util/view-mri-data.py

   1 #!/usr/bin/python3
   2
   3 """
   4 Display volumetric data from the Stanford Volume Data Archive. The
   5 data (layers) are expected to be concatenated together.
   6 """
   7
   8 from mayavi import mlab
   9 import os
  10 import sys
  11
  12 def usage():
  13     binary = sys.argv[0]
  14     print(f"Usage: {binary} <data file>")
  15
  16 if len(sys.argv) < 2:
  17     usage()
  18     raise SystemExit
  19
  20
  21 def cube_root(n):
  22     """
  23     For integers, this probably even works.
  24     """
  25     for x in range(0,n+1):
  26         if x**3 == n:
  27             return x
  28
  29     return None
  30
  31
  32 # Read the data in a numpy 3D array
  33 import numpy as np
  34 data = np.fromfile(sys.argv[1], dtype='>u2')
  35
  36 original_data_length = 109*256*256
  37 multiplier = cube_root(len(data) // original_data_length)
  38 data.shape = (109*multiplier, 256*multiplier, 256*multiplier)
  39 data = data.T
  40
  41 # Display the data
  42 mlab.figure( bgcolor=(0,0,0), size=(1000,1000) )
  43
  44 # Our data is scalar (grayscale), but not equally spaced in all
  45 # directions.
  46 src = mlab.pipeline.scalar_field(data)
  47 src.spacing = [1, 1, 1.5]
  48 src.update_image_data = True
  49
  50 mlab.pipeline.volume(src, vmin=1400, vmax=2500)
  51 mlab.show()