Python RecToolsDIR.FBP 예제들

예제 #1

파일: Model2D_t.py 프로젝트: world2005/TomoPhantom

sino = TomoP2D.ModelSinoTemporal(model, N_size, P, angles, path_library2D)

plt.figure(2)
plt.rcParams.update({'font.size': 21})
plt.title('{}''{}'.format('2D+t sinogram of model no.',model))
for sl in range(0,np.shape(phantom_2Dt)[0]):
    im = sino[sl,:,:].transpose()
    plt.imshow(im, vmin=0, vmax=180)
    plt.pause(.1)
    plt.draw
#%%
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("Reconstructing analytical sinogram using FBP (tomobar)...")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
# initialise tomobar reconstruction class ONCE
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(DetectorsDimH = P,  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
                    CenterRotOffset = None, # Center of Rotation (CoR) scalar (for 3D case only)
                    AnglesVec = angles_rad, # array of angles in radians
                    ObjSize = N_size, # a scalar to define reconstructed object dimensions
                    device_projector='cpu')

FBPrec = RectoolsDIR.FBP(sino[15,:,:].transpose()) # reconstruct one frame

plt.figure(3) 
plt.imshow(FBPrec, vmin=0, vmax=1)
plt.title('FBP Reconstructed Phantom')
#%%

예제 #2

plt.colorbar(ticks=[0, 150, 250], orientation='vertical')
plt.title('{}' '{}'.format('Analytical noisy sinogram', model))
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(
    DetectorsDimH=P,  # Horizontal detector dimension
    DetectorsDimV=None,  # Vertical detector dimension (3D case)
    CenterRotOffset=0.001,  # Center of Rotation scalar
    AnglesVec=angles_rad,  # A vector of projection angles in radians
    ObjSize=N_size,  # Reconstructed object dimensions (scalar)
    device_projector='gpu')

FBPrec = RectoolsDIR.FBP(noisy_sino)  # perform FBP reconstruction

plt.figure()
plt.rcParams.update({'font.size': 20})
plt.imshow(FBPrec, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('FBP reconstruction')
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("Reconstructing with FISTA method (ASTRA used for projection)")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsIR import RecToolsIR

# set parameters and initiate a class object
Rectools = RecToolsIR(
    DetectorsDimH=P,  # Horizontal detector dimension

예제 #3

파일: Demo_SimulData_Recon_SX.py 프로젝트: zhengyi-beijing/CCPi-Regularisation-Toolkit

plt.title('Vertical (Y-Z) view', fontsize=19)
plt.show()
#plt.savefig('projdata.pdf', format='pdf', dpi=1200)
#%%
# initialise tomobar DIRECT reconstruction class ONCE
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(
    DetectorsDimH=Horiz_det,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    Vert_det,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    AnglesVec=proj_angles,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device='gpu')
#%%
print("Reconstruction using FBP from tomobar")
recFBP = RectoolsDIR.FBP(projdata_norm)  # FBP reconstruction
#%%
x0, y0 = 0, 127  # These are in _pixel_ coordinates!!
x1, y1 = 255, 127

sliceSel = int(0.5 * N_size)
max_val = 1
plt.figure(figsize=(20, 5))
gs1 = gridspec.GridSpec(1, 3)
gs1.update(wspace=0.1, hspace=0.05)  # set the spacing between axes.
ax1 = plt.subplot(gs1[0])
plt.imshow(recFBP[sliceSel, :, :], vmin=0, vmax=max_val, cmap="PuOr")
ax1.plot([x0, x1], [y0, y1], 'ko-', linestyle='--')
plt.colorbar(ax=ax1)
plt.title('FBP Reconstruction, axial (X-Y) view', fontsize=19)
ax1.set_aspect('equal')

예제 #4

plt.title('Tangentogram view')
plt.show()
#%%
# initialise tomobar DIRECT reconstruction class ONCE
from tomobar.methodsDIR import RecToolsDIR
Rectools = RecToolsDIR(
    DetectorsDimH=Horiz_det,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    Vert_det,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=0.0,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device_projector='gpu')

print("Reconstruction using FBP from tomobar")
recNumerical = Rectools.FBP(projData3D_analyt_noisy)  # FBP reconstruction

sliceSel = int(0.5 * N_size)
max_val = 1
#plt.gray()
plt.figure()
plt.subplot(131)
plt.imshow(recNumerical[sliceSel, :, :], vmin=0, vmax=max_val)
plt.title('3D Reconstruction, axial view')

plt.subplot(132)
plt.imshow(recNumerical[:, sliceSel, :], vmin=0, vmax=max_val)
plt.title('3D Reconstruction, coronal view')

plt.subplot(133)
plt.imshow(recNumerical[:, :, sliceSel], vmin=0, vmax=max_val)

예제 #5

sliceSel = 150
plt.figure() 
plt.subplot(131)
plt.imshow(projData3D_analyt_noisy[:,sliceSel,:],vmin=0, vmax=intens_max)
plt.title('2D noisy Projection (analytical)')
plt.subplot(132)
plt.imshow(projData3D_analyt_noisy[sliceSel,:,:],vmin=0, vmax=intens_max)
plt.title('Noisy sinogram view')
plt.subplot(133)
plt.imshow(projData3D_analyt_noisy[:,:,sliceSel],vmin=0, vmax=intens_max)
plt.title('Noisy tangentogram view')
plt.show()
"""
#%%
print("Reconstruction using FBP from tomobar")
recNumerical = RectoolsDIR.FBP(ProjData3D)  # FBP reconstruction

sliceSel = int(0.5 * N3D_size)
max_val = 1
#plt.gray()
plt.figure()
plt.subplot(131)
plt.imshow(recNumerical[sliceSel, :, :], vmin=0, vmax=max_val)
plt.title('3D Reconstruction, axial view')

plt.subplot(132)
plt.imshow(recNumerical[:, sliceSel, :], vmin=0, vmax=max_val)
plt.title('3D Reconstruction, coronal view')

plt.subplot(133)
plt.imshow(recNumerical[:, :, sliceSel], vmin=0, vmax=max_val)

예제 #6

파일: Demo_RealData.py 프로젝트: jacksky64/ToMoBAR

#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(
    DetectorsDimH=
    detectorHoriz,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=None,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device='gpu')

FBPrec = RectoolsDIR.FBP(data_norm[:, :, slice_to_recon])

plt.figure()
plt.imshow(FBPrec[150:550, 150:550], vmin=0, vmax=0.005, cmap="gray")
plt.title('FBP reconstruction')

from tomobar.methodsIR import RecToolsIR
# set parameters and initiate a class object
Rectools = RecToolsIR(
    DetectorsDimH=
    detectorHoriz,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=None,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions

예제 #7

    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device_projector='cpu')
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("Reconstructing analytical sinogram using Fourier Slice method")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
RecFourier = RectoolsDIR.FOURIER(noisy_sino, 'linear')
plt.figure()
plt.imshow(RecFourier, vmin=0, vmax=1, cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('Fourier slice reconstruction')
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("Reconstructing analytical sinogram using FBP (tomobar)...")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
FBPrec = RectoolsDIR.FBP(noisy_sino)  # ideal reconstruction

plt.figure()
plt.imshow(FBPrec, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('FBP reconstruction')
#%%
# initialise tomobar ITERATIVE reconstruction class ONCE
from tomobar.methodsIR import RecToolsIR
RectoolsIR = RecToolsIR(
    DetectorsDimH=P,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=None,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions

예제 #8

#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(
    DetectorsDimH=Horiz_det,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    Vert_det,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=None,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device_projector='gpu')

FBPrec = RectoolsDIR.FBP(projData3D_analyt_noise)  #perform FBP

sliceSel = int(0.5 * N_size)
max_val = 1
plt.figure()
plt.subplot(131)
plt.imshow(FBPrec[sliceSel, :, :], vmin=0, vmax=max_val)
plt.title('3D FBP Reconstruction, axial view')

plt.subplot(132)
plt.imshow(FBPrec[:, sliceSel, :], vmin=0, vmax=max_val)
plt.title('3D FBP Reconstruction, coronal view')

plt.subplot(133)
plt.imshow(FBPrec[:, :, sliceSel], vmin=0, vmax=max_val)
plt.title('3D FBP Reconstruction, sagittal view')

예제 #9

파일: DemoFISTA_artifacts2D.py 프로젝트: dkazanc/ToMoBAR

plt.colorbar(ticks=[0, 150, 250], orientation='vertical')
plt.title('{}' '{}'.format('Analytical noisy sinogram with artifacts.', model))
#%%
from tomobar.methodsDIR import RecToolsDIR
Rectools = RecToolsDIR(
    DetectorsDimH=P,  # Horizontal detector dimension
    DetectorsDimV=None,  # Vertical detector dimension (3D case)
    CenterRotOffset=0.0,  # Center of Rotation scalar
    AnglesVec=angles_rad,  # A vector of projection angles in radians
    ObjSize=N_size,  # Reconstructed object dimensions (scalar)
    device_projector='gpu')

print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("Reconstructing analytical sinogram using FBP (tomobar)...")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
FBPrec_ideal = Rectools.FBP(sino_an)  # ideal reconstruction
FBPrec_error = Rectools.FBP(sino_artifacts)  # reconstruction with artifacts
FBPrec_misalign = Rectools.FBP(
    sino_misalign)  # reconstruction with misalignment

plt.figure()
plt.subplot(131)
plt.imshow(FBPrec_ideal, vmin=0, vmax=2, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 2], orientation='vertical')
plt.title('Ideal FBP reconstruction')
plt.subplot(132)
plt.imshow(FBPrec_error, vmin=0, vmax=2, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 2], orientation='vertical')
plt.title('Erroneous data FBP Reconstruction')
plt.subplot(133)
plt.imshow(FBPrec_misalign, vmin=0, vmax=2, cmap="gray")

예제 #10

plt.subplot(133)
plt.imshow(projData3D_analyt_noisy[:,:,sliceSel],vmin=0, vmax=intens_max)
plt.title('Tangentogram view')
plt.show()
#%%
# initialise tomobar DIRECT reconstruction class ONCE
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(DetectorsDimH = Horiz_det,  # Horizontal detector dimension
                    DetectorsDimV = Vert_det,         # Vertical detector dimension (3D case)
                    CenterRotOffset  = None,          # Centre of Rotation scalar
                    AnglesVec = angles_rad,           # A vector of projection angles in radians
                    ObjSize = N_size,                 # Reconstructed object dimensions (scalar)
                    device_projector='gpu')

print ("Reconstruction using FBP from tomobar")
Rec_FBP= RectoolsDIR.FBP(projData3D_analyt_noisy) # FBP reconstruction

sliceSel = int(0.5*N_size)
max_val = 1
#plt.gray()
plt.figure() 
plt.subplot(131)
plt.imshow(Rec_FBP[sliceSel,:,:],vmin=0, vmax=max_val)
plt.title('3D FBP Reconstruction, axial view')

plt.subplot(132)
plt.imshow(Rec_FBP[:,sliceSel,:],vmin=0, vmax=max_val)
plt.title('3D FBP Reconstruction, coronal view')

plt.subplot(133)
plt.imshow(Rec_FBP[:,:,sliceSel],vmin=0, vmax=max_val)

예제 #11

파일: Demo_RealData2.py 프로젝트: shisteve/ToMoBAR

#%%
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR

N_size = 2000
det_y_crop = [i for i in range(0,2374)]

RectoolsDIR = RecToolsDIR(DetectorsDimH = np.size(det_y_crop),  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
                    AnglesVec = angles_rad, # array of angles in radians
                    ObjSize = N_size, # a scalar to define reconstructed object dimensions
                    device='gpu')

FBPrec = RectoolsDIR.FBP(np.transpose(data_norm[det_y_crop,:,0]))

plt.figure()
#plt.imshow(FBPrec[500:1500,500:1500], vmin=0, vmax=1, cmap="gray")
plt.imshow(FBPrec, vmin=0, vmax=1, cmap="gray")
plt.title('FBP reconstruction')

#%%
from tomobar.methodsIR import RecToolsIR

# set parameters and initiate a class object
Rectools = RecToolsIR(DetectorsDimH = np.size(det_y_crop),  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
                    CenterRotOffset = None, # Center of Rotation (CoR) scalar (for 3D case only)
                    AnglesVec = angles_rad, # array of angles in radians
                    ObjSize = N_size, # a scalar to define reconstructed object dimensions

예제 #12

파일: Demo_RealData.py 프로젝트: shisteve/ToMoBAR

detectorHoriz = np.size(data_norm,0)
N_size = 1000
slice_to_recon = 19 # select which slice to reconstruct
angles_rad = angles*(np.pi/180.0)
#%%
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(DetectorsDimH = detectorHoriz,  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
                    AnglesVec = angles_rad, # array of angles in radians
                    ObjSize = N_size, # a scalar to define reconstructed object dimensions                   
                    device='gpu')

FBPrec = RectoolsDIR.FBP(np.transpose(data_norm[:,:,slice_to_recon]))

plt.figure()
plt.imshow(FBPrec[150:550,150:550], vmin=0, vmax=0.005, cmap="gray")
plt.title('FBP reconstruction')

from tomobar.methodsIR import RecToolsIR
# set parameters and initiate a class object
Rectools = RecToolsIR(DetectorsDimH = detectorHoriz,  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
                    CenterRotOffset = None, # Center of Rotation (CoR) scalar (for 3D case only)
                    AnglesVec = angles_rad, # array of angles in radians
                    ObjSize = N_size, # a scalar to define reconstructed object dimensions
                    datafidelity='PWLS',# data fidelity, choose LS, PWLS, GH (wip), Student (wip)
                    nonnegativity='ENABLE', # enable nonnegativity constraint (set to 'ENABLE')
                    OS_number = 12, # the number of subsets, NONE/(or > 1) ~ classical / ordered subsets

예제 #13

angles_rad = np.zeros(N_size)
angles_step_rad = (360.0 / float(N_size)) * np.pi / 180.0
for i in range(0, N_size):
    angles_rad[i] = i * angles_step_rad

RectoolsDIR = RecToolsDIR(
    DetectorsDimH=N_cut,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=-118.0,  # Center of Rotation (CoR) scalar 
    AnglesVec=np.float32(angles_rad),  # array of angles in radians
    ObjSize=1600,  # a scalar to define reconstructed object dimensions
    device_projector='cpu')

print("Reconstruction using FBP from tomobar")
recFBP = RectoolsDIR.FBP(projections_norm[:, 5, :])  # FBP reconstruction

plt.figure()
plt.imshow(recFBP, vmin=0, vmax=0.00095, cmap="gray")

#%%
# do reconstruction
angles_rad = np.zeros(N_cut)
angles_step_rad = (360.0 / float(N_cut)) * np.pi / 180.0
for i in range(0, N_cut):
    angles_rad[i] = i * angles_step_rad

RectoolsDIR = RecToolsDIR(
    DetectorsDimH=N_cut,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only

예제 #14

파일: DemoFISTA_real_artifacts3D.py 프로젝트: dkazanc/ToMoBAR

plt.title('Tangentogram view')
plt.show()
#%%
# initialise tomobar DIRECT reconstruction class ONCE
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(
    DetectorsDimH=Horiz_det,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    Vert_det,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=None,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device_projector='gpu')

print("Reconstruction using FBP from tomobar")
recNumerical_conventional = RectoolsDIR.FBP(
    projData3D_norm)  # FBP reconstruction
recNumerical_conventional *= intens_max_clean

recNumerical_dynamic = RectoolsDIR.FBP(
    projData3D_norm_dyn)  # FBP reconstruction
recNumerical_dynamic *= intens_max_clean

sliceSel = int(0.5 * N_size)
max_val = 1
#plt.gray()
plt.figure()
plt.subplot(131)
plt.imshow(recNumerical_conventional[sliceSel, :, :], vmin=0, vmax=max_val)
plt.title('3D Reconstruction, axial view')

plt.subplot(132)

예제 #15

파일: Demo_RealData3.py 프로젝트: dkazanc/ToMoBAR

plt.title('Sinogram of i23 data')
plt.show()
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(
    DetectorsDimH=detectorHoriz,  # Horizontal detector dimension
    DetectorsDimV=None,  # Vertical detector dimension (3D case)
    CenterRotOffset=13.0,  # Centre of Rotation scalar
    AnglesVec=angles_rad,  # A vector of projection angles in radians
    ObjSize=N_size,  # Reconstructed object dimensions (scalar)
    device_projector='gpu')

FBPrec = RectoolsDIR.FBP(np.transpose(sinogram))

fig = plt.figure()
plt.imshow(FBPrec, vmin=0, vmax=0.005, cmap="gray")
plt.title('FBP reconstruction')
#fig.savefig('dendr_FPP.png', dpi=200)
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("Reconstructing with FISTA PWLS-OS-TV method %%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsIR import RecToolsIR
# Set scanning geometry parameters and initiate a class object
Rectools = RecToolsIR(
    DetectorsDimH=detectorHoriz,  # Horizontal detector dimension
    DetectorsDimV=None,  # Vertical detector dimension
    CenterRotOffset=None,  # Center of Rotation scalar

예제 #16

    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device='cpu')
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("Reconstructing analytical sinogram using Fourier Slice method")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
RecFourier = RectoolsDIR.fourier(sino_an, 'linear')
plt.figure()
plt.imshow(RecFourier, vmin=0, vmax=1, cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('Fourier slice reconstruction')
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("Reconstructing analytical sinogram using FBP (tomobar)...")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
FBPrec_ideal = RectoolsDIR.FBP(sino_an)  # ideal reconstruction
FBPrec_error = RectoolsDIR.FBP(
    noisy_zing_stripe)  # reconstruction with artifacts
FBPrec_misalign = RectoolsDIR.FBP(
    noisy_sino_misalign)  # reconstruction with misalignment

plt.figure()
plt.subplot(131)
plt.imshow(FBPrec_ideal, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('Ideal FBP reconstruction')
plt.subplot(132)
plt.imshow(FBPrec_error, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('Erroneous data FBP Reconstruction')
plt.subplot(133)

예제 #17

print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
#x = Atools.backproj(sino_an) # generate backprojection (A'b)

plt.figure()
plt.subplot(121)
plt.imshow(sino_an, cmap="BuPu")
plt.title('Analytical sinogram')
plt.subplot(122)
plt.imshow(sino_num_ASTRA, cmap="BuPu")
plt.title('Numerical sinogram')
plt.show()
#calculate norm
#rmse1 = np.linalg.norm(sino_an - sino_num_ASTRA)/np.linalg.norm(sino_num_ASTRA)

print("Reconstructing analytical sinogram using FBP (astra TB)...")
FBPrec1 = Rectools.FBP(sino_an)
plt.figure()
plt.imshow(FBPrec1, vmin=0, vmax=1, cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('FBP Reconstructed Phantom (analyt)')

print("Reconstructing numerical sinogram using FBP (astra TB)...")
FBPrec2 = Rectools.FBP(sino_num_ASTRA)

plt.figure()
plt.imshow(FBPrec2, vmin=0, vmax=1, cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('FBP Reconstructed Phantom (numeric)')

plt.figure()
plt.imshow(abs(FBPrec1 - FBPrec2), vmin=0, vmax=0.05, cmap="BuPu")

예제 #18

파일: DemoReconASTRA3D_sim.py 프로젝트: zhyh329/TomoPhantom

plt.title('Sinogram view')
plt.subplot(133)
plt.imshow(projData3D_norm[:,:,sliceSel],vmin=0, vmax=intens_max)
plt.title('Tangentogram view')
plt.show()
#%%
# initialise tomobar DIRECT reconstruction class ONCE
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(DetectorsDimH = Horiz_det,  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = Vert_det,  # DetectorsDimV # detector dimension (vertical) for 3D case only
                    AnglesVec = angles_rad, # array of angles in radians
                    ObjSize = N_size, # a scalar to define reconstructed object dimensions
                    device = 'gpu')
#%%
print ("Reconstruction using FBP from tomobar")
recNumerical= RectoolsDIR.FBP(projData3D_norm) # FBP reconstruction

sliceSel = int(0.5*N_size)
max_val = 1
#plt.gray()
plt.figure() 
plt.subplot(131)
plt.imshow(recNumerical[sliceSel,:,:],vmin=0, vmax=max_val)
plt.title('3D Reconstruction, axial view')

plt.subplot(132)
plt.imshow(recNumerical[:,sliceSel,:],vmin=0, vmax=max_val)
plt.title('3D Reconstruction, coronal view')

plt.subplot(133)
plt.imshow(recNumerical[:,:,sliceSel],vmin=0, vmax=max_val)

예제 #19

파일: Demo_RealData.py 프로젝트: alperelli/ToMoBAR

N_size = 1000
slice_to_recon = 19 # select which slice to reconstruct
angles_rad = angles[:,0]*(np.pi/180.0)
#%%
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(DetectorsDimH = detectorHoriz, # Horizontal detector dimension
                    DetectorsDimV = None,            # Vertical detector dimension (3D case)
                    CenterRotOffset = None,          # Center of Rotation scalar
                    AnglesVec = angles_rad,          # A vector of projection angles in radians
                    ObjSize = N_size,                # Reconstructed object dimensions (scalar)
                    device_projector='gpu')

FBPrec = RectoolsDIR.FBP(data_norm[slice_to_recon,:,:])

fig = plt.figure()
plt.imshow(FBPrec[100:900,100:900], vmin=0, vmax=0.004, cmap="gray")
plt.title('FBP reconstruction')
#fig.savefig('dendr_FPP.png', dpi=200)
#%%
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("Reconstructing with FISTA PWLS-OS-TV method %%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsIR import RecToolsIR
# Set scanning geometry parameters and initiate a class object
Rectools = RecToolsIR(DetectorsDimH = detectorHoriz, # Horizontal detector dimension
                    DetectorsDimV = None,            # Vertical detector dimension (3D case)
                    CenterRotOffset = None,          # Center of Rotation scalar
                    AnglesVec = angles_rad,          # A vector of projection angles in radians

예제 #20

파일: DemoFISTA_2D.py 프로젝트: jacksky64/ToMoBAR

plt.colorbar(ticks=[0, 150, 250], orientation='vertical')
plt.title('{}''{}'.format('Analytical noisy sinogram',model))
#%%

print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR
RectoolsDIR = RecToolsDIR(DetectorsDimH = P,  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
                    CenterRotOffset = None, # Center of Rotation (CoR) scalar (for 3D case only)
                    AnglesVec = angles_rad, # array of angles in radians
                    ObjSize = N_size, # a scalar to define reconstructed object dimensions
                    device='gpu')

FBPrec = RectoolsDIR.FBP(noisy_sino) #perform FBP

plt.figure()
plt.rcParams.update({'font.size': 20})
plt.imshow(FBPrec, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('FBP reconstruction')
#%%
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("Reconstructing with FISTA method (ASTRA used for projection)")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsIR import RecToolsIR

# set parameters and initiate a class object
Rectools = RecToolsIR(DetectorsDimH = P,  # DetectorsDimH # detector dimension (horizontal)
                    DetectorsDimV = None,  # DetectorsDimV # detector dimension (vertical) for 3D case only

예제 #21

from tomobar.methodsDIR import RecToolsDIR

N_size = 2000
det_y_crop = [i for i in range(0, 2374)]

RectoolsDIR = RecToolsDIR(
    DetectorsDimH=np.size(
        det_y_crop),  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=None,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions
    device_projector='gpu')

FBPrec = RectoolsDIR.FBP(data_norm[:, det_y_crop])

plt.figure()
#plt.imshow(FBPrec[500:1500,500:1500], vmin=0, vmax=1, cmap="gray")
plt.imshow(FBPrec, vmin=0, vmax=1, cmap="gray")
plt.title('FBP reconstruction')

#%%
from tomobar.methodsIR import RecToolsIR

# set parameters and initiate a class object
Rectools = RecToolsIR(
    DetectorsDimH=np.size(
        det_y_crop),  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only

예제 #22

파일: Demo_RealData2.py 프로젝트: dkazanc/ToMoBAR

angles_number, detectorHoriz = np.shape(data_norm)
#%%
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%Reconstructing with FBP method %%%%%%%%%%%%%%%%%")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
from tomobar.methodsDIR import RecToolsDIR

RectoolsDIR = RecToolsDIR(
    DetectorsDimH=detectorHoriz,  # Horizontal detector dimension
    DetectorsDimV=None,  # Vertical detector dimension (3D case)
    CenterRotOffset=92,  # Center of Rotation scalar
    AnglesVec=angles_rad,  # A vector of projection angles in radians
    ObjSize=N_size,  # Reconstructed object dimensions (scalar)
    device_projector='gpu')

FBPrec = RectoolsDIR.FBP(data_norm)

plt.figure()
#plt.imshow(FBPrec[500:1500,500:1500], vmin=0, vmax=1, cmap="gray")
plt.imshow(FBPrec, vmin=0, vmax=1, cmap="gray")
plt.title('FBP reconstruction')
#%%
from tomobar.methodsIR import RecToolsIR
# set parameters and initiate a class object
Rectools = RecToolsIR(
    DetectorsDimH=detectorHoriz,  # Horizontal detector dimension
    DetectorsDimV=None,  # Vertical detector dimension (3D case)
    CenterRotOffset=92,  # Center of Rotation scalar
    AnglesVec=angles_rad,  # A vector of projection angles in radians
    ObjSize=N_size,  # Reconstructed object dimensions (scalar)
    datafidelity='PWLS',  # Data fidelity, choose from LS, KL, PWLS

예제 #23

    'percentage': 0.75,
    'maxthickness': 2.0,
    'intensity': 0.15,
    'type': 'mix',
    'variability': 0.005
}

sino_num_artifacts = _Artifacts_(sino_num, _noise_, _zingers_, _stripes_,
                                 _sinoshifts_)

plt.figure(3)
plt.rcParams.update({'font.size': 21})
plt.imshow(sino_num_artifacts, cmap="BuPu")
plt.title('{}'.format('Distorted Phantom'))
#%%
FBPrec = Rectools.FBP(sino_num_artifacts)  # perform FBP reconstruction

plt.figure()
plt.rcParams.update({'font.size': 20})
plt.imshow(FBPrec, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('FBP reconstruction')
#%%
from tomobar.methodsIR import RecToolsIR
RectoolsIR = RecToolsIR(
    DetectorsDimH=P,  # DetectorsDimH # detector dimension (horizontal)
    DetectorsDimV=
    None,  # DetectorsDimV # detector dimension (vertical) for 3D case only
    CenterRotOffset=None,  # Center of Rotation (CoR) scalar (for 3D case only)
    AnglesVec=angles_rad,  # array of angles in radians
    ObjSize=N_size,  # a scalar to define reconstructed object dimensions