def importOS():
IMAGE = pr.image_read('TomoData/PhantomData/sl.mat')
counts = pr.image_read('TomoData/noisyphantom/nslcounts.mat',
dtype=np.float32)
print 'counts', counts.shape
dark = pr.image_read('TomoData/noisyphantom/nsldark.mat', dtype=np.float32)
print 'dark', dark.shape
flat = pr.image_read('TomoData/noisyphantom/nslflat.mat', dtype=np.float32)
print 'flat', flat.shape
# flat = np.zeros(counts.shape)
#pp.imshow( sino, cmap = 'gray_r', interpolation = 'nearest',
#extent = ( sl.top_left[ 0 ], sl.bottom_right[ 0 ], sl.bottom_right[ 1 ], sl.top_left[ 1 ] ))
#pp.show()
fast_radon, fast_transp = fs.make_fourier_slice_radon_transp(counts)
#pp.imshow( sino, cmap = 'gray_r', interpolation = 'nearest',
#extent = ( sino.top_left[ 0 ], sino.bottom_right[ 0 ], sino.bottom_right[ 1 ], sino.top_left[ 1 ] ))
#pp.show()
return IMAGE, counts, dark, flat, fast_radon, fast_transp
def importSino():
sino = pr.image_read('egg_slice_1097.mat')
#pp.imshow( sino, cmap = 'gray_r', interpolation = 'nearest',
#extent = ( sl.top_left[ 0 ], sl.bottom_right[ 0 ], sl.bottom_right[ 1 ], sl.top_left[ 1 ] ))
#pp.show()
fast_radon, fast_transp = fs.make_fourier_slice_radon_transp(sino)
#pp.imshow( sino, cmap = 'gray_r', interpolation = 'nearest',
#extent = ( sino.top_left[ 0 ], sino.bottom_right[ 0 ], sino.bottom_right[ 1 ], sino.top_left[ 1 ] ))
#pp.show()
return sino, fast_radon, fast_transp
def importPhoto():
sl = pr.image_read('sl.mat')
#pp.imshow( sl, cmap = 'gray_r', interpolation = 'nearest',
#extent = ( sl.top_left[ 0 ], sl.bottom_right[ 0 ], sl.bottom_right[ 1 ], sl.top_left[ 1 ] ))
#pp.show()
sino = pr.image(np.zeros((1024, 1024)),
top_left=(0, 1),
bottom_right=(math.pi, -1))
fast_radon, fast_transp = fs.make_fourier_slice_radon_transp(sino)
sino = fast_radon(sl)
#pp.imshow( sino, cmap = 'gray_r', interpolation = 'nearest',
#extent = ( sino.top_left[ 0 ], sino.bottom_right[ 0 ], sino.bottom_right[ 1 ], sino.top_left[ 1 ] ))
#pp.show()
return sino, fast_radon, fast_transp
def P_INTERP_PP(In1):
#%=====================================================================
#% This function performs interpolation from the Polar-Grid to the
#% Pseudo-Polar domain for use in the adjoint. The interpolation is in
#% two stages first along each ray to obtain non-equispaced points, then
#% along each row to obtain non-equiangular rays on the concentric square
#% grid.
#% In - 2D-FFT on the Polar Grid (r, theta)
#% Out- 2D-FFT on the Pseudo-Polar Grid (r, theta)
#%=====================================================================
if In1 is None:
In1 = pr.image_read('TomoData/noisyphantom/nslcounts.mat',dtype=np.float32)
OS1=1;
OS2=1;
K = np.shape(In1)
In = In1
print('import done')
N = min(np.shape(In)); #assuming square input
# C. resampling the rays to the Pseudo-Polar locations
F=In[:,0:N/2]
Fout = np.zeros((OS2*N,N/2))*0j
Xcor = np.arange(-2.0*np.pi,2.0*np.pi-np.pi/(N*OS2),2.0*np.pi/(N*OS2)) #these are the current locations
Xcor1 = np.arange(-np.pi*1.0,np.pi-np.pi/(2*N*OS2),2.0*np.pi/(2.0*N*OS2))
print('initialization done')
for k in range(1,N/2+1):
Ray=np.transpose(F[:,k-1])
Factor=np.cos((k-N/4.0)*np.pi/(N)); # completion of current locations
#f2 = interp1d(Xcor, Ray, kind='linear')
f2 = CubicSpline(Xcor,Ray)
Fout[:,k-1]=np.transpose(f2(Xcor1[0::2*OS2]/Factor));
# C. resampling the rays to the Pseudo-Polar locations
G=In[:,N/2::];
Gout = np.zeros((N,N/2))*0j;
Ycor = np.arange(-2.0*np.pi,2.0*np.pi-np.pi/(N*OS2),2.0*np.pi/(N*OS2)) #these are the current locations
Ycor1 = np.arange(-np.pi*1.0,np.pi-np.pi/(2*N*OS2),2.0*np.pi/(2.0*N*OS2))
for k in range(1,N/2+1):
Ray=G[:,k-1]
Factor=np.cos((k-N/4.0 )*np.pi/(N)); # completion of current locations
#f2 = interp1d(Xcor, Ray,kind='linear')
f2 = CubicSpline(Ycor,Ray)
Gout[:,k-1]=np.transpose(f2(Ycor1[0::2*OS2]/Factor))
# B. row/columnwise interpolation to obatain equi-distant slope
Xcor1 = 2.0*np.pi/(N*OS2)*np.arange(-OS1*N/2.0,OS1*N/2.0-1,2)/OS1/N
Xcor2 = 1.0*np.pi/(N*OS2)*np.tan(np.pi*np.arange(-N/2.0,N/2.0-1,2)/N/2.0)
steps = range(-N/2*OS2,N/2*OS2)
for ll in steps:
Temp1=Fout[ll+OS2*N/2,:]
if ll != 0:
#f2 = interp1d(Xcor2*ll,Temp1,kind='linear', fill_value='extrapolate')
if ll > 0:
f2 = CubicSpline(Xcor2*ll,Temp1)
Fout[ll+OS2*N/2,0:N/2]=f2(Xcor1*ll);
else:
f2 = CubicSpline(np.flip(Xcor2*ll,0),np.flip(Temp1,0))
Fout[ll+OS2*N/2,0:N/2]=f2(Xcor1*ll);
else:
Fout[ll+OS2*N/2,0:N/2]=Temp1[0::OS1];
# B. row/columnwise interpolation to obatain equi-distant slope
Ycor1 = 2.0*np.pi/(N*OS2)*np.arange(-OS1*N/2.0,OS1*N/2.0-1,2)/OS1/N
Ycor2 = 1.0*np.pi/(N*OS2)*np.tan(np.pi*np.arange(-N/2.0,N/2.0-1,2)/N/2.0)
steps = range(-N/2*OS2,N/2*OS2)
for ll in steps:
Temp2=Gout[ll+OS2*N/2,:];
if ll !=0:
#f2 = interp1d(Ycor2*ll,Temp1, kind='linear',fill_value='extrapolate')
if ll > 0:
f2 = CubicSpline(Ycor2*ll,Temp2)
Gout[ll+OS2*N/2,0:N/2]= f2(Ycor1*ll)
else:
f2 = CubicSpline(np.flip(Ycor2*ll,0),np.flip(Temp2,0))
Gout[ll+OS2*N/2,0:N/2]=f2(Ycor1*ll);
else:
Gout[ll+OS2*N/2,0:N/2]= Temp2[0::OS1];
Out = np.concatenate(((Fout), Gout),1)
return Out
import pyraft as pr
import matplotlib.pyplot as pp
import fourier_slice as fs
import numpy as np
import math
# From Fullerton_Example
# implementation of FISTA
# uses actual data (seed data)
yy = pr.image_read('counts.mat', dtype=np.float32)
r = pr.image_read('dark.mat', dtype=np.float32)
b = pr.image_read('flat.mat', dtype=np.float32)
dim = 2048
# USE THIS TO CHANGE DIMENSIONS OF DATA
sino = yy # given sinogram data
fast_radon, fast_transp = fs.make_fourier_slice_radon_transp(sino)
#pp.imshow(sino, interpolation = 'nearest', cmap = 'gray_r', extent = ( sino.top_left[ 0 ], sino.bottom_right[ 0 ], sino.bottom_right[ 1 ], sino.top_left[ 1 ] ) )
#pp.show()
def gradient(xz):
temp = (b * yy) / (
b + np.exp(fast_radon(xz)) * r) - b * np.exp(-fast_radon(xz))
return fast_transp(temp)
told = 1 # initial t val
data1 = sino # locate image
def pseudoimportSino(data_case):
#You can custom import data by loading into directory and changing string
#Sinogram must by NxN wher N is doubly even. It may be useful to develop
#interpolation function in feature domain to create artificial oversampling
#this way any data can be made NxN with N divisible by 4.
if data_case ==0:
sl = pr.image_read( 'TomoData/PhantomData/sl2.mat', dtype=np.float32)
flat = pr.image_read( 'TomoData/PhantomData/slflat.mat', dtype=np.float32 )
dark = pr.image_read( 'TomoData/PhantomData/sldark.mat', dtype=np.float32 )
counts = pr.image_read( 'TomoData/PhantomData/slcount.mat', dtype=np.float32 )
elif data_case == 1:
sl = pr.image_read( 'TomoData/PhantomData/sl2.mat', dtype=np.float32)
flat = pr.image_read( 'TomoData/noisyphantom/nslflat.mat', dtype=np.float32 )
dark = pr.image_read( 'TomoData/noisyphantom/nsldark.mat', dtype=np.float32 )
counts = pr.image_read( 'TomoData/noisyphantom/nslcounts.mat', dtype=np.float32 )
elif data_case ==2:
sl = pr.image(np.ones((1024,1024)), top_left =(-1,1), bottom_right = (1,-1))
flat = pr.image_read( 'TomoData/SeedData/flati.mat', dtype=np.float32 )
dark = pr.image_read( 'TomoData/SeedData/darki.mat', dtype=np.float32 )
counts = pr.image_read( 'TomoData/SeedData/countsi.mat', dtype=np.float32 )
else:
print('not a valid data_case, you can insert custom data here')
quit()
#the lines below must always be performed regardless of data
n,k = sl.shape
#Form sino for interpolation step
sino = np.log(flat/counts)
#Pad Sino to eliminate need for extrapolation, oversample
sino = PIPP.Pad2x(sino)
print(np.max(sino))
#Convert to frequency domain
fsino = np.fft.fftshift(sino, axes = 0)
fsino = np.fft.fft( fsino, axis = 0 )
fsino = np.fft.fftshift(fsino)
#Interpolate via 2 stage interpolation (reverse of averbuch et. al)
fsino = PIPP.P_INTERP_PP(fsino)
#Convert back to feature domain
fsino = np.fft.fftshift(fsino )
fsino = np.fft.ifft( fsino, axis = 0 )
sino= (np.real(np.fft.ifftshift(fsino, axes=0)))
sino= pr.image(np.concatenate((np.fliplr(np.flipud(sino[:,0:n])),np.fliplr(sino[:,n::])),1), top_left = (0,1), bottom_right = (np.pi,-1) )
print(np.min(counts))
#Reparse into counts,flat,dark
counts = pr.image(flat/np.exp(sino), top_left = (0,1), bottom_right = (np.pi,-1) )
function = ppfs.make_fourier_slice_radon_transp
fast_radon, fast_transp = function( sino )
return sl, sino, counts, dark, flat, fast_radon, fast_transp, function
def nonuimportSino(data_case):
if data_case ==0:
sl = pr.image_read( 'TomoData/PhantomData/sl.mat')
flat = pr.image_read( 'TomoData/PhantomData/slflat.mat', dtype=np.float32 )
dark = pr.image_read( 'TomoData/PhantomData/sldark.mat', dtype=np.float32 )
counts = pr.image_read( 'TomoData/PhantomData/slcount.mat', dtype=np.float32 )
elif data_case ==1:
sl = pr.image_read( 'TomoData/PhantomData/sl.mat')
counts = pr.image_read( 'TomoData/noisyphantom/nslcounts.mat', dtype=np.float32 )
flat = pr.image_read( 'TomoData/noisyphantom/nslflat.mat', dtype=np.float32 )
dark = pr.image_read( 'TomoData/noisyphantom/nsldark.mat', dtype=np.float32 )
elif data_case ==2:
sl = pr.image(np.ones((2048,2048)), top_left =(-1,1), bottom_right = (1,-1))
flat = pr.image_read( 'TomoData/SeedData/flati.mat', dtype=np.float32 )
dark = pr.image_read( 'TomoData/SeedData/darki.mat', dtype=np.float32 )
counts = pr.image_read( 'TomoData/SeedData/countsi.mat', dtype=np.float32 )
else:
print('not a valid data_case, you can insert custom data here')
quit()
sino = pr.image(np.log(flat/counts), top_left = (0,1),bottom_right=(np.pi,-1))
function = fs.make_fourier_slice_radon_transp
fast_radon, fast_transp = function( sino )
return sl, sino, counts, dark, flat, fast_radon, fast_transp, function
