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segmenter: save a bigger area than needed

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(cherry picked from commit b1d0c4988e80eef2cc3c83618bc62787aa72c6df)
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Romain Bazile 2021-06-02 14:08:29 +02:00 committed by Romain Bazile
parent 396c5623e9
commit 4dca53e2e4
1 changed files with 33 additions and 3 deletions
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36
scripts/planktoscope/segmenter/__init__.py
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@ -21,6 +21,7 @@ import io
import threading import threading
import functools import functools
import select
# Basic planktoscope libraries # Basic planktoscope libraries
import planktoscope.mqtt import planktoscope.mqtt
@ -414,6 +415,30 @@ class SegmenterProcess(multiprocessing.Process):
Returns: Returns:
tuple: (Number of saved objects, original number of objects before size filtering) tuple: (Number of saved objects, original number of objects before size filtering)
""" """
def __augment_slice(dim_slice, max_dims, size=10):
# transform tuple in list
dim_slice = list(dim_slice)
# dim_slice[0] is the vertical component
# dim_slice[1] is the horizontal component
# dim_slice[1].start,dim_slice[0].start is the top left corner
for i in range(2):
if dim_slice[i].start < size:
dim_slice[i] = slice(0, dim_slice[i].stop)
else:
dim_slice[i] = slice(dim_slice[i].start - size, dim_slice[i].stop)
# dim_slice[1].stop,dim_slice[0].stop is the bottom right corner
for i in range(2):
if dim_slice[i].stop + size == max_dims[i]:
dim_slice[i] = slice(dim_slice[i].start, max_dims[i])
else:
dim_slice[i] = slice(dim_slice[i].start, dim_slice[i].stop + size)
# transform back list in tuple
dim_slice = tuple(dim_slice)
return dim_slice
# TODO retrieve here all those from the global metadata # TODO retrieve here all those from the global metadata
minESD = 40 # microns minESD = 40 # microns
minArea = math.pi * (minESD / 2) * (minESD / 2) minArea = math.pi * (minESD / 2) * (minESD / 2)
@ -437,9 +462,17 @@ class SegmenterProcess(multiprocessing.Process):
"status/segmenter/object_id", "status/segmenter/object_id",
f'{{"object_id":"{region.label}"}}', f'{{"object_id":"{region.label}"}}',
) )
# First extract to get all the metadata about the image
obj_image = img[region.slice] obj_image = img[region.slice]
colors = self._get_color_info(obj_image, region.filled_image)
metadata = self._extract_metadata_from_regionprop(region)
# Second extract to get a bigger image for saving
obj_image = img[__augment_slice(region.slice, labels.shape, 10)]
object_id = f"{name}_{i}" object_id = f"{name}_{i}"
object_fn = os.path.join(self.__working_obj_path, f"{object_id}.jpg") object_fn = os.path.join(self.__working_obj_path, f"{object_id}.jpg")
self._save_image(obj_image, object_fn) self._save_image(obj_image, object_fn)
self._stream(obj_image) self._stream(obj_image)
@ -449,9 +482,6 @@ class SegmenterProcess(multiprocessing.Process):
os.path.join(self.__working_debug_path, f"obj_{i}_mask.jpg"), os.path.join(self.__working_debug_path, f"obj_{i}_mask.jpg"),
) )
colors = self._get_color_info(obj_image, region.filled_image)
metadata = self._extract_metadata_from_regionprop(region)
object_metadata = { object_metadata = {
"name": f"{object_id}", "name": f"{object_id}",
"metadata": {**metadata, **colors}, "metadata": {**metadata, **colors},