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"""
Demonstrates GLVolumeItem for displaying volumetric data.
"""
import sys
import numpy as np
import pyqtgraph as pg
from pyqtgraph.Qt import QtGui
import pyqtgraph.opengl as gl
from pyqtgraph import functions as fn
if 'darwin' in sys.platform:
fmt = QtGui.QSurfaceFormat()
fmt.setRenderableType(fmt.RenderableType.OpenGL)
fmt.setProfile(fmt.OpenGLContextProfile.CoreProfile)
fmt.setVersion(4, 1)
QtGui.QSurfaceFormat.setDefaultFormat(fmt)
app = pg.mkQApp("GLVolumeItem Example")
w = gl.GLViewWidget()
w.show()
w.setWindowTitle('pyqtgraph example: GLVolumeItem')
w.setCameraPosition(distance=200)
g = gl.GLGridItem()
g.scale(10, 10, 1)
w.addItem(g)
## Hydrogen electron probability density
def psi(i, j, k, offset=(50,50,100)):
x = i-offset[0]
y = j-offset[1]
z = k-offset[2]
th = np.arctan2(z, np.hypot(x, y))
r = np.sqrt(x**2 + y**2 + z **2)
a0 = 2
return (
(1.0 / 81.0)
* 1.0 / (6.0 * np.pi) ** 0.5
* (1.0 / a0) ** (3 / 2)
* (r / a0) ** 2
* np.exp(-r / (3 * a0))
* (3 * np.cos(th) ** 2 - 1)
)
data = np.fromfunction(psi, (100,100,200))
with np.errstate(divide = 'ignore'):
positive = np.log(fn.clip_array(data, 0, data.max())**2)
negative = np.log(fn.clip_array(-data, 0, -data.min())**2)
d2 = np.empty(data.shape + (4,), dtype=np.ubyte)
# Original Code
# d2[..., 0] = positive * (255./positive.max())
# d2[..., 1] = negative * (255./negative.max())
# Reformulated Code
# Both positive.max() and negative.max() are negative-valued.
# Thus the next 2 lines are _not_ bounded to [0, 255]
positive = positive * (255./positive.max())
negative = negative * (255./negative.max())
# When casting to ubyte, the original code relied on +Inf to be
# converted to 0. On arm64, it gets converted to 255.
# Thus the next 2 lines change +Inf explicitly to 0 instead.
positive[np.isinf(positive)] = 0
negative[np.isinf(negative)] = 0
# When casting to ubyte, the original code relied on the conversion
# to do modulo 256. The next 2 lines do it explicitly instead as
# documentation.
d2[..., 0] = positive.astype(int) % 256
d2[..., 1] = negative.astype(int) % 256
d2[..., 2] = d2[...,1]
d2[..., 3] = d2[..., 0]*0.3 + d2[..., 1]*0.3
d2[..., 3] = (d2[..., 3].astype(float) / 255.) **2 * 255
d2[:, 0, 0] = [255,0,0,100]
d2[0, :, 0] = [0,255,0,100]
d2[0, 0, :] = [0,0,255,100]
v = gl.GLVolumeItem(d2)
v.translate(-50,-50,-100)
w.addItem(v)
ax = gl.GLAxisItem()
w.addItem(ax)
if __name__ == '__main__':
pg.exec()
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