diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py index db04f99..54169a4 100644 --- a/nd2reader/__init__.py +++ b/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 diff --git a/nd2reader/service/__init__.py b/nd2reader/service/__init__.py index 03dcc28..c93079f 100644 --- a/nd2reader/service/__init__.py +++ b/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):