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likeajumpropelikeajumprope
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uncomment remaining tests
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‎PhysIO/tests/unit/readin/tapas_physio_readin_bids_test.m‎

Lines changed: 94 additions & 94 deletions
Original file line numberDiff line numberDiff line change
@@ -27,100 +27,100 @@
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tests = functiontests(localfunctions);
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end
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% % compare raw read-in PPU trace data from BIDS example to previously saved reference
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% % results
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% function test_readin_bids_ppu3t(testCase)
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%
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% % Get PhysIO public repo base folder from this file's location
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% pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
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%pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);
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%
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%
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% % load SPM matlabbatch, but convert to pure script before executing
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% % remove unnecessary (beyond read-in) part from job exeuction (e.g.
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% % visualization, modeling)
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% % ...still needs SPM at the moment for conversion
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% % TODO: parse matlab-script.m file apart from last, execution line
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%
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% pathCurrentExample = fullfile(pathExamples, 'BIDS/PPU3T');
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% pathNow = pwd;
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% cd(pathCurrentExample); % for prepending absolute paths correctly
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% fileExample = fullfile(pathCurrentExample, 'bids_ppu3t_spm_job.mat');
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% load(fileExample, 'matlabbatch');
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%
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% physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
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% physio.verbose.level = 0;
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% physio.preproc.cardiac.initial_cpulse_select.method = 'load_from_logfile'; % faster
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% physio = tapas_physio_main_create_regressors(physio);
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% cd(pathNow)
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%
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% actPhysio = physio;
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%
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% % load physio from reference data
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% fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
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% 'physio_readin_bids_ppu3t.mat');
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% load(fileReferenceData, 'physio');
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% expPhysio = physio;
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%
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% % extract cpulse from actual and expected solution and compare
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% actRaw = actPhysio.ons_secs.raw;
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% expRaw = expPhysio.ons_secs.raw;
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%
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% verifyEqual(testCase, actRaw.t, expRaw.t, 'RelTol', 1e-6, 'Raw time vector does not match');
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% verifyEqual(testCase, actRaw.c, expRaw.c, 'RelTol', 1e-6, 'Raw cardiac trace does not match');
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% verifyEqual(testCase, actRaw.r, expRaw.r, 'RelTol', 1e-6, 'Raw respiratory trace does not match');
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%
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% end
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%
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%
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% % compare raw read-in CPULSE data from BIDS example to previously saved reference
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% % results
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% function test_readin_bids_cpulse3t(testCase)
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%
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% % run BIDS cpulse3t example and extract physio
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% pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
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% pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);
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%
84-
% % load SPM matlabbatch, but convert to pure script before executing
85-
% % remove unnecessary (beyond read-in) part from job exeuction (e.g.
86-
% % visualization, modeling)
87-
% % ...still needs SPM at the moment for conversion
88-
% % TODO: parse matlab-script.m file apart from last, execution line
89-
%
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% pathCurrentExample = fullfile(pathExamples, 'BIDS/CPULSE3T');
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% pathNow = pwd;
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% cd(pathCurrentExample); % for prepending absolute paths correctly
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% fileExample = fullfile(pathCurrentExample, 'bids_cpulse3t_spm_job.mat');
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% load(fileExample, 'matlabbatch');
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%
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% physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
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% physio.verbose.level = 0;
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% % Some modeling has to be done, otherwise no raw data preprocessed
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% %physio.model.retroicor.include = 0;
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% physio.model.retroicor.order.cr = 0;
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% physio.model.retroicor.order.r = 0;
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% physio.model.hrv.include = 0;
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% physio.model.rvt.include = 0;
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% physio = tapas_physio_main_create_regressors(physio);
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% cd(pathNow)
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%
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% actPhysio = physio;
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%
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% % load physio from reference data
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% fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
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% 'physio_readin_bids_cpulse3t.mat');
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% load(fileReferenceData, 'physio');
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% expPhysio = physio;
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%
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% % extract cpulse from actual and expected solution and compare
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% actRaw = actPhysio.ons_secs.raw;
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% expRaw = expPhysio.ons_secs.raw;
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%
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% verifyEqual(testCase, actRaw.t, expRaw.t, 'Raw time vector does not match');
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% verifyEqual(testCase, actRaw.cpulse, expRaw.cpulse, 'Raw cardiac trace does not match');
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% verifyEqual(testCase, actRaw.r, expRaw.r, 'Raw respiratory trace does not match');
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%
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% end
30+
% compare raw read-in PPU trace data from BIDS example to previously saved reference
31+
% results
32+
function test_readin_bids_ppu3t(testCase)
33+
34+
% Get PhysIO public repo base folder from this file's location
35+
pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
36+
pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);
37+
38+
39+
% load SPM matlabbatch, but convert to pure script before executing
40+
% remove unnecessary (beyond read-in) part from job exeuction (e.g.
41+
% visualization, modeling)
42+
% ...still needs SPM at the moment for conversion
43+
% TODO: parse matlab-script.m file apart from last, execution line
44+
45+
pathCurrentExample = fullfile(pathExamples, 'BIDS/PPU3T');
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pathNow = pwd;
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cd(pathCurrentExample); % for prepending absolute paths correctly
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fileExample = fullfile(pathCurrentExample, 'bids_ppu3t_spm_job.mat');
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load(fileExample, 'matlabbatch');
50+
51+
physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
52+
physio.verbose.level = 0;
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physio.preproc.cardiac.initial_cpulse_select.method = 'load_from_logfile'; % faster
54+
physio = tapas_physio_main_create_regressors(physio);
55+
cd(pathNow)
56+
57+
actPhysio = physio;
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% load physio from reference data
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fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
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'physio_readin_bids_ppu3t.mat');
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load(fileReferenceData, 'physio');
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expPhysio = physio;
64+
65+
% extract cpulse from actual and expected solution and compare
66+
actRaw = actPhysio.ons_secs.raw;
67+
expRaw = expPhysio.ons_secs.raw;
68+
69+
verifyEqual(testCase, actRaw.t, expRaw.t, 'RelTol', 1e-6, 'Raw time vector does not match');
70+
verifyEqual(testCase, actRaw.c, expRaw.c, 'RelTol', 1e-6, 'Raw cardiac trace does not match');
71+
verifyEqual(testCase, actRaw.r, expRaw.r, 'RelTol', 1e-6, 'Raw respiratory trace does not match');
72+
73+
end
74+
75+
76+
% compare raw read-in CPULSE data from BIDS example to previously saved reference
77+
% results
78+
function test_readin_bids_cpulse3t(testCase)
79+
80+
% run BIDS cpulse3t example and extract physio
81+
pathPhysioPublic = fullfile(fileparts(mfilename('fullpath')), '..', '..', '..');
82+
pathExamples = tapas_physio_get_path_examples(pathPhysioPublic);
83+
84+
% load SPM matlabbatch, but convert to pure script before executing
85+
% remove unnecessary (beyond read-in) part from job exeuction (e.g.
86+
% visualization, modeling)
87+
% ...still needs SPM at the moment for conversion
88+
% TODO: parse matlab-script.m file apart from last, execution line
89+
90+
pathCurrentExample = fullfile(pathExamples, 'BIDS/CPULSE3T');
91+
pathNow = pwd;
92+
cd(pathCurrentExample); % for prepending absolute paths correctly
93+
fileExample = fullfile(pathCurrentExample, 'bids_cpulse3t_spm_job.mat');
94+
load(fileExample, 'matlabbatch');
95+
96+
physio = tapas_physio_job2physio(matlabbatch{1}.spm.tools.physio);
97+
physio.verbose.level = 0;
98+
% Some modeling has to be done, otherwise no raw data preprocessed
99+
%physio.model.retroicor.include = 0;
100+
physio.model.retroicor.order.cr = 0;
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physio.model.retroicor.order.r = 0;
102+
physio.model.hrv.include = 0;
103+
physio.model.rvt.include = 0;
104+
physio = tapas_physio_main_create_regressors(physio);
105+
cd(pathNow)
106+
107+
actPhysio = physio;
108+
109+
% load physio from reference data
110+
fileReferenceData = fullfile(pathExamples, 'TestReferenceResults', 'readin', ...
111+
'physio_readin_bids_cpulse3t.mat');
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load(fileReferenceData, 'physio');
113+
expPhysio = physio;
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115+
% extract cpulse from actual and expected solution and compare
116+
actRaw = actPhysio.ons_secs.raw;
117+
expRaw = expPhysio.ons_secs.raw;
118+
119+
verifyEqual(testCase, actRaw.t, expRaw.t, 'Raw time vector does not match');
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verifyEqual(testCase, actRaw.cpulse, expRaw.cpulse, 'Raw cardiac trace does not match');
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verifyEqual(testCase, actRaw.r, expRaw.r, 'Raw respiratory trace does not match');
122+
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end
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% compare newly written bids output file from the Phillips ECG V3 test case to
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% saved files

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