#!/usr/bin/env python
# coding: utf-8

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# Requirements
# !pip install nibabel vtk


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import k3d
import math
import numpy as np
import nibabel as nib
from k3d.helpers import download


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import vtk
from vtk.util import numpy_support

filename = download('https://github.com/marcomusy/vtkplotter-examples/raw/master/vtkplotter_examples/data/embryo.slc')
reader = vtk.vtkSLCReader()
reader.SetFileName(filename)
reader.Update()
vti = reader.GetOutput()

bounds = vti.GetBounds()
x, y, z = vti.GetDimensions()
volume_data = numpy_support.vtk_to_numpy(vti.GetPointData().GetArray(0)).reshape(-1, y, x)


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embryo = k3d.volume(volume_data.astype(np.float16), 
                    color_map=np.array(k3d.basic_color_maps.BlackBodyRadiation, dtype=np.float32), 
                    bounds=bounds)

plot = k3d.plot()
plot += embryo
plot.display()


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filename = download('https://github.com/FNNDSC/data/raw/master/nifti/adi_brain/adi_brain.nii.gz')

nii_source = nib.load(filename)
img = nii_source.get_fdata()
dx, dy, dz = nii_source.header.get_zooms()
img = np.swapaxes(img,0,2).astype(np.float32)
nz, ny, nx = img.shape

volume = k3d.volume(img, color_range=[50,1000], color_map=np.array(k3d.basic_color_maps.Jet, dtype=np.float32))

plot = k3d.plot()
plot += volume
plot.display()


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volume.samples = 1024.0


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volume.color_range = [650, 1500]


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