Utils¶

Visualization Utils¶

Visualization utilities.

staintools.utils.visual.build_stack(images)[source]¶

Build a stack of images from a tuple/list of images.

Parameters:	images – A tuple/list of images.
Returns:

staintools.utils.visual.patch_grid(ims, width=5, sub_sample=False, rand=False, save_name=None)[source]¶

Display a grid of patches.

Parameters:	ims – A patch ‘stack’ width – Images per row. sub_sample – Should we take a subsample? rand – Randomize subsample?
Returns:

staintools.utils.visual.read_image(path)[source]¶

Read an image to RGB uint8. Read with opencv (cv) and covert from BGR colorspace to RGB.

Parameters:	path – The path to the image.
Returns:	RGB uint8 image.

staintools.utils.visual.show(image, now=True, fig_size=(10, 10))[source]¶

Show an image (np.array). Caution! Rescales image to be in range [0,1].

Parameters:	image – now – plt.show() now? fig_size – Figure size.
Returns:

staintools.utils.visual.show_colors(C)[source]¶

Visualize rows of C as colors (RGB)

Parameters:	C – An array N x 3 where the rows are considered as RGB colors.
Returns:

Misc Utils¶

Other utilities.

staintools.utils.misc.OD_to_RGB(OD)[source]¶

Convert from optical density (OD_RGB) to RGB RGB = 255 * exp(-1*OD_RGB)

Parameters:	OD – Optical denisty RGB image.
Returns:	Image RGB uint8.

staintools.utils.misc.RGB_to_OD(I)[source]¶

Convert from RGB to optical density (OD_RGB) space. RGB = 255 * exp(-1*OD_RGB).

Parameters:	I – Image RGB uint8.
Returns:	Optical denisty RGB image.

staintools.utils.misc.array_equal(A, B, eps=1e-09)[source]¶

Are arrays A and B equal?

Parameters:	A – Array. B – Array. eps – Tolerance.
Returns:	True/False.

staintools.utils.misc.check_image(x)[source]¶

Check if is an image. If gray make sure it is ‘squeezed’ correctly.

Parameters:	x – Input.
Returns:	True/False.

staintools.utils.misc.is_gray_image(x)[source]¶

Is x a gray image?

Parameters:	x – Input.
Returns:	True/False.

staintools.utils.misc.is_image(x)[source]¶

Is x an image? i.e. numpy array of 2 or 3 dimensions.

Parameters:	x – Input.
Returns:	True/False.

staintools.utils.misc.is_uint8_image(x)[source]¶

Is x a uint8 image?

Parameters:	x – Input.
Returns:	True/False.

staintools.utils.misc.normalize_rows(A)[source]¶

Normalize the rows of an array.

Parameters:	A – An array.
Returns:	Array with rows normalized.

staintools.utils.misc.notwhite_mask(I, thresh=0.8)[source]¶

Get a binary mask where true denotes ‘not white’. Specifically, a pixel is not white if its luminance (in LAB color space) is less than the specified threshold.

Parameters:	I – RGB uint 8 image. thresh – Luminosity threshold.
Returns:	Binary mask where true denotes ‘not white’.

staintools.utils.misc.remove_zeros(I)[source]¶

Remove zeros in an image, replace with 1’s.

Parameters:	I – An Array.
Returns:	New array where 0’s have been replaced with 1’s.

staintools.utils.misc.sign(x)[source]¶

Returns the sign of x.

Parameters:	x – A scalar x.
Returns:	The sign of x in (+1, -1, 0).

staintools.utils.misc.standardize_brightness(I, percentile=95)[source]¶

Standardize brightness.

Parameters:	I – Image uint8 RGB.
Returns:	Image uint8 RGB with standardized brightness.