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[WIP] Function to copy derivatives #162

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nbeliy
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@nbeliy nbeliy commented Feb 19, 2021

Added a functionderivate(BIDS, out_path, name, varargin) which exports the files from current BIDS layout into out_path/name folder. In other words exports data into derivatives.

varargin are the query options same as in bids.query, in fact they are passed directly to it.

To do (help needed!):

  • Options -- when created derivatives, there a list of usefull options to fine tune, but adding them will make list of parameters to long. Options that I would like to include are below.
  • Script add a line to dataset_description a new structure each time it is run. But on the third run it crashes (see below)
  • Add version of bids-matlab (does it exists?)
  • Optimise the loop on files (see Provide easy way to loop over files as structure #161)
  • Copy of derivatives. Actually it supports only full paths in dependencies.* field.
  • Copy of participants.tsv and scans.tsv files
  • Tests

Options

  • unzip -- if true, then zipped files are unzipped
  • copy_dependencies -- if true, the files that current file depend on are copied even if they are not explicitely queried
  • force -- copy file even if he already exists in output. Mutually exclusve with copy_dependencies to avoid circular copy

Crashes during dataset_description generation:

Error using horzcat
Dimensions of matrices being concatenated are not consistent.

Error in bids.derivate (line 68)
    description.GeneratedBy = [description.GeneratedBy pipeline];

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codecov bot commented Feb 19, 2021

Codecov Report

Merging #162 (5f6b991) into dev (ac3bb7f) will not change coverage.
The diff coverage is 0.00%.

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@@          Coverage Diff          @@
##             dev    #162   +/-   ##
=====================================
  Coverage   0.00%   0.00%           
=====================================
  Files         25      26    +1     
  Lines        920     975   +55     
=====================================
- Misses       920     975   +55     
Flag Coverage Δ
unittests 0.00% <0.00%> (ø)

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Impacted Files Coverage Δ
+bids/derivate.m 0.00% <0.00%> (ø)

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@Remi-Gau
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Thanks for starting this!!!!

Will have a look and make suggestions where I can.

One think I can already tell you: we don't have bids-matlab version... YET but the issue has been opened and we should try to have some sort of pre-alpha soon.

@Remi-Gau Remi-Gau mentioned this pull request Feb 23, 2021
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@Remi-Gau
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Closing as this has been moved to #171

@Remi-Gau Remi-Gau closed this Feb 23, 2021
@nbeliy nbeliy deleted the beliy-derivate branch November 14, 2022 15:09
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