force three zoom levels

nd2reader/__init__.py

@@ -11,8 +11,8 @@ class Nd2(BaseNd2):
     def __init__(self, filename):
         super(Nd2, self).__init__(filename)
 
-    def get_image(self, timepoint, fov, channel_name, z_level):
-        image_set_number = self._calculate_image_set_number(timepoint, fov, z_level)
+    def get_image(self, time_index, fov, channel_name, z_level):
+        image_set_number = self._calculate_image_set_number(time_index, fov, z_level)
         timestamp, raw_image_data = self._reader.get_raw_image_data(image_set_number, self.channel_offset[channel_name])
         return Image(timestamp, raw_image_data, fov, channel_name, z_level, self.height, self.width)
 
@@ -34,7 +34,7 @@ class Nd2(BaseNd2):
         """
         Gets all the images for a given field of view and
         """
-        timepoint_set = xrange(self.timepoint_count) if time_indices is None else time_indices
+        timepoint_set = xrange(self.time_index_count) if time_indices is None else time_indices
         channel_set = [channel.name for channel in self.channels] if channels is None else channels
         z_level_set = xrange(self.z_level_count) if z_levels is None else z_levels
 

nd2reader/service/__init__.py

@@ -61,7 +61,7 @@ class BaseNd2(object):
         return self._metadata['ImageEvents']['RLxExperimentRecord']['uiCount']
 
     @property
-    def timepoint_count(self):
+    def time_index_count(self):
         """
         The number of images for a given field of view, channel, and z_level combination.
         Effectively the number of frames.
@@ -73,7 +73,8 @@ class BaseNd2(object):
 
     @property
     def z_level_count(self):
-        return self._image_count / self._sequence_count
+        # return self._image_count / self._sequence_count
+        return 3
 
     @property
     def field_of_view_count(self):
@@ -106,8 +107,8 @@ class BaseNd2(object):
     def _metadata(self):
         return self._reader.metadata
 
-    def _calculate_image_set_number(self, timepoint, fov, z_level):
-        return timepoint * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level)
+    def _calculate_image_set_number(self, time_index, fov, z_level):
+        return time_index * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level)
 
 
 class Nd2Reader(object):