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124 lines
4.7 KiB
124 lines
4.7 KiB
# -*- coding: utf-8 -*-
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from collections import namedtuple
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from nd2reader.model import Channel
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import logging
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from nd2reader.model import Image, ImageSet
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from nd2reader.reader import Nd2FileReader
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chunk = namedtuple('Chunk', ['location', 'length'])
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field_of_view = namedtuple('FOV', ['number', 'x', 'y', 'z', 'pfs_offset'])
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print(__name__)
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log = logging.getLogger(__name__)
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log.setLevel(logging.WARN)
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class Nd2(Nd2FileReader):
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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, 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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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, time_indices=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.time_index_count) if time_indices is None else time_indices
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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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self._channel_offset = None
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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 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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name = chan['sDescription']
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exposure_time = metadata['sSampleSetting'][label]['dExposureTime']
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camera = metadata['sSampleSetting'][label]['pCameraSetting']['CameraUserName']
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yield Channel(name, camera, exposure_time)
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@property
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def channel_names(self):
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"""
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A convenience method for getting an alphabetized list of channel names.
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:return: list[str]
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"""
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for channel in sorted(self.channels, key=lambda x: x.name):
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yield channel.name
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@property
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def _image_count(self):
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return self._metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount']
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@property
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def _sequence_count(self):
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return self._metadata['ImageEvents']['RLxExperimentRecord']['uiCount']
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@property
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def channel_offset(self):
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if self._channel_offset is None:
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self._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 self._channel_offset
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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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