# -*- coding: utf-8 -*- from nd2reader.model import ImageGroup from nd2reader.parser import get_parser from nd2reader.version import get_version import warnings class Nd2(object): """ Allows easy access to NIS Elements .nd2 image files. """ def __init__(self, filename): self._filename = filename self._fh = open(filename, "rb") major_version, minor_version = get_version(self._fh) parser = get_parser(self._fh, major_version, minor_version) self._driver = parser.driver self._metadata = parser.metadata def __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): if self._fh is not None: self._fh.close() def __repr__(self): return "\n".join(["" % self._filename, "Created: %s" % (self.date if self.date is not None else "Unknown"), "Image size: %sx%s (HxW)" % (self.height, self.width), "Frames: %s" % len(self.frames), "Channels: %s" % ", ".join(["'%s'" % str(channel) for channel in self.channels]), "Fields of View: %s" % len(self.fields_of_view), "Z-Levels: %s" % len(self.z_levels) ]) def __len__(self): """ This should be the total number of images in the ND2, but it may be inaccurate. If the ND2 contains a different number of images in a cycle (i.e. there are "gap" images) it will be higher than reality. :rtype: int """ return self._metadata.total_images_per_channel * len(self.channels) def __getitem__(self, item): """ Allows slicing ND2s. :type item: int or slice :rtype: nd2reader.model.Image() or generator """ if isinstance(item, int): try: image = self._driver.get_image(item) except KeyError: raise IndexError else: return image elif isinstance(item, slice): return self._slice(item.start, item.stop, item.step) raise IndexError def _slice(self, start, stop, step): """ Allows for iteration over a selection of the entire dataset. :type start: int :type stop: int :type step: int :rtype: nd2reader.model.Image() """ start = start if start is not None else 0 step = step if step is not None else 1 stop = stop if stop is not None else len(self) # This weird thing with the step allows you to iterate backwards over the images for i in range(start, stop)[::step]: yield self[i] @property def image_sets(self): """ Iterates over groups of related images. This is useful if your ND2 contains multiple fields of view. A typical use case might be that you have, say, four areas of interest that you're monitoring, and every minute you take a bright field and GFP image of each one. For each cycle, this method would produce four ImageSet objects, each containing one bright field and one GFP image. :return: model.ImageSet() """ warnings.warn("Nd2.image_sets will be removed from the nd2reader library in the near future.", DeprecationWarning) for frame in self.frames: image_group = ImageGroup() for fov in self.fields_of_view: for channel_name in self.channels: for z_level in self.z_levels: image = self.get_image(frame, fov, channel_name, z_level) if image is not None: image_group.add(image) yield image_group @property def date(self): return self._metadata.date @property def z_levels(self): return self._metadata.z_levels @property def fields_of_view(self): return self._metadata.fields_of_view @property def channels(self): return self._metadata.channels @property def frames(self): return self._metadata.frames @property def height(self): """ :return: height of each image, in pixels :rtype: int """ return self._metadata.height @property def width(self): """ :return: width of each image, in pixels :rtype: int """ return self._metadata.width def get_image(self, frame_number, field_of_view, channel_name, z_level): """ Returns an Image if data exists for the given parameters, otherwise returns None. :type frame_number: int :param field_of_view: the label for the place in the XY-plane where this image was taken. :type field_of_view: int :param channel_name: the name of the color of this image :type channel_name: str :param z_level: the label for the location in the Z-plane where this image was taken. :type z_level: int :rtype: nd2reader.model.Image() """ return self._driver.get_image_by_attributes(frame_number, field_of_view, channel_name, z_level, self.height, self.width) def close(self): self._fh.close()