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Dev fork joel #3

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joelyancey
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@joelyancey joelyancey commented Mar 30, 2022

Fixes for daisy v1.0 support:

  • dims = in_array.roi.dims() -> dims = in_array.roi.dims
  • num_channels = 1 -> num_channels = None
  • replace deprecated call to daisy.run_blockwise with new daisy.Task

Improvements:

  • when create_scale_pyramid is called programmatically, compressor can be supplied as an argument ("cname"/"clevel") . The value it accepts is a dict where key 'id' holds a string value for compressor type; key 'level' holds an integer value for compression level.
  • zstd swapped for gzip as default compressor
  • print statements added to create_scale_pyramid that aid in debugging when arguments are chosen by the user from a GUI at runtime

@sheridana
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@joelyancey thanks for the contribution! Could you write test(s) that hit each of these fixes? Don't think pytest/unittest is necessary here - you can see some examples in the daisy and lsd repos. One thing I could envision is that I believe n5 sometimes has problems with non-gzip compression (although this might be fixed now).

@joelyancey
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Will do. Thinking about the conversation we just had... I suppose tests are more for verifying code integrity, while exceptions are for handling unexpected runtime behavior. I will add some of both when I get back to working on this.

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