def svd_power_method(arr, geo, angles, **kwargs):
"""
method to determine the largest singular value for the rectangular A
projection matrix.
:param arr: (np.ndarray, dtype=np.float32)
random vector
:param geo: (tigre.geometry())
geometry of the set up
:param angles: (np.ndarray, dtype=np.float32)
angles of projection
:param kwargs:
optional arguments
:keyword maxiter: (int)
number of iterations to run unless margin of error epsilon has
been reached. Default: 100
:keyword epsilon: (float)
margin of error for the algorithm. Default: 0.001
:keyword verbose: (bool)
print stuff. Default: False
:return: (float)
the largest singular value of the A matrix.
"""
maxiter = 100
if "maxiter" in kwargs:
maxiter = kwargs["maxiter"]
# very optimistic value for epsilon (it turns out)
epsilon = 0.001
if "epsilon" in kwargs:
epsilon = kwargs["epsilon"]
verbose = False
if "verbose" in kwargs:
verbose = kwargs["verbose"]
error = np.inf
arr_old = arr.copy()
i = 0
while error >= epsilon:
if verbose:
if i == 0:
print("using SVD power method to calculate " "Lipschitz const")
if np.mod(i, 10) == 0:
print("error for val is:" + str(error))
# very verbose and inefficient for now
omega = tigre.Ax(arr_old, geo, angles)
alpha = np.linalg.norm(omega)
u = (1.0 / alpha) * omega
z = tigre.Atb(u, geo, angles)
beta = np.linalg.norm(z)
arr = (1.0 / beta) * z
error = np.linalg.norm(tigre.Ax(arr, geo, angles) - beta * u)
sigma = beta
arr_old = arr
i += 1
if i >= maxiter:
return sigma
return sigma
def run_main_iter(self):
self.l2l = np.zeros([self.niter], dtype=np.float32)
avgtime = []
for i in range(self.niter):
if i == 0:
print("CGLS Algorithm in progress.")
toc = time.clock()
if i == 1:
tic = time.clock()
print('Esitmated time until completetion (s): ' +
str((self.niter - 1) * (tic - toc)))
avgtic = time.clock()
q = tigre.Ax(self.__p__, self.geo, self.angles, 'ray-voxel')
q_norm = np.linalg.norm(q)
alpha = self.__gamma__ / (q_norm * q_norm)
self.res += alpha * self.__p__
avgtoc = time.clock()
avgtime.append(abs(avgtic - avgtoc))
for item in self.__dict__:
if isinstance(getattr(self, item), np.ndarray):
if np.isnan(getattr(self, item)).any():
raise ValueError('nan found for ' + item +
' at iteraton ' + str(i))
aux = self.proj - \
tigre.Ax(self.res, self.geo, self.angles, 'ray-voxel')
self.l2l[i] = np.linalg.norm(aux)
if i > 0 and self.l2l[i] > self.l2l[i - 1]:
print('re-initilization of CGLS called at iteration:' + str(i))
if self.re_init_at_iteration + 1 == i:
print(
'Algorithm exited with two consecutive reinitializations.'
)
return self.res
self.res -= alpha * self.__p__
self.reinitialise_cgls()
self.re_init_at_iteration = i
self.__r__ -= alpha * q
s = tigre.Atb(self.__r__, self.geo, self.angles)
s_norm = np.linalg.norm(s)
gamma1 = s_norm * s_norm
beta = gamma1 / self.__gamma__
if self.log_parameters:
self.parameter_history['alpha'][i] = alpha
self.parameter_history['beta'][i] = beta
self.parameter_history['gamma'][i] = self.__gamma__
self.parameter_history['q_norm'][i] = q_norm
self.parameter_history['s_norm'][i] = s_norm
self.__gamma__ = gamma1
self.__p__ = s + beta * self.__p__
print('Average time taken for each iteration for CGLS:' +
str(sum(avgtime) / len(avgtime)) + '(s)')
def update_image(self, geo, angle, iteration):
"""
VERBOSE:
for j in range(angleblocks):
angle = np.array([alpha[j]], dtype=np.float32)
proj_err = proj[angle_index[j]] - Ax(res, geo, angle, 'Siddon')
backprj = Atb(proj_err, geo, angle, 'FDK')
res += backprj
res[res<0]=0
:return: None
"""
self.res += (
self.__bm__
* 2
* tigre.Atb(
(
self.proj[self.angle_index[iteration]]
- tigre.Ax(self.res, geo, angle, "interpolated", gpuids=self.gpuids)
),
geo,
angle,
"matched",
gpuids=self.gpuids,
)
)
def ray_trace(self, phantom2, tile):
if self.tigre_works: # resort to astra if tigre doesn't work
try:
return np.squeeze(tigre.Ax(phantom2, self.geomet, self.angles))
except Exception:
logging.info("WARNING: Tigre GPU not working")
self.tigre_works = False
def setUp(**kwargs):
if kwargs.get('mode') == 'cone':
geo = tigre.geometry(mode='cone',
nVoxel=kwargs.get('nVoxel'),
default_geo=True)
angles_1 = np.linspace(0, 2 * np.pi, 100, dtype=np.float32)
angles_3 = np.zeros((100), dtype=np.float32)
angles = np.vstack((angles_1, angles_3, angles_3)).T
img = data_loader.load_head_phantom(number_of_voxels=geo.nVoxel)
proj = tigre.Ax(img, geo, angles, kwargs.get('krylov'))
if kwargs.get('alglist') == 'all':
alglist = ['sart', 'sirt', 'ossart', 'asd_pocs', 'FDK', 'cgls']
else:
alglist = kwargs.pop('alglist').split()
plot_algs(alglist,
proj,
geo,
angles,
niter=int(kwargs.pop('niter')),
**kwargs)
if kwargs.get('mode') == 'parallel':
geo = tigre.geometry(mode='parallel',
nVoxel=kwargs.get('nVoxel'),
default_geo=True)
angles_1 = np.linspace(0, 2 * np.pi, 100, dtype=np.float32)
angles_3 = np.zeros((100), dtype=np.float32)
angles = np.vstack((angles_1, angles_3, angles_3)).T
img = data_loader.load_head_phantom(number_of_voxels=geo.nVoxel)
proj = tigre.Ax(img, geo, angles, kwargs.get('krylov'))
if kwargs.get('alglist') == 'all':
alglist = ['sart', 'sirt', 'ossart', 'asd_pocs', 'fbp', 'cgls']
else:
alglist = kwargs.pop('alglist').split()
plot_algs(alglist,
proj,
geo,
angles,
niter=int(kwargs.pop('niter')),
**kwargs)
def svd_power_method(arr, geo, angles, **kwargs):
maxiter = 100
if 'maxiter' in kwargs:
maxiter = kwargs['maxiter']
#very optimistic value for epsilon (it turns out)
epsilon = 0.001
if 'epsilon' in kwargs:
epsilon = kwargs['epsilon']
verbose = False
if 'verbose' in kwargs:
verbose = kwargs['verbose']
error = np.inf
arr_old = arr.copy()
i = 0
while error >= epsilon:
if verbose:
if i == 0:
print('using SVD power method to calculate ' 'Lipschitz const')
if np.mod(i, 10) == 0:
print('error for val is:' + str(error))
# very verbose and inefficient for now
omega = tigre.Ax(arr_old, geo, angles)
alpha = np.linalg.norm(omega)
u = (1. / alpha) * omega
z = tigre.Atb(u, geo, angles)
beta = np.linalg.norm(z)
arr = (1. / beta) * z
error = np.linalg.norm(tigre.Ax(arr, geo, angles) - beta * u)
sigma = beta
arr_old = arr
i += 1
if i >= maxiter:
return sigma
return sigma
# http://www.anstuocmath.ro/mathematics/anale2015vol2/Bentbib_A.H.__Kanber_A..pdf
def test(self):
head = load_head_phantom(self.geo.nVoxel)
proj = tigre.Ax(head, self.geo, self.angles)
if self.algorithm in ["FDK", "fbp"]:
self.output = getattr(tigre.algorithms, self.algorithm)(proj, self.geo, self.angles)
self.rmse = Measure_Quality(self.output, head, ["nRMSE"])
self.algorithm_finished = True
return
self.timestarted = time.asctime()
self.output = getattr(tigre.algorithms, self.algorithm)(
proj, self.geo, self.angles, self.niter, **self.kwargs
)
self.timeended = time.asctime()
self.algorithm_finished = True
self.rmse = Measure_Quality(self.output, head, ["nRMSE"])
def test(self):
if self.algorithm == 'fbp' and self.geo.mode != 'parallel':
print('WARNING: fbp was implemented in cone beam.')
print('Test ignored.\n')
raise SystemExit()
head = load_head_phantom(self.geo.nVoxel)
proj = tigre.Ax(head, self.geo, self.angles)
if self.algorithm in ['FDK', 'fbp']:
self.output = getattr(tigre.algorithms,
self.algorithm)(proj, self.geo, self.angles)
self.rmse = Measure_Quality(self.output, head, ['nRMSE'])
self.algorithm_finished = True
return
self.timestarted = time.asctime()
self.output = getattr(tigre.algorithms,
self.algorithm)(proj, self.geo, self.angles,
self.niter, **self.kwargs)
self.timeended = time.asctime()
self.algorithm_finished = True
self.rmse = Measure_Quality(self.output, head, ['nRMSE'])
import time
import sys
from tigre.demos.Test_data import data_loader
from matplotlib import pyplot as plt
from tigre.utilities.Measure_Quality import Measure_Quality
#geo1 = tigre.geometry(mode='cone', high_quality=False, default=True)
geo = tigre.geometry(mode='cone', nVoxel=np.array([256,256,256]),default=True)
geo.dDetector = np.array([0.8, 0.8])*2 # size of each pixel (mm)
geo.sDetector = geo.dDetector * geo.nDetector
niter = 10
nangles = 100
angles = np.linspace(0, 2 * np.pi, nangles, dtype=np.float32)
#head = np.load('src_img_cubic_256.npy') #data_loader.load_head_phantom(geo.nVoxel)
head = data_loader.load_head_phantom(geo.nVoxel)
proj = tigre.Ax(head,geo,angles)
fdkout = algs.fdk(proj,geo,angles)
sirtout = algs.ossart(proj,geo,angles,20,blocksize=20)
# 'RMSE'
# 'MSSIM'
# 'SSD'
# 'UQI'
print('RMSE fdk:')
print(Measure_Quality(fdkout,head,['nRMSE']))
print('RMSE ossart')
print(Measure_Quality(sirtout,head,['nRMSE']))
plt.subplot(211)
plt.imshow(fdkout[geo.nVoxel[0]//2])
plt.subplot(212)
plt.imshow(sirtout[geo.nVoxel[0]//2])
geo.accuracy = 0.5
# Accuracy of FWD proj (vx/sample)
# lets do just one angles
angles = np.array([0])
#%% Description
# The difference between them is that `Siddon` will compute the
# intersection of a ray crossing each voxel, and the `interpolated` will
# sample the voxels at a given sample rate.
#%% Main difference
head = sample_loader.load_head_phantom(geo.nVoxel)
start_time = time.time()
projInterp = tigre.Ax(head, geo, angles, "interpolated")
interptime = time.time() - start_time
start_time = time.time()
projray = tigre.Ax(head, geo, angles, "Siddon")
raytime = time.time() - start_time
# It is relatively clear that discretization artefacts appear with the
# ray-voxel approach (middle one)
tigre.plotproj(
np.concatenate([np.abs(projInterp - projray), projray, projInterp],
axis=1), angles)
# But also the ray voxel approach is faster (more obvious at bigger sizes)
print("Time interpolated: " + str(interptime))
print("Time Siddon : " + str(raytime))
#%% With small voxel the errors are more obvious
def run_main_iter(self):
self.l2l = np.zeros([self.niter], dtype=np.float32)
avgtime = []
for i in range(self.niter):
if i == 0:
if self.verbose:
print("CGLS Algorithm in progress.")
toc = default_timer()
if i == 1:
tic = default_timer()
if self.verbose:
print("Esitmated time until completetion (s): " +
str((self.niter - 1) * (tic - toc)))
avgtic = default_timer()
q = tigre.Ax(self.__p__,
self.geo,
self.angles,
"Siddon",
gpuids=self.gpuids)
q_norm = np.linalg.norm(q)
alpha = self.__gamma__ / (q_norm * q_norm)
self.res += alpha * self.__p__
avgtoc = default_timer()
avgtime.append(abs(avgtic - avgtoc))
for item in self.__dict__:
if isinstance(getattr(self, item), np.ndarray):
if np.isnan(getattr(self, item)).any():
raise ValueError("nan found for " + item +
" at iteraton " + str(i))
aux = self.proj - tigre.Ax(
self.res, self.geo, self.angles, "Siddon", gpuids=self.gpuids)
self.l2l[i] = np.linalg.norm(aux)
if i > 0 and self.l2l[i] > self.l2l[i - 1]:
if self.verbose:
print("re-initilization of CGLS called at iteration:" +
str(i))
if self.re_init_at_iteration + 1 == i:
if self.verbose:
print(
"Algorithm exited with two consecutive reinitializations."
)
return self.res
self.res -= alpha * self.__p__
self.reinitialise_cgls()
self.re_init_at_iteration = i
self.__r__ -= alpha * q
s = tigre.Atb(self.__r__,
self.geo,
self.angles,
gpuids=self.gpuids)
s_norm = np.linalg.norm(s)
gamma1 = s_norm * s_norm
beta = gamma1 / self.__gamma__
if self.log_parameters:
self.parameter_history["alpha"][i] = alpha
self.parameter_history["beta"][i] = beta
self.parameter_history["gamma"][i] = self.__gamma__
self.parameter_history["q_norm"][i] = q_norm
self.parameter_history["s_norm"][i] = s_norm
self.__gamma__ = gamma1
self.__p__ = s + beta * self.__p__
if self.verbose:
print("Average time taken for each iteration for CGLS:" +
str(sum(avgtime) / len(avgtime)) + "(s)")
import numpy as np
from tigre.utilities import sample_loader
from tigre.utilities import CTnoise
import tigre.algorithms as algs
from matplotlib import pyplot as plt
#%% Geometry
geo = tigre.geometry_default(high_resolution=False)
#%% Load data and generate projections
# define angles
angles = np.linspace(0, 2 * np.pi, 100)
# Load thorax phatom data
head = sample_loader.load_head_phantom(geo.nVoxel)
# generate projections
projections = tigre.Ax(head, geo, angles)
# add noise
noise_projections = CTnoise.add(projections,
Poisson=1e5,
Gaussian=np.array([0, 10]))
## FISTA is a quadratically converging algorithm.
# 'hyper': This parameter should approximate the largest
# eigenvalue in the A matrix in the equation Ax-b and Atb.
# Empirical tests show that for, the headphantom object:
#
# geo.nVoxel = [64,64,64]' , hyper (approx=) 2.e8
# geo.nVoxel = [512,512,512]' , hyper (approx=) 2.e4
# Default: 2.e8
# 'tviter': Number of iterations of Im3ddenoise to use. Default: 20
class TestStdout(unittest.TestCase):
pass
def test_generator(algorithm, proj, geo, angles, niter):
def test(self):
capturedOutput = StringIO.StringIO()
sys.stdout = capturedOutput
getattr(algs, algorithm)(proj, geo, angles, niter=niter, verbose=False)
self.assertIs(capturedOutput.getvalue(), "")
sys.stdout = sys.__stdout__
return test
if __name__ == "__main__":
geo = tigre.geometry(mode="cone", default=True, high_quality=False)
print(geo)
true_img = data_loader.load_head_phantom(geo.nVoxel)
angles = np.linspace(0, 2 * np.pi, 100)
niter = 5
proj = tigre.Ax(true_img, geo, angles)
for alg in algs.__all__:
if alg != "fbp":
test_name = "test_print_%s" % (alg)
test = test_generator(alg, proj, geo, angles, niter)
setattr(TestStdout, test_name, test)
unittest.main()
# Geometry
#geo1 = tigre.geometry(mode='cone', high_quality=False, default=True)
geo = tigre.geometry(mode='cone',
nVoxel=np.array([256, 256, 256]),
default=True)
geo.dDetector = np.array([0.8, 0.8]) * 2 # size of each pixel (mm)
geo.sDetector = geo.dDetector * geo.nDetector
# print(geo)
nangles = 100
angles = np.linspace(0, 2 * np.pi, nangles, endpoint=False, dtype=np.float32)
# Prepare projection data
#head = np.load('src_img_cubic_256.npy')
head = data_loader.load_head_phantom(geo.nVoxel)
proj = tigre.Ax(head, geo, angles, gpuids=gpuids)
# Reconstruct
niter = 20
fdkout = algs.fdk(proj, geo, angles, gpuids=gpuids)
sirtout = algs.ossart(proj, geo, angles, niter, blocksize=20, gpuids=gpuids)
# Measure Quality
# 'RMSE', 'MSSIM', 'SSD', 'UQI'
print('RMSE fdk:')
print(Measure_Quality(fdkout, head, ['nRMSE']))
print('RMSE ossart')
print(Measure_Quality(sirtout, head, ['nRMSE']))
# Plot
fig, axes = plt.subplots(3, 2)
geo = tigre.geometry_default(high_resolution=False)
angles = np.linspace(0, 2 * np.pi, 100)
angles = np.hstack([angles, angles, angles]) # loop 3 times
# Load thorax phatom data
head = sample_loader.load_head_phantom(geo.nVoxel)
# This makes it helical
geo.offOrigin = np.zeros((angles.shape[0], 3))
geo.offOrigin[:, 2] = np.linspace(
-1024 / 2 + 128, 1024 / 2 - 128,
angles.shape[0]) # about 256^3 images fit int he detector with this size.
# project data
data = tigre.Ax(head, geo, angles)
# Uncomment if you want to see the data
# plotProj(data,angles);
## Reconstruct Helical
SIRTimg = algs.sirt(data, geo, angles, 30)
# SARTimg=SART(data,geo,angles,30); # takes time
CGLSimg = algs.cgls(data, geo, angles, 20)
## Plot results
# CGLS and SIRT
tigre.plotImg(np.concatenate([head, SIRTimg, CGLSimg], axis=1),
dim="z",
step=3,
clims=[0, 1])
import tigre
import tigre.algorithms as algs
import numpy as np
geo = tigre.geometry(mode='cone',
nVoxel=np.array([32, 64, 128]),
default_geo=True)
from tigre.demos.Test_data import data_loader
img = data_loader.load_head_phantom(geo.nVoxel)
angles = np.linspace(0, np.pi * 2, 100, dtype=np.float32)
proj = tigre.Ax(img, geo, angles)
algs.fdk(proj, geo, angles)
# --------------------------- CGLS for both modes---------------------------------------
do_algs(['cgls'], proj_par, geo_par, angles, mode='Parallel', **dict(nVoxel = [64 ,64 ,64]))
do_algs(['cgls'], proj_con, geo_con, angles, mode='Cone', **dict(nVoxel = [64 ,64 ,64]))
"""
import tigre.algorithms as algs
nangles = 100
angles_1 = np.linspace(0, 2 * np.pi, nangles, dtype=np.float32)
angles_2 = np.ones(
(nangles), dtype=np.float32) * np.array(np.pi / 4, dtype=np.float32)
angles_3 = np.zeros((nangles), dtype=np.float32)
angles = np.vstack((angles_1, angles_3, angles_3)).T
geo = tigre.geometry(mode='cone', nVoxel=nVoxel, default_geo=True)
source_img = data_loader.load_head_phantom(number_of_voxels=geo.nVoxel)
proj = tigre.Ax(source_img, geo, angles)
res = algs.awasd_pocs(proj, geo, angles, niter=10, **dict(blocksize=nangles))
from matplotlib import pyplot as plt
plt.imshow(res[32])
plt.show()
"""
from tigre.utilities.Atb import Atb
Atb(proj,geo,angles,'FDK')[32]
#plt.colorbar()
#plt.title('FDK')
mat = Atb(proj,geo,angles,'matched')
plt.subplot(221)
plt.imshow(mat[32])
plt.subplot(222)
plt.imshow(mat[:,32])
plt.subplot(223)
from tigre.utilities import sample_loader from tigre.utilities import CTnoise import tigre.algorithms as algs from matplotlib import pyplot as plt from tigre.utilities.im3Dnorm import im3DNORM #%% Geometry geo = tigre.geometry_default(high_resolution=False) #%% Load data and generate projections # define angles angles = np.linspace(0, 2 * np.pi, 100) # Load thorax phatom data head = sample_loader.load_head_phantom(geo.nVoxel) # generate projections projections = tigre.Ax(head, geo, angles) # add noise noise_projections = CTnoise.add(projections, Poisson=1e5, Gaussian=np.array([0, 10])) #%% Lets create a OS-SART test for comparison imgOSSART = algs.ossart(noise_projections, geo, angles, 10) #%% Total Variation algorithms # # ASD-POCS: Adaptative Steeppest Descent-Projection On Convex Subsets # Often called POCS # ========================================================================== # ========================================================================== # ASD-POCS minimizes At-B and the TV norm separately in each iteration, # i.e. reconstructs the image first and then reduces the TV norm, every # iteration. As the other algorithms the mandatory inputs are projections,
def testandlog(alglist,
geo,
angles,
niter,
saveresult=False,
newsubdirectory=False,
**kwargs):
nangles = angles.shape[0]
# createlogfile
dirname = os.path.dirname(__file__)
kwargs.update(dict(blocksize=20))
# create top level folder if this does not exist
if 'logs' not in os.listdir(dirname):
os.system('mkdir ' + 'logs')
logdirectory = os.path.join(dirname, 'logs')
logdate = time.strftime("%a_%b_%d")
if logdate not in os.listdir(logdirectory):
os.system('mkdir ' + os.path.join(logdirectory, logdate))
subdirectory = os.path.join(logdirectory, logdate)
if 'subdirectoryname' in kwargs:
subdirectoryname = kwargs['subdirectoryname']
else:
subdirectoryname = 'test' + str(len(os.listdir(subdirectory)) - 1)
if newsubdirectory:
subdirectoryname = 'test' + str(len(os.listdir(subdirectory)))
# create subdirectory for test if this does not exist
if subdirectoryname not in os.listdir(subdirectory):
os.system('mkdir ' + os.path.join(subdirectory, subdirectoryname))
subdirectory = os.path.join(logdirectory, logdate, subdirectoryname)
timestamp = str(time.asctime()).replace(' ', '_')
# create/append to log file
logfilename = None
for filename in os.listdir(subdirectory):
if os.path.splitext(filename)[-1] == '.log':
logfilename = os.path.split(filename)[-1]
logflist = []
if logfilename is not None:
logflist.extend(
open(os.path.join(subdirectory, logfilename), 'r').readlines())
else:
logfilename = timestamp + '.log'
try:
algsuccess = np.load(
os.path.join(subdirectory,
os.path.splitext(logfilename)[0]) + '.npy').item()
except Exception:
algsuccess = dict()
# TODO: need to fix directory path here.
repo_path = os.path.join(dirname, '..', '..', '.git/')
repo = Repo(repo_path)
commit = list(repo.iter_commits(repo.active_branch))[0]
uname = str(os.uname())
current_config = dict(uname=uname, commithash=commit.hexsha)
try:
prev_config = open(
os.path.join(subdirectory,
os.path.splitext(logfilename)[0] + '_config') +
'.npy').item()
except Exception:
prev_config = dict()
prev_config.update(current_config)
for item in current_config:
if prev_config[item] != current_config[item]:
logflist.append(
'------------------------------------------------\n')
logflist.append('Configuration changed for' + item + ':\n')
logflist.append('From: ' + str(prev_config[item]))
logflist.append('To : ' + str(current_config[item]))
if len(logflist) == 0: # If file is empty
# MACHINE
logflist.append(uname + '\n')
# GIT header for logfile
if not repo.bare:
logflist.append(
'------------------------------------------------\n')
logflist.append(make_repository_str(repo))
# create list of commits then print some of them to stdout
logflist.append(make_commit_str(commit))
logflist.append(
'\n------------------------------------------------\n')
else:
print('Could not load repository at {} :('.format(repo_path))
logflist.append('GEOMETRY used for instance of testandlog: \n')
for item in geo.__dict__:
logflist.append(item + ': ' + str(getattr(geo, item)) + '\n')
logflist.append('------------------------------------------------\n')
# Run the algorithms
source_img = data_loader.load_head_phantom(number_of_voxels=geo.nVoxel)
proj = tigre.Ax(source_img, geo, angles)
for alg in alglist:
logflist.append(str(alg).upper() + ' ' + time.asctime() + '\n')
logflist.append('nproj: ' + str(nangles) + ' niter: ' + str(niter) +
'\n')
if np.sum(angles[:, 1]) != 0 or np.sum(angles[:, 2]) != 0:
spherical = True
else:
spherical = False
logflist.append('spherical projection: ' + str(spherical) + '\n')
algpassed = False
try:
tic = time.clock()
res = getattr(algs, alg)(proj, geo, angles, niter=niter, **kwargs)
algpassed = True
except Exception:
formatedlines = traceback.format_exc()
logflist.append('ERROR at ' +
str(time.strftime("%H:%M:%S") + '\n'))
logflist.append(''.join(formatedlines) + '\n')
finally:
toc = time.clock()
algsuccess.update({alg: algpassed})
np.save(
os.path.join(subdirectory,
os.path.splitext(logfilename)[0]), algsuccess)
np.save(
os.path.join(subdirectory,
os.path.splitext(logfilename)[0]) + '_config',
current_config)
pass
if algpassed:
logflist.append('total time taken: ' + str(abs(tic - toc)) + '\n')
logflist.append('------------------------------------------------\n')
logf = open(os.path.join(subdirectory, logfilename), 'w')
logf.write(''.join(logflist))
logf.close()
if saveresult and algpassed:
warnings.filterwarnings("ignore")
plt.figure()
plt.subplot(3, 1, 1)
plt.imshow(res[geo.nVoxel[0] / 2])
plt.title('results for ' + alg)
plt.ylabel('dim 0')
plt.subplot(3, 1, 2)
plt.imshow(res[:, geo.nVoxel[1] / 2])
plt.ylabel('dim 1')
plt.subplot(3, 1, 3)
plt.imshow(res[:, :, geo.nVoxel[2] / 2])
plt.ylabel('dim 2')
plt.savefig(
os.path.join(subdirectory,
alg + '_' + geo.mode + '_' + timestamp + '.png'))
warnings.filterwarnings("error")
def run_main_iter(self):
self.l2l = np.zeros((1, self.niter), dtype=np.float32)
avgtime = []
for i in range(self.niter):
if self.verbose:
self._estimate_time_until_completion(i)
if self.Quameasopts is not None:
res_prev = copy.deepcopy(self.res)
avgtic = default_timer()
q = tigre.Ax(self.__p__,
self.geo,
self.angles,
"Siddon",
gpuids=self.gpuids)
q_norm = np.linalg.norm(q)
alpha = self.__gamma__ / (q_norm * q_norm)
self.res += alpha * self.__p__
avgtoc = default_timer()
avgtime.append(abs(avgtic - avgtoc))
for item in self.__dict__:
if (isinstance(getattr(self, item), np.ndarray)
and np.isnan(getattr(self, item)).any()):
raise ValueError("nan found for " + item +
" at iteraton " + str(i))
aux = self.proj - tigre.Ax(
self.res, self.geo, self.angles, "Siddon", gpuids=self.gpuids)
self.l2l[0, i] = np.linalg.norm(aux)
if i > 0 and self.l2l[0, i] > self.l2l[0, i - 1]:
if self.verbose:
print("re-initilization of CGLS called at iteration:" +
str(i))
if self.re_init_at_iteration + 1 == i:
if self.verbose:
print(
"Algorithm exited with two consecutive reinitializations."
)
return self.res
self.res -= alpha * self.__p__
self.reinitialise_cgls()
self.re_init_at_iteration = i
self.__r__ -= alpha * q
s = tigre.Atb(self.__r__,
self.geo,
self.angles,
backprojection_type="matched",
gpuids=self.gpuids)
s_norm = np.linalg.norm(s)
gamma1 = s_norm * s_norm
beta = gamma1 / self.__gamma__
if self.log_parameters:
self.parameter_history["alpha"][i] = alpha
self.parameter_history["beta"][i] = beta
self.parameter_history["gamma"][i] = self.__gamma__
self.parameter_history["q_norm"][i] = q_norm
self.parameter_history["s_norm"][i] = s_norm
self.__gamma__ = gamma1
self.__p__ = s + beta * self.__p__
if self.Quameasopts is not None:
self.error_measurement(res_prev, i)
if self.verbose:
print("Average time taken for each iteration for CGLS:" +
str(sum(avgtime) / len(avgtime)) + "(s)")