def thing(expos=0.008, gain=2, mycube='spare', TDI_flag = 0):
"""
Process command line. This is used
"""
IlluminateWidth = 1920
IlluminateHeight = 1080
CameraWidth = 1000
CameraHeight = 1000
#MF = MaestroFunctions.Maestro_Functions()
MF = MaestroFunctions()
# process the numeric arguments
int_time = float(expos)
em_gain = int(gain)
"""
Set up imaging
"""
MF.darkfield_off()
print "the third argument is %s\n" % mycube
MF.filter_goto(mycube)
"""
set up release hardware
"""
# initialize the release system
print "Initializing release system\n"
PI.py_clear_memory();
if PI.py_illuminate_init(IlluminateWidth, IlluminateHeight, \
CameraWidth, CameraHeight) < 0:
sys.exit(-1)
#end if
# load an identity map for alignment parameters
# CRUCIAL as for now!!!!!!!!!!!!
PI.py_illuminate_alignment_load_identity()
# enable release hardware
PI.py_illuminate_enable()
# generate an image
"""
im = Image.open("test.png")
if im.size[0] > im.size[1]:
scaler = IlluminateWidth/(im.size[0])
im = im.resize((IlluminateWidth, scaler*im.size[1]),Image.BICUBIC)
#end if
else:
scaler = IlluminateHeight/(im.size[1])
im = im.resize((scaler*im.size[0], IlluminateHeight),Image.BICUBIC)
#end else
im.convert('L')
im.show()
im.save("testout.png")
"""
#im = Image.open("wyss_HD_R3.bmp")
im = Image.open("../data/alignment_DMD5.bmp")
#im = Image.open("George_Church_03.bmp")
#im = Image.open("all_white.bmp")
#im = im.rotate(90)
im = im.transpose(Image.FLIP_LEFT_RIGHT)
im = im.transpose(Image.FLIP_TOP_BOTTOM)
#im = im.offset(50, -300)
pix = im.load()
mask_number = 0
y_step = 1
x_step = 1
#PI.py_clear_mask(mask_number)
PI.py_clear_framebuffer()
#PI.py_clear_memory() # must run this or you will get line artifacts!!!!
PI.py_illum_mask_radius(0,mask_number)
#done = 0
for y in range(0,IlluminateHeight,y_step):
for x in range(0,IlluminateWidth,x_step):
#if pix[y,x] != 0:
if pix[y,x] == 0:# and done == 0:
#x = 1920/2
#y = 1080/2
PI.py_illuminate_point(x,y,mask_number)
#print x, y
#done = 1;
#end if
# end for
# end for
# expose image, so that it stays displayed
#PI.py_illuminate_disable()
PI.py_illuminate_expose()
"""
start imaging
"""
# open shutter
MF.shutter_open()
return 0
MaestroF = MaestroFunctions()
#my_color = "spare"
my_color = "cy3"
LEN = 1000000
data_size = LEN#+4
MAX_BEADS_PERFRAME = 1000000
img_array = np.empty(data_size, dtype=np.uint16)
img_array2 = np.empty(data_size, dtype=np.uint16)
beadpos_xcol = np.empty(MAX_BEADS_PERFRAME, dtype=np.uint16)
beadpos_yrow = np.empty(MAX_BEADS_PERFRAME, dtype=np.uint16)
segmask_image = np.empty(data_size, dtype=np.uint16)
MaestroF.darkfield_off()
MaestroF.filter_home()
MaestroF.filter_goto(my_color)
time.sleep(1)
MapFunc.init_illum()
MapFunc.light_all()
PC.py_snapPtr(img_array, .35,80,my_color)
#invert for images where beads are lighter than background
img_array = 16383 - img_array # invert the 14 bit image
num_beads = FO.find_objects(1000, 1000, \
img_array, \
beadpos_xcol, beadpos_yrow, \
segmask_image)
print("The number of beads found: %d" % num_beads)
def main(argv=None):
"""
Process command line
"""
IlluminateWidth = 1920
IlluminateHeight = 1080
CameraWidth = 1000
CameraHeight = 1000
if argv is None:
argv = sys.argv
# end if
argc = len(argv)
print "newline\n"
print "There are %d arguments\n" % argc
# make sure we have the correct number of arguments */
if (argc < 3) or (argc > 5):
#testDMD.show_usage()
show_usage()
sys.exit(-1)
#end if
MF = MaestroFunctions()
# process the numeric arguments
int_time = float(argv[1])
em_gain = int(argv[2])
# process cube name
if argc < 4:
mycube = DEFAULT_CUBE
# end if
else:
mycube = str(argv[3])
# end else
# process TDI flag
if argc < 5:
TDI_flag = DEFAULT_TDI
# end if
else:
TDI_flag = int(argv[4])
# end else
"""
Set up imaging
"""
MF.darkfield_off()
print "the third argument is %s\n" % mycube
MF.filter_goto(mycube)
"""
set up release hardware
"""
# initialize the release system
print "Initializing release system\n"
# if PI.py_illuminate_init( IlluminateWidth, \
# IlluminateHeight, \
# CameraWidth, \
# CameraHeight) < 0:
# sys.exit(-1)
#end if
# load an identity map for alignment parameters
#PI.py_illuminate_alignment_load_identity()
# enable release hardware
#PI.py_illuminate_enable()
#PI.py_clear_memory() # must run this or you will get line artifacts!!!!
# generate an image
#PI.generate_image()
# expose image, so that it stays displayed
#PI.py_illuminate_expose()
"""
start imaging
"""
# open shutter
MF.shutter_open()
# start imaging
myargc = 3;
myargv = ['0' ,'0','c','d'] # create a list of length 4
myargv[2] = argv[1]
myargv[3] = argv[2]
# start in a separate process to avoid crash if window is closed
pid = os.fork() # this is a UNIX only syscall
if pid == 0:
#child process
PC.py_camera_live(myargc, myargv, TDI_flag)
return 0;
# end if
# in parent process
# wait for child to terminate
#os.waitpid(pid,os.WNOHANG) # this option WNOHANG is UNIX only
os.wait()
# close shutter
MF.shutter_close()
return 0
def main(argv=None):
"""
Process command line
"""
IlluminateWidth = 1920
IlluminateHeight = 1080
CameraWidth = 1000
CameraHeight = 1000
if argv is None:
argv = sys.argv
# end if
argc = len(argv)
print "newline\n"
print "There are %d arguments\n" % argc
# make sure we have the correct number of arguments */
if (argc < 3) or (argc > 5):
show_usage()
sys.exit(-1)
#end if
MF = MaestroFunctions()
# process the numeric arguments
int_time = float(argv[1])
em_gain = int(argv[2])
# process cube name
if argc < 4:
mycube = DEFAULT_CUBE
# end if
else:
mycube = str(argv[3])
# end else
# process TDI flag
if argc < 5:
TDI_flag = DEFAULT_TDI
# end if
else:
TDI_flag = int(argv[4])
# end else
"""
Set up imaging
"""
MF.darkfield_off()
print "the third argument is %s\n" % mycube
MF.filter_goto(mycube)
"""
set up release hardware
"""
# initialize the release system
print "Initializing release system\n"
PI.py_clear_memory();
if PI.py_illuminate_init(IlluminateWidth, IlluminateHeight, \
CameraWidth, CameraHeight) < 0:
sys.exit(-1)
#end if
# load an identity map for alignment parameters
PI.py_illuminate_alignment_load_identity()
# enable release hardware
PI.py_illuminate_enable()
# generate an image
"""
im = Image.open("test.png")
if im.size[0] > im.size[1]:
scaler = IlluminateWidth/(im.size[0])
im = im.resize((IlluminateWidth, scaler*im.size[1]),Image.BICUBIC)
#end if
else:
scaler = IlluminateHeight/(im.size[1])
im = im.resize((scaler*im.size[0], IlluminateHeight),Image.BICUBIC)
#end else
im.convert('L')
im.show()
im.save("testout.png")
"""
#im = Image.open("wyss_HD_R3.bmp")
#im = Image.open("alignment_DMD.bmp")
im = Image.open("George_Church_03.bmp")
#im = Image.open("all_white.bmp")
#im = im.rotate(90)
im = im.transpose(Image.FLIP_LEFT_RIGHT)
im = im.transpose(Image.FLIP_TOP_BOTTOM)
#im = im.offset(50, -300)
pix = im.load()
mask_number = 0
y_step = 1
x_step = 1
#PI.py_clear_mask(mask_number)
PI.py_clear_framebuffer()
#PI.py_clear_memory() # must run this or you will get line artifacts!!!!
PI.py_illum_mask_radius_dmd(0,mask_number)
for y in range(0,IlluminateHeight,y_step):
for x in range(0,IlluminateWidth,x_step):
#if pix[y,x] != 0:
if pix[y,x] == 0:
PI.py_illuminate_point(x,y,mask_number)
#end if
# end for
# end for
# expose image, so that it stays displayed
#PI.py_illuminate_disable()
PI.py_illuminate_expose()
"""
start imaging
"""
# open shutter
MF.shutter_open()
# start imaging
myargc = 3;
myargv = ['0' ,'0','c','d'] # create a list of length 4
myargv[2] = argv[1]
myargv[3] = argv[2]
# start in a separate process to avoid crash if window is closed
#pid = os.fork() # this is a UNIX only syscall
#if pid == 0:
#child process
# PC.py_camera_live(myargc, myargv, TDI_flag)
# return 0;
# end if
# in parent process
# wait for child to terminate
#os.waitpid(pid,os.WNOHANG) # this option WNOHANG is UNIX only
#os.wait()
# close shutter
#MF.shutter_close()
return 0