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segmenter:retrieve initial size data from metadata.json

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Romain Bazile 2021-08-11 18:39:31 +02:00
parent 9b0383a277
commit f3e6d90a4d
1 changed files with 3 additions and 3 deletions
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scripts/planktoscope/segmenter/__init__.py
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@ -456,10 +456,10 @@ class SegmenterProcess(multiprocessing.Process):
dim_slice = tuple(dim_slice) dim_slice = tuple(dim_slice)
return dim_slice return dim_slice
# TODO retrieve here all those from the global metadata minMesh = self.__global_metadata.get("acq_minimum_mesh", 20) # microns
minESD = 40 # microns minESD = minMesh * 2
minArea = math.pi * (minESD / 2) * (minESD / 2) minArea = math.pi * (minESD / 2) * (minESD / 2)
pixel_size = 1.01 # to be retrieved from metadata pixel_size = self.__global_metadata.get("process_pixels", 1.0)
# minsizepix = minArea / pixel_size / pixel_size # minsizepix = minArea / pixel_size / pixel_size
minsizepix = (minESD / pixel_size) ** 2 minsizepix = (minESD / pixel_size) ** 2