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Improve pmod handling in pspm_glm #700

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merged 4 commits into from
Jun 3, 2024
Merged

Improve pmod handling in pspm_glm #700

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c7a762a
improve pmod handling in GLM
Apr 26, 2024
ff0715d
fix tests
Apr 27, 2024
30ebf89
Merge branch 'develop' into glm-pmod
dominikbach May 28, 2024
d312ba3
Merge branch 'develop' into glm-pmod
dominikbach Jun 3, 2024
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75 changes: 56 additions & 19 deletions src/pspm_get_timing.m
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Original file line number Diff line number Diff line change
Expand Up @@ -294,27 +294,64 @@
end
end
% ensure same names exist for all sessions and re-sort if
% necesssary
% necesssary; collect number and names of all pmods
outtiming = struct('names', {}, 'onsets', {}, 'durations', {});
for iFile = 1:nFiles
for iCond = 1:numel(allnames)
name_idx = find(strcmpi(temptiming(iFile).names, allnames{iCond}));
if numel(name_idx) > 1
warning('Names must be unique within each session.');
return;
elseif numel(name_idx) == 1
outtiming(iFile).onsets{iCond} = temptiming(iFile).onsets{name_idx};
outtiming(iFile).durations{iCond} = temptiming(iFile).durations{name_idx};
if isfield(temptiming, 'pmod') && numel(temptiming(iFile).pmod) >= name_idx
outtiming(iFile).pmod(iCond) = temptiming(iFile).pmod(name_idx);
end
elseif numel(name_idx) == 0
outtiming(iFile).onsets{iCond} = [];
outtiming(iFile).durations{iCond} = [];
end
outtiming(iFile).names{iCond} = allnames{iCond};
end
pmodname = {};
try
for iFile = 1:nFiles
for iCond = 1:numel(allnames)
name_idx = find(strcmpi(temptiming(iFile).names, allnames{iCond}));
if numel(name_idx) > 1
warning('Names must be unique within each session.');
return;
elseif numel(name_idx) == 1
outtiming(iFile).onsets{iCond} = temptiming(iFile).onsets{name_idx};
outtiming(iFile).durations{iCond} = temptiming(iFile).durations{name_idx};
% assign pmods
if isfield(temptiming, 'pmod') && ...
~isempty(temptiming(iFile).pmod) && ...
numel(temptiming(iFile).pmod) >= name_idx
outtiming(iFile).pmod(iCond) = temptiming(iFile).pmod(name_idx);
% store pmod number and name for later use
pmodno(iFile, iCond) = numel(temptiming(iFile).pmod(name_idx).param);
% get pmodname from first session
if isempty(pmodname) || ...
numel(pmodname) < iCond || ...
isempty(pmodname{iCond})
pmodname{iCond} = temptiming(iFile).pmod(name_idx).name;
end
else
pmodno(iFile, iCond) = 0;
end
elseif numel(name_idx) == 0
outtiming(iFile).onsets{iCond} = [];
outtiming(iFile).durations{iCond} = [];
pmodno(iFile, iCond) = 0;
end
outtiming(iFile).names{iCond} = allnames{iCond};
end
end
if nFiles > 1
pmodno = max(pmodno);
end
% initialise pmods
for iFile = 1:nFiles
for iCond = 1:numel(allnames)
% insert pmods if they exist in other sessions
if pmodno(iCond) > 0 && ...
(numel(outtiming(iFile).pmod) < iCond || ...
isempty(outtiming(iFile).pmod(iCond).param))
for i_pmod = 1:pmodno(iCond)
outtiming(iFile).pmod(iCond).param{i_pmod} = [];
outtiming(iFile).pmod(iCond).name{i_pmod} = pmodname{iCond}{i_pmod};
end
end
end
end
catch
keyboard
end

% clear local variables
clear iParam iParamNew iCond iFile iPmod
else
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9 changes: 8 additions & 1 deletion test/pspm_get_timing_test.m
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Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,8 @@ function case_onsets(this)
this.verifyEqual(outtiming.names(:), names(:));
this.verifyTrue(isfield(outtiming, 'durations'));
% test 4
% this checks github issue 191: a pmod is defined on a condition
% that is not present in the first session
names = {'name1', 'name2'};
onsets = {[1 2 3], [3 4 5]};
durations = {[3 4 5]', [5 6 7]'};
Expand All @@ -139,7 +141,12 @@ function case_onsets(this)
this.verifyEqual(outtiming(1).names, {'name1', 'name2', 'name5'});
this.verifyTrue(isfield(outtiming(1), 'durations'));
this.verifyEqual(outtiming(1).durations, [durations, {[]}]);
this.verifyEqual(outtiming(1).pmod.param, {[2 3 4], [4 9 16], [4 5 6]});
this.verifyEqual(outtiming(1).pmod(1).param, {[2 3 4], [4 9 16], [4 5 6]});
this.verifyEqual(outtiming(1).pmod(2).param, []);
this.verifyEqual(outtiming(1).pmod(3).param, {[], [], []});
this.verifyEqual(outtiming(1).pmod(1).name, {'name3^1' 'name3^2' 'name4^1'});
this.verifyEqual(outtiming(1).pmod(2).name,[]);
this.verifyEqual(outtiming(1).pmod(3).name, {'name6^1' 'name6^2' 'name4^1'});
load(fn_mat2);
this.verifyTrue(sts==1);
this.verifyEqual(outtiming(2).onsets, [onsets{2}, {[]}, onsets{1}]);
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27 changes: 27 additions & 0 deletions test/pspm_glm_test.m
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Expand Up @@ -491,6 +491,33 @@ function test_eye(this, cutoff)
delete(model.datafile);
delete(model.modelfile);
end
function test_pmod(this)
% this checks github issue 191: a pmod is defined on a condition
% that is not present in the first session
bf1 = 1; offset = 0; sr = 100; duration = 120;
model.modelfile = 'Test_GLM_pmod_model.mat';
model.datafile = {'Test_GLM_pmod_data_1.mat', 'Test_GLM_pmod_data_2.mat'};
model.timeunits = 'seconds';
model.timing{1}.names{1} = 'cond_a';
model.timing{1}.onsets{1} = [10 40 70 100]';
model.timing{2}.names{1} = 'cond_b';
model.timing{2}.onsets{1} = [20 50 80 110]';
model.timing{2}.pmod(1).param = {[1, 2, 3, 4]; [1, 3, 3, 1]};
model.timing{2}.pmod(1).name = {'pmod1', 'pmod2'};
Y1 = pspm_glm_test.testdata_gen(model.timing{1}.onsets{1}, bf1, offset, 0, sr, duration);
Y2 = pspm_glm_test.testdata_gen(model.timing{2}.onsets{1}, bf1, offset, 0, sr, duration);
pspm_glm_test.save_datafile(Y1, sr, duration, model.datafile{1});
pspm_glm_test.save_datafile(Y2, sr, duration, model.datafile{2});
model.channel = 'scr';
model.modelspec = 'scr';
model.modality = 'scr';
[sts, glm] = this.verifyWarningFree(@() pspm_glm(model));
this.verifyEqual(glm.names, ...
{'cond_a, bf 1', 'cond_a, bf 2', 'cond_b, bf 1', 'cond_b, bf 2', ...
'cond_b x pmod1^1, bf 1', 'cond_b x pmod1^1, bf 2', 'cond_b x pmod2^1, bf 1', ...
'cond_b x pmod2^1, bf 2', 'Constant 1', 'Constant 2'}');
delete(model.modelfile);
end
end
methods(Test, ParameterCombination='exhaustive')
function glm = test_extract_missing(this, cutoff, nan_percent)
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