Very basic Reader test

nd2reader/reader.py

@@ -108,15 +108,27 @@ class ND2Reader(FramesSequenceND):
         """
         return self._dtype
 
+    def _get_metadata_property(self, key, default=None):
+        if self.metadata is None:
+            return default
+
+        if key not in self.metadata:
+            return default
+
+        if self.metadata[key] is None:
+            return default
+
+        return self.metadata[key]
+
     def _setup_axes(self):
         """Setup the xyctz axes, iterate over t axis by default
 
         """
-        self._init_axis('x', self.metadata["width"])
-        self._init_axis('y', self.metadata["height"])
-        self._init_axis('c', len(self.metadata["channels"]))
-        self._init_axis('t', len(self.metadata["frames"]))
-        self._init_axis('z', len(self.metadata["z_levels"]))
+        self._init_axis('x', self._get_metadata_property("width", default=0))
+        self._init_axis('y', self._get_metadata_property("height", default=0))
+        self._init_axis('c', len(self._get_metadata_property("channels", default=[])))
+        self._init_axis('t', len(self._get_metadata_property("frames", default=[])))
+        self._init_axis('z', len(self._get_metadata_property("z_levels", default=[])))
 
         # provide the default
         self.iter_axes = 't'

tests/test_reader.py

@@ -1,8 +1,30 @@
 import unittest
+from os import path
+import numpy as np
 
+from nd2reader.artificial import ArtificialND2
 from nd2reader.reader import ND2Reader
 
 
 class TestReader(unittest.TestCase):
+    def create_test_nd2(self):
+        with ArtificialND2(self.test_file) as artificial:
+            artificial.close()
+
+    def setUp(self):
+        dir_path = path.dirname(path.realpath(__file__))
+        self.test_file = path.join(dir_path, 'test_data/test.nd2')
+
+    def test_can_open_test_file(self):
+        self.create_test_nd2()
+        with ND2Reader(self.test_file) as reader:
+            self.assertEqual(reader.filename, self.test_file)
+            self.assertEqual(reader.pixel_type, np.float64)
+            self.assertEqual(reader.sizes['x'], 0)
+            self.assertEqual(reader.sizes['y'], 0)
+            self.assertEqual(reader.sizes['z'], 1)
+            self.assertEqual(reader.sizes['c'], 0)
+            self.assertEqual(reader.sizes['t'], 1)
+
     def test_extension(self):
         self.assertTrue('nd2' in ND2Reader.class_exts())