From 8f3d5bc401303f15b4747652c2fefa9160543112 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 29 Nov 2024 15:09:29 +0100
Subject: [PATCH] Deserialization does not solve deprojection a second time; a
deprojected RoiSet is serialized as 3D. Tight patch mask format depends on
dimensions of ROIs themselves, so 2d PNGs are possible in a 3D set if no ROI
is thicker than 1
---
model_server/base/roiset.py | 11 ++++++-----
tests/base/test_roiset_pipeline.py | 23 ++++++++++++-----------
2 files changed, 18 insertions(+), 16 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 509650a2..ccd79c2d 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -320,6 +320,7 @@ def make_df_from_object_ids(
return rel_argzmax + r.z0
df['zi'] = df.apply(_get_zi_from_label, axis=1)
+ df['nz'] = df['z1'] - df['z0']
def _make_binary_mask(r):
r = r.convert_dtypes()
@@ -809,7 +810,10 @@ class RoiSet(object):
def export_patch_masks(self, where: Path, pad_to: int = None, prefix='mask', expanded=False) -> pd.DataFrame:
patches_df = self.get_patch_masks(pad_to=pad_to, expanded=expanded).copy()
- ext = 'tif' if is_df_3d(patches_df) else 'png'
+ if 'nz' in patches_df.columns and any(patches_df['nz'] > 1):
+ ext = 'tif'
+ else:
+ ext = 'png'
def _export_patch_mask(roi):
patch = InMemoryDataAccessor.from_mono(roi.patch_mask)
@@ -1214,10 +1218,7 @@ class RoiSet(object):
df['binary_mask'] = df.apply(_read_binary_mask, axis=1)
id_mask = make_object_ids_from_df(df, acc_raw.shape_dict)
- if not is_3d and id_mask.nz > 1:
- return cls.from_object_ids(acc_raw, id_mask.get_mip())
- else:
- return cls.from_object_ids(acc_raw, id_mask)
+ return cls.from_object_ids(acc_raw, id_mask)
else: # assume bounding boxes, exclusively 2d objects
df['y'] = df['y0']
diff --git a/tests/base/test_roiset_pipeline.py b/tests/base/test_roiset_pipeline.py
index 15c32145..641c887a 100644
--- a/tests/base/test_roiset_pipeline.py
+++ b/tests/base/test_roiset_pipeline.py
@@ -33,16 +33,17 @@ class BaseTestRoiSetMonoProducts(object):
def _get_export_params(self):
return {
- 'patches_3d': None,
- 'annotated_patches_2d': {
- 'draw_bounding_box': True,
- 'rgb_overlay_channels': [3, None, None],
- 'rgb_overlay_weights': [0.2, 1.0, 1.0],
- 'pad_to': 512,
- },
- 'patches_2d': {
- 'draw_bounding_box': False,
- 'draw_mask': False,
+ 'patches': {
+ '2d_annotated': {
+ 'draw_bounding_box': True,
+ 'rgb_overlay_channels': [3, None, None],
+ 'rgb_overlay_weights': [0.2, 1.0, 1.0],
+ 'pad_to': 512,
+ },
+ '2d': {
+ 'draw_bounding_box': False,
+ 'draw_mask': False,
+ },
},
'annotated_zstacks': None,
'object_classes': True,
@@ -102,7 +103,7 @@ class TestRoiSetWorkflow(BaseTestRoiSetMonoProducts, unittest.TestCase):
{f'{k}_': v['model'] for k, v in self._get_models().items()},
**params.dict()
)
- self.assertEqual(trace.pop('annotated_patches_2d').count, n_rois)
+ self.assertEqual(trace.pop('patches_2d_annotated').count, n_rois)
self.assertEqual(trace.pop('patches_2d').count, n_rois)
trace.write_interm(Path(output_path) / 'trace', 'roiset_worfklow_trace', skip_first=False, skip_last=False)
self.assertTrue('ob_id' in trace.keys())
--
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