Module: io

Utilities to read and write images in various formats.

The following plug-ins are available:

Plugin	Description
qt	Fast image display using the Qt library. Deprecated since 0.18. Will be removed in 0.20.
imread	Image reading and writing via imread
gdal	Image reading via the GDAL Library (www.gdal.org)
simpleitk	Image reading and writing via SimpleITK
gtk	Fast image display using the GTK library
pil	Image reading via the Python Imaging Library
fits	FITS image reading via PyFITS
matplotlib	Display or save images using Matplotlib
tifffile	Load and save TIFF and TIFF-based images using tifffile.py
imageio	Image reading via the ImageIO Library

`skimage.io.call_plugin`(kind, args, *kwargs)	Find the appropriate plugin of ‘kind’ and execute it.
`skimage.io.concatenate_images`(ic)	Concatenate all images in the image collection into an array.
`skimage.io.find_available_plugins`([loaded])	List available plugins.
`skimage.io.imread`(fname[, as_gray, plugin])	Load an image from file.
`skimage.io.imread_collection`(load_pattern[, …])	Load a collection of images.
`skimage.io.imread_collection_wrapper`(imread)
`skimage.io.imsave`(fname, arr[, plugin, …])	Save an image to file.
`skimage.io.imshow`(arr[, plugin])	Display an image.
`skimage.io.imshow_collection`(ic[, plugin])	Display a collection of images.
`skimage.io.load_sift`(f)	Read SIFT or SURF features from externally generated file.
`skimage.io.load_surf`(f)	Read SIFT or SURF features from externally generated file.
`skimage.io.plugin_info`(plugin)	Return plugin meta-data.
`skimage.io.plugin_order`()	Return the currently preferred plugin order.
`skimage.io.pop`()	Pop an image from the shared image stack.
`skimage.io.push`(img)	Push an image onto the shared image stack.
`skimage.io.reset_plugins`()
`skimage.io.show`()	Display pending images.
`skimage.io.use_plugin`(name[, kind])	Set the default plugin for a specified operation.
`skimage.io.ImageCollection`(load_pattern[, …])	Load and manage a collection of image files.
`skimage.io.MultiImage`(filename[, …])	A class containing all frames from multi-frame images.
`skimage.io.collection`	Data structures to hold collections of images, with optional caching.
`skimage.io.manage_plugins`	Handle image reading, writing and plotting plugins.
`skimage.io.sift`
`skimage.io.util`

call_plugin

skimage.io.call_plugin(kind, *args, **kwargs) [source]

Find the appropriate plugin of ‘kind’ and execute it.

Parameters

kind{‘imshow’, ‘imsave’, ‘imread’, ‘imread_collection’}: Function to look up.
pluginstr, optional: Plugin to load. Defaults to None, in which case the first matching plugin is used.
*args, **kwargsarguments and keyword arguments: Passed to the plugin function.

concatenate_images

skimage.io.concatenate_images(ic) [source]

Concatenate all images in the image collection into an array.

Parameters

ican iterable of images: The images to be concatenated.

Returns

array_catndarray: An array having one more dimension than the images in ic.

Raises

ValueError: If images in ic don’t have identical shapes.

Notes

concatenate_images receives any iterable object containing images, including ImageCollection and MultiImage, and returns a NumPy array.

find_available_plugins

skimage.io.find_available_plugins(loaded=False) [source]

List available plugins.

Parameters

loadedbool: If True, show only those plugins currently loaded. By default, all plugins are shown.

Returns

pdict: Dictionary with plugin names as keys and exposed functions as values.

imread

skimage.io.imread(fname, as_gray=False, plugin=None, **plugin_args) [source]

Load an image from file.

Parameters

fnamestring: Image file name, e.g. test.jpg or URL.
as_graybool, optional: If True, convert color images to gray-scale (64-bit floats). Images that are already in gray-scale format are not converted.
pluginstr, optional: Name of plugin to use. By default, the different plugins are tried (starting with imageio) until a suitable candidate is found. If not given and fname is a tiff file, the tifffile plugin will be used.

Returns

img_arrayndarray: The different color bands/channels are stored in the third dimension, such that a gray-image is MxN, an RGB-image MxNx3 and an RGBA-image MxNx4.

Other Parameters

plugin_argskeywords: Passed to the given plugin.

imread_collection

skimage.io.imread_collection(load_pattern, conserve_memory=True, plugin=None, **plugin_args) [source]

Load a collection of images.

Parameters

load_patternstr or list: List of objects to load. These are usually filenames, but may vary depending on the currently active plugin. See the docstring for ImageCollection for the default behaviour of this parameter.
conserve_memorybool, optional: If True, never keep more than one in memory at a specific time. Otherwise, images will be cached once they are loaded.

Returns

icImageCollection: Collection of images.

Other Parameters

plugin_argskeywords: Passed to the given plugin.

imread_collection_wrapper

skimage.io.imread_collection_wrapper(imread) [source]

imsave

skimage.io.imsave(fname, arr, plugin=None, check_contrast=True, **plugin_args) [source]

Save an image to file.

Parameters

fnamestr: Target filename.
arrndarray of shape (M,N) or (M,N,3) or (M,N,4): Image data.
pluginstr, optional: Name of plugin to use. By default, the different plugins are tried (starting with imageio) until a suitable candidate is found. If not given and fname is a tiff file, the tifffile plugin will be used.
check_contrastbool, optional: Check for low contrast and print warning (default: True).

Other Parameters

plugin_argskeywords: Passed to the given plugin.

Notes

When saving a JPEG, the compression ratio may be controlled using the quality keyword argument which is an integer with values in [1, 100] where 1 is worst quality and smallest file size, and 100 is best quality and largest file size (default 75). This is only available when using the PIL and imageio plugins.

imshow

skimage.io.imshow(arr, plugin=None, **plugin_args) [source]

Display an image.

Parameters

arrndarray or str: Image data or name of image file.
pluginstr: Name of plugin to use. By default, the different plugins are tried (starting with imageio) until a suitable candidate is found.

Other Parameters

plugin_argskeywords: Passed to the given plugin.

Examples using `skimage.io.imshow`

Explore 3D images (of cells)

imshow_collection

skimage.io.imshow_collection(ic, plugin=None, **plugin_args) [source]

Display a collection of images.

Parameters

icImageCollection: Collection to display.
pluginstr: Name of plugin to use. By default, the different plugins are tried until a suitable candidate is found.

Other Parameters

plugin_argskeywords: Passed to the given plugin.

load_sift

skimage.io.load_sift(f) [source]

Read SIFT or SURF features from externally generated file.

This routine reads SIFT or SURF files generated by binary utilities from http://people.cs.ubc.ca/~lowe/keypoints/ and http://www.vision.ee.ethz.ch/~surf/.

This routine does not generate SIFT/SURF features from an image. These algorithms are patent encumbered. Please use skimage.feature.CENSURE instead.

Parameters

filelikestring or open file: Input file generated by the feature detectors from http://people.cs.ubc.ca/~lowe/keypoints/ or http://www.vision.ee.ethz.ch/~surf/ .
mode{‘SIFT’, ‘SURF’}, optional: Kind of descriptor used to generate filelike.

Returns

datarecord array with fields

row: int

row position of feature
column: int

column position of feature
scale: float

feature scale
orientation: float

feature orientation
data: array

feature values

load_surf

skimage.io.load_surf(f) [source]

Read SIFT or SURF features from externally generated file.

This routine reads SIFT or SURF files generated by binary utilities from http://people.cs.ubc.ca/~lowe/keypoints/ and http://www.vision.ee.ethz.ch/~surf/.

This routine does not generate SIFT/SURF features from an image. These algorithms are patent encumbered. Please use skimage.feature.CENSURE instead.

Parameters

filelikestring or open file: Input file generated by the feature detectors from http://people.cs.ubc.ca/~lowe/keypoints/ or http://www.vision.ee.ethz.ch/~surf/ .
mode{‘SIFT’, ‘SURF’}, optional: Kind of descriptor used to generate filelike.

Returns

datarecord array with fields

row: int

row position of feature
column: int

column position of feature
scale: float

feature scale
orientation: float

feature orientation
data: array

feature values

plugin_info

skimage.io.plugin_info(plugin) [source]

Return plugin meta-data.

Parameters

pluginstr: Name of plugin.

Returns

mdict: Meta data as specified in plugin .ini.

plugin_order

skimage.io.plugin_order() [source]

Return the currently preferred plugin order.

Returns

pdict: Dictionary of preferred plugin order, with function name as key and plugins (in order of preference) as value.

pop

skimage.io.pop() [source]

Pop an image from the shared image stack.

Returns

imgndarray: Image popped from the stack.

push

skimage.io.push(img) [source]

Push an image onto the shared image stack.

Parameters

imgndarray: Image to push.

reset_plugins

skimage.io.reset_plugins() [source]

show

skimage.io.show() [source]

Display pending images.

Launch the event loop of the current gui plugin, and display all pending images, queued via imshow. This is required when using imshow from non-interactive scripts.

A call to show will block execution of code until all windows have been closed.

Examples

>>> import skimage.io as io

>>> for i in range(4):
...     ax_im = io.imshow(np.random.rand(50, 50))
>>> io.show()

use_plugin

skimage.io.use_plugin(name, kind=None) [source]

Set the default plugin for a specified operation. The plugin will be loaded if it hasn’t been already.

Parameters

namestr: Name of plugin.
kind{‘imsave’, ‘imread’, ‘imshow’, ‘imread_collection’, ‘imshow_collection’}, optional: Set the plugin for this function. By default, the plugin is set for all functions.

Examples

To use Matplotlib as the default image reader, you would write:

>>> from skimage import io
>>> io.use_plugin('matplotlib', 'imread')

To see a list of available plugins run io.available_plugins. Note that this lists plugins that are defined, but the full list may not be usable if your system does not have the required libraries installed.

ImageCollection

class skimage.io.ImageCollection(load_pattern, conserve_memory=True, load_func=None, **load_func_kwargs) [source]

Bases: object

Load and manage a collection of image files.

Parameters

load_patternstr or list of str: Pattern string or list of strings to load. The filename path can be absolute or relative.
conserve_memorybool, optional: If True, ImageCollection does not keep more than one in memory at a specific time. Otherwise, images will be cached once they are loaded.

Other Parameters

load_funccallable: imread by default. See notes below.

Notes

Note that files are always returned in alphanumerical order. Also note that slicing returns a new ImageCollection, not a view into the data.

ImageCollection can be modified to load images from an arbitrary source by specifying a combination of load_pattern and load_func. For an ImageCollection ic, ic[5] uses load_func(load_pattern[5]) to load the image.

Imagine, for example, an ImageCollection that loads every third frame from a video file:

video_file = 'no_time_for_that_tiny.gif'

def vidread_step(f, step):
    vid = imageio.get_reader(f)
    seq = [v for v in vid.iter_data()]
    return seq[::step]

ic = ImageCollection(video_file, load_func=vidread_step, step=3)

ic  # is an ImageCollection object of length 1 because there is 1 file

x = ic[0]  # calls vidread_step(video_file, step=3)
x[5]  # is the sixth element of a list of length 8 (24 / 3)

Another use of load_func would be to convert all images to uint8:

def imread_convert(f):
    return imread(f).astype(np.uint8)

ic = ImageCollection('/tmp/*.png', load_func=imread_convert)

Examples

>>> import skimage.io as io
>>> from skimage import data_dir

>>> coll = io.ImageCollection(data_dir + '/chess*.png')
>>> len(coll)
2
>>> coll[0].shape
(200, 200)

>>> ic = io.ImageCollection(['/tmp/work/*.png', '/tmp/other/*.jpg'])

Attributes

fileslist of str: If a pattern string is given for load_pattern, this attribute stores the expanded file list. Otherwise, this is equal to load_pattern.

__init__(load_pattern, conserve_memory=True, load_func=None, **load_func_kwargs) [source]: Load and manage a collection of images.

concatenate() [source]

Concatenate all images in the collection into an array.

Returns

arnp.ndarray: An array having one more dimension than the images in self.

Raises

ValueError: If images in the ImageCollection don’t have identical shapes.

MultiImage

class skimage.io.MultiImage(filename, conserve_memory=True, dtype=None, **imread_kwargs) [source]

Bases: skimage.io.collection.ImageCollection

A class containing all frames from multi-frame images.

Parameters

load_patternstr or list of str: Pattern glob or filenames to load. The path can be absolute or relative.
conserve_memorybool, optional: Whether to conserve memory by only caching a single frame. Default is True.

Other Parameters

load_funccallable: imread by default. See notes below.

Notes

If conserve_memory=True the memory footprint can be reduced, however the performance can be affected because frames have to be read from file more often.

The last accessed frame is cached, all other frames will have to be read from file.

The current implementation makes use of tifffile for Tiff files and PIL otherwise.

Examples

>>> from skimage import data_dir

>>> img = MultiImage(data_dir + '/multipage.tif') 
>>> len(img) 
2
>>> for frame in img: 
...     print(frame.shape) 
(15, 10)
(15, 10)

__init__(filename, conserve_memory=True, dtype=None, **imread_kwargs) [source]: Load a multi-img.

property filename

© 2019 the scikit-image team
Licensed under the BSD 3-clause License.
https://scikit-image.org/docs/0.18.x/api/skimage.io.html

Module: io

call_plugin

concatenate_images

Notes

find_available_plugins

imread

imread_collection

imread_collection_wrapper

imsave

Notes

imshow

Examples using skimage.io.imshow

imshow_collection

load_sift

load_surf

plugin_info

plugin_order

pop

push

reset_plugins

show

Examples

use_plugin

Examples

ImageCollection

Notes

Examples

MultiImage

Notes

Examples

Examples using `skimage.io.imshow`