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189 lines
7.1 KiB
189 lines
7.1 KiB
# -*- coding: utf-8 -*-
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import array
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from datetime import datetime
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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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import numpy as np
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import re
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import struct
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log = logging.getLogger(__name__)
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log.addHandler(logging.StreamHandler())
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log.setLevel(logging.WARN)
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class Nd2(Nd2Parser):
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def __init__(self, filename, image_sets=False):
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super(Nd2, self).__init__(filename)
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self._use_image_sets = image_sets
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def __iter__(self):
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if self._use_image_sets:
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return self.image_sets()
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else:
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return self.images()
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def images(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 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):
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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_valid:
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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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timestamp, raw_image_data = self._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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@property
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def channels(self):
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metadata = self.metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes']
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try:
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validity = self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['ppNextLevelEx'][''][0]['pItemValid']
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except KeyError:
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# If none of the channels have been deleted, there is no validity list, so we just make one
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validity = [True for i in metadata]
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# Channel information is contained in dictionaries with the keys a0, a1...an where the number
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# indicates the order in which the channel is stored. So by sorting the dicts alphabetically
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# we get the correct order.
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for (label, chan), valid in zip(sorted(metadata['sPlaneNew'].items()), validity):
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if not valid:
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continue
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yield chan['sDescription']
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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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@property
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def absolute_start(self):
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if self._absolute_start is None:
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for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values():
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absolute_start_12 = None
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absolute_start_24 = None
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# ND2s seem to randomly switch between 12- and 24-hour representations.
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try:
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absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S")
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except ValueError:
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pass
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try:
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absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p")
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except ValueError:
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pass
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if not absolute_start_12 and not absolute_start_24:
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continue
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self._absolute_start = absolute_start_12 if absolute_start_12 else absolute_start_24
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return self._absolute_start
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@property
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def channel_count(self):
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pattern = r""".*?λ\((\d+)\).*?"""
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try:
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count = int(re.match(pattern, self._dimensions).group(1))
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except AttributeError:
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return 1
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else:
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return count
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@property
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def field_of_view_count(self):
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"""
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The metadata contains information about fields of view, but it contains it even if some fields
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of view were cropped. We can't find anything that states which fields of view are actually
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in the image data, so we have to calculate it. There probably is something somewhere, since
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NIS Elements can figure it out, but we haven't found it yet.
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"""
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pattern = r""".*?XY\((\d+)\).*?"""
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try:
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count = int(re.match(pattern, self._dimensions).group(1))
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except AttributeError:
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return 1
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else:
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return count
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@property
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def time_index_count(self):
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"""
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The number of image sets. If images were acquired using some kind of cycle, all images at each step in the
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program will have the same timestamp (even though they may have varied by a few seconds in reality). For example,
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if you have four fields of view that you're constantly monitoring, and you take a bright field and GFP image of
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each, and you repeat that process 100 times, you'll have 800 individual images. But there will only be 400
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time indexes.
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:rtype: int
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"""
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pattern = r""".*?T'\((\d+)\).*?"""
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try:
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count = int(re.match(pattern, self._dimensions).group(1))
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except AttributeError:
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return 1
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else:
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return count
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@property
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def z_level_count(self):
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pattern = r""".*?Z\((\d+)\).*?"""
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try:
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count = int(re.match(pattern, self._dimensions).group(1))
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except AttributeError:
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return 1
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else:
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return count
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@staticmethod
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def as_numpy_array(arr):
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return np.frombuffer(arr)
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@property
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def _channel_offset(self):
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"""
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Image data is interleaved for each image set. That is, if there are four images in a set, the first image
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will consist of pixels 1, 5, 9, etc, the second will be pixels 2, 6, 10, and so forth. Why this would be the
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case is beyond me, but that's how it works.
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"""
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channel_offset = {}
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for n, channel in enumerate(self.channels):
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self._channel_offset[channel.name] = n
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return channel_offset
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def _get_raw_image_data(self, image_set_number, channel_offset):
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chunk = self._label_map["ImageDataSeq|%d!" % image_set_number]
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data = self._read_chunk(chunk)
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timestamp = struct.unpack("d", data[:8])[0]
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# The images for the various channels are interleaved within each other.
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image_data = array.array("H", data)
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image_data_start = 4 + channel_offset
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return timestamp, image_data[image_data_start::self.channel_count]
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def _calculate_image_set_number(self, time_index, fov, z_level):
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return time_index * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level)
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