#123 switched to the new LabelMap object, added support for another metadata field

nd2reader/model/label.py

@@ -1,12 +1,8 @@
 import six
 import struct
-from collections import namedtuple
 import re
 
 
-data_location = namedtuple("DataLocation", ["location", "length"])
-
-
 class LabelMap(object):
     """
     """
@@ -22,12 +18,16 @@ class LabelMap(object):
 
     def _parse_data_location(self, label_location):
         location, length = struct.unpack("QQ", self._data[label_location: label_location + 16])
-        return data_location(location=location, length=length)
+        return location
 
     @property
     def image_text_info(self):
         return self._get_location(six.b("ImageTextInfoLV!"))
 
+    @property
+    def image_metadata(self):
+        return self._get_location(six.b("ImageMetadataLV!"))
+
     @property
     def image_metadata_sequence(self):
         # there is always only one of these, even though it has a pipe followed by a zero, which is how they do indexes
@@ -39,7 +39,6 @@ class LabelMap(object):
         regex = re.compile(six.b("""ImageDataSeq\|(\d+)!"""))
         for match in regex.finditer(self._data):
             if match:
-                print(match.start(), match.end())
                 location = self._parse_data_location(match.end())
                 image_data[int(match.group(1))] = location
         return image_data

nd2reader/parser/v3.py

@@ -42,14 +42,34 @@ class V3Parser(BaseParser):
         return V3Driver(self.metadata, self._label_map, self._fh)
 
     def _build_metadata_dict(self):
-        metadata_dict = {}
         self._label_map = self._build_label_map()
-        for label in self._label_map.keys():
-            if label.endswith(six.b("LV!")) or six.b("LV|") in label:
-                data = read_chunk(self._fh, self._label_map[label])
-                stop = label.index(six.b("LV"))
-                metadata_dict[label[:stop]] = self._read_metadata(data, 1)
-        return metadata_dict
+        raw_data = {"image_text_info": read_chunk(self._fh, self._label_map.image_text_info),
+                    "image_metadata_sequence": read_chunk(self._fh, self._label_map.image_metadata_sequence),
+                    # "image_data": read_chunk(self._fh, self._label_map.image_data),
+                    "image_calibration": read_chunk(self._fh, self._label_map.image_calibration),
+                    "image_attributes": read_chunk(self._fh, self._label_map.image_attributes),
+                    # "x_data": read_chunk(self._fh, self._label_map.x_data),
+                    # "y_data": read_chunk(self._fh, self._label_map.y_data),
+                    # "z_data": read_chunk(self._fh, self._label_map.z_data),
+                    # "roi_metadata": read_chunk(self._fh, self._label_map.roi_metadata),
+                    # "pfs_status": read_chunk(self._fh, self._label_map.pfs_status),
+                    # "pfs_offset": read_chunk(self._fh, self._label_map.pfs_offset),
+                    # "guid": read_chunk(self._fh, self._label_map.guid),
+                    # "description": read_chunk(self._fh, self._label_map.description),
+                    # "camera_exposure_time": read_chunk(self._fh, self._label_map.camera_exposure_time),
+                    # "camera_temp": read_chunk(self._fh, self._label_map.camera_temp),
+                    # "acquisition_times": read_chunk(self._fh, self._label_map.acquisition_times),
+                    # "acquisition_times_2": read_chunk(self._fh, self._label_map.acquisition_times_2),
+                    # "acquisition_frames": read_chunk(self._fh, self._label_map.acquisition_frames),
+                    # "lut_data": read_chunk(self._fh, self._label_map.lut_data),
+                    # "grabber_settings": read_chunk(self._fh, self._label_map.grabber_settings),
+                    # "custom_data": read_chunk(self._fh, self._label_map.custom_data),
+                    # "app_info": read_chunk(self._fh, self._label_map.app_info)
+                    }
+        if self._label_map.image_metadata:
+            raw_data["image_metadata"] = read_chunk(self._fh, self._label_map.image_metadata)
+
+        return {key: self._read_metadata(data, 1) for key, data in raw_data.items()}
 
     def _parse_metadata(self):
         """
@@ -209,28 +229,15 @@ class V3Parser(BaseParser):
         as some of the bytes contain the value 33, which is the ASCII code for "!". So we iteratively find each label,
         grab the subsequent data (always 16 bytes long), advance to the next label and repeat.
 
-        :rtype: dict
+        :rtype: LabelMap
 
         """
-        # label_map = {}
         self._fh.seek(-8, 2)
         chunk_map_start_location = struct.unpack("Q", self._fh.read(8))[0]
         self._fh.seek(chunk_map_start_location)
         raw_text = self._fh.read(-1)
-        # label_start = raw_text.index(V3Parser.CHUNK_MAP_START) + 32
         return LabelMap(raw_text)
 
-        # while True:
-        #     data_start = raw_text.index(six.b("!"), label_start) + 1
-        #     key = raw_text[label_start: data_start]
-        #     location, length = struct.unpack("QQ", raw_text[data_start: data_start + 16])
-        #     if key == V3Parser.CHUNK_MAP_END:
-        #         # We've reached the end of the chunk map
-        #         break
-        #     label_map[key] = location
-        #     label_start = data_start + 16
-        # return label_map
-
     def _parse_unsigned_char(self, data):
         return struct.unpack("B", data.read(1))[0]