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Add BIDS-compatible automatic reformatting of units of measure #222

Merged
merged 56 commits into from
Jun 2, 2020
Merged

Add BIDS-compatible automatic reformatting of units of measure #222

merged 56 commits into from
Jun 2, 2020
+101 −0

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vinferrer
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Closes #127

Proposed Changes

  • add bids_untits.py
  • This file contains dictionaries and fucntions to convert units strings to proper bids formatting.
  • bidify_units converts unit string to bids formatting
  • this function doesn't do unit conversion it only puts the unit string in the right format

vinferrer and others added 30 commits March 30, 2020 13:23
@vinferrer
add check_trigger_amount_std method
a494a27
@vinferrer
add option to activate check_trigger_amount_std
d8f58cb
@vinferrer
add if condition to use either check_trigger_amount or check_trigger_…
eee1223 
…amount_std
@vinferrer
correct linting
2148737
@vinferrer
merge check_trigger_amount functions in one
7e40f0d
@vinferrer
delete std_option and if statement
e99dcbd
@vinferrer
delete std_option and make 0 the threshold defalut
98c7ba1
@vinferrer
change legend so it's more understandable
640159a
@vinferrer
change thr default to None
9e9a67b
@vinferrer
delete unused function
64efe10
@vinferrer @eurunuela
Update phys2bids/cli/run.py
6920301 
Co-Authored-By: Eneko Uruñuela <13706448+eurunuela@users.noreply.github.com>
@vinferrer @eurunuela
Update phys2bids/physio_obj.py
b604650 
Co-Authored-By: Eneko Uruñuela <13706448+eurunuela@users.noreply.github.com>
@vinferrer @eurunuela
Update phys2bids/physio_obj.py
dde563e 
Co-Authored-By: Eneko Uruñuela <13706448+eurunuela@users.noreply.github.com>
@vinferrer
now we don't use the derivative, we only use the trigger channel
a31c167
@vinferrer
now -tr and -ntp is needed to run the check_trigger_amount function
161ca65
@vinferrer
Update phys2bids/cli/run.py
8314d0e 
change help description

Co-Authored-By: Stefano Moia <s.moia@bcbl.eu>
@vinferrer
Update phys2bids/cli/run.py
5d17060 
Co-Authored-By: Stefano Moia <s.moia@bcbl.eu>
@vinferrer
correct syntax errors
d09e977
@vinferrer
adding thr as attribute to the class and define it as float
714f38b
@vinferrer
delete thr=phys_in.thr line
fdc123a
@vinferrer
add space to log message
112827b
@vinferrer
change a bit log message
adda4ff
@vinferrer
change or statement for and statement
0a530dd
@vinferrer
change log
97ce038
@eurunuela
Fixes integration tests
6eb8b8f
Very tiny text changes
9531927
@vinferrer
initialize self.num_timepoints_found = None
fc50a05
@vinferrer
update docstring
170431e
@vinferrer
Update phys2bids/physio_obj.py
f5b8ecf 
Co-Authored-By: Stefano Moia <s.moia@bcbl.eu>
Add unit aliases dictionary
4cf435d
smoia
smoia reviewed May 28, 2020
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smoia
smoia reviewed May 28, 2020
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smoia
smoia reviewed May 28, 2020
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rmarkello
rmarkello reviewed May 28, 2020
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Thanks for making those changes, @vinferrer !

I have a few new comments based on the updates. Thanks for bearing with !

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@vinferrer vinferrer requested a review from rmarkello May 29, 2020 08:40
@smoia smoia mentioned this pull request Jun 1, 2020
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@rmarkello I think we are done with this, unless someone has any comments?

@vinferrer vinferrer assigned smoia and vinferrer and unassigned eurunuela Jun 2, 2020
@vinferrer vinferrer added this to the phys2bids first non-beta milestone Jun 2, 2020
rmarkello
rmarkello approved these changes Jun 2, 2020
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LGTM! Thanks for integrating all the changes.

@rmarkello rmarkello merged commit a60e951 into physiopy:master Jun 2, 2020
@smoia smoia mentioned this pull request Jun 2, 2020
Merged
@vinferrer vinferrer mentioned this pull request Jun 10, 2020
Closed
@vinferrer vinferrer deleted the bids_units branch June 16, 2020 06:59
@smoia smoia added the released This issue/pull request has been released. label Oct 14, 2020
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@smoia smoia smoia left review comments

@rmarkello rmarkello rmarkello approved these changes

@eurunuela eurunuela eurunuela approved these changes

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Minormod This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0) released This issue/pull request has been released.
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Adhering to BIDS units standards
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@vinferrer @smoia @eurunuela @rmarkello