protoclass.extraction.SpatialExtraction

class protoclass.extraction.SpatialExtraction(base_modality, kind='position', coord_system='euclidean', reference='centre')

Spatial extraction from standalone modality.

Parameters:

base_modality : object

The base modality on which the normalization will be applied. The base modality should inherate from StandaloneModality class.

kind : str, optional (default=’position’)

The type of spatial feature to extract. Can be either ‘position’ or ‘distance’.

coord_system : str, optional (default=’euclidean’)

The type of coordinate system to use. Can be either ‘euclidean’ or ‘cylindrical’.

reference : str, optional (default=’centre’)

If type is ‘distance’, the reference can be either ‘centre’ or ‘nn-contour-point’

Attributes

base_modality_	(object) The base modality on which the normalization will be applied. The base modality should inherate from StandaloneModality class.
roi_data_	(ndarray, shape flexible) Corresponds to the index to consider in order to fit the data.
data_	(ndarray,) Containing the data of all the slices according to the desired spatial information

Methods

fit(modality[, ground_truth, cat])	Compute the images images.
load_from_pickles(filename)	Function to load a normalization object.
save_to_pickles(filename)	Function to save a normalizatio object using pickles.
transform(modality[, ground_truth, cat])	Extract the data from the given modality.

__init__(base_modality, kind='position', coord_system='euclidean', reference='centre')

Methods

__init__(base_modality[, kind, ...])
fit(modality[, ground_truth, cat])	Compute the images images.
load_from_pickles(filename)	Function to load a normalization object.
save_to_pickles(filename)	Function to save a normalizatio object using pickles.
transform(modality[, ground_truth, cat])	Extract the data from the given modality.

fit(modality, ground_truth=None, cat=None)

Compute the images images.

Parameters:

modality : object of type TemporalModality

The modality object of interest.

ground-truth : object of type GTModality or None

The ground-truth of GTModality. If None, the whole data will be considered.

cat : str or None

String corresponding at the ground-truth of interest. Cannot be None if ground-truth is not None.

load_from_pickles(filename)

Function to load a normalization object.

Parameters:

filename : str

Filename to the pickle file. The extension should be .p.

Returns:

bpp : object

Returns the loaded object.

save_to_pickles(filename)

Function to save a normalizatio object using pickles.

Parameters:

filename : str

Filename to the pickle file. The extension should be .p.

Returns:

None

transform(modality, ground_truth=None, cat=None)

Extract the data from the given modality.

Parameters:

modality : object of type StandaloneModality

The modality object of interest.

ground-truth : object of type GTModality or None

The ground-truth of GTModality. If None, the whole data will be considered.

cat : str or None

String corresponding at the ground-truth of interest. Cannot be None if ground-truth is not None.

Returns

——

data : ndarray, shape (n_sample, n_feature)

A matrix containing the features extracted. The number of samples is equal to the number of positive label in the ground-truth. If distance, a single feature is returned. If position, 3 features are returned.