import logging from nd2reader.service import BaseNd2 from nd2reader.model import Image, ImageSet log = logging.getLogger("nd2reader") log.addHandler(logging.StreamHandler()) log.setLevel(logging.DEBUG) 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) 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) def __iter__(self): """ Just return every image in order (might not be exactly the order that the images were physically taken, but it will be within a few seconds). A better explanation is probably needed here. """ for i in range(self._image_count): for fov in range(self.field_of_view_count): for z_level in range(self._z_level_count): for channel in self.channels: image = self.get_image(i, fov, channel.name, z_level) if image.is_valid: yield image def image_sets(self, field_of_view, timepoints=None, channels=None, z_levels=None): """ Gets all the images for a given field of view and """ timepoint_set = xrange(self._timepoint_count) if timepoints is None else timepoints 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 for timepoint in timepoint_set: image_set = ImageSet() for channel_name in channel_set: for z_level in z_level_set: image = self.get_image(timepoint, field_of_view, channel_name, z_level) if image.is_valid: image_set.add(image) yield image_set