def main(select=3, **kwargs):
"""Script main function.
select: int
1: Medical data
2: Blocky data, different every time
3: Two donuts
4: Ellipsoid
"""
import visvis as vv # noqa: delay import visvis and GUI libraries
# Create test volume
if select == 1:
vol = vv.volread('stent')
isovalue = kwargs.pop('level', 800)
elif select == 2:
vol = vv.aVolume(20, 128)
isovalue = kwargs.pop('level', 0.2)
elif select == 3:
with timer('computing donuts'):
vol = donuts()
isovalue = kwargs.pop('level', 0.0)
# Uncommenting the line below will yield different results for
# classic MC
# vol *= -1
elif select == 4:
vol = ellipsoid(4, 3, 2, levelset=True)
isovalue = kwargs.pop('level', 0.0)
else:
raise ValueError('invalid selection')
# Get surface meshes
with timer('finding surface lewiner'):
vertices1, faces1 = marching_cubes_lewiner(vol, isovalue, **kwargs)[:2]
with timer('finding surface classic'):
vertices2, faces2 = marching_cubes_classic(vol, isovalue, **kwargs)
# Show
vv.figure(1)
vv.clf()
a1 = vv.subplot(121)
vv.title('Lewiner')
m1 = vv.mesh(np.fliplr(vertices1), faces1)
a2 = vv.subplot(122)
vv.title('Classic')
m2 = vv.mesh(np.fliplr(vertices2), faces2)
a1.camera = a2.camera
# visvis uses right-hand rule, gradient_direction param uses left-hand rule
m1.cullFaces = m2.cullFaces = 'front' # None, front or back
vv.use().Run()
def main(select=3, **kwargs):
"""Script main function.
select: int
1: Medical data
2: Blocky data, different every time
3: Two donuts
4: Ellipsoid
"""
import visvis as vv # noqa: delay import visvis and GUI libraries
# Create test volume
if select == 1:
vol = vv.volread('stent')
isovalue = kwargs.pop('level', 800)
elif select == 2:
vol = vv.aVolume(20, 128)
isovalue = kwargs.pop('level', 0.2)
elif select == 3:
with timer('computing donuts'):
vol = donuts()
isovalue = kwargs.pop('level', 0.0)
# Uncommenting the line below will yield different results for
# classic MC
# vol *= -1
elif select == 4:
vol = ellipsoid(4, 3, 2, levelset=True)
isovalue = kwargs.pop('level', 0.0)
else:
raise ValueError('invalid selection')
# Get surface meshes
with timer('finding surface lewiner'):
vertices1, faces1 = marching_cubes_lewiner(vol, isovalue, **kwargs)[:2]
with timer('finding surface classic'):
vertices2, faces2 = marching_cubes_classic(vol, isovalue, **kwargs)
# Show
vv.figure(1)
vv.clf()
a1 = vv.subplot(121)
vv.title('Lewiner')
m1 = vv.mesh(np.fliplr(vertices1), faces1)
a2 = vv.subplot(122)
vv.title('Classic')
m2 = vv.mesh(np.fliplr(vertices2), faces2)
a1.camera = a2.camera
# visvis uses right-hand rule, gradient_direction param uses left-hand rule
m1.cullFaces = m2.cullFaces = 'front' # None, front or back
vv.use().Run()
while not cropper3d._finished:
vv.processEvents()
time.sleep(0.01)
# Clean up figure (close if we opened it)
fig.Clear()
fig.DrawNow()
if figCleanup:
fig.Destroy()
# Obtain ranges
rx = cropper3d._range_transversal._rangex
ry = cropper3d._range_transversal._rangey
rz = cropper3d._range_coronal._rangey
# Perform crop
vol2 = vol[rz.min:rz.max, ry.min:ry.max, rx.min:rx.max]
# Done
return vol2
if __name__ == '__main__':
# testing
import os
vol1 = vv.aVolume(size=128)
vol2 = crop3d(vol1)
print('shape1:', vol1.shape)
print('shape2:', vol2.shape)
while not cropper3d._finished:
vv.processEvents()
time.sleep(0.01)
# Clean up figure (close if we opened it)
fig.Clear()
fig.DrawNow()
if figCleanup:
fig.Destroy()
# Obtain ranges
rx = cropper3d._range_transversal._rangex
ry = cropper3d._range_transversal._rangey
rz = cropper3d._range_coronal._rangey
# Perform crop
vol2 = vol[rz.min:rz.max, ry.min:ry.max, rx.min:rx.max]
# Done
return vol2
if __name__ == '__main__':
# testing
import os
vol1 = vv.aVolume(size=128)
vol2 = crop3d(vol1)
print('shape1:', vol1.shape)
print('shape2:', vol2.shape)
#!/usr/bin/env python
""" This example demonstrates rendering a color volume.
This example demonstrates two render styles. Note that
all render styles are capable of rendering color data.
"""
import numpy as np
import visvis as vv
app = vv.use()
# Use vv.aVolume to create random bars for each color plane
N = 64
vol = np.empty((N, N, N, 3), dtype='float32')
for i in range(3):
vol[:, :, :, i] = vv.aVolume(10, N)
# Show
vv.figure()
a1 = vv.subplot(121)
t1 = vv.volshow(vol[:, :, :, :], renderStyle='mip')
vv.title('color MIP render')
a2 = vv.subplot(122)
t2 = vv.volshow(vol[:, :, :, :], renderStyle='iso')
t2.isoThreshold = 0.5
vv.title('color ISO-surface render')
# Share cameras
a1.camera = a2.camera
# Run app
app.Run()
#!/usr/bin/env python
""" This example illustrates visualizing a four dimensional data set
(a series of 3D volumes). The same method can be used to visualize
the motion of lines, images, meshes, etc.
"""
import visvis as vv
# create multiple instances of the same volume (simulate motion)
vols = [vv.aVolume()]
for i in range(9):
vol = vols[i].copy()
vol[2:] = vol[:-2]
vol[:2] = 0
vols.append(vol)
# create figure, axes, and data container object
f = vv.clf()
a = vv.gca()
m = vv.MotionDataContainer(a)
# create volumes, loading them into opengl memory, and insert into container.
for vol in vols:
t = vv.volshow(vol)
t.parent = m
t.colormap = vv.CM_HOT
# Remove comments to use iso-surface rendering
#t.renderStyle = 'iso'
#t.isoThreshold = 0.2
# set some settings
a.daspect = 1,1,-1
# Create test volume
SELECT = 3
if SELECT == 0:
import pirt
vol = np.zeros((100, 100, 100), 'float32')
vol[50, 50, 50] = 200.0
vol = pirt.gfilter(vol, 20)
isovalue = vol.max() * 0.5
elif SELECT == 1:
s = vv.ssdf.load(
'/home/almar/data/cropped/stents_valve/cropped_pat102.bsdf')
vol = s.vol.astype('float32')
isovalue = 800
elif SELECT == 2:
vol = vv.aVolume(20, 256) # Different every time
isovalue = 0.2
elif SELECT == 3:
n = 48
a, b = 2.5 / n, -1.25
isovalue = 0.0
#
vol = np.empty((n, n, n), 'float32')
for iz in range(vol.shape[0]):
for iy in range(vol.shape[1]):
for ix in range(vol.shape[2]):
z, y, x = float(iz) * a + b, float(iy) * a + b, float(
ix) * a + b
vol[iz, iy,
ix] = (((8 * x)**2 + (8 * y - 2)**2 +
(8 * z)**2 + 16 - 1.85 * 1.85) *
for i in range(3):
vv.SliceTexture(proxy, vol, i, centre[i])
# set clim
if isinstance(clim,list):
clim = tuple(clim)
if isinstance(clim, tuple):
proxy.SetClim(clim)
# set colormap
if cm is not None:
proxy.colormap = cm
# adjust axes
if axesAdjust:
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.cameraType = '3d'
axes.SetLimits()
# done
axes.Draw()
return proxy
if __name__ == "__main__":
import visvis as vv
vol = vv.aVolume()
vol[:30,:30,:30] += 0.3
t = volshow2(vol)
#!/usr/bin/env python
""" This example demonstrates rendering a color volume.
This example demonstrates two render styles. Note that
all render styles are capable of rendering color data.
"""
import numpy as np
import visvis as vv
app = vv.use()
# Use vv.aVolume to create random bars for each color plane
N = 64
vol = np.empty((N,N,N,3), dtype='float32')
for i in range(3):
vol[:,:,:,i] = vv.aVolume(10,N)
# Show
vv.figure()
a1 = vv.subplot(121);
t1 = vv.volshow(vol[:,:,:,:], renderStyle = 'mip')
vv.title('color MIP render')
a2 = vv.subplot(122);
t2 = vv.volshow(vol[:,:,:,:], renderStyle = 'iso')
t2.isoThreshold = 0.5
vv.title('color ISO-surface render')
# Share cameras
a1.camera = a2.camera
# Run app
app.Run()
from skimage.measure import marching_cubes_classic, marching_cubes_lewiner
from skimage.draw import ellipsoid
# Create test volume
SELECT = 3
gradient_dir = 'descent' # ascent or descent
if SELECT == 1:
# Medical data
vol = vv.volread('stent')
isovalue = 800
elif SELECT == 2:
# Blocky data
vol = vv.aVolume(20, 128) # Different every time
isovalue = 0.2
elif SELECT == 3:
# Generate two donuts using a formula by Thomas Lewiner
n = 48
a, b = 2.5 / n, -1.25
isovalue = 0.0
#
vol = np.empty((n, n, n), 'float32')
for iz in range(vol.shape[0]):
for iy in range(vol.shape[1]):
for ix in range(vol.shape[2]):
z, y, x = float(iz)*a+b, float(iy)*a+b, float(ix)*a+b
vol[iz, iy, ix] = ( (
(8*x)**2 + (8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) * ( (8*x)**2 +
# The appearance of the line objects can be set in their # constructor, or by using their properties line1.lc, line1.mc = 'g', 'b' line2.lc, line2.mc = 'y', 'r' # Display a legend a1.legend = "Astronaut's face", "Astronaut's helmet" # Create second axes (with a black background) a2 = vv.subplot(122) a2.bgcolor = 'k' a2.axis.axisColor = 'w' # Display a texture vol = vv.aVolume(2) # returns a test volume as a numpy array texture3d = vv.volshow(vol) # Display a mesh using one of the "solid" functions mesh = vv.solidTeapot((32, 32, 80), scaling=(50, 50, 50)) mesh.faceColor = 0.4, 1, 0.4 mesh.specular = 'r' # Set orthographic projection a2.camera.fov = 45 # Create labels for the axis a2.axis.xLabel = 'x-axis' a2.axis.yLabel = 'y-axis' a2.axis.zLabel = 'z-axis'
# The appearance of the line objects can be set in their # constructor, or by using their properties line1.lc, line1.mc = 'g', 'b' line2.lc, line2.mc = 'y', 'r' # Display a legend a1.legend = "Lena's face", "Lena's shoulder" # Create second axes (with a black background) a2 = vv.subplot(122) a2.bgcolor = 'k' a2.axis.axisColor = 'w' # Display a texture vol = vv.aVolume(2) # returns a test volume as a numpy array texture3d = vv.volshow(vol) # Display a mesh using one of the "solid" functions mesh = vv.solidTeapot((32,32,80), scaling=(50,50,50)) mesh.faceColor = 0.4, 1, 0.4 mesh.specular = 'r' # Set orthographic projection a2.camera.fov = 45 # Create labels for the axis a2.axis.xLabel = 'x-axis' a2.axis.yLabel = 'y-axis' a2.axis.zLabel = 'z-axis'
#!/usr/bin/env python
""" This example illustrates visualizing a four dimensional data set
(a series of 3D volumes). The same method can be used to visualize
the motion of lines, images, meshes, etc.
"""
import visvis as vv
# create multiple instances of the same volume (simulate motion)
vols = [vv.aVolume()]
for i in range(9):
vol = vols[i].copy()
vol[2:] = vol[:-2]
vol[:2] = 0
vols.append(vol)
# create figure, axes, and data container object
f = vv.clf()
a = vv.gca()
m = vv.MotionDataContainer(a)
# create volumes, loading them into opengl memory, and insert into container.
for vol in vols:
t = vv.volshow(vol)
t.parent = m
t.colormap = vv.CM_HOT
# Remove comments to use iso-surface rendering
#t.renderStyle = 'iso'
#t.isoThreshold = 0.2
# set some settings
a.daspect = 1,1,-1
#!/usr/bin/env python
""" This example demonstrates rendering a color volume.
We demonstrate two renderers capable of rendering color data:
the colormip and coloriso renderer.
"""
import visvis as vv
app = vv.use()
# Create volume (smooth a bit)
if True:
vol0 = vv.aVolume()
vol = vol0.copy() * 0.5
vol[1:, :, :] += 0.3 * vol0[:-1, :, :]
vol[:-1, :, :] += 0.3 * vol0[1:, :, :]
vol[:, 1:, :] += 0.3 * vol0[:, :-1, :]
vol[:, :-1, :] += 0.3 * vol0[:, 1:, :]
vol[:, :, 1:] += 0.3 * vol0[:, :, :-1]
vol[:, :, :-1] += 0.3 * vol0[:, :, 1:]
else:
# My personal test
from visvis import ssdf
s = ssdf.load(
'/home/almar/data/dicom/cropped/croppedReg_pat01_gravity.bsdf')
vol = s.vol
##
# Create figure and make subplots with different renderers
#!/usr/bin/env python
import visvis as vv
import numpy as np
app = vv.use()
vv.clf()
# create volume
vol = vv.aVolume(size=64)
# set labels
vv.xlabel('x axis')
vv.ylabel('y axis')
vv.zlabel('z axis')
# show
t = vv.volshow(vol, renderStyle='mip')
# try the differtent render styles, for examample
# "t.renderStyle='iso'" or "t.renderStyle='ray'"
# If the drawing hangs, your video drived decided to render in software mode.
# This is unfortunately (as far as I know) not possible to detect.
# It might help if your data is shaped a power of 2.
# Get axes and set camera to orthographic mode (with a field of view of 70)
a = vv.gca()
a.camera.fov = 45
# Create colormap editor wibject.
vv.ColormapEditor(a)
# Start app
#!/usr/bin/env python
import visvis as vv
import numpy as np
app = vv.use()
vv.clf()
# create volume
vol = vv.aVolume(size=64)
# set labels
vv.xlabel('x axis')
vv.ylabel('y axis')
vv.zlabel('z axis')
# show
t = vv.volshow(vol, renderStyle='mip')
# try the differtent render styles, for examample
# "t.renderStyle='iso'" or "t.renderStyle='ray'"
# If the drawing hangs, your video drived decided to render in software mode.
# This is unfortunately (as far as I know) not possible to detect.
# It might help if your data is shaped a power of 2.
# Get axes and set camera to orthographic mode (with a field of view of 70)
a = vv.gca()
a.camera.fov = 45
# Create colormap editor wibject.
vv.ColormapEditor(a)
# Start app
from skimage.measure import marching_cubes_classic, marching_cubes_lewiner
from skimage.draw import ellipsoid
# Create test volume
SELECT = 3
gradient_dir = 'descent' # ascent or descent
if SELECT == 1:
# Medical data
vol = vv.volread('stent')
isovalue = 800
elif SELECT == 2:
# Blocky data
vol = vv.aVolume(20, 128) # Different every time
isovalue = 0.2
elif SELECT == 3:
# Generate two donuts using a formula by Thomas Lewiner
n = 48
a, b = 2.5 / n, -1.25
isovalue = 0.0
#
vol = np.empty((n, n, n), 'float32')
for iz in range(vol.shape[0]):
for iy in range(vol.shape[1]):
for ix in range(vol.shape[2]):
z, y, x = float(iz) * a + b, float(iy) * a + b, float(
ix) * a + b
vol[iz, iy, ix] = (((8 * x)**2 + (8 * y - 2)**2 +
# Create test volume
SELECT = 3
if SELECT == 0:
import pirt
vol = np.zeros((100,100,100), 'float32')
vol[50,50,50] = 200.0
vol = pirt.gfilter(vol, 20)
isovalue = vol.max() *0.5
elif SELECT == 1:
s = vv. ssdf.load('/home/almar/data/cropped/stents_valve/cropped_pat102.bsdf')
vol = s.vol.astype('float32')
isovalue = 800
elif SELECT == 2:
vol = vv.aVolume(20, 256) # Different every time
isovalue = 0.2
elif SELECT == 3:
n = 48
a, b = 2.5/n, -1.25
isovalue = 0.0
#
vol = np.empty((n,n,n), 'float32')
for iz in range(vol.shape[0]):
for iy in range(vol.shape[1]):
for ix in range(vol.shape[2]):
z, y, x = float(iz)*a+b, float(iy)*a+b, float(ix)*a+b
vol[iz,iy,ix] = ( (
(8*x)**2 + (8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) * ( (8*x)**2 +
(8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) - 64 * ( (8*x)**2 + (8*y-2)**2 )
) * ( ( (8*x)**2 + ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2 + 16 - 1.85*1.85 )
#!/usr/bin/env python
""" This example demonstrates rendering a color volume.
We demonstrate two renderers capable of rendering color data:
the colormip and coloriso renderer.
"""
import visvis as vv
app = vv.use()
# Create volume (smooth a bit)
if True:
vol0 = vv.aVolume()
vol = vol0.copy()*0.5
vol[1:,:,:] += 0.3 * vol0[:-1,:,:]
vol[:-1,:,:] += 0.3 * vol0[1:,:,:]
vol[:,1:,:] += 0.3 * vol0[:,:-1,:]
vol[:,:-1,:] += 0.3 * vol0[:,1:,:]
vol[:,:,1:] += 0.3 * vol0[:,:,:-1]
vol[:,:,:-1] += 0.3 * vol0[:,:,1:]
else:
# My personal test
from visvis import ssdf
s = ssdf.load('/home/almar/data/dicom/cropped/croppedReg_pat01_gravity.bsdf')
vol = s.vol
##
# Create figure and make subplots with different renderers
vv.figure(1); vv.clf()
RS = ['mip', 'iso', 'edgeray', 'ray', 'litray']