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Merge pull request #12 from xylar/update_from_hererra_pyevtk
Bring in 3 commits from PyEVTK BitBucket repo and 1 from paulo-herrera/PyEVTK on github
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‎README.md‎

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@@ -104,4 +104,10 @@ That should create a points.vtu file in the current directory.
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SUPPORT:
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=======
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I will continue releasing this package as open source, so it is free to be used in any kind of project. I will also continue providing support for simple questions and making incremental improvements as time allows. However, I also provide contract based support for commercial or research projects interested in this package or in topics related to data analysis and scientific programming with Python, Java, MATLAB/Octave, C/C++ or Fortran. For further details, please contact me to: paulo.herrera.eirl@gmail.com.
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I will continue releasing this package as open source, so it is free to be used in any kind of project.
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I will also continue providing support for simple questions and making incremental improvements as time
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allows. However, I also provide contract based support for commercial or research projects interested
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in this package or in topics related to data analysis and scientific programming with Python, Java, MATLAB/Octave, C/C++ or Fortran.
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For further details, please contact me to: paulo.herrera.eirl@gmail.com.
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**NOTE: PyEVTK moved to GitHub. The new official page is this one (https://github.com/paulo-herrera/PyEVTK)**

‎examples/lines.py‎

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#! /usr/bin/env python
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# ***********************************************************************************
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# * Copyright 2010 - 2016 Paulo A. Herrera. All rights reserved. *
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# * *
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# * Redistribution and use in source and binary forms, with or without *
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# * modification, are permitted provided that the following conditions are met: *
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# * *
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# * 1. Redistributions of source code must retain the above copyright notice, *
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# * this list of conditions and the following disclaimer. *
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# * *
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# * 2. Redistributions in binary form must reproduce the above copyright notice, *
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# * this list of conditions and the following disclaimer in the documentation *
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# * and/or other materials provided with the distribution. *
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# * *
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# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR *
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# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
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# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO *
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# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, *
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# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, *
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# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, *
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# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
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# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
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# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS *
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# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
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# ***********************************************************************************
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# **************************************************************
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# * Example of how to use the high level pointsToVTK function. *
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# **************************************************************
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from pyevtk.hl import linesToVTK
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import numpy as np
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# Example 1
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npoints = 4
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x = np.zeros(npoints)
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y = np.zeros(npoints)
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z = np.zeros(npoints)
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pressure = np.random.rand(npoints)
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temp = np.random.rand(npoints)
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vel = np.zeros(2)
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vel[0] = 1.0
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vel[1] = 5.0
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x[0], y[0], z[0] = 0.0, 0.0, 0.0
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x[1], y[1], z[1] = 1.0, 1.0, 1.0
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x[2], y[2], z[2] = 0.0, 0.0, 0.0
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x[3], y[3], z[3] = -1.0, 1.0, 1.0
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linesToVTK("./lines", x, y, z, cellData = {"vel" : vel}, pointData = {"temp" : temp, "pressure" : pressure})
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‎examples/poly_lines.py‎

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#! /usr/bin/env python
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# ***********************************************************************************
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# * Copyright 2010 - 2016 Paulo A. Herrera. All rights reserved. *
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# * *
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# * Redistribution and use in source and binary forms, with or without *
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# * modification, are permitted provided that the following conditions are met: *
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# * *
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# * 1. Redistributions of source code must retain the above copyright notice, *
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# * this list of conditions and the following disclaimer. *
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# * *
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# * 2. Redistributions in binary form must reproduce the above copyright notice, *
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# * this list of conditions and the following disclaimer in the documentation *
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# * and/or other materials provided with the distribution. *
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# * *
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# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR *
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# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
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# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO *
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# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, *
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# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, *
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# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, *
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# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
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# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
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# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS *
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# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
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# ***********************************************************************************
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# **************************************************************
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# * Example of how to use the high level pointsToVTK function. *
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# **************************************************************
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from pyevtk.hl import polyLinesToVTK
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import numpy as np
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# Positions of points that define lines
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npoints = 7
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x = np.zeros(npoints)
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y = np.zeros(npoints)
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z = np.zeros(npoints)
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# First line
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x[0], y[0], z[0] = 0.0, 0.0, 0.0
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x[1], y[1], z[1] = 1.0, 1.0, 0.0
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x[2], y[2], z[2] = 2.0, 0.0, 0.0
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x[3], y[3], z[3] = 3.0, -1.0, 0.0
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# Second line
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x[4], y[4], z[4] = 0.0, 0.0, 3.0
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x[5], y[5], z[5] = 1.0, 1.0, 3.0
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x[6], y[6], z[6] = 2.0, 0.0, 3.0
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# Connectivity of the lines
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pointsPerLine = np.zeros(2)
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pointsPerLine[0] = 4
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pointsPerLine[1] = 3
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# Some variables
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pressure = np.random.rand(npoints)
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temp = np.random.rand(npoints)
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vel = np.zeros(6)
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vel[0:3] = 1.0
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vel[4:6] = 5.0
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polyLinesToVTK("./poly_lines", x, y, z, pointsPerLine = pointsPerLine, cellData = {"vel" : vel}, pointData = {"temp" : temp, "pressure" : pressure})
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‎examples/unstructured.py‎

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#! /usr/bin/env python
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# ***********************************************************************************
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# * Copyright 2010 - 2017 Paulo A. Herrera. All rights reserved. *
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# * *
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# * Redistribution and use in source and binary forms, with or without *
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# * modification, are permitted provided that the following conditions are met: *
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# * *
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# * 1. Redistributions of source code must retain the above copyright notice, *
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# * this list of conditions and the following disclaimer. *
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# * *
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# * 2. Redistributions in binary form must reproduce the above copyright notice, *
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# * this list of conditions and the following disclaimer in the documentation *
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# * and/or other materials provided with the distribution. *
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# * *
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# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR *
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# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
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# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO *
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# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, *
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# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, *
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# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, *
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# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
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# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
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# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS *
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# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
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# ***********************************************************************************
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# ************************************************************************
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# * Example of how to use the high level unstructuredGridToVTK function. *
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# * This example shows how to export a unstructured grid give its *
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# * nodes and topology through a connectivity and offset lists. *
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# * Check the VTK file format for details of the unstructured grid. *
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# ************************************************************************
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from pyevtk.hl import unstructuredGridToVTK
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from pyevtk.vtk import VtkTriangle, VtkQuad
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import numpy as np
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# Define vertices
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x = np.zeros(6)
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y = np.zeros(6)
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z = np.zeros(6)
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x[0], y[0], z[0] = 0.0, 0.0, 0.0
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x[1], y[1], z[1] = 1.0, 0.0, 0.0
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x[2], y[2], z[2] = 2.0, 0.0, 0.0
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x[3], y[3], z[3] = 0.0, 1.0, 0.0
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x[4], y[4], z[4] = 1.0, 1.0, 0.0
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x[5], y[5], z[5] = 2.0, 1.0, 0.0
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# Define connectivity or vertices that belongs to each element
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conn = np.zeros(10)
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conn[0], conn[1], conn[2] = 0, 1, 3 # first triangle
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conn[3], conn[4], conn[5] = 1, 4, 3 # second triangle
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conn[6], conn[7], conn[8], conn[9] = 1, 2, 5, 4 # rectangle
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# Define offset of last vertex of each element
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offset = np.zeros(3)
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offset[0] = 3
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offset[1] = 6
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offset[2] = 10
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# Define cell types
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ctype = np.zeros(3)
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ctype[0], ctype[1] = VtkTriangle.tid, VtkTriangle.tid
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ctype[2] = VtkQuad.tid
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unstructuredGridToVTK("unstructured", x, y, z, connectivity = conn, offsets = offset, cell_types = ctype, cellData = None, pointData = None)

‎pyevtk/hl.py‎

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import numpy as np
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# =================================
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# Helper functions
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# Helper functions
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# =================================
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def _addDataToFile(vtkFile, cellData, pointData):
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# Point data
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if pointData != None:
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if pointData:
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keys = list(pointData.keys())
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vtkFile.openData("Point", scalars = keys[0])
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for key in keys:
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vtkFile.closeData("Point")
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4747
# Cell data
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if cellData != None:
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if cellData:
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keys = list(cellData.keys())
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vtkFile.openData("Cell", scalars = keys[0])
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for key in keys:
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202202
# ==============================================================================
203-
def pointsToVTK(path, x, y, z, data):
203+
def pointsToVTK(path, x, y, z, data = None):
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"""
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Export points and associated data as an unstructured grid.
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return w.getFileName()
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435435
# ==============================================================================
436-
def cylindricalToVTK(path, x, y, z, sh, cellData):
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def cylinderToVTK(path, x0, y0, z0, z1, radius, nlayers, npilars = 16, cellData=None, pointData=None):
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"""
438-
Export points and associated data as an unstructured grid.
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A cylindrical mesh connectivity is assumed. That is, the mesh is a
441-
function
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f: D --> R^3
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(x,y,z)=f(i,j,k)
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where D is the cartesian product of graphs between a cycle (C_j)
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and two path graphs (P_i and P_k).
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D= P_i x C_j x P_k
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for further explanation see:
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https://en.wikipedia.org/wiki/Cartesian_product_of_graphs
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https://en.wikipedia.org/wiki/Path_graph
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https://en.wikipedia.org/wiki/Cycle_graph
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Export cylinder as VTK unstructured grid.
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PARAMETERS:
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path: path to file without extension.
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x0, yo: center of cylinder.
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z0, z1: lower and top elevation of the cylinder.
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radius: radius of cylinder.
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nlayers: Number of layers in z direction to divide the cylinder.
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npilars: Number of points around the diameter of the cylinder.
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Higher value gives higher resolution to represent the curved shape.
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cellData: dictionary with 1D arrays that store cell data.
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Arrays should have number of elements equal to ncells = npilars * nlayers.
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pointData: dictionary with 1D arrays that store point data.
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Arrays should have number of elements equal to npoints = npilars * (nlayers + 1).
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PARAMETERS:
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path: name of the file without extension where data should be saved.
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x, y, z: 1D arrays with coordinates of the points.
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sh: number of cells in each direction
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cellData: dictionary with variables associated to each cell.
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Keys should be the names of the variable stored in each array.
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All arrays must have the same number of elements.
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RETURNS:
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RETURNS:
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Full path to saved file.
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NOTE: This function only export vertical shapes for now. However, it should be easy to
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rotate the cylinder to represent other orientations.
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"""
469-
assert(x.size==y.size==z.size)
470-
s=sh+(1,0,1)
471-
npoints = np.prod(s)
472-
ncells = np.prod(sh)
459+
import math as m
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474-
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assert(npoints==x.size)
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# create some temporary arrays to write grid topology
478-
offsets = np.arange(start = 8, stop = 8*(ncells + 1), step=8, dtype = 'int32') # index of last node in each cell
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cell_types = np.empty(ncells, dtype = 'uint8')
480-
cell_types[:] = VtkHexahedron.tid
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# create connectivity
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connectivity = np.empty(8*ncells, dtype = 'int32')
484-
i=0
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# Define x, y coordinates from polar coordinates.
462+
dpi = 2.0 * m.pi / npilars
463+
angles = np.arange(0.0, 2.0 * m.pi, dpi)
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486-
for zeta in range(0,sh[2]):
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for tita in range(0,sh[1]):
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for r in range(0,sh[0]):
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for d in ((0,0,0),(1,0,0),(1,1,0),(0,1,0),(0,0,1),(1,0,1),(1,1,1),(0,1,1)):
490-
connectivity[i]=r+d[0]+s[0]*((tita+d[1])%s[1])+s[0]*s[1]*(zeta+d[2])
491-
i+=1
465+
x = radius * np.cos(angles) + x0
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y = radius * np.sin(angles) + y0
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493-
w = VtkFile(path, VtkUnstructuredGrid)
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w.openGrid()
495-
w.openPiece(ncells = ncells, npoints = npoints)
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w.openElement("Points")
498-
w.addData("points", (x,y,z))
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w.closeElement("Points")
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w.openElement("Cells")
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w.addData("connectivity", connectivity)
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w.addData("offsets", offsets)
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w.addData("types", cell_types)
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w.closeElement("Cells")
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# adaptar cellData segun formato!!!
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_addDataToFile(w, cellData = cellData, pointData = None)
468+
dz = (z1 - z0) / nlayers
469+
z = np.arange(z0, z1+dz, step = dz)
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510-
w.closePiece()
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w.closeGrid()
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w.appendData( (x,y,z) )
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w.appendData(connectivity).appendData(offsets).appendData(cell_types)
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515-
_appendDataToFile(w, cellData = cellData, pointData = None)
471+
npoints = npilars * (nlayers + 1)
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ncells = npilars * nlayers
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517-
w.save()
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return w.getFileName()
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xx = np.zeros(npoints)
475+
yy = np.zeros(npoints)
476+
zz = np.zeros(npoints)
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478+
ii = 0
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for k in range(nlayers + 1):
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for p in range(npilars):
481+
xx[ii] = x[p]
482+
yy[ii] = y[p]
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zz[ii] = z[k]
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ii = ii + 1
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# Define connectivity
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conn = np.zeros(4 * ncells, dtype = np.int64)
488+
ii = 0
489+
for l in range(nlayers):
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for p in range(npilars):
491+
p0 = p
492+
if(p + 1 == npilars):
493+
p1 = 0
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else:
495+
p1 = p + 1 # circular loop
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497+
n0 = p0 + l * npilars
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n1 = p1 + l * npilars
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n2 = n0 + npilars
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n3 = n1 + npilars
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conn[ii + 0] = n0
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conn[ii + 1] = n1
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conn[ii + 2] = n3
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conn[ii + 3] = n2
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ii = ii + 4
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# Define offsets
509+
offsets = np.zeros(ncells, dtype = np.int64)
510+
for i in range(ncells):
511+
offsets[i] = (i + 1) * 4
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# Define cell types
514+
ctype = np.ones(ncells) + VtkPixel.tid
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return unstructuredGridToVTK(path, xx, yy, zz, connectivity = conn, offsets = offsets, cell_types = ctype, cellData = cellData, pointData = pointData)

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