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

-i, --interactive

If passed, the annotations will be rendered as napari objects rather than rendered together and displayed as an image. [default: False]

Arguments

ANNOTATIONS

Required argument

image

viewmask image [OPTIONS] IMAGE

Arguments

IMAGE

Required argument

overlay

viewmask overlay [OPTIONS] IMAGE ANNOTATIONS

Options

-i, --interactive

If passed, the annotations will be rendered as napari objects rather than rendered together and displayed as an image. [default: False]

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])

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.

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.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

Indices and tables