From 25ed79557e98d166a0a302526bcc07a6313d0238 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 2 Nov 2023 15:20:24 +0100
Subject: [PATCH] Added method to cast patch as YXCZ array
---
extensions/chaeo/accessors.py | 3 +++
extensions/chaeo/tests/test_accessors.py | 9 ++++++++-
2 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/extensions/chaeo/accessors.py b/extensions/chaeo/accessors.py
index 5d2987fa..2b23318b 100644
--- a/extensions/chaeo/accessors.py
+++ b/extensions/chaeo/accessors.py
@@ -44,6 +44,9 @@ class MonoPatchStack(InMemoryDataAccessor):
def iat(self, i):
return self.data[:, :, 0, i]
+ def iat_yxcz(self, i):
+ return np.expand_dims(self.iat(i), (2, 3))
+
def get_list(self):
n = self.nz
return [self.data[:, :, 0, zi] for zi in range(0, n)]
diff --git a/extensions/chaeo/tests/test_accessors.py b/extensions/chaeo/tests/test_accessors.py
index 40192575..c74fdd86 100644
--- a/extensions/chaeo/tests/test_accessors.py
+++ b/extensions/chaeo/tests/test_accessors.py
@@ -43,4 +43,11 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_raises_filenotfound(self):
from extensions.chaeo.accessors import FileNotFoundError
with self.assertRaises(FileNotFoundError):
- acc = MonoPatchStackFromFile('c:/fake/file/name.tif')
\ No newline at end of file
+ acc = MonoPatchStackFromFile('c:/fake/file/name.tif')
+
+ def test_patch_as_yxcz_array(self):
+ w = 256
+ h = 512
+ n = 4
+ acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, 4)])
+ self.assertEqual(acc.iat_yxcz(0).shape, (h, w, 1, 1))
\ No newline at end of file
--
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