diff --git a/README.md b/README.md index 954c641..cef4c08 100644 --- a/README.md +++ b/README.md @@ -43,31 +43,45 @@ https://www.cs.ubc.ca/~schmidtm/Software/minConf.html https://www.mathworks.com/matlabcentral/fileexchange/9416-3d-shepp-logan-phantom -## Examples: +## Scripts: -Seven examples are provided with the code. Before running any example, please run the startup.m script first. Each example uses a different phantom: -1. example_SheppLogan: +Eight examples are provided with the code. Before running any example, please run the startup.m script first. +1. example1_SheppLogan: The classic Shepp-Logan phantom with variable size -2. example_Disk: +2. example2_Disk: A custom-made disk example with variable size and number of disks -3. example_Thorax: +3. example3_Thorax: The synthetic phantom mimics internal body structure in an abstract fashion (taken from the CONRAD software framework: https://git5.cs.fau.de/PyConrad/pyCONRAD) -4. example_SheppLogan_SparseAngle: +4. example4_SheppLogan_SparseAngle: The Shepp-Logan phantom with only 10 projection angles (adjustable) -5. example_SheppLogan_LimitedView: +5. example5_SheppLogan_LimitedView: The Shepp-Logan phantom with a missing wedge of 60 degrees (adjustable) -6. example_MixedDisk: +6. example6_MixedDisk: A custom-made disk example with variable size and number of disks, where the disks consists of multiple materials -7. example_SheppLogan3D: +7. example7_SheppLogan3D: 3D version of the Shepp-Logan phnatom with adjustable size +8. example8_microCTData.m: +A demonstration of the approach on real micro-CT data from a natural rock sample. The source of the data can be found further below. -On each phantom the four implemented algorithms (UR, RU, cJoint and ADJUST) are performed. The perfomance of these algorithms are captured by computing and presenting the MSE, PSNR, and the SSIM between the reconstructed material maps and the ground truth. Below are results for a numerical study on the Shepp-Logan phantom: +On each case the four implemented algorithms (UR, RU, cJoint and ADJUST) can be tested. The perfomance of these algorithms are captured by computing and presenting the MSE, PSNR, and the SSIM between the reconstructed material spatial maps and the ground truth. + + +## Example results: + +As an example, below are results for a numerical study on the Shepp-Logan phantom:

+ +For the micro-CT dataset, four different materials (lead, tungsten, quartz and gold) can be reconstructed. An example reconstruction is shown below: + +

+ +

+ ## Generation of spectral data @@ -77,17 +91,35 @@ These scripts are written in Python (version 3.7 or higher). Apart from this, ph ## References -The algorithms implemented in this MATLAB package are described in following paper: +The algorithms implemented in this MATLAB package are described in following [paper](https://iopscience.iop.org/article/10.1088/1361-6420/ac932e): ``` @article{ title={ADJUST: A Dictionary-Based Joint Reconstruction and Unmixing Method for Spectral Tomography}, author={Zeegers, Math{\'e} T and Kadu, Ajinkya and van Leeuwen, Tristan and Batenburg, Kees Joost}, - journal={arXiv preprint arXiv:2112.11406}, - year={2021} + journal={Inverse Problems}, + year={2022}, + publisher={IOP Publishing}, + doi={10.1088/1361-6420/ac932e} +} +``` +The preprint can be found [here](https://arxiv.org/abs/2112.11406) + +The micro-CT dataset required to run the eighth script is introduced in the paper below: + +``` +@article{sittner2021spectral, + title={Spectral X-ray computed micro tomography: 3-dimensional chemical imaging}, + author={Sittner, Jonathan and Godinho, Jose RA and Renno, Axel D and Cnudde, Veerle and Boone, Marijn and De Schryver, Thomas and Van Loo, Denis and Merkulova, Margarita and Roine, Antti and Liipo, Jussi}, + journal={X-Ray Spectrometry}, + volume={50}, + number={2}, + pages={92--105}, + year={2021}, + publisher={Wiley Online Library} } ``` -The preprint can be found [here](https://arxiv.org/pdf/2112.11406.pdf). +The dataset can be found [here](https://rodare.hzdr.de/record/1627). ## Authors diff --git a/data/AllOtherPhantoms_MatrixTXray100chan_42_MinEn5_MaxEn35_mat_CORRECTED.csv b/data/AllOtherPhantoms_MatrixTXray100chan_42_MinEn5_MaxEn35_mat_CORRECTED.csv new file mode 100644 index 0000000..2946a51 --- /dev/null +++ b/data/AllOtherPhantoms_MatrixTXray100chan_42_MinEn5_MaxEn35_mat_CORRECTED.csv @@ -0,0 +1,42 @@ 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diff --git a/examples/example1_SheppLogan.m b/examples/example1_SheppLogan.m new file mode 100644 index 0000000..41f109c --- /dev/null +++ b/examples/example1_SheppLogan.m @@ -0,0 +1,118 @@ +%%% Spectral Tomography +%%% Shepp Logan phantom of size 512 x 512 +%%% 5 materials +%%% 100 channels +%%% Full-view setting: 60 angles from 0 to 180 degrees +%%% Non-inverse crime configuration: measurements are simulated on 2x +%%% high-resolution grid and corrupted with mild Poisson noise. +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 512; % spatial resolution of phantom +phantom = 'SheppLogan'; % phantom name + +%% load phantom (for measurement and inversion) + +% load matrices for measurements (phantom discretized on 2x resolution grid) +[Am,Fm,Tm,Qm] = loadSpectralPhantom(phantom,2*n); + +% load matrices for inversion +[A,F,T,Q] = loadSpectralPhantom(phantom,n); + +% number of materials (in phantom) +k = size(A,2); + +% problem structure +strProb.A = A; +strProb.F = F; +strProb.k = k; +strProb.T = T; +strProb.n = [n n]; + +%% generate spectral measurements (on 2x resolution grid) + +% spectral volume +Um = Am*Fm; + +% tomography operator +n_ang = 180; +theta = linspace(0,pi,n_ang); + +volGeo = astra_create_vol_geom(2*n, 2*n); +projGeo= astra_create_proj_geom('parallel', 2, n,theta); +Wm = opTomo('cuda', projGeo, volGeo); + +% spectral tomographic measurements with noise +Y0 = (Wm*Um)/2; % the factor of 2 division required for 2x grid +Y = 0*Y0; +for i=1:size(Y0,2) + Y(:,i) = astra_add_noise_to_sino(Y0(:,i), Qm(i)); +end + +%% (non-inverse-crime) forward operator to be used for inversion + +volGeo = astra_create_vol_geom(n, n); +projGeo= astra_create_proj_geom('parallel', 1, n,theta); +W = opTomo('cuda', projGeo, volGeo); + +% (only for checking) measurments with forward operator +U = A*F; +Y1 = W*U; + +strProb.angles = theta; +strProb.Y = Y; +strProb.Yclean = Y1; + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 1000; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; + +%%% ADJUST +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% plots and tables + +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_SheppLogan.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example2_Disk.m b/examples/example2_Disk.m new file mode 100644 index 0000000..809ca37 --- /dev/null +++ b/examples/example2_Disk.m @@ -0,0 +1,118 @@ +%%% Spectral Tomography +%%% Disk phantom of size 512 x 512 +%%% 8 materials +%%% 100 channels +%%% Full-view setting: 180 angles from 0 to 180 degrees +%%% Non-inverse crime configuration: measurements are simulated on 2x +%%% high-resolution grid and corrupted with mild Poisson noise. +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 512; % spatial resolution of phantom +phantom = 'Disks'; % phantom name + +%% load phantom (for measurement and inversion) + +% load matrices for measurements (phantom discretized on 2x resolution grid) +[Am,Fm,Tm,Qm] = loadSpectralPhantom(phantom,2*n); + +% load matrices for inversion +[A,F,T,Q] = loadSpectralPhantom(phantom,n); + +% number of materials (in phantom) +k = size(A,2); + +% problem structure +strProb.A = A; +strProb.F = F; +strProb.k = k; +strProb.T = T; +strProb.n = [n n]; + +%% generate spectral measurements (on 2x resolution grid) + +% spectral volume +Um = Am*Fm; + +% tomography operator +n_ang = 180; +theta = linspace(0,pi,n_ang); + +volGeo = astra_create_vol_geom(2*n, 2*n); +projGeo= astra_create_proj_geom('parallel', 2, n,theta); +Wm = opTomo('cuda', projGeo, volGeo); + +% spectral tomographic measurements with noise +Y0 = (Wm*Um)/2; % the factor of 2 division required for 2x grid +Y = 0*Y0; +for i=1:size(Y0,2) + Y(:,i) = astra_add_noise_to_sino(Y0(:,i), Qm(i)); +end + +%% (non-inverse-crime) forward operator to be used for inversion + +volGeo = astra_create_vol_geom(n, n); +projGeo= astra_create_proj_geom('parallel', 1, n,theta); +W = opTomo('cuda', projGeo, volGeo); + +% (only for checking) measurments with forward operator +U = A*F; +Y1 = W*U; + +strProb.angles = theta; +strProb.Y = Y; +strProb.Yclean = Y1; + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 1000; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; + +%%% ADJUST +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% plots and tables + +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_Disk.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example3_Thorax.m b/examples/example3_Thorax.m new file mode 100644 index 0000000..fad2265 --- /dev/null +++ b/examples/example3_Thorax.m @@ -0,0 +1,124 @@ +%%% Spectral Tomography +%%% Thorax phantom of size 512 x 512 +%%% 5 materials (3 are identified) +%%% 100 channels +%%% Full-view setting: 180 angles from 0 to 180 +%%% Non-inverse crime configuration: measurements are simulated on 2x +%%% high-resolution grid and corrupted with mild Poisson noise. +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 512; % spatial resolution of phantom +phantom = 'Thorax'; % phantom name + +%% load phantom + +% load matrices for inversion +[A,F,T,Q] = loadSpectralPhantom(phantom,n); + +% number of materials (to be reconstructed) +k = 3; + +% problem structure +strProb.A = A; +strProb.F = F; +strProb.k = k; +strProb.T = T; +strProb.n = [n n]; + +%% generate spectral measurements (on 2x resolution grid) + +% create matrices for measurements (phantom discretized on 2x resolution grid, +% by upsampling the original phantom) +Am = zeros(size(A,1)*4, size(A,2)); +for i=1:size(A,2) + Am(:,i) = reshape(imresize(reshape(A(:,i),n,n),2, 'nearest'), n*n*4, 1); +end + +% spectral volume +Um = Am*F; + +% tomography operator +n_ang = 180; +theta = linspace(0,pi,n_ang); + +volGeo = astra_create_vol_geom(2*n, 2*n); +projGeo= astra_create_proj_geom('parallel', 2, n, theta); +Wm = opTomo('cuda', projGeo, volGeo); + +% spectral tomographic measurements with noise +Y0 = (Wm*Um)/2; % the factor of 2 division required for 2x grid +Y = 0*Y0; +for i=1:size(Y0,2) + Y(:,i) = astra_add_noise_to_sino(Y0(:,i), Q(i)); +end + +%% (non-inverse-crime) forward operator to be used for inversion + +volGeo = astra_create_vol_geom(n, n); +projGeo= astra_create_proj_geom('parallel', 1, n, theta); +W = opTomo('cuda', projGeo, volGeo); + +% (only for checking) measurments with forward operator +U = A*F; +Y1 = W*U; + +strProb.angles = theta; +strProb.Y = Y; +strProb.Yclean = Y1; + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 2000; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; +%% +%%% ADJUST +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% plots and tables + +A1 = [A(:,1) A(:,2) A(:,3)+A(:,4)+A(:,5)]; +strProb.A = A1; +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_Thorax.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example4_SheppLogan_SparseAngle.m b/examples/example4_SheppLogan_SparseAngle.m new file mode 100644 index 0000000..8cd0d0f --- /dev/null +++ b/examples/example4_SheppLogan_SparseAngle.m @@ -0,0 +1,118 @@ +%%% Spectral Tomography +%%% Shepp Logan phantom of size 512 x 512 +%%% 5 materials +%%% 100 channels +%%% Sparse-angle tomography setting: only 10 angles between 0 and 180 deg +%%% Non-inverse crime configuration: measurements are simulated on 2x +%%% high-resolution grid and corrupted with mild Poisson noise. +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 512; % spatial resolution of phantom +phantom = 'SheppLogan'; % phantom name + +%% load phantom (for measurement and inversion) + +% load matrices for measurements (phantom discretized on 2x resolution grid) +[Am,Fm,Tm,Qm] = loadSpectralPhantom(phantom,2*n); + +% load matrices for inversion +[A,F,T,Q] = loadSpectralPhantom(phantom,n); + +% number of materials (in phantom) +k = size(A,2); + +% problem structure +strProb.A = A; +strProb.F = F; +strProb.k = k; +strProb.T = T; +strProb.n = [n n]; + +%% generate spectral measurements (on 2x resolution grid) + +% spectral volume +Um = Am*Fm; + +% tomography operator +n_ang = 10; +theta = linspace(0,pi,n_ang); + +volGeo = astra_create_vol_geom(2*n, 2*n); +projGeo= astra_create_proj_geom('parallel', 2, n, theta); +Wm = opTomo('cuda', projGeo, volGeo); + +% spectral tomographic measurements with noise +Y0 = (Wm*Um)/2; % the factor of 2 division required for 2x grid +Y = 0*Y0; +for i=1:size(Y0,2) + Y(:,i) = astra_add_noise_to_sino(Y0(:,i), Qm(i)); +end + +%% (non-inverse-crime) forward operator to be used for inversion + +volGeo = astra_create_vol_geom(n, n); +projGeo= astra_create_proj_geom('parallel', 1, n, theta); +W = opTomo('cuda', projGeo, volGeo); + +% (only for checking) measurments with forward operator +U = A*F; +Y1 = W*U; + +strProb.angles = theta; +strProb.Y = Y; +strProb.Yclean = Y1; + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 1000; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; + +%%% ADJUST +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% plots and tables + +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_SheppLogan_SparseAngle.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example5_SheppLogan_LimitedView.m b/examples/example5_SheppLogan_LimitedView.m new file mode 100644 index 0000000..596d589 --- /dev/null +++ b/examples/example5_SheppLogan_LimitedView.m @@ -0,0 +1,118 @@ +%%% Spectral Tomography +%%% Shepp Logan phantom of size 512 x 512 +%%% 5 materials +%%% 100 channels +%%% Limited-view setting: parallel-beam 60 angles from 0 to 120 degrees +%%% Non-inverse crime configuration: measurements are simulated on 2x +%%% high-resolution grid and corrupted with mild Poisson noise. +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 512; % spatial resolution of phantom +phantom = 'SheppLogan'; % phantom name + +%% load phantom (for measurement and inversion) + +% load matrices for measurements (phantom discretized on 2x resolution grid) +[Am,Fm,Tm,Qm] = loadSpectralPhantom(phantom,2*n); + +% load matrices for inversion +[A,F,T,Q] = loadSpectralPhantom(phantom,n); + +% number of materials (in phantom) +k = size(A,2); + +% problem structure +strProb.A = A; +strProb.F = F; +strProb.k = k; +strProb.T = T; +strProb.n = [n n]; + +%% generate spectral measurements (on 2x resolution grid) + +% spectral volume +Um = Am*Fm; + +% tomography operator +n_ang = 60; +theta = linspace(0,2*pi/3,n_ang); + +volGeo = astra_create_vol_geom(2*n, 2*n); +projGeo= astra_create_proj_geom('parallel', 2, n, theta); +Wm = opTomo('cuda', projGeo, volGeo); + +% spectral tomographic measurements with noise +Y0 = (Wm*Um)/2; % the factor of 2 division required for 2x grid +Y = 0*Y0; +for i=1:size(Y0,2) + Y(:,i) = astra_add_noise_to_sino(Y0(:,i), Qm(i)); +end + +%% (non-inverse-crime) forward operator to be used for inversion + +volGeo = astra_create_vol_geom(n, n); +projGeo= astra_create_proj_geom('parallel', 1, n, theta); +W = opTomo('cuda', projGeo, volGeo); + +% (only for checking) measurments with forward operator +U = A*F; +Y1 = W*U; + +strProb.angles = theta; +strProb.Y = Y; +strProb.Yclean = Y1; + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 1000; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; + +%%% ADJUST +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% plots and tables + +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_SheppLogan_LimitedView.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example6_MixedDisk.m b/examples/example6_MixedDisk.m new file mode 100644 index 0000000..2053bf2 --- /dev/null +++ b/examples/example6_MixedDisk.m @@ -0,0 +1,118 @@ +%%% Spectral Tomography +%%% Mixed Disk phantom of size 512 x 512 +%%% 5 materials +%%% 100 channels +%%% Full-view setting: 180 angles from 0 to 180 deg +%%% Non-inverse crime configuration: measurements are simulated on 2x +%%% high-resolution grid and corrupted with mild Poisson noise. +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 512; % spatial resolution of phantom +phantom = 'MixedDisk'; % phantom name + +%% load phantom + +% load matrices for measurements (phantom discretized on 2x resolution grid) +[Am,Fm,Tm,Qm] = loadSpectralPhantom(phantom,2*n); + +% load matrices for inversion +[A,F,T,Q] = loadSpectralPhantom(phantom,n); + +% number of materials (in phantom) +k = size(A,2); + +% problem structure +strProb.A = A; +strProb.F = F; +strProb.k = k; +strProb.T = T; +strProb.n = [n n]; + +%% generate spectral measurements (on 2x resolution grid) + +% spectral volume +Um = Am*Fm; + +% tomography operator +n_ang = 180; +theta = linspace(0,pi,n_ang); + +volGeo = astra_create_vol_geom(2*n, 2*n); +projGeo= astra_create_proj_geom('parallel', 2, n, theta); +Wm = opTomo('cuda', projGeo, volGeo); + +% spectral tomographic measurements with noise +Y0 = (Wm*Um)/2; % the factor of 2 division required for 2x grid +Y = 0*Y0; +for i=1:size(Y0,2) + Y(:,i) = astra_add_noise_to_sino(Y0(:,i), Qm(i)); +end + +%% (non-inverse-crime) forward operator to be used for inversion + +volGeo = astra_create_vol_geom(n, n); +projGeo= astra_create_proj_geom('parallel', 1, n, theta); +W = opTomo('cuda', projGeo, volGeo); + +% (only for checking) measurments with forward operator +U = A*F; +Y1 = W*U; + +strProb.angles = theta; +strProb.Y = Y; +strProb.Yclean = Y1; + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 1000; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; + +%%% ADJUST +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% plots and tables + +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_MixedDisk.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example7_SheppLogan3D.m b/examples/example7_SheppLogan3D.m new file mode 100644 index 0000000..c4251eb --- /dev/null +++ b/examples/example7_SheppLogan3D.m @@ -0,0 +1,125 @@ +%%% Spectral Tomography +%%% 3D Shepp Logan phantom of size 128 x 128 x 128 +%%% 3 materials +%%% 100 channels +%%% Full-view setting: parallel beam geometry, 60 angles from 0 to 180 deg +%%% Non-inverse crime configuration: measurements are simulated on 2x +%%% high-resolution grid and corrupted with mild Poisson noise. +%%% The phantom by Matthias Schabel can be found at: +%%% https://nl.mathworks.com/matlabcentral/fileexchange/9416-3d-shepp-logan-phantom +%%% Please note: +%%% The spectral reconstruction algorithms requires around 32-48 GB memory +%%% and hence, we advice to run this script only if you have PC with 64 GB +%%% RAM. Otherwise, please reduce the size of phantom to either 32 or 64 +%%% px. +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 128; % spatial resolution of phantom +phantom = 'SheppLogan3D'; % phantom name + +%% load phantom (for measurement and inversion) + +% load matrices for measurements (phantom discretized on 2x resolution grid) +[Am,Fm,Tm,Qm] = loadSpectralPhantom(phantom,2*n); + +% load matrices for inversion +[A,F,T,Q] = loadSpectralPhantom(phantom,n); + +% number of materials (in phantom) +k = size(A,2); + +% problem structure +strProb.A = A; +strProb.F = F; +strProb.k = k; +strProb.T = T; +strProb.n = [n n n]; + +%% generate spectral measurements (on 2x resolution grid) + +% spectral volume +Um = Am*Fm; + +% tomography operator +n_ang = 60; +theta = linspace(0,pi,n_ang); + +volGeo = astra_create_vol_geom(2*n, 2*n, 2*n); +projGeo= astra_create_proj_geom('parallel3d', 2, 2, n, n, theta); +Wm = opTomo('cuda', projGeo, volGeo); + +% spectral tomographic measurements with noise +Y0 = (Wm*Um)/2; % the factor of 2 division required for 2x grid +Y = 0*Y0; +for i=1:size(Y0,2) + Y(:,i) = astra_add_noise_to_sino(Y0(:,i), Qm(i)); +end + +%% (non-inverse-crime) forward operator to be used for inversion + +volGeo = astra_create_vol_geom(n, n, n); +projGeo= astra_create_proj_geom('parallel3d', 1, 1, n, n, theta); +W = opTomo('cuda', projGeo, volGeo); + +% (only for checking) measurments with forward operator +U = A*F; +Y1 = W*U; + +strProb.angles = theta; +strProb.Y = Y; +strProb.Yclean = Y1; + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 500; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; + +%%% ADJUST +Dopt.rho = 1e-2; +Dopt.iterMax = 500; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% plots and tables + +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_SheppLogan3D.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example8_microCTData.m b/examples/example8_microCTData.m new file mode 100644 index 0000000..4a15f72 --- /dev/null +++ b/examples/example8_microCTData.m @@ -0,0 +1,169 @@ +%%% Spectral Tomography +%%% MicroCT data of size 1 x 257 +%%% 4 materials +%%% 64 channels (reduced from 128) +%%% Full-view setting: 600 angles from 0 to 360 +%%% Data acquired by Jonathan Sittner et al. (2022) +%%% Data taken from: https://rodare.hzdr.de/record/1627 +%%% More information: https://doi.org/10.1002/xrs.3200 +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +clc; clearvars; close all; + +% setting random stream +myStream = RandStream('mt19937ar','Seed',10); +RandStream.setGlobalStream(myStream) + +% directory for saving results +saveDir = [pwd '\results\']; +if ~exist(saveDir,'dir'), mkdir(saveDir); end + +%% settings + +n = 255; % spatial resolution the data +phantom = 'Real'; + +%% data preprocessing + +% data with particles - change the path to location of the data +datapath = '/Spectral_CT_W_Au_Pb/'; + +% dark and flatfield correction +darkfield = double(imread(strcat(datapath, 'di000000.tif'))); +flatfield = double(imread(strcat(datapath, 'io000000.tif'))); +data = zeros(128,257,600); +datacor = zeros(128,257,600); +for i=1:size(data,3) + data(:,:,i) = imread(strcat(datapath, 'scan_', sprintf('%06d',i-1), '.tif')); + datacor(:,:,i) = log((flatfield-darkfield)./(data(:,:,i) - darkfield)); +end + +% flip the sinograms for correct alignment with angles +data = flipdim(data,3); +datacor = flipdim(datacor,3); + +%% make reconstruction of every spectral channel +n_ang = 600; +theta = linspace(0,2*pi,n_ang); + +% values taken from the settings file +DETSIZE = 0.80; +SOD = 57.999001; +SDD = 883.081116; +MAGN = SDD/SOD; +CONV = MAGN/DETSIZE; + +volGeo = astra_create_vol_geom(255, 255); +projGeo = astra_create_proj_geom('fanflat', DETSIZE*CONV, 257, theta, SOD*CONV, (SDD-SOD)*CONV); + +cor_shift = 257/2-127.379570; +projGeo_cor = astra_geom_postalignment(projGeo, cor_shift); + +recsParticles = zeros(128,255,255); + +ALG = 'SIRT_CUDA'; +ITER = 100; + +for i=1:128 + fprintf('running spectral idx=%d \n',i); + + sinogram_id = astra_mex_data2d('create', '-sino', projGeo_cor, permute(datacor(i,:,:), [3 2 1])); + rec_id = astra_mex_data2d('create', '-vol', volGeo); + cfg = astra_struct(ALG); + cfg.ReconstructionDataId = rec_id; + cfg.ProjectionDataId = sinogram_id; + + alg_id = astra_mex_algorithm('create', cfg); + + astra_mex_algorithm('iterate', alg_id, ITER); + + recsParticles(i,:,:) = astra_mex_data2d('get', rec_id); + +end + + +%% forward operator to be used for inversion + +W = opTomo('cuda', projGeo_cor, volGeo); + +Y0 = permute(datacor, [3 2 1]); +Y0 = reshape(Y0, [] , size(Y0,3)); + +%% load and adjust data + +T1 = readmatrix('NISTequivalentofRealData_MatrixTXray128chan_42_MinEn20.35_MaxEn161.15.csv'); +T1 = 0.015*T1; + +% add quartz extracted from data to dictionary +T1(43,:) = mean(recsParticles(:,130:140,130:140),[2,3]); + +% number of materials (to be reconstructed) +k = 4; + +%restrict data and dictionary to 64 spectral bins +Y = Y0(:,30:94); +T = T1(:,30:94); +T_gt = T1(:,30:94); + +strProb.k = k; +strProb.T = T; +strProb.n = [n n]; + + +%% Spectral Tomography algorithms + +%%% Reconstruction and then Unmixing +[Aru,Fru] = RU(Y,W,k); + +strRU.A = Aru; +strRU.F = Fru; + +%%% Unmixing then Reconstruction +[Aur,Fur] = UR(Y,W,k); + +strUR.A = Aur; +strUR.F = Fur; + +%% cJoint +Jopt.rho = 1e-2; +Jopt.iterMax = 500; +Jopt.showIter = 2; +[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); + +strJ.A = Aj; +strJ.F = Fj; + +%% ADJUST + +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +Dopt.innerIter = 2; +Dopt.showIter = 2; +[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); + +strD.A = Ad; +strD.F = Fd; + +%% ADJUST-true + +Dopt.rho = 1e-2; +Dopt.iterMax = 1000; +Dopt.innerIter = 2; +Dopt.showIter = 2; +[Ad_gt,Fd_gt,Rd_gt,hist_gt] = ADJUST(Y,W,k,T_gt,Dopt); + +strProb.A = Ad_gt; +strProb.F = Fd_gt; + +%% plots and tables + +strOut = computeResults(strProb,strRU,strUR,strJ,strD); + +%% save results + +save([saveDir 'example_microCTData.mat'],'strOut'); \ No newline at end of file diff --git a/examples/example_Disk.m b/examples/example_Disk.m deleted file mode 100644 index da813f7..0000000 --- a/examples/example_Disk.m +++ /dev/null @@ -1,88 +0,0 @@ -%%% Spectral Tomography -%%% Disk phantom of size 256 x 256 -%%% 8 materials -%%% 100 channels -%%% Full-view setting: 60 angles from 0 to 180 -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -clc; clearvars; close all; - -% setting random stream -myStream = RandStream('mt19937ar','Seed',10); -RandStream.setGlobalStream(myStream) - -%% settings - -n = 256; -phantom = 'Disks'; - -%% load phantom - -% load matrices -[A,F,T,Q] = loadSpectralPhantom(phantom,n); -k = size(A,2); - -strProb.A = A; -strProb.F = F; -strProb.k = k; -strProb.T = T; -strProb.n = [n n]; - -%% generate spectral measurements - -U0 = A*F; - -% tomography -n_ang = 60; -theta = linspace(0,180,n_ang); - -volGeo = astra_create_vol_geom(n, n); -projGeo= astra_create_proj_geom('parallel', 1, n,theta); -W = opTomo('cuda', projGeo, volGeo); - -% measurements with noise -Y0 = W*U0; -Y = 0*Y0; -for i=1:size(Y0,2) - Y(:,i) = astra_add_noise_to_sino(Y0(:,i),Q(i)); -end - -%% Spectral Tomography algorithms - -%%% Reconstruction and then Unmixing -[Aru,Fru] = RU(Y,W,k); - -strRU.A = Aru; -strRU.F = Fru; - -%%% Unmixing then Reconstruction -[Aur,Fur] = UR(Y,W,k); - -strUR.A = Aur; -strUR.F = Fur; - -%%% cJoint -Jopt.rho = 1e-2; -Jopt.iterMax = 500; -[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); - -strJ.A = Aj; -strJ.F = Fj; - -%%% ADJUST -Dopt.rho = 1e-2; -Dopt.iterMax = 500; -[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); - -strD.A = Ad; -strD.F = Fd; - -%% plots and tables - -strOut = computeResults(strProb,strRU,strUR,strJ,strD); - diff --git a/examples/example_MixedDisk.m b/examples/example_MixedDisk.m deleted file mode 100644 index c0cd8ba..0000000 --- a/examples/example_MixedDisk.m +++ /dev/null @@ -1,89 +0,0 @@ -%%% Spectral Tomography -%%% Mixed Disk phantom of size 128 x 128 -%%% 5 materials -%%% 100 channels -%%% Full-view setting: 60 angles from 0 to 180 -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -clc; clearvars; close all; - -% setting random stream -myStream = RandStream('mt19937ar','Seed',10); -RandStream.setGlobalStream(myStream) - -%% settings - -n = 128; -phantom = 'MixedDisk'; - -%% load phantom - -% load matrices -[A,F,T,Q] = loadSpectralPhantom(phantom,n); -k = size(A,2); - -strProb.A = A; -strProb.F = F; -strProb.k = k; -strProb.T = T; -strProb.n = [n n]; - -%% generate spectral measurements - -U0 = A*F; - -% tomography -N = sqrt(size(A,1)); -n_ang = 60; -theta = linspace(0,180,n_ang); - -volGeo = astra_create_vol_geom(n, n); -projGeo= astra_create_proj_geom('parallel', 1, n,theta); -W = opTomo('cuda', projGeo, volGeo); - -% measurements with noise -Y0 = W*U0; -Y = 0*Y0; -for i=1:size(Y0,2) - Y(:,i) = astra_add_noise_to_sino(Y0(:,i),Q(i)); -end - -%% Spectral Tomography algorithms - -%%% Reconstruction and then Unmixing -[Aru,Fru] = RU(Y,W,k); - -strRU.A = Aru; -strRU.F = Fru; - -%%% Unmixing then Reconstruction -[Aur,Fur] = UR(Y,W,k); - -strUR.A = Aur; -strUR.F = Fur; - -%%% cJoint -Jopt.rho = 1e-2; -Jopt.iterMax = 500; -[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); - -strJ.A = Aj; -strJ.F = Fj; - -%%% ADJUST -Dopt.rho = 1e-2; -Dopt.iterMax = 500; -[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); - -strD.A = Ad; -strD.F = Fd; - -%% plots and tables - -strOut = computeResults(strProb,strRU,strUR,strJ,strD); - diff --git a/examples/example_SheppLogan.m b/examples/example_SheppLogan.m deleted file mode 100644 index 645798a..0000000 --- a/examples/example_SheppLogan.m +++ /dev/null @@ -1,88 +0,0 @@ -%%% Spectral Tomography -%%% Shepp Logan phantom of size 128 x 128 -%%% 5 materials -%%% 100 channels -%%% Full-view setting: 60 angles from 0 to 180 -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -clc; clearvars; close all; - -% setting random stream -myStream = RandStream('mt19937ar','Seed',10); -RandStream.setGlobalStream(myStream) - -%% settings - -n = 128; -phantom = 'SheppLogan'; - -%% load phantom - -% load matrices -[A,F,T,Q] = loadSpectralPhantom(phantom,n); -k = size(A,2); - -strProb.A = A; -strProb.F = F; -strProb.k = k; -strProb.T = T; -strProb.n = [n n]; - -%% generate spectral measurements - -U0 = A*F; - -% tomography -%N = sqrt(size(A,1)); -n_ang = 60; -theta = linspace(0,180,n_ang); - -volGeo = astra_create_vol_geom(n, n); -projGeo= astra_create_proj_geom('parallel', 1, n,theta); -W = opTomo('cuda', projGeo, volGeo); - -% measurements with noise -Y0 = W*U0; -Y = 0*Y0; -for i=1:size(Y0,2) - Y(:,i) = astra_add_noise_to_sino(Y0(:,i),Q(i)); -end - -%% Spectral Tomography algorithms - -%%% Reconstruction and then Unmixing -[Aru,Fru] = RU(Y,W,k); - -strRU.A = Aru; -strRU.F = Fru; - -%%% Unmixing then Reconstruction -[Aur,Fur] = UR(Y,W,k); - -strUR.A = Aur; -strUR.F = Fur; - -%%% cJoint -Jopt.rho = 1e-2; -Jopt.iterMax = 500; -[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); - -strJ.A = Aj; -strJ.F = Fj; - -%%% ADJUST -Dopt.rho = 1e-2; -Dopt.iterMax = 500; -[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); - -strD.A = Ad; -strD.F = Fd; - -%% plots and tables - -strOut = computeResults(strProb,strRU,strUR,strJ,strD); diff --git a/examples/example_SheppLogan3D.m b/examples/example_SheppLogan3D.m deleted file mode 100644 index 680732e..0000000 --- a/examples/example_SheppLogan3D.m +++ /dev/null @@ -1,87 +0,0 @@ -%%% Spectral Tomography -%%% 3D Shepp Logan phantom of size 128 x 128 x 128 -%%% 3 materials -%%% 100 channels -%%% Full-view setting: parallel beam geometry, 60 angles from 0 to 180 -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -clc; clearvars; close all; - -% setting random stream -myStream = RandStream('mt19937ar','Seed',10); -RandStream.setGlobalStream(myStream) - -%% settings - -n = 128; -phantom = 'SheppLogan3D'; - -%% load phantom - -% load matrices -[A,F,T,Q] = loadSpectralPhantom(phantom,n); -k = size(A,2); - -strProb.A = A; -strProb.F = F; -strProb.k = k; -strProb.T = T; -strProb.n = [n n n]; - -%% generate spectral measurements - -U0 = A*F; - -% tomography -n_ang = 60; -theta = linspace(0,180,n_ang); - -volGeo= astra_create_vol_geom(n, n, n); -projGeo= astra_create_proj_geom('parallel3d', 1, 1, n, n,theta); -W = opTomo('cuda', projGeo, volGeo); - -% measurements with noise -Y0 = W*U0; -Y = 0*Y0; -for i=1:size(Y0,2) - Y(:,i) = astra_add_noise_to_sino(Y0(:,i),Q(i)); -end - -%% Spectral Tomography algorithms - -%%% Reconstruction and then Unmixing -[Aru,Fru] = RU(Y,W,k); - -strRU.A = Aru; -strRU.F = Fru; - -%%% Unmixing then Reconstruction -[Aur,Fur] = UR(Y,W,k); - -strUR.A = Aur; -strUR.F = Fur; - -%%% cJoint -Jopt.rho = 1e-2; -Jopt.iterMax = 500; -[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); - -strJ.A = Aj; -strJ.F = Fj; - -%%% ADJUST -Dopt.rho = 1e-2; -Dopt.iterMax = 500; -[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); - -strD.A = Ad; -strD.F = Fd; - -%% plots and tables - -strOut = computeResults(strProb,strRU,strUR,strJ,strD); \ No newline at end of file diff --git a/examples/example_SheppLogan_LimitedView.m b/examples/example_SheppLogan_LimitedView.m deleted file mode 100644 index c075b1f..0000000 --- a/examples/example_SheppLogan_LimitedView.m +++ /dev/null @@ -1,88 +0,0 @@ -%%% Spectral Tomography -%%% Shepp Logan phantom of size 128 x 128 -%%% 5 materials -%%% 100 channels -%%% Limited-view setting: parallel-beam 60 angles from 0 to 120 degrees -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -clc; clearvars; close all; - -% setting random stream -myStream = RandStream('mt19937ar','Seed',10); -RandStream.setGlobalStream(myStream) - -%% settings - -n = 128; -phantom = 'SheppLogan'; - -%% load phantom - -% load matrices -[A,F,T,Q] = loadSpectralPhantom(phantom,n); -k = size(A,2); - -strProb.A = A; -strProb.F = F; -strProb.k = k; -strProb.T = T; -strProb.n = [n n]; - -%% generate spectral measurements - -U0 = A*F; - -% tomography -n_ang = 60; -theta = linspace(0,120,n_ang); - -volGeo = astra_create_vol_geom(n, n); -projGeo= astra_create_proj_geom('parallel', 1, n,theta); -W = opTomo('cuda', projGeo, volGeo); - -% measurements with noise -Y0 = W*U0; -Y = 0*Y0; -for i=1:size(Y0,2) - Y(:,i) = astra_add_noise_to_sino(Y0(:,i),Q(i)); -end - -%% Spectral Tomography algorithms - -%%% Reconstruction and then Unmixing -[Aru,Fru] = RU(Y,W,k); - -strRU.A = Aru; -strRU.F = Fru; - -%%% Unmixing then Reconstruction -[Aur,Fur] = UR(Y,W,k); - -strUR.A = Aur; -strUR.F = Fur; - -%%% cJoint -Jopt.rho = 1e-2; -Jopt.iterMax = 200; -[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); - -strJ.A = Aj; -strJ.F = Fj; - -%%% ADJUST -Dopt.rho = 1e-2; -Dopt.iterMax = 200; -[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); - -strD.A = Ad; -strD.F = Fd; - -%% plots and tables - -strOut = computeResults(strProb,strRU,strUR,strJ,strD); - diff --git a/examples/example_SheppLogan_SparseAngle.m b/examples/example_SheppLogan_SparseAngle.m deleted file mode 100644 index 476c0a3..0000000 --- a/examples/example_SheppLogan_SparseAngle.m +++ /dev/null @@ -1,88 +0,0 @@ -%%% Spectral Tomography -%%% Shepp Logan phantom of size 128 x 128 -%%% 5 materials -%%% 100 channels -%%% Sparse-angle setting: 10 angles from 0 to 180 -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -clc; clearvars; close all; - -% setting random stream -myStream = RandStream('mt19937ar','Seed',10); -RandStream.setGlobalStream(myStream) - -%% settings - -n = 128; -phantom = 'SheppLogan'; - -%% load phantom - -% load matrices -[A,F,T,Q] = loadSpectralPhantom(phantom,n); -k = size(A,2); - -strProb.A = A; -strProb.F = F; -strProb.k = k; -strProb.T = T; -strProb.n = [n n]; - -%% generate spectral measurements - -U0 = A*F; - -% tomography -n_ang = 10; -theta = linspace(0,180,n_ang); - -volGeo = astra_create_vol_geom(n, n); -projGeo= astra_create_proj_geom('parallel', 1, n,theta); -W = opTomo('cuda', projGeo, volGeo); - -% measurements with noise -Y0 = W*U0; -Y = 0*Y0; -for i=1:size(Y0,2) - Y(:,i) = astra_add_noise_to_sino(Y0(:,i),Q(i)); -end - -%% Spectral Tomography algorithms - -%%% Reconstruction and then Unmixing -[Aru,Fru] = RU(Y,W,k); - -strRU.A = Aru; -strRU.F = Fru; - -%%% Unmixing then Reconstruction -[Aur,Fur] = UR(Y,W,k); - -strUR.A = Aur; -strUR.F = Fur; - -%%% cJoint -Jopt.rho = 1e-2; -Jopt.iterMax = 500; -[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); - -strJ.A = Aj; -strJ.F = Fj; - -%%% ADJUST -Dopt.rho = 1e-2; -Dopt.iterMax = 500; -[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); - -strD.A = Ad; -strD.F = Fd; - -%% plots and tables - -strOut = computeResults(strProb,strRU,strUR,strJ,strD); - diff --git a/examples/example_Thorax.m b/examples/example_Thorax.m deleted file mode 100644 index 7093db8..0000000 --- a/examples/example_Thorax.m +++ /dev/null @@ -1,100 +0,0 @@ -%%% Spectral Tomography -%%% Thorax phantom of size 512 x 512 -%%% 5 materials (3 soft + 2 hard) -%%% 100 channels -%%% Full-view setting: 60 angles from 0 to 180 degrees -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -clc; clearvars; close all; - -% setting random stream -myStream = RandStream('mt19937ar','Seed',10); -RandStream.setGlobalStream(myStream) - -%% settings - -%Thorax phantom size is fixed to 512 -n = 512; -phantom = 'Thorax'; - -%% load phantom - -% load matrices -[A,F,T,Q] = loadSpectralPhantom(phantom); - - -%% generate spectral measurements - -U0 = A*F; - -% tomography -n_ang = 60; -theta = linspace(0,180,n_ang); - -volGeo = astra_create_vol_geom(n, n); -projGeo= astra_create_proj_geom('parallel', 1, n,theta); -W = opTomo('cuda', projGeo, volGeo); - -% measurements with noise -Y0 = W*U0; -Y = 0*Y0; -for i=1:size(Y0,2) - Y(:,i) = astra_add_noise_to_sino(Y0(:,i),Q(i)); -end - -%% problem setting -% Please note that we only distinguish hard materials from soft materials. -% There are 3 soft materials and 2 hard materials. Hence, we use k = 3 -% (2 hard and 1 combined soft) here. - -% number of materials -k = 3; - -% convert 3 softer ones to 1 soft -[A_Thorax,F_Thorax] = modifyThorax(A,F); - -strProb.A = A_Thorax; -strProb.F = F_Thorax; -strProb.k = k; -strProb.T = T; -strProb.n = [n n]; - -%% Spectral Tomography algorithms - -%%% Reconstruction and then Unmixing -[Aru,Fru] = RU(Y,W,k); - -strRU.A = Aru; -strRU.F = Fru; - -%%% Unmixing then Reconstruction -[Aur,Fur] = UR(Y,W,k); - -strUR.A = Aur; -strUR.F = Fur; - -%%% cJoint -Jopt.rho = 1e-2; -Jopt.iterMax = 500; -[Aj,Fj,histJ] = cJoint(Y,W,k,Jopt); - -strJ.A = Aj; -strJ.F = Fj; - -%%% ADJUST -Dopt.rho = 1e-2; -Dopt.iterMax = 10; -[Ad,Fd,Rd,hist] = ADJUST(Y,W,k,T,Dopt); - -strD.A = Ad; -strD.F = Fd; - -%% plots and tables - -strOut = computeResults(strProb,strRU,strUR,strJ,strD); - diff --git a/images/micro_ct_dataset_result.png b/images/micro_ct_dataset_result.png new file mode 100644 index 0000000..8f7f26b Binary files /dev/null and b/images/micro_ct_dataset_result.png differ diff --git a/mbin/ADJUST.m b/mbin/ADJUST.m index 4f0e306..2661d7e 100644 --- a/mbin/ADJUST.m +++ b/mbin/ADJUST.m @@ -76,15 +76,16 @@ resTol = getoptions(options,'resTol',1e-6); % tolerance for residual relTol = getoptions(options,'relTol',1e-9); % tolerance for residual progress progTol = getoptions(options,'progTol',1e-6);% tolerance for iterate progress -rho = getoptions(options,'rho',1e-2); -EQ_A = getoptions(options,'EQ_A',0); -dynUpd = getoptions(options,'dynUpd',1); +rho = getoptions(options,'rho',1e-2); % acceleration parameter +EQ_A = getoptions(options,'EQ_A',0); % equality constraints on A (1: strong, 0: weak) +dynUpd = getoptions(options,'dynUpd',1); % dynamic update of acceleration parameter (experimental) +showIter= getoptions(options,'showIter',1); % show iterates (1: yes, 0: no) %% initialization A0 = rand(n,k); -for i=1:size(A0,1) % normalize the rows +for i=1:size(A0,1) % normalize the rows by their sum A0(i,:) = A0(i,:)/sum(A0(i,:)); end @@ -138,7 +139,6 @@ R = minConf_SPG(funObjR,R(:),funProjR,Opt); R = reshape(R,k,p); - % channel matrix F = R*T; @@ -152,6 +152,7 @@ res = (Y - W*(A*F)); Q = Q + res; + % register time time_iter = toc; time_hist = time_hist + time_iter; @@ -165,9 +166,11 @@ hist.res_prog(i)=1; end - % show iterate and progress + % show iterate and progress (every 100 iterations) + if ((showIter == 1) && (rem(i,100)==0)) || (showIter > 1) fprintf('%10d %12.3e %12.3e %12.3e [%4.2e/%4.2e]\n',i,... hist.res(i),hist.res_prog(i),hist.prog(i),time_iter,time_hist); + end % record solution if i==1 @@ -188,7 +191,7 @@ break; end - % dynamic update of rho + % dynamic update of rho (this is an experimental feature) if dynUpd if (rho > 5e-2) && (hist.res_prog(i) > 1e-3) rho = 1e-2; @@ -210,6 +213,7 @@ function [f,g] = misfitR(R,Y,W,A,T,k,nY) % misfit function for matrix R, where Y = W * A * R * T. +% provides functional value and gradient at particular point % get the size of U and reshape matrix R [m,t] = size(Y); @@ -226,6 +230,7 @@ function [f,g] = misfitA(A,F,Y,W,k,nY) % misfit function handle for matrix A, where Y = W * A * F +% provides functional value and gradient at particular point % get the size of U and reshape A [m,n] = size(W); @@ -252,9 +257,9 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function [x] = projSimplexR(x,m,n) +% projector for matrix R (simplex constraints on both rows and columns) R = reshape(x,m,n); % reshape matrix R - R = projectTwoSimplexConstr(R); x = R(:); @@ -265,18 +270,23 @@ [m,n] = size(R); MAX_ITER = 1e4; -%%% solve using ADMM - +%%% solve using alternating projections (similar to Dijkstra's algorithm) x = R; + if sum(x(:)) >= 1 for i=1:MAX_ITER + % row projection x1 = transpose(proj_simplex_q(0.5*(x+R)',1,1)); + + % column projection x = proj_simplex_q(x1,1,0); + % stopping criterion if norm(x1-x,'fro') < 1e-6 break; end + end end @@ -287,7 +297,7 @@ function [x] = proj_simplex_q(x,q,EQ) % simplex projector -% EQ = 0; % Equality constraints indicator (set to 1 if required) +% EQ = 0; % Equality constraints indicator (set to 1 if required) VECTORIZE = false; % vectorization indictor ('false' to keep it as matrix) diff --git a/mbin/cJoint.m b/mbin/cJoint.m index 06f36c7..d6912f3 100644 --- a/mbin/cJoint.m +++ b/mbin/cJoint.m @@ -59,6 +59,7 @@ resTol = getoptions(options, 'resTol' , 1e-6); % tolerance for residual progTol = getoptions(options, 'progTol' , 1e-6);% tolerance for progress rho = getoptions(options, 'rho' , 0.01); % acceleration parameter +showIter= getoptions(options, 'showIter', 1); % display iter %% initialization @@ -123,6 +124,7 @@ res = (Y - W*(A*F)); Q = Q + res; + % register time time_iter = toc; time_hist = time_hist + time_iter; @@ -137,10 +139,12 @@ end % show iterate and progress + if ((showIter == 1) && (rem(i,100)==0)) || (showIter > 1) fprintf('%10d %12.3e %12.3e %12.3e [%4.2e/%4.2e]\n',i,... hist.res(i),hist.res_prog(i),hist.prog(i),time_iter,time_hist); + end - % record solution + % record solution with least residual (since the convegence is non-monotonic) if i==1 Asol = A;Fsol = F; hist.resmin = hist.res(i); @@ -167,6 +171,7 @@ function [f,g] = misfitF(F,Y,W,A,k,nY) % misfit function for matrix F, where Y = W * A * F. +% provide functional value and gradient at given point % get the size of U and reshape matrix R [m,c] = size(Y); @@ -181,6 +186,7 @@ function [f,g] = misfitA(A,F,Y,W,k,nY) % misfit function handle for matrix A +% provide functional value and gradient at given point % get the size of U and reshape A [m,n] = size(W); @@ -196,7 +202,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function [x] = projA(x) -% projector for matrix A (simplex constraints - on rows) +% projector for matrix A (bounds constraints) x(x < 0) = 0; x(x > 1) = 1; diff --git a/mbin/computeResults.m b/mbin/computeResults.m index fa119b1..5ec6734 100644 --- a/mbin/computeResults.m +++ b/mbin/computeResults.m @@ -1,273 +1,304 @@ -function [sO] = computeResults(strProb,strRU,strUR,strJ,strD,sliceNo) -% computeResults Plot various comparison plots and tables for methods -% 1) RU - Reconstruction-then-Unmixing -% 2) UR - Unmixing-the-Reconstruction -% 3) cJoint - classical joint reconstruction algorithm -% 4) ADJUST - proposed method -% -% Input: -% strProb - problem structure containing A (spatial maps), F (spectral -% maps) and n (size of spatial images) -% strRU - numerical results of RU method that contains A and F -% strUR - numerical results of UR method that contains A and F -% strJ - numerical results of classical Joint method that contains A -% and F -% strD - numerical results of ADJUST method that contains A and F -% -% Output: -% sO - output structure containing sO.UR, sO.RU, sO.cJoint, sO.ADJUST -% that have the following details -% A : reconstructed spatial maps aligned with true maps -% (size: n x k) -% F : reconstructed spectral maps aligned with true maps -% (size: k x c) -% psnr : peak signal-to-noise ratio for each reconstructed material -% spatial map w.r.t. true map (size: kx1) -% ssim : structural similarity index for each reconstructed material -% spatial map w.r.t. true map (size: kx1) -% imse : mean-squared error for each reconstructed material -% spatial map w.r.t true map (size: kx1) -% psnrM: mean PSNR over all materials -% ssimM: mean SSIM over all materials -% imseM: mean MSE over all materials -% -% -% Authors: -% Ajinkya Kadu, -% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) -% Mathé Zeegers, -% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) - -%% - -n = strProb.n; -A = strProb.A; -F = strProb.F; - -Aur = strUR.A; -Fur = strUR.F; -Aru = strRU.A; -Fru = strRU.F; -Aj = strJ.A; -Fj = strJ.F; -Ad = strD.A; -Fd = strD.F; - - -%% UR - -[Aurf,Furf] = alignMatrices(A,Aur,Fur,n); -sO.UR = computePerformance(Aurf,A,n); -sO.UR.A = Aurf; -sO.UR.F = Furf; - -%% RU - -[Aruf,Fruf] = alignMatrices(A,Aru,Fru,n); -sO.RU = computePerformance(Aruf,A,n); -sO.RU.A = Aruf; -sO.RU.F = Fruf; - -%% cJoint - -[Ajf,Fjf] = alignMatrices(A,Aj,Fj,n); -sO.cJoint = computePerformance(Ajf,A,n); -sO.cJoint.A = Ajf; -sO.cJoint.F = Fjf; - -%% ADJUST - -[Adf,Fdf] = alignMatrices(A,Ad,Fd,n); -sO.ADJUST = computePerformance(Adf,A,n); -sO.ADJUST.A = Adf; -sO.ADJUST.F = Fdf; - -%% print - -fprintf('\n--------------------------------------------------------------------------\n'); - -fprintf('%12s | %12s | %12s | %12s | %12s \n','','RU','UR',... - 'cJoint','ADJUST'); - -fprintf('--------------------------------------------------------------------------\n'); - -fprintf('%12s | %12.4f | %12.4f | %12.4f | %12.4f \n','PSNR',sO.RU.psnrM,... - sO.UR.psnrM,sO.cJoint.psnrM,sO.ADJUST.psnrM); - -fprintf('%12s | %12.4f | %12.4f | %12.4f | %12.4f \n','SSIM',sO.RU.ssimM,... - sO.UR.ssimM,sO.cJoint.ssimM,sO.ADJUST.ssimM); - -fprintf('%12s | %12.4f | %12.4f | %12.4f | %12.4f \n','MSE',sO.RU.imseM,... - sO.UR.imseM,sO.cJoint.imseM,sO.ADJUST.imseM); - -fprintf('--------------------------------------------------------------------------\n'); - - -%% plot figure - -k = size(A,2); - -if length(n) == 2 - fig = figure(100);colormap hot; - for i=1:k - AtI = reshape(A(:,i),n); - AruI = reshape(Aurf(:,i),n); - AurI = reshape(Aurf(:,i),n); - AjI = reshape(Ajf(:,i),n); - AdI = reshape(Adf(:,i),n); - - subplot(k,5,5*(i-1)+1);imagesc(AtI,[0 1]);title(sprintf('True-%d',i)); - axis image;set(gca,'XTick',[],'YTick',[]); - subplot(k,5,5*(i-1)+2);imagesc(AruI,[0 1]);title(sprintf('RU-%d',i)); - axis image;set(gca,'XTick',[],'YTick',[]); - subplot(k,5,5*(i-1)+3);imagesc(AurI,[0 1]);title(sprintf('UR-%d',i)); - axis image;set(gca,'XTick',[],'YTick',[]); - subplot(k,5,5*(i-1)+4);imagesc(AjI,[0 1]);title(sprintf('cJoint-%d',i)); - axis image;set(gca,'XTick',[],'YTick',[]); - subplot(k,5,5*(i-1)+5);imagesc(AdI,[0 1]);title(sprintf('ADJUST-%d',i)); - axis image;set(gca,'XTick',[],'YTick',[]); - pause(1); - end - h = axes(fig,'visible','off'); - colorbar(h,'Position',[0.93 0.168 0.022 0.7]); - -elseif length(n) == 3 - figure(100); - for i=1:k - AtI = reshape(A(:,i),n); - AruI = reshape(Aurf(:,i),n); - AurI = reshape(Aurf(:,i),n); - AjI = reshape(Ajf(:,i),n); - AdI = reshape(Adf(:,i),n); - - if nargin < 7 - sliceNo = floor(n(3)/2); - end - - subplot(k,5,5*(i-1)+1);imshow(AtI(:,:,sliceNo));title(sprintf('True-%d',i)); - subplot(k,5,5*(i-1)+2);imshow(AruI(:,:,sliceNo));title(sprintf('RU-%d',i)); - subplot(k,5,5*(i-1)+3);imshow(AurI(:,:,sliceNo));title(sprintf('UR-%d',i)); - subplot(k,5,5*(i-1)+4);imshow(AjI(:,:,sliceNo));title(sprintf('cJoint-%d',i)); - subplot(k,5,5*(i-1)+5);imshow(AdI(:,:,sliceNo));title(sprintf('ADJUST-%d',i)); - pause(1); - end - -end - -end - -function [strOut] = computePerformance(A,At,n) - -k = size(At,2); - -psnrI = zeros(k,1); -ssimI = zeros(k,1); -imseI = zeros(k,1); - - -for i=1:k - Ix = reshape(A(:,i),n); - Iy = reshape(At(:,i),n); - Ix = double(Ix); - Iy = double(Iy); - psnrI(i,1) = psnr(Ix,Iy); - ssimI(i,1) = ssim(Ix,Iy); - imseI(i,1) = immse(Ix,Iy); -end - -strOut.psnr = psnrI; -strOut.ssim = ssimI; -strOut.imse = imseI; - -strOut.psnrM = mean(psnrI); -strOut.ssimM = mean(ssimI); -strOut.imseM = mean(imseI); - -end - - -function [A2f,F2f,cumError,ErrorMatrix] = alignMatrices(A,A1,F1,n) - - Amax = max(A1(:)); - A2 = A1/Amax; - F2 = F1*Amax; - - [cumError,ErrorMatrix,minrowI,mincolI] = computeError(A2,A); - - [~,idD]= sort(mincolI); - A2f = A2(:, minrowI(idD)); - F2f = F2(minrowI(idD),:); - -end - - -%%% Function for calculating the error measure per image -function [cumError,ErrorMatrix,minrowI,mincolI] = computeError(A,Atrue) - - B = A; - Btrue = Atrue; - - nmat = size(Atrue,2); - nPix = size(Atrue,1); - - %First compute the errors for all image pairs - ErrorMatrix = zeros(nmat, nmat); - for i = 1:nmat - for j = 1:nmat - ErrorMatrix(i,j) = norm(B(:,i) - Btrue(:,j)); - end - end - - % ErrorMatrix - - %Now do the matching and iteratively removing rows and colums - cumError = 0; - minrowI = zeros(nmat,1); - mincolI = zeros(nmat,1); - psnrv = zeros(nmat,1); - ssimv = zeros(nmat,1); - immsev = zeros(nmat,1); - - for k = 1:nmat - - %Find minimum value and indices in error array - [minvalue, minindex] = min(ErrorMatrix(:)); - [minrow, mincol] = ind2sub(size(ErrorMatrix), minindex); - - trueI = Btrue(:,mincol); - recI = B(:,minrow); - - errorPair = ErrorMatrix(minrow,mincol); - cumError = cumError + errorPair; - - % fprintf("Matched image %d to true image %d with error %f \n", minrow, mincol, errorPair) - - minrowI(k,1) = minrow; - mincolI(k,1) = mincol; - - %Remove the corresponding row and column from the array - - ErrorMatrix(minrow,:) = Inf; - ErrorMatrix(:,mincol) = Inf; - - end - - % fprintf("The total error is %f \n", cumError) - -end - -function [Af] = buildSingleImageforA(A,idx) - -[m,n] = size(A); - -if nargin < 2 - idx = linspace(1,n,n); -end - -vdx = linspace(1,n,n); - -Af = A(:,idx)*vdx'; - - -end - +function [sO] = computeResults(strProb,strRU,strUR,strJ,strD,sliceNo) +% computeResults Plot various comparison plots and tables for methods +% 1) RU - Reconstruction-then-Unmixing +% 2) UR - Unmixing-the-Reconstruction +% 3) cJoint - classical joint reconstruction algorithm +% 4) ADJUST - proposed method +% +% Input: +% strProb - problem structure containing A (spatial maps), F (spectral +% maps) and n (size of spatial images) +% strRU - numerical results of RU method that contains A and F +% strUR - numerical results of UR method that contains A and F +% strJ - numerical results of classical Joint method that contains A +% and F +% strD - numerical results of ADJUST method that contains A and F +% sliceNo- slice number for visualizing results on 3d phantom +% +% Output: +% sO - output structure containing sO.UR, sO.RU, sO.cJoint, sO.ADJUST +% that have the following details +% A : reconstructed spatial maps aligned with true maps +% (size: n x k) +% F : reconstructed spectral maps aligned with true maps +% (size: k x c) +% psnr : peak signal-to-noise ratio for each reconstructed material +% spatial map w.r.t. true map (size: kx1) +% ssim : structural similarity index for each reconstructed material +% spatial map w.r.t. true map (size: kx1) +% imse : mean-squared error for each reconstructed material +% spatial map w.r.t true map (size: kx1) +% psnrM: mean PSNR over all materials +% ssimM: mean SSIM over all materials +% imseM: mean MSE over all materials +% +% +% Authors: +% Ajinkya Kadu, +% Centrum Wiskunde & Informatica, Amsterdam (aak@cwi.nl) +% Mathé Zeegers, +% Centrum Wiskunde & Informatica, Amsterdam (M.T.Zeegers@cwi.nl) + +%% + +n = strProb.n; +A = strProb.A; +F = strProb.F; + +Aur = strUR.A; +Fur = strUR.F; +Aru = strRU.A; +Fru = strRU.F; +Aj = strJ.A; +Fj = strJ.F; +Ad = strD.A; +Fd = strD.F; + +sO.strProb = strProb; +sO.GT.A = A; +sO.GT.F = F; +%% UR + +[Aurf,Furf] = alignMatrices(A,Aur,Fur); +sO.UR = computePerformance(Aurf,A,n); +sO.UR.A = Aurf; +sO.UR.F = Furf; + +%% RU + +[Aruf,Fruf] = alignMatrices(A,Aru,Fru,n); +sO.RU = computePerformance(Aruf,A,n); +sO.RU.A = Aruf; +sO.RU.F = Fruf; + +%% cJoint + +[Ajf,Fjf] = alignMatrices(A,Aj,Fj,n); +sO.cJoint = computePerformance(Ajf,A,n); +sO.cJoint.A = Ajf; +sO.cJoint.F = Fjf; + +%% ADJUST + +[Adf,Fdf] = alignMatrices(A,Ad,Fd,n); +sO.ADJUST = computePerformance(Adf,A,n); +sO.ADJUST.A = Adf; +sO.ADJUST.F = Fdf; + +%% print + +fprintf('\n--------------------------------------------------------------------------\n'); + +fprintf('%12s | %12s | %12s | %12s | %12s \n','','RU','UR',... + 'cJoint','ADJUST'); + +fprintf('--------------------------------------------------------------------------\n'); + +fprintf('%12s | %12.4f | %12.4f | %12.4f | %12.4f \n','PSNR',sO.RU.psnrM,... + sO.UR.psnrM,sO.cJoint.psnrM,sO.ADJUST.psnrM); + +fprintf('%12s | %12.4f | %12.4f | %12.4f | %12.4f \n','SSIM',sO.RU.ssimM,... + sO.UR.ssimM,sO.cJoint.ssimM,sO.ADJUST.ssimM); + +fprintf('%12s | %12.4f | %12.4f | %12.4f | %12.4f \n','MSE',sO.RU.imseM,... + sO.UR.imseM,sO.cJoint.imseM,sO.ADJUST.imseM); + +fprintf('--------------------------------------------------------------------------\n'); + + +%% plot figure + +k = size(A,2); + +if length(n) == 2 + fig = figure(100);colormap hot; + for i=1:k + AtI = reshape(A(:,i),n); + AruI = reshape(Aurf(:,i),n); + AurI = reshape(Aurf(:,i),n); + AjI = reshape(Ajf(:,i),n); + AdI = reshape(Adf(:,i),n); + + subplot(k,5,5*(i-1)+1);imagesc(AtI,[0 1]);title(sprintf('True-%d',i)); + axis image;set(gca,'XTick',[],'YTick',[]); + subplot(k,5,5*(i-1)+2);imagesc(AruI,[0 1]);title(sprintf('RU-%d',i)); + axis image;set(gca,'XTick',[],'YTick',[]); + subplot(k,5,5*(i-1)+3);imagesc(AurI,[0 1]);title(sprintf('UR-%d',i)); + axis image;set(gca,'XTick',[],'YTick',[]); + subplot(k,5,5*(i-1)+4);imagesc(AjI,[0 1]);title(sprintf('cJoint-%d',i)); + axis image;set(gca,'XTick',[],'YTick',[]); + subplot(k,5,5*(i-1)+5);imagesc(AdI,[0 1]);title(sprintf('ADJUST-%d',i)); + axis image;set(gca,'XTick',[],'YTick',[]); + pause(1); + end + h = axes(fig,'visible','off'); + colorbar(h,'Position',[0.93 0.168 0.022 0.7]); + +elseif length(n) == 3 + figure(100); + for i=1:k + AtI = reshape(A(:,i),n); + AruI = reshape(Aurf(:,i),n); + AurI = reshape(Aurf(:,i),n); + AjI = reshape(Ajf(:,i),n); + AdI = reshape(Adf(:,i),n); + + if nargin < 7 + sliceNo = floor(n(3)/2); + end + + subplot(k,5,5*(i-1)+1);imshow(rescale(AtI(:,:,sliceNo)));title(sprintf('True-%d',i)); + subplot(k,5,5*(i-1)+2);imshow(rescale(AruI(:,:,sliceNo)));title(sprintf('RU-%d',i)); + subplot(k,5,5*(i-1)+3);imshow(rescale(AurI(:,:,sliceNo)));title(sprintf('UR-%d',i)); + subplot(k,5,5*(i-1)+4);imshow(rescale(AjI(:,:,sliceNo)));title(sprintf('cJoint-%d',i)); + subplot(k,5,5*(i-1)+5);imshow(rescale(AdI(:,:,sliceNo)));title(sprintf('ADJUST-%d',i)); + pause(1); + end + +end + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% +% Supporting functions +% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function [strOut] = computePerformance(A,At,n) +% computes the performance measures algorithm by comparing reconstructed +% spatial maps with ground truth spatial maps +% We look at PSNR, SSIM and IMMSE +% Input - +% A - reconstructed spatial maps +% At- ground truth spatial maps +% n - size of images +% +% Output: +% strOut - structure containing +% psnr - peak signal-to-noise-ratio of individual spatial map +% ssim - structural similarity index of individual spatial map +% imse - mean-squared-error of individual spatial map +% psnrM, ssimM, imseM - mean of these measures +% +k = size(At,2); + +psnrI = zeros(k,1); +ssimI = zeros(k,1); +imseI = zeros(k,1); + +% compute for each spatial map +for i=1:k + Ix = reshape(A(:,i),n); + Iy = reshape(At(:,i),n); + Ix = double(Ix); + Iy = double(Iy); + psnrI(i,1) = psnr(Ix,Iy); + ssimI(i,1) = ssim(Ix,Iy); + imseI(i,1) = immse(Ix,Iy); +end + +strOut.psnr = psnrI; +strOut.ssim = ssimI; +strOut.imse = imseI; + +% compute the averages +strOut.psnrM = mean(psnrI); +strOut.ssimM = mean(ssimI); +strOut.imseM = mean(imseI); + +end + + +function [A2f,F2f,cumError,ErrorMatrix] = alignMatrices(A,A1,F1) +% align the reconstructed spatial and spectral maps based on the ground +% truth or given spatial and spectral maps +% +% Input: +% A - ground truth or given spatial maps +% A1 - spatial maps that needs to be aligned +% F1 - spectral maps that needs to be aligned +% +% Output: +% A2f - aligned spatial maps +% F2f - aligned spectral maps +% cumError - cumulative errors +% ErrorMatrix - mean-squared error for each pair (spatial maps only). + +Amax = max(A1(:)); +A2 = A1/Amax; +F2 = F1*Amax; + +[cumError,ErrorMatrix,minrowI,mincolI] = computeError(A2,A); + +[~,idD]= sort(mincolI); +A2f = A2(:, minrowI(idD)); +F2f = F2(minrowI(idD),:); + +end + + +function [cumError,ErrorMatrix,minrowI,mincolI] = computeError(A,Atrue) +% Function for calculating the error measure per image +% +% Input: +% A - reconstructed spatial maps +% Atrue - ground truth spatial maps +% +% Output: +% cumError - cumulative error for each material +% ErrorMatrix - mean-squared-error for each material spatial maps pair +% minrowI - +% mincolI - +% + +nmat = size(Atrue,2); +nPix = size(Atrue,1); + +% First compute the errors for all image pairs +ErrorMatrix = zeros(nmat, nmat); +for i = 1:nmat + for j = 1:nmat + ErrorMatrix(i,j) = norm(A(:,i) - Atrue(:,j)); + end +end + +% ErrorMatrix + +% Now do the matching and iteratively removing rows and colums +cumError = 0; +minrowI = zeros(nmat,1); +mincolI = zeros(nmat,1); + +% psnrv = zeros(nmat,1); +% ssimv = zeros(nmat,1); +% immsev = zeros(nmat,1); + +for k = 1:nmat + + %Find minimum value and indices in error array + [minvalue, minindex] = min(ErrorMatrix(:)); + [minrow, mincol] = ind2sub(size(ErrorMatrix), minindex); + + % trueI = Atrue(:,mincol); + % recI = A(:,minrow); + + errorPair = ErrorMatrix(minrow,mincol); + cumError = cumError + errorPair; + + % fprintf("Matched image %d to true image %d with error %f \n", minrow, mincol, errorPair) + + minrowI(k,1) = minrow; + mincolI(k,1) = mincol; + + %Remove the corresponding row and column from the array + + ErrorMatrix(minrow,:) = Inf; + ErrorMatrix(:,mincol) = Inf; + +end + +% fprintf("The total error is %f \n", cumError) + +end + diff --git a/mbin/loadSpectralPhantom.m b/mbin/loadSpectralPhantom.m index b67d0ce..3cb0350 100644 --- a/mbin/loadSpectralPhantom.m +++ b/mbin/loadSpectralPhantom.m @@ -1,48 +1,68 @@ -function [A,F,T,q] = loadSpectralPhantom(phantomId,n) -% loadSpectralPhantom gives the spatial and material maps for various -% phantoms. It also gives the spectral dictionary that may be required for -% ADJUST algorithm. - -if nargin < 2 - if(phantomId == 'Thorax') - n = 512; - else - n = 128; - end -end - -switch phantomId - case 'SheppLogan' - A = spectralSheppLogan(n); - T = readmatrix('MatrixTXrayHard100chan_93mat_20MinEn_119MaxEn.csv'); - F = T(0+(1:size(A,2)),:); - q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); - case 'Disks' - k = 8; - A = spectralPhantomCircles(n,k); - T = readmatrix('MatrixTXrayHard100chan_93mat_20MinEn_119MaxEn.csv'); - F = T(10+(1:size(A,2)),:); - q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); - case 'Thorax' - A0 = spectralThoraxPhantom(); - A = [A0(:,1)+A0(:,2) A0(:,3)+A0(:,4) A0(:,5)+A0(:,7) A0(:,6) A0(:,8)]; - T = readmatrix('Thorax_MatrixTXray100chan_60mat_MinEn20_MaxEn80.csv'); - F = readmatrix('Thorax_MatrixFXray100chan_6matBoneBloodIodineSofttissueBloodLungsIodine_MinEn20_MaxEn80.csv'); - F = F(1:5,:); %remove the pure iodine from the dictionary - q = readmatrix('VectorIXrayMatWEn100Min20Max80.csv'); - case 'MixedDisk' - k = 5; - A = spectralPhantomCirclesMixed(n, k); - T = readmatrix('MatrixTXrayHard100chan_93mat_20MinEn_119MaxEn.csv'); - F = T(0+(1:size(A,2)),:); - q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); - case 'SheppLogan3D' - A = spectralSheppLogan3D(n); - T = readmatrix('MatrixTXrayHard100chan_93mat_20MinEn_119MaxEn.csv'); - F = T(0+(1:size(A,2)),:); - q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); - otherwise - error('phantom can either be SheppLogan, Disks, Thorax or Mixed \n'); -end - -end +function [A,F,T,q] = loadSpectralPhantom(phantomId,n) +% loadSpectralPhantom gives the spatial and material maps for various +% phantoms. It also gives the spectral dictionary that may be required for +% ADJUST algorithm. +% +% Input: +% phantomId - one of 'SheppLogan', 'Disks', 'Thorax', 'MixedDisk', +% 'SheppLogan3D' +% n - spatial resolution of phantom (e.g. 256) +% +% Output: +% A - spatial map of materials +% F - spectral map of materials +% T - spectral dictionary +% q - source spectrum + +% making sure that Thorax phantom resolution is 512, and otherwise default +% 128 + +if nargin < 2 + if(phantomId == 'Thorax') + n = 512; + else + n = 128; + end +end + +switch phantomId + case 'SheppLogan' + A = spectralSheppLogan(n); + T = readmatrix('AllOtherPhantoms_MatrixTXray100chan_42_MinEn5_MaxEn35_mat_CORRECTED.csv'); + F = T(0+(1:size(A,2)),:); + q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); + + case 'Disks' + k = 8; + A = spectralPhantomCircles(n,k); + T = readmatrix('AllOtherPhantoms_MatrixTXray100chan_42_MinEn5_MaxEn35_mat_CORRECTED.csv'); + F = T(10+(1:size(A,2)),:); + q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); + + case 'Thorax' + A0 = spectralThoraxPhantom(); + A = [A0(:,1)+A0(:,2) A0(:,3)+A0(:,4) A0(:,5)+A0(:,7) A0(:,6) A0(:,8)]; + T = readmatrix('Thorax_MatrixTXray100chan_60mat_MinEn20_MaxEn80.csv'); + F = readmatrix('Thorax_MatrixFXray100chan_6matBoneBloodIodineSofttissueBloodLungsIodine_MinEn20_MaxEn80.csv'); + F = F(1:5,:); %remove the pure iodine from the dictionary + q = readmatrix('VectorIXrayMatWEn100Min20Max80.csv'); + + case 'MixedDisk' + k = 5; + A = spectralPhantomCirclesMixed(n, k); + T = readmatrix('AllOtherPhantoms_MatrixTXray100chan_42_MinEn5_MaxEn35_mat_CORRECTED.csv'); + F = T(10+(1:size(A,2)),:); + q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); + + case 'SheppLogan3D' + A = spectralSheppLogan3D(n); + T = readmatrix('AllOtherPhantoms_MatrixTXray100chan_42_MinEn5_MaxEn35_mat_CORRECTED.csv'); + F = T(20+(1:size(A,2)),:); + q = readmatrix('VectorIXrayMatMoEn100Min5Max35.csv'); + + otherwise + error('phantom can either be SheppLogan, Disks, Thorax or Mixed \n'); +end + + +end