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Diffusion Motion correction paper (workstation) Browse

R6289/test.m
3b07d0e78f1eworkstation

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test.m
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close all;
clear all;
warn = warning ('off','all');
poolobj = gcp('nocreate');
if isempty(poolobj)
parpool;
end
pctRunOnAll warning('off','all')
%% set path
%fnIJ='/Applications/MATLAB_R2016a.app/java/jar/ij.jar'; % Path to "ij.jar"
%fnMIJ='/Applications/MATLAB_R2016a.app/java/jar/mij.jar'; % Path to "mij.jar"
%javaaddpath(fnIJ);
%javaaddpath(fnMIJ);
addpath('code');
addpath('code/external/utils');
addpath(genpath('code/external/InvPbLib'));
%% Parameters
param = default_parameters();
param.lambda = 1000; % Regularization parameter
param.gamma = 100; % Sets the strength of the feature matching constraint
%% Input - Output
type=0; % 0 for Mac users, 1 for Linux users
fnMatch='data/1_Horizontal_VNC/tdTom.tif'; % Sequence used for the feature matching similarity term
fnIn1='data/1_Horizontal_VNC/GC6s.tif'; % Sequence used for the brightness constancy term
fnIn2='data/1_Horizontal_VNC/tdTom.tif'; % Sequence warped with the motion field estimated from fnIn1 and fnMatch
N=10; % Motion is estimated on frames 1 to N. If N=-1, motion is estimated on
% the whole sequence
fnSave='results/test/'; % Folder where the results are saved
mkdir(fnSave);
fnOut1=[fnSave,'warped1.tif']; % Sequence fnIn1 warped
fnOut2=[fnSave,'warped2.tif']; % Sequence fnIn2 warped
fnColor=[fnSave,'colorFlow.tif']; % Color visualization of the motion field
if type==0
fnDeepMatching='code/external/deepmatching_1.2.2_c++_mac';
elseif type==1
fnDeepMatching='code/external/deepmatching_1.2.2_c++_linux';
end
addpath(fnDeepMatching);
%% Perform motion compensation
motion_compensate(fnIn1,fnIn2,fnMatch,fnDeepMatching,fnOut1,fnOut2,fnColor,N,param);
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