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)