Test color channels, fix a bug in color channel encoding

nd2reader/artificial.py

@@ -197,6 +197,8 @@ class ArtificialND2(object):
             raw_data = struct.pack('I', data)
         elif isinstance(data, float):
             raw_data = struct.pack('d', data)
+        elif isinstance(data, str):
+            raw_data = self._str_to_padded_bytes(data)
 
         return raw_data
 
@@ -205,15 +207,21 @@ class ArtificialND2(object):
             return self.data_types['metadata_item']
         elif isinstance(data, int):
             return self.data_types['unsigned_int']
+        elif isinstance(data, str):
+            return self.data_types['string']
         else:
             return self.data_types['double']
 
+    @staticmethod
+    def _str_to_padded_bytes(data):
+        return six.b('').join([struct.pack('cx', six.b(s)) for s in data]) + struct.pack('xx')
+
     def _pack_dict_with_metadata(self, data):
         raw_data = b''
 
         for data_key in data.keys():
             # names have always one character extra and are padded in zero bytes???
-            b_data_key = six.b('').join([struct.pack('cx', six.b(s)) for s in data_key]) + struct.pack('xx')
+            b_data_key = self._str_to_padded_bytes(data_key)
 
             # header consists of data type and length of key name, it is represented by 2 unsigned chars
             raw_data += struct.pack('BB', self._get_data_type(data[data_key]), len(data_key) + 1)
@@ -256,7 +264,20 @@ class ArtificialND2(object):
             },  # ImageAttributesLV!",
             7,  # ImageTextInfoLV!",
             7,  # ImageMetadataLV!",
-            7,  # ImageMetadataSeqLV|0!",
+            {
+                'SLxPictureMetadata':
+                    {
+                        'sPicturePlanes':
+                            {
+                                'sPlaneNew': {
+                                    # channels are numbered a0, a1, ..., aN
+                                    'a0': {
+                                        'sDescription': 'TRITC'
+                                    }
+                                }
+                            }
+                    }
+            },  # ImageMetadataSeqLV|0!",
             7,  # ImageCalibrationLV|0!",
             7,  # CustomData|X!",
             7,  # CustomData|Y!",

nd2reader/common.py

@@ -165,7 +165,7 @@ def _parse_string(data):
     try:
         decoded = value.decode("utf16")[:-1].encode("utf8")
     except UnicodeDecodeError:
-        decoded = value.decode('utf8')
+        decoded = value.decode('utf8').encode("utf8")
 
     return decoded
 

nd2reader/raw_metadata.py

@@ -136,7 +136,10 @@ class RawMetadata(object):
         for (label, chan), valid in zip(sorted(metadata[six.b('sPlaneNew')].items()), validity):
             if not valid:
                 continue
-            channels.append(chan[six.b('sDescription')].decode("utf8"))
+            if chan[six.b('sDescription')] is not None:
+                channels.append(chan[six.b('sDescription')].decode("utf8"))
+            else:
+                channels.append('Unknown')
         return channels
 
     def _parse_fields_of_view(self):

tests/test_common.py

@@ -104,7 +104,7 @@ class TestCommon(unittest.TestCase):
         test_string = 'colloid'
         file = self._prepare_bin_stream("%ds" % len(test_string), six.b(test_string))
         parsed = _parse_string(file)
-        self.assertEqual(parsed, test_string)
+        self.assertEqual(parsed, six.b(test_string))
 
         test_data = [1, 2, 3, 4, 5]
         file = self._prepare_bin_stream("Q" + ''.join(['B'] * len(test_data)), len(test_data), *test_data)

tests/test_raw_metadata.py

@@ -57,3 +57,8 @@ class TestRawMetadata(unittest.TestCase):
         parsed_dict = self.metadata.image_attributes
 
         self._assert_dicts_equal(parsed_dict, self.file_data['image_attributes'])
+
+    def test_color_channels(self):
+        parsed_channels = self.metadata.get_parsed_metadata()['channels']
+
+        self.assertEquals(parsed_channels, ['TRITC'])