First git commit. Version 1.1.1

LICENSE

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+***********************************************************************************
+* Copyright 2010 - 2019 Paulo A. Herrera. All rights reserved.                    * 
+*                                                                                 *
+* Redistribution and use in source and binary forms, with or without              *
+* modification, are permitted provided that the following conditions are met:     *
+*                                                                                 *
+*  1. Redistributions of source code must retain the above copyright notice,      *
+*  this list of conditions and the following disclaimer.                          *
+*                                                                                 *
+*  2. Redistributions in binary form must reproduce the above copyright notice,   *
+*  this list of conditions and the following disclaimer in the documentation      *
+*  and/or other materials provided with the distribution.                         *
+*                                                                                 *
+* THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR      *
+* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF    *
+* MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO      *
+* EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,        *
+* INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,  *
+* BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,    *
+* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY           *
+* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING  *
+* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS              *
+* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.                    *
+***********************************************************************************

MANIFEST

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+README.txt
+setup.py
+LICENSE
+src/__init__.py
+src/hl.py
+src/vtk.py
+src/xml.py
+src/examples/__init__.py
+src/examples/group.py
+src/examples/image.py
+src/examples/lowlevel.py
+src/examples/points.py
+src/examples/rectilinear.py
+src/examples/structured.py

README.md

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+INTRODUCTION:
+=============
+
+EVTK (Export VTK) package allows exporting data to binary VTK files for
+visualization and data analysis with any of the visualization packages that
+support VTK files, e.g.  Paraview, VisIt and Mayavi. EVTK does not depend on any
+external library (e.g. VTK), so it is easy to install in different systems.
+
+Since version 0.9 the package is composed only of a set of pure Python files, hence
+it is straightforwrd to install and run in any system where Python is installed.
+EVTK provides low and high level interfaces.  While the low level interface 
+can be used to export data that is stored in any type of container, the high 
+level functions make easy to export data stored in Numpy arrays.
+
+INSTALLATION:
+=============
+
+Go to the source directory and type:
+python setup.py install
+
+DOCUMENTATION:
+==============
+
+This file together with the included examples in the examples directory in the
+source tree provide enough information to start using the package.
+
+DESIGN GUIDELINES:
+==================
+
+The design of the package considered the following objectives:
+
+1. Self-contained. The package does not require any external library with
+the exception of Numpy, which is becoming a standard package in many Python
+installations.
+
+2. Flexibility. It is possible to use EVTK to export data stored in any
+container and in any of the grid formats supported by VTK by using the low level
+interface.
+
+3. Easy of use. The high level interface makes very easy to export data stored
+in Numpy arrays. The high level interface provides functions to export most of
+the grids supported by VTK: image data, rectilinear and structured grids. It
+also includes a function to export point sets and associated data that can be
+used to export results from particle and meshless numerical simulations.
+
+4. Performance. The aim of the package is to be used as a part of
+post-processing tools. Thus, good performance is important to handle the results
+of large simulations.  However, latest versions give priority to ease of installation
+and use over performance.
+
+REQUIREMENTS:
+=============
+
+    - Numpy. Tested with Numpy 1.8.0 to 1.13.3.
+
+It is compatible with both Python 2 (2.7+) and Python 3 (3.3+). Since version 0.9 it is only compatible
+with VTK 6.0 and newer versions.
+
+DEVELOPER NOTES:
+================
+
+It is useful to build and install the package to a temporary location without
+touching the global python site-packages directory while developing. To do
+this, while in the root directory, one can type:
+
+    1. python setup.py build --debug install --prefix=./tmp
+    2. export PYTHONPATH=./tmp/lib/python2.7/site-packages/:$PYTHONPATH
+
+NOTE: you may have to change the Python version depending of the installed
+version on your system.
+
+To test the package one can run some of the examples, e.g.:
+./tmp/lib/python2.7/site-packages/examples/points.py
+
+That should create a points.vtu file in the current directory.
+
+SUPPORT:
+=======
+
+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: [email protected].

setup.py

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+# ***********************************************************************************
+# * Copyright 2010-2017 Paulo A. Herrera. All rights reserved.                           * 
+# *                                                                                 *
+# * Redistribution and use in source and binary forms, with or without              *
+# * modification, are permitted provided that the following conditions are met:     *
+# *                                                                                 *
+# *  1. Redistributions of source code must retain the above copyright notice,      *
+# *  this list of conditions and the following disclaimer.                          *
+# *                                                                                 *
+# *  2. Redistributions in binary form must reproduce the above copyright notice,   *
+# *  this list of conditions and the following disclaimer in the documentation      *
+# *  and/or other materials provided with the distribution.                         *
+# *                                                                                 *
+# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR      *
+# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF    *
+# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO      *
+# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,        *
+# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,  *
+# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,    *
+# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY           *
+# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING  *
+# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS              *
+# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.                    *
+# ***********************************************************************************
+
+# CHECK THIS PATCH
+#try:
+#    from setuptools import setup
+#except ImportError:
+from distutils.core import setup
+
+import numpy as np
+
+def readme(fname):
+    with open(fname, 'r') as f:
+        return f.read()
+
+setup(
+    name = 'evtk',
+    version = '1.1.1',
+    description = 'Export data as binary VTK files',
+    long_description = readme('README.txt'),
+    author = 'Paulo Herrera',
+    author_email = '[email protected]',
+    url = 'https://bitbucket.org/pauloh/pyevtk',
+    packages = ['evtk'],
+    package_dir = {'evtk' : 'src'},
+    package_data = {'evtk' :  ['LICENSE', 'examples/*.py']}
+)
+

src/__init__.py

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+# *************************************************************************
+# * Copyright 2010 - 2016 Paulo Herrera                                   *
+# *                                                                       *
+# * This file is part of EVTK.                                            *
+# *                                                                       *
+# * EVTK is free software: you can redistribute it and/or modify          *
+# * it under the terms of the GNU General Public License as published by  *
+# * the Free Software Foundation, either version 3 of the License, or     *
+# * (at your option) any later version.                                   *
+# *                                                                       *
+# * EVTK is distributed in the hope that it will be useful,               *
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of        *
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
+# * GNU General Public License for more details.                          *
+# *                                                                       *
+# * You should have received a copy of the GNU General Public License     *
+# * along with EVTK.  If not, see <http://www.gnu.org/licenses/>.         *
+# *************************************************************************
+

src/evtk.py

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+# ***********************************************************************************
+# * Copyright 2010 - 2016 Paulo A. Herrera. All rights reserved.                    * 
+# *                                                                                 *
+# * Redistribution and use in source and binary forms, with or without              *
+# * modification, are permitted provided that the following conditions are met:     *
+# *                                                                                 *
+# *  1. Redistributions of source code must retain the above copyright notice,      *
+# *  this list of conditions and the following disclaimer.                          *
+# *                                                                                 *
+# *  2. Redistributions in binary form must reproduce the above copyright notice,   *
+# *  this list of conditions and the following disclaimer in the documentation      *
+# *  and/or other materials provided with the distribution.                         *
+# *                                                                                 *
+# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR      *
+# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF    *
+# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO      *
+# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,        *
+# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,  *
+# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,    *
+# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY           *
+# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING  *
+# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS              *
+# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.                    *
+# ***********************************************************************************
+
+import struct
+import numpy as np
+import sys
+
+# Map numpy dtype to struct format
+np_to_struct = { 'int8'    : 'b',
+                 'uint8'   : 'B',
+                 'int16'   : 'h',
+                 'uint16'  : 'H',
+                 'int32'   : 'i',
+                 'uint32'  : 'I',
+                 'int64'   : 'q',
+                 'uint64'  : 'Q',
+                 'float32' : 'f',
+                 'float64' : 'd' }
+
+def _get_byte_order_char():
+# Check format in https://docs.python.org/3.5/library/struct.html
+    if sys.byteorder == "little":
+        return '<'
+    else:
+        return '>'
+
+# ================================
+#        Python interface
+# ================================  
+def writeBlockSize(stream, block_size):
+    fmt = _get_byte_order_char() + 'Q' # Write size as unsigned long long == 64 bits unsigned integer
+    stream.write(struct.pack(fmt, block_size))
+
+def writeArrayToFile(stream, data):
+    #stream.flush() # this should not be necessary          
+    assert (data.ndim == 1 or data.ndim == 3)
+    fmt = _get_byte_order_char() + str(data.size) + np_to_struct[data.dtype.name]  # > for big endian
+
+    # Check if array is contiguous
+    assert (data.flags['C_CONTIGUOUS'] or data.flags['F_CONTIGUOUS'])
+
+    # NOTE: VTK expects data in FORTRAN order
+    # This is only needed when a multidimensional array has C-layout
+    dd = np.ravel(data, order='F')
+
+    bin = struct.pack(fmt, *dd)
+    stream.write(bin)
+
+# ==============================================================================
+def writeArraysToFile(stream, x, y, z):
+    # Check if arrays have same shape and data type
+    assert ( x.size == y.size == z.size ), "Different array sizes."
+    assert ( x.dtype.itemsize == y.dtype.itemsize == z.dtype.itemsize ), "Different item sizes."
+
+    nitems = x.size
+    itemsize = x.dtype.itemsize
+
+    fmt = _get_byte_order_char() + str(1) + np_to_struct[x.dtype.name]  # > for big endian
+
+    # Check if arrays are contiguous
+    assert (x.flags['C_CONTIGUOUS'] or x.flags['F_CONTIGUOUS'])
+    assert (y.flags['C_CONTIGUOUS'] or y.flags['F_CONTIGUOUS'])
+    assert (z.flags['C_CONTIGUOUS'] or z.flags['F_CONTIGUOUS'])
+
+
+    # NOTE: VTK expects data in FORTRAN order
+    # This is only needed when a multidimensional array has C-layout
+    xx = np.ravel(x, order='F')
+    yy = np.ravel(y, order='F')
+    zz = np.ravel(z, order='F')    
+
+    # eliminate this loop by creating a composed array.
+    for i in range(nitems):
+        bx = struct.pack(fmt, xx[i])
+        by = struct.pack(fmt, yy[i])
+        bz = struct.pack(fmt, zz[i])
+        stream.write(bx)
+        stream.write(by)
+        stream.write(bz)

src/examples/group.py

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+#! /usr/bin/env python
+
+# ***********************************************************************************
+# * Copyright 2010 - 2016 Paulo A. Herrera. All rights reserved.                    * 
+# *                                                                                 *
+# * Redistribution and use in source and binary forms, with or without              *
+# * modification, are permitted provided that the following conditions are met:     *
+# *                                                                                 *
+# *  1. Redistributions of source code must retain the above copyright notice,      *
+# *  this list of conditions and the following disclaimer.                          *
+# *                                                                                 *
+# *  2. Redistributions in binary form must reproduce the above copyright notice,   *
+# *  this list of conditions and the following disclaimer in the documentation      *
+# *  and/or other materials provided with the distribution.                         *
+# *                                                                                 *
+# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR      *
+# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF    *
+# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO      *
+# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,        *
+# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,  *
+# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,    *
+# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY           *
+# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING  *
+# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS              *
+# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.                    *
+# ***********************************************************************************
+
+# **************************************************************
+# * Example of how to create a VTK group to visualize time     *
+# * dependent data.                                            *
+# **************************************************************
+
+from evtk.vtk import VtkGroup
+
+g = VtkGroup("./group")
+g.addFile(filepath = "sim0000.vtu", sim_time = 0.0)
+g.addFile(filepath = "sim0001.vtu", sim_time = 1.0)
+g.addFile(filepath = "sim0002.vtu", sim_time = 2.0)
+g.addFile(filepath = "sim0003.vtu", sim_time = 3.0)
+g.save()

src/examples/image.py

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+#! /usr/bin/env python
+
+# ***********************************************************************************
+# * Copyright 2010 - 2016 Paulo A. Herrera. All rights reserved.                    * 
+# *                                                                                 *
+# * Redistribution and use in source and binary forms, with or without              *
+# * modification, are permitted provided that the following conditions are met:     *
+# *                                                                                 *
+# *  1. Redistributions of source code must retain the above copyright notice,      *
+# *  this list of conditions and the following disclaimer.                          *
+# *                                                                                 *
+# *  2. Redistributions in binary form must reproduce the above copyright notice,   *
+# *  this list of conditions and the following disclaimer in the documentation      *
+# *  and/or other materials provided with the distribution.                         *
+# *                                                                                 *
+# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR      *
+# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF    *
+# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO      *
+# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,        *
+# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,  *
+# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,    *
+# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY           *
+# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING  *
+# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS              *
+# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.                    *
+# ***********************************************************************************
+
+# **************************************************************
+# * Example of how to use the high level imageToVTK function.  *
+# **************************************************************
+
+from evtk.hl import imageToVTK
+import numpy as np
+
+# Dimensions
+nx, ny, nz = 6, 6, 2
+ncells = nx * ny * nz
+npoints = (nx + 1) * (ny + 1) * (nz + 1)
+
+# Variables
+pressure = np.random.rand(ncells).reshape( (nx, ny, nz), order = 'C')
+temp = np.random.rand(npoints).reshape( (nx + 1, ny + 1, nz + 1))
+
+imageToVTK("./image", cellData = {"pressure" : pressure}, pointData = {"temp" : temp} )
+