From 2958fa629cfcdff78d846c3bec443d0637f44b0b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 27 Sep 2023 15:46:46 +0200
Subject: [PATCH] Updated test data for zmask
---
extensions/chaeo/conf/testing.py | 12 ++++++------
extensions/chaeo/test_zstack.py | 2 ++
model_server/accessors.py | 12 ++++++++++++
3 files changed, 20 insertions(+), 6 deletions(-)
diff --git a/extensions/chaeo/conf/testing.py b/extensions/chaeo/conf/testing.py
index 13b5ea89..7a6b6953 100644
--- a/extensions/chaeo/conf/testing.py
+++ b/extensions/chaeo/conf/testing.py
@@ -2,12 +2,12 @@ from pathlib import Path
root = Path.home() / 'model-server'
-czi_multichannel_zstack = {
- 'path': root / 'testing' / 'proj0004-exp0038-SelectionA10-01.czi',
- 'w': 2048,
- 'h': 2048,
- 'c': 5,
- 'z': 21,
+multichannel_zstack = {
+ 'path': root / 'testing' / 'zmask-test-stack.tif',
+ 'w': 512,
+ 'h': 512,
+ 'c': 2,
+ 'z': 7,
}
pixel_classifier = {
diff --git a/extensions/chaeo/test_zstack.py b/extensions/chaeo/test_zstack.py
index 1f9fcf96..78baa64c 100644
--- a/extensions/chaeo/test_zstack.py
+++ b/extensions/chaeo/test_zstack.py
@@ -1,5 +1,6 @@
import unittest
+from extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier
from extensions.chaeo.zstack import build_stack_mask
from model_server.accessors import InMemoryDataAccessor
@@ -7,6 +8,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
def setUp(self) -> None:
# need test data incl obj map
+ self.zstack =
self.obmap = None
self.stack = None
diff --git a/model_server/accessors.py b/model_server/accessors.py
index d2b4da24..a2a28aaa 100644
--- a/model_server/accessors.py
+++ b/model_server/accessors.py
@@ -67,6 +67,18 @@ class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded
raise FileAccessorError(f'Could not find file at {fpath}')
self.fpath = fpath
+class ImageJTiffFileAccessor(GenericImageFileAccessor):
+ def __init__(self, fpath: Path):
+ super().__init__(fpath)
+
+ try:
+ tf = tifffile.TiffFile(fpath)
+ self.tf = tf
+ except Exception:
+ FileAccessorError(f'Unable to access data in {fpath}')
+
+ self._data = tf.asarray()
+
class CziImageFileAccessor(GenericImageFileAccessor):
"""
Image that is stored in a Zeiss .CZI file; may be multi-channel, and/or a z-stack,
--
GitLab