Merge pull request #124 from jimrybarski/123-expose-label-map

123 expose label map

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

@@ -0,0 +1,120 @@
+import six
+import struct
+import re
+
+
+class LabelMap(object):
+    """
+    """
+    def __init__(self, raw_binary_data):
+        self._data = raw_binary_data
+        self._image_data = {}
+
+    def _get_location(self, label):
+        try:
+            label_location = self._data.index(label) + len(label)
+            return self._parse_data_location(label_location)
+        except ValueError:
+            return None
+
+    def _parse_data_location(self, label_location):
+        location, length = struct.unpack("QQ", self._data[label_location: label_location + 16])
+        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
+        return self._get_location(six.b("ImageMetadataSeqLV|0!"))
+
+    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):
+        return self._get_location(six.b("ImageCalibrationLV|0!"))
+
+    @property
+    def image_attributes(self):
+        return self._get_location(six.b("ImageAttributesLV!"))
+
+    @property
+    def x_data(self):
+        return self._get_location(six.b("CustomData|X!"))
+
+    @property
+    def y_data(self):
+        return self._get_location(six.b("CustomData|Y!"))
+
+    @property
+    def z_data(self):
+        return self._get_location(six.b("CustomData|Z!"))
+
+    @property
+    def roi_metadata(self):
+        return self._get_location(six.b("CustomData|RoiMetadata_v1!"))
+
+    @property
+    def pfs_status(self):
+        return self._get_location(six.b("CustomData|PFS_STATUS!"))
+
+    @property
+    def pfs_offset(self):
+        return self._get_location(six.b("CustomData|PFS_OFFSET!"))
+
+    @property
+    def guid(self):
+        return self._get_location(six.b("CustomData|GUIDStore!"))
+
+    @property
+    def description(self):
+        return self._get_location(six.b("CustomData|CustomDescriptionV1_0!"))
+
+    @property
+    def camera_exposure_time(self):
+        return self._get_location(six.b("CustomData|Camera_ExposureTime1!"))
+
+    @property
+    def camera_temp(self):
+        return self._get_location(six.b("CustomData|CameraTemp1!"))
+
+    @property
+    def acquisition_times(self):
+        return self._get_location(six.b("CustomData|AcqTimesCache!"))
+
+    @property
+    def acquisition_times_2(self):
+        return self._get_location(six.b("CustomData|AcqTimes2Cache!"))
+
+    @property
+    def acquisition_frames(self):
+        return self._get_location(six.b("CustomData|AcqFramesCache!"))
+
+    @property
+    def lut_data(self):
+        return self._get_location(six.b("CustomDataVar|LUTDataV1_0!"))
+
+    @property
+    def grabber_settings(self):
+        return self._get_location(six.b("CustomDataVar|GrabberCameraSettingsV1_0!"))
+
+    @property
+    def custom_data(self):
+        return self._get_location(six.b("CustomDataVar|CustomDataV2_0!"))
+
+    @property
+    def app_info(self):
+        return self._get_location(six.b("CustomDataVar|AppInfo_V1_0!"))

nd2reader/parser/v3.py

@@ -3,6 +3,7 @@
 import array
 from datetime import datetime
 from nd2reader.model.metadata import Metadata
+from nd2reader.model.label import LabelMap
 from nd2reader.parser.base import BaseParser
 from nd2reader.driver.v3 import V3Driver
 from nd2reader.common.v3 import read_chunk
@@ -40,21 +41,44 @@ class V3Parser(BaseParser):
     def driver(self):
         return V3Driver(self.metadata, self._label_map, self._fh)
 
+    def _build_metadata_dict(self):
+        self._label_map = self._build_label_map()
+        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):
         """
         Reads all metadata and instantiates the Metadata object.
 
         """
-        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)
-
-        height = metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiHeight')]
-        width = metadata_dict[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiWidth')]
+        metadata_dict = self._build_metadata_dict()
+        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)
@@ -71,7 +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
@@ -99,9 +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]
@@ -157,7 +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
@@ -197,7 +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):
         """
@@ -205,26 +229,14 @@ 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
-
-        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
+        return LabelMap(raw_text)
 
     def _parse_unsigned_char(self, data):
         return struct.unpack("B", data.read(1))[0]