Source code for nd2reader.legacy

"""
Legacy class for backwards compatibility
"""

import warnings

from nd2reader import ND2Reader


[docs]class Nd2(object): """ Warning: this module is deprecated and only maintained for backwards compatibility with the non-PIMS version of nd2reader. """ def __init__(self, filename): warnings.warn( "The 'Nd2' class is deprecated, please consider using the new ND2Reader interface which uses pims.", DeprecationWarning) self.reader = ND2Reader(filename) def __repr__(self): return "\n".join(["<Deprecated ND2 %s>" % self.reader.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 __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): if self.reader is not None: self.reader.close() def __len__(self): return len(self.reader) def __getitem__(self, item): return self.reader[item]
[docs] def select(self, fields_of_view=None, channels=None, z_levels=None, start=0, stop=None): """Select images based on criteria. Args: fields_of_view: the fields of view channels: the color channels z_levels: the z levels start: the starting frame stop: the last frame Returns: ND2Reader: Sliced ND2Reader which contains the frames """ if stop is None: stop = len(self.frames) return self.reader[start:stop]
[docs] def get_image(self, frame_number, field_of_view, channel_name, z_level): """Deprecated. Returns the specified image from the ND2Reader class. Args: frame_number: the frame number field_of_view: the field of view number channel_name: the name of the color channel z_level: the z level number Returns: Frame: the specified image """ return self.reader.parser.get_image_by_attributes(frame_number, field_of_view, channel_name, z_level, self.height, self.width)
[docs] def close(self): """Closes the ND2Reader """ if self.reader is not None: self.reader.close()
@property def height(self): """Deprecated. Fetches the height of the image. Returns: int: the pixel height of the image """ return self._get_width_or_height("height") @property def width(self): """Deprecated. Fetches the width of the image. Returns: int: the pixel width of the image """ return self._get_width_or_height("width") def _get_width_or_height(self, key): return self.reader.metadata[key] if self.reader.metadata[key] is not None else 0 @property def z_levels(self): """Deprecated. Fetches the available z levels. Returns: list: z levels. """ return self.reader.metadata["z_levels"] @property def fields_of_view(self): """Deprecated. Fetches the fields of view. Returns: list: fields of view. """ return self.reader.metadata["fields_of_view"] @property def channels(self): """Deprecated. Fetches all color channels. Returns: list: the color channels. """ return self.reader.metadata["channels"] @property def frames(self): """Deprecated. Fetches all frames. Returns: list: list of frames """ return self.reader.metadata["frames"] @property def date(self): """Deprecated. Fetches the acquisition date. Returns: string: the date """ return self.reader.metadata["date"] @property def pixel_microns(self): """Deprecated. Fetches the amount of microns per pixel. Returns: float: microns per pixel """ return self.reader.metadata["pixel_microns"]