Welcome to viewmask’s documentation!¶
Command Line Interface¶
viewmask¶
viewmask [OPTIONS] COMMAND [ARGS]...
Package¶
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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.
- Return type
list of tuple of int
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viewmask.utils.centers_to_image(centers, shape=(1000, 1000, 3), radius=4)¶ Determine the line color for annotations from a TCGA annotations file.
- 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.
shape (tuple of int, optional) – The shape of the mask. shape defaults to (1000, 1000, 3), since most images in the TCGA dataset have a height and width of 1000 pixels and have 3 channels (red, green, and blue). If shape provides a 3rd value with value 3, the centers will be drawn in red; otherwise, if shape has only 2 values, the centers will be drawn in white.
radius (int, optional) – The radius of each center, defaults to 4.
- Returns
rendered_annotations – An N-dimensional NumPy array representing the RGB output image with the shape defined as shape.async
- Return type
numpy.ndarray
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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
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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
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viewmask.utils.xml_to_contours(xml_tree, contour_drawer)¶ Extract contours from a TCGA XML annotations file.
- Parameters
xml_tree (xml.etree.ElementTree) – The XML tree of the TCGA annotations file.
contour_drawer ({'napari', 'cv2'}) – If contour_drawer is ‘napari’ then the contours will be transposed over its main diagonal. When contour_drawer is ‘cv2’, no changes will be made to the returned contours.
- Returns
contours – A list of contours, where each contour is a list of coordinates, where each coordinate is a list with exactly 2 integers, representing the X and Y coordinates, respectively.
- Return type
list of numpy.ndarray
Notes
The main diagonal is defined as the line that connects the top-left corner and the bottom right corner.
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viewmask.utils.xml_to_image(xml_tree, shape=(1000, 1000, 3))¶ Convert a TCGA annotations file to a binary mask.
- Parameters
xml_tree (xml.etree.ElementTree) – The XML tree of the TCGA annotations file.
shape (tuple of int, optional) – The shape of the mask. shape defaults to (1000, 1000, 3), since most images in the TCGA dataset have a height and width of 1000 pixels and have 3 channels (red, green, and blue).
- Returns
rendered_annotations – An N-dimensional NumPy array representing the RGB output image with the shape defined as shape.
- Return type
numpy.ndarray