View GitHub Repository niprov

Schedule Inspection
Subscribe
Completed
Pull Request — master (#136)
by Jasper
01:24
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
2 
import webbrowser
3 

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    4
                

                                    
                                                    
                
                
                

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    5
                

                                    
                                                    
                
                
                
class Polaroid(object):

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    6
                

                                    
                                                    
                
                
                

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    7
                

                                    
                                                    
                
                
                
    def __init__(self, dependencies):

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    8
                

                                    
                                                    
                
                
                
        pass

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    9
                

                                    
                                                    
                
                
                

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    10
                

                                    
                                                    
                
                
                
    def saveSnapshot(self, data, to):

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    11
                

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

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    12
                

                                    
                                                    
                
                
                

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    13
                

                                    
                                                    
                
                
                
        Args:

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    14
                

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

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    15
                

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

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    16
                

                                    
                                                    
                
                
                
                handle to save the plotted picture to.

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    17
                

                                    
                                                    
                
                
                
        """

            


            
                                                                                                            
                            
            
                                    
            
            

                
                    18
                

                                    
                                                    
                
                
                
        pass

            


            
                                                                                                            
                                                                
            
                                    
            
            

                
                    19
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    20
                

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

            


            
                                                        
            
                                    
            
            

                
                    21
                

                                    
                                                    
                
                
                
        libs = dependencies.getLibraries()

            


            
                                                        
            
                                    
            
            

                
                    22
                

                                    
                                                    
                
                
                
        plt = libs.pyplot

            


            
                                                        
            
                                    
            
            

                
                    23
                

                                    
                                                    
                
                
                
        nibabel = libs.nibabel

            


            
                                                        
            
                                    
            
            

                
                    24
                

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

            


            
                                                        
            
                                    
            
            

                
                    25
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    26
                

                                    
                                                    
                
                
                
        ## 3D

            


            
                                                        
            
                                    
            
            

                
                    27
                

                                    
                                                    
                
                
                
        ndims = len(data.shape)

            


            
                                                        
            
                                    
            
            

                
                    28
                

                                    
                                                    
                
                
                
        sliceOrder = [1, 0, 2]

            


            
                                                        
            
                                    
            
            

                
                    29
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    30
                

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

            


            
                                                        
            
                                    
            
            

                
                    31
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    32
                

                                    
                                                    
                
                
                
        for d in range(ndims):

            


            
                                                        
            
                                    
            
            

                
                    33
                

                                    
                                                    
                
                
                
            slicing = [slice(None)]*ndims

            


            
                                                        
            
                                    
            
            

                
                    34
                

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

            


            
                                                        
            
                                    
            
            

                
                    35
                

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

            


            
                                                        
            
                                    
            
            

                
                    36
                

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

            


            
                                                        
            
                                    
            
            

                
                    37
                

                                    
                                                    
                
                
                
            axs[d].locator_params(nbins=3)

            


            
                                                        
            
                                    
            
            

                
                    38
                

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

            


            
                                                        
            
                                    
            
            

                
                    39
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    40
                

                                    
                                                    
                
                
                
        plt.tight_layout()

            


            
                                                        
            
                                    
            
            

                
                    41
                

                                    
                                                    
                
                
                

            


            
                                                        
            
                                    
            
            

                
                    42
                

                                    
                                                    
                
                
                
        fname = 'myplot.png'

            


            
                                                        
            
                                    
            
            

                
                    43
                

                                    
                                                    
                
                
                
        plt.savefig(fname)

            


            
                                                        
            
                                    
            
            

                
                    44
                

                                    
                                                    
                
                
                
        webbrowser.open(fname)

            


            
                                                        
            
                                    
            
            

                
                    45