From 40be402fb4d097432a30d760d0fd709dccc91c12 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 2 Nov 2023 15:40:12 +0100
Subject: [PATCH] Added 3D patch accessor
---
extensions/chaeo/accessors.py | 33 ++++++++++++++++++++++++
extensions/chaeo/tests/test_accessors.py | 29 +++++++++++++++++----
2 files changed, 57 insertions(+), 5 deletions(-)
diff --git a/extensions/chaeo/accessors.py b/extensions/chaeo/accessors.py
index 2b23318b..c62a7ff5 100644
--- a/extensions/chaeo/accessors.py
+++ b/extensions/chaeo/accessors.py
@@ -63,6 +63,39 @@ class MonoPatchStackFromFile(MonoPatchStack):
def fpath(self):
return self.file_acc.fpath
+class PatchStack3D(InMemoryDataAccessor):
+
+ def __init__(self, data):
+ """
+ A sequence of n monochrome 3D images of the same size
+ :param data: a list of np.ndarrays of size YXZ
+ """
+
+ if isinstance(data, list): # list of YXZ patches
+ nda = np.array(data).squeeze()
+ assert nda.ndim == 4
+ self._data = np.moveaxis(
+ nda,
+ [1, 2, 0, 3],
+ [0, 1, 2, 3]
+ )
+ else:
+ raise InvalidDataForPatchStackError(f'Cannot create accessor from {type(data)}')
+
+ def iat(self, i):
+ return self.data[:, :, i, :]
+
+ def iat_yxcz(self, i):
+ return np.expand_dims(self.iat(i), 2)
+
+ @property
+ def chroma(self):
+ return 1
+
+ @property
+ def count(self):
+ return self.shape[2]
+
class Error(Exception):
pass
diff --git a/extensions/chaeo/tests/test_accessors.py b/extensions/chaeo/tests/test_accessors.py
index c74fdd86..461c34d7 100644
--- a/extensions/chaeo/tests/test_accessors.py
+++ b/extensions/chaeo/tests/test_accessors.py
@@ -3,7 +3,7 @@ import unittest
import numpy as np
from conf.testing import monozstackmask
-from extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile
+from extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile, PatchStack3D
@@ -11,7 +11,7 @@ class TestCziImageFileAccess(unittest.TestCase):
def setUp(self) -> None:
pass
- def test_make_patch_stack_from_list(self):
+ def test_make_patch_stack_from_3d_array(self):
w = 256
h = 512
n = 4
@@ -20,11 +20,11 @@ class TestCziImageFileAccess(unittest.TestCase):
self.assertEqual(acc.hw, (h, w))
self.assertEqual(acc.make_tczyx().shape, (n, 1, 1, h, w))
- def test_make_patch_stack_from_3d_array(self):
+ def test_make_patch_stack_from_list(self):
w = 256
h = 512
n = 4
- acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, 4)])
+ acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, n)])
self.assertEqual(acc.count, n)
self.assertEqual(acc.hw, (h, w))
self.assertEqual(acc.make_tczyx().shape, (n, 1, 1, h, w))
@@ -50,4 +50,23 @@ class TestCziImageFileAccess(unittest.TestCase):
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
+ self.assertEqual(acc.iat_yxcz(0).shape, (h, w, 1, 1))
+
+ def test_make_3d_patch_stack_from_list(self):
+ w = 256
+ h = 512
+ nz = 5
+ n = 4
+ acc = PatchStack3D([np.random.rand(h, w, nz) for _ in range(0, n)])
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.chroma, 1)
+ self.assertEqual(acc.iat(0).shape, (h, w, nz))
+
+ def test_3d_patch_as_yxcz_array(self):
+ w = 256
+ h = 512
+ nz = 5
+ n = 4
+ acc = PatchStack3D([np.random.rand(h, w, nz) for _ in range(0, n)])
+ self.assertEqual(acc.iat_yxcz(0).shape, (h, w, 1, nz))
\ No newline at end of file
--
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