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Completed
Pull Request — master (#136)
by Jasper
01:17
created

NiftiFile.attach()   A

↳ Parent: NiftiFile

Complexity

Conditions 1

Size

Total Lines 15

Duplication

Lines 0
Ratio 0 %

Importance

Changes 0
Metric Value
cc 1
c 0
b 0
f 0
dl 0
loc 15
rs 9.4285
1 
from datetime import datetime
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from niprov.basefile import BaseFile
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class NiftiFile(BaseFile):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    def __init__(self, location, **kwargs):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        super(NiftiFile, self).__init__(location, **kwargs)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        self.libs = self.dependencies.getLibraries()

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        self.camera = self.dependencies.getCamera()

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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    def attach(self, form='json'):

            


            
                                                                        
                            
            
                                    
            
            

                
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        """

            


            
                                                                        
                            
            
                                    
            
            

                
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        Attach the current provenance to the file by injecting it as a 

            


            
                                                                        
                            
            
                                    
            
            

                
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        json-encoded extension to the nifti header.

            


            
                                                                        
                            
            
                                    
            
            

                
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        Args:

            


            
                                                                        
                            
            
                                    
            
            

                
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            form (str): Data format in which to serialize provenance. Defaults 

            


            
                                                                        
                            
            
                                    
            
            

                
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                to 'json'.

            


            
                                                                        
                            
            
                                    
            
            

                
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        """

            


            
                                                                        
                            
            
                                    
            
            

                
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        img = self.libs.nibabel.load(self.path)

            


            
                                                                        
                            
            
                                    
            
            

                
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        provstr = self.getProvenance(form)

            


            
                                                                        
                            
            
                                    
            
            

                
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        ext = self.libs.nibabel.nifti1.Nifti1Extension('comment', provstr)

            


            
                                                                        
                            
            
                                    
            
            

                
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        hdr = img.get_header()

            


            
                                                                        
                            
            
                                    
            
            

                
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        hdr.extensions.append(ext)

            


            
                                                                        
                            
            
                                    
            
            

                
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        img.to_filename(self.path)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    def inspect(self):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        provenance = super(NiftiFile, self).inspect()

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        img = self.libs.nibabel.load(self.path)

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        self.camera.saveSnapshot(img.get_data(), for_=self)

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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        return provenance

            


            
                                                        
            
                                    
            
            

                
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