beg of day

andor_repo/andor/andor_driver.py

@@ -29,7 +29,7 @@ def __init__(self):
         (ret) = self.cam.SetBaselineClamp(1)
         (ret) = self.cam.SetOutputAmplifier(0) # 0 is EMCCD. David added this
         (ret) = self.cam.SetEMGainMode(3) # Max is 300? David added this
-        (ret) = self.cam.SetEMCCDGain(11) # Max is 300? David added this ###########################################################
+        (ret) = self.cam.SetEMCCDGain(100) # Max is 300? David added this ###########################################################
         (ret) = self.cam.SetCountConvertMode(1) # 1 is electron, 2 is photon
         (ret) = self.cam.SetFrameTransferMode(0)
         # (ret) = self.cam.SetCountConvertWavelength(float(852))
@@ -53,7 +53,7 @@ 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! 0.012
+        (ret) = self.cam.SetExposureTime(0.010) # Set exposure time here! WAS 0.010 ms!
         (ret, self.fminExposure, self.fAccumulate, self.fKinetic) = self.cam.GetAcquisitionTimings()
 
         (ret) = self.cam.PrepareAcquisition()
@@ -82,26 +82,34 @@ def __init__(self):
         # # # else:
             # # # print("shift_speed_change failed")
 
-    def retrieve_trigger(self,images=1,timeout = 0): # Time out time in seconds
-        # print("Retrieving trigger...")
-        # time1 = time.time()
+    def retrieve_trigger(self,images=2,timeout = 0): # Time out time in milliseconds
+
         for i in range(images):
-            win32event.WaitForSingleObject(self.event, (timeout*1000 + 1000)) # 12000 is 12 second timeout
-        # print(time.time()-time1)
+            # win32event.WaitForSingleObject(self.event, (timeout*1000 + 1000)) # This was the old, working one
+            ret = win32event.WaitForSingleObject(self.event, (timeout)) # 1 second extra delay was removed as of 7/29
+        # time.sleep(0.07)
+        # ret = win32event.WaitForSingleObject(self.event, (timeout)) # 1 second extra delay was removed as of 7/29
+        return np.int32(ret)
 
     def reset_image(self):
         self.cam.CancelWait()
         self.cam.AbortAcquisition()
 
     def start_acquisition_event(self):
         self.event = win32event.CreateEvent(None, 0, 0, None)
-        self.cam.SetDriverEvent(self.event)
-        self.cam.StartAcquisition()
+        ret = self.cam.SetDriverEvent(self.event)
+        if atmcd.DRV_SUCCESS==ret:
+            ret = self.cam.StartAcquisition()
+        else:
+            pass
+
+        return np.int32(ret)
+        # print('started')
 
     def trigger_count(self):
-        _,__,x = self.cam.GetNumberAvailableImages()
-        print(x,"triggers received")
-        return x
+        x = self.cam.GetNumberAvailableImages()[2]
+        # print(x,"triggers received")
+        return np.int32(x)
 
     def get_last_image(self):
         (ret, fullFrameBuffer) = self.cam.GetMostRecentImage(self.imageSize) # GetImages(somethinghere) might be a better command if we want to do background subtraction
@@ -112,7 +120,35 @@ def get_specific_image(self, image_number):
         (ret, fullFrameBuffer, validfirst, validlast) = self.cam.GetImages(image_number,image_number,self.imageSize)
         image = np.reshape(fullFrameBuffer, (512,512)) #Converts c_long 262k array to 512x512 image numpy array
         return image
-
+
+    def get_crop_image(self, cropx_min = 401, cropx_max = 441, cropy_min = 358, cropy_max = 398, image_number = 1, zero = False):
+        (ret, fullFrameBuffer, validfirst, validlast) = self.cam.GetImages(image_number,image_number,self.imageSize)
+        image = np.reshape(fullFrameBuffer, (512,512))
+        image = image[cropx_min:cropx_max,cropy_min:cropy_max]*1
+        # image[17:20,18:21] = image[17:20,18:21] + 10000 # This line is used for visualizing pixels of interest on image in artiq
+        if zero == False:
+            image = image * 1
+        if zero == True:
+            image = image * 0
+        return image
+
+    def get_both_crop_image(self, cropx_min = 401, cropx_max = 441, cropy_min = 358, cropy_max = 398, zero = False):
+        (ret, image0, validfirst, validlast) = self.cam.GetImages(1,1,self.imageSize)
+        image0 = np.reshape(image0, (512,512))
+        image0 = image0[cropx_min:cropx_max,cropy_min:cropy_max]           
+
+        (ret, image1, validfirst, validlast) = self.cam.GetImages(2,2,self.imageSize)
+        image1 = np.reshape(image1, (512,512))
+        image1 = image1[cropx_min:cropx_max,cropy_min:cropy_max]
+        if zero == False:
+            image0 = image0 * 1
+            image1 = image1 * 1
+        if zero == True:
+            image0 = image0 * 0
+            image1 = image1 * 0
+        return image0
+
+
     def get_all_images(self,image_number = 2):
         image_arr = [0]*image_number
         for i in range(image_number):
@@ -162,4 +198,4 @@ def take_pic(self):
     def reset(self):
         (ret) = self.cam.SetShutter(0,2,50,50)
         (ret) = self.cam.ShutDown()
-        print("Camera Reset Successful...")
+        print("Camera Reset Successful...")

andor_repo/andor/andor_testing.py

@@ -0,0 +1,86 @@
+from pyAndorSDK2 import atmcd
+import win32event
+import numpy as np
+import matplotlib.pyplot as plt
+import time
+''' To be run in Spyder. Run andor_driver first then run this in the same terminal '''
+
+
+
+cam = atmcd()# atmcd("") was working. Switch back if a problem! Without the "" also appears to be working #load the atmcd library
+# reset()
+
+(ret) = cam.Initialize("/usr/local/etc/andor") #initialise camera # C:\Program Files\Andor SDK
+(ret, iSerialNumber) = cam.GetCameraSerialNumber()
+(ret) = cam.CoolerON()    
+(ret) = cam.SetCoolerMode(1)  
+(ret) = cam.SetTemperature(-60) 
+(ret) = cam.SetADChannel(0) # Added 4/6/22
+(ret) = cam.SetHSSpeed(0,0) # 0 corresponds to 17MHz on AD channel 0 (the only channel for our camera) in EM Gain mode
+# print("HSSpeed",cam.GetHSSpeed(0, 0, 0))
+(ret) = cam.SetVSSpeed(4) # 4 corresponds to 3.3us. 0 is .3
+# print("VSSpeed",cam.GetVSSpeed(4))
+(ret) = cam.SetVSAmplitude(0) # 0 corresponds to 'Normal'   3 required for good image at 0.3 usec VSSpeed 
+# print("Number VSAmplitudes is",cam.GetNumberVSAmplitudes())
+(ret) = cam.SetPreAmpGain(2) # 2 corresponds to a gain of 3.0
+# print("PreAmpGain", cam.GetPreAmpGain(2))
+
+(ret) = cam.SetBaselineClamp(1)
+(ret) = cam.SetOutputAmplifier(0) # 0 is EMCCD. David added this
+(ret) = cam.SetEMGainMode(3) # Max is 300? David added this
+(ret) = cam.SetEMCCDGain(100) # Max is 300? David added this ###########################################################
+(ret) = cam.SetCountConvertMode(1) # 1 is electron, 2 is photon
+(ret) = cam.SetFrameTransferMode(0)
+# (ret) = cam.SetCountConvertWavelength(float(852))
+(ret) = cam.SetShutter(0,1,50,50) # (0,1,50,50) opens shutter. (0,2,50,50) closes shutter.   
+# (ret) = cam.SetAcquisitionMode(1)
+##############################################################
+(ret) = cam.SetFastExtTrigger(1) #when FastExtTrigger is active, set to 1, camera will NOT wait until a Keep Clean cycle is complete before taking an image
+(ret) = cam.SetAcquisitionMode(3) #3 is Kinetics 
+(ret) = cam.SetNumberKinetics(2) #number of images taken in an acquisition
+(ret) = cam.EnableKeepCleans(1)
+(ret) = cam.SetNumberAccumulations(1) #Default value is 1. Excplicitly stating this is probably unnecessary. 
+# (ret) = cam.SaveEEPROMToFile(r'C:\Users\hoodl\Desktop\EEPROM.txt') # This breaks the camera initialization.
+#(ret) = SetIsolatedCropMode(1, 30, 30, 1, 1)
+##############################################################
+(ret) = cam.SetReadMode(4)
+(ret) = cam.SetTriggerMode(1) # 0 is internal, 1 is external, 6 is external start?
+(ret, xpixels, ypixels) = cam.GetDetector()
+imageSize = xpixels*ypixels
+(ret) = cam.SetImage(1, 1, 1, xpixels, 1, ypixels)
+(ret) = cam.SetExposureTime(0.010) # Set exposure time here! WAS 0.010 ms!
+(ret, fminExposure, fAccumulate, fKinetic) = cam.GetAcquisitionTimings()
+(ret) = cam.PrepareAcquisition()
+
+if atmcd.DRV_SUCCESS==ret:
+    print("Andor Initializiation was successful...")
+else:
+    print("Andor Initializiation failed...Try restarting Artiq and/or powercycling camera")
+
+#%%
+
+event = win32event.CreateEvent(None, 0, 0, None)
+cam.SetDriverEvent(event)
+ret = cam.StartAcquisition() # It needs time.sleep(0.07) between StartAcq and WaitForSingleObject
+#%% 
+
+time.sleep(0.07) # Needed
+print(cam.GetNumberAvailableImages()[2])
+# retrieve_trigger
+# for i in range(2):
+ret = win32event.WaitForSingleObject(event, 1) # 1 second extra delay was removed as of 7/29
+    # print(ret)
+
+# time.sleep(0.5)
+
+(ret, image,_,_) = cam.GetImages(1,1,imageSize)
+img0 = np.reshape(image, (512,512)) #Converts c_long 262k array to 512x512 image numpy array
+(ret, image,_,_) = cam.GetImages(2,2,imageSize)
+img1 = np.reshape(image, (512,512)) #Converts c_long 262k array to 512x512 image numpy array  
+
+# plt.imshow(img0)
+
+print('img0/img1',np.mean(img0),np.mean(img1))
+
+cam.CancelWait()
+cam.AbortAcquisition()

flir_repo/flir/driver.py

@@ -53,8 +53,8 @@ def __init__(self):
         # try:
 
         # Set camera serial numbers
-        serial_1 = '20343286' # currently replacing Andor
-        #serial_1 = '20409335'  # diagonal flourescence (on stage carriage)
+        #serial_1 = '20343286' # Back objective camera
+        serial_1 = '20409335'  # Diagonal fluorescence (on stage carriage)
 
         # Get system
         self.system = PySpin.System.GetInstance()
@@ -75,7 +75,7 @@ def __init__(self):
         cam.AcquisitionMode.SetValue(PySpin.AcquisitionMode_Continuous)     
         cam.ExposureAuto.SetValue(PySpin.ExposureAuto_Off)
         cam.ExposureMode.SetValue(PySpin.ExposureMode_Timed) #Timed or TriggerWidth (must comment out trigger parameters other that Line)
-        cam.ExposureTime.SetValue(100) #us
+        cam.ExposureTime.SetValue(50) #us
         cam.GainAuto.SetValue(PySpin.GainAuto_Off)
         cam.Gain.SetValue(23.8)# Previously 23.8
 
@@ -131,16 +131,14 @@ def await_trigger(self, EXPOSURE_TIME):
             except:
                 pass
             print("Error in await_trigger(), try restarting artiq")
-
-
-
+
     def get_image(self,num_of_im):
         # try:
         # Acquire images.  Output is python list of images as numpy arrays
         images=[]
         for i in range(num_of_im):
             # print("Before GetNextImage")
-            image = self.cam_1.GetNextImage(50000) #timeout (ms) 20000
+            image = self.cam_1.GetNextImage(6000) #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()
@@ -153,7 +151,21 @@ def get_image(self,num_of_im):
             # except:
                 # pass
             # print("Error in get_image(), try restarting artiq")
+
+    def get_next_image(self):
+        # try:
+        # Acquire images.  Output is python list of images as numpy arrays
+
+        # print("Before GetNextImage")
+        image = self.cam_1.GetNextImage(20000) #timeout (ms) 20000
+        # print("Picture Successfully taken at: ",time.strftime("%d %b %Y %H:%M:%S", time.localtime()))
+        img = np.array(image.GetData(),dtype="uint16").reshape((image.GetHeight(),image.GetWidth())) #convert PySpin ImagePtr into numpy array 
+        image.Release()
 
+        return img
+
+    def end_acquisition(self):
+        self.cam_1.EndAcquisition()
 
     def save_image(self, imagearray):#,image_1, image_2):
         try: