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When using the
--save_png
flag, theio.save_masks()
method attempts to make a PNG of the original image/predicted outlines/predicted masks/cell pose. This takes a lot of time, especially for large images. I've added a default flag to disable the block inio.save_masks()
that makes the matplotlib figure. I've exposed this flag to the CLI and API.Alternatively, the image data could be reshaped manually, rather than letting matplotlib do the work. (@carsen-stringer)
Example CLI data after setting default behavior to skip matplotlib:
--save_png
: 105 seconds--save_png
and--save_mpl
: 121 seconds--save_png
: 668 seconds--save_png
and--save_mpl
: 1562 secondsThis also is related to the OOM issues #735, since the memory spikes at the end of matplotlib figure creation.