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Diffusion Motion correction paper (cluster_pipeline) Browse

R6289/test.m
3e35ee179701cluster_pipeline

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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='/home/aymanns/registration/ij.jar'; % Path to "ij.jar"
fnMIJ='/home/aymanns/registration/mij.jar'; % Path to "mij.jar"
javaaddpath(fnIJ);
javaaddpath(fnMIJ);
addpath('code');
addpath('code/external/utils');
addpath(genpath('code/external/InvPbLib'));
%% load file names
fname = 'files.json';
fid = fopen(fname);
raw = fread(fid,inf);
str = char(raw');
fclose(fid);
files = parse_json(str);
%% Parameters
param = default_parameters();
param.lambda = 1000; % Regularization parameter
param.gamma = 100; % Sets the strength of the feature matching constraint
%% Input - Output
type=1; % 0 for Mac users, 1 for Linux users
fnMatch=files.tdTom_input;%'/home/aymanns/data/1_Horizontal_VNC/tdTom.tif'; % Sequence used for the feature matching similarity term
fnIn1=files.GC6s_input; % Sequence used for the brightness constancy term
fnIn2=files.tdTom_input; % Sequence warped with the motion field estimated from fnIn1 and fnMatch
N=3; % Motion is estimated on frames 1 to N. If N=-1, motion is estimated on
% the whole sequence
fnOut1=files.GC6s_registered; % Sequence fnIn1 warped
fnOut2=files.tdTom_registered; % Sequence fnIn2 warped
fnColor=files.color_flow_out; % Color visualization of the motion field
fnVector=files.vectors_out;
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,fnVector,N,param);
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