Welcome to viewmask’s documentation!¶
Command Line Interface¶
viewmask¶
viewmask [OPTIONS] COMMAND [ARGS]...
Options
- --version¶
Show the version and exit.
annotations¶
viewmask annotations [OPTIONS] ANNOTATIONS
Options
- -o, --output <output>¶
Arguments
- ANNOTATIONS¶
Required argument
image¶
viewmask image [OPTIONS] IMAGE
Arguments
- IMAGE¶
Required argument
overlay¶
viewmask overlay [OPTIONS] IMAGE ANNOTATIONS
Options
- -o, --output <output>¶
Arguments
- IMAGE¶
Required argument
- ANNOTATIONS¶
Required argument
Package¶
- viewmask.utils.centers_of_contours(contours)¶
Return the centers of a list of OpenCV contours.
- Parameters
contours (list of numpy.ndarray) – A list of cv2 contours; each contour’s center will be calculated. Each contour is a list with 1 element, which is a list with 2 elements, representing the X and Y coordinates as integers, respectively.
- Returns
centers – A list of coordinates, where each coordinate is a tuple with exactly 2 ints, representing the X and Y coordinates, respectively. Each coordinate represents the center of the corresponding contour in contours. In this method, the center is defined as the centroid of the contour. If the centroid cannot be calculated, the circumcenter of the center is used.
- Return type
list of tuple of int
- viewmask.utils.centers_to_image(centers, radius=4, write_color=[255, 0, 0], shape=None)¶
Draw coordinates of centers to a static image.
- Parameters
centers (list of tuple of int) – A list of coordinates, where each coordinate is a tuple with exactly 2 ints, representing the X and Y coordinates, respectively. Each coordinate represents the center of the corresponding contour in contours.
radius (int, optional) – The radius of each center, defaults to 4.
write_color (array_like of int, optional) – The RGB color that should be used to draw the centers, defaults to [255, 0, 0], which is red. write_color have a length of 3; each integer represents red, green, and blue, respectively.
shape (tuple of int, optional) – The shape of the output image. Defaults to (x_max, y_max, 3), where x_max are the maximum x-coordinate and y-coordinate, respectively, of the centers.
- Returns
rendered_annotations – An N-dimensional NumPy array representing the RGB output image with the shape defined as shape.
- Return type
numpy.ndarray
- viewmask.utils.file_to_dask_array(path, tile_size=1000, overlap=0, remove_last=True, allow_unknown_chunksizes=False)¶
Load an image to a dask array.
- Parameters
path (str) – The path to the image file as a string.
tile_size (int, optional) – Size of chunk to be read in.
overlap (int, optional) – Do not modify, overlap between neighboring tiles.
remove_last (bool, optional) – Remove last tile because it has a custom size.
allow_unknown_chunksizes (bool, optional) – Allow different chunk sizes, more flexible, but slowdown.
- Returns
arr – A Dask Array representing the contents of the image file.
- Return type
dask.array.Array
Examples
>>> da_img = file_to_dask_array(path) >>> npa_img = arr.compute() # convert the dask array to a numpy array >>> pil_img = Image.fromarray(cv2.resize( ... npa_img, ... dsize=(1440, 700), ... interpolation=cv2.INTER_CUBIC ... )) >>> pil_img.save(test_image_name)
- viewmask.utils.fit_spline_to_points(points)¶
Fit a B-spline through a sequence of points.
- Parameters
points (numpy.ndarray) – A list of sample vector arrays representing the curve.
- Returns
spline_points – An N-dimensional NumPy array representing the RGB output image with the shape defined as shape.
- Return type
numpy.ndarray
- viewmask.utils.get_hematoxylin(rgb)¶
Extract the hematoxylin layer from an RGB image.
- Parameters
rgb ((..., 3) array_like) – The RGB input image to process.
- Returns
arr_hema – A 2-dimensional array representing the hematoxylin intensity.
- Return type
ndarray
- Raises
ValueError – If rgb is not at least 2-D with shape (…, 3).
References
- 1
A. C. Ruifrok and D. A. Johnston, “Quantification of histochemical staining by color deconvolution.,” Analytical and quantitative cytology and histology / the International Academy of Cytology [and] American Society of Cytology, vol. 23, no. 4, pp. 291-9, Aug. 2001.
Examples
>>> from skimage import data >>> from viewmask.utils import get_hematoxylin >>> rgb = data.immunohistochemistry() >>> he_layer = get_hematoxylin(rgb)
- viewmask.utils.get_stroke_color(xml_tree)¶
Determine the line color for annotations from a TCGA annotations file.
- Parameters
xml_tree (xml.etree.ElementTree) – The XML tree of the TCGA annotations file.
- Returns
line_color – A string representing the proper hex code to use for the stroke color. The output is always 6 characters and does not include the hashtag.
- Return type
str
- viewmask.utils.mask_to_contours(mask)¶
Determine the line color for annotations from a TCGA annotations file.
- Parameters
mask (numpy.ndarray) – A NumPy N-dimensional array representing the image. If mask has 3 dimensions, the image is assumed to be RGB, and will be converted to grayscale. If mask only has 2 dimensions, the image is assumed to be grayscale. The values in the input should be in the range [0, 255].
- Returns
contours – A list of contours, where each contour is a list of coordinates, where each coordinate is a list of a list of X and Y integers.
- Return type
list of numpy.ndarray
- viewmask.utils.region_to_contour(region, fit_spline=False)¶
Convert an XML region to a contour.
- Parameters
region (list of vertices) – A list of vertices, where each vertex is a dict with an ‘X’ and a ‘Y’ key which correspond to a number (int or float).
fit_spline (bool, optional) – Whether a B-spline should be fit through the contour.
- Returns
contour – A list of points, where each point is a two-element list representing an (X, Y) coordinate pair.
- Return type
list of list of float
See also
fit_spline_to_points
Fit a B-spline through a contour.