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function [varargout] = bart(cmd, varargin)
% BART Call BART command from Matlab.
% [varargout] = BART(cmd, varargin) to run given bart command (cmd) using the
% data arrays/matrices passed as varargin.
%
% [A, B] = BART('command', X, Y) call command with inputs X Y and outputs A B
%
% To output a list of available bart commands simply run "bart". To
% output the help for a specific bart command type "bart command -h".
%
% Parameters:
% cmd: Command to run as string (including non data parameters)
% varargin: Data arrays/matrices used as input
%
% Example:
% bart traj -h
% [reco] = bart('nufft -i traj', data) call nufft with inputs data and outputs reco
%
% Authors:
% 2014-2016 Martin Uecker <uecker@med.uni-goettingen.de>
% 2018 (Edited for WSL) Soumick Chatterjee <soumick.chatterjee@ovgu.de>
% 2020 Martin Krämer <martin.kraemer@med.uni-jena.de>
% 2022 Jon Tamir <jtamir.utexas.edu>
% Check input variables
if nargin==0 || isempty(cmd)
fprintf('Usage: bart <command> <arguments...>\n\n');
cmd = '';
end
% Check bart toolbox path
[bart_path, isWSL] = get_bart_path();
if isempty(bart_path)
error('BART path not detected.');
end
% Clear the LD_LIBRARY_PATH environment variable (to work around a bug in Matlab).
% Store original library path to be restored later.
if ismac==1
libPath = getenv('DYLD_LIBRARY_PATH');
setenv('DYLD_LIBRARY_PATH', '');
else
libPath = getenv('LD_LIBRARY_PATH');
setenv('LD_LIBRARY_PATH', '');
end
% Strip string arguments that were passed as varargin
strArgsInd = cellfun(@ischar,varargin);
strArgs = varargin(strArgsInd);
dataArgs = varargin(~strArgsInd);
if (~isempty(strArgs)) % append to cmd
cmd = sprintf('%s %s', cmd, sprintf('%s ', strArgs{:}));
cmd(end) = [];
end
% Root path for temporary file
name = tempname;
% Files used for input
in = cell(1, length(dataArgs));
for iFile = 1:length(dataArgs)
in{iFile} = strcat(name, 'in', num2str(iFile));
writecfl(in{iFile}, dataArgs{iFile});
end
in_str = sprintf(' %s', in{:});
% Files used for output
out = cell(1, nargout);
for iFile = 1:nargout
out{iFile} = strcat(name, 'out', num2str(iFile));
end
out_str = sprintf(' %s', out{:});
% Run bart
if ispc % running windows?
if isWSL
% For WSL and modify paths
in_strWSL = wslPathCorrection(in_str);
out_strWSL = wslPathCorrection(out_str);
final_strWSL = ['wsl ', bart_path, '/bart ', cmd, ' ', in_strWSL, ' ', out_strWSL];
ERR = system(final_strWSL);
else
% For cygwin use bash and modify paths
ERR = system(['bash.exe --login -c ', ...
strrep(bart_path, filesep, '/'), ...
'"', '/bart ', strrep(cmd, filesep, '/'), ' ', ...
strrep(in_str, filesep, '/'), ...
' ', strrep(out_str, filesep, '/'), '"']);
end
else
ERR = system([bart_path, '/bart ', cmd, ' ', in_str, ' ', out_str]);
end
% Remove input files
for iFile = 1:length(in)
if (exist(strcat(in{iFile}, '.cfl'),'file'))
delete(strcat(in{iFile}, '.cfl'));
end
if (exist(strcat(in{iFile}, '.hdr'),'file'))
delete(strcat(in{iFile}, '.hdr'));
end
end
% Remove output files
for iFile = 1:length(out)
if ERR == 0
varargout{iFile} = readcfl(out{iFile});
end
if (exist(strcat(out{iFile}, '.cfl'),'file'))
delete(strcat(out{iFile}, '.cfl'));
end
if (exist(strcat(out{iFile}, '.hdr'),'file'))
delete(strcat(out{iFile}, '.hdr'));
end
end
% Restore Library Path to it's original value
if (~isempty(libPath))
if ismac==1
setenv('DYLD_LIBRARY_PATH', libPath);
else
setenv('LD_LIBRARY_PATH', libPath);
end
end
% Check if running BART was successful
if (ERR~=0) && (~isempty(cmd))
error('command exited with an error');
end
end
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