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236 lines
8.3 KiB
236 lines
8.3 KiB
# -*- coding: utf-8 -*-
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from nd2reader.parser import get_parser, get_version
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import six
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class Nd2(object):
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""" Allows easy access to NIS Elements .nd2 image files. """
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def __init__(self, filename):
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self._filename = filename
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self._fh = open(filename, "rb")
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major_version, minor_version = get_version(self._fh)
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self._parser = get_parser(self._fh, major_version, minor_version)
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self._metadata = self._parser.metadata
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self._roi_metadata = self._parser.roi_metadata
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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.date if self.date is not None else "Unknown"),
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"Image size: %sx%s (HxW)" % (self.height, self.width),
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"Frames: %s" % len(self.frames),
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"Channels: %s" % ", ".join(["%s" % str(channel) for channel in self.channels]),
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"Fields of View: %s" % len(self.fields_of_view),
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"Z-Levels: %s" % len(self.z_levels)
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])
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def __enter__(self):
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return self
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def __exit__(self, exc_type, exc_val, exc_tb):
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if self._fh is not None:
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self._fh.close()
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def __len__(self):
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"""
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This should be the total number of images in the ND2, but it may be inaccurate. If the ND2 contains a
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different number of images in a cycle (i.e. there are "gap" images) it will be higher than reality.
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:rtype: int
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"""
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return self._metadata.total_images_per_channel * len(self.channels)
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def __getitem__(self, item):
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"""
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Allows slicing ND2s.
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:type item: int or slice
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:rtype: nd2reader.model.Image() or generator
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"""
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if isinstance(item, int):
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try:
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image = self._parser.driver.get_image(item)
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except KeyError:
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raise IndexError
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else:
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return image
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elif isinstance(item, slice):
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return self._slice(item.start, item.stop, item.step)
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raise IndexError
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def select(self, fields_of_view=None, channels=None, z_levels=None, start=0, stop=None):
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"""
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Iterates over images matching the given criteria. This can be 2-10 times faster than manually iterating over
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the Nd2 and checking the attributes of each image, as this method skips disk reads for any images that don't
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meet the criteria.
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:type fields_of_view: int or tuple or list
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:type channels: str or tuple or list
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:type z_levels: int or tuple or list
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:type start: int
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:type stop: int
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"""
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fields_of_view = self._to_tuple(fields_of_view, self.fields_of_view)
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channels = self._to_tuple(channels, self.channels)
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z_levels = self._to_tuple(z_levels, self.z_levels)
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# By default, we stop after the last image. Otherwise we make sure the user-provided value is valid
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stop = len(self) if stop is None else max(0, min(stop, len(self)))
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for frame in range(start, stop):
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field_of_view, channel, z_level = self._parser.driver.calculate_image_properties(frame)
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if field_of_view in fields_of_view and channel in channels and z_level in z_levels:
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image = self._parser.driver.get_image(frame)
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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 height(self):
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"""
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The height of each image in pixels.
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:rtype: int
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"""
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return self._metadata.height
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@property
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def width(self):
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"""
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The width of each image in pixels.
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:rtype: int
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"""
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return self._metadata.width
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@property
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def z_levels(self):
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"""
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A list of integers that represent the different levels on the Z-axis that images were taken. Currently this is
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just a list of numbers from 0 to N. For example, an ND2 where images were taken at -3µm, 0µm, and +5µm from a
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set position would be represented by 0, 1 and 2, respectively. ND2s do store the actual offset of each image
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in micrometers and in the future this will hopefully be available. For now, however, you will have to match up
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the order yourself.
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:return: list of int
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"""
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return self._metadata.z_levels
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@property
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def fields_of_view(self):
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"""
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A list of integers representing the various stage locations, in the order they were taken in the first round
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of acquisition.
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:return: list of int
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"""
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return self._metadata.fields_of_view
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@property
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def channels(self):
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"""
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A list of channel (i.e. wavelength) names. These are set by the user in NIS Elements.
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:return: list of str
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"""
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return self._metadata.channels
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@property
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def frames(self):
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"""
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A list of integers representing groups of images. ND2s consider images to be part of the same frame if they
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are in the same field of view and don't have the same channel. So if you take a bright field and GFP image at
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four different fields of view over and over again, you'll have 8 images and 4 frames per cycle.
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:return: list of int
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"""
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return self._metadata.frames
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@property
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def date(self):
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"""
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The date and time that the acquisition began. Not guaranteed to have been recorded.
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:rtype: datetime.datetime() or None
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"""
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return self._metadata.date
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@property
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def pixel_microns(self):
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"""
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The width of a pixel in microns. Note that the user can override this in NIS Elements so it may not reflect reality.
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:rtype: float
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"""
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return self._metadata.pixel_microns
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def get_image(self, frame_number, field_of_view, channel_name, z_level):
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"""
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Attempts to return the image with the unique combination of given attributes. None will be returned if a match
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is not found.
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:type frame_number: int
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:param field_of_view: the label for the place in the XY-plane where this image was taken.
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:type field_of_view: int
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:param channel_name: the name of the color of this image
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:type channel_name: str
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:param z_level: the label for the location in the Z-plane where this image was taken.
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:type z_level: int
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:rtype: nd2reader.model.Image() or None
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"""
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return self._parser.driver.get_image_by_attributes(frame_number,
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field_of_view,
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channel_name,
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z_level,
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self.height,
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self.width)
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def close(self):
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"""
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Closes the file handle to the image. This actually sometimes will prevent problems so it's good to do this or
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use Nd2 as a context manager.
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"""
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self._fh.close()
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def _slice(self, start, stop, step):
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"""
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Allows for iteration over a selection of the entire dataset.
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:type start: int
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:type stop: int
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:type step: int
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:rtype: nd2reader.model.Image()
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"""
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start = start if start is not None else 0
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step = step if step is not None else 1
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stop = stop if stop is not None else len(self)
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# This weird thing with the step allows you to iterate backwards over the images
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for i in range(start, stop)[::step]:
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yield self[i]
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def _to_tuple(self, value, default):
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"""
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Idempotently converts a value to a tuple. This allows users to pass in scalar values and iterables to
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select(), which is more ergonomic than having to remember to pass in single-member lists
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:type value: int or str or tuple or list
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:type default: tuple or list
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:rtype: tuple
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"""
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value = default if value is None else value
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return (value,) if isinstance(value, int) or isinstance(value, six.string_types) else tuple(value)
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