Lang (AE) renamed neighbour to neighbor

.gitignore

@@ -84,3 +84,4 @@ python/pygimli/core/*.dll
 .vscode/settings.json
 
 python/pygimli/testing/synth.ves
+.vscode/launch.json

cmake/Findpygccxml.cmake

@@ -5,7 +5,6 @@
 # PYGCCXML_FOUND, If false, do not try to use pygccxml
 # PYPLUSPLUS_FOUND, If false, do not try to use pyplusplus
 
-
 find_python_module(pygccxml)
 
 if (pygccxml_FOUND)
@@ -25,7 +24,12 @@ else()
         message( STATUS "NOT Found pygccxml: we try to get a copy or cannot build pygimli.")
         find_package(Subversion REQUIRED)
     endif(PYGCCXML_PATH)
-
+
+endif()
+
+if (PYGCCXML_PATH)
+    message(STATUS "Found pygccxml path: ${PYGCCXML_PATH}")
+    STRING(REGEX REPLACE "\\\\" "/" PYGCCXML_PATH ${PYGCCXML_PATH})
+    message(STATUS "Found pygccxml path: ${PYGCCXML_PATH}")
 endif()
-
 mark_as_advanced(PYGCCXML)

doc/examples/seismics/plot_4_rays_layered_and_gradient_models.py

@@ -117,7 +117,7 @@ def analyticalSolutionGradient(x, a=1000, b=100):
         boundary.setMarker(0)
 
     xmin, xmax = mesh.xmin(), mesh.xmax()
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
 
     # In order to use the Dijkstra, we extract the surface positions >0
     mx = pg.x(mesh)
@@ -144,7 +144,7 @@ def analyticalSolutionGradient(x, a=1000, b=100):
     pg.show(mesh, vel, ax=ax[0, j], label="Velocity (m/s)", hold=True,
             logScale=False, cMap="summer_r", coverage=0.7)
     drawMesh(ax[0, j], mesh, color="white", lw=0.21)
-    
+
     # We compare the accuracy for 0-5 secondary nodes
     sec_nodes = [0, 1, 5]
     t_all = []
@@ -161,7 +161,7 @@ def analyticalSolutionGradient(x, a=1000, b=100):
         # Perform traveltime calculations and log time with pg.tic() & pg.toc()
         pg.tic()
         res = mgr.simulate(vel=vel, scheme=data, mesh=mesh, secNodes=n)
-        # We need to copy res['t'] here because res['t'] is a reference to 
+        # We need to copy res['t'] here because res['t'] is a reference to
         # an array in res, and res will be removed in the next iteration.
         # Unfortunately, we don't have any reverence counting for core objects yet.
         t_all.append(res['t'].array())
@@ -173,7 +173,7 @@ def analyticalSolutionGradient(x, a=1000, b=100):
                 lab = "Raypath with %d sec nodes" % n
             else:
                 lab = None
-            
+
             recNode = mgr.fop.mesh().findNearestNode([sensors[p], 0.0])
             sourceNode = mgr.fop.mesh().findNearestNode([0.0, 0.0])
 
@@ -196,7 +196,7 @@ def analyticalSolutionGradient(x, a=1000, b=100):
         ax[2, j].plot(px, np.abs(t_all[i] - t_ana) * 1000)
 
     ax[1, j].legend()
-   
+
     # Draw sensor positions for the selected receivers
     for p in recs:
         ax[0, j].plot(sensors[p], 0.0, "kv", ms=10)

doc/paper/cg17/example-2_visualization.py

@@ -145,7 +145,7 @@ def showModel(outPath):
     pg.wait()
     pg.show(fopMesh, ax=ax, linewidth=0.2)
 
-    paraMesh.createNeighbourInfos()
+    paraMesh.createNeighborInfos()
     bs = []
     for b in paraMesh.boundaries():
         if b.leftCell() and b.rightCell():

python/generate_pygimli_code.py

@@ -18,6 +18,11 @@
 
 (options, args) = optionParser.parse_args()
 
+print('##############')
+print(options)
+print(args)
+print('##############')
+
 if options.caster:
     settings.caster_path = options.caster
 

python/pygimli/core/__init__.py

@@ -861,6 +861,8 @@ def abs(v):
     """
     if isinstance(v, _pygimli_.CVector):
         return _pygimli_.mag(v)
+    elif isinstance(v, list):
+        return _pygimli_.absR3(np.array(v).T)
     elif isinstance(v, _pygimli_.R3Vector):
         return _pygimli_.absR3(v)
     elif isinstance(v, np.ndarray):

python/pygimli/core/mesh.py

@@ -16,8 +16,6 @@ def __Mesh_str(self):
         st += " secNodes: " + str(self.secondaryNodeCount())
 
     return st
-
-
 Mesh.__str__ = __Mesh_str
 
 
@@ -26,8 +24,6 @@ def __addPLCs__(self, other):
         return mergePLC([self, other])
     else:
         error("Addition is only supported for PLCs, i.e. meshs without cells.")
-
-
 Mesh.__add__ = __addPLCs__
 
 
@@ -44,8 +40,6 @@ def __MeshEntity_str(self):
         for n in self.nodes():
             s += '\t' + str(n.id()) + " " + str(n.pos()) + "\n"
     return s
-
-
 MeshEntity.__str__ = __MeshEntity_str
 
 
@@ -56,11 +50,9 @@ def __Node_str(self):
          ', Marker: ' + str(self.marker())
     s += '\t' + str(self.pos()) + '\n'
     return s
-
-
 Node.__str__ = __Node_str
 
-# For Jupyer Notebook use.. checkme
+# For Jupyer Notebook use.. check me
 # Node.__repr__ = Node_str
 # Mesh.__repr__ = Mesh_str
 # MeshEntity.__repr__ = MeshEntity_str
@@ -69,8 +61,6 @@ def __Node_str(self):
 def __Mesh_setVal(self, key, val):
     """Index access to the mesh data"""
     self.addData(key, val)
-
-
 Mesh.__setitem__ = __Mesh_setVal
 
 
@@ -80,8 +70,6 @@ def __Mesh_getVal(self, key):
         return self.data(key)
     else:
         error('The mesh does not have the requested data:', key)
-
-
 Mesh.__getitem__ = __Mesh_getVal
 
 
@@ -90,8 +78,6 @@ def __MeshBoundingBox__(self):
     mi = [bb.min()[i] for i in range(self.dim())]
     ma = [bb.max()[i] for i in range(self.dim())]
     return [mi, ma]
-
-
 Mesh.bb = __MeshBoundingBox__
 
 
@@ -108,7 +94,6 @@ def __MeshSetCellMarker__(self, m):
 def __MeshHoleMarkers__(self):
     return self.holeMarker()
 
-
 Mesh.cellMarker = __MeshGetCellMarker__
 Mesh.setCellMarker = __MeshSetCellMarker__
 Mesh.holeMarkers = __MeshHoleMarkers__
@@ -130,7 +115,7 @@ def __createSecondaryNodes__(self, n=3, verbose=False):
     pg.Mesh
         Copy of the given mesh with secondary nodes.
     """
-    self.createNeighbourInfos()
+    self.createNeighborInfos()
 
     if self.boundary(0).nodeCount() != self.boundary(0).allNodeCount():
         warn("Mesh already contains secondary nodes. Not adding any more.")
@@ -148,10 +133,10 @@ def __createSecondaryNodes__(self, n=3, verbose=False):
             for b in self.boundaries():
                 bs = b.shape()
                 for sx in range(n):
-                    nmax = n
+                    nMax = n
                     if isinstance(b, TriangleFace):
-                        nmax = n - sx
-                    for sy in range(nmax):
+                        nMax = n - sx
+                    for sy in range(nMax):
                         if isinstance(b, TriangleFace):
                             pos = bs.xyz([(sx + 1) / (n + 2),
                                           (sy + 1) / (n + 2)])
@@ -216,9 +201,16 @@ def __createMeshWithSecondaryNodes__(self, n=3, verbose=False):
     m = Mesh(self)
     m.createSecondaryNodes(n, verbose)
     return m
-
-
 Mesh.createSecondaryNodes = __createSecondaryNodes__
 Mesh.createMeshWithSecondaryNodes = __createMeshWithSecondaryNodes__
 
 Mesh.exportPLC = exportPLC
+
+# just to keep backward compatibility 20191120
+Mesh.createNeighbourInfos = Mesh.createNeighborInfos
+Mesh.xmin = Mesh.xMin
+Mesh.ymin = Mesh.yMin
+Mesh.zmin = Mesh.zMin
+Mesh.xmax = Mesh.xMax
+Mesh.ymax = Mesh.yMax
+Mesh.zmax = Mesh.zMax

python/pygimli/meshtools/grid.py

@@ -283,7 +283,7 @@ def appendTriangleBoundary(mesh, xbound=10, ybound=10, marker=1, quality=34.0,
         mesh2.copyCell(cell)
 
     # old neighbor infos need to be cleaned since the new cells are added
-    mesh2.createNeighbourInfos(force=True)
+    mesh2.createNeighborInfos(force=True)
 
     for b in mesh2.boundaries():
         if b.leftCell() is None or b.rightCell() is None:

python/pygimli/meshtools/mapping.py

@@ -215,17 +215,17 @@ def fillEmptyToCellArray(mesh, vals, slope=True):
     # atts = pg.Vector(mesh.cellCount(), 0.0)  # not used
     # oldAtts = mesh.cellAttributes()  # not used
     mesh.setCellAttributes(vals)
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
     # std::vector< Cell * >
     # empties = []
 
     if slope:
-        # search all cells with empty neighbours
+        # search all cells with empty neighbors
         ids = pg.find(mesh.cellAttributes() != 0.0)
 
         for c in mesh.cells(ids):
-            for i in range(c.neighbourCellCount()):
-                nc = c.neighbourCell(i)
+            for i in range(c.neighborCellCount()):
+                nc = c.neighborCell(i)
 
                 if nc:
                     if nc.attribute() == 0.0:
@@ -240,7 +240,7 @@ def fillEmptyToCellArray(mesh, vals, slope=True):
                         while startCell:
 
                             startCell.shape().isInside(pos, sf, False)
-                            nextC = startCell.neighbourCell(sf)
+                            nextC = startCell.neighborCell(sf)
                             if nextC:
                                 if nextC.attribute() == 0.0:
                                     nextC.setAttribute(c.attribute())
@@ -495,7 +495,7 @@ def interpolate(*args, **kwargs):
     * 2D parametric to points (method=['linear, 'spline', 'harmonic'])
     * 2D/3D point cloud to points/grids
         ('Delauney', 'linear, 'spline', 'harmonic')
-    * Mesh to points based on nearest neighbour values (pg.core)
+    * Mesh to points based on nearest neighbor values (pg.core)
 
     Examples
     --------

python/pygimli/meshtools/mesh.py

@@ -196,7 +196,7 @@ def refineQuad2Tri(mesh, style=1):
                 out.createBoundary([b.node(0).id(), b.node(1).id()],
                                    b.marker())
 
-    out.createNeighbourInfos()
+    out.createNeighborInfos()
 
     return out
 
@@ -520,7 +520,7 @@ def readGmsh(fname, verbose=False):
                 mesh.node(int(cell[2] - 1)), mesh.node(int(cell[3] - 1)),
                 marker=int(cell[4]))
 
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
 
     # Set Neumann on outer edges by default (can be overriden by Gmsh info)
     for b in mesh.boundaries():
@@ -605,7 +605,7 @@ def readTetgen(fname, comment='#', verbose=False, defaultCellMarker=0,
         are loaded or not. Note that without the -f in during the tetgen call,
         the faces in the .face file will only contain the faces of the original
         input poly file and not all faces. If only a part of the faces are
-        imported, a createNeighbourInfos call of the mesh will fail.
+        imported, a createNeighborInfos call of the mesh will fail.
 
     quadratic: boolean (False)
         Returns a P2 (quadratic) refined mesh when True (to be removed, as soon
@@ -754,7 +754,7 @@ def readHydrus2dMesh(fileName='MESHTRIA.TXT'):
                 mesh.node(int(line[3]) - 1), mesh.node(int(line[4]) - 1), 1)
 
     fid.close()
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
     return mesh
 
 
@@ -808,7 +808,7 @@ def readHydrus3dMesh(fileName='MESHTRIA.TXT'):
         cells.append(c)
 
     f.close()
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
     return mesh
 
 
@@ -969,7 +969,7 @@ def readGambitNeutral(fileName, verbose=False):
     if verbose:
         print("Gambit neutral file imported: ", mesh)
 
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
     return mesh
 
 
@@ -1023,7 +1023,7 @@ def convertHDF5Mesh(h5Mesh, group='mesh', indices='cell_indices',
     for i, cell in enumerate(mesh_cells):
         mesh.createCell(pg.core.IndexArray(cell), marker=int(mesh_marker[i]))
 
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
 
     if verbose:
         print('converted mesh:', mesh)

python/pygimli/mplviewer/meshview.py

@@ -22,7 +22,7 @@ def __new__(cls):
         if CellBrowserCacheSingleton.__instance is None:
             CellBrowserCacheSingleton.__instance = object.__new__(cls)
         return CellBrowserCacheSingleton.__instance
-# 
+#
     def add(self, c):
         self.cbCache_.append(c)
 
@@ -545,7 +545,7 @@ def drawMeshBoundaries(ax, mesh, hideMesh=False, useColorMap=False,
 
 #    drawAA = True
 #    swatch = pg.core.Stopwatch(True)
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
 
     if not hideMesh:
         drawSelectedMeshBoundaries(ax,
@@ -875,7 +875,7 @@ def drawField(ax, mesh, data=None, levels=[], nLevs=5,
     gci = None
 
     if len(levels) == 0:
-        levels = autolevel(data, nLevs, 
+        levels = autolevel(data, nLevs,
                            zmin=cMin, zmax=cMax, logScale=logScale)
 
     if len(z) == len(triangles):
@@ -913,7 +913,7 @@ def drawField(ax, mesh, data=None, levels=[], nLevs=5,
 
                 gci = ax.tricontourf(x, y, triangles, z, levels=levs,
                                      **kwargs)
-                            
+
             if contourLines:
                 ax.tricontour(x, y, triangles, z, levels=levels,
                               colors=kwargs.pop('colors', ['0.5']), **kwargs)
@@ -1167,11 +1167,11 @@ def drawStreams(ax, mesh, data, startStream=3, coarseMesh=None, quiver=False,
     if coarseMesh is not None:
         viewMesh = coarseMesh
         dataMesh = mesh
-        dataMesh.createNeighbourInfos()
+        dataMesh.createNeighborInfos()
     else:
         viewMesh = mesh
 
-    viewMesh.createNeighbourInfos()
+    viewMesh.createNeighborInfos()
 
     for c in viewMesh.cells():
         c.setValid(True)

python/pygimli/physics/gravimetry/gravMagModelling.py

@@ -663,7 +663,7 @@ def solveGravimetry(mesh, dDensity=None, pnts=None, complete=False):
     if pnts is None:
         pnts = [[0.0, 0.0]]
 
-    mesh.createNeighbourInfos()
+    mesh.createNeighborInfos()
 
     Gdg = None
     Gdgz = None

python/pygimli/physics/traveltime/refraction.py

@@ -298,7 +298,7 @@
 #             solution.
 #         """
 #         self.mesh = mesh
-#         self.mesh.createNeighbourInfos()
+#         self.mesh.createNeighborInfos()
 #         self.fop.setMesh(self.mesh)
 #         self.fop.regionManager().setConstraintType(1)