def pointTransform(self,x,y, check=0):
"""
illuminates a single point while performing a mapping transform
function exists primarily for testing
"""
MF = self.MF
coord = self.ccd_to_dmd(x,y)
# TODO:
# multiplying by 4 because of confusing SUBPIXEL stuff fix in image
# generator
# do all floats in FUTURE
PI.py_illuminate_enable()
PI.py_clear_framebuffer()
PI.py_illuminate_point(coord[0],coord[1], MF.mask_number1)
PI.py_illuminate_expose() # turn on the frame buffer
if check == 1:
img_array = PC.snapPtr(0.35,180,"spare")
# just clobber the illumination point
a = numpy.array([coord[0]])
b = numpy.array([coord[1]])
max_val = PI.py_illuminate_spot_find(img_array, a,b)
if max_val < 100:
print("point not found")
# end if
else:
print("found(%d,%d)" % (a[0],b[0]))
# end else
PC.cameraClose() # also frees up image buffer memory
def grid(self,grid_spacing=10, square_size=1):
"""
illuminates a single point while performing a mapping transform
function exists primarily for testing
"""
MF = self.MF
pix = numpy.zeros((1000,1000), dtype=numpy.uint8)
period = grid_spacing+square_size
for i in range(1000/period):
for j in range(1000/period):
for p in range(square_size):
for q in range(square_size):
pix[period*i+p,period*j+q] = 1
# end for
#end for
# end for
# end for
itemind = numpy.where(pix==1)
PI.py_clear_framebuffer()
points_illum = self.n_ccd_to_dmd(itemind[1],itemind[0])
PI.py_illuminate_enable()
PI.py_illuminate_vector(points_illum[0],points_illum[1], \
MF.mask_number1, points_illum[0].size)
PI.py_illuminate_expose()
def bitmap(self,transform=1):
"""
illuminates a single point while performing a mapping transform
function exists primarily for testing
"""
MF = self.MF
#im = Image.open("wyss_1000.bmp")
#im = Image.open("wyss_1000_i2.bmp")
#im = Image.open("alignment_DMD2.bmp")
#im = Image.open("George_Church_04.bmp")
#im = Image.open("George_Church_05.bmp")
im = Image.open("../../data/TitlePres.bmp")
#im = Image.open("all_white.bmp")
pix = numpy.array(im.getdata(), dtype=numpy.uint8)
pix = pix.reshape((1000,1000))
#print("array created")
itemind = numpy.where(pix==0)
#print("points found")
PI.py_clear_framebuffer()
#print("framebuff cleared")
points_illum = self.n_ccd_to_dmd(itemind[1],itemind[0])
#print("transformed")
PI.py_illuminate_enable()
PI.py_illuminate_vector(points_illum[0],points_illum[1], \
MF.mask_number1, points_illum[0].size)
PI.py_illuminate_expose()
def wyss(self,inverse=0,decimate=0):
"""
illuminates a single point while performing a mapping transform
function exists primarily for testing
"""
MF = self.MF
im = Image.open("../../data/wyss_1000_i2.bmp")
pix = numpy.array(im.getdata(), dtype=numpy.uint8)
# decimate it down
if decimate > 0:
if inverse == 1:
for i in range(pix.size/decimate):
for j in range(decimate-1):
pix[decimate*i+j+1] = 0
# end for
# end for
# end if
else:
for i in range(pix.size/decimate):
for j in range(decimate-1):
pix[decimate*i+j+1] = 1
# end for
# end for
# end else
# end if
pix = pix.reshape((1000,1000))
itemind = numpy.where(pix==inverse)
PI.py_clear_framebuffer()
points_illum = self.n_ccd_to_dmd(itemind[1],itemind[0])
PI.py_illuminate_enable()
PI.py_illuminate_vector(points_illum[0],points_illum[1], \
MF.mask_number1, points_illum[0].size)
PI.py_illuminate_expose()
def george(self,inverse=0,decimate=0):
"""
illuminates a single point while performing a mapping transform
function exists primarily for testing
"""
MF = self.MF
im = Image.open("../../data/George_Church_05.bmp")
pix = numpy.array(im.getdata(), dtype=numpy.uint8)
pix = pix.reshape((1000,1000))
itemind = numpy.where(pix==inverse)
PI.py_clear_framebuffer()
points_illum = self.n_ccd_to_dmd(itemind[1],itemind[0])
PI.py_illuminate_enable()
PI.py_illuminate_vector(points_illum[0],points_illum[1], \
MF.mask_number1, points_illum[0].size)
PI.py_illuminate_expose()
def off():
PI.py_illuminate_disable()
def clear():
PI.py_clear_framebuffer()
def floaty():
PI.py_illuminate_float()
def expose():
PI.py_illuminate_enable()
PI.py_illuminate_expose()
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
def illumInit(self):
"""
initialize the illumination system for use in the mapping process
"""
MF = self.MF
print "Initializing release system\n"
PI.py_clear_memory();
# initialize module values
if PI.py_illuminate_init(int(MF.IlluminateWidth),\
int(MF.IlluminateHeight),\
int(MF.CameraWidth),\
int(MF.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()
# Create a group of masks
PI.py_illum_mask_radius(MF.mask_radius0,MF.mask_number0)
PI.py_illum_mask_radius(MF.mask_radius1,MF.mask_number1)
PI.py_illum_mask_radius(MF.mask_radius2,MF.mask_number2)
PI.py_illum_mask_radius(MF.mask_radius3,MF.mask_number3)
def mapGen(self, test_me = False):
"""
This function generates the mapping it:
1) loads the points to illuminate
2) generates a image for the DMD based on said coordinates
3) illuminates the image
4) takes a picture
5) copies the picture from the frame buffer
6) finds the illuminated points in the camera coordinates
7) generates a mapping to the DMD using a pseudoinverse
8) writes the mapping to class memory
9) writes the mapping to file
Polonator_IlluminateFunctions is SWIGed as follows
Illuminate and Hardware coordinates are mapped using the SWIG
This allows you to access an array of Coordinates in C and python
as follows once the IlluminateCoords_type struct is also interfaced
in SWIG :
new_coordArray(int size) -- creates an array of size
delete_coordArray(IlluminateCoords_type * arry) -- deletes and array
coordArray_get_x(IlluminateCoords_type *c_xy, int i) -- gets an value
coordArray_set_x(IlluminateCoords_type *c_xy, int i, signed short
int val) -- sets a value
ptr_coordArray(IlluminateCoords_type *c_xy, int i) returns a
pointer to an index
"""
"""
get points for bitmap and load them SWIG style
mapping_basis is just a list of points to to illuminate to
generate a good and sufficient mapping basis coordinates are given
as a range from -1 to 1 with 0,0 being the image center
"""
MF = self.MF
print("STATUS:\tMappingFunctions: opening frame buffer\n")
mapping_basis = open(MF.config_dir +'/mapping_basis.coordinates')
print( "STATUS:\tMappingFunctions: getting list of points \
to illuminate from file\n")
idx = -1
num_points = 0
for line in mapping_basis:
if line[0] != '#':
# '#' is reserved for comments on a separate line
basis_coordinate = line.split() # tab delimited fields
print(basis_coordinate)
if basis_coordinate[0] == 'number':
# this is the number of basis points we need to illuminate
num_points = int(basis_coordinate[1])
idx = num_points
# this creates the array of coordinates to illuminate
points_to_illum_x = numpy.empty(idx, dtype=numpy.int32)
# this is the array containing the found points on the CCD
points_found_x = numpy.empty(idx, dtype=numpy.int32)
points_to_illum_y = numpy.empty(idx, dtype=numpy.int32)
points_found_y = numpy.empty(idx, dtype=numpy.int32)
# write coordinates in reverse
idx = idx - 1
print("number of Points to Illuminate: " + str(num_points))
elif (basis_coordinate[0] == 'XY') and (idx > -1):
# make sure its tagged as a coordinate and the index is positive
# scale to dimensions of the DMD
bc_x = int( float(MF.IlluminateWidth)/2 \
*float(basis_coordinate[1]) ) \
+ (float(MF.IlluminateWidth)-1)/2
bc_y = int( float(MF.IlluminateHeight)/2 \
*float(basis_coordinate[2]) ) \
+ (float(MF.IlluminateHeight)-1)/2
print("read(%d,%d)\n" % (bc_x, bc_y))
points_to_illum_x[idx] = bc_x
points_to_illum_y[idx] = bc_y
idx = idx - 1
#end if
#end if
#end for
"""
Set up imaging
"""
MaestroF = MF.MaestroF
MaestroF.darkfield_off()
MaestroF.filter_home()
MaestroF.filter_goto("spare")
time.sleep(1)
#MaestroF.filter_unlock()
"""
set up release hardware
"""
#self.illumInit()
num_sub = 0 # keeps track of not found points
data_size = 1000000
img_array = numpy.empty(data_size, dtype=numpy.uint16)
#img_array_out = numpy.empty(data_size, dtype=numpy.uint16)
img_array_float = numpy.zeros(data_size, dtype=numpy.float)
for idx in range(num_points):
# generate bitmap
print("STATUS:\tMappingFunctions: clearing frame buffer\n")
PI.py_clear_framebuffer()
print("STATUS:\tMappingFunctions: creating mask\n")
print("STATUS:\tMappingFunctions: generating one image of with ' + \
'one pixel\n")
PI.py_illuminate_point( int(points_to_illum_x[idx]),\
int(points_to_illum_y[idx]),\
MF.mask_number0)
# illuminate just ONE spot
print("STATUS:\tMappingFunctions: illuminating one point\n")
print("illuminating (%d,%d)\n" % \
(int(points_to_illum_x[idx]), int(points_to_illum_y[idx])))
PI.py_illuminate_expose() # turn on the frame buffer
#time.sleep(1)
# analyze image for centroid
print("STATUS:\tMappingFunctions: taking picture \
of one illuminated point\n")
# take a picture and get a pointer to the picture
frames = 5
for i in range(frames):
PC.py_snapPtr(img_array, MF.expose,MF.gain,"spare")
# sum accumulator
img_array_float += img_array.astype(numpy.float)
# end for
# average over frames
img_array_out = (img_array_float/frames).astype(numpy.uint16)
img_array_float *= 0 # reset accumulator
self.convertPicPNG(img_array_out, \
points_to_illum_x[idx], points_to_illum_y[idx])
# read in the config file. must be formated correctly
print("STATUS:\tMappingFunctions: find illuminated point\n")
# SWIGged function for finding the centroid
# doing array[x:x+1] returns a pointer to an index x in an array
# essentially in numpy
a = points_found_x[idx:idx+1]
b = points_found_y[idx:idx+1]
max_val = PI.py_illuminate_spot_find(img_array_out,a,b)
if max_val < 100:
print("point not found")
num_sub += 1
# end if
else:
print("found(%d,%d)" % \
(points_found_x[idx],points_found_y[idx]) )
# end else
# free up memory
#unload_camera_image(img_array)
PI.py_clear_framebuffer()
PI.py_illuminate_float()
#PC.cameraClose() # also frees up image buffer memory
#end for
num_points -= num_sub
# perform mapping operation
print("STATUS:\tMappingFunctions: generating mapping\n")
PC.cameraClose() # also frees up image buffer memory
self.generateMapping(points_found_x, points_found_y, \
points_to_illum_x, points_to_illum_y, num_points)
self.writeMappingFile()
for i in range(num_points):
print("illuminated(%d,%d)" % \
(points_to_illum_x[i],points_to_illum_y[i]) )
print("found(%d,%d)" % (points_found_x[i],points_found_y[i]) )
print(" ")
# end for
print("Finished map generation\n")
def on():
PI.py_light_all()
def closeDMD(self):
"""
Float the DMD and clear the frame buffer
"""
PI.py_illuminate_float()
PI.py_clear_framebuffer()
def vector(self,vx,vy, num_points,spot_size=0):
MF = self.MF
outpoints = self.n_ccd_to_dmd(vx,vy)
a = outpoints[0]
b = outpoints[1]
PI.py_illuminate_enable()
PI.py_clear_framebuffer()
if spot_size == 1:
PI.py_illuminate_vector(a,b, MF.mask_number2, num_points)
elif spot_size == 2:
PI.py_illuminate_vector(a,b, MF.mask_number3, num_points)
else:
PI.py_illuminate_vector(a,b, MF.mask_number1, num_points)
PI.py_illuminate_expose() # turn on the frame buffer
def lightAll(self):
PI.py_light_all()
def enableDMD(self):
# enable release hardware
PI.py_illuminate_enable()
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
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.cameraLive(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
