search

catalystneuro / nwb-conversion-tools

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.
https://nwb-conversion-tools.readthedocs.io/en/main/
BSD 3-Clause "New" or "Revised" License
25 stars 12 forks source link

Add optical physiology interfaces to conversion gallery I #585

Closed h-mayorquin closed 2 years ago

h-mayorquin commented 2 years ago

Related to catalystneuro/nwb-conversion-tools#442

This is the first batch of the conversion gallery with all the imaging extractors.

The only missing is ScanImage as I am waiting for catalystneuro/nwb-conversion-tools#580.

In a second batch I will add the segmentation extractors. See latest discussion at catalystneuro/nwb-conversion-tools#442 for the blocker on this.

I also changed the structure of the main index. I re-arranged the main terms so the conversion gallery is before the developer guide trying to mimic (expected) order to frequency of use. I am wondering on whether the conversion gallery should come before the user guide as its the most simple use case and the user guide explains the abstractions /concepts of the library and deals with combining more than one interface.

There were also some remnants missing from catalystneuro/neuroconv#42 that needed to be completed.

EDIT. The documentation is working but there is a problem with locating one of the files. Trying some git data trickery.

h-mayorquin commented 2 years ago

After https://github.com/catalystneuro/nwb-conversion-tools/pull/580 I adeed ScanImage.

codecov[bot] commented 2 years ago

Codecov Report

Merging #585 (000a67b) into main (9dc42a0) will not change coverage. The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##             main     catalystneuro/nwb-conversion-tools#585   +/-   ##
=======================================
  Coverage   88.34%   88.34%           
=======================================
  Files          59       59           
  Lines        3218     3218           
=======================================
  Hits         2843     2843           
  Misses        375      375
Flag Coverage Δ
unittests 88.34% <100.00%> (ø)

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

Impacted Files Coverage Δ
...ols/datainterfaces/ophys/hdf5/hdf5datainterface.py 100.00% <ø> (ø)
...ainterfaces/ophys/baseimagingextractorinterface.py 95.34% <100.00%> (ø)
...tools/datainterfaces/ophys/sbx/sbxdatainterface.py 100.00% <100.00%> (ø)
...faces/ophys/scanimage/scanimageimaginginterface.py 88.37% <100.00%> (ø)
...ols/datainterfaces/ophys/tiff/tiffdatainterface.py 100.00% <100.00%> (ø)
...version_tools/tools/roiextractors/roiextractors.py 80.00% <100.00%> (ø)