87 lines
2.3 KiB
Python
87 lines
2.3 KiB
Python
# -*- coding: utf-8 -*-
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"""
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Demonstrates GLVolumeItem for displaying volumetric data.
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"""
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## Add path to library (just for examples; you do not need this)
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import initExample
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import numpy as np
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import pyqtgraph as pg
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import pyqtgraph.opengl as gl
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from pyqtgraph import functions as fn
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app = pg.mkQApp("GLVolumeItem Example")
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w = gl.GLViewWidget()
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w.show()
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w.setWindowTitle('pyqtgraph example: GLVolumeItem')
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w.setCameraPosition(distance=200)
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g = gl.GLGridItem()
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g.scale(10, 10, 1)
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w.addItem(g)
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## Hydrogen electron probability density
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def psi(i, j, k, offset=(50,50,100)):
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x = i-offset[0]
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y = j-offset[1]
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z = k-offset[2]
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th = np.arctan2(z, np.hypot(x, y))
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r = np.sqrt(x**2 + y**2 + z **2)
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a0 = 2
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return (
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(1.0 / 81.0)
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* 1.0 / (6.0 * np.pi) ** 0.5
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* (1.0 / a0) ** (3 / 2)
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* (r / a0) ** 2
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* np.exp(-r / (3 * a0))
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* (3 * np.cos(th) ** 2 - 1)
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)
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data = np.fromfunction(psi, (100,100,200))
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with np.errstate(divide = 'ignore'):
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positive = np.log(fn.clip_array(data, 0, data.max())**2)
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negative = np.log(fn.clip_array(-data, 0, -data.min())**2)
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d2 = np.empty(data.shape + (4,), dtype=np.ubyte)
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# Original Code
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# d2[..., 0] = positive * (255./positive.max())
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# d2[..., 1] = negative * (255./negative.max())
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# Reformulated Code
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# Both positive.max() and negative.max() are negative-valued.
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# Thus the next 2 lines are _not_ bounded to [0, 255]
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positive = positive * (255./positive.max())
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negative = negative * (255./negative.max())
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# When casting to ubyte, the original code relied on +Inf to be
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# converted to 0. On arm64, it gets converted to 255.
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# Thus the next 2 lines change +Inf explicitly to 0 instead.
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positive[np.isinf(positive)] = 0
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negative[np.isinf(negative)] = 0
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# When casting to ubyte, the original code relied on the conversion
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# to do modulo 256. The next 2 lines do it explicitly instead as
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# documentation.
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d2[..., 0] = positive.astype(int) % 256
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d2[..., 1] = negative.astype(int) % 256
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d2[..., 2] = d2[...,1]
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d2[..., 3] = d2[..., 0]*0.3 + d2[..., 1]*0.3
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d2[..., 3] = (d2[..., 3].astype(float) / 255.) **2 * 255
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d2[:, 0, 0] = [255,0,0,100]
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d2[0, :, 0] = [0,255,0,100]
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d2[0, 0, :] = [0,0,255,100]
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v = gl.GLVolumeItem(d2)
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v.translate(-50,-50,-100)
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w.addItem(v)
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ax = gl.GLAxisItem()
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w.addItem(ax)
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if __name__ == '__main__':
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pg.exec()
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