From caea291c6582f5ae3adfb2c5101ea525832f1e0f Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 20 Sep 2024 11:58:24 +0200
Subject: [PATCH] Can create RoiSet from bounding boxes; now working on
patch-level accessors
---
model_server/base/roiset.py | 41 +++++++++++++++----------------------
tests/base/test_roiset.py | 9 +++++---
2 files changed, 23 insertions(+), 27 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index ed8f44f8..fa622930 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -414,39 +414,32 @@ class RoiSet(object):
# deproject if zi is not specified
if bbox_zi is None:
- def _slice_zmax(r):
- acc_raw.crop_hw(
- r.y0,
- r.x0,
- r.y1 - r.y0,
- r.x1 - r.x0
- )
- # TODO: use accessor.get_z_argmax
- zmax = acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16')
+ dch = params.deproject_channel
+ if dch is None or dch >= acc_raw.chroma or dch < 0:
+ if acc_raw.chroma == 1:
+ dch = 0
+ else:
+ raise NoDeprojectChannelSpecifiedError(
+ f'When labeling objects, either their z-coordinates or a valid deprojection channel are required.'
+ )
+ bbox_df['zi'] = acc_raw.get_mono(dch).get_focus_vector().argmax()
else:
bbox_df['zi'] = bbox_zi
+ bbox_df['y0'] = bbox_df['y']
+ bbox_df['x0'] = bbox_df['x']
+ bbox_df['y1'] = bbox_df['y0'] + bbox_df['h']
+ bbox_df['x1'] = bbox_df['x0'] + bbox_df['w']
+
+
df = df_insert_slices(
- bbox_df,
+ bbox_df[['y0', 'x0', 'y1', 'x1', 'zi']],
acc_raw.shape_dict,
- params.get('expand_box_by', 0)
+ params.expand_box_by,
)
# TODO: don't even make binary_mask column in obj det case
- # def _make_binary_mask(r):
- # # 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)
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 497bcb03..6a516be0 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -645,22 +645,25 @@ class TestRoiSetObjectDetection(unittest.TestCase):
table = pd.DataFrame(
regionprops_table(labels)
).rename(
- columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'zi', 'bbox-3': 'y1', 'bbox-4': 'x1'}
+ columns={'bbox-0': 'y', 'bbox-1': 'x', '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']
+ table['w'] = table['x1'] - table['x']
+ table['h'] = table['y1'] - table['y']
+ bboxes = table[['y', 'x', 'h', 'w']].to_dict(orient='records')
roiset = RoiSet.from_bounding_boxes(
self.stack_ch_pa,
+ bboxes,
)
# test segments reside in bounding boxes
self.assertFalse(roiset.contains_segmentation)
+ patches = roiset.get_patches_acc()
self.assertTrue(False)
class TestRoiSetPolygons(BaseTestRoiSetMonoProducts, unittest.TestCase):
--
GitLab