AbstractSingleImage

class AbstractSingleImage[source]

Bases: object

Abstract Class to define a SingleImage-API

_crop(*args, **kwargs)[source]

Internal implementation of AbstractSingleImage.crop()

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
_crop_lmks(*args, **kwargs)[source]

Crops the landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
_crop_to_landmarks(*args, **kwargs)[source]

Internal implementation of AbstractSingleImage.crop_to_landmarks()

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
_normalize_rotation(*args, **kwargs)[source]

Internal implementation of AbstractSingleImage.normalize_rotation()

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
_save_landmarks(*args, **kwargs)[source]

Abstract internal Function to save landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
_transform_img(*args, **kwargs)[source]

Applies a given transformation to image

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
_transform_lmk(*args, **kwargs)[source]

Applies a given transformation to landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
apply_trafo(*args, **kwargs)[source]

Applies a given transformation to image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
cartesian_coordinates()[source]

Transforms the landmarks into cartesian coordinates

Raises:NotImplementedError – if not overwritten by subclass
crop(*args, **kwargs)[source]

Crops image and landmarks to given range

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
crop_to_landmarks(*args, **kwargs)[source]

Crops image and landmarks to bounding box specified by landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
classmethod from_files(*args, **kwargs)[source]

Creates a class instance from files

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError
get_landmark_bounds(*args, **kwargs)[source]

Calculates bounds of landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
homogeneous_coordinates()[source]

Transforms the landmarks into homogeneous coordinates

Raises:NotImplementedError – if not overwritten by subclass
img

Property to get the actual image pixels

Returns:image pixels
Return type:np.array
is_gray

Property returning whether the image is a grayscale image

Raises:NotImplementedError – if not overwritten by subclass
is_homogeneous

Property returning whether the landmarks are in homogeneous coordinates

Raises:NotImplementedError – if not overwritten by subclass
normalize_rotation(*args, **kwargs)[source]

Rotates image and landmarks in a way, that the vector between two given points is parallel to horizontal axis

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
rescale(*args, **kwargs)[source]

Rescales image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
resize(*args, **kwargs)[source]

Resizes image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
rotate(*args, **kwargs)[source]

Rotates image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
save(*args, **kwargs)[source]

Abstract Function to save image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
save_image(*args, **kwargs)[source]

Abstract Function to save image

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
save_landmarks(*args, **kwargs)[source]

Abstract Function to save landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
to_grayscale()[source]

Converts image to grayscale

Raises:NotImplementedError – if not overwritten by subclass
transform(*args, **kwargs)[source]

Applies a given transformation to image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
transform_about_centre(*args, **kwargs)[source]

Applies a given transformation to image and landmarks at image center (internally shifts image and landmarks center to origin, applies transformation and shifts back)

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
translate(*args, **kwargs)[source]

Translates image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
view(*args, **kwargs)[source]

Plots image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass

BaseSingleImage

class BaseSingleImage(img: <sphinx.ext.autodoc.importer._MockObject object at 0x7f8f65aab898>, *args, **kwargs)[source]

Bases: shapedata.base_data_processing.AbstractSingleImage

Holds Single Image

_crop(min_y, min_x, max_y, max_x)[source]

Implements actual cropping inplace

Parameters:
  • min_y (int) – minimum y value
  • min_x (int) – minimum x value
  • max_y (int) – maximum y value
  • max_x (int) – maximum x value
Raises:

NotImplementedError – if not overwritten by subclass
static _crop_lmks(lmks, min_y, min_x, max_y, max_x)[source]

Crops landmarks to given values

Parameters:
  • lmks (np.ndarray) – landmarks to crop
  • min_y (int) – minimum y value
  • min_x (int) – minimum x value
  • max_y (int) – maximum y value
  • max_x (int) – maximum x value
Returns:

cropped landmarks
Return type:

np.ndarray
_crop_to_landmarks(proportion=0.0, **kwargs)[source]

Crop to landmarks inplace

Parameters:
  • proportion (float) – boundary proportion of cropping
  • **kwargs – additional keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
_normalize_rotation(lmks, index_left, index_right, **kwargs)[source]

normalizes rotation based on two keypoints

Parameters:
  • lmks (np.ndarray) – landmarks for rotation normalization
  • index_left (int) – index for left point
  • index_right (int) – index for right point
  • **kwargs – additional keyword arguments (passed to skimage.transform.warp())
Returns:

transformed Image
Return type:

BaseSingleImage
_save_landmarks(filepath, lmk_type, **kwargs)[source]

Saves landmarks to file

Parameters:
  • filepath (str) – path to file the landmarks should be saved to
  • lmk_type (str) – specifies the type of landmark file
  • **kwargs – additional keyword arguments passed to save function
Raises:

NotImplementedError – If not overwritten by subclass
_transform_img(transformation: <sphinx.ext.autodoc.importer._MockObject object at 0x7f8f65aab438>, **kwargs)[source]

Apply transformation inplace to image

Parameters:
Returns:

Transformed Image with original Landmarks
Return type:

BaseSingleImage
_transform_lmk(transformation: <sphinx.ext.autodoc.importer._MockObject object at 0x7f8f65aab438>)[source]

Apply transformation inplace to landmarks

Parameters:transformation (skimage.transform.AffineTransform) – transformation to apply
Returns:Image with Transformed Landmarks
Return type:BaseSingleImage
apply_trafo(transformation: <sphinx.ext.autodoc.importer._MockObject object at 0x7f8f65aab438>, **kwargs)[source]

Apply transformation inplace to image and landmarks

Parameters:
Returns:

Transformed Image and Landmarks
Return type:

BaseSingleImage
cartesian_coordinates()[source]

Transforms landmark coordinates inplace to cartesian coordinates

Returns:Image with Landmarks in cartesian Coordinates
Return type:BaseSingleImage
crop(min_y, min_x, max_y, max_x)[source]

Crops Image by specified values

Parameters:
  • min_y (int) – minimum y value
  • min_x (int) – minimum x value
  • max_y (int) – maximum y value
  • max_x (int) – maximum x value
Returns:

cropped image
Return type:

BaseSingleImage
crop_to_landmarks(proportion=0.0, **kwargs)[source]

Crop image to landmarks

Parameters:
  • proportion (float) – image proportion to add to size of bounding box
  • **kwargs – additional keyword arguments
Returns:

cropped image
Return type:

BaseSingleImage
classmethod from_files(file, extension=None, **kwargs)[source]

Creates a class instance from files

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError
classmethod from_ljson_files(img_file, **kwargs)[source]

Create class from image or landmark file

Parameters:file (str) – path to image or landmarkfile
Returns:
Return type:BaseSingleImage
classmethod from_npy_files(file, **kwargs)[source]

Create class from image or landmark file

Parameters:file (str) – path to image or landmarkfile
Returns:
Return type:BaseSingleImage
classmethod from_pts_files(file, **kwargs)[source]

Create class from image or landmark file :param file: path to image or landmarkfile :type file: string

Returns:
Return type:BaseSingleImage
static get_landmark_bounds(lmks)[source]

Function to calculate the landmark bounds

Parameters:lmks (np.ndarray) – landmarks
Returns:
  • int (min_y)
  • int (min_x)
  • int (max_y)
  • int (max_x)
homogeneous_coordinates()[source]

Transforms landmark coordinates inplace to homogeneous coordinates

Returns:Image with Landmarks in Homogeneous Coordinates
Return type:BaseSingleImage
img

Property to get the actual image pixels

Returns:image pixels
Return type:np.array
is_gray

Property returning whether the image is a grayscale image

Raises:NotImplementedError – if not overwritten by subclass
is_homogeneous

Property returning whether the landmarks are in homogeneous coordinates

Raises:NotImplementedError – if not overwritten by subclass
normalize_rotation(*args, **kwargs)[source]

Rotates image and landmarks in a way, that the vector between two given points is parallel to horizontal axis

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass
rescale(scale, **kwargs)[source]

Scale Image and landmarks

Parameters:
  • scale – scale parameter
  • **kwargs – additional keyword arguments (passed to skimage.transform.warp())
Returns:

transformed Image
Return type:

BaseSingleImage
resize(target_shape, **kwargs)[source]

resize image and scale landmarks :param target_shape: target shape for resizing :type target_shape: tuple or list :param **kwargs: additional keyword arguments (passed to

skimage.transform.warp())
Returns:transformed Image
Return type:BaseSingleImage
rotate(angle, degree=True, **kwargs)[source]

Rotates the image and landmarks by given angle

Parameters:
  • angle (float or int) – rotation angle
  • degree (bool) – whether the angle is given in degree or radiant
  • **kwargs – additional keyword arguments (passed to skimage.transform.warp())
Returns:

transformed Image
Return type:

BaseSingleImage
save(directory, filename, lmk_type='LJSON', **kwargs)[source]

Saves Image and optionally landmarks to files

Parameters:
  • directory (str) – string containing the directory to save
  • filename (str) – string containing the filename (without the extension)
  • lmk_type (str or None) – if None: no landmarks will be saved if str: specifies type of landmark file
  • **kwargs – additional keyword arguments passed to save function for landmarks
save_image(filepath)[source]

Saves Image to file

Parameters:filepath (str) – file to save the image to
save_landmarks(filepath, lmk_type='LJSON', **kwargs)[source]

Saves landmarks to file

Parameters:
  • filepath (str) – path to file the landmarks should be saved to
  • lmk_type (str) – specifies the type of landmark file
  • **kwargs – additional keyword arguments passed to save function
to_grayscale()[source]

Convert Image to grayscale

Returns:Grayscale Image
Return type:BaseSingleImage
transform(transform=None, rotation=None, scale=None, translation=None, shear=None, trafo_matrix=None, return_matrix=False, **kwargs)[source]

transform image and landmarks by parameters or transformation matrix See skimage.transform.AffineTransform for a detailed parameter explanation

Parameters:
  • transform (skimage.transform.AffineTransform) – if transform is specified it overwrites all other arguments
  • rotation (float or None) – rotation angle in radiant
  • scale (float or None) – scale value
  • translation – translation params
  • shear – shear params
  • trafo_matrix – transformation matrix
  • return_matrix (bool) – whether to return the transformation matrix along the transformed object
  • **kwargs – additional keyword arguments
Returns:

  • BaseSingleImage – transformed Image
  • [optional] np.ndarray – transformation matrix
transform_about_centre(transform=None, rotation=None, scale=None, translation=None, shear=None, trafo_matrix=None, return_matrix=False, **kwargs)[source]

Perform transformations about the image center. (internally shifting image to origin, perform transformation and shift it back)

Parameters:
  • transform (skimage.transform.AffineTransform) – if transform is specified it overwrites all other arguments
  • rotation (float) – rotation angle in radiant
  • scale (float) – scale value
  • translation – translation params
  • shear – shear params
  • trafo_matrix – transformation matrix
  • return_matrix (bool) – whether to return the transformation matrix along the transformed object
  • **kwargs – additional keyword arguments
Returns:

  • BaseSingleImage – transformed Image
  • [optional] np.ndarray – transformation matrix
translate(translation, relative=False, **kwargs)[source]

translates image and landmarks

translation :
translation parameters
relative : bool
whether translation parameters are relative to image size
**kwargs :
additional keyword arguments (passed to skimage.transform.warp())
BaseSingleImage
transformed Image
view(*args, **kwargs)[source]

Plots image and landmarks

Parameters:
  • *args – positional arguments
  • **kwargs – keyword arguments
Raises:

NotImplementedError – if not overwritten by subclass