def getFrame(self, t_exp=None, bitdepth=None):
t_exp = t_exp or self.t_exp
bitdepth = bitdepth or self.bitdepth
# open lib
ic_ic = IC_ImagingControl()
ic_ic.init_library()
cam_names = ic_ic.get_unique_device_names()
cam = ic_ic.get_device(cam_names[0])
cam.open()
# change camera properties
cam.gain.auto = False # enable auto gain
cam.gain.value = cam.gain.min
t_exp_reg = int(
np.round(np.log2(t_exp))
) # convert exposure time into register value (nearest power of 2)
if t_exp_reg in range(cam.exposure.min, cam.exposure.max + 1):
cam.exposure.value = int(np.round(np.log2(t_exp)))
else:
cam.exposure.value = int(cam.exposure.max + cam.exposure.min) / 2
print('Exposure out of range. Setting to half of exposure range')
cam.formats = cam.list_video_formats()
cam.sensor_height = 1080
cam.sensor_width = 1920
cam.set_video_format(
b'Y800 (1920x1080)') # use first available video format
cam.enable_continuous_mode(True) # image in continuous mode
cam.start_live(show_display=False) # start imaging
cam.enable_trigger(True) # camera will wait for trigger
if not cam.callback_registered:
cam.register_frame_ready_callback(
) # needed to wait for frame ready callback
cam.reset_frame_ready() # reset frame ready flag
# send hardware trigger OR call cam.send_trigger() here
cam.send_trigger()
# get image data...
cam.wait_til_frame_ready(10) # wait for frame ready due to trigger
im = cam.get_image_data()
img = np.ndarray(buffer=im[0],
dtype=np.uint8,
shape=(cam.sensor_height, cam.sensor_width, 3))
cam.stop_live()
cam.close()
ic_ic.close_library()
cam.start_live()
def handle_frame(handle_ptr, p_data, frame_num, data):
print 'callback called!', frame_num
print time.time()
cam.register_frame_ready_callback(C_FRAME_READY_CALLBACK(handle_frame))
cam.snap_image(1000)
cam.snap_image(1000)
cam.snap_image(1000)
raw_input('Waiting for callback')
cam.save_image('output.jpg')
data, width, height, depth = cam.get_image_data()
print width, height
frame = np.ndarray(buffer=data,
dtype=np.uint8,
shape=(height, width, depth))
cam.stop_live()
cam.close()
ic.close_library()
class IC(daq_device):
"""
This class sets up data acquisition for (theoretically) all cameras from the imaging source.
This sets all of the camera properties relevant to a given camera. It utilizes the py-ic-ic wrapper
downloaded from github for the IC C library given on the imaging source website. It seems to mostly
work, but it takes a few tries to figure out how to use this program with each model of camera.
Test out different parameters in the .ini file until you get a good image from the camera.
Attributes
----------
ic_ic : idk what type
IC library grabber.
cam : idk what type
Camera being used.
software_trigger : bool
A boolean value which determines whether to use a software trigger or not.
video_index : int
An index which determines which video format the camera will be using.
width : int
The horizontal number of pixels used in the image being captured.
height : int
The vertical number of pixels used in the image being captured.
depth : int
The number of color channels used in the image being captured.
Methods
-------
figure_of_merit
Measure the figure of merit of the system.
shut_down
Shut down the Imaging Source camera.
"""
def __init__(self, device_string, fom_num):
"""
Initialize the Imaging Source camera.
Set all of the parameters for the chosen Imaging Source camera so that it is ready to
take an image.
Parameters
----------
device_string : str
A string naming which daq device to use.
fom_num : int
An int denoting which figure of merit this daq device will be using.
"""
super().__init__(device_string,
fom_num) # call the daq_device __init__ function
self.ic_ic = IC_ImagingControl(
) # initialize the imaging control grabber
self.ic_ic.init_library(
) # Use the grabber to initialze the library of IC functions we can use
# Determine the Imaging Source cameras connected to the computer
cam_names = self.ic_ic.get_unique_device_names()
if (len(cam_names) == 0): # no IC camera is connected
print("Error: No IC cameras connected to the computer.")
exit()
print("\nThese are the available cameras:")
print(cam_names)
print(
"Please select an IC camera to use by inputting the index of the camera."
)
print("The indices go from 0 to ", len(cam_names) - 1)
# Iterate through an infinite loop until the user defines which camera they want to use
while True:
index = int(input())
if ((index <= len(cam_names) - 1) and (index >= 0)):
self.cam = self.ic_ic.get_device(cam_names[index])
break
else:
print("You didn't enter a correct index.")
self.cam.open() # open the camera they chose
# Go through an infinite loop with user to decide to initialize with the .ini file or by setting all of the values
print(
"\nWould you like to set all of the camera initialization values yourself, or use the IC properties.ini file?"
)
print(
'Enter either "set" for setting all of the values or "ini" for the .ini file'
)
while True:
init = input()
if (init == "set"):
set_all = True
break
elif (init == "ini"):
set_all = False
break
else:
print("You didn't enter 'set' or 'ini'. Try again.")
# reset all properties before setting them
self.cam.reset_properties()
# Go through each property available and set its value
cam_properties = self.cam.list_property_names()
print(
"Note: this only goes through the camera properties available for this specific camera."
)
for attribute_index in range(
len(cam_properties
)): # for loop through each of the camera properties
if (getattr(self.cam, cam_properties[attribute_index]).available ==
True): # if the attribute can be set
if (set_all == True): # if the user wants to set everything
print("You are setting the",
cam_properties[attribute_index])
print(
"Its current value is ",
getattr(self.cam,
cam_properties[attribute_index]).value)
print(
"The range of values you can set this to is ",
getattr(self.cam,
cam_properties[attribute_index]).range)
print("What would you like to set this property to?")
while True:
change_value = input()
print("You entered", change_value,
"\nIs this okay? (enter 'y' or 'n')")
input_is_good = input()
if (input_is_good == 'y'):
break
elif (input_is_good == 'n'):
print(
"Type in what you'd like to change this property to instead"
)
else:
print(
"You didn't enter a y or an n. Enter what value you'd like to change the property to again."
)
else: # if the user is using the .ini file
if (self.initialize_array[attribute_index] == "auto"
): # if the .ini file has "auto" for this property
if (getattr(
self.cam,
cam_properties[attribute_index]).auto_available
== True):
getattr(
self.cam,
cam_properties[attribute_index]).auto = True
print("Set the camera",
cam_properties[attribute_index], "to auto")
else:
print("Auto setting unavailable for",
cam_properties[attribute_index])
print("Did not set",
cam_properties[attribute_index])
elif (self.initialize_array[attribute_index] == "none"
): # if the .ini file has "none" for this property
print("Did not set", cam_properties[attribute_index])
else: # if the .ini file has a value for its setting
if (type(
getattr(self.cam,
cam_properties[attribute_index]).value)
== int):
getattr(
self.cam,
cam_properties[attribute_index]).value = int(
self.initialize_array[attribute_index])
if (type(
getattr(self.cam,
cam_properties[attribute_index]).value)
== float):
getattr(
self.cam,
cam_properties[attribute_index]).value = float(
self.initialize_array[attribute_index])
print(
"Set the camera", cam_properties[attribute_index],
"to",
getattr(self.cam,
cam_properties[attribute_index]).value,
"within the range",
getattr(self.cam,
cam_properties[attribute_index]).range)
# the last property in the .ini file is whether the person wants the trigger
self.software_trigger = (
self.initialize_array[len(cam_properties)]
) == "True" # set the software trigger to True or False
# Determine the video format the user would like to use
formats = self.cam.list_video_formats()
print("\nThese are the available video formats:")
print(formats)
print(
"Please select video format to use by inputting the index of the format."
)
print("The indices go from 0 to ", len(formats) - 1)
# Iterate through an infinite loop until the user defines which video format they want to use
while True:
self.video_index = int(input())
if ((self.video_index <= len(formats) - 1)
and (self.video_index >= 0)):
self.cam.set_video_format(formats[self.video_index])
break
else:
print("You didn't enter a correct index.")
current_video_format = self.cam.get_video_format(
self.video_index) # set the video format
# if the video format stores the pixels left to right and top to bottom, set flip_image to True
if any(string in str(current_video_format)
for string in PIXEL_FORMAT_TOP_DOWN):
self.flip_image = True
else:
self.flip_image = False
self.cam.enable_continuous_mode(True) # image in continuous mode
self.cam.start_live(show_display=False) # start imaging
self.cam.enable_trigger(
self.software_trigger) # camera will wait for trigger
if not self.cam.callback_registered:
self.cam.register_frame_ready_callback(
) # needed to wait for frame ready callback
# determine the image dimensions
self.width, self.height, depth, color_format = self.cam.get_image_description(
)
self.depth = depth // 8 # I have no idea why the open source pyicic library does this
# take an image because for some cameras, the first image doesn't work correctly and then the rest work
self.__acquire()
def figure_of_merit(self):
"""
Determine the figure of merit using the Imaging Source camera.
Capture an image using the imaging source camera and then calculate the figure of merit.
"""
self.__acquire() # acquire an image from the camera
return figure_of_merit_f.ic_FOM(self.frameout, self.fom_num)
def __acquire(self):
"""
Capture an image.
Capture an image using the given IC camera and then save the image as frameout.
"""
self.cam.reset_frame_ready(
) # reset the frame ready flag to False so that we can wait for the frame to be ready
if (self.software_trigger):
self.cam.send_trigger(
) # send a software trigger if it was specified to do so
self.cam.wait_til_frame_ready(
1000) # wait for frame ready due to trigger
data, width, height, depth = self.cam.get_image_data(
) # Get the image from the camera
frame = np.ndarray(
buffer=data,
dtype=np.uint8,
shape=(self.height, self.width,
self.depth)) # turn this buffer into a numpy array
frameout = copy.deepcopy(
frame
) # deep copy this data so that if anything overwrites the camera memory, we still have the image
if self.flip_image: # if the pixels are written top to bottom, flip the image upside down
frameout = np.flipud(frameout)
del frame # take care of memory allocation
self.frameout = frameout # save the image
def shut_down(self):
"""
Shut down the camera and close the IC grabber.
"""
self.cam.stop_live() # stop capturing video from the camera
self.cam.close() # shut down the camera
self.ic_ic.close_library() # stop accessing the IC dll
def _previewCam(self, t_exp, bitdepth, displaythresh):
t_exp = t_exp or self.t_exp
bitdepth = bitdepth or self.bitdepth
# open lib
ic_ic = IC_ImagingControl()
ic_ic.init_library()
cam_names = ic_ic.get_unique_device_names()
cam = ic_ic.get_device(cam_names[0])
cam.open()
# change camera properties
cam.gain.auto = False # enable auto gain
cam.gain.value = cam.gain.min
t_exp_reg = int(
np.round(np.log2(t_exp))
) # convert exposure time into register value (nearest power of 2)
if t_exp_reg in range(cam.exposure.min, cam.exposure.max + 1):
cam.exposure.value = int(np.round(np.log2(t_exp)))
else:
cam.exposure.value = int(cam.exposure.max + cam.exposure.min) / 2
print('Exposure out of range. Setting to half of exposure range')
cam.formats = cam.list_video_formats()
cam.sensor_height = 1080
cam.sensor_width = 1920
cam.set_video_format(
b'Y800 (1920x1080)') # use first available video format
cam.enable_continuous_mode(True) # image in continuous mode
cam.start_live(show_display=False) # start imaging
cam.enable_trigger(True) # camera will wait for trigger
if not cam.callback_registered:
cam.register_frame_ready_callback(
) # needed to wait for frame ready callback
window_width = 800
resize_scale = window_width / cam.sensor_width
rescaled_size = (window_width, int(cam.sensor_height * resize_scale))
cv2.namedWindow('Camera Preview',
flags=cv2.WINDOW_KEEPRATIO | cv2.WINDOW_NORMAL)
cv2.resizeWindow('Camera Preview', rescaled_size[0], rescaled_size[1])
class MouseControl:
def __init__(self):
self.xy = [0, 0]
self.im_val = 0
self.stopflag = 0
self.markers = 0
def process_events(self, event, x, y, flags, param):
if event == cv2.EVENT_LBUTTONDOWN:
self.stopflag = not (self.stopflag)
elif event == cv2.EVENT_MOUSEMOVE:
x_val = int(x)
y_val = int(y)
self.xy = [x_val, y_val]
elif event == cv2.EVENT_RBUTTONDOWN:
self.markers = (self.markers + 1) % 3
#instantiate class
mouse = MouseControl()
cv2.setMouseCallback('Camera Preview', mouse.process_events)
while (cv2.getWindowProperty('Camera Preview', 0) >= 0):
try:
if not (mouse.stopflag):
t = time.time()
cam.reset_frame_ready() # reset frame ready flag
# send hardware trigger OR call cam.send_trigger() here
cam.send_trigger()
# get image data...
cam.wait_til_frame_ready(
10) # wait for frame ready due to trigger
im = cam.get_image_data()
img = np.ndarray(buffer=im[0],
dtype=np.uint8,
shape=(cam.sensor_height,
cam.sensor_width, 3))
cv2.imshow('Camera Preview', img)
k = cv2.waitKey(1)
if k == 0x1b:
cv2.destroyAllWindows()
break
fps = 1 / (time.time() - t)
else:
cv2.imshow('Camera Preview', img)
k = cv2.waitKey(1)
if k == 0x1b:
cv2.destroyAllWindows()
break
except:
print('There was an error')
cam.stop_live()
cam.close()
ic_ic.close_library()
raise
cam.stop_live()
cam.close()
ic_ic.close_library()
def ic():
ic_ic = IC_ImagingControl()
ic_ic.init_library()
# open first available camera device
cam_names = ic_ic.get_unique_device_names()
# print(cam_names)
cam = ic_ic.get_device(cam_names[0])
cam.open()
cam.reset_properties()
# change camera properties
# print(cam.list_property_names()) # ['gain', 'exposure', 'hue', etc...]
cam.gain.auto = False # enable auto gain
cam.exposure.value = -5
# change camera settings
formats = cam.list_video_formats()
# print formats
cam.set_video_format(formats[0]) # use first available video format
cam.enable_continuous_mode(True) # image in continuous mode
cam.start_live(show_display=False) # start imaging
cam.enable_trigger(True) # camera will wait for trigger
if not cam.callback_registered:
cam.register_frame_ready_callback(
) # needed to wait for frame ready callback
cam.reset_frame_ready()
cam.send_trigger()
cam.wait_til_frame_ready(1000) # wait for frame ready due to trigger
data, width, height, depth = cam.get_image_data()
frame = np.ndarray(buffer=data,
dtype=np.uint8,
shape=(height, width, depth))
frameout = copy.deepcopy(frame).astype(float)
del frame
# print(frameout.max())
cam.stop_live()
cam.close()
ic_ic.close_library()
imgray = rgb2gray(frameout) # convert rgb image into grayscale
satu = imgray[imgray > 254].shape[0]
if satu > 0:
print('Image saturated with %d pixels' % satu)
return 0
else:
# FOM1
# I = abs(imgray)**2
# x = np.arange(imgray.shape[1]).astype(float)
# y = np.arange(imgray.shape[0]).astype(float)
# mu0 = np.trapz(np.trapz(I, x ),y)
# mean_x = np.trapz(np.trapz(I * x, x), y)/mu0
# mean_y = np.trapz(np.trapz(I, x)*y, y)/mu0
# r0 = 50
# X, Y= np.meshgrid(x,y)
# r = (Y - mean_y)**2 + (X - mean_x)**2
# fom = (1-np.sum(imgray[r>=r0**2]) / np.sum(imgray) ) * np.sum(imgray[r<r0**2])
# y_peak, x_peak = np.unravel_index(imgray.argmax(), imgray.shape) # find the target position for FOM calculation, here the maximum point is the target position
#FOM2 (Image Moment)
# x_peak = 520
# y_peak = 554
# xx = np.arange(imgray.shape[1]).astype(float)
# yy = np.arange(imgray.shape[0]).astype(float)
# X, Y= np.meshgrid(xx,yy)
# d1 = (Y - y_peak)**2
# d2 = (X - x_peak)**2
# d = (d1+d2)**4
# d[y_peak,x_peak]=1
# fom = imgray / d
# fom[y_peak,x_peak]=0
# fom = np.sum(fom)
#FOM3
# fom = np.sum(imgray**2);
#FOM4
fom = np.sum(imgray)
print(frameout.max(), fom)
return fom
def ic():
ic_ic = IC_ImagingControl()
ic_ic.init_library()
cam_names = ic_ic.get_unique_device_names()
print("These are the available cameras:")
print(cam_names)
print(
"Please select an IC camera to use by inputting the index of the camera."
)
print("The indices go from 0 to ", len(cam_names) - 1)
while True:
index = int(input())
if ((index <= len(cam_names) - 1) and (index >= 0)):
cam = ic_ic.get_device(cam_names[index])
break
else:
print("You didn't enter a correct index.")
cam.open()
cam.reset_properties()
# change camera properties
print(cam.list_property_names()) # ['gain', 'exposure', 'hue', etc...]
cam.gain.auto = False # enable auto gain
cam.exposure.value = -5
# change camera settings
formats = cam.list_video_formats()
# print formats
print(formats)
cam.set_video_format(formats[0]) # use first available video format
cam.enable_continuous_mode(True) # image in continuous mode
cam.start_live(show_display=False) # start imaging
cam.enable_trigger(True) # camera will wait for trigger
if not cam.callback_registered:
cam.register_frame_ready_callback(
) # needed to wait for frame ready callback
cam.reset_frame_ready()
cam.send_trigger()
cam.wait_til_frame_ready(1000) # wait for frame ready due to trigger
data, width, height, depth = cam.get_image_data()
frame = np.ndarray(buffer=data,
dtype=np.uint8,
shape=(height, width, depth))
frameout = copy.deepcopy(frame).astype(float)
plt.imsave('figure_of_merit.png', frameout, cmap=cm.gray)
del frame
# print(frameout.max())
cam.stop_live() # stop capturing video from the camera
cam.close() # shut down the camera
ic_ic.close_library() # stop accessing the IC dll
return frameout
class data_acqusition(object):
"""This object is used to initialize, acquire data from, and shut down various different hardware for data acquisition
"""
def __init__(self, device, fom_num):
self.device = device # save which acquisition device is being used
initialize_array = file_f.read_initialization_variables(
"\\" + self.device + "\\" + self.device + " properties.ini"
) # read in the initialization information from the file at device/device properites.ini
self.fom_num = fom_num
# initialize the specific device being called
if (device == DAQ_DEVICES[0]): # if the device name is "Andor"
self.__initialize_andor(initialize_array)
elif (device == DAQ_DEVICES[1]): # if the device name is "NI_DAQ"
self.__initialize_NI_DAQ(initialize_array)
elif (device == DAQ_DEVICES[2]): # if the device name is "IC"
self.__initialize_IC(initialize_array)
else:
print(
"Error: The device you entered into data acquisition wasn't valid"
)
print("The possible devices are: ", DAQ_DEVICES)
exit()
def __check_success(self, error_value, function_name):
"""Check whether or not the program was able to perform the given function for the Andor camera
Parameters
----------
error_value : error value, int
This is the error value returned from any Andor function
function_name : function name, string
This is a string which denotes which function returned this error value
"""
if (error_value != DRV_SUCCESS): # if the error value wasn't success
print("Andor", function_name, "Error", error_value)
exit()
def __initialize_andor(self, initialize_array):
"""Initialize the Andor camera to be ready to capture images
Parameters
----------
initialize_array : initialization array, numpy array
This contains information from the "Andor/Andor properties.ini" file about what Andor properties to use for image capture
"""
# get the information from the .ini file
read_mode_top = int(
initialize_array[0]
) # readout mode options: 0 Full Vertical binning; 1 Multi-Track; 2 Random-Track; 3 Single-Track; 4 Image;
acquisition_mode_top = int(
initialize_array[1]
) # acquisition mode options: 1 Single scan; 2 Accumulate; 3 Kinetics; 4 Fast Kinetics; 5 Run till abort;
exposure_time_top = float(initialize_array[2]) # time in seconds
trigger_mode_top = int(
initialize_array[3]
) # trigger mode options: 0 internal; 1 external; 6 external start; 7 external exposure (bulb); 9 external FVB EM; 10 software trigger; 12 external charge shifting;
horizontal_binning_top = int(
initialize_array[4]) # set the horizontal binning
vertical_binning_top = int(
initialize_array[5]) # set the vertical binning
horizontal_start_top = int(
initialize_array[6]
) # set the horizontal start pixel of the subregion of the camera which to take a picture from
horizontal_end_top = int(
initialize_array[7]) # set the horizontal end pixel
vertical_start_top = int(
initialize_array[8]) # set the vertical start pixel
vertical_end_top = int(
initialize_array[9]) # set the vertical end pixel
# Load the atmcd64.dll file
directory_path = os.path.dirname(
os.path.abspath(__file__)) # get the current directory's path
self.andor_dll = ctypes.windll.LoadLibrary(
directory_path + '\\Andor\\atmcd32d.dll'
) # load the andor dll from the directory Andor/
# Initialize camera
aBuffer = ctypes.c_char_p(
) # The buffer tells the initialize function where the driver files are. Currently, they're in the same folder as this .py file
error_value = self.andor_dll.Initialize(aBuffer)
self.__check_success(error_value, "Initialize")
# Determine size (in pixels of camera)
gblXPixels = ctypes.c_int() # Total number of horizontal pixels
gblYPixels = ctypes.c_int() # Total number of vertical pixels
error_value = self.andor_dll.GetDetector(ctypes.byref(gblXPixels),
ctypes.byref(gblYPixels))
self.__check_success(error_value, "GetDetector")
# Set vertical shift speed to recommended value
vertical_shift_index = ctypes.c_int(
) # the index to access specific vertical shift speeds
vertical_speed = ctypes.c_float(
) # speed of the vertical speed shift in microseconds per pixel shift
error_value = self.andor_dll.GetFastestRecommendedVSSpeed(
ctypes.byref(vertical_shift_index), ctypes.byref(vertical_speed))
self.__check_success(error_value,
"Get Fastest Recommended Vertical Shift Speed")
error_value = self.andor_dll.SetVSSpeed(vertical_shift_index)
self.__check_success(error_value, "Set Vertical Shift Speed")
# Set horizontal shift speed to the maximum
horizontal_shift_index = ctypes.c_int(
0) # the index to access specific horizontal shift speeds
AD_converter_index = ctypes.c_int(
) # the specific index to access a given A-D converter
number_AD = ctypes.c_int(
0) # the number of A-D converters in the camera
number_speeds = ctypes.c_int() # number of speeds available
horizontal_speed = ctypes.c_float() # horizontal shift speed
max_horizontal_speed = ctypes.c_float(0) # maximum horizontal speed
error_value = self.andor_dll.GetNumberADChannels(
ctypes.byref(number_AD))
self.__check_success(error_value, "Get Number AD Channels")
for each_AD in range(number_AD.value):
error_value = self.andor_dll.GetNumberHSSpeeds(
AD_converter_index, ctypes.c_int(0),
ctypes.byref(number_speeds))
self.__check_success(error_value,
"Get Number Horizontal Shift Speeds")
for each_speed_index in range(number_speeds.value):
error_value = self.andor_dll.GetHSSpeed(
ctypes.c_int(each_AD), ctypes.c_int(0),
ctypes.c_int(each_speed_index),
ctypes.byref(horizontal_speed))
self.__check_success(error_value, "Get Horizontal Shift Speed")
if (horizontal_speed.value > max_horizontal_speed.value):
max_horizontal_speed.value = horizontal_speed.value
horizontal_shift_index = ctypes.c_int(each_speed_index)
AD_converter_index = ctypes.c_int(each_AD)
error_value = self.andor_dll.SetADChannel(AD_converter_index)
self.__check_success(error_value, "Set AD Channel")
error_value = self.andor_dll.SetHSSpeed(ctypes.c_int(0),
horizontal_shift_index)
self.__check_success(error_value, "Set Horizontal Speed Index")
# Turn the camera cooler on
error_value = self.andor_dll.CoolerON()
self.__check_success(error_value, "Turn Cooler On")
# Check to make sure cooler is on
cooler_on = ctypes.c_int()
error_value = self.andor_dll.IsCoolerOn(ctypes.byref(cooler_on))
self.__check_success(error_value, "Check if cooler is on")
if (cooler_on.value != 1):
print("Error: Cooler not on", "Exiting...")
exit()
# Set the readout mode of the camera
read_mode = ctypes.c_int(read_mode_top)
error_value = self.andor_dll.SetReadMode(read_mode)
self.__check_success(error_value, "Set Read Mode")
# Set the acquisition mode
acquisition_mode = ctypes.c_int(acquisition_mode_top)
error_value = self.andor_dll.SetAcquisitionMode(acquisition_mode)
self.__check_success(error_value, "Set Acquisition Mode")
# Set exposure time
exposure_time = ctypes.c_float(exposure_time_top) # time in seconds
error_value = self.andor_dll.SetExposureTime(exposure_time)
self.__check_success(error_value, "Set Exposure Time")
# Set trigger mode
trigger_mode = ctypes.c_int(trigger_mode_top)
error_value = self.andor_dll.SetTriggerMode(trigger_mode)
self.__check_success(error_value, "Set Trigger Mode")
# TODO Set up accumulation and kinetic capture & probs not video
"""
// only needed for accumulation acquisition
//float accumulation_cycle_time = .1; // seconds
//errorValue = SetAccumulationCycleTime(accumulation_cycle_time);
//if (errorValue != DRV_SUCCESS) {
//std::cout << "Set accumulation cycle time Error\n";
//std::cout << "Error: " << errorValue << "\n";
//}
//Only needed for kinetic capture
//errorValue = SetBaselineClamp(1);
//if (errorValue != DRV_SUCCESS) {
//std::cout << "Set Baseline Clamp Error\n";
//std::cout << "Error: " << errorValue << "\n";
//}
"""
# Determine the actual times the camera is using for acquisition
actual_exposure_time = ctypes.c_float()
actual_accumulate_time = ctypes.c_float()
actual_kinetic_time = ctypes.c_float()
error_value = self.andor_dll.GetAcquisitionTimings(
ctypes.byref(actual_exposure_time),
ctypes.byref(actual_accumulate_time),
ctypes.byref(actual_kinetic_time))
self.__check_success(error_value, "Get Acquisition Timings")
print('Exposure time is ', actual_exposure_time.value)
# Set the horizontal and vertical binning and the area of the image to be captured
horizontal_binning = ctypes.c_int(
horizontal_binning_top) # Number of pixels to bin horizontally
vertical_binning = ctypes.c_int(
vertical_binning_top) # Number of pixels to bin vertically
horizontal_start = ctypes.c_int(
horizontal_start_top
) # Start column of image to be taken (inclusive)
horizontal_end = ctypes.c_int(
horizontal_end_top) # End column of image to be taken (inclusive)
vertical_start = ctypes.c_int(
vertical_start_top) # Start row of image to be taken (inclusive)
vertical_end = ctypes.c_int(
vertical_end_top) # End row of image to be taken (inclusive)
# Determine number of horizontal and vertical pixels, and set the region and settings for image capture
self.number_x_pixels = horizontal_end_top - horizontal_start_top + 1
self.number_y_pixels = vertical_end_top - vertical_start_top + 1
error_value = self.andor_dll.SetImage(horizontal_binning,
vertical_binning,
horizontal_start, horizontal_end,
vertical_start, vertical_end)
self.__check_success(error_value, "Set Image")
def __initialize_NI_DAQ(self, initialize_array):
"""Initialize the NI daq to be ready to read in voltages
Parameters
----------
initialize_array : initialization array, numpy array
This contains information from the "NI_DAQ/NI_DAQ properties.ini" file
"""
self.number_of_reads = int(
initialize_array[0]) # determine number voltages to average over
directory_path = os.path.dirname(
os.path.abspath(__file__)) # get the current directory's path
LabVIEW = win32com.client.Dispatch(
"Labview.Application") # Start running Labview
self.pci0VI = LabVIEW.getvireference(
directory_path + '\\NI_DAQ\\get_average_photodiode_voltage.vi'
) # get the path to the LabVIEW VI
def __initialize_IC(self, initialize_array):
"""TODO comments"""
self.ic_ic = IC_ImagingControl()
self.ic_ic.init_library()
cam_names = self.ic_ic.get_unique_device_names()
if (len(cam_names) == 0):
print("Error: No IC cameras connected to the computer.")
exit()
print("\nThese are the available cameras:")
print(cam_names)
print(
"Please select an IC camera to use by inputting the index of the camera."
)
print("The indices go from 0 to ", len(cam_names) - 1)
while True:
index = int(input())
if ((index <= len(cam_names) - 1) and (index >= 0)):
self.cam = self.ic_ic.get_device(cam_names[index])
break
else:
print("You didn't enter a correct index.")
self.cam.open()
print(
"\nWould you like to set all of the camera initialization values yourself, or use the IC properties.ini file?"
)
print(
'Enter either "set" for setting all of the values or "ini" for the .ini file'
)
while True:
init = input()
if (init == "set"):
set_all = True
break
elif (init == "ini"):
set_all = False
break
else:
print("You didn't enter 'set' or 'ini'. Try again.")
self.cam.reset_properties()
cam_properties = self.cam.list_property_names()
print(
"Note: this only goes through the camera properties available for this specific camera."
)
for attribute_index in range(len(cam_properties)):
if (getattr(self.cam,
cam_properties[attribute_index]).available == True):
if (set_all == True): # if they want to go through everything
print("You are setting the",
cam_properties[attribute_index])
print(
"Its current value is ",
getattr(self.cam,
cam_properties[attribute_index]).value)
print(
"The range of values you can set this to is ",
getattr(self.cam,
cam_properties[attribute_index]).range)
print("What would you like to set this property to?")
while True:
change_value = input()
print("You entered", change_value,
"\nIs this okay? (enter 'y' or 'n')")
input_is_good = input()
if (input_is_good == 'y'):
break
elif (input_is_good == 'n'):
print(
"Type in what you'd like to change this property to instead"
)
else:
print(
"You didn't enter a y or an n. Enter what value you'd like to change the property to again."
)
else:
if (initialize_array[attribute_index] == "auto"):
if (getattr(
self.cam,
cam_properties[attribute_index]).auto_available
== True):
getattr(
self.cam,
cam_properties[attribute_index]).auto = True
print("Set the camera",
cam_properties[attribute_index], "to auto")
else:
print("Auto setting unavailable for",
cam_properties[attribute_index])
print("Did not set",
cam_properties[attribute_index])
elif (initialize_array[attribute_index] == "none"):
print("Did not set", cam_properties[attribute_index])
else:
if (type(
getattr(self.cam,
cam_properties[attribute_index]).value)
== int):
getattr(
self.cam,
cam_properties[attribute_index]).value = int(
initialize_array[attribute_index])
if (type(
getattr(self.cam,
cam_properties[attribute_index]).value)
== float):
getattr(
self.cam,
cam_properties[attribute_index]).value = float(
initialize_array[attribute_index])
print(
"Set the camera", cam_properties[attribute_index],
"to",
getattr(self.cam,
cam_properties[attribute_index]).value,
"within the range",
getattr(self.cam,
cam_properties[attribute_index]).range)
formats = self.cam.list_video_formats()
print("\nThese are the available video formats:")
print(formats)
print(
"Please select video format to use by inputting the index of the format."
)
print("The indices go from 0 to ", len(formats) - 1)
while True:
index = int(input())
if ((index <= len(formats) - 1) and (index >= 0)):
self.cam.set_video_format(formats[index])
break
else:
print("You didn't enter a correct index.")
self.cam.enable_continuous_mode(True) # image in continuous mode
self.cam.start_live(show_display=False) # start imaging
self.cam.enable_trigger(True) # camera will wait for trigger
if not self.cam.callback_registered:
self.cam.register_frame_ready_callback(
) # needed to wait for frame ready callback
self.width, self.height, depth, color_format = self.cam.get_image_description(
)
self.depth = depth // 8 # I have no idea why the library does this
self.acquire()
def figure_of_merit(self):
"""Determine the figure of merit using the selected device
Parameters
----------
fom_num: figure of merit number, int
This determines which calculation to use when calculating the figure of merit
"""
self.acquire()
if (self.device == DAQ_DEVICES[0]): # if the device name is "Andor"
figure_of_merit_f.Andor_FOM(self.image, self.fom_num)
elif (self.device == DAQ_DEVICES[1]): # if the device name is "NI_DAQ"
figure_of_merit_f.NI_DAQ_FOM(self.voltage, self.fom_num)
elif (self.device == DAQ_DEVICES[2]): # if the device name is "IC"
figure_of_merit_f.ic_FOM(self.frameout, self.fom_num)
def acquire(self):
"""Acquire data from the appropriate data acquisition hardware
"""
if (self.device == DAQ_DEVICES[0]): # if the device name is "Andor"
self.__acquire_andor()
elif (self.device == DAQ_DEVICES[1]): # if the device name is "NI_DAQ"
self.__acquire_NI_DAQ()
elif (self.device == DAQ_DEVICES[2]): # if the device name is "IC"
self.__acquire_IC()
def __acquire_andor(self):
"""This function acquires an image from the andor camera and returns the image
Returns
-------
image : image, numpy 2d array
This is the image which the Andor camera captured
"""
# Wait until the camera is in an idle state
camera_status = ctypes.c_int()
error_value = self.andor_dll.GetStatus(ctypes.byref(camera_status))
self.__check_success(error_value, "Get Camera Status")
while (camera_status.value != DRV_IDLE):
error_value = self.andor_dll.GetStatus(ctypes.byref(camera_status))
self.__check_success(error_value, "Get Camera Status")
# Start the acquisition process
error_value = self.andor_dll.StartAcquisition()
acquiring = self.__check_success(error_value, "Start Acquisition")
if (acquiring == False):
self.andor_dll.AbortAcquisition()
# Wait until the acquisition is complete
error_value = self.andor_dll.GetStatus(ctypes.byref(camera_status))
self.__check_success(error_value, "Get Camera Status")
while (camera_status.value != DRV_IDLE):
error_value = self.andor_dll.GetStatus(ctypes.byref(camera_status))
self.__check_success(error_value, "Get Camera Status")
# Get the image data from the camera
size = ctypes.c_int(self.number_x_pixels * self.number_y_pixels)
image_pointer = ctypes.cast(
ctypes.create_string_buffer(size.value *
ctypes.sizeof(ctypes.c_long())),
ctypes.POINTER(ctypes.c_long))
error_value = self.andor_dll.GetAcquiredData(image_pointer, size)
self.__check_success(error_value, "Get Acquired Data")
# Deep copy the image from dereferencing a pointer to a numpy array
image = np.zeros((self.number_y_pixels, self.number_x_pixels))
for x in range(self.number_x_pixels):
for y in range(self.number_y_pixels):
image[y, x] = image_pointer[x + y * self.number_x_pixels]
self.image = image
def __acquire_NI_DAQ(self):
"""Compute figure of merit that is average voltage reading from DAQ
Returns
-------
voltage: voltage, variable type unknown -> maybe float
the averaged voltage read by the NI DAQ hardware
"""
self.pci0VI._FlagAsMethod(
"Call") # Flag "Call" as the method to run the VI in this path
self.pci0VI.setcontrolvalue('error in (no error)', 0) # set error in
self.pci0VI.setcontrolvalue('number of reads',
self.number_of_reads) # set addresses
self.pci0VI.Call() # Run the VI
voltage = self.pci0VI.getcontrolvalue('voltage') # retrieve error out
error = self.pci0VI.getcontrolvalue('error out') # retrieve error out
if (error[1] != 0): # check whether there was an error
print('There was an error writing to board 0 at PXI4::5::INSTR')
print('Error: ', error)
print('Press anything and enter to exit...')
input()
exit()
self.voltage = voltage
def __acquire_IC(self):
self.cam.reset_frame_ready()
self.cam.send_trigger()
self.cam.wait_til_frame_ready(
1000) # wait for frame ready due to trigger
data, width, height, depth = self.cam.get_image_data()
frame = np.ndarray(buffer=data,
dtype=np.uint8,
shape=(self.height, self.width, self.depth))
frameout = copy.deepcopy(frame)
plt.imshow(frameout)
plt.colorbar()
plt.show()
# self.cam.save_image(b"image.jpg", 1)
del frame
self.frameout = frameout
def shut_down(self):
"""Shut down the appropriate data acquisition hardware
"""
if (self.device == DAQ_DEVICES[0]): # if the device name is "Andor"
self.__shut_down_andor()
elif (self.device == DAQ_DEVICES[1]): # if the device name is "NI_DAQ"
self.__shut_down_NI_DAQ()
elif (self.device == DAQ_DEVICES[2]): # if the device name is "IC"
self.__shut_down_IC()
def __shut_down_andor(self):
"""Shut down the Andor camera
"""
error_value = self.andor_dll.ShutDown()
self.__check_success(error_value, "Shut down")
def __shut_down_NI_DAQ(self):
"""Nothing needs to be done to shut down the NI DAQ device
"""
return
def __shut_down_IC(self):
"""TODO"""
self.cam.stop_live() # stop capturing video from the camera
self.cam.close() # shut down the camera
self.ic_ic.close_library() # stop accessing the IC dll