2*1000, "millisecond")
+        #########################Save to datadepot############################################
+
+        # print((post2-post1)*1000, "millisecond lag between datadepot and local saves")
+
+
+# def reset():
+#     cam_1.DeInit()
+#     cam_1.EndAcquisition()
+#     del cam
+#     cam_list.Clear()
+#     PySpin.System.CloseInstance()
+
+
+
+  #####################################################################
+      # async def _ser_readline():
+        # c = await port.read(1)
+        # print(c)
+        # r = c
+        # while c != b"\n":
+            # c = await port.read(1)
+            # r += c
+        # return r
+
+    # async def _ser_send( cmd, get_response=True):
+        # """Send a string to the serial port."""
+
+        # Low-level routine for sending serial commands to device. It sends
+        # strings and listens for a response terminated by a carriage return.
+        # example:
+        # ser_send("F0 1.0") # sets the freq of channel 0 to 1.0 MHz
+
+        # if simulation:
+            # logger.info("simulation _ser_send(\"%s\")", cmd)
+        # else:
+            # logger.debug("_ser_send(\"%s\")", cmd)
+            # port.ser.reset_input_buffer()
+            # await port.write((cmd + "\r\n").encode())
+            # if get_response:
+                # result = (await _ser_readline()).rstrip().decode()
+                # logger.debug("got response from device: %s", result)
+                # if result != "OK":
+                    # errstr = error_codes.get(result, "Unrecognized reply")
+                    # s = "Erroneous reply from device: {ec}, {ecs}".format(
+                        # ec=result, ecs=errstr)
+                    # raise ValueError(s)
+            # else:
+                # pass
+
+    # async def setup():
+        # """Initial setup of FLIR."""
+        # await _ser_send("E d", get_response=False)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# 1. Get image
+# 2. Convert to array immediately
+# 3. Bin it (roi) (trash most of array)
+# 4. (For abs imaging: background )
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

flir_repo/flir.egg-info/PKG-INFO

@@ -1,10 +1,9 @@
-Metadata-Version: 1.0
+Metadata-Version: 2.1
 Name: flir
 Version: 0.0.0
 Summary: UNKNOWN
-Home-page: UNKNOWN
-Author: UNKNOWN
-Author-email: UNKNOWN
 License: UNKNOWN
-Description: UNKNOWN
 Platform: UNKNOWN
+
+UNKNOWN
+

flir_repo/flir.egg-info/entry_points.txt

@@ -1,3 +1,2 @@
 [console_scripts]
 aqctl_flir = flir.aqctl_flir:main
-

flir_repo/flir/driver.py

@@ -29,7 +29,7 @@
 global trigtype
 SOFTWARE = 1
 HARDWARE = 2
-trigtype=SOFTWARE
+trigtype=HARDWARE
 class TriggerType():
     def __init__(self, softtrig):
         global trigtype
@@ -53,8 +53,7 @@ def __init__(self):
         # try:
 
         # Set camera serial numbers
-        serial_1 = '20343286' # abs camera
-        #serial_2 = '20409335'# fluorescence camera
+        serial_1 = '20409335' # 20343286' # abs camera (286 was the original abs camera and 335 is the new one)
 
         # Get system
         self.system = PySpin.System.GetInstance()
@@ -77,7 +76,7 @@ def __init__(self):
         cam.ExposureMode.SetValue(PySpin.ExposureMode_Timed) #Timed or TriggerWidth (must comment out trigger parameters other that Line)
         cam.ExposureTime.SetValue(100) #us
         cam.GainAuto.SetValue(PySpin.GainAuto_Off)
-        cam.Gain.SetValue(1)# Previously 23.8
+        cam.Gain.SetValue(23.8)# Previously 23.8
 
         #cam.Gamma.SetValue(GAMMA_VALUE)                       #always fails?
         #cam.AdcBitDepth.SetValue(PySpin.AdcBitDepth_Bit16)    #always fails?
@@ -109,7 +108,7 @@ def __init__(self):
 
     def await_trigger(self, EXPOSURE_TIME):
         try:
-            time.sleep(0.01)
+            # time.sleep(0.01)
             self.cam_1.ExposureTime.SetValue(int(EXPOSURE_TIME))
             self.cam_1.BeginAcquisition()
 
@@ -140,7 +139,7 @@ def get_image(self,num_of_im):
         images=[]
         for i in range(num_of_im):
             # print("Before GetNextImage")
-            image = self.cam_1.GetNextImage(20000) #timeout (ms) 10000
+            image = self.cam_1.GetNextImage(50000) #timeout (ms) 20000
             # print("Picture Successfully taken at: ",time.strftime("%d %b %Y %H:%M:%S", time.localtime()))
             images.append(np.array(image.GetData(),dtype="uint16").reshape((image.GetHeight(),image.GetWidth()))) #convert PySpin ImagePtr into numpy array 
             image.Release()