def main():
slabsize=4
h5chunksize=4
if len(sys.argv) <= 4 :
print " "
print sys.argv[0]
print "USAGE: %s h5file chunkstart chunkstop h5outputfile "%sys.argv[0]
print "chunk must not be smaller than %i projections"%h5chunksize
sys.exit(0)
npad=0 # should be 0
input=sys.argv[1] #first argument, filename of h5 file , should contain /entry/instrument/detector/data and be uint16
chunkstart=int(sys.argv[2]) # the start of the chunk (without padding)
chunkstop=int(sys.argv[3]) #the end of the chunk (without padding)
outname=sys.argv[4] #the output file
infp=h5py.File(input)
#data=infp['/entry/instrument/detector/data']
data=infp['/entry1/tomo_entry/data/data']
chunksize=chunkstop-chunkstart
nslabs = int(chunksize/slabsize)
h5outp=h5py.File(outname,"w")
outgrp=h5outp.create_group("/entry1/tomo_entry/data")
outdset=outgrp.create_dataset("data",(chunksize,data.shape[1],data.shape[2]),chunks=(h5chunksize,h5chunksize,data.shape[2]))
print "nslabs=%i"%nslabs
lastslabsize=chunksize-(nslabs*slabsize)
print "lastslabsize=%i"%lastslabsize
#set the coefficients -- this coudl be rolled into setup with additional args?
#unwarp.setcoeff(1,-1e-3,-6e-7,5e-10,-4e-13) #fisheye test
#unwarp.setctr(500,1000) #fisheye test
#unwarp.setcoeff(1,0,0,0,0)
unwarp.setcoeff(1.00015076,1.9289e-6,-2.4325e-8,1.00439e-11,-3.99352e-15)
unwarp.setctr(1283.25,data.shape[1]-1164.765)
outim=np.empty((slabsize+2*npad,data.shape[1],data.shape[2]),dtype=np.uint16) #create an empty array , the program will fill it up
firststop=chunkstart+slabsize
instack=read_image_set(data,chunkstart,firststop,npad) #npad is optional, default is 2
unwarp.setup(instack,outim) #call the program to initialize the arrays
for slab in range(nslabs):
print "SLAB %i of %i"%(slab,nslabs)
slabstart=slab*slabsize
slabstop=slabstart+slabsize
instack=read_image_set(data,slabstart,slabstop,npad) #npad is optional, default is 2
unwarp.run(instack,outim) #could call again with a different instack before cleaning up, if it is teh same size
output=outim[npad:outim.shape[0]-npad] #discard the padded area
for slice in range(slabstart,slabstop):
tifffile.imsave("/dls/i12/data/2015/cm12163-5/tmp/out_%05d.tif"%slice,outim[slice-slabstart]) #example, save the chunk
outdset[slabstart-chunkstart:slabstop-chunkstart,:,:]=output
unwarp.cleanup() #call the program to de-allocate the arrays
#now the last slab
if lastslabsize > 0:
outim=np.empty((lastslabsize+2*npad,data.shape[1],data.shape[2]),dtype=np.uint16) #create an empty array , the program will fill it up
print "last outim shape",outim.shape
laststart=chunkstart+nslabs*slabsize
slabstart=laststart
slabstop=chunkstop
instack=read_image_set(data,slabstart,slabstop,npad) #npad is optional, default is 2
unwarp.setup(instack,outim) #call the program to initialize the arrays
unwarp.run(instack,outim) #could call again with a different instack before cleaning up, if it is teh same size
output=outim[npad:outim.shape[0]-npad] #discard the padded area
for slice in range(slabstart,slabstop):
tifffile.imsave("/dls/i12/data/2015/cm12163-5/tmp/out_%05d.tif"%slice,outim[slice-slabstart]) #example, save the chunk
print "slabstart=",slabstart, "slabstop=",slabstop
print "output shape",output.shape
print "outdset shape",outdset.shape
print "chunksize",chunksize
outdset[slabstart-chunkstart:slabstop-chunkstart,:,:]=output
unwarp.cleanup() #call the program to de-allocate the arrays
rot=infp[ "/entry1/tomo_entry/data/rotation_angle"]
key=infp["/entry1/tomo_entry/instrument/detector/image_key"]
outrot=h5outp.create_dataset("/entry1/tomo_entry/data/rotation_angle",data=rot[chunkstart:chunkstop])
outkey=h5outp.create_dataset("/entry1/tomo_entry/instrument/detector/image_key",data=key[chunkstart:chunkstop])
h5outp.close()
def main():
slabsize = 4
h5chunksize = 4
if len(sys.argv) <= 4:
print " "
print sys.argv[0]
print "USAGE: %s h5file chunkstart chunkstop h5outputfile " % sys.argv[
0]
print "chunk must not be smaller than %i projections" % h5chunksize
sys.exit(0)
npad = 0 # should be 0
input = sys.argv[
1] #first argument, filename of h5 file , should contain /entry/instrument/detector/data and be uint16
chunkstart = int(sys.argv[2]) # the start of the chunk (without padding)
chunkstop = int(sys.argv[3]) #the end of the chunk (without padding)
outname = sys.argv[4] #the output file
infp = h5py.File(input)
#data=infp['/entry/instrument/detector/data']
data = infp['/entry1/tomo_entry/data/data']
chunksize = chunkstop - chunkstart
nslabs = int(chunksize / slabsize)
h5outp = h5py.File(outname, "w")
outgrp = h5outp.create_group("/entry1/tomo_entry/data")
outdset = outgrp.create_dataset("data",
(chunksize, data.shape[1], data.shape[2]),
chunks=(h5chunksize, h5chunksize,
data.shape[2]))
print "nslabs=%i" % nslabs
lastslabsize = chunksize - (nslabs * slabsize)
print "lastslabsize=%i" % lastslabsize
#set the coefficients -- this coudl be rolled into setup with additional args?
#unwarp.setcoeff(1,-1e-3,-6e-7,5e-10,-4e-13) #fisheye test
#unwarp.setctr(500,1000) #fisheye test
#unwarp.setcoeff(1,0,0,0,0)
unwarp.setcoeff(1.00015076, 1.9289e-6, -2.4325e-8, 1.00439e-11,
-3.99352e-15)
unwarp.setctr(1283.25, data.shape[1] - 1164.765)
outim = np.empty(
(slabsize + 2 * npad, data.shape[1], data.shape[2]),
dtype=np.uint16) #create an empty array , the program will fill it up
firststop = chunkstart + slabsize
instack = read_image_set(data, chunkstart, firststop,
npad) #npad is optional, default is 2
unwarp.setup(instack, outim) #call the program to initialize the arrays
for slab in range(nslabs):
print "SLAB %i of %i" % (slab, nslabs)
slabstart = slab * slabsize
slabstop = slabstart + slabsize
instack = read_image_set(data, slabstart, slabstop,
npad) #npad is optional, default is 2
unwarp.run(
instack, outim
) #could call again with a different instack before cleaning up, if it is teh same size
output = outim[npad:outim.shape[0] - npad] #discard the padded area
for slice in range(slabstart, slabstop):
tifffile.imsave("/dls/i12/data/2015/cm12163-5/tmp/out_%05d.tif" %
slice,
outim[slice - slabstart]) #example, save the chunk
outdset[slabstart - chunkstart:slabstop - chunkstart, :, :] = output
unwarp.cleanup() #call the program to de-allocate the arrays
#now the last slab
if lastslabsize > 0:
outim = np.empty(
(lastslabsize + 2 * npad, data.shape[1], data.shape[2]),
dtype=np.uint16
) #create an empty array , the program will fill it up
print "last outim shape", outim.shape
laststart = chunkstart + nslabs * slabsize
slabstart = laststart
slabstop = chunkstop
instack = read_image_set(data, slabstart, slabstop,
npad) #npad is optional, default is 2
unwarp.setup(instack,
outim) #call the program to initialize the arrays
unwarp.run(
instack, outim
) #could call again with a different instack before cleaning up, if it is teh same size
output = outim[npad:outim.shape[0] - npad] #discard the padded area
for slice in range(slabstart, slabstop):
tifffile.imsave("/dls/i12/data/2015/cm12163-5/tmp/out_%05d.tif" %
slice,
outim[slice - slabstart]) #example, save the chunk
print "slabstart=", slabstart, "slabstop=", slabstop
print "output shape", output.shape
print "outdset shape", outdset.shape
print "chunksize", chunksize
outdset[slabstart - chunkstart:slabstop - chunkstart, :, :] = output
unwarp.cleanup() #call the program to de-allocate the arrays
rot = infp["/entry1/tomo_entry/data/rotation_angle"]
key = infp["/entry1/tomo_entry/instrument/detector/image_key"]
outrot = h5outp.create_dataset("/entry1/tomo_entry/data/rotation_angle",
data=rot[chunkstart:chunkstop])
outkey = h5outp.create_dataset(
"/entry1/tomo_entry/instrument/detector/image_key",
data=key[chunkstart:chunkstop])
h5outp.close()
#inim=np.expand_dims(tifffile.imread("index-1.tif"),0)
#inim=np.expand_dims(tifffile.imread("p_00600.tif"),0)
inim = np.expand_dims(tifffile.imread("i32.tif"), 0)
inimt = np.tile(inim, (nbatch, 1, 1))
inim3 = np.ascontiguousarray(inimt.astype(np.uint16))
print "shape: ", inim3.shape
outim = np.empty_like(inim3)
return (inim3, outim)
#end of get_image_array
(inarray, outarray) = get_image_array()
#set the coefficients -- this coudl be rolled into setup with additional args?
unwarp.setcoeff(1, -1e-3, -6e-7, 5e-10, -4e-13)
unwarp.setctr(1000, 1000)
#call setup routine
unwarp.setup(inarray, outarray)
unwarp.run(inarray, outarray)
#multiple calls so long as centre and parameters are fixed
#could be different data solong as it is same type/size/etc
unwarp.run(inarray, outarray)
unwarp.cleanup()
print(
"Writing the files to /dls/i12/data/2015/cm12163-5/tmp/unwarptest/cython_out"
)
def get_image_array():
global nbatch
#inim=np.expand_dims(tifffile.imread("index-1.tif"),0)
#inim=np.expand_dims(tifffile.imread("p_00600.tif"),0)
inim=np.expand_dims(tifffile.imread("i32.tif"),0)
inimt=np.tile(inim,(nbatch,1,1))
inim3=np.ascontiguousarray(inimt.astype(np.uint16))
print "shape: ",inim3.shape
outim=np.empty_like(inim3)
return(inim3,outim)
#end of get_image_array
(inarray,outarray)=get_image_array()
#set the coefficients -- this coudl be rolled into setup with additional args?
unwarp.setcoeff(1,-1e-3,-6e-7,5e-10,-4e-13)
unwarp.setctr(1000,1000)
#call setup routine
unwarp.setup(inarray,outarray)
unwarp.run(inarray,outarray)
#multiple calls so long as centre and parameters are fixed
#could be different data solong as it is same type/size/etc
unwarp.run(inarray,outarray)
unwarp.cleanup()
print("Writing the files to /dls/i12/data/2015/cm12163-5/tmp/unwarptest/cython_out")
try: