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Pull Request — master (#136)
by Jasper
01:18
created

Polaroid.view()   B

↳ Parent: Polaroid

Complexity

Conditions 2

Size

Total Lines 25

Duplication

Lines 0
Ratio 0 %

Importance

Changes 1
Bugs 0 Features 0
Metric Value
cc 2
c 1
b 0
f 0
dl 0
loc 25
rs 8.8571
1 
from niprov.dependencies import Dependencies
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import webbrowser
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class Polaroid(object):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    def __init__(self, dependencies):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        pass

            


            
                                                                                                            
                            
            
                                    
            
            

                
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    def saveSnapshot(self, data, to):

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        """Plot an overview of the image and store it.

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        Args:

            


            
                                                                                                            
                            
            
                                    
            
            

                
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            data (numpy.ndarray): Array of 2, 3 or 4 dimensions with image data.

            


            
                                                                                                            
                            
            
                                    
            
            

                
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            to (:class:`.PictureCache`): Service that provides a file-like 

            


            
                                                                                                            
                            
            
                                    
            
            

                
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                handle to save the plotted picture to.

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        """

            


            
                                                                                                            
                            
            
                                    
            
            

                
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        pass

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
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    def view(img, dependencies=Dependencies()):

            


            
                                                        
            
                                    
            
            

                
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        libs = dependencies.getLibraries()

            


            
                                                        
            
                                    
            
            

                
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        plt = libs.pyplot

            


            
                                                        
            
                                    
            
            

                
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        nibabel = libs.nibabel

            


            
                                                        
            
                                    
            
            

                
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        data = nibabel.load(img.path).get_data()

            


            
                                                        
            
                                    
            
            

                
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        ## 3D

            


            
                                                        
            
                                    
            
            

                
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        ndims = len(data.shape)

            


            
                                                        
            
                                    
            
            

                
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        sliceOrder = [1, 0, 2]

            


            
                                                        
            
                                    
            
            

                
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        fig, axs = plt.subplots(nrows=1, ncols=ndims)

            


            
                                                        
            
                                    
            
            

                
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        for d in range(ndims):

            


            
                                                        
            
                                    
            
            

                
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            slicing = [slice(None)]*ndims

            


            
                                                        
            
                                    
            
            

                
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            slicing[sliceOrder[d]] = int(data.shape[d]/2)

            


            
                                                        
            
                                    
            
            

                
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            axs[d].matshow(data[slicing].T, origin='lower', 

            


            
                                                        
            
                                    
            
            

                
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                cmap = plt.get_cmap('gray'), vmin = 0, vmax = data.max())

            


            
                                                        
            
                                    
            
            

                
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            axs[d].locator_params(nbins=3)

            


            
                                                        
            
                                    
            
            

                
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            axs[d].tick_params(axis='both', which='major', labelsize=8)

            


            
                                                        
            
                                    
            
            

                
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        plt.tight_layout()

            


            
                                                        
            
                                    
            
            

                
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        fname = 'myplot.png'

            


            
                                                        
            
                                    
            
            

                
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        plt.savefig(fname)

            


            
                                                        
            
                                    
            
            

                
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        webbrowser.open(fname)

            


            
                                                        
            
                                    
            
            

                
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