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48 lines
2.1 KiB
48 lines
2.1 KiB
import logging
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from nd2reader.service import BaseNd2
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from nd2reader.model import Image, ImageSet
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log = logging.getLogger("nd2reader")
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log.addHandler(logging.StreamHandler())
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log.setLevel(logging.DEBUG)
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class Nd2(BaseNd2):
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def __init__(self, filename):
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super(Nd2, self).__init__(filename)
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def get_image(self, timepoint, fov, channel_name, z_level):
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image_set_number = self._calculate_image_set_number(timepoint, fov, z_level)
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timestamp, raw_image_data = self._reader.get_raw_image_data(image_set_number, self.channel_offset[channel_name])
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return Image(timestamp, raw_image_data, fov, channel_name, z_level, self.height, self.width)
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def __iter__(self):
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"""
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Just return every image in order (might not be exactly the order that the images were physically taken, but it will
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be within a few seconds). A better explanation is probably needed here.
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"""
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for i in range(self._image_count):
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for fov in range(self.field_of_view_count):
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for z_level in range(self.z_level_count):
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for channel in self.channels:
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image = self.get_image(i, fov, channel.name, z_level)
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if image.is_valid:
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yield image
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def image_sets(self, field_of_view, timepoints=None, channels=None, z_levels=None):
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"""
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Gets all the images for a given field of view and
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"""
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timepoint_set = xrange(self.timepoint_count) if timepoints is None else timepoints
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channel_set = [channel.name for channel in self.channels] if channels is None else channels
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z_level_set = xrange(self.z_level_count) if z_levels is None else z_levels
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for timepoint in timepoint_set:
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image_set = ImageSet()
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for channel_name in channel_set:
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for z_level in z_level_set:
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image = self.get_image(timepoint, field_of_view, channel_name, z_level)
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if image.is_valid:
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image_set.add(image)
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yield image_set
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