resolves #123: the label map and raw metadata are now accessible, so we can more easily compare what they contain to the information in the XML (which we're still not parsing)

functional_tests/single.py

@@ -25,6 +25,13 @@ class FunctionalTests(unittest.TestCase):
     def test_length(self):
         self.assertEqual(len(self.nd2), 1)
 
+    def test_actual_length(self):
+        count = 0
+        for image in self.nd2:
+            if image is not None:
+                count += 1
+        self.assertEqual(len(self.nd2), count)
+
     def test_frames(self):
         self.assertEqual(len(self.nd2.frames), 1)
 

nd2reader/driver/v3.py

@@ -130,7 +130,7 @@ class V3Driver(object):
         :raises:    NoImageError
 
         """
-        chunk = self._label_map[six.b("ImageDataSeq|%d!" % image_group_number)]
+        chunk = self._label_map.get_image_data_location(image_group_number)
         data = read_chunk(self._file_handle, chunk)
         # All images in the same image group share the same timestamp! So if you have complicated image data,
         # your timestamps may not be entirely accurate. Practically speaking though, they'll only be off by a few

nd2reader/model/label.py

@@ -8,6 +8,7 @@ class LabelMap(object):
     """
     def __init__(self, raw_binary_data):
         self._data = raw_binary_data
+        self._image_data = {}
 
     def _get_location(self, label):
         try:
@@ -33,15 +34,14 @@ class LabelMap(object):
         # there is always only one of these, even though it has a pipe followed by a zero, which is how they do indexes
         return self._get_location(six.b("ImageMetadataSeqLV|0!"))
 
-    @property
-    def image_data(self):
-        image_data = {}
-        regex = re.compile(six.b("""ImageDataSeq\|(\d+)!"""))
-        for match in regex.finditer(self._data):
-            if match:
-                location = self._parse_data_location(match.end())
-                image_data[int(match.group(1))] = location
-        return image_data
+    def get_image_data_location(self, index):
+        if not self._image_data:
+            regex = re.compile(six.b("""ImageDataSeq\|(\d+)!"""))
+            for match in regex.finditer(self._data):
+                if match:
+                    location = self._parse_data_location(match.end())
+                    self._image_data[int(match.group(1))] = location
+        return self._image_data[index]
 
     @property
     def image_calibration(self):

nd2reader/parser/v3.py

@@ -77,8 +77,8 @@ class V3Parser(BaseParser):
 
         """
         metadata_dict = self._build_metadata_dict()
-        height = metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiHeight')]
-        width = metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiWidth')]
+        height = metadata_dict['image_attributes'][six.b('SLxImageAttributes')][six.b('uiHeight')]
+        width = metadata_dict['image_attributes'][six.b('SLxImageAttributes')][six.b('uiWidth')]
         channels = self._parse_channels(metadata_dict)
         date = self._parse_date(metadata_dict)
         fields_of_view = self._parse_fields_of_view(metadata_dict)
@@ -95,7 +95,7 @@ class V3Parser(BaseParser):
         :rtype: datetime.datetime() or None
 
         """
-        for line in metadata_dict[six.b('ImageTextInfo')][six.b('SLxImageTextInfo')].values():
+        for line in metadata_dict['image_text_info'][six.b('SLxImageTextInfo')].values():
             line = line.decode("utf8")
             absolute_start_12 = None
             absolute_start_24 = None
@@ -123,9 +123,9 @@ class V3Parser(BaseParser):
 
         """
         channels = []
-        metadata = metadata_dict[six.b('ImageMetadataSeq')][six.b('SLxPictureMetadata')][six.b('sPicturePlanes')]
+        metadata = metadata_dict['image_metadata_sequence'][six.b('SLxPictureMetadata')][six.b('sPicturePlanes')]
         try:
-            validity = metadata_dict[six.b('ImageMetadata')][six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][six.b('ppNextLevelEx')][six.b('')][0][six.b('pItemValid')]
+            validity = metadata_dict['image_metadata'][six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][six.b('ppNextLevelEx')][six.b('')][0][six.b('pItemValid')]
         except KeyError:
             # If none of the channels have been deleted, there is no validity list, so we just make one
             validity = [True for _ in metadata]
@@ -181,7 +181,7 @@ class V3Parser(BaseParser):
         :rtype:    str
 
         """
-        for line in metadata_dict[six.b('ImageTextInfo')][six.b('SLxImageTextInfo')].values():
+        for line in metadata_dict['image_text_info'][six.b('SLxImageTextInfo')].values():
             if six.b("Dimensions:") in line:
                 metadata = line
                 break
@@ -221,7 +221,7 @@ class V3Parser(BaseParser):
         :rtype: int
 
         """
-        return metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiSequenceCount')]
+        return metadata_dict['image_attributes'][six.b('SLxImageAttributes')][six.b('uiSequenceCount')]
 
     def _build_label_map(self):
         """