mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 23:59:11 +09:00
169 lines
7.4 KiB
Matlab
169 lines
7.4 KiB
Matlab
% TESTING SCRIPT for ASTRA wrappers
|
||
% This script will run some basic features in the ASTRA wrapper code
|
||
% ie reconstruciton , splitting on GPU, splitting between multiple workers
|
||
% compare results with expected values to detect inconsistencies
|
||
% recompile commands
|
||
% (Linux, GCC 4.8.5) mexcuda -outdir private ASTRA_GPU_wrapper/ASTRA_GPU_wrapper.cu ASTRA_GPU_wrapper/util3d.cu ASTRA_GPU_wrapper/par3d_fp.cu ASTRA_GPU_wrapper/par3d_bp.cu
|
||
% (Windows) mexcuda -outdir private ASTRA_GPU_wrapper\ASTRA_GPU_wrapper.cu ASTRA_GPU_wrapper\util3d.cu ASTRA_GPU_wrapper\par3d_fp.cu ASTRA_GPU_wrapper\par3d_bp.cu
|
||
|
||
cd(fullfile( fileparts(mfilename('fullpath')), '..'))
|
||
addpath('tests')
|
||
addpath('utils')
|
||
addpath('./')
|
||
addpath(find_base_package)
|
||
utils.verbose(0)
|
||
|
||
utils.verbose(0,'Creating data for ASTRA wrapper tests')
|
||
if ~exist('GPU_id', 'var'); GPU_id = [1]; end
|
||
gpuDevice(GPU_id);
|
||
|
||
% volume settings
|
||
Npix_vol = [300, 300, 200] ;
|
||
Nangles = 400;
|
||
Npix_proj = [400, 400];
|
||
|
||
% create "data"
|
||
angles = linspace(0, 180, Nangles);
|
||
lamino_angle = 60; % 90 deg is normal tomo
|
||
tilt_angle = 10; % rotation in plane of the projection
|
||
CoR_offset = [20,10]; % offset of the center of rotation
|
||
pixel_scale = [1,1] ; % relative scale of the pixels
|
||
volData = ones(Npix_vol, 'single');
|
||
|
||
% generate geometry
|
||
[cfg, vectors] = astra.ASTRA_initialize(Npix_vol, Npix_proj, angles, lamino_angle, tilt_angle, pixel_scale,Npix_proj/2+CoR_offset);
|
||
% find optimal split, for small volumes below 600^3 no split is needed
|
||
split = astra.ASTRA_find_optimal_split(cfg);
|
||
|
||
% generate projections
|
||
projData = astra.Ax_partial(volData, cfg, vectors, split);
|
||
|
||
% plot the projections
|
||
figure
|
||
plotting.imagesc3D(projData, 'init_frame', 50); axis off image; colormap bone
|
||
title('Volume projection')
|
||
drawnow
|
||
|
||
% do backprojection projections !!! not FBP !!!
|
||
backprojData = astra.Atx_partial(projData, cfg, vectors, split);
|
||
|
||
utils.verbose(0,'Simple ASTRA wrapper tested')
|
||
%% =============== tests simple "on GPU" splitting ============
|
||
split = [2,2,2,2];
|
||
|
||
% generate projections
|
||
projData_split = astra.Ax_partial(volData, cfg, vectors, split);
|
||
|
||
err = norm(projData(:) - projData_split(:)) / norm(projData(:));
|
||
% plotting.imagesc3D(projData - projData_split); colorbar; axis off image; colormap bone
|
||
assert(err < 1e-5, "Splitted projections solver is not fully consistent with the unsplitted one")
|
||
|
||
|
||
% do backprojection projections !!! not FBP !!!
|
||
backprojData_split = astra.Atx_partial(projData, cfg, vectors, split);
|
||
err = norm(backprojData(:) - backprojData_split(:)) / norm(backprojData(:));
|
||
assert(err < 1e-6, "Splitted backprojections solver is not fully consistent with the unsplitted one")
|
||
|
||
|
||
utils.verbose(0,'On GPU splitting tested')
|
||
%% =============== tests additional splitting for tomography ============
|
||
|
||
split = [2,2,2,1];
|
||
projData_split = tomo.Ax_sup_partial(volData, cfg, vectors, split);
|
||
err = norm(projData(:) - projData_split(:)) / norm(projData(:));
|
||
if err > 1e-5
|
||
figure
|
||
plotting.imagesc3D(projData - projData_split); colorbar; axis off image; colormap bone
|
||
title('Projection data difference')
|
||
drawnow
|
||
end
|
||
if err > 1e-3
|
||
error("Sup-splitted projections solver is not fully consistent with the unsplitted one")
|
||
elseif err > 1e-5
|
||
warning("Sup-splitted projections solver is not fully consistent with the unsplitted one, most likely only subpixel errors are present")
|
||
end
|
||
|
||
|
||
|
||
backprojData_split = tomo.Atx_sup_partial(projData, cfg, vectors, split);
|
||
err = norm(backprojData(:) - backprojData_split(:)) / norm(backprojData(:));
|
||
if err > 1e-5
|
||
figure
|
||
plotting.imagesc_tomo(backprojData - backprojData_split); colorbar; axis off image; colormap bone
|
||
title('Backprojection data difference')
|
||
drawnow
|
||
end
|
||
if err > 1e-3
|
||
error("Sup-splitted backprojections solver is not fully consistent with the unsplitted one")
|
||
elseif err > 1e-5
|
||
warning("Sup-splitted backprojections solver is not fully consistent with the unsplitted one, most likely only subpixel errors are present")
|
||
end
|
||
|
||
utils.verbose(0,'Extra splitting tested')
|
||
|
||
%% =============== tests multiGPU solvers ============
|
||
|
||
utils.verbose(0,'Testing multiGPU solver')
|
||
|
||
c = parcluster('local');
|
||
if exist('local_cluster_jobs', 'dir')
|
||
rmdir('local_cluster_jobs', 's') % delete folder with jobs (prevent accumulation )
|
||
end
|
||
mkdir('local_cluster_jobs') % recreate the folder
|
||
c.JobStorageLocation = ['local_cluster_jobs'];
|
||
|
||
|
||
GPU = [1:gpuDeviceCount];
|
||
split = [2,2,2,2];
|
||
projData_split = tomo.Ax_sup_partial(volData, cfg, vectors, split, 'GPU', GPU);
|
||
err = norm(projData(:) - projData_split(:)) / norm(projData(:));
|
||
% plotting.imagesc3D(projData - projData_split); colorbar; axis off image; colormap bone
|
||
assert(err < 1e-5, "Sup-splitted projections solver is not fully consistent with the unsplitted one")
|
||
|
||
|
||
backprojData_split = tomo.Atx_sup_partial(projData, cfg, vectors, split, 'GPU', GPU);
|
||
err = norm(backprojData(:) - backprojData_split(:)) / norm(backprojData(:));
|
||
assert(err < 1e-6, "Sup-splitted backprojections solver is not fully consistent with the unsplitted one")
|
||
|
||
utils.verbose(0,'Multi GPU solver tested')
|
||
rmdir('local_cluster_jobs', 's') % delete folder with jobs (prevent accumulation )
|
||
|
||
utils.verbose(0,'==== All ASTRA wrapper tests passed ===== ')
|
||
|
||
%*-----------------------------------------------------------------------*
|
||
%| |
|
||
%| Except where otherwise noted, this work is licensed under a |
|
||
%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
|
||
%| International (CC BY-NC-SA 4.0) license. |
|
||
%| |
|
||
%| Copyright (c) 2018 by Paul Scherrer Institute (http://www.psi.ch) |
|
||
%| |
|
||
%| Author: CXS group, PSI |
|
||
%*-----------------------------------------------------------------------*
|
||
% You may use this code with the following provisions:
|
||
%
|
||
% If the code is fully or partially redistributed, or rewritten in another
|
||
% computing language this notice should be included in the redistribution.
|
||
%
|
||
% If this code, or subfunctions or parts of it, is used for research in a
|
||
% publication or if it is fully or partially rewritten for another
|
||
% computing language the authors and institution should be acknowledged
|
||
% in written form in the publication: “Data processing was carried out
|
||
% using the “cSAXS matlab package” developed by the CXS group,
|
||
% Paul Scherrer Institut, Switzerland.”
|
||
% Variations on the latter text can be incorporated upon discussion with
|
||
% the CXS group if needed to more specifically reflect the use of the package
|
||
% for the published work.
|
||
%
|
||
% A publication that focuses on describing features, or parameters, that
|
||
% are already existing in the code should be first discussed with the
|
||
% authors.
|
||
%
|
||
% This code and subroutines are part of a continuous development, they
|
||
% are provided “as they are” without guarantees or liability on part
|
||
% of PSI or the authors. It is the user responsibility to ensure its
|
||
% proper use and the correctness of the results.
|
||
|
||
|
||
|