From dc31a371a7f5c66e32226698999f345e350f3049 Mon Sep 17 00:00:00 2001 From: Folkert Bleichrodt Date: Wed, 8 Apr 2015 16:03:41 +0200 Subject: Added ASTRA-Spot operator opTomo A Spot operator for the ASTRA projectors. Wraps the forward and backprojection operation into a Spot operator, which can be used with matrix-vector syntax in Matlab. --- samples/matlab/s017_opTomo.m | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 samples/matlab/s017_opTomo.m (limited to 'samples') diff --git a/samples/matlab/s017_opTomo.m b/samples/matlab/s017_opTomo.m new file mode 100644 index 0000000..4886cc5 --- /dev/null +++ b/samples/matlab/s017_opTomo.m @@ -0,0 +1,44 @@ +% load a phantom image +im = phantom(256); +% and flatten it to a vector +x = im(:); + +%% Setting up the geometry +% projection geometry +proj_geom = astra_create_proj_geom('parallel', 1, 256, linspace2(0,pi,180)); +% object dimensions +vol_geom = astra_create_vol_geom(256,256); + +%% Generate projection data +% Create the Spot operator for ASTRA using the GPU. +W = opTomo('cuda', proj_geom, vol_geom); + +p = W*x; + +% reshape the vector into a sinogram +sinogram = reshape(p, W.proj_size); +imshow(sinogram, []); + + +%% Reconstruction +% We use a least squares solver lsqr from Matlab to solve the +% equation W*x = p. +% Max number of iterations is 100, convergence tolerance of 1e-6. +y = lsqr(W, p, 1e-6, 100); + +% the output is a vector, so we reshape it into an image +reconstruction = reshape(y, W.vol_size); + +subplot(1,3,1); +imshow(reconstruction, []); +title('Reconstruction'); + +subplot(1,3,2); +imshow(im, []); +title('Ground truth'); + +% The transpose of the operator corresponds to the backprojection. +backProjection = W'*p; +subplot(1,3,3); +imshow(reshape(backProjection, W.vol_size), []); +title('Backprojection'); -- cgit v1.2.3 From e5bbcf730e1f5049b3dfd7f0ee46a7e477042231 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 15 May 2015 13:31:01 +0200 Subject: Add note about Spot to sample script --- samples/matlab/s017_opTomo.m | 8 ++++++++ 1 file changed, 8 insertions(+) (limited to 'samples') diff --git a/samples/matlab/s017_opTomo.m b/samples/matlab/s017_opTomo.m index 4886cc5..e23b53d 100644 --- a/samples/matlab/s017_opTomo.m +++ b/samples/matlab/s017_opTomo.m @@ -1,3 +1,11 @@ +% This sample illustrates the use of opTomo. +% +% opTomo is a wrapper around the FP and BP operations of the ASTRA Toolbox, +% to allow you to use them as you would a matrix. +% +% This class requires the Spot Linear-Operator Toolbox to be installed. +% You can download this at http://www.cs.ubc.ca/labs/scl/spot/ + % load a phantom image im = phantom(256); % and flatten it to a vector -- cgit v1.2.3 From a6bdde8d391566972642090cb71cf752da92f69a Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 15 May 2015 13:43:17 +0200 Subject: Add copyright header --- samples/matlab/s017_opTomo.m | 10 ++++++++++ 1 file changed, 10 insertions(+) (limited to 'samples') diff --git a/samples/matlab/s017_opTomo.m b/samples/matlab/s017_opTomo.m index e23b53d..891a93d 100644 --- a/samples/matlab/s017_opTomo.m +++ b/samples/matlab/s017_opTomo.m @@ -1,3 +1,13 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + % This sample illustrates the use of opTomo. % % opTomo is a wrapper around the FP and BP operations of the ASTRA Toolbox, -- cgit v1.2.3 From 732a647d658230b682c6eaf3b61e3ea34af9cdbc Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 15 May 2015 13:56:04 +0200 Subject: Create python sample for OpTomo --- samples/python/s017_OpTomo.py | 61 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 samples/python/s017_OpTomo.py (limited to 'samples') diff --git a/samples/python/s017_OpTomo.py b/samples/python/s017_OpTomo.py new file mode 100644 index 0000000..967fa64 --- /dev/null +++ b/samples/python/s017_OpTomo.py @@ -0,0 +1,61 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np +import scipy.sparse.linalg + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) + +# construct the OpTomo object +W = astra.OpTomo(proj_id) + +sinogram = W * P +sinogram = sinogram.reshape([180, 384]) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Run the lsqr linear solver +output = scipy.sparse.linalg.lsqr(W, sinogram.flatten(), iter_lim=150) +rec = output[0].reshape([256, 256]) + +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. +astra.projector.delete(proj_id) -- cgit v1.2.3