Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[WIP] refactor narrowing, add test, run narrow before copying #29

Open
wants to merge 3 commits into
base: master
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from 2 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 25 additions & 0 deletions narrow_participants.m
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
function BIDS = narrow_participants(BIDS, labels)
% NARROW_PARTICIPANTS - restrict BIDS struct to only requested labels
%
Remi-Gau marked this conversation as resolved.
Show resolved Hide resolved

% nothing to do if no labels to change?
if isempty(labels)
return
end

idx = ismember({BIDS.subjects.name},labels);
BIDS.subjects = BIDS.subjects(idx);

idx = ismember(BIDS.participants.participant_id,labels);
for fn=fieldnames(BIDS.participants)'
replace = BIDS.participants.(char(fn));
% BIDS.participants.meta is 1x1. other fields are 1xN
if(length(replace) < length(idx))
warning('BIDS participants field "%s" too short: ID idx len %d > number of field values %d; ignored', ...
char(fn), length(idx), length(replace))
continue
end
BIDS.participants.(char(fn)) = replace(idx);
end

end
14 changes: 3 additions & 11 deletions spm_BIDS_App.m
Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,9 @@
spm('defaults','fmri');
spm_jobman('initcfg');

% if we used --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
BIDS = narrow_participants(BIDS, BIDS_App.participants);

%==========================================================================
%-(Temporary) Copy of input data and uncompress image files
%==========================================================================
Expand Down Expand Up @@ -253,17 +256,6 @@
BIDS = spm_changepath(BIDS,'.nii.gz','.nii',false);
end

%-Simplify BIDS structure to only contain participants under study
%--------------------------------------------------------------------------
idx = ismember({BIDS.subjects.name},BIDS_App.participants);
BIDS.subjects = BIDS.subjects(idx);
if ~isempty(BIDS.participants)
idx = ismember(BIDS.participants.participant_id,BIDS_App.participants);
for fn=fieldnames(BIDS.participants)'
BIDS.participants.(char(fn)) = BIDS.participants.(char(fn))(idx);
end
end

%==========================================================================
%-Analysis level: participant*
%==========================================================================
Expand Down
30 changes: 30 additions & 0 deletions test_narrow_participants.m
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Do you think you could rewrite this test to be used directly by matlab testing framework?

Ideally with setup and teardown functions.

https://nl.mathworks.com/help/matlab/matlab_prog/write-test-using-setup-and-teardown-functions.html

If you don't have the bandwidth, let me know and I can give it a go

Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
%
% script based testing for narrow_participants
% participants.json adds a 'meta' field that can be avoided when selecting only some participants
%

bids_dir = [tempname '_bids_test'];
try
% build minimal BIDS filesystem: participants.json and 1 anat file pair
system(['mkdir -p ' bids_dir '/sub-{a,b}/ses-{1,2}/anat/']);
system([ 'touch ' bids_dir '/sub-{a,b}/ses-{1,2}/anat/T1.{json,nii.gz}']);
system(['echo -e ''participant_id\nsub-a\nsub-a\nsub-b\nsub-b'' > ' bids_dir '/participants.tsv']);
system(['echo ''{ "Name": "test", "BIDSVersion": "1.4.1"}'' > ' bids_dir '/dataset_description.json']);
system(['echo ''{ "age": { "Description": "xyz" } }'' > ' bids_dir '/participants.json']);

% get what we built -- matches expectations
BIDS = spm_BIDS(bids_dir);
assert(length(BIDS.participants.participant_id) == 4)

% narrowing works
BIDS_narrow = narrow_participants(BIDS, {'sub-a'})
assert(length(BIDS_narrow.participants.participant_id) == 2)

% no change on empty
BIDS_nochange = narrow_participants(BIDS, {}); % TODO: {{}}?
assert(length(BIDS_nochange.participants.participant_id) == 4)

catch me
rmdir(bids_dir,'s')
rethrow(me)
end