Utils

This package provides utility functions as image operations, various decorators, path operations and time operations.

classtype_func(class_object)[source]

Decorator to Check whether the first argument of the decorated function is a subclass of a certain type

Parameters:class_object (Any) – type the first function argument should be subclassed from
Returns:
Return type:Wrapped Function
Raises:AssertionError – First argument of decorated function is not a subclass of given type
dtype_func(class_object)[source]

Decorator to Check whether the first argument of the decorated function is of a certain type

Parameters:class_object (Any) – type the first function argument should have
Returns:
Return type:Wrapped Function
Raises:AssertionError – First argument of decorated function is not of given type
make_deprecated(new_func)[source]

Decorator which raises a DeprecationWarning for the decorated object

Parameters:new_func (Any) – new function which should be used instead of the decorated one
Returns:
Return type:Wrapped Function
Raises:Deprecation Warning
numpy_array_func(func)
torch_module_func(func)
torch_tensor_func(func)
bounding_box(mask, margin=None)[source]

Calculate bounding box coordinates of binary mask

Parameters:
  • mask (SimpleITK.Image) – Binary mask
  • margin (int, default: None) – margin to be added to min/max on each dimension
Returns:

bounding box coordinates of the form (xmin, xmax, ymin, ymax, zmin, zmax)

Return type:

tuple

calculate_origin_offset(new_spacing, old_spacing)[source]

Calculates the origin offset of two spacings

Parameters:
  • new_spacing (list or np.ndarray or tuple) – new spacing
  • old_spacing (list or np.ndarray or tuple) – old spacing
Returns:

origin offset

Return type:

np.ndarray

max_energy_slice(img)[source]

Determine the axial slice in which the image energy is max

Parameters:img (SimpleITK.Image) – given image
Returns:slice index
Return type:int
sitk_copy_metadata(img_source, img_target)[source]

Copy metadata (=DICOM Tags) from one image to another

Parameters:
  • img_source (SimpleITK.Image) – Source image
  • img_target (SimpleITK.Image) – Source image
Returns:

Target image with copied metadata

Return type:

SimpleITK.Image

sitk_new_blank_image(size, spacing, direction, origin, default_value=0.0)[source]

Create a new blank image with given properties

Parameters:
  • size (list or np.ndarray or tuple) – new image size
  • spacing (list or np.ndarray or tuple) – spacing of new image
  • direction – new image’s direction
  • origin – new image’s origin
  • default_value (float) – new image’s default value
Returns:

Blank image with given properties

Return type:

SimpleITK.Image

sitk_resample_to_image(image, reference_image, default_value=0.0, interpolator=<sphinx.ext.autodoc.importer._MockObject object>, transform=None, output_pixel_type=None)[source]

Resamples Image to reference image

Parameters:
  • image (SimpleITK.Image) – the image which should be resampled
  • reference_image (SimpleITK.Image) – the resampling target
  • default_value (float) – default value
  • interpolator (Any) – implements the actual interpolation
  • transform (Any (default: None)) – transformation
  • output_pixel_type (Any (default:None)) – type of output pixels
Returns:

resampled image

Return type:

SimpleITK.Image

sitk_resample_to_shape(img, x, y, z, order=1)[source]

Resamples Image to given shape

Parameters:
  • img (SimpleITK.Image) –
  • x (int) – shape in x-direction
  • y (int) – shape in y-direction
  • z (int) – shape in z-direction
  • order (int) – interpolation order
Returns:

Resampled Image

Return type:

SimpleITK.Image

sitk_resample_to_spacing(image, new_spacing=(1.0, 1.0, 1.0), interpolator=<sphinx.ext.autodoc.importer._MockObject object>, default_value=0.0)[source]

Resamples SITK Image to a given spacing

Parameters:
  • image (SimpleITK.Image) – image which should be resampled
  • new_spacing (list or np.ndarray or tuple) – target spacing
  • interpolator (Any) – implements the actual interpolation
  • default_value (float) – default value
Returns:

resampled Image with target spacing

Return type:

SimpleITK.Image

subdirs(d)[source]

For a given directory, return a list of all subdirectories (full paths)

Parameters:d (string) – given root directory
Returns:list of strings of all subdirectories
Return type:list
now()[source]

Return current time as YYYY-MM-DD_HH-MM-SS

Returns:current time
Return type:string
class LookupConfig(*args, **kwargs)[source]

Bases: sphinx.ext.autodoc.importer._MockObject

Helper class to have nested lookups in all subdicts of Config

nested_get(key, *args, **kwargs)[source]

Returns all occurances of key in self and subdicts

Parameters:
  • key (str) – the key to search for
  • *args – positional arguments to provide default value
  • **kwargs – keyword arguments to provide default value
Raises:

KeyError – Multiple Values are found for key (unclear which value should be returned) OR No Value was found for key and no default value was given

Returns:

value corresponding to key (or default if value was not found)

Return type:

Any