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KeepLargestComponent.apply_transform()   A

↳ Parent: torchio.transforms.preprocessing.label.keep_largest_component

Complexity

Conditions 2

Size

Total Lines 10
Code Lines 10

Duplication

Lines 0
Ratio 0 %

Importance

Changes 0
Metric Value
cc 2
eloc 10
nop 2
dl 0
loc 10
rs 9.9
c 0
b 0
f 0
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import SimpleITK as sitk
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from .label_transform import LabelTransform

            


            
                                                                                                            
                            
            
                                    
            
            

                
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class KeepLargestComponent(LabelTransform):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    r"""Keep only the largest connected component in a binary label map.

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    Args:

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        **kwargs: See :class:`~torchio.transforms.Transform` for additional

            


            
                                                                                                            
                            
            
                                    
            
            

                
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            keyword arguments.

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    .. note:: For now, this transform only works for binary images, i.e., label

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        maps with a background and a foreground class. If you are interested in

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        extending this transform `open a new issue`_.

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    .. _open a new issue: https://github.com/fepegar/torchio/issues/new?assignees=&labels=enhancement&template=feature_request.md&title=Improve%20KeepLargestComponent%20transform

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    """  # noqa: E501

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    def __init__(self, **kwargs):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        super().__init__(**kwargs)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        self.args_names = []

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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    def apply_transform(self, subject):

            


            
                                                        
            
                                    
            
            

                
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        for image in self.get_images(subject):

            


            
                                                        
            
                                    
            
            

                
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            assert image.data.ndim == 4 and image.data.shape[0] == 1

            


            
                                                        
            
                                    
            
            

                
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            sitk_image = image.as_sitk()

            


            
                                                        
            
                                    
            
            

                
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            connected_components = sitk.ConnectedComponent(sitk_image)

            


            
                                                        
            
                                    
            
            

                
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            labeled_cc = sitk.RelabelComponent(connected_components)

            


            
                                                        
            
                                    
            
            

                
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            largest_cc = labeled_cc == 1

            


            
                                                        
            
                                    
            
            

                
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            tensor, _ = self.sitk_to_nib(largest_cc)

            


            
                                                        
            
                                    
            
            

                
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            image.set_data(tensor)

            


            
                                                        
            
                                    
            
            

                
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        return subject

            


            
                                                        
            
                                    
            
            

                
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