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sepiaIO.m
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sepiaIO.m
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%% sepiaIO(input,output,maskFullName,algorParam)
%
% Input
% --------------
% input : input directory contains NIfTI files or structure containing filenames
% output : output directory that stores the output
% maskFullName : mask filename
% algorParam : structure contains method and method specific parameters
%
% Description: This is a I/O level wrapper to coordinate SEPIA processing
% pipeline based on input algorithm parameter (sub)structure
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 29 June 2020 (v0.8.0)
% Date modified: 27 Jan 2021 (v0.8.1)
%
%
function sepiaIO(input,output,maskFullName,algorParam)
%%% Step 1 %%%
currDir = pwd;
% 1.1: get and create output directory
output_index = strfind(output, filesep);
outputDir = output(1:output_index(end));
% if the output directory does not exist then create the directory
if exist(outputDir,'dir') ~= 7
mkdir(outputDir);
end
% move to output directory
cd(outputDir)
% 1.2 log command window display to a text file
% use current time as unique identifier
identifier = datestr(datetime('now'),'yymmddHHMMSSFFF');
logFilename = fullfile(outputDir, ['run_sepia.log' identifier]);
while exist(logFilename,'file') == 2
% update current time as unique identifier
identifier = datestr(datetime('now'),'yymmddHHMMSSFFF');
logFilename = fullfile(outputDir, ['run_sepia.log' identifier]);
end
diary(logFilename)
% check if any sepia config file exists in the output directory, if not
% then create one
check_and_create_sepia_config(input,output,maskFullName,algorParam,identifier);
% display the parent script
fn = dbstack('-completenames');
if length(fn) >=2
fprintf('Running script: %s\n',fn(2).file);
end
%%% Step 2 %%%
try
% check if the input algorithm parameters contain any specific tasks
isUnwrapParam = isfield(algorParam,'unwrap');
isBRFParam = isfield(algorParam,'bfr');
isQSMParam = isfield(algorParam,'qsm');
isR2sParam = isfield(algorParam,'r2s');
% input algorithm parameters must have at least one specific task
isValid = or(or(or(isUnwrapParam,isBRFParam),isQSMParam),isR2sParam);
if ~isValid
error(['Input ''algorParam'' contains no parameter for any tasks in SEPIA.',...
'Please check your pipeline configuration file.']);
end
% One-stop processing contains all task parameter
isOneStop = and(and(isUnwrapParam,isBRFParam),isQSMParam);
%%% Step 3 %%%
% determine which pipeline the data will go
if isOneStop
% if algorParam contains all three task, then execute one-stop
% processing pipeline
disp('Running one-stop processing pipeline...');
SepiaIOWrapper(input,output,maskFullName,algorParam);
else
if and(isUnwrapParam,isBRFParam) || and(isUnwrapParam,isQSMParam) || and(isBRFParam,isQSMParam)
% pipeline with 2 tasks is not allowed. Either 3 tasks or 1 task is
% allowed
error(['Input ''algorParam'' contains parameters for two tasks.',...
'It can only contain parameters for either all three tasks (One-stop processing) or a single task.',...
'Please check your pipeline configuration file.']);
else
% single task application pipeline
if isUnwrapParam
disp('Running total field recovery and phase unwrapping processing pipeline...');
UnwrapPhaseMacroIOWrapper(input,output,maskFullName,algorParam);
elseif isBRFParam
disp('Running background field removal processing pipeline...');
BackgroundRemovalMacroIOWrapper(input,output,maskFullName,algorParam);
elseif isQSMParam
disp('Running QSM dipole inversion processing pipeline...');
QSMMacroIOWrapper(input,output,maskFullName,algorParam);
elseif isR2sParam
disp('Running R2* mapping processing pipeline...');
R2sIOWrapper(input,output,maskFullName,algorParam);
end
end
end
% turn off the log
diary off
% move back to original directory
cd(currDir)
catch ME
% close log file
disp('There was an error! Please check the command window/error message file for more information.');
diary off
% move back to original directory
cd(currDir)
% open a new text file for error message
errorMessageFilename = fullfile(outputDir, ['run_sepia.error' identifier]);
fid = fopen(errorMessageFilename,'w');
fprintf(fid,'The identifier was:\n%s\n\n',ME.identifier);
fprintf(fid,'The message was:\n\n');
msgString = getReport(ME,'extended','hyperlinks','off');
fprintf(fid,'%s',msgString);
fclose(fid);
% rethrow the error message to command window
rethrow(ME);
end
%%
function check_and_create_sepia_config(input,output,maskFullName,algorParam,identifier)
sepia_universal_variables;
isConfigFileExist = false;
%%%%%%%%%%%% Step 1: Check if config file exists in the output dir %%%%%%%%%%%%
output_index = strfind(output, filesep);
outputDir = output(1:output_index(end));
% create a new m file
configFileList = dir(fullfile(outputDir,'*sepia_config*.m*'));
if ~isempty(configFileList)
isConfigFileExist = true;
disp('SEPIA configuration file already exists in the output directory.')
else
configFilename = fullfile(outputDir, ['sepia_config' identifier '.m']);
end
%%%%%%%%%%%% Step 2: Write config file %%%%%%%%%%%%
if ~isConfigFileExist
fid = fopen(configFilename,'w');
% specify config file version
fprintf(fid,'%% This file is generated by SEPIA version: %s\n',SEPIA_version);
% general path
fprintf(fid,'%% add general Path\n');
fprintf(fid,'sepia_addpath\n\n');
fprintf(fid,'%% Input/Output filenames\n');
% 2.1: input data
if isstruct(input)
fprintf(fid,'input(1).name = ''%s'' ;\n',input(1).name);
fprintf(fid,'input(2).name = ''%s'' ;\n',input(2).name);
fprintf(fid,'input(3).name = ''%s'' ;\n',input(3).name);
fprintf(fid,'input(4).name = ''%s'' ;\n',input(4).name);
else
fprintf(fid,'input = ''%s'' ;\n',input);
end
% 2.2: output
fprintf(fid,'output_basename = ''%s'' ;\n',output);
% 2.3: mask
fprintf(fid,'mask_filename = [''%s''] ;\n\n',maskFullName);
% 2.4: algorithm parameters
task_field = fieldnames(algorParam);
fprintf(fid,'algorParam=struct();\n');
% loop all the tasks
for k = 1:length(task_field)
% task separator
switch task_field{k}
case 'general'
fprintf(fid,'%% General algorithm parameters\n');
case 'unwrap'
fprintf(fid,'%% Total field recovery algorithm parameters\n');
case 'bfr'
fprintf(fid,'%% Background field removal algorithm parameters\n');
case 'qsm'
fprintf(fid,'%% QSM algorithm parameters\n');
end
curr_task_field = algorParam.(task_field{k});
method_field = fieldnames(curr_task_field);
% loop all method parameters
for kk = 1:length(method_field)
curr_method_value = curr_task_field.(method_field{kk});
if ischar(curr_method_value)
curr_method_value = sprintf('''%s''',curr_method_value);
elseif ~isscalar(curr_method_value)
curr_method_value = sprintf('[%s]',num2str(curr_method_value));
elseif isnumeric(curr_method_value)
curr_method_value = num2str(curr_method_value);
end
% export to config file
fprintf(fid,'%s.%s.%s = %s;\n','algorParam',task_field{k},method_field{kk},curr_method_value);
end
end
fprintf(fid,'\nsepiaIO(input,output_basename,mask_filename,algorParam);\n');
disp('No SEPIA configuration file exists in the output directory. The file is now generated.')
end