get_mask

formatreader.get_mask(selected_path: str, file_format: str, n_interp: int = 10, smooth_slices: bool = True, **kwargs)

Calls the corresponding function depending on the file format selected and retrieves its outputs.

Parameters:

• selected_path (string) – Path to the selected folder or file.

• file_format (string) – File format chosen in the GUI (nifti, tiff, dicom-seg, image).

• n_interp (int) – Number of interpolated slices to generate between two real slices. The default is 10.

• smooth_slices (boolean) – If True, calls the function smooth_mask() on each of the real slices. The default is True.

• **kwargs –

  Additional keyword arguments passed. mask_id : list of int

  Merge the specified mask ids into a single volume. Default = [0]. If [0] all masks are merged into a single point cloud.

  zsizefloat

  Distance between slices. Needed when loading slices from multiple single images.

Returns:

• contours (Numpy array) – Contains the contours of every slice in voxel coordinates.

• covers (Numpy array) – Contains the points from the top and bottom slices. Needed to close the .stl geometry.

• transf_mat (Numpy array) – Transformation matrix to convert from voxel coordinates to space coordinates.