Utils¶

Contour related util functions

munge.utils.contour.get_dcm_num_for_contour(contour_file_name)¶

Gets the DICOM series number for a given contour file name or full file path

Ex: For ‘data/contourfiles/SC-HF-I-1/i-contours/IM-0001-0048-icontour-manual.txt’ the return value will be 48

Parameters:	contour_file_name – name of the contour file
Returns:	Integer corresponding to the DICOM series number

munge.utils.contour.parse_contour_file(filename)¶

Parse the given contour filename

Parameters:	filename – filepath to the contourfile to parse
Returns:	list of tuples holding x, y coordinates of the contour

munge.utils.contour.poly_to_mask(polygon, width, height)¶

Convert polygon to mask

Parameters:	polygon – list of pairs of x, y coords [(x1, y1), (x2, y2), …] in units of pixels width – scalar image width height – scalar image height
Returns:	Boolean mask of shape (height, width)

Image related util functions

munge.utils.image.get_dcm_resolution(dcm_img)¶

Gets the resolution of the DICOM image

Parameters:	dcm_img – pydicom instance of DICOM image
Returns:	Resolution of the DICOM image i.e equivalent spacing of 1 pixel in millimeters

munge.utils.image.grayscale_to_rgb(img_raw)¶

Converts the given grayscale image to a three channel image

Parameters:	img_raw – the raw grayscale image
Returns:	3 Channel RGB image

munge.utils.image.parse_dicom_file(filename)¶

Parse the given DICOM filename

Parameters:	filename – filepath to the DICOM file to parse
Returns:	dictionary with DICOM image data

Miscellaneous util functions

munge.utils.misc.csv2dict(csv_file)¶

Converts and returns a CSV file to Dict

Parameters:	csv_file – Path to the CSV file
Returns:	Dict representation of the CSV file

munge.utils.misc.get_app_config(config_file)¶

Gets the application configuration as a dict from the given file

Parameters:	config_file – path to the configuration file
Returns:	Dict containing the application configuration

munge.utils.misc.get_bounding_box_coords(contour, window=30)¶

Given a contour and window, get the min and max co-ordinates of a bounding box around that window

Parameters:	contour – Array of co-ordinates defining the contour window – The window size of the bounding box
Returns:	min_x, max_x, min_y and max_y of the bounding box

munge.utils.misc.get_ocontour_for_icontour(icontour_file, ocontour_dir)¶

Gets the ocontour file corresponding to the given icontour_path. If the ocontour file does not exist, None is returned.

Parameters:	icontour_path – Full path to the icontour file
Returns:	Path of the corresponding ocontour file, if exists or None

munge.utils.misc.get_uuid()¶

Generates and returns a random GUID

Returns:	Random GUID V4

Munge