From 74f655f87a12503f54cc1459c5d18cf618182b10 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 5 Sep 2023 15:45:29 +0200
Subject: [PATCH] Isolated and corrected bug pulling single-channel data from
z-stack
---
model_server/image.py | 5 +++--
tests/test_image.py | 10 ++++++++++
2 files changed, 13 insertions(+), 2 deletions(-)
diff --git a/model_server/image.py b/model_server/image.py
index c700ea66..5d16d980 100644
--- a/model_server/image.py
+++ b/model_server/image.py
@@ -24,7 +24,7 @@ class GenericImageDataAccessor(ABC):
@staticmethod
def conform_data(data):
- if len(data.shape) > 4:
+ if len(data.shape) > 4 or (0 in data.shape):
raise DataShapeError(f'Cannot handle image with dimensions other than X, Y, C, and Z: {data.shape}')
ones = [1 for i in range(0, 4 - len(data.shape))]
return data.reshape(*data.shape, *ones)
@@ -33,7 +33,8 @@ class GenericImageDataAccessor(ABC):
return True if self.shape_dict['Z'] > 1 else False
def get_one_channel_data (self, channel: int):
- return InMemoryDataAccessor(self.data[:, :, int(channel), :])
+ c = int(channel)
+ return InMemoryDataAccessor(self.data[:, :, c:(c+1), :])
@property
def data(self):
diff --git a/tests/test_image.py b/tests/test_image.py
index 7f6df822..83d25ba1 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -20,6 +20,16 @@ class TestCziImageFileAccess(unittest.TestCase):
self.assertEqual(cf.shape[0], czifile['h'])
self.assertEqual(cf.shape[1], czifile['w'])
+ def test_get_single_channel_from_zstack(self):
+ w = 256
+ h = 512
+ nc = 4
+ nz = 11
+ c = 3
+ cf = InMemoryDataAccessor(np.random.rand(w, h, nc, nz))
+ sc = cf.get_one_channel_data(c)
+ self.assertEqual(sc.shape, (w, h, 1, nz))
+
def test_write_single_channel_tif(self):
ch = 4
cf = CziImageFileAccessor(czifile['path'])
--
GitLab