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catalystneuro / roiextractors

Python-based module for extracting from, converting between, and handling optical imaging data from several file formats. Inspired by SpikeInterface.
https://roiextractors.readthedocs.io/en/latest/index.html
BSD 3-Clause "New" or "Revised" License
11 stars 7 forks source link

add stub option #103

Closed bendichter closed 2 years ago

bendichter commented 2 years ago

A stub option should limit the conversion to the first ~100 frames so that conversions can be tested quickly without reading/writing all of the data.

CodyCBakerPhD commented 2 years ago

An excellent request - very surprised this isn't already supported. I'll get on this today along with the other roiextractors improvements.

CodyCBakerPhD commented 2 years ago

~100

Also, I'd vote for n_frames_stub=largest_axis_length+1 to avoid the NWBInspector check_data_orientation from getting raised on stub files.

CodyCBakerPhD commented 2 years ago

@bendichter Oh, I forgot - so, stubbing is something done at the tools+DataInterface level on NWBCT, it's not a native argument to extractor objects either here or on SpikeInterface.

For all of the extractors here, everything except the non-memmap TIFF should have fully lazy access, so a stub option for read operations here would only be for that case (also not entirely sure how to go about it through the tifffile library context used to call as_array).

Is that what you wanted to try to get working to make testing faster? Or just the option on the NWBCT side?

Separate usage: Technically we could support the stub option here for all of our static methods for writing back to proprietary formats, but NWB is usually what we care about most, and that's not handled here.

CodyCBakerPhD commented 2 years ago

Ahhh but as I look into that it seems that what is needed at the roiextractors level is either

a) SubImagingExtractor + SubSegmentationExtractor

OR the new SpikeInterface approach

b) .frame_slice() method of the base class.

I prefer (b), how about you @bendichter?

bendichter commented 2 years ago

Let's use the new method to keep up with the latest from SpikeInterface