In [38]:

    

%pylab inline
import io3d
import numpy as np
import matplotlib.pyplot as plt

orig_data = (np.random.random([30, 100, 120]) * 30).astype(np.int16)
orig_data[0:15, 20:60, 60:70] += 60
metadata = {'voxelsize_mm': [0.5, 0.5, 4]}


import sed3
plt.figure(figsize=(10,5))
sed3.show_slices(orig_data)


    

    




Populating the interactive namespace from numpy and matplotlib






    

In [35]:

    

new_data = io3d.misc.resize_to_mm(orig_data, metadata["voxelsize_mm"], [3,3,3])

# sed3.show_slices(new_data)
segmentation = new_data > 30
# sed3.show_slices(segmentation)
plt.figure(figsize=(10,5))
sed3.show_slices(new_data, contour=segmentation)
print(segmentation.shape)


    

    













    




(5, 17, 160)

In [37]:

    

orig_size_segmentation = io3d.misc.resize_to_shape(segmentation, shape=orig_data.shape)
plt.figure(figsize=(10,5))
sed3.show_slices(orig_data, contour=orig_size_segmentation)