Bring in 3 commits from PyEVTK BitBucket repo and 1 from paulo-herrera/PyEVTK on github

README.md

@@ -104,4 +104,10 @@ 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: paulo.herrera.eirl@gmail.com.
+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.
+
+**NOTE: PyEVTK moved to GitHub. The new official page is this one (https://github.com/paulo-herrera/PyEVTK)**

examples/lines.py

@@ -0,0 +1,53 @@
+#! /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 pointsToVTK function. *
+# **************************************************************
+
+from pyevtk.hl import linesToVTK
+import numpy as np
+
+# Example 1
+npoints = 4
+x = np.zeros(npoints)
+y = np.zeros(npoints)
+z = np.zeros(npoints)
+pressure = np.random.rand(npoints)
+temp = np.random.rand(npoints)
+vel = np.zeros(2)
+vel[0] = 1.0
+vel[1] = 5.0
+
+x[0], y[0], z[0] = 0.0, 0.0, 0.0
+x[1], y[1], z[1] = 1.0, 1.0, 1.0
+x[2], y[2], z[2] = 0.0, 0.0, 0.0
+x[3], y[3], z[3] = -1.0, 1.0, 1.0
+
+linesToVTK("./lines", x, y, z, cellData = {"vel" : vel}, pointData = {"temp" : temp, "pressure" : pressure})
+
+

examples/poly_lines.py

@@ -0,0 +1,66 @@
+#! /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 pointsToVTK function. *
+# **************************************************************
+
+from pyevtk.hl import polyLinesToVTK
+import numpy as np
+
+# Positions of points that define lines
+npoints = 7
+x = np.zeros(npoints)
+y = np.zeros(npoints)
+z = np.zeros(npoints)
+
+# First line
+x[0], y[0], z[0] = 0.0, 0.0, 0.0
+x[1], y[1], z[1] = 1.0, 1.0, 0.0
+x[2], y[2], z[2] = 2.0, 0.0, 0.0
+x[3], y[3], z[3] = 3.0, -1.0, 0.0
+
+# Second line
+x[4], y[4], z[4] = 0.0, 0.0, 3.0
+x[5], y[5], z[5] = 1.0, 1.0, 3.0
+x[6], y[6], z[6] = 2.0, 0.0, 3.0
+
+# Connectivity of the lines
+pointsPerLine = np.zeros(2)
+pointsPerLine[0] = 4
+pointsPerLine[1] = 3
+
+# Some variables
+pressure = np.random.rand(npoints)
+temp = np.random.rand(npoints)
+vel = np.zeros(6)
+vel[0:3] = 1.0
+vel[4:6] = 5.0
+
+polyLinesToVTK("./poly_lines", x, y, z, pointsPerLine = pointsPerLine, cellData = {"vel" : vel}, pointData = {"temp" : temp, "pressure" : pressure})
+
+

examples/unstructured.py

@@ -0,0 +1,70 @@
+#! /usr/bin/env python
+
+# ***********************************************************************************
+# * 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.                    *
+# ***********************************************************************************
+
+# ************************************************************************
+# * Example of how to use the high level unstructuredGridToVTK function. *
+# * This example shows how to export a unstructured grid give its        *
+# * nodes and topology through a connectivity and offset lists.          *
+# * Check the VTK file format for details of the unstructured grid.      *
+# ************************************************************************
+
+from pyevtk.hl import unstructuredGridToVTK
+from pyevtk.vtk import VtkTriangle, VtkQuad
+import numpy as np
+
+# Define vertices
+x = np.zeros(6)
+y = np.zeros(6)
+z = np.zeros(6)
+
+x[0], y[0], z[0] = 0.0, 0.0, 0.0
+x[1], y[1], z[1] = 1.0, 0.0, 0.0
+x[2], y[2], z[2] = 2.0, 0.0, 0.0
+x[3], y[3], z[3] = 0.0, 1.0, 0.0
+x[4], y[4], z[4] = 1.0, 1.0, 0.0
+x[5], y[5], z[5] = 2.0, 1.0, 0.0
+
+# Define connectivity or vertices that belongs to each element
+conn = np.zeros(10)
+
+conn[0], conn[1], conn[2] = 0, 1, 3              # first triangle
+conn[3], conn[4], conn[5] = 1, 4, 3              # second triangle
+conn[6], conn[7], conn[8], conn[9] = 1, 2, 5, 4  # rectangle
+
+# Define offset of last vertex of each element
+offset = np.zeros(3)
+offset[0] = 3
+offset[1] = 6
+offset[2] = 10
+
+# Define cell types
+
+ctype = np.zeros(3)
+ctype[0], ctype[1] = VtkTriangle.tid, VtkTriangle.tid
+ctype[2] = VtkQuad.tid
+
+unstructuredGridToVTK("unstructured", x, y, z, connectivity = conn, offsets = offset, cell_types = ctype, cellData = None, pointData = None)

pyevtk/hl.py

@@ -32,11 +32,11 @@
 import numpy as np
 
 # =================================
-#       Helper functions      
+#       Helper functions
 # =================================
 def _addDataToFile(vtkFile, cellData, pointData):
     # Point data
-    if pointData != None:
+    if pointData:
         keys = list(pointData.keys())
         vtkFile.openData("Point", scalars = keys[0])
         for key in keys:
@@ -45,7 +45,7 @@ def _addDataToFile(vtkFile, cellData, pointData):
         vtkFile.closeData("Point")
 
     # Cell data
-    if cellData != None:
+    if cellData:
         keys = list(cellData.keys())
         vtkFile.openData("Cell", scalars = keys[0])
         for key in keys:
@@ -200,7 +200,7 @@ def gridToVTK(path, x, y, z, cellData = None, pointData = None):
 
 
 # ==============================================================================
-def pointsToVTK(path, x, y, z, data):
+def pointsToVTK(path, x, y, z, data = None):
     """
         Export points and associated data as an unstructured grid.
 
@@ -433,88 +433,84 @@ def unstructuredGridToVTK(path, x, y, z, connectivity, offsets, cell_types, cell
     return w.getFileName()
 
 # ==============================================================================
-def cylindricalToVTK(path, x, y, z, sh, cellData):
+def cylinderToVTK(path, x0, y0, z0, z1, radius, nlayers, npilars = 16, cellData=None, pointData=None):
     """
-        Export points and associated data as an unstructured grid.
-
-        A cylindrical mesh connectivity is assumed. That is, the mesh is a 
-        function
-
-        f: D --> R^3
-        (x,y,z)=f(i,j,k)
-
-        where D is the cartesian product of graphs between a cycle (C_j)
-        and two path graphs (P_i and P_k).
-
-        D= P_i x C_j x P_k
-
-        for further explanation see:
-        https://en.wikipedia.org/wiki/Cartesian_product_of_graphs
-        https://en.wikipedia.org/wiki/Path_graph
-        https://en.wikipedia.org/wiki/Cycle_graph
+        Export cylinder as VTK unstructured grid.
+
+      PARAMETERS:
+        path: path to file without extension.
+        x0, yo: center of cylinder.
+        z0, z1: lower and top elevation of the cylinder.
+        radius: radius of cylinder.
+        nlayers: Number of layers in z direction to divide the cylinder.
+        npilars: Number of points around the diameter of the cylinder. 
+                 Higher value gives higher resolution to represent the curved shape.
+        cellData: dictionary with 1D arrays that store cell data. 
+                  Arrays should have number of elements equal to ncells = npilars * nlayers.
+        pointData: dictionary with 1D arrays that store point data.
+                  Arrays should have number of elements equal to npoints = npilars * (nlayers + 1).
 
-
-        PARAMETERS:
-            path: name of the file without extension where data should be saved.
-            x, y, z: 1D arrays with coordinates of the points.
-            sh: number of cells in each direction
-            cellData: dictionary with variables associated to each cell.
-                  Keys should be the names of the variable stored in each array.
-                  All arrays must have the same number of elements.
-
-        RETURNS:
+      RETURNS: 
             Full path to saved file.
-
+
+        NOTE: This function only export vertical shapes for now. However, it should be easy to 
+              rotate the cylinder to represent other orientations.
     """
-    assert(x.size==y.size==z.size)
-    s=sh+(1,0,1)
-    npoints = np.prod(s)
-    ncells = np.prod(sh)
+    import math as m
 
-
-    assert(npoints==x.size)
-
-    # create some temporary arrays to write grid topology
-    offsets = np.arange(start = 8, stop = 8*(ncells + 1), step=8, dtype = 'int32')   # index of last node in each cell
-    cell_types = np.empty(ncells, dtype = 'uint8') 
-    cell_types[:] = VtkHexahedron.tid
-
-    # create connectivity
-    connectivity = np.empty(8*ncells, dtype = 'int32') 
-    i=0
+    # Define x, y coordinates from polar coordinates.
+    dpi = 2.0 * m.pi / npilars
+    angles = np.arange(0.0, 2.0 * m.pi, dpi)
 
-    for zeta in range(0,sh[2]):
-        for tita in range(0,sh[1]):
-            for r in range(0,sh[0]):
-                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)):
-                    connectivity[i]=r+d[0]+s[0]*((tita+d[1])%s[1])+s[0]*s[1]*(zeta+d[2])
-                    i+=1
+    x = radius * np.cos(angles) + x0
+    y = radius * np.sin(angles) + y0
 
-    w = VtkFile(path, VtkUnstructuredGrid)
-    w.openGrid()
-    w.openPiece(ncells = ncells, npoints = npoints)
-
-    w.openElement("Points")
-    w.addData("points", (x,y,z))
-    w.closeElement("Points")
-    w.openElement("Cells")
-    w.addData("connectivity", connectivity)
-    w.addData("offsets", offsets)
-    w.addData("types", cell_types)
-    w.closeElement("Cells")
-
-    # adaptar cellData segun formato!!! 
-
-    _addDataToFile(w, cellData = cellData, pointData = None)
+    dz = (z1 - z0) / nlayers
+    z = np.arange(z0, z1+dz, step = dz)
 
-    w.closePiece()
-    w.closeGrid()
-    w.appendData( (x,y,z) )
-    w.appendData(connectivity).appendData(offsets).appendData(cell_types)
-
-    _appendDataToFile(w, cellData = cellData, pointData = None)
+    npoints = npilars * (nlayers + 1)
+    ncells  = npilars * nlayers
 
-    w.save()
-    return w.getFileName()
+    xx = np.zeros(npoints)
+    yy = np.zeros(npoints)
+    zz = np.zeros(npoints)
 
+    ii = 0
+    for k in range(nlayers + 1):
+        for p in range(npilars):
+            xx[ii] = x[p]
+            yy[ii] = y[p]
+            zz[ii] = z[k]
+            ii = ii + 1
+
+    # Define connectivity
+    conn = np.zeros(4 * ncells, dtype = np.int64)
+    ii = 0
+    for l in range(nlayers):
+        for p in range(npilars):
+            p0 = p
+            if(p + 1 == npilars):
+                p1 = 0 
+            else: 
+                p1 = p + 1 # circular loop
+
+            n0 = p0 + l * npilars
+            n1 = p1 + l * npilars 
+            n2 = n0 + npilars
+            n3 = n1 + npilars
+
+            conn[ii + 0] = n0
+            conn[ii + 1] = n1
+            conn[ii + 2] = n3
+            conn[ii + 3] = n2 
+            ii = ii + 4
+
+    # Define offsets 
+    offsets = np.zeros(ncells, dtype = np.int64)
+    for i in range(ncells):
+        offsets[i] = (i + 1) * 4
 
+    # Define cell types
+    ctype = np.ones(ncells) + VtkPixel.tid
+
+    return unstructuredGridToVTK(path, xx, yy, zz, connectivity = conn, offsets = offsets, cell_types = ctype, cellData = cellData, pointData = pointData)