From ee6740a1d59f1525ce63bdf047a0af5fd8a3e3e8 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sat, 7 Dec 2024 08:58:31 +0100
Subject: [PATCH] Getting a patch mask can optionally update patch focus
---
model_server/base/roiset.py | 22 +++++++++++++++-------
tests/base/test_roiset.py | 26 ++++++++++++++++++++++++++
2 files changed, 41 insertions(+), 7 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 510b9fe3..0a8775e6 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -40,6 +40,10 @@ class PatchParams(BaseModel):
pad_to: Union[int, None] = 256
expanded: bool = False
force_tif: bool = False
+ update_focus_zi: bool = Field(
+ False,
+ description='If generating 2d patches with a 3d focus metric, update the RoiSet patch focus zi accordingly'
+ )
class AnnotatedPatchParams(PatchParams):
bounding_box_channel: int = 1
@@ -888,6 +892,7 @@ class RoiSet(object):
rgb_overlay_weights: list = [1.0, 1.0, 1.0],
white_channel: int = None,
expanded=False,
+ update_focus_zi=False,
**kwargs
) -> pd.Series:
@@ -937,7 +942,7 @@ class RoiSet(object):
else:
stack = raw.data
- def _make_patch(roi):
+ def _make_patch(roi): # extract, focus, and annotate a patch
if expanded:
patch3d = stack[roi.expanded_slice]
subpatch = patch3d[roi.relative_slice]
@@ -947,11 +952,11 @@ class RoiSet(object):
ph, pw, pc, pz = patch3d.shape
- # make a 3d patch
+ # make a 3d patch, focus stays where it is
if make_3d:
patch = patch3d.copy()
+ zif = roi.zi
- # TODO: somehow persist the result of patch focusing for use by patch mask exporter
# make a 2d patch, find optimal z-position determined by focus_metric function on each channel separately
elif focus_metric is not None:
foc = focus_metrics()[focus_metric]
@@ -965,8 +970,8 @@ class RoiSet(object):
# make a 2d patch from middle of z-stack
else:
- zim = floor(pz / 2)
- patch = patch3d[:, :, :, [zim]]
+ zif = floor(pz / 2)
+ patch = patch3d[:, :, :, [zif]]
assert len(patch.shape) == 4
@@ -1012,9 +1017,12 @@ class RoiSet(object):
if pad_to and expanded:
patch = pad(patch, pad_to)
- return patch
+ return {'patch': patch, 'zif': zif}
- return self._df.apply(lambda r: _make_patch(r), axis=1)
+ df_processed_patches = self._df.apply(lambda r: _make_patch(r), axis=1, result_type='expand')
+ if update_focus_zi:
+ self._df['zi'] = df_processed_patches['zif']
+ return df_processed_patches['patch']
@property
def classification_columns(self):
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index e0b9168d..376b8b44 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -296,6 +296,7 @@ class TestRoiSet3dProducts(unittest.TestCase):
'draw_mask': False,
'pad_to': None,
'rgb_overlay_channels': None,
+ 'update_focus_zi': False,
},
'3d_masks': {
'make_3d': True,
@@ -324,6 +325,31 @@ class TestRoiSet3dProducts(unittest.TestCase):
self.assertTrue(any([_get_nz_from_file(f) > 1 for f in res['patches_3d_masks']]))
self.assertTrue(all([_get_nz_from_file(f) == 1 for f in res['patches_2d_masks']]))
+ def test_run_update_focus_during_patch_export(self):
+ p = RoiSetExportParams(**{
+ 'patches': {
+ '2d': {
+ 'make_3d': False,
+ 'focus_metric': 'max_sobel',
+ 'white_channel': -1,
+ 'draw_bounding_box': False,
+ 'draw_mask': False,
+ 'pad_to': None,
+ 'rgb_overlay_channels': None,
+ 'update_focus_zi': True,
+ },
+ },
+ })
+ roiset = self.test_create_roiset_from_3d_obj_ids()
+ starting_zi = roiset.get_df()['zi']
+
+ res = roiset.run_exports(
+ self.where,
+ prefix='test',
+ params=p
+ )
+ updated_zi = roiset.get_df()['zi']
+ self.assertTrue((starting_zi != updated_zi).any())
def test_run_export_mono_3d_labels_overlay(self):
# export via .run_exports() method
--
GitLab