From 1263a4e6cde070d73474005c6d98710b844f798b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 4 Apr 2024 15:17:40 +0200
Subject: [PATCH] Allow None as an argument to rgb_overlay_channels, indicating
export of mono patches
---
model_server/base/roiset.py | 2 +-
tests/test_roiset.py | 31 ++++++++++++++++++++++++++++++-
2 files changed, 31 insertions(+), 2 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index e50068d7..dd3139a1 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -28,7 +28,7 @@ class PatchParams(BaseModel):
draw_mask: bool = False
rescale_clip: float = 0.001
focus_metric: str = 'max_sobel'
- rgb_overlay_channels: List[Union[int, None]] = [None, None, None]
+ rgb_overlay_channels: Union[List[Union[int, None]], None] = None
rgb_overlay_weights: List[float] = [1.0, 1.0, 1.0]
pad_to: int = 256
expanded: bool = False
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index de58f25f..e281b7a0 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -428,9 +428,38 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertEqual(pacc.hw, (256, 256))
print('res')
+ def test_run_export_mono_2d_patch(self):
+ p = RoiSetExportParams(**{
+ 'patches_2d': {
+ 'draw_bounding_box': False,
+ 'draw_mask': False,
+ 'expanded': True,
+ 'pad_to': 256,
+ 'rgb_overlay_channels': None,
+ },
+ })
+ self.assertTrue(hasattr(p.patches_2d, 'pad_to'))
+ self.assertTrue(hasattr(p.patches_2d, 'expanded'))
+
+ where = output_path / 'run_exports_mono_2d_patch'
+ res = self.roiset.run_exports(
+ where,
+ channel=-1,
+ prefix='test',
+ params=p
+ )
+
+ # test that exported patches are padded dimension
+ for fn in res['patches_2d']:
+ pa = where / fn
+ self.assertTrue(pa.exists())
+ pacc = generate_file_accessor(pa)
+ self.assertEqual(pacc.chroma, 1)
+ print('res')
+
-class TestRoiSetFromZmask(unittest.TestCase):
+class TestRoiSetSerialization(unittest.TestCase):
def setUp(self) -> None:
# set up test raw data and segmentation from file
--
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