pyiron_contrib.image.image module

class pyiron_contrib.image.image.Image(source, metadata=None, as_gray=False)[source]

Bases: object

A base class for storing image data in the form of numpy arrays. Functionality of the skimage library can be leveraged using the sub-module name and an activate method.

source

The raw data source.

Type: str/numpy.ndarray

data

The image data. Not loaded until called, so first call may be slow. Modifications are made to this field, leaving the source untouched. NOT saved to hdf.

Type: numpy.ndarray

as_gray

Whether to interpret the image as grayscale.

Type: bool

metadata

Metadata associated with the source.

Type: Metadata

convert_to_grayscale()[source]: Flattens (NxMx3) data into (NxM) grayscale data.

property data

from_hdf(hdf, group_name=None)[source]

property metadata

overwrite_source(new_source, new_metadata=None, as_gray=False)[source]

Apply a new source of image data to the image object.

Parameters

new_source (str/numpy.ndarray) – The filepath to the data, or the raw array of data itself.
new_metadata (Metadata) – The metadata associated with the new source. (Default is None.)
as_gray (bool) – Whether to interpret the new data as grayscale. (Default is False.)

plot(ax=None, subplots_kwargs=None, imshow_kwargs=None, hide_axes=True)[source]

Make a simple matplotlib imshow plot of the data.

Parameters

ax (matplotlib.axes.Axes) – The axis to plot on. (Default is None, make a new figure.)
subplots_kwargs (dict) – Keyword arguments to pass to the figure generation. Only used if no axis is provided. (Default is None.)
imshow_kwargs (dict) – Keyword arguments to pass to the imshow plotting command. (Default is None.)
hide_axes (bool) – Whether to hide axis ticks and labels. (Default is True.)

Returns

The figure the plot is in. (matplotlib.axes.Axes): The axis the plot is on.

Return type

(matplotlib.figure.Figure)

reload_data()[source]: Reverts the data attribute to the source, i.e. the most recently read file (if set by reading data), or the originally assigned array (if set by direct array assignment).

property shape

property source

to_hdf(hdf, group_name=None)[source]

class pyiron_contrib.image.image.Metadata(dict=None, /, **kwargs)[source]

Bases: UserDict

TODO: Leverage the generic to and from hdf functions written by Dominik over in pyiron_contrib/protocol

from_hdf(hdf, group_name=None)[source]

to_hdf(hdf, group_name=None)[source]

pyiron_contrib.image.image.pass_and_set_image_data(image)[source]

Decorator which connects function input and output to image.data.

Parameters: image (Image) – The image whose data to set.
Returns: Decorated function.
Return type: (fnc)

pyiron_contrib.image.image.pass_image_data(image)[source]

Decorator to see if the signature of the function starts with a particular variable (_IMAGE_VARIABLE). If so, automatically passes an attribute of the argument (image.data) as the first argument.

Parameters: image (Image) – The image whose data to use.
Returns: Decorated function.
Return type: (fnc)

pyiron_contrib.image.image.set_image_data(image)[source]

Decorator which checks the returned value of the function. If that value is of type numpy.ndarray, uses it to set an attribute of the argument (image.data) instead of returning it.

Parameters: image (Image) – The image whose data to set.
Returns: Decorated function.
Return type: (fnc)