From 2491ddf1f4c2c5f80948828e3fdbdcaa00876845 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Dec 2023 14:50:25 +0100
Subject: [PATCH] Can make patch stack from itself
---
extensions/chaeo/accessors.py | 10 +++++++---
extensions/chaeo/tests/test_accessors.py | 8 ++++++++
2 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/extensions/chaeo/accessors.py b/extensions/chaeo/accessors.py
index 60cc2c70..c24ab7d6 100644
--- a/extensions/chaeo/accessors.py
+++ b/extensions/chaeo/accessors.py
@@ -12,9 +12,13 @@ class MonoPatchStack(InMemoryDataAccessor):
:param data: either np.ndarray of dimensions YXn, or a list of np.ndarrays of size YX
"""
- if isinstance(data, np.ndarray): # interpret as YXZ
- assert data.ndim == 3
- self._data = np.expand_dims(data, 2)
+ if isinstance(data, np.ndarray):
+ if data.ndim == 3: # interpret as YXZ
+ self._data = np.expand_dims(data, 2)
+ elif data.ndim == 4: # interpret as a copy another patch stack
+ self._data = data
+ else:
+ raise InvalidDataForPatchStackError()
elif isinstance(data, list): # list of YX patches
if len(data) == 0:
self._data = np.ndarray([0, 0, 0, 0], dtype='uin9')
diff --git a/extensions/chaeo/tests/test_accessors.py b/extensions/chaeo/tests/test_accessors.py
index c2194581..52935598 100644
--- a/extensions/chaeo/tests/test_accessors.py
+++ b/extensions/chaeo/tests/test_accessors.py
@@ -28,6 +28,14 @@ class TestCziImageFileAccess(unittest.TestCase):
self.assertEqual(acc.count, n)
self.assertEqual(acc.hw, (h, w))
self.assertEqual(acc.make_tczyx().shape, (n, 1, 1, h, w))
+ return acc
+
+ def test_make_patch_stack_clone(self):
+ w = 256
+ h = 512
+ n = 4
+ acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, n)])
+ self.assertEqual(MonoPatchStack(acc.data).shape, acc.shape)
def test_make_patch_stack_from_file(self):
h = monozstackmask['h']
--
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