def main(argv=None):
global curr_averageimgnum
global num_to_average
if argv is None:
argv = sys.argv
# end if
argc = len(argv)
if argc < 2:
show_usage()
sys.exit(-1)
# end if
filename = argv[1]
if argc > 2:
autolevel = argv[2]
# end if
mf = maestro.MaestroFunctions()
img_buffer_cpy = numpy.empty(data_size, dtype=np.uint16)
TOTAL_FCS = 1
first_average_image = 1
auto_exposure = 0
base_dir = "%s/polonator/G.007/acquisition" % (os.environ["HOME"])
log_dir = "%s/logs" % (base_dir)
command_buffer = "mkdir -p %s" % log_dir
system(command_buffer)
logfilename = log_dir + "/" + config.get("Log", "logfilename") + \
"." + argv[1] + ".log"
PL.start_logger(logfilename, 1)
TOTAL_IMGS = int(config.get("Flowcell", "imgs_per_array"))
image_timeout = int(config.get("Motion", "image_timeout"))
PHX_buffersize = int(config.get("Camera", "PHX_buffersize"))
proc_portnum = int(config.get("Processor", "proc_portnum"))
PHX_configfilename = polpath + "/config_files/" + \
config.get("Camera", "PHX_configfilename")
auto_exposure = int(config.get("Stage_Align", "auto_exposure"))
argc = len(argv)
if argc == 7:
# number of images to average was specified
log_string = "%s called with %d args: <%s> <%d> <%d> <%d> <%d> <%d>" %
(argv[0], argc-1, argv[1], \
int(argv[2]), int(argv[3]), int(argv[4]),\
int(argv[5]), int(argv[6]) )
PL.p_log(log_string)
# num_to_avg consecutive images should be averaged together,
# then transmitted
num_to_average = int(argv[6])
if num_to_average == 1:
num_to_average = 0
def writeMappingFile(self):
"""
This function writes a mapping function after it has been generated
within the class and is in memory
To a file
"""
MF = self.MF
# write mapping to file
PL.p_log("Status:\tMF: writing camera to DMD map to file")
mapping_file = open('camera_to_DMD.map', 'w')
mapping_file.write('#This is the mapping file for the camera to DMD\n')
mapping_file.write( '#Generated on: ' \
+ time.strftime("%Y-%m-%d %H:%M:%S") + '\n')
mapping_file.write('#A0\tA1\tA2\tA3\tA4\tA5\tA6\tA7\tA8\tA9\n')
mapping_file.write( str(MF.A_map[0]) + \
'\t' + str(MF.A_map[1]) + \
'\t' + str(MF.A_map[2]) + \
'\t' + str(MF.A_map[3]) + \
'\t' + str(MF.A_map[4]) + \
'\t' + str(MF.A_map[5]) + \
'\t' + str(MF.A_map[6]) + \
'\t' + str(MF.A_map[7]) + \
'\t' + str(MF.A_map[8]) + \
'\t' + str(MF.A_map[9]) + '\n' )
mapping_file.close()
def __init__(self):
"""
This configures the class by loading key parameters from a
configuration file
"""
PL.p_log("STATUS:\tMappingFunctions: initializing")
self.MF.config = ConfigParser.ConfigParser()
self.MF.config_dir = os.environ['POLONATOR_PATH'] + \
'/config_files'
self.MF.config_path = self.MF.config_dir \
+ '/camera_to_DMD_params.config'
self.MF.A_map = numpy.empty(10,dtype=numpy.float)
# make sure something is in the file
if self.MF.config.read(self.MF.config_path) == []:
self.defaultConfigFile()
self.MF.config.read(self.MF.config_path)
#end if
elif not self.MF.config.has_section('Main'):
print "No main"
self.defaultConfigFile()
# end elif
self.MF.IlluminateWidth = \
int(self.MF.config.get( 'Main', 'IlluminateWidth'))
self.MF.IlluminateHeight = \
int(self.MF.config.get( 'Main', 'IlluminateHeight'))
self.MF.CameraWidth = \
int(self.MF.config.get( 'Main', 'CameraWidth'))
self.MF.CameraHeight = \
int(self.MF.config.get( 'Main', 'CameraHeight'))
self.MF.ImageExposure = \
float(self.MF.config.get('Main', 'ImageExposure'))
self.MF.ImageGain = \
int(self.MF.config.get( 'Main', 'ImageGain'))
self.MF.ImageColor = \
self.MF.config.get( 'Main', 'ImageColor')
self.MF.ImageFilename = \
self.MF.config.get( 'Main', 'ImageFilename')
self.MF.ImageCCD_BytesPerPixel = \
int(self.MF.config.get( 'Main', 'ImageCCD_BytesPerPixel'))
self.MF.MaestroF = PM.MaestroFunctions()
self.MF.mask_number0 = 0
self.MF.mask_radius0 = 1
self.MF.mask_number1 = 1
self.MF.mask_radius1 = 0
self.MF.mask_number2 = 2
self.MF.mask_radius2 = 1
self.MF.mask_number3 = 3
self.MF.mask_radius3 = 3
self.MF.expose = 0.25
self.MF.gain = 200
self.illumInit()
def mapReinit(self):
"""
This configures the class by loading key parameters from a
configuration file
"""
# read in the config file. must be formated correctly
PL.p_log("STATUS:\tMappingFunctions: initializing")
MF = self.MF
MF.config = ConfigParser.ConfigParser()
MF.config_dir = os.environ['POLONATOR_PATH'] + '/config_files'
MF.config_path = MF.config_dir + '/camera_to_DMD_params.config'
# make sure something is in the file
if MF.config.read(MF.config_path) == []:
self.defaultConfigFile()
MF.config.read(MF.config_path)
#end if
elif not MF.config.has_section('Main'):
print "No main"
MF.defaultConfigFile()
# end elif
MF.IlluminateWidth = int(MF.config.get( 'Main', \
'IlluminateWidth'))
MF.IlluminateHeight = int(MF.config.get('Main', \
'IlluminateHeight'))
MF.CameraWidth = int(MF.config.get( 'Main', \
'CameraWidth'))
MF.CameraHeight = int(MF.config.get( 'Main', \
'CameraHeight'))
MF.ImageExposure = float(MF.config.get( 'Main', \
'ImageExposure'))
MF.ImageGain = int(MF.config.get( 'Main', \
'ImageGain'))
MF.ImageColor = MF.config.get( 'Main', \
'ImageColor')
MF.ImageFilename = MF.config.get( 'Main', \
'ImageFilename')
MF.ImageCCD_BytesPerPixel = \
int(MF.config.get('Main', 'ImageCCD_BytesPerPixel'))
def readMappingFile(self):
"""
This reads a mapping data from file into memory. Assumes the
mapping file already exists
TODO: Should add exception in the case the file does not exist
"""
MF = self.MF
PL.p_log("Status:\tMF: reading camera to DMD map to file")
mapping_file = open('camera_to_DMD.map', 'r')
for line in mapping_file:
# the mapping data starts on the first line without a # to start it
if line[0] != '#':
map_line = line.split()
for i in range(len(map_line)):
MF.A_map[i] = float(map_line[i]);
print MF.A_map[i]
# end for
break;
# end if
# end for
mapping_file.close()
def send_initial_raw_images(num_array):
#Network transfer declarations
# int serv_sock; # socket for the server (this machine)
i = 0
global datasize
# prepare the network connection and send
# open the port, and wait for processor to connect
net.py_network_startserver(proc_portnum)
while i < num_array:
# read and send the auto_exposure raw images
stagealign_rawimgfilename = "%s/polonator/G.007/acquisition/stagealign/stagealign-image0_%d.raw" % (os.environ["HOME"], i)
PL.p_log_simple(stagealign_rawimgfilename)
log_string = "STATUS:\t 1try to send the autoexposure images %s to processor, port %d..." % (stagealign_rawimgfilename, proc_portnum)
PL.p_log(log_string)
baseimage = numpy.fromfile(file=stagealign_rawimgfilename, dtype=np.uint16)
log_string = "STATUS:\t 2try to send the autoexposure images %s to processor, port %d..." % (stagealign_rawimgfilename, proc_portnum)
PL.p_log(log_string)
blank_image = numpy.copy(baseimage)
log_string = "STATUS:\t 3try to send the autoexposure images %s to processor, port %d..." % (stagealign_rawimgfilename, proc_portnum)
PL.p_log(log_string)
while net.py_network_waitforsend() != 1:
log_string = "Waiting to send the autoexposure images"
PL.p_log(log_string)
# end while
log_string = "Trying to send autoexposure images %d" % (i)
PL.p_log_simple(log_string)
net.py_network_sendimage( 0, 0, i, blank_image)
log_string = "Sent autoexposure images %d" % (i)
PL.p_log_simple(log_string)
i += 1
def send_FL_images(mystring, num_array):
# prepare the network connection and send
# open the port, and wait for processor to connect
net.py_network_startserver(proc_portnum)
string1 = mystring + len(mystring) - 1
PL.p_log(string1)
log_string = "string1 length %d" % (len(string1))
PL.p_log(log_string)
if string1 == "G":
log_string = "success_%d.raw" % (0)
PL.p_log(log_string)
stagealign_dir_name = "%s/polonator/G.007/acquisition/autoexp_FL_images/fam/" % (os.environ["HOME"])
PL.p_log(stagealign_dir_name)
elif string1 == "A":
log_string = "success_%d.raw" % (0)
PL.p_log(log_string)
stagealign_dir_name = "%s/polonator/G.007/acquisition/autoexp_FL_images/cy3/" % (os.environ["HOME"])
PL.p_log(stagealign_dir_name)
# elif
elif string1 == "C":
log_string = "success_%d.raw" % (0)
PL.p_log(log_string)
stagealign_dir_name = "%s/polonator/G.007/acquisition/autoexp_FL_images/txred/" % (os.environ["HOME"])
PL.p_log(stagealign_dir_name)
# end elif
elif string1 == "T":
log_string = "success_%d.raw" % (0)
PL.p_log(log_string)
stagealign_dir_name = "%s/polonator/G.007/acquisition/autoexp_FL_images/cy5/" % (os.environ["HOME"])
PL.p_log(stagealign_dir_name)
# end elif
i = 0
while i < num_array:
# read and send the FL autoe images
stagealign_rawimgfilename = "%simage_%d.raw" % (stagealign_dir_name, 60+i*10)
log_string = "STATUS:\t 1try to send the autoexposure images %s to processor, port %d..." % (stagealign_rawimgfilename, proc_portnum)
PL.p_log(log_string)
baseimage = numpy.fromfile(file=stagealign_rawimgfilename, dtype=np.uint16)
log_string = "STATUS:\t 2try to send the autoexposure images %s to processor, port %d..." % (stagealign_rawimgfilename, proc_portnum)
PL.p_log(log_string)
blank_image = numpy.copy(baseimage)
log_string = "STATUS:\t 3try to send the autoexposure images %s to processor, port %d..." % (stagealign_rawimgfilename, proc_portnum)
PL.p_log(log_string)
while net.py_network_waitforsend() != 1:
log_string = "Waiting to send the autoexposure images"
PL.p_log(log_string)
# end while
log_string = "Trying to send autoexposure FL images %d" % (i)
PL.p_log_simple(log_string)
net.py_network_sendimage(0, 0, i, blank_image)
log_string = "Sent autoexposure FL images %d" % i
PL.p_log_simple(log_string)
i += 1
# end while
i = 0
while i < 2:
i = net.py_network_waitforsend()
log_string = "waiting to receive the gain value back"
PL.p_log(log_string)
# end while
gain = (i - 97)*10 + 60
log_string = "the autoexposure gain to use will be %d" % (gain)
PL.p_log_simple(log_string)
return gain
(argv[0], argc-1, argv[1], \
int(argv[2]), int(argv[3]), int(argv[4]),\
int(argv[5]), int(argv[6]) )
PL.p_log(log_string)
# num_to_avg consecutive images should be averaged together,
# then transmitted
num_to_average = int(argv[6])
if num_to_average == 1:
num_to_average = 0
elif argc == 6:
# number of images to average was not specified; assume no averaging
log_string = "%s called with %d args: <%s> <%d> <%d> <%d> <%d>" % \
(argv[0], argc-1, argv[1], \
int(argv[2]), int(argv[3]), \
int(argv[4]), int(argv[5]) )
PL.p_log(log_string)
num_to_average = 0 # don't do image averaging
else:
print "ERROR: %s called with %d args, must be called as\n" % (argv[0], argc-1)
print " %s <cycle_name> <integration time in seconds> <EM gain> <flowcell number> <number of arrays> <num_imgs_to_average> OR\n" % (argv[0])
print " %s <cycle_name> <integration time in seconds> <EM gain> <flowcell number> <number of arrays> IF no image averaging desired.\n" % (argv[0])
sys.exit(1)
fcnum = int(argv[4])
TOTAL_ARRAYS = int(argv[5])
# CAMERA SETUP
# configure framegrabber
exposure = float(argv[2])
gain = int(arg[3])
PC.camera_initAcq(0, exposure, gain)