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add 1-dim probability map shader to chunkflow neuroglancer command #302

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merged 1 commit into from
Feb 24, 2024

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eschombu
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This adds a user-controllable colored shader to 1-dimensional probability map neuroglancer layers. The color can be specified in the chunkflow command parameters with the following syntax:

chunkflow \
  ...
  neuroglancer -i img,seg,glia[color=red],mito

Above, the glia variable contains the glia probability prediction at each voxel in the chunk. When this layer is added via the _append_probability_map_layer, a new color parameter takes its value from the parameters specified inside the [...] brackets. Extracting this parameter value is implemented in the neuroglancer operator's __call__ method by checking for comma-separated key=value pairs within such square brackets. This mechanism can be reused for other layer-type-specific keyword parameters in the future.

…using brackets after name; use for coloring probability vars
@xiuliren
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this is a very useful feature to have!

@xiuliren xiuliren merged commit 0dc816a into seung-lab:master Feb 24, 2024
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@eschombu eschombu deleted the neuroglancer-proba-color branch February 28, 2024 00:34
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2 participants