Placeholder.

Return the path to a file in the tests/test_files directory. :param name: The name of the file. :returns: the path to the file.

Parse ground truth mask and gets contours for annotations. Parameters ---------- MASK : nd array ground truth mask (m,n) where pi

Placeholder.

Placeholder.

Given dataframe of contours, get list of annotation documents. This method parses a dataframe of contours to a list of dictionaries, each of

Get how much is request region smaller than base. This also gets the string to append to server request for getting rgb. Parameters ----

Shifts labels in a label image to fill in gaps corresponding to missing values. Parameters ---------- im_label : array_like

Given a slide annotation list, gets information on bounding boxes. Parameters ---------- slide_annotations : list of dicts respon

Given a histomicsTK girder response, get np array image. Parameters ---------- resp : object response from server request

Placeholder.

Scales up or down annotations in a slide. Works in place, but returns slide_annotations anyways. Parameters ---------- slide_annotat

Get x-, y- coordinates in a list format (Internal).

Placeholder.

Get binary tissue mask from slide thumbnail. Parameters ---------- thumbnail_im : np array (m, n, 3) nd array of thumbnail RGB im

Placeholder.

Unmix stains mixing followed by deconvolution (wrapper). Parameters ---------- im_rgb : array_like An RGB image (m x n x 3) to co

Parse region from the slide and get its corresponding labeled mask. This is a wrapper around get_roi_mask() which should be referred to for i

Perform Reinhard color normalization. Transform the color characteristics of an image to a desired standard. The standard is defined by the m

Run workflow for all slides.

Performs exterior boundary tracing of one or more objects in a label mask. If a starting point is not provided then a raster scan will be performe

Get indices of ROIs within the element_infos dataframe. (Internal)

Process annotations to get RGB and contours without intermediate masks. Parameters ---------- gc : object girder client object to

Wrapper around assert_array_almost_equal to work around scikit-image bug. `skimage.transform.resize()` can return different results on different

Placeholder.

Perform color normalization using color deconvolution to transform the. ... color characteristics of an image to a desired standard. After th

Delete all annotations in a slide.

Compute the mean and standard deviation of the intensities. ... of each channel of the given RGB image in LAB color space. The outputs of thi

Transforms input optical density image `im_od` into RGB space Parameters ---------- im_od : array_like A floating-point image of

Given a slide annotation list, parse into convenient tabular format. If the annotation is a point, then it is just treated as if it is a rect

Transforms input RGB image `im_rgb` into optical density space for color deconvolution. Parameters ---------- im_rgb : array_like

Transform input RGB image or matrix `im_rgb` into SDA (stain darkness) space for color deconvolution. Parameters ---------- im_rgb :

Yield information on one slide at a time.

If a background group contour is NOT fully enclosed, discard it. This is a purely aesthetic method, makes sure that the background group cont

Get element coords and mask and add to ROI (Internal).

Apply callback to all annotations and return output list.

Generates a complemented stain matrix Used to fill out empty columns of a stain matrix for use with color_deconvolution. Replaces right-most c

Placeholder.

Placeholder.

Get all ROIs for a slide without an intermediate mask form. This mainly relies on contours_to_labeled_object_mask(), which should be referred

Parse annotations and gets a ground truth mask for a single ROI. This will look at all slide annotations and get ones that overlap with the r

Given data on rectangular ROI center/width/height/rotation. Get the unrotated abounding box coordinates around rotated ROI. This of course is

Get slide thumbnail using girder client. Parameters ---------- gc : object girder client to use slide_id : str girder

Placeholder.

Transforms an image from RGB to LAB color space Parameters ---------- im_rgb : array_like An RGB image Returns -------

Init Slide_iterator object. Arguments: --------- gc : object girder client object source_folder_id : str

Add single polygon to ROI given mask (Internal).

Add single contour to self.merged_contours (Internal).

Connect a girder client to the local DSA docker

A version of count_image that doesn't compute the label image and only computes the sums.

Compute the distance between two sets of points. Has signature (i),(i)->().

Parse ground truth mask and gets contours (Internal).

Get coordinates and mask for annotation element. (Internal)

Search docker containers for a DSA docker container and fetch its IP address

Simplifies the given list of points by removing colinear spurs

Reorder stains in a stain matrix to a specific order. This is particularly relevant in macenco where the order of stains is not preserved dur

Placeholder.

Do the extra computations to convert an OutputTotals to an Output

Placeholder.

Placeholder.

Placeholder.

Compares image maxima Compare that the maxima found in an image matches the maxima found in a ground truth image. This function is a wrapper

Calculate intensity features from an intensity image. Parameters ---------- im_label : array_like A labeled mask image wherein in

Convert an image (MxNx3 array) to a column matrix of pixels (3x(M*N)). It will pass through a 2D array unchanged.

Placeholder.

Create a binary mask from given vertices coordinates. Source: This is modified from code by Juan Carlos from David Gutman Lab. Parameters

Deletes objects with values in 'indices' from label image, writing them over with zeros to assimilate with background. Parameters --

Deletes objects touching the border of the image and relabel Parameters ---------- im_label : array_like A label mask genera

Dump annotations of folder and subfolders locally recursively. This reproduces this tiered structure locally and (possibly) dumps annotations

Estimates variance of a peak in a histogram using the FWHM of an approximate normal distribution. Starting from a user-supplied peak and histo

Get absolute path for a girder folder. Parameters ---------- gc : girder_client.GirderClient authenticated girder client fold

Parse annotations and saves ground truth masks for ALL ROIs. Get all ROIs in a single slide. This is mainly uses get_image_and_mask_from_slid

Find indices of **potentially** included annotations within the ROI. We say "potentially" because this uses the IoU of roi and annotation as a

Get annotation documents of tissue boundaries to visualize on DSA. Parameters ---------- gc : object girder client to use sli

Placeholder.

Apply wrapper that calls perturb_stain_concentration() on RGB. Parameters ---------- im_rgb : array_like An RGB image (m x n x 3)

Compute the stain matrix for color deconvolution with the "Macenko" method from an RGB image or matrix. Parameters ---------- im_rgb

Convert to HSI the RGB pixels in im. Adapted from https://en.wikipedia.org/wiki/HSL_and_HSV#Hue_and_chroma.

Version of histomicstk.utils.sample_pixels that takes a Namespace and handles the special default values.

Transform input SDA image or matrix `im_sda` into RGB space. This is the inverse of `rgb_to_sda` with respect to the first parameter Paramet