From b0847605bf7d00177938a4a26b2e288089be1f38 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 2 Nov 2023 15:50:09 +0100
Subject: [PATCH] Expanded 3d patch stack as 3d multichannel patch stack
---
extensions/chaeo/accessors.py | 47 +++++++++++++++---------
extensions/chaeo/tests/test_accessors.py | 14 ++++---
2 files changed, 38 insertions(+), 23 deletions(-)
diff --git a/extensions/chaeo/accessors.py b/extensions/chaeo/accessors.py
index c62a7ff5..f606470e 100644
--- a/extensions/chaeo/accessors.py
+++ b/extensions/chaeo/accessors.py
@@ -63,38 +63,51 @@ class MonoPatchStackFromFile(MonoPatchStack):
def fpath(self):
return self.file_acc.fpath
-class PatchStack3D(InMemoryDataAccessor):
+class Multichannel3dPatchStack(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
+ A sequence of n (generally) color 3D images of the same size
+ :param data: a list of np.ndarrays of size YXCZ
"""
- 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]
- )
+ if isinstance(data, list): # list of YXCZ patches
+ nda = np.array(data)
+ assert nda.ndim == 5
+ # self._data = np.moveaxis( # pos-YXCZ
+ # nda,
+ # [0, 1, 2, 0, 3],
+ # [0, 1, 2, 3]
+ # )
+ self._data = nda
else:
raise InvalidDataForPatchStackError(f'Cannot create accessor from {type(data)}')
def iat(self, i):
- return self.data[:, :, i, :]
+ return self.data[i, :, :, :, :]
def iat_yxcz(self, i):
- return np.expand_dims(self.iat(i), 2)
+ return self.iat(i)
@property
- def chroma(self):
- return 1
+ def count(self):
+ return self.shape_dict['P']
@property
- def count(self):
- return self.shape[2]
+ def data(self):
+ """
+ Return data as 5d with axes in order of pos, Y, X, C, Z
+ :return: np.ndarray
+ """
+ return self._data
+
+ @property
+ def shape(self):
+ return self._data.shape
+
+ @property
+ def shape_dict(self):
+ return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
class Error(Exception):
pass
diff --git a/extensions/chaeo/tests/test_accessors.py b/extensions/chaeo/tests/test_accessors.py
index 461c34d7..c2194581 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, PatchStack3D
+from extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile, Multichannel3dPatchStack
@@ -55,18 +55,20 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_make_3d_patch_stack_from_list(self):
w = 256
h = 512
+ c = 1
nz = 5
n = 4
- acc = PatchStack3D([np.random.rand(h, w, nz) for _ in range(0, n)])
+ acc = Multichannel3dPatchStack([np.random.rand(h, w, c, 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))
+ self.assertEqual(acc.chroma, c)
+ self.assertEqual(acc.iat(0).shape, (h, w, c, nz))
def test_3d_patch_as_yxcz_array(self):
w = 256
h = 512
nz = 5
+ c = 1
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
+ acc = Multichannel3dPatchStack([np.random.rand(h, w, c, nz) for _ in range(0, n)])
+ self.assertEqual(acc.iat_yxcz(0).shape, (h, w, c, nz))
\ No newline at end of file
--
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