curf += 1
average_psf = average_psf/total
# force psf to be zero (on average) at the boundaries.
if 1:
edge = numpy.concatenate((average_psf[0,:],
average_psf[-1,:],
average_psf[:,0],
average_psf[:,-1]))
average_psf -= numpy.mean(edge)
# save PSF (in image form).
if 1:
import sa_library.daxwriter as daxwriter
daxwriter.singleFrameDax("psf.dax", 1000.0*average_psf+100)
# save PSF (in numpy form).
numpy.save(sys.argv[3],average_psf)
#
# The MIT License
#
# Copyright (c) 2012 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# save hres results.
hr_xo = i * keep_size * scale
hr_xf = hr_xo + keep_size * scale
hr_yo = j * keep_size * scale
hr_yf = hr_yo + keep_size * scale
ht_hres[hr_xo:hr_xf, hr_yo:hr_yf] = ht_xvec.reshape(
(scale * keep_size, scale * keep_size))
fista_hres[hr_xo:hr_xf, hr_yo:hr_yf] = fista_xvec.reshape(
(scale * keep_size, scale * keep_size))
# Save results.
ht.printProfilingData()
fista.printProfilingData()
daxwriter.singleFrameDax("low_hres.dax", low_res)
daxwriter.singleFrameDax("ht_hres.dax", ht_hres)
daxwriter.singleFrameDax("fista_hres.dax", fista_hres)
#
# The MIT License
#
# Copyright (c) 2013 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
x = start
for i in range(s_size):
y = start
for j in range(s_size):
np_spline[j, i] = xy_spline.f(y, x)
y += 1.0
x += 1.0
print("Calculating spline coefficients.")
spline = spline2D.Spline2D(np_spline)
if 1:
import sa_library.daxwriter as daxwriter
daxwriter.singleFrameDax("spline.dax", 1000.0 * np_spline + 100)
# 3D spline
else:
print("Generating 3D spline.")
s_size = 2 * s_size
np_spline = numpy.zeros((s_size, s_size, s_size))
xy_splines = []
print("Generating XY splines.")
for i in range(np_psf.shape[0]):
xy_splines.append(spline2D.Spline2D(np_psf[i, :, :]))
print("Generating fitting spline.")
x = start
peaks_used += 1
curf += 1
average_psf = average_psf / total
# force psf to be zero (on average) at the boundaries.
if 1:
edge = numpy.concatenate((average_psf[0, :], average_psf[-1, :],
average_psf[:, 0], average_psf[:, -1]))
average_psf -= numpy.mean(edge)
# save PSF (in image form).
if 1:
import sa_library.daxwriter as daxwriter
daxwriter.singleFrameDax("psf.dax", 1000.0 * average_psf + 100)
# save PSF (in numpy form).
numpy.save(sys.argv[3], average_psf)
#
# The MIT License
#
# Copyright (c) 2012 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
sx = numpy.ones(np) * float(sigma)
sy = numpy.ones(np) * float(sigma)
objects = numpy.concatenate(
(x[:, None], y[:, None], h[:, None], sx[:, None], sy[:, None]), axis=1)
image = cDrawGaussians(image, objects, 1)
return image
if __name__ == "__main__":
import sa_library.daxwriter as daxwriter
x = 4.0 * numpy.arange(10) + 10
y = 4.0 * numpy.arange(10) + 5
image = drawGaussiansXY([100, 100], x, y, height=100.0)
daxwriter.singleFrameDax("dg_test.dax", image)
#
# The MIT License
#
# Copyright (c) 2016 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
x = numpy.arange(0.0, 2.001, 0.125)
y = numpy.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0], [6.0, 7.0, 8.0]])
s = Spline2D(y)
surf = numpy.zeros((x.size, x.size))
dx_surf = numpy.zeros((x.size, x.size))
dy_surf = numpy.zeros((x.size, x.size))
for i in range(x.size):
for j in range(x.size):
surf[i, j] = s.f(x[i], x[j])
dx_surf[i, j] = s.dxf(x[i], x[j])
dy_surf[i, j] = s.dyf(x[i], x[j])
print surf
#print dx_surf
#print dy_surf
if 0:
surf = 100.0 + 100.0 * surf
dx_surf = 100.0 + 100.0 * dx_surf
dy_surf = 100.0 + 100.0 * dy_surf
daxwriter.singleFrameDax("surf.dax", surf)
daxwriter.singleFrameDax("dx_surf.dax", dx_surf)
daxwriter.singleFrameDax("dy_surf.dax", dy_surf)
#pw = pyqtgraph.plot()
#raw_input("return to continue")
import sa_library.arraytoimage as arraytoimage
import sa_library.daxwriter as daxwriter
if (len(sys.argv) != 3):
print "usage: <in_hres> <out_img>"
exit()
hres = HResFile(sys.argv[1])
image = hres.sumFrames(verbose=True)
ext = os.path.splitext(sys.argv[2])[1]
if (ext == ".png"):
arraytoimage.singleColorImage(image, sys.argv[2])
elif (ext == ".dax"):
daxwriter.singleFrameDax(sys.argv[2], image)
else:
print "unrecognized extension ", ext
#
# The MIT License
#
# Copyright (c) 2012 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# save hres results.
hr_xo = i * keep_size * scale
hr_xf = hr_xo + keep_size * scale
hr_yo = j * keep_size * scale
hr_yf = hr_yo + keep_size * scale
ht_hres[hr_xo:hr_xf, hr_yo:hr_yf] = ht_xvec.reshape((scale * keep_size, scale * keep_size))
fista_hres[hr_xo:hr_xf, hr_yo:hr_yf] = fista_xvec.reshape((scale * keep_size, scale * keep_size))
# Save results.
ht.printProfilingData()
fista.printProfilingData()
daxwriter.singleFrameDax("low_hres.dax", low_res)
daxwriter.singleFrameDax("ht_hres.dax", ht_hres)
daxwriter.singleFrameDax("fista_hres.dax", fista_hres)
#
# The MIT License
#
# Copyright (c) 2013 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
x = start
for i in range(s_size):
y = start
for j in range(s_size):
np_spline[j,i] = xy_spline.f(y,x)
y += 1.0
x += 1.0
print "Calculating spline coefficients."
spline = spline2D.Spline2D(np_spline)
if 1:
import sa_library.daxwriter as daxwriter
daxwriter.singleFrameDax("spline.dax", 1000.0*np_spline + 100)
# 3D spline
else:
print "Generating 3D spline."
s_size = 2*s_size
np_spline = numpy.zeros((s_size, s_size, s_size))
xy_splines = []
print "Generating XY splines."
for i in range(np_psf.shape[0]):
xy_splines.append(spline2D.Spline2D(np_psf[i,:,:]))
print "Generating fitting spline."
y[:,None],
h[:,None],
sx[:,None],
sy[:,None]),
axis = 1)
image = cDrawGaussians(image, objects, 1)
return image
if __name__ == "__main__":
import sa_library.daxwriter as daxwriter
x = 4.0*numpy.arange(10) + 10
y = 4.0*numpy.arange(10) + 5
image = drawGaussiansXY([100,100], x, y, height = 100.0)
daxwriter.singleFrameDax("dg_test.dax", image)
#
# The MIT License
#
# Copyright (c) 2016 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
[3.0, 4.0, 5.0],
[6.0, 7.0, 8.0]])
s = Spline2D(y)
surf = numpy.zeros((x.size, x.size))
dx_surf = numpy.zeros((x.size, x.size))
dy_surf = numpy.zeros((x.size, x.size))
for i in range(x.size):
for j in range(x.size):
surf[i,j] = s.f(x[i],x[j])
dx_surf[i,j] = s.dxf(x[i],x[j])
dy_surf[i,j] = s.dyf(x[i],x[j])
print surf
#print dx_surf
#print dy_surf
if 0:
surf = 100.0 + 100.0 * surf
dx_surf = 100.0 + 100.0 * dx_surf
dy_surf = 100.0 + 100.0 * dy_surf
daxwriter.singleFrameDax("surf.dax", surf)
daxwriter.singleFrameDax("dx_surf.dax", dx_surf)
daxwriter.singleFrameDax("dy_surf.dax", dy_surf)
#pw = pyqtgraph.plot()
#raw_input("return to continue")
import sa_library.arraytoimage as arraytoimage
import sa_library.daxwriter as daxwriter
if (len(sys.argv) != 3):
print "usage: <in_hres> <out_img>"
exit()
hres = HResFile(sys.argv[1])
image = hres.sumFrames(verbose = True)
ext = os.path.splitext(sys.argv[2])[1]
if (ext == ".png"):
arraytoimage.singleColorImage(image, sys.argv[2])
elif (ext == ".dax"):
daxwriter.singleFrameDax(sys.argv[2], image)
else:
print "unrecognized extension ", ext
#
# The MIT License
#
# Copyright (c) 2012 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
