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