Updated test data for zmask

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 = {

extensions/chaeo/test_zstack.py

 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
 

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,