

In [1]:

    
%pylab inline

import io3d









    



Populating the interactive namespace from numpy and matplotlib

Data reader



In [2]:

    
dr = io3d.DataReader()
datap = dr.Get3DData('../sample_data/jatra_5mm/', dataplus_format=True)
datap.keys()









    Out[2]:





['SeriesNumber',
 'voxelsize_mm',
 'SeriesDescription',
 'dcmfilelist',
 'ImageComments',
 'datadir',
 'data3d',
 'series_number',
 'Modality']

Visualization



In [3]:

    
plt.imshow(datap["data3d"][50,:,:], cmap='gray')
print("pixel spacing = ", datap["voxelsize_mm"])









    



('pixel spacing = ', [5.0, 0.75, 0.75])



In [4]:

    
datap["data3d"]









    Out[4]:





array([[[-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        ..., 
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024]],

       [[-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        ..., 
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024]],

       [[-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        ..., 
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024]],

       ..., 
       [[-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        ..., 
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024]],

       [[-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        ..., 
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024]],

       [[-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        ..., 
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024],
        [-1024, -1024, -1024, ..., -1024, -1024, -1024]]], dtype=int16)



In [5]:

    
import sed3
ed = sed3.show_slices(datap["data3d"], slice_step=10)