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Formatting tool for user friendly converting to spaceTX format #1318
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Proposalfiles are to be named: <image_type>-f<fov_number>-r<round_number>-c<ch_number>-z<zplane_number>.<image_extension> image_type is like primary, dots, etc. coordinates are to be read from a specified csv file, where the columns are filename, xmin, xmax, ymin, ymax, zmin, zmax. images where num_zplanes==1 should declare num_zplane to be any value they desire, and assign NaN to the z coordinates. |
codebook is still the hardest part of this, IMO... |
There are a few formalisms for codebooks that we might want to support conversion from: csv where each row is csv where each row is |
I don't have a good solution for codebooks that aren't 1-hot. Fortunately 1-hot appears to be very common. |
I would prefer just doing:
|
@ttung so each column defines a coordinate? I would find the tidy version more intuitive, where each row corresponds to a single value in the codebook...
the xarray |
example roundtrip from codebook to csv and back (technically to xarray on the return) https://gist.github.com/neuromusic/87267d7e20279585517c8cd46a0c5601 |
correct. for one-hot encodings, it's very easy to sanity check (sums across rows or columns should always be 1)
that's a lot more "rows". riskier to get it wrong, potentially? not sure. |
Define file name convention
Have tile fetcher example that works with above convention
Document in readthedocs
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