From 25a7d75b79f180e8a616472edd5b8f23bfe39d57 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 26 Nov 2024 06:58:27 +0100
Subject: [PATCH] Merged in changes from remote
---
model_server/base/roiset.py | 17 +++++++++--------
tests/base/test_roiset.py | 15 +++++++++------
2 files changed, 18 insertions(+), 14 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index bd94b33e..8190377a 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -19,7 +19,7 @@ from skimage.morphology import binary_dilation, disk
from .accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from .models import InstanceMaskSegmentationModel
-from .process import get_safe_contours, pad, rescale, make_rgb
+from .process import get_safe_contours, pad, rescale, make_rgb, resample_to_8bit
from .annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
from .accessors import generate_file_accessor, PatchStack
from .process import mask_largest_object
@@ -42,6 +42,11 @@ class AnnotatedPatchParams(PatchParams):
bounding_box_channel: int = 1
bounding_box_linewidth: int = 2
+class RoiSetLabelsOverlayParams(BaseModel):
+ white_channel: int
+ transparency: float = 0.5
+ mip: bool = False
+ rescale_clip: Union[float, None] = None
class AnnotatedZStackParams(BaseModel):
draw_label: bool = False
@@ -67,10 +72,6 @@ class RoiSetMetaParams(BaseModel):
class RoiSetExportParams(BaseModel):
- class RoiSetLabelsOverlayParams(BaseModel):
- transparency: float = 0.5
- mip: bool = False
- rescale_clip: Union[float, None] = None
patches_3d: Union[PatchParams, None] = None
annotated_patches_2d: Union[AnnotatedPatchParams, None] = None
patches_2d: Union[PatchParams, None] = None
@@ -769,7 +770,7 @@ class RoiSet(object):
fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
if patch.dtype == 'uint16':
- resampled = patch.apply(resample_to_8bit)
+ resampled = patch.to_8bit()
write_accessor_data_to_file(where / fname, resampled)
else:
write_accessor_data_to_file(where / fname, patch)
@@ -997,7 +998,7 @@ class RoiSet(object):
dacc.export_pyxcz(fp)
record[k].append(str(fp))
if k == 'labels_overlay':
- fn = self.export_object_identities_overlay_map(subdir, prefix=prefix, white_channel=channel, **kp)
+ fn = self.export_object_identities_overlay_map(subdir, prefix=prefix, **kp)
record[k] = str(Path(k) / fn)
# export dataframe and patch masks
@@ -1034,7 +1035,7 @@ class RoiSet(object):
for n in cnames:
interm[f'{k}_{n}'] = self.get_object_class_map(n)
if k == 'labels_overlay':
- interm[k] = self.get_object_identities_overlay_map(channel, **kp)
+ interm[k] = self.get_object_identities_overlay_map(**kp)
return interm
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index c9d01b2c..9fc1ff74 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -373,8 +373,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
# export z-stack product
acc_out = self.roiset.get_export_product_accessors(
- channel=-1,
- params=RoiSetExportParams(**{'labels_overlay': {'transparency': 0.5}})
+ params=RoiSetExportParams(**{'labels_overlay': {'white_channel': -1, 'transparency': 0.5}})
)['labels_overlay']
self.assertEqual(acc_out.chroma, 3)
self.assertGreater(acc_out.nz, 1)
@@ -382,8 +381,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
# export MIP product
acc_out = self.roiset.get_export_product_accessors(
- channel=0,
- params=RoiSetExportParams(**{'labels_overlay': {'transparency': 0.2, 'mip': True}})
+ params=RoiSetExportParams(**{'labels_overlay': {'white_channel': 0, 'transparency': 0.2, 'mip': True}})
)['labels_overlay']
self.assertEqual(acc_out.chroma, 3)
self.assertEqual(acc_out.nz, 1)
@@ -392,9 +390,14 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
# export via .run_exports() method
self.roiset.run_exports(
where,
- channel=-1,
prefix='run_exports',
- params=RoiSetExportParams(**{'labels_overlay': {'transparency': 0.2, 'mip': True, 'rescale_clip': 0.00}})
+ params=RoiSetExportParams(
+ **{
+ 'labels_overlay': {
+ 'white_channel': -1, 'transparency': 0.2, 'mip': True, 'rescale_clip': 0.00
+ }
+ }
+ )
)
--
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