def choix_fichier(self):
# L'utilisateur choisi le dossier dans lequel se trouve les fichiers
path = QtWidgets.QFileDialog.getExistingDirectory(
self,
"Open a folder",
os.sep.join(
(os.path.expanduser('~'), 'Desktop'
)), #Permet d'afficher le bureau à l'ouverture de la fenêtre
options=QtWidgets.QFileDialog.ShowDirsOnly)
#Gestion de l'exception dans le cas où l'utilisateur choisit un mauvais dossier
#Si aucun dossier n'est sélectionné path = 0 et il ne se passe rien
if path:
try:
MatrixGeneration(path + '/*.tif')
except IndexError:
return tomopy.project(tomopy.shepp3d(), tomopy.angles(180))
def choix_fichier(self):
factor = float(str(self.selectFactor.currentText()))
# L'utilisateur choisi le dossier dans lequel se trouve les fichiers
path = QtWidgets.QFileDialog.getExistingDirectory(
self,
"Open a folder",
os.sep.join((os.path.expanduser('~'), 'Desktop')), #Permet d'afficher le bureau à l'ouverture de la fenêtre
options = QtWidgets.QFileDialog.ShowDirsOnly
)
#Gestion de l'exception dans le cas où l'utilisateur choisit un mauvais dossier
#Dans ce cas on envoie des projections générées virtuellement par tomopy
#Si aucun dossier n'est sélectionné path = 0 et il ne se passe rien
if path:
try:
MatrixGeneration(self, path, factor)
except IndexError:
return tomopy.project(tomopy.shepp3d(), tomopy.angles(180))
# preform the adjoint warp
x = adjoint_backward_warp_3D(x_warped,
self.u,
self.v,
self.w,
degree=self.degree)
# return as flattened array
return x.ravel()
# we start by preforming the same warp as in e04_3D_warping.py
import tomopy
im_size = 512
print("generating 3D images and DVFs")
shepp = tomopy.shepp3d(im_size).astype(np.float32)
u = 10 * np.repeat(
np.sin(np.linspace(0, 4 * np.pi, im_size, dtype=np.float32)), im_size**
2).reshape((im_size, ) * 3)
v = 8 * np.repeat(np.cos(np.linspace(0, 4 * np.pi, im_size, dtype=np.float32)),
im_size**2).reshape((im_size, ) * 3)
w = 2 * np.repeat(np.cos(np.linspace(0, 4 * np.pi, im_size, dtype=np.float32)),
im_size**2).reshape((im_size, ) * 3)
# this time, we can preform the warp with more high level syntax,
# as if warping is a matrix vector multiplication (which it is).
A = WarpingOperator(u, v, w)
b = A @ shepp.ravel() # @ is matrix mult
warped_shepp = b.reshape(shepp.shape)
# we will now try to reconstruct shepp form the warped version "warped_shepp"
comm = MPI.COMM_WORLD
print("Hello! I'm rank %d from %d running in total..." %
(comm.rank, comm.size))
comm.Barrier() # wait for everybody to synchronize _here_
num_slice = 512
num_col = 2560
num_angles = 1024
blk_size = np.int(num_slice / comm.size)
ang = tomopy.angles(num_angles) # Generate uniformly spaced tilt angles.
obj_recv = np.zeros(blk_size * num_col * num_col, dtype=np.float32)
if (comm.rank == 0):
# obj = np.random.rand(num_slice,num_col,num_col).astype(np.float32)
obj = np.float32(tomopy.shepp3d(
(num_slice, num_col, num_col))) # Generate an object.
vol = np.zeros((num_slice, num_col, num_col), dtype=np.float32)
else:
obj = None
chunks = None
vol = np.empty(num_slice * num_col * num_col)
comm.Scatter(obj, obj_recv, root=0)
#proj_data = np.random.rand(ang.size,num_slice,num_col) # Calculate projections for the relevant chunk
proj_data = tomopy.project(obj_recv.reshape(blk_size, num_col, num_col),
ang) # Calculate projections for the relevant chunk
theta, rows, cols = proj_data.shape
proj_data = proj_data[:, :, cols / 2 - num_col / 2:cols / 2 + num_col / 2]
t_start = MPI.Wtime()
rec = np.float32(reconMBIR_tomocam(proj_data, ang, comm.rank))
import tomopy import pylab obj = tomopy.shepp3d() # Generate an object. ang = tomopy.angles(180) # Generate uniformly spaced tilt angles. sim = tomopy.project(obj, ang) # Calculate projections. # rec = tomopy.recon_accelerated(sim, ang, algorithm='ospml_quad', hardware='Xeon_Phi', implementation='tomoperi') # Reconstruct object. rec = tomopy.recon_accelerated(sim, ang, algorithm="ospml_hybrid") # Show 64th slice of the reconstructed object. pylab.imshow(rec[64], cmap="gray") pylab.show()
import tomopy import pylab obj = tomopy.shepp3d() # Generate an object. ang = tomopy.angles(180) # Generate uniformly spaced tilt angles. sim = tomopy.project(obj, ang) # Calculate projections. #rec = tomopy.recon_accelerated(sim, ang, algorithm='ospml_quad', hardware='Xeon_Phi', implementation='tomoperi') # Reconstruct object. rec = tomopy.recon_accelerated(sim, ang, algorithm='ospml_hybrid') # Show 64th slice of the reconstructed object. pylab.imshow(rec[64], cmap='gray') pylab.show()
#import pyqtgraph as pg
import afnumpy as afnp
import math
from XT_argsParser import bl832inputs_parser
from XT_ForwardModel import forward_project, init_nufft_params, back_project
from XT_Common import padmat
from normalize import normalize_bo
num_slice = 50
im_size = 512 #A n X n X n volume
sino_center = im_size / 2
num_angles = 256
slice_idx = num_slice / 2
obj = tomopy.shepp3d((num_slice, im_size, im_size)) # Generate an object.
#obj = tomopy.shepp3d(im_size) # Generate an object.
ang = tomopy.angles(num_angles) # Generate uniformly spaced tilt angles.
### Comparing to tomopy
sim = tomopy.project(obj, ang)
sino = {}
geom = {}
sino['Ns'] = 768 #3624#im_size*2 #Sinogram size after padding
sino['Ns_orig'] = im_size #size of original sinogram
sino['center'] = sino_center + (sino['Ns'] / 2 - sino['Ns_orig'] / 2
) #for padded sinogram
sino['angles'] = ang
params = init_nufft_params(sino, geom)
import numpy as np
import cupy as cp
from cupy_optomo import OpTomo
import tomopy
import astra
from time import time
im_size = 256
x = cp.asarray(tomopy.shepp3d(im_size), dtype=np.float32)
vol_geom = astra.create_vol_geom(x.shape[1], x.shape[2], x.shape[0])
proj_geom = astra.create_proj_geom('parallel3d', 1, 1, x.shape[1], x.shape[2],
np.linspace(0, np.pi, 200))
proj_id = astra.create_projector('cuda3d', proj_geom, vol_geom)
# the astra version of OpTomo only accepts numpy arrays (CPU)
# so we have to copy x to CPU before we can pass it to W1.
W1 = astra.OpTomo(proj_id)
# This would crash:
# p1 = W1 @ x.ravel()
# so we do this instead
t0 = time()
p1 = W1 @ (x.ravel().get())
print("Projected with ASTRA OpTomo in", time() - t0, "seconds")
# with the cupy friendly OpTomo we can work on cupy arrays (GPU)
# directly (and it still works on numpy arrays)
W = OpTomo(proj_id)
