Source code for allensdk.core.sitk_utilities

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import warnings

import SimpleITK as sitk
import numpy as np


[docs]def get_sitk_image_information(image):
    ''' Extract information about a SimpleITK image

    Parameters
    ----------
    image : sitk.Image
        Extract information about this image.

    Returns
    -------
    dict : 
        Extracted information. Includes spacing, origin, size, direction, and 
        number of components per pixel

    '''

    return {'spacing': image.GetSpacing(),
            'origin': image.GetOrigin(),
            'size': image.GetSize(),
            'direction': image.GetDirection(),
            'ncomponents': image.GetNumberOfComponentsPerPixel()}


[docs]def set_sitk_image_information(image, information):
    ''' Set information on a SimpleITK image

    Parameters
    ----------
    image : sitk.Image
        Set information on this image.
    information : dict
        Stores information to be set. Supports spacing, origin, direction. Also 
        checks (but cannot set) size and number of components per pixel

    '''

    if 'spacing' in information:
        image.SetSpacing(information.pop('spacing'))
    if 'origin' in information:
        image.SetOrigin(information.pop('origin'))
    if 'direction' in information:
        image.SetDirection(information.pop('direction'))

    if 'size' in information:
        assert(np.array_equal( information.pop('size'), image.GetSize() ))
    if 'ncomponents' in information:
        assert( information.pop('ncomponents') == image.GetNumberOfComponentsPerPixel() )
    
    if not len(information) == 0:
        warnings.warn('unwritten keys: {}'.format(','.join(information.keys())))


[docs]def fix_array_dimensions(array, ncomponents=1):
    ''' Convenience function that reorders ndarray dimensions for io with SimpleITK

    Parameters
    ----------
    array : np.ndarray
        The array to be reordered
    ncomponents : int, optional
        Number of components per pixel, default 1. 

    Returns
    -------
    np.ndarray : 
        Reordered array

    '''

    act_size = list(array.shape)
    ndims = len(act_size)
    multicomponent = ncomponents > 1

    from_order = list(range( ndims - multicomponent ))
    to_order = list(range( ndims - multicomponent ))[::-1]

    if multicomponent:
        from_order += [-1]
        to_order += [-1]

    return np.ascontiguousarray(np.moveaxis(array, from_order, to_order))


[docs]def read_ndarray_with_sitk(path):
    ''' Read a numpy array from a file using SimpleITK

    Parameters
    ----------
    path : str
        Read from this path
    
    Returns
    -------
    image : np.ndarray
        Obtained array
    information : dict
        Additional information about the array

    '''

    image = sitk.ReadImage(str(path))
    information = get_sitk_image_information(image)
    image = sitk.GetArrayFromImage(image)

    image = fix_array_dimensions(image, information['ncomponents'])
    return image, information


[docs]def write_ndarray_with_sitk(array, path, **information):
    ''' Write a numpy array to a file using SimpleITK

    Parameters
    ----------
    array : np.ndarray
        Array to be written.
    path : str
        Write to here
    **information : dict
        Contains additional information to be stored in the image file. 
        See set_sitk_image_information for more information.

    '''

    if not 'ncomponents' in information:
        information['ncomponents'] = 1
    ncomponents = information.pop('ncomponents')

    array = fix_array_dimensions(array, ncomponents)
    
    array = sitk.GetImageFromArray(array, ncomponents > 1)
    set_sitk_image_information(array, information)

    sitk.WriteImage(array, str(path))
Source code for allensdk.core.sitk_utilities

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