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[ENH] refactor removing date entity and allow to use bids fitler to only convert certain files from source to raw #197

Merged
merged 4 commits into from
Apr 27, 2022
Merged

[ENH] refactor removing date entity and allow to use bids fitler to only convert certain files from source to raw #197

merged 4 commits into from
Apr 27, 2022

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Remi-Gau
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@Remi-Gau Remi-Gau commented Apr 16, 2022 •
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fixes #196

@Remi-Gau Remi-Gau changed the base branch from master to dev April 16, 2022 09:00
@Remi-Gau Remi-Gau requested a review from CerenB April 16, 2022 09:00
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codecov bot commented Apr 16, 2022 •
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Codecov Report

Merging #197 (7bc55c0) into dev (627ceef) will decrease coverage by 3.68%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##              dev     #197      +/-   ##
==========================================
- Coverage   81.71%   78.02%   -3.69%     
==========================================
  Files          30       31       +1     
  Lines         678      710      +32     
==========================================
  Hits          554      554              
- Misses        124      156      +32
Flag Coverage Δ
unittests 78.02% <0.00%> (-3.69%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/convertSourceToRaw.m 0.00% <0.00%> (ø)
src/utils/removeDateEntity.m 0.00% <0.00%> (ø)

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Remi-Gau
Remi-Gau commented Apr 16, 2022
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src/convertSourceToRaw.m
%
% Function attempts to convert a source dataset created with CPP_BIDS into a valid
% BIDS data set.
%
%
% USAGE::
%
% convertSourceToRaw(cfg)
% convertSourceToRaw(cfg, 'filter', filter)
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Should now be possible to use a typical bids.query fitler to only convert a subset of files (only those from beh or from a given subject)

Remi-Gau
Remi-Gau commented Apr 16, 2022
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src/convertSourceToRaw.m
% add dummy README and CHANGE file
templateFolder = fullfile(fileparts(mfilename('fullpath')), '..', 'templates');
% trick use bids matlab copy dataset function
bids.copy_to_derivative(sourceDir, ...
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reuse the bids matlab "copy dataset" function as it was literally made for this.

Remi-Gau
Remi-Gau commented Apr 16, 2022
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src/utils/removeDateEntity.m
Comment on lines +1 to +11
function removeDateEntity(varargin)
%
% Removes the date entity from all the files in a BIDS data set
%
%
% USAGE::
%
% removeDateEntity(pathToDataSet, 'filter', filter)
%
%
% (C) Copyright 2022 CPP_BIDS developers
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There is now a stand alone function to remove date entities

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CerenB commented Apr 26, 2022

Thank you! I used removeDateEntity !
with the master branch of CPP-SPM repo, bids-matlab submodule is on a HEAD (detached?) branch. And I was using CPP-BIDS with CPP-SPM submodules together. And it was giving an error during BIDS data reading.
If CPP-SPM is not in the same repo, I bet it'll work as it is.
In my case, I updated bids-matlab branch in CPP-SPM repo to be compatible with CPP-BIDS functions.

BIDS = bids.layout(pathToDataSet,  'use_schema', false);
K>> BIDS = bids.layout(pathToDataSet,  'use_schema', false)
Undefined function or variable 'function_name'.

Error in bids.Schema/load (line 75)
        bids.internal.error_handling(function_name,
        'missingDirectory', msg, false, true);

Error in bids.Schema (line 34)
      obj = load(obj, use_schema);

Error in bids.layout (line 110)
  schema = bids.Schema(use_schema);

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yeah there might be a bit of branch juggling indeed.

@Remi-Gau Remi-Gau merged commit e97fcce into cpp-lln-lab:dev Apr 27, 2022
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yeah there might be a bit of branch juggling indeed.

@Remi-Gau Remi-Gau deleted the rm_data branch April 27, 2022 06:31
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@CerenB CerenB CerenB approved these changes

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