View GitHub Repository niprov

Schedule Inspection
Subscribe

NiftiFile.attach()   A
last analyzed

↳ 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
2 
from niprov.basefile import BaseFile
3 

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    4
                

                                    
                                                    
                
                
                

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    5
                

                                    
                                                    
                
                
                
class NiftiFile(BaseFile):

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    6
                

                                    
                                                    
                
                
                

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    7
                

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

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    8
                

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

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    9
                

                                    
                                                    
                
                
                
        self.libs = self.dependencies.getLibraries()

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    10
                

                                    
                                                    
                
                
                
        self.camera = self.dependencies.getCamera()

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
                    11
                

                                    
                                                    
                
                
                

            


            
                                                                        
                            
            
                                    
            
            

                
                    12
                

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

            


            
                                                                        
                            
            
                                    
            
            

                
                    13
                

                                    
                                                    
                
                
                
        """

            


            
                                                                        
                            
            
                                    
            
            

                
                    14
                

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

            


            
                                                                        
                            
            
                                    
            
            

                
                    15
                

                                    
                                                    
                
                
                
        json-encoded extension to the nifti header.

            


            
                                                                        
                            
            
                                    
            
            

                
                    16
                

                                    
                                                    
                
                
                

            


            
                                                                        
                            
            
                                    
            
            

                
                    17
                

                                    
                                                    
                
                
                
        Args:

            


            
                                                                        
                            
            
                                    
            
            

                
                    18
                

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

            


            
                                                                        
                            
            
                                    
            
            

                
                    19
                

                                    
                                                    
                
                
                
                to 'json'.

            


            
                                                                        
                            
            
                                    
            
            

                
                    20
                

                                    
                                                    
                
                
                
        """

            


            
                                                                        
                            
            
                                    
            
            

                
                    21
                

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

            


            
                                                                        
                            
            
                                    
            
            

                
                    22
                

                                    
                                                    
                
                
                
        provstr = self.getProvenance(form)

            


            
                                                                        
                            
            
                                    
            
            

                
                    23
                

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

            


            
                                                                        
                            
            
                                    
            
            

                
                    24
                

                                    
                                                    
                
                
                
        hdr = img.get_header()

            


            
                                                                        
                            
            
                                    
            
            

                
                    25
                

                                    
                                                    
                
                
                
        hdr.extensions.append(ext)

            


            
                                                                        
                            
            
                                    
            
            

                
                    26
                

                                    
                                                    
                
                
                
        img.to_filename(self.path)

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    27
                

                                    
                                                    
                
                
                

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    28
                

                                    
                                                    
                
                
                
    def inspect(self):

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    29
                

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

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    30
                

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

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    31
                

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

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
                    32
                

                                    
                                                    
                
                
                
        return provenance

            


            
                                                        
            
                                    
            
            

                
                    33