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
open the port, and wait for processor to connect
"""
if auto_exposure == 1:
net.py_network_startserver(proc_portnum)
array_string = argv[1]
PL.p_log(array_string)
if array_string == "0" or array_string == "1":
PL.p_log(array_string)
send_initial_raw_images(1)
else:
log_string = "STATUS:\tPolonator-acquirer: running autoexposure, server sending filename %s to processor, port %d..." % (argv[1], proc_portnum)
PL.p_log_simple(log_string)
# now send the filename for the current image set
log_string = "STATUS:\tPolonator-acquirer: server sending filename %s to processor, port %d..." % (argv[1], proc_portnum)
PL.p_log(log_string)
net.py_network_sendfilename(array_string)
# close connection, then re-open for flowcell number
net.py_network_stopserver()
net.py_network_startserver(proc_portnum)
autoe_gain = send_FL_images(array_string,15)
PC.setGain(autoe_gain)
log_string = "STATUS:\tPolonator-acquirer: using the auto-exposure gain %d..." % (autoe_gain)
