From 531fac85288fcac6f6ceb6344e40b2049db6b72b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 31 Jul 2024 16:48:04 +0200
Subject: [PATCH] Implemented polygon fitting
---
model_server/base/roiset.py | 39 ++++++++++++++++++++++++++++++++++++-
tests/base/test_roiset.py | 26 ++++++++++++++++++++++++-
2 files changed, 63 insertions(+), 2 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 854a53da..12310bec 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -10,7 +10,8 @@ from pydantic import BaseModel
from scipy.stats import moment
from skimage.filters import sobel
-from skimage.measure import label, regionprops_table, shannon_entropy
+from skimage.measure import approximate_polygon, find_contours, label, points_in_poly, regionprops, regionprops_table, shannon_entropy
+from skimage.morphology import binary_dilation, disk
from .accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from .models import InstanceSegmentationModel
@@ -180,6 +181,10 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame
)
return df
+# TODO: implement
+def make_df_from_polygons(acc_raw, polygons:np.ndarray) -> pd.DataFrame:
+ pass
+
def df_insert_slices(df: pd.DataFrame, sd: dict, expand_box_by) -> pd.DataFrame:
h = sd['Y']
@@ -347,6 +352,11 @@ class RoiSet(object):
"""
return RoiSet.from_object_ids(acc_raw, get_label_ids(acc_seg, allow_3d=allow_3d, connect_3d=connect_3d), params)
+ @staticmethod
+ #TODO: implement
+ def from_polygons(acc_raw, polygons: np.ndarray):
+ pass
+
# TODO: get overlapping segments
def get_overlap_seg(self) -> pd.DataFrame:
@@ -764,6 +774,33 @@ class RoiSet(object):
record['tight_patch_masks'] = list(se_pa)
return record
+ def get_polygons(self, poly_threshold=0, dilation_radius=1):
+ pad_to = 1
+
+ def _poly_from_mask(roi):
+ # mask = generate_file_accessor(roi.mask_path).data[:, :, 0, 0]
+ mask = roi.binary_mask
+
+ # label and fill holes
+ labeled = label(mask)
+ filled = [rp.image_filled for rp in regionprops(labeled)]
+ assert (np.unique(labeled)[-1] == 1) and (len(filled) == 1), 'Cannot fit multiple polygons in a single patch mask'
+
+ closed = binary_dilation(filled[0], footprint=disk(dilation_radius))
+ padded = np.pad(closed, pad_to) * 1.0
+ all_contours = find_contours(padded)
+
+ nc = len(all_contours)
+ for j in range(0, nc):
+ if all([points_in_poly(all_contours[k], all_contours[j]).all() for k in range(0, nc)]):
+ contour = all_contours[j]
+ break
+
+ rel_polygon = approximate_polygon(contour[:, [1, 0]], poly_threshold) - [pad_to, pad_to]
+ return rel_polygon + [roi.x0, roi.y0]
+
+ return self._df.apply(_poly_from_mask, axis=1)
+
# TODO: implement
def serialize_coco(self, where: Path, prefix='') -> dict:
"""
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 6264d41e..892445bf 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -1,4 +1,3 @@
-import os
import re
import unittest
@@ -6,6 +5,7 @@ import numpy as np
from pathlib import Path
import pandas as pd
+from skimage import draw
from model_server.base.roiset import filter_overlap_bbox, RoiSetExportParams, RoiSetMetaParams
from model_server.base.roiset import RoiSet
@@ -664,3 +664,27 @@ class TestRoiSetSerialization(unittest.TestCase):
)
roiset.serialize_coco(output_path / 'serialize_coco')
self.assertEqual(1, 0)
+
+class TestRoiSetPolygons(BaseTestRoiSetMonoProducts, unittest.TestCase):
+
+ def test_compute_polygons(self):
+ roiset = RoiSet.from_binary_mask(
+ self.stack_ch_pa,
+ self.seg_mask,
+ params=RoiSetMetaParams(
+ mask_type='contours',
+ filters={'area': {'min': 1e1, 'max': 1e6}}
+ )
+ )
+
+ poly = roiset.get_polygons()
+ binary_poly = np.zeros(self.seg_mask.hw, dtype=bool)
+ for p in poly:
+ pidcs = draw.polygon(p[:, 1], p[:, 0])
+ binary_poly[pidcs] = True
+
+ test_mask = np.logical_and(
+ np.logical_not(binary_poly),
+ (self.seg_mask.data[:, :, 0, 0] == 255)
+ )
+ self.assertLess(test_mask.sum() / test_mask.size, 0.001) # most mask pixels are within in fitted polygon
\ No newline at end of file
--
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