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Remove rgbchannels and MetadataOnly blocks #20

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merged 4 commits into from
Apr 29, 2020

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melissalinkert
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Resurrects https://github.com/glencoesoftware/raw2ometiff/compare/master...chris-allan:fix-legacy?expand=1 with conflicts fixed. Replaces #19, and requires glencoesoftware/isyntax2raw#15.

Running the full conversion against both iSyntax files and something like bf-data-repo/automated-tests/curated/jpeg/big-images/8kx8k.jpg should result in a readable OME-TIFF with multiple channels (and no errors).

@chris-allan
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isyntax2raw --> raw2ometiff stack seems to be functioning correctly but we will need some work to ensure that the resultant OME-TIFF metadata reflects the "RGBness" of the source data. Otherwise downstream software is going to have a rough time telling the difference between 3 channel flourescence and H+E.

RGB data is only written if exactly 3 channels exist and there are
no Z sections or timepoints.  The Z/T restriction could be removed
once full multi-dimensional support is added.
@melissalinkert
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raw2ometiff --rgb /path/to/pyramid rgb.ome.tiff should now produce an RGB TIFF, with the caveats listed in the 4dae7b0 commit message.

This was referenced Apr 26, 2020
@chris-allan chris-allan merged commit 20cf5bd into glencoesoftware:master Apr 29, 2020
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2 participants