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73 lines
2.7 KiB
73 lines
2.7 KiB
# -*- coding: utf-8 -*-
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import logging
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from nd2reader.model import Image, ImageSet
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from nd2reader.parser import Nd2Parser
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log = logging.getLogger(__name__)
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log.addHandler(logging.StreamHandler())
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log.setLevel(logging.WARNING)
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class Nd2(Nd2Parser):
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def __init__(self, filename):
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super(Nd2, self).__init__(filename)
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self._filename = filename
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def __repr__(self):
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return "\n".join(["<ND2 %s>" % self._filename,
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"Created: %s" % self._absolute_start.strftime("%Y-%m-%d %H:%M:%S"),
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"Image size: %sx%s (HxW)" % (self.height, self.width),
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"Image cycles: %s" % self._time_index_count,
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"Channels: %s" % ", ".join(["'%s'" % channel for channel in self._channels]),
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"Fields of View: %s" % self._field_of_view_count,
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"Z-Levels: %s" % self._z_level_count
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])
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def __iter__(self):
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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_name in self._channels:
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image = self.get_image(i, fov, channel_name, z_level)
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if image is not None:
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yield image
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@property
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def image_sets(self):
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for time_index in xrange(self._time_index_count):
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image_set = ImageSet()
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for fov in range(self._field_of_view_count):
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for channel_name in self._channels:
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for z_level in xrange(self._z_level_count):
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image = self.get_image(time_index, fov, channel_name, z_level)
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if image is not None:
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image_set.add(image)
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yield image_set
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def get_image(self, time_index, fov, channel_name, z_level):
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image_set_number = self._calculate_image_set_number(time_index, fov, z_level)
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try:
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timestamp, raw_image_data = self._get_raw_image_data(image_set_number, self._channel_offset[channel_name])
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image = Image(timestamp, raw_image_data, fov, channel_name, z_level, self.height, self.width)
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except TypeError:
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return None
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else:
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return image
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@property
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def height(self):
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"""
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:return: height of each image, in pixels
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"""
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return self.metadata['ImageAttributes']['SLxImageAttributes']['uiHeight']
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@property
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def width(self):
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"""
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:return: width of each image, in pixels
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"""
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return self.metadata['ImageAttributes']['SLxImageAttributes']['uiWidth']
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