routine

andor_repo/andor/andor_driver.py

@@ -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(0.010) # seoncds, Set exposure time here! 
+        (ret) = self.cam.SetExposureTime(0.030) # seoncds, Set exposure time here! 
         (ret, self.fminExposure, self.fAccumulate, self.fKinetic) = self.cam.GetAcquisitionTimings()
 
         (ret) = self.cam.PrepareAcquisition()
@@ -125,8 +125,7 @@ def get_crop_image(self, cropx_min = 419, cropx_max = 459, cropy_min = 358, crop
         (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
-        #[18:21,17:20] for 3x3 array as of 11/16/22
-        # image[19:20,18:20] = image[19:20,18:20] + 10000 # This line is used for visualizing pixels of interest on image in artiq
+        # image[19:21,18:20] = image[19:21,18:20] + 10000 # This line is used for visualizing pixels of interest on image in artiq
         if zero == False:
             image = image * 1
         if zero == True:

flir_repo/flir/driver.py

@@ -53,8 +53,8 @@ def __init__(self):
         # try:
 
         # Set camera serial numbers
-        #serial_1 = '20343286' # Back objective camera
-        serial_1 = '20409335'  # Diagonal fluorescence (on stage carriage)
+        serial_1 = '20343286' # Back objective camera
+        # serial_1 = '20409335'  # Diagonal fluorescence (on stage carriage)
 
         # Get system
         self.system = PySpin.System.GetInstance()
@@ -109,36 +109,39 @@ def __init__(self):
 
     def await_trigger(self, EXPOSURE_TIME):
         try:
-            # time.sleep(0.01)
-            self.cam_1.ExposureTime.SetValue(int(EXPOSURE_TIME))
-            self.cam_1.BeginAcquisition()
-
-            # This is a trigger test
-            # for i in range(1000):
-                # if self.cam_1.LineStatus() == True:
-                    # self.postpicture()
-                    # self.cam_1.TriggerMode.SetValue(PySpin.TriggerMode_Off)
-                    # time.sleep(1)
-                # else:
-                    # time.sleep(0.01)
-                    # print("Trying again or exiting")
-
-
-            print("Awaiting trigger...")
+            self.cam_1.EndAcquisition()
         except:
             try:
-                self.cam_1.EndAcquisition()
+                # time.sleep(0.01)
+                self.cam_1.ExposureTime.SetValue(int(EXPOSURE_TIME))
+                self.cam_1.BeginAcquisition()
+
+                # This is a trigger test
+                # for i in range(1000):
+                    # if self.cam_1.LineStatus() == True:
+                        # self.postpicture()
+                        # self.cam_1.TriggerMode.SetValue(PySpin.TriggerMode_Off)
+                        # time.sleep(1)
+                    # else:
+                        # time.sleep(0.01)
+                        # print("Trying again or exiting")
+
+
+                print("Awaiting trigger...")
             except:
-                pass
-            print("Error in await_trigger(), try restarting artiq")
+                try:
+                    self.cam_1.EndAcquisition()
+                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(6000) #timeout (ms) 20000
+            image = self.cam_1.GetNextImage(10000) #timeout (ms) 6000
             # 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()
@@ -157,11 +160,11 @@ def get_next_image(self):
         # Acquire images.  Output is python list of images as numpy arrays
 
         # print("Before GetNextImage")
-        image = self.cam_1.GetNextImage(20000) #timeout (ms) 20000
+        image = self.cam_1.GetNextImage(10000) #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()
-
+        # self.cam_1.EndAcquisition()
         return img
 
     def end_acquisition(self):

flir_repo/flir/testing.py

@@ -1,22 +1,3 @@
-# #%%
-# import matplotlib.pyplot as plt
-# import driver
-# t = driver.FLIR()
-
-# #%%
-
-# t.await_trigger(int(50))
-
-# output = t.convert_image(1)
-# img = output[0]
-
-
-
-# plt.imshow(img)
-
-# t.reset()
-
-
 #%%  Import libraries
 import math
 import logging
@@ -26,18 +7,19 @@
 import matplotlib.pyplot as plt
 import keyboard
 import time
-imporKeyboardInterrupt
+# imporKeyboardInterrupt
 import sys
 import time
 import numpy as np
 from PIL import Image
+import PySpin
 
 
 
-#%%   Initialize camera
+#%   Initialize camera
 # Set camera serial numbers
-serial_1 = '20343286' # abs camera
-#serial_2 = '20409335'# fluorescence camera
+serial = '20343286' # abs camera
+# serial = '20409335'# fluorescence camera
 
 # Get system
 system = PySpin.System.GetInstance()
@@ -46,7 +28,7 @@
 cam_list = system.GetCameras()
 
 # Get cameras by serial
-cam = cam_list.GetBySerial(serial_1)
+cam = cam_list.GetBySerial(serial)
 
 # Initialize cameras
 cam.Init()
@@ -75,43 +57,49 @@
 #cam.EndAcquisition()
 
 print("FLIR driver initialization successful... (pretrig)")
-#%%
+##%%
 cam.V3_3Enable.SetValue(True)
 cam.TriggerMode.SetValue(PySpin.TriggerMode_Off)
 cam.TriggerSource.SetValue(PySpin.TriggerSource_Line0)
 cam.TriggerMode.SetValue(PySpin.TriggerMode_On)
 
 cam.TriggerSelector.SetValue(1)   #0,1 PySpin.TriggerSelector_FrameStart
 cam.TriggerActivation.SetValue(PySpin.TriggerActivation_RisingEdge)
-
+    
 
 
 print("FLIR driver initialization successful... (posttrig)")
 
-#%%  Begin Acquisition
+##%  Begin Acquisition
 #cam.TriggerMode.SetValue(PySpin.TriggerMode_Off)
-cam.ExposureTime.SetValue(int(50))  #min value 49.2us
+# cam.ExposureTime.SetValue(int(50))  #min value 49.2us
+
+
 
 cam.BeginAcquisition()
+print("Beginning acquisition")
 
 
 #%%  Get Images
-num_of_im = 1
+num_of_im = 5
 images=[]
 for i in range(num_of_im):
-    print("Before GetNextImage")
-    #print('num images in use',cam.GetNumImagesInUse())
-    #print('data streams', cam.GetNumDataStreams())
-    image = cam.GetNextImage(5000) #timeout (ms) 10000
-    #print('num images in use',cam.GetNumImagesInUse())
-    #print('data streams', cam.GetNumDataStreams())
-    print(image.IsIncomplete())
-    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()
-    #print('num images in use',  cam.GetNumImagesInUse())
-    #print('data streams', cam.GetNumDataStreams())
-
+    try:
+        print("Before GetNextImage")
+        # print('num images in use',cam.GetNumImagesInUse())
+        # print('data streams', cam.GetNumDataStreams())
+        image = cam.GetNextImage(1000) #timeout (ms) 10000
+        # print('num images in use',cam.GetNumImagesInUse())
+        # print('data streams', cam.GetNumDataStreams())
+        print(image.IsIncomplete())
+        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()
+        # print('num images in use',  cam.GetNumImagesInUse())
+        # print('data streams', cam.GetNumDataStreams())
+    except:
+        print("failed")
+        cam.EndAcquisition()
 #%% Plot image
 for i in range(num_of_im):
     img = images[i]
@@ -123,10 +111,10 @@
 
 
 #%%
-cam.EndAcquisition()
+# cam.EndAcquisition()
 
 #%%
-f = plt.figure()
+# f = plt.figure()
 
 
 #%%  Close camera

flir_repo/flir/testing_2.py

@@ -0,0 +1,135 @@
+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
+
+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 = 960 #964 is max #OFFSET #964 pixels default
+IMAGE_WIDTH  = 1280 #1288 is max #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
+
+global trigtype
+SOFTWARE = 1
+HARDWARE = 2
+trigtype=HARDWARE
+class TriggerType():
+    def __init__(self, softtrig):
+        global trigtype
+        if softtrig is True:
+            trigtype=SOFTWARE
+        else:
+            trigtype=HARDWARE
+
+CHOSEN_TRIGGER = trigtype
+
+logger = logging.getLogger(__name__)
+
+# try:
+
+# Set camera serial numbers
+serial_1 = '20343286' # Back objective camera
+# serial_1 = '20409335'  # Diagonal fluorescence (on stage carriage)
+
+# Get system
+system = PySpin.System.GetInstance()
+
+# Get camera list
+cam_list = system.GetCameras()
+
+
+# Get cameras by serial
+cam = cam_list.GetBySerial(serial_1)
+
+# Initialize cameras
+cam.Init()
+
+#cam.FactoryReset()
+
+# 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.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(50) #us
+cam.GainAuto.SetValue(PySpin.GainAuto_Off)
+cam.Gain.SetValue(23.8)# Previously 23.8
+
+#cam.Gamma.SetValue(GAMMA_VALUE)                       #always fails?
+#cam.AdcBitDepth.SetValue(PySpin.AdcBitDepth_Bit16)    #always fails?
+
+cam.PixelFormat.SetValue(PySpin.PixelFormat_Mono16)
+cam.Width.SetValue(1280)
+cam.Height.SetValue(960)
+# cam.OffsetX.SetValue(WIDTH_OFFSET)
+# cam.OffsetY.SetValue(HEIGHT_OFFSET)
+
+#This takes an image quickly. The first image is always corrupt for whatever reason. This picture is not saved.
+#cam.BeginAcquisition()
+#cam.EndAcquisition()
+
+cam.V3_3Enable.SetValue(True)
+cam.TriggerMode.SetValue(PySpin.TriggerMode_Off)
+cam.TriggerSource.SetValue(PySpin.TriggerSource_Line0)
+cam.TriggerMode.SetValue(PySpin.TriggerMode_On)
+
+cam.TriggerSelector.SetValue(1)   #0,1 PySpin.TriggerSelector_FrameStart
+cam.TriggerActivation.SetValue(PySpin.TriggerActivation_RisingEdge)
+
+
+cam_1=cam
+
+print("FLIR driver initialization successful...")
+# except:
+   # print("Error in __init__(), try restarting artiq")
+
+# Await Trigger
+
+cam_1.ExposureTime.SetValue(int(50))
+cam_1.BeginAcquisition()
+
+print("Awaiting trigger...")
+
+# cam_1.EndAcquisition()
+
+#%% Get Image
+
+num_of_im = 5
+images=[]
+try:
+    for i in range(num_of_im):
+        print("Before GetNextImage")
+        image = cam_1.GetNextImage(1000) #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()
+
+except:
+    cam_1.EndAcquisition()
+    print("failed...ending acquisition")
+
+#%% Plot image
+for i in range(num_of_im):
+    img = images[i]
+    print( np.amax(img) , np.amin(img) )
+    plt.imshow(img)
+    plt.colorbar()
+    plt.show()
+
+

picomotor_repo/picomotor/aqctl_picomotor.py

@@ -37,7 +37,7 @@ def main():
     # if args.device is None:
         # print("Starting in Simulation mode...")
         # dev = andor(args.device if not args.simulation else None)
-    dev = picomotor("COM4")
+    dev = picomotor("COM3")
     #asyncio.get_event_loop().run_until_complete(dev.setup())
     try:
         print("picomotor server startup on port",args.port,"successful...")