From 18f28496eadae26dd3b0e9572bf1b026a7f727a3 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 19 Feb 2024 12:45:14 +0100
Subject: [PATCH] Added PCZYX getter mainly for ilastik use
---
model_server/extensions/chaeo/accessors.py | 11 +++++++++--
.../extensions/chaeo/tests/test_accessors.py | 13 ++++++++++++-
2 files changed, 21 insertions(+), 3 deletions(-)
diff --git a/model_server/extensions/chaeo/accessors.py b/model_server/extensions/chaeo/accessors.py
index ee9bfd07..45eee67b 100644
--- a/model_server/extensions/chaeo/accessors.py
+++ b/model_server/extensions/chaeo/accessors.py
@@ -127,11 +127,18 @@ class PatchStack(InMemoryDataAccessor):
@property
def pyxcz(self):
- return self._data
+ return self.data
@property
+ def pczyx(self):
+ return np.moveaxis(
+ self.data,
+ [0, 3, 4, 1, 2],
+ [0, 1, 2, 3, 4]
+ )
+ @property
def shape(self):
- return self._data.shape
+ return self.data.shape
@property
def shape_dict(self):
diff --git a/model_server/extensions/chaeo/tests/test_accessors.py b/model_server/extensions/chaeo/tests/test_accessors.py
index 086b405c..0aa364c7 100644
--- a/model_server/extensions/chaeo/tests/test_accessors.py
+++ b/model_server/extensions/chaeo/tests/test_accessors.py
@@ -61,4 +61,15 @@ class TestMultipositionCziImageFileAccess(unittest.TestCase):
self.assertEqual(acc.hw, (h, 2 * w))
self.assertEqual(acc.chroma, c)
self.assertEqual(acc.iat(0).shape, (h, 2 * w, c, nz))
- self.assertEqual(acc.iat_yxcz(0).shape, (h, 2 * w, c, nz))
\ No newline at end of file
+ self.assertEqual(acc.iat_yxcz(0).shape, (h, 2 * w, c, nz))
+
+ def test_pczyx(self):
+ w = 256
+ h = 512
+ n = 4
+ nz = 15
+ nc = 2
+ acc = PatchStack(np.random.rand(n, h, w, nc, nz))
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.pczyx.shape, (n, nc, nz, h, w))
+ self.assertEqual(acc.hw, (h, w))
--
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