From 8f33b530a85f23a6fab71f3f055a2995504d987b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 13 Sep 2024 16:41:47 +0200
Subject: [PATCH] Still implementing generation of RoiSet from bounding boxes
alone
---
model_server/base/roiset.py | 47 +++++++++++++++++++++++++++----------
tests/base/test_roiset.py | 26 ++++++++++++++++++++
2 files changed, 61 insertions(+), 12 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 60cb5912..f529da22 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -221,6 +221,7 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame
"""
# build dataframe of objects, assign z index to each object
+ # TODO: don't assume that channel 0 is the basis of z-argmax
if acc_obj_ids.nz == 1: # deproject objects' z-coordinates from argmax of raw image
df = pd.DataFrame(regionprops_table(
acc_obj_ids.data_xy,
@@ -328,7 +329,6 @@ def make_object_ids_from_df(df: pd.DataFrame, sd: dict) -> InMemoryDataAccessor:
class RoiSet(object):
- # TODO: __init__ to take bounding boxes e.g. from obj det model; flag if overlaps are allowed
def __init__(
self,
acc_raw: GenericImageDataAccessor,
@@ -383,17 +383,40 @@ class RoiSet(object):
@staticmethod
def from_bounding_boxes(
acc_raw: GenericImageDataAccessor,
- yxhw_list: List,
+ bbox_df: pd.DataFrame,
params: RoiSetMetaParams = RoiSetMetaParams()
):
- df = pd.DataFrame([
- {
- 'y0': yxhw[0],
- 'y1': yxhw[0] + yxhw[2],
- 'x0': yxhw[1],
- 'x1': yxhw[1] + yxhw[3],
- } for yxhw in yxhw_list
- ])
+
+ # deproject if zi is not provided
+ if 'zi' not in bbox_df.columns:
+ def _slice_zmax(r):
+ acc_raw.crop_hw(
+ r.y0,
+ r.x0,
+ r.y1 - r.y0,
+ r.x1 - r.x0
+ )
+ zmax = acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16')
+ bbox_df['zi'] = 0
+
+ df = df_insert_slices(
+ bbox_df,
+ acc_raw.shape_dict,
+ params.get('expand_box_by', 0)
+ )
+
+ def _make_binary_mask(r):
+ # TODO: make square mask array
+ # acc = InMemoryDataAccessor(acc_obj_ids.data == r.label)
+ # cropped = acc.get_mono(0, mip=True).crop_hw((r.y0, r.x0, (r.y1 - r.y0), (r.x1 - r.x0))).data_xy
+ return cropped
+
+ df['binary_mask'] = df.apply(
+ _make_binary_mask,
+ axis=1,
+ result_type='reduce',
+ )
+
return RoiSet(acc_raw, df, params)
@@ -945,14 +968,14 @@ class RoiSet(object):
# TODO: make this work with obj det dataset
@staticmethod
- def deserialize(acc_raw: GenericImageDataAccessor, where: Path, prefix=''):
+ def deserialize(acc_raw: GenericImageDataAccessor, where: Path, prefix='') -> Self:
"""
Create an RoiSet object from saved files and an image accessor
:param acc_raw: accessor to image that contains ROIs
:param where: path to directory containing RoiSet serialization files, namely dataframe.csv and a subdirectory
named tight_patch_masks
:param prefix: starting prefix of patch mask filenames
- :return:
+ :return: RoiSet object
"""
df = pd.read_csv(where / 'dataframe' / (prefix + '.csv'))[['label', 'zi', 'y0', 'y1', 'x0', 'x1']]
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 75a9b775..6794dac2 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -623,6 +623,32 @@ class TestRoiSetSerialization(unittest.TestCase):
t_acc = generate_file_accessor(pt)
self.assertTrue(np.all(r_acc.data == t_acc.data))
+ def test_create_roiset_from_bounding_boxes(self):
+ from skimage.measure import label, regionprops, regionprops_table
+
+
+ mask = self.seg_mask_3d.data_xyz
+ labels = label(mask)
+ table = pd.DataFrame(
+ regionprops_table(labels)
+ ).rename(
+ columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'zi', 'bbox-3': 'y1', 'bbox-4': 'x1'}
+ ).drop(
+ columns=['bbox-5']
+ )
+ table['w'] = table['x1'] - table['x0']
+ table['h'] = table['y1'] - table['y0']
+
+
+ # bbox =
+ self.assertTrue(False)
+ # RoiSet.from_bounding_boxes(
+ # self.stack_ch_pa,
+ #
+ # )
+
+ # test segments reside in bounding boxes
+
class TestRoiSetPolygons(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_compute_polygons(self):
--
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