Merge pull request #82 from jimrybarski/81-get-time-index

resolves #81: images now include the frame number (formerly called th…

nd2reader/__init__.py

@@ -58,8 +58,9 @@ class Nd2(Nd2Parser):
                 channel = self._calculate_channel(item)
                 z_level = self._calculate_z_level(item)
                 image_group_number = int(item / len(self.channels))
+                frame_number = self._calculate_frame_number(image_group_number, fov, z_level)
                 timestamp, raw_image_data = self._get_raw_image_data(image_group_number, channel_offset)
-                image = Image(timestamp, raw_image_data, fov, channel, z_level, self.height, self.width)
+                image = Image(timestamp, frame_number, raw_image_data, fov, channel, z_level, self.height, self.width)
             except (TypeError, ValueError):
                 return None
             except KeyError:
@@ -126,13 +127,12 @@ class Nd2(Nd2Parser):
         """
         return self.metadata[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiWidth')]
 
-    def get_image(self, time_index, field_of_view, channel_name, z_level):
+    def get_image(self, frame_number, field_of_view, channel_name, z_level):
         """
         Returns an Image if data exists for the given parameters, otherwise returns None. In general, you should avoid
         using this method unless you're very familiar with the structure of ND2 files.
 
-        :param time_index: the frame number
-        :type time_index: int
+        :type frame_number: int
         :param field_of_view: the label for the place in the XY-plane where this image was taken.
         :type field_of_view: int
         :param channel_name: the name of the color of this image
@@ -142,10 +142,10 @@ class Nd2(Nd2Parser):
         :rtype: nd2reader.model.Image() or None
 
         """
-        image_group_number = self._calculate_image_group_number(time_index, field_of_view, z_level)
+        image_group_number = self._calculate_image_group_number(frame_number, field_of_view, z_level)
         try:
             timestamp, raw_image_data = self._get_raw_image_data(image_group_number, self._channel_offset[channel_name])
-            image = Image(timestamp, raw_image_data, field_of_view, channel_name, z_level, self.height, self.width)
+            image = Image(timestamp, frame_number, raw_image_data, field_of_view, channel_name, z_level, self.height, self.width)
         except TypeError:
             return None
         else:

nd2reader/model/__init__.py

@@ -8,10 +8,12 @@ log = logging.getLogger(__name__)
 
 
 class Image(object):
-    def __init__(self, timestamp, raw_array, field_of_view, channel, z_level, height, width):
+    def __init__(self, timestamp, frame_number, raw_array, field_of_view, channel, z_level, height, width):
         """
         A wrapper around the raw pixel data of an image.
 
+        :param timestamp: The frame number relative to the .
+        :type timestamp: int
         :param timestamp: The number of milliseconds after the beginning of the acquisition that this image was taken.
         :type timestamp: int
         :param raw_array: The raw sequence of bytes that represents the image.
@@ -29,6 +31,7 @@ class Image(object):
 
         """
         self._timestamp = timestamp
+        self._frame_number = int(frame_number)
         self._raw_data = raw_array
         self._field_of_view = field_of_view
         self._channel = channel
@@ -41,6 +44,7 @@ class Image(object):
         return "\n".join(["<ND2 Image>",
                           "%sx%s (HxW)" % (self._height, self._width),
                           "Timestamp: %s" % self.timestamp,
+                          "Frame: %s" % self._frame_number,
                           "Field of View: %s" % self.field_of_view,
                           "Channel: %s" % self.channel,
                           "Z-Level: %s" % self.z_level,
@@ -83,6 +87,10 @@ class Image(object):
         """
         return self._timestamp / 1000.0
 
+    @property
+    def frame_number(self):
+        return self._frame_number
+
     @property
     def channel(self):
         """
@@ -144,4 +152,4 @@ class ImageSet(object):
         :type image:    nd2reader.model.Image()
 
         """
-        self._images[image.channel][image.z_level] = image
+        self._images[image.channel][image.z_level] = image

nd2reader/parser.py

@@ -69,7 +69,7 @@ class Nd2Parser(object):
         These are labels created by the NIS Elements user. Typically they may a short description of the filter cube
         used (e.g. "bright field", "GFP", etc.)
 
-        :rtype: str
+        :rtype: list
 
         """
         if not self._channels:
@@ -97,7 +97,7 @@ class Nd2Parser(object):
         in the image data, so we have to calculate it. There probably is something somewhere, since
         NIS Elements can figure it out, but we haven't found it yet.
 
-        :rtype: int
+        :rtype: list
 
         """
         if self._fields_of_view is None:
@@ -109,7 +109,7 @@ class Nd2Parser(object):
         """
         The number of cycles.
 
-        :rtype:     int
+        :rtype:     list
 
         """
         if self._time_indexes is None:
@@ -121,7 +121,7 @@ class Nd2Parser(object):
         """
         The different levels in the Z-plane. Just a sequence from 0 to n.
 
-        :rtype: int
+        :rtype: list
 
         """
         if self._z_levels is None:
@@ -214,6 +214,9 @@ class Nd2Parser(object):
         """
         return time_index * len(self.fields_of_view) * len(self.z_levels) + (fov * len(self.z_levels) + z_level)
 
+    def _calculate_frame_number(self, image_group_number, fov, z_level):
+        return (image_group_number - (fov * len(self.z_levels) + z_level)) / (len(self.fields_of_view) * len(self.z_levels))
+
     @property
     def _channel_offset(self):
         """