Test legacy Nd2, parser, reader fixes

nd2reader/raw_metadata.py

@@ -321,23 +321,21 @@ class RawMetadata(object):
         """Parse the metadata of the ND experiment
 
         """
+        self._metadata_parsed['experiment'] = {
+            'description': 'unknown',
+            'loops': []
+        }
+
         if self.image_metadata is None or six.b('SLxExperiment') not in self.image_metadata:
             return
 
         raw_data = self.image_metadata[six.b('SLxExperiment')]
 
-        experimental_data = {
-            'description': 'unknown',
-            'loops': []
-        }
-
         if six.b('wsApplicationDesc') in raw_data:
-            experimental_data['description'] = raw_data[six.b('wsApplicationDesc')].decode('utf8')
+            self._metadata_parsed['experiment']['description'] = raw_data[six.b('wsApplicationDesc')].decode('utf8')
 
         if six.b('uLoopPars') in raw_data:
-            experimental_data['loops'] = self._parse_loop_data(raw_data[six.b('uLoopPars')])
-
-        self._metadata_parsed['experiment'] = experimental_data
+            self._metadata_parsed['experiment']['loops'] = self._parse_loop_data(raw_data[six.b('uLoopPars')])
 
     @staticmethod
     def _get_loops_from_data(loop_data):

nd2reader/reader.py

@@ -180,6 +180,7 @@ class ND2Reader(FramesSequenceND):
 
         timesteps = np.array([])
         current_time = 0.0
+
         for loop in self.metadata['experiment']['loops']:
             if loop['stimulation']:
                 continue

tests/test_legacy.py

@@ -0,0 +1,38 @@
+import unittest
+import warnings
+
+from nd2reader.legacy import Nd2
+from nd2reader.reader import ND2Reader
+from nd2reader.artificial import ArtificialND2
+
+
+class TestLegacy(unittest.TestCase):
+    def test_init(self):
+        with ArtificialND2('test_data/legacy.nd2'):
+            with warnings.catch_warnings(record=True) as w:
+                # Cause all warnings to always be triggered.
+                warnings.simplefilter("always")
+                with Nd2('test_data/legacy.nd2') as reader:
+                    self.assertIsInstance(reader.reader, ND2Reader)
+                self.assertTrue(issubclass(w[0].category, DeprecationWarning))
+                self.assertEquals(str(w[0].message), "The 'Nd2' class is deprecated, please consider using the new" +
+                                  " ND2Reader interface which uses pims.")
+
+    def test_misc(self):
+        with ArtificialND2('test_data/legacy.nd2'):
+            with Nd2('test_data/legacy.nd2') as reader:
+                representation = "\n".join(["<Deprecated ND2 %s>" % reader.reader.filename,
+                                            "Created: Unknown",
+                                            "Image size: %sx%s (HxW)" % (reader.height, reader.width),
+                                            "Frames: %s" % len(reader.frames),
+                                            "Channels: %s" % ", ".join(["%s" % str(channel) for channel
+                                                                        in reader.channels]),
+                                            "Fields of View: %s" % len(reader.fields_of_view),
+                                            "Z-Levels: %s" % len(reader.z_levels)
+                                            ])
+                self.assertEquals(representation, str(reader))
+
+                # not implemented yet
+                self.assertEquals(reader.pixel_microns, None)
+
+                self.assertEquals(len(reader), 1)

tests/test_parser.py

@@ -25,8 +25,8 @@ class TestParser(unittest.TestCase):
             self.assertTrue(parser.supported)
 
     def test_cannot_open_wrong_version(self):
-        with ArtificialND2(self.test_file, version=('a', 'b')) as artificial:
-            artificial.close()
-
-        with open(self.test_file, 'rb') as fh:
-            self.assertRaises(InvalidVersionError, Parser, fh)
+        with ArtificialND2(self.test_file, version=('0', '0')) as _:
+            with open(self.test_file, 'rb') as fh:
+                with self.assertRaises(InvalidVersionError) as exception:
+                    Parser(fh)
+            self.assertEqual(str(exception.exception), "No parser is available for that version.")

tests/test_reader.py

@@ -4,6 +4,7 @@ import numpy as np
 from nd2reader.artificial import ArtificialND2
 from nd2reader.exceptions import EmptyFileError
 from nd2reader.reader import ND2Reader
+from nd2reader.parser import Parser
 
 
 class TestReader(unittest.TestCase):
@@ -12,20 +13,31 @@ class TestReader(unittest.TestCase):
 
     def test_init_and_init_axes(self):
         with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
-            reader = ND2Reader('test_data/test_nd2_reader.nd2')
+            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
+                attributes = artificial.data['image_attributes']['SLxImageAttributes']
+                self.assertEqual(reader.metadata['width'], attributes['uiWidth'])
+                self.assertEqual(reader.metadata['height'], attributes['uiHeight'])
 
-            attributes = artificial.data['image_attributes']['SLxImageAttributes']
-            self.assertEqual(reader.metadata['width'], attributes['uiWidth'])
-            self.assertEqual(reader.metadata['height'], attributes['uiHeight'])
+                self.assertEqual(reader.metadata['width'], reader.sizes['x'])
+                self.assertEqual(reader.metadata['height'], reader.sizes['y'])
 
-            self.assertEqual(reader.metadata['width'], reader.sizes['x'])
-            self.assertEqual(reader.metadata['height'], reader.sizes['y'])
-
-            self.assertEqual(reader._dtype, np.float64)
-            self.assertEqual(reader.iter_axes, ['t'])
+                self.assertEqual(reader.pixel_type, np.float64)
+                self.assertEqual(reader.iter_axes, ['t'])
 
     def test_init_empty_file(self):
         with ArtificialND2('test_data/empty.nd2', skip_blocks=['label_map_marker']):
             with self.assertRaises(EmptyFileError) as exception:
-                ND2Reader('test_data/empty.nd2')
+                with ND2Reader('test_data/empty.nd2'):
+                    pass
             self.assertEqual(str(exception.exception), "No axes were found for this .nd2 file.")
+
+    def test_get_parser(self):
+        with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
+            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
+                self.assertIsInstance(reader.parser, Parser)
+
+    def test_get_timesteps(self):
+        with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
+            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
+                timesteps = reader.timesteps
+                self.assertEquals(list(timesteps), [])