ageorgou commented 4 years ago

Will fix #36.

[x] New header version for latest LabView setup
[x] Put reading/handling of ROI information in its own class for more flexibility
[x] Read extra columns in newer setup (resolution, FOV, ...)
[x] Create an imaging plane for each ROI acquisition series if needed

ageorgou commented 4 years ago

This is still far from done but it's a start! It may be that subclasses for RoiReader are not the way to go (instead, we could create the mappings and specify behaviour through functions or other classes -- composition rather than inheritance). Since there is no immediate prospect of further LabView versions, however, we might as well not overcomplicate this right now.

The main remaining changes are:

adding the new ROI.dat columns and their types to RoiReaderv300
adding a method to RoiReader that takes a ROI number and an NWBFile (or perhaps our own NwbFile) and creates/returns the imaging plane corresponding to the acquisition for that ROI. For older versions, this should give the ImagingPlane created for the corresponding Z-plane. For the latest version, and only if variable shapes are enabled, it should create a new ImagingPlane based on that ROI's coordinates and resolution (thinking about this, maybe it should take a channel too, so we don't duplicate between Red and Green ROIs?) This method should be called from read_functional_data, when determining the imaging plane for the acquisition named ROI_NNN_Red/Green.

codecov-io commented 3 years ago

Codecov Report

Merging #74 (8115f8f) into master (358c551) will increase coverage by 1.48%. The diff coverage is 85.59%.

@@            Coverage Diff             @@
##           master      #74      +/-   ##
==========================================
+ Coverage   59.32%   60.80%   +1.48%     
==========================================
  Files          17       19       +2     
  Lines        1866     2008     +142     
  Branches      275      292      +17     
==========================================
+ Hits         1107     1221     +114     
- Misses        716      738      +22     
- Partials       43       49       +6

Impacted Files	Coverage Δ
src/silverlabnwb/signature.py	`56.73% <ø> (ø)`
tests/test_labview_import.py	`75.71% <50.00%> (-0.76%)`	:arrow_down:
src/silverlabnwb/rois.py	`78.31% <78.31%> (ø)`
src/silverlabnwb/nwb_file.py	`90.21% <82.43%> (-1.93%)`	:arrow_down:
src/silverlabnwb/header.py	`88.96% <87.50%> (+0.32%)`	:arrow_up:
src/silverlabnwb/metadata.py	`89.04% <100.00%> (ø)`
src/silverlabnwb/timings.py	`98.24% <100.00%> (+4.39%)`	:arrow_up:
tests/test_header.py	`100.00% <100.00%> (ø)`
tests/test_rois.py	`100.00% <100.00%> (ø)`
tests/test_timings.py	`100.00% <100.00%> (ø)`
... and 2 more

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ageorgou commented 3 years ago

Latest changes look good. Making a note to check that everything works with variable-shape ROIs as it's not yet tested on Travis.

ageorgou commented 3 years ago

I suggest we merge this (without creating a new release yet). Have created #80 and #81 for the remaining issues/questions.

SilverLabUCL / PySilverLabNWB

Support for ROIs with different size or resolution #74

Codecov Report