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Fix incorrect segmenter object size thresholding calculations #50

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merged 6 commits into from
Nov 29, 2024
Merged

Fix incorrect segmenter object size thresholding calculations #50

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14b4318
Implement Fabien's proposed size thresholding calculations
ethanjli Oct 29, 2024
56273cb
Try pinning cryptography package to last wheel available on armv7
ethanjli Oct 29, 2024
c50ca27
Fix incorrect variable name
ethanjli Oct 30, 2024
c93d0d0
Bump cryptography package
ethanjli Nov 29, 2024
dc3a1b3
Merge branch 'main' into fix/segmenter-object-size-threshold
ethanjli Nov 29, 2024
aff1ae1
Update `CHANGELOG.md`
ethanjli Nov 29, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,10 @@ All dates in this file are given in the [UTC time zone](https://en.wikipedia.org
- (Hardware controller) The bitrate of the camera preview stream has been reduced slightly from ~8 Mbps to ~7 Mbps.
- (Hardware controller) The framerate of the camera preview stream is now explicitly limited to 25 fps.

### Fixed

- (Breaking change; segmenter) The previously incorrect method for filtering segmented objects by size has now been corrected to filter object sizes by filled area rather than bounding box area, and directly using the mesh size as the threshold for equivalent spherical diameter (ESD) instead of calculating a fictional ESD.

## v2024.0.0-beta.2 - 2024-08-19

### Changed
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13 changes: 6 additions & 7 deletions processing/segmenter/planktoscope/segmenter/__init__.py
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Expand Up @@ -474,17 +474,16 @@ def __augment_slice(dim_slice, max_dims, size=10):
dim_slice = tuple(dim_slice)
return dim_slice

minMesh = self.__global_metadata.get("acq_minimum_mesh", 20) # microns
minESD = minMesh * 2
minArea = math.pi * (minESD / 2) * (minESD / 2)
pixel_size = self.__global_metadata.get("process_pixel", 1.0)
# minsizepix = minArea / pixel_size / pixel_size
minsizepix = (minESD / pixel_size) ** 2
min_mesh = self.__global_metadata.get("acq_minimum_mesh", 20) # microns
min_esd = min_mesh # or process_min_ESD in the future (microns)
pixel_size = self.__global_metadata["process_pixel"]
min_radius = min_esd / 2 / pixel_size # (pixels)
min_area = math.pi * min_radius * min_radius

labels, nlabels = skimage.measure.label(mask, return_num=True)
regionprops = skimage.measure.regionprops(labels)
regionprops_filtered = [
region for region in regionprops if region.bbox_area >= minsizepix
region for region in regionprops if region.filled_area >= min_area
]
object_number = len(regionprops_filtered)
logger.debug(f"Found {nlabels} labels, or {object_number} after size filtering")
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