curious.bio/planktoscope
curious.bio/planktoscope
9
0
Fork 0
Code Issues 10 Pull requests Packages Projects 7 Releases Wiki Activity

segmenter:retrieve initial size data from metadata.json

Browse source
This commit is contained in:
Romain Bazile 2021-08-11 18:39:31 +02:00
parent 9b0383a277
commit f3e6d90a4d
1 changed files with 3 additions and 3 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

6
scripts/planktoscope/segmenter/__init__.py
View file

@ -456,10 +456,10 @@ class SegmenterProcess(multiprocessing.Process):
dim_slice = tuple(dim_slice)
return dim_slice
# TODO retrieve here all those from the global metadata
minESD = 40 # microns
minMesh = self.__global_metadata.get("acq_minimum_mesh", 20) # microns
minESD = minMesh * 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 = (minESD / pixel_size) ** 2