From 5ccb314a28e3f7797d8b446471ef82e315a5da25 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 20 Sep 2024 10:33:24 +0200
Subject: [PATCH] Added and tested accessor method to run argmax on z-axis
---
model_server/base/accessors.py | 4 +++-
tests/base/test_accessors.py | 11 +++++++++++
2 files changed, 14 insertions(+), 1 deletion(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 98aba201..7f2f74d7 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -67,10 +67,12 @@ class GenericImageDataAccessor(ABC):
"""
return self.apply(lambda x: x.max(axis=self._ga('Z'), keepdims=True))
-
def get_mono(self, channel: int, mip: bool = False):
return self.get_channels([channel], mip=mip)
+ def get_z_argmax(self):
+ return self.apply(lambda x: x.argmax(axis=self.get_axis('Z')))
+
@property
def data_xy(self) -> np.ndarray:
if not self.chroma == 1 and self.nz == 1:
diff --git a/tests/base/test_accessors.py b/tests/base/test_accessors.py
index b4203070..452cb3c0 100644
--- a/tests/base/test_accessors.py
+++ b/tests/base/test_accessors.py
@@ -61,6 +61,17 @@ class TestCziImageFileAccess(unittest.TestCase):
sc = cf.get_mono(c, mip=True)
self.assertEqual(sc.shape, (h, w, 1, 1))
+ def test_get_single_channel_argmax_from_zstack(self):
+ w = 256
+ h = 512
+ nc = 4
+ nz = 11
+ c = 3
+ cf = InMemoryDataAccessor(np.random.rand(h, w, nc, nz))
+ am = cf.get_mono(c).get_z_argmax()
+ self.assertEqual(am.shape, (h, w, 1, 1))
+ self.assertTrue(np.all(am.unique()[0] == range(0, nz)))
+
def test_get_zi(self):
w = 256
h = 512
--
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