You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
 
 
 

48 lines
2.1 KiB

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