From 3bf6161ca420838381db33e35d8c186c90a9a0b5 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 16 Jul 2024 14:48:34 +0200
Subject: [PATCH] Removed image-flattening from focal points
---
model_server/base/roiset.py | 26 +++++--------
tests/base/test_roiset.py | 78 ++++++++++++++++++++++++-------------
2 files changed, 60 insertions(+), 44 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 360d86f9..23748e60 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -218,14 +218,14 @@ class RoiSet(object):
df = pd.DataFrame(regionprops_table(
acc_obj_ids.data[:, :, 0, 0],
intensity_image=acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16'),
- properties=('label', 'area', 'intensity_mean', 'bbox', 'centroid')
+ properties=('label', 'area', 'intensity_mean', 'bbox')
)).rename(columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'y1', 'bbox-3': 'x1'})
df['zi'] = df['intensity_mean'].round().astype('int')
else: # objects' z-coordinates come from arg of max count in object identities map
df = pd.DataFrame(regionprops_table(
acc_obj_ids.data[:, :, 0, :],
- properties=('label', 'area', 'bbox', 'centroid')
+ properties=('label', 'area', 'bbox')
)).rename(columns={
'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'z0', 'bbox-3': 'y1', 'bbox-4': 'x1', 'bbox-5': 'z1'
})
@@ -285,7 +285,14 @@ class RoiSet(object):
# TODO: get overlapping segments
def get_overlap_seg(self) -> pd.DataFrame:
- df_overlap_bbox = self.get_overlap_bbox()
+ dfbb = _filter_overlap_bbox(self._df)
+ def _iou(roi_i):
+ roi1 = self._df.loc[roi_i.index]
+ roi2 = self._df.loc[roi_i.overlaps_with]
+ print(roi1)
+ print(roi2)
+
+ dfbb['iou'] = dfbb.apply()
# TODO: test if overlaps exist
@@ -311,19 +318,6 @@ class RoiSet(object):
def add_df_col(self, name, se: pd.Series) -> None:
self._df[name] = se
- def get_multichannel_projection(self):
- if self.count:
- projected = project_stack_from_focal_points(
- self._df['centroid-0'].to_numpy(),
- self._df['centroid-1'].to_numpy(),
- self._df['zi'].to_numpy(),
- self.acc_raw,
- degree=4,
- )
- else: # else just return MIP
- projected = self.acc_raw.data.max(axis=-1)
- return projected
-
def get_patches_acc(self, channels: list = None, **kwargs) -> PatchStack: # padded, un-annotated 2d patches
if channels and len(channels) == 1:
patches_df = self.get_patches(white_channel=channels[0], **kwargs)
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 6f39f239..b06499c9 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -19,20 +19,62 @@ params = conf.meta['roiset']
class TestOverlapLogic(unittest.TestCase):
- def test_overlap_bbox(self):
- df = pd.DataFrame({
- 'x0': [0, 1, 3, 1, 1],
+ def setUp(self) -> None:
+ self.df = pd.DataFrame({
+ 'x0': [0, 1, 2, 1, 1],
'x1': [2, 3, 4, 3, 3],
- 'y0': [0, 0, 0, 1, 0],
- 'y1': [1, 1, 1, 2, 1],
+ 'y0': [0, 0, 0, 2, 0],
+ 'y1': [2, 2, 2, 3, 2],
'zi': [0, 0, 0, 0, 1],
})
- res = _filter_overlap_bbox(df)
- print(res)
+ self.mask = np.array([
+ [1, 1, 0, 0, 0],
+ [1, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0],
+ ])
+
+ self.mask = np.array([
+ [0, 0, 1, 0, 0],
+ [0, 1, 1, 0, 0],
+ [0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0],
+ ])
+
+ self.mask = np.array([
+ [0, 0, 1, 1, 0],
+ [0, 0, 1, 1, 0],
+ [0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0],
+ ])
+
+ # first and second overlap bounding boxes but not segmentation
+ # second and third overlap both ways
+ self.masks = [
+ [
+ [1, 1],
+ [1, 0]
+ ],
+ [
+ [0, 1],
+ [1, 1]
+ ],
+ [
+ [1, 1],
+ [1, 1]
+ ],
+ ]
- self.assertEqual(len(res), 1)
+ def test_overlap_bbox(self):
+ res = _filter_overlap_bbox(self.df)
+ print(res)
+ self.assertEqual(len(res), 2)
self.assertTrue((res.loc[0, 'overlaps_with'] == 1).all())
+ self.assertTrue((res.loc[1, 'overlaps_with'] == 2).all())
class BaseTestRoiSetMonoProducts(object):
@@ -181,26 +223,6 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
result = generate_file_accessor(where / file)
self.assertEqual(result.shape, roiset.acc_raw.shape)
- def test_flatten_image(self):
- roiset = RoiSet.from_binary_mask(self.stack_ch_pa, self.seg_mask, params=RoiSetMetaParams(mask_type='boxes'))
- df = roiset.get_df()
-
- from model_server.base.roiset import project_stack_from_focal_points
-
- img = project_stack_from_focal_points(
- df['centroid-0'].to_numpy(),
- df['centroid-1'].to_numpy(),
- df['zi'].to_numpy(),
- self.stack,
- degree=4,
- )
-
- self.assertEqual(img.shape[0:2], self.stack.shape[0:2])
-
- write_accessor_data_to_file(
- output_path / 'flattened.tif',
- InMemoryDataAccessor(img)
- )
def test_make_binary_masks(self):
roiset = self._make_roi_set()
--
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