From 6b7cdc2ee4c13b5debdc44cb61947ced87eabe0e Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 27 Nov 2024 13:33:32 +0100
Subject: [PATCH] Added alternate constructor for RoiSet from either YX or YXZ
monochromatic data
---
model_server/base/accessors.py | 9 +++++++++
tests/base/test_accessors.py | 23 +++++++++++++++++++++--
2 files changed, 30 insertions(+), 2 deletions(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 7f1e763d..6dd63bc1 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -223,6 +223,15 @@ class InMemoryDataAccessor(GenericImageDataAccessor):
self._data = self.conform_data(data)
self.lazy = False
+ @classmethod
+ def from_mono(cls, data):
+ if len(data.shape) == 2: # interpret as YX
+ return cls(np.expand_dims(data, (2, 3)))
+ if len(data.shape) == 3:
+ return cls(np.expand_dims(data, 2))
+ else:
+ raise InvalidDataShape(f'Expecting either YX or YXZ monochromatic data')
+
class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded from a file
def __init__(self, fpath: Path, lazy=False):
"""
diff --git a/tests/base/test_accessors.py b/tests/base/test_accessors.py
index cdaa8345..f216f0ca 100644
--- a/tests/base/test_accessors.py
+++ b/tests/base/test_accessors.py
@@ -114,6 +114,25 @@ class TestCziImageFileAccess(unittest.TestCase):
acc = InMemoryDataAccessor(_random_int(h, w, nc, nz))
self.assertEqual(acc.get_mono(0).data_mono.shape, (h, w, nz))
+ def test_make_from_mono_2d(self):
+ w = 256
+ h = 512
+ nda = _random_int(h, w)
+ acc = InMemoryDataAccessor.from_mono(nda)
+ self.assertEqual(acc.chroma, 1)
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.nz, 1)
+
+ def test_make_from_mono_3d(self):
+ w = 256
+ h = 512
+ nz = 11
+ nda = _random_int(h, w, nz)
+ acc = InMemoryDataAccessor.from_mono(nda)
+ self.assertEqual(acc.chroma, 1)
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.nz, nz)
+
def test_crop_yx(self):
w = 256
h = 512
@@ -320,8 +339,8 @@ class TestPatchStackAccessor(unittest.TestCase):
# test that this persists after channel selection
for i in range(0, acc.count):
- self.assertEqual(patches[i].shape[0:2], acc.get_channels([0]).iat_data(i, crop=True).shape[0:2])
- self.assertEqual(patches[i].shape[3], acc.get_channels([0]).iat_data(i, crop=True).shape[3])
+ self.assertEqual(patches[i].shape[0:2], acc.get_channels([0]).iat(i, crop=True).shape[0:2])
+ self.assertEqual(patches[i].shape[3], acc.get_channels([0]).iat(i, crop=True).shape[3])
def test_write_nonuniform_patches(self):
w = 256
--
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