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uncomment remaining tests
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@likeajumprope
likeajumprope committed Dec 7, 2022
1 parent 9ee6a32 commit ed0c1f8
Showing 1 changed file with 94 additions and 94 deletions.
188 changes: 94 additions & 94 deletions PhysIO/tests/unit/readin/tapas_physio_readin_bids_test.m
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Original file line number Diff line number Diff line change
Expand Up @@ -27,100 +27,100 @@
tests = functiontests(localfunctions);
end

% % compare raw read-in PPU trace data from BIDS example to previously saved reference
% % results
% function test_readin_bids_ppu3t(testCase)
%
% % Get PhysIO public repo base folder from this file's location
% pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
%pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);
%
%
% % load SPM matlabbatch, but convert to pure script before executing
% % remove unnecessary (beyond read-in) part from job exeuction (e.g.
% % visualization, modeling)
% % ...still needs SPM at the moment for conversion
% % TODO: parse matlab-script.m file apart from last, execution line
%
% pathCurrentExample = fullfile(pathExamples, 'BIDS/PPU3T');
% pathNow = pwd;
% cd(pathCurrentExample); % for prepending absolute paths correctly
% fileExample = fullfile(pathCurrentExample, 'bids_ppu3t_spm_job.mat');
% load(fileExample, 'matlabbatch');
%
% physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
% physio.verbose.level = 0;
% physio.preproc.cardiac.initial_cpulse_select.method = 'load_from_logfile'; % faster
% physio = tapas_physio_main_create_regressors(physio);
% cd(pathNow)
%
% actPhysio = physio;
%
% % load physio from reference data
% fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
% 'physio_readin_bids_ppu3t.mat');
% load(fileReferenceData, 'physio');
% expPhysio = physio;
%
% % extract cpulse from actual and expected solution and compare
% actRaw = actPhysio.ons_secs.raw;
% expRaw = expPhysio.ons_secs.raw;
%
% verifyEqual(testCase, actRaw.t, expRaw.t, 'RelTol', 1e-6, 'Raw time vector does not match');
% verifyEqual(testCase, actRaw.c, expRaw.c, 'RelTol', 1e-6, 'Raw cardiac trace does not match');
% verifyEqual(testCase, actRaw.r, expRaw.r, 'RelTol', 1e-6, 'Raw respiratory trace does not match');
%
% end
%
%
% % compare raw read-in CPULSE data from BIDS example to previously saved reference
% % results
% function test_readin_bids_cpulse3t(testCase)
%
% % run BIDS cpulse3t example and extract physio
% pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
% pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);
%
% % load SPM matlabbatch, but convert to pure script before executing
% % remove unnecessary (beyond read-in) part from job exeuction (e.g.
% % visualization, modeling)
% % ...still needs SPM at the moment for conversion
% % TODO: parse matlab-script.m file apart from last, execution line
%
% pathCurrentExample = fullfile(pathExamples, 'BIDS/CPULSE3T');
% pathNow = pwd;
% cd(pathCurrentExample); % for prepending absolute paths correctly
% fileExample = fullfile(pathCurrentExample, 'bids_cpulse3t_spm_job.mat');
% load(fileExample, 'matlabbatch');
%
% physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
% physio.verbose.level = 0;
% % Some modeling has to be done, otherwise no raw data preprocessed
% %physio.model.retroicor.include = 0;
% physio.model.retroicor.order.cr = 0;
% physio.model.retroicor.order.r = 0;
% physio.model.hrv.include = 0;
% physio.model.rvt.include = 0;
% physio = tapas_physio_main_create_regressors(physio);
% cd(pathNow)
%
% actPhysio = physio;
%
% % load physio from reference data
% fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
% 'physio_readin_bids_cpulse3t.mat');
% load(fileReferenceData, 'physio');
% expPhysio = physio;
%
% % extract cpulse from actual and expected solution and compare
% actRaw = actPhysio.ons_secs.raw;
% expRaw = expPhysio.ons_secs.raw;
%
% verifyEqual(testCase, actRaw.t, expRaw.t, 'Raw time vector does not match');
% verifyEqual(testCase, actRaw.cpulse, expRaw.cpulse, 'Raw cardiac trace does not match');
% verifyEqual(testCase, actRaw.r, expRaw.r, 'Raw respiratory trace does not match');
%
% end
% compare raw read-in PPU trace data from BIDS example to previously saved reference
% results
function test_readin_bids_ppu3t(testCase)

% Get PhysIO public repo base folder from this file's location
pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);


% load SPM matlabbatch, but convert to pure script before executing
% remove unnecessary (beyond read-in) part from job exeuction (e.g.
% visualization, modeling)
% ...still needs SPM at the moment for conversion
% TODO: parse matlab-script.m file apart from last, execution line

pathCurrentExample = fullfile(pathExamples, 'BIDS/PPU3T');
pathNow = pwd;
cd(pathCurrentExample); % for prepending absolute paths correctly
fileExample = fullfile(pathCurrentExample, 'bids_ppu3t_spm_job.mat');
load(fileExample, 'matlabbatch');

physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
physio.verbose.level = 0;
physio.preproc.cardiac.initial_cpulse_select.method = 'load_from_logfile'; % faster
physio = tapas_physio_main_create_regressors(physio);
cd(pathNow)

actPhysio = physio;

% load physio from reference data
fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
'physio_readin_bids_ppu3t.mat');
load(fileReferenceData, 'physio');
expPhysio = physio;

% extract cpulse from actual and expected solution and compare
actRaw = actPhysio.ons_secs.raw;
expRaw = expPhysio.ons_secs.raw;

verifyEqual(testCase, actRaw.t, expRaw.t, 'RelTol', 1e-6, 'Raw time vector does not match');
verifyEqual(testCase, actRaw.c, expRaw.c, 'RelTol', 1e-6, 'Raw cardiac trace does not match');
verifyEqual(testCase, actRaw.r, expRaw.r, 'RelTol', 1e-6, 'Raw respiratory trace does not match');

end


% compare raw read-in CPULSE data from BIDS example to previously saved reference
% results
function test_readin_bids_cpulse3t(testCase)

% run BIDS cpulse3t example and extract physio
pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);

% load SPM matlabbatch, but convert to pure script before executing
% remove unnecessary (beyond read-in) part from job exeuction (e.g.
% visualization, modeling)
% ...still needs SPM at the moment for conversion
% TODO: parse matlab-script.m file apart from last, execution line

pathCurrentExample = fullfile(pathExamples, 'BIDS/CPULSE3T');
pathNow = pwd;
cd(pathCurrentExample); % for prepending absolute paths correctly
fileExample = fullfile(pathCurrentExample, 'bids_cpulse3t_spm_job.mat');
load(fileExample, 'matlabbatch');

physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
physio.verbose.level = 0;
% Some modeling has to be done, otherwise no raw data preprocessed
%physio.model.retroicor.include = 0;
physio.model.retroicor.order.cr = 0;
physio.model.retroicor.order.r = 0;
physio.model.hrv.include = 0;
physio.model.rvt.include = 0;
physio = tapas_physio_main_create_regressors(physio);
cd(pathNow)

actPhysio = physio;

% load physio from reference data
fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
'physio_readin_bids_cpulse3t.mat');
load(fileReferenceData, 'physio');
expPhysio = physio;

% extract cpulse from actual and expected solution and compare
actRaw = actPhysio.ons_secs.raw;
expRaw = expPhysio.ons_secs.raw;

verifyEqual(testCase, actRaw.t, expRaw.t, 'Raw time vector does not match');
verifyEqual(testCase, actRaw.cpulse, expRaw.cpulse, 'Raw cardiac trace does not match');
verifyEqual(testCase, actRaw.r, expRaw.r, 'Raw respiratory trace does not match');

end

% compare newly written bids output file from the Phillips ECG V3 test case to
% saved files
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