from . import Request from ..typing import ArrayLike import numpy as np from typing import Optional, Dict, Any, Tuple, Union, List, Iterator from dataclasses import dataclass @dataclass class ImageProperties: """Standardized Metadata ImageProperties represent a set of standardized metadata that is available under the same name for every supported format. If the ImageResource (or format) does not specify the value, a sensible default value is chosen instead. Attributes ---------- shape : Tuple[int, ...] The shape of the loaded ndimage. dtype : np.dtype The dtype of the loaded ndimage. n_images : int Number of images in the file if ``index=...``, `None` for single images. is_batch : bool If True, the first dimension of the ndimage represents a batch dimension along which several images are stacked. spacing : Tuple A tuple describing the spacing between pixels along each axis of the ndimage. If the spacing is uniform along an axis the value corresponding to that axis is a single float. If the spacing is non-uniform, the value corresponding to that axis is a tuple in which the i-th element indicates the spacing between the i-th and (i+1)-th pixel along that axis. """ shape: Tuple[int, ...] dtype: np.dtype n_images: Optional[int] = None is_batch: bool = False spacing: Optional[tuple] = None class PluginV3: """A ImageIO Plugin. This is an abstract plugin that documents the v3 plugin API interface. A plugin is an adapter/wrapper around a backend that converts a request from iio.core (e.g., read an image from file) into a sequence of instructions for the backend that fulfill the request. Plugin authors may choose to subclass this class when implementing a new plugin, but aren't obliged to do so. As long as the plugin class implements the interface (methods) described below the ImageIO core will treat it just like any other plugin. Parameters ---------- request : iio.Request A request object that represents the users intent. It provides a standard interface to access the various ImageResources and serves them to the plugin as a file object (or file). Check the docs for details. **kwargs : Any Additional configuration arguments for the plugin or backend. Usually these match the configuration arguments available on the backend and are forwarded to it. Raises ------ InitializationError During ``__init__`` the plugin tests if it can fulfill the request. If it can't, e.g., because the request points to a file in the wrong format, then it should raise an ``InitializationError`` and provide a reason for failure. This reason may be reported to the user. ImportError Plugins will be imported dynamically when listed in ``iio.config.known_plugins`` to fulfill requests. This way, users only have to load plugins/backends they actually use. If this plugin's backend is not installed, it should raise an ``ImportError`` either during module import or during class construction. Notes ----- Upon successful construction the plugin takes ownership of the provided request. This means that it is the plugin's responsibility to call request.finish() to close the resource when it is no longer needed. Plugins _must_ implement a context manager that closes and cleans any resources held by the plugin upon exit. """ def __init__(self, request: Request) -> None: """Initialize a new Plugin Instance. See Plugin's docstring for detailed documentation. Notes ----- The implementation here stores the request as a local variable that is exposed using a @property below. If you inherit from PluginV3, remember to call ``super().__init__(request)``. """ self._request = request def read(self, *, index: int = 0) -> np.ndarray: """Read a ndimage. The ``read`` method loads a (single) ndimage, located at ``index`` from the requested ImageResource. It is at the plugin's descretion to decide (and document) what constitutes a single ndimage. A sensible way to make this decision is to choose based on the ImageResource's format and on what users will expect from such a format. For example, a sensible choice for a TIFF file produced by an ImageJ hyperstack is to read it as a volumetric ndimage (1 color dimension followed by 3 spatial dimensions). On the other hand, a sensible choice for a MP4 file produced by Davinci Resolve is to treat each frame as a ndimage (2 spatial dimensions followed by 1 color dimension). The value ``index=None`` is special. It requests the plugin to load all ndimages in the file and stack them along a new first axis. For example, if a MP4 file is read with ``index=None`` and the plugin identifies single frames as ndimages, then the plugin should read all frames and stack them into a new ndimage which now contains a time axis as its first axis. If a PNG file (single image format) is read with ``index=None`` the plugin does a very similar thing: It loads all ndimages in the file (here it's just one) and stacks them along a new first axis, effectively prepending an axis with size 1 to the image. If a plugin does not wish to support ``index=None`` it should set a more sensible default and raise a ``ValueError`` when requested to read using ``index=None``. Parameters ---------- index : int If the ImageResource contains multiple ndimages, and index is an integer, select the index-th ndimage from among them and return it. If index is an ellipsis (...), read all ndimages in the file and stack them along a new batch dimension. If index is None, let the plugin decide. If the index is out of bounds a ``ValueError`` is raised. **kwargs : Any The read method may accept any number of plugin-specific keyword arguments to further customize the read behavior. Usually these match the arguments available on the backend and are forwarded to it. Returns ------- ndimage : np.ndarray A ndimage containing decoded pixel data (sometimes called bitmap). Notes ----- The ImageResource from which the plugin should read is managed by the provided request object. Directly accessing the managed ImageResource is _not_ permitted. Instead, you can get FileLike access to the ImageResource via request.get_file(). If the backend doesn't support reading from FileLike objects, you can request a temporary file to pass to the backend via ``request.get_local_filename()``. This is, however, not very performant (involves copying the Request's content into a temporary file), so you should avoid doing this whenever possible. Consider it a fallback method in case all else fails. """ raise NotImplementedError() def write(self, ndimage: Union[ArrayLike, List[ArrayLike]]) -> Optional[bytes]: """Write a ndimage to a ImageResource. The ``write`` method encodes the given ndimage into the format handled by the backend and writes it to the ImageResource. It overwrites any content that may have been previously stored in the file. If the backend supports only a single format then it must check if the ImageResource matches that format and raise an exception if not. Typically, this should be done during initialization in the form of a ``InitializationError``. If the backend supports more than one format it must determine the requested/desired format. Usually this can be done by inspecting the ImageResource (e.g., by checking ``request.extension``), or by providing a mechanism to explicitly set the format (perhaps with a - sensible - default value). If the plugin can not determine the desired format, it **must not** write to the ImageResource, but raise an exception instead. If the backend supports at least one format that can hold multiple ndimages it should be capable of handling ndimage batches and lists of ndimages. If the ``ndimage`` input is a list of ndimages, the plugin should not assume that the ndimages are not stackable, i.e., ndimages may have different shapes. Otherwise, the ``ndimage`` may be a batch of multiple ndimages stacked along the first axis of the array. The plugin must be able to discover this, either automatically or via additional `kwargs`. If there is ambiguity in the process, the plugin must clearly document what happens in such cases and, if possible, describe how to resolve this ambiguity. Parameters ---------- ndimage : ArrayLike The ndimage to encode and write to the current ImageResource. **kwargs : Any The write method may accept any number of plugin-specific keyword arguments to customize the writing behavior. Usually these match the arguments available on the backend and are forwarded to it. Returns ------- encoded_image : bytes or None If the chosen ImageResource is the special target ``""`` then write should return a byte string containing the encoded image data. Otherwise, it returns None. Notes ----- The ImageResource to which the plugin should write to is managed by the provided request object. Directly accessing the managed ImageResource is _not_ permitted. Instead, you can get FileLike access to the ImageResource via request.get_file(). If the backend doesn't support writing to FileLike objects, you can request a temporary file to pass to the backend via ``request.get_local_filename()``. This is, however, not very performant (involves copying the Request's content from a temporary file), so you should avoid doing this whenever possible. Consider it a fallback method in case all else fails. """ raise NotImplementedError() def iter(self) -> Iterator[np.ndarray]: """Iterate the ImageResource. This method returns a generator that yields ndimages in the order in which they appear in the file. This is roughly equivalent to:: idx = 0 while True: try: yield self.read(index=idx) except ValueError: break It works very similar to ``read``, and you can consult the documentation of that method for additional information on desired behavior. Parameters ---------- **kwargs : Any The iter method may accept any number of plugin-specific keyword arguments to further customize the reading/iteration behavior. Usually these match the arguments available on the backend and are forwarded to it. Yields ------ ndimage : np.ndarray A ndimage containing decoded pixel data (sometimes called bitmap). See Also -------- PluginV3.read """ raise NotImplementedError() def properties(self, index: int = 0) -> ImageProperties: """Standardized ndimage metadata. Parameters ---------- index : int If the ImageResource contains multiple ndimages, and index is an integer, select the index-th ndimage from among them and return its properties. If index is an ellipsis (...), read all ndimages in the file and stack them along a new batch dimension and return their properties. If index is None, the plugin decides the default. Returns ------- properties : ImageProperties A dataclass filled with standardized image metadata. """ raise NotImplementedError() def metadata(self, index: int = 0, exclude_applied: bool = True) -> Dict[str, Any]: """Format-Specific ndimage metadata. The method reads metadata stored in the ImageResource and returns it as a python dict. The plugin is free to choose which name to give a piece of metadata; however, if possible, it should match the name given by the format. There is no requirement regarding the fields a plugin must expose; however, if a plugin does expose any,``exclude_applied`` applies to these fields. If the plugin does return metadata items, it must check the value of ``exclude_applied`` before returning them. If ``exclude applied`` is True, then any metadata item that would be applied to an ndimage returned by ``read`` (or ``iter``) must not be returned. This is done to avoid confusion; for example, if an ImageResource defines the ExIF rotation tag, and the plugin applies the rotation to the data before returning it, then ``exclude_applied`` prevents confusion on whether the tag was already applied or not. The `kwarg` ``index`` behaves similar to its counterpart in ``read`` with one exception: If the ``index`` is None, then global metadata is returned instead of returning a combination of all metadata items. If there is no global metadata, the Plugin should return an empty dict or raise an exception. Parameters ---------- index : int If the ImageResource contains multiple ndimages, and index is an integer, select the index-th ndimage from among them and return its metadata. If index is an ellipsis (...), return global metadata. If index is None, the plugin decides the default. exclude_applied : bool If True (default), do not report metadata fields that the plugin would apply/consume while reading the image. Returns ------- metadata : dict A dictionary filled with format-specific metadata fields and their values. """ raise NotImplementedError() def close(self) -> None: """Close the ImageResource. This method allows a plugin to behave similar to the python built-in ``open``:: image_file = my_plugin(Request, "r") ... image_file.close() It is used by the context manager and deconstructor below to avoid leaking ImageResources. If the plugin has no other cleanup to do it doesn't have to overwrite this method itself and can rely on the implementation below. """ self.request.finish() @property def request(self) -> Request: return self._request def __enter__(self) -> "PluginV3": return self def __exit__(self, type, value, traceback) -> None: self.close() def __del__(self) -> None: self.close()