Merge pull request #7 from Jimbles/dev

Fixed writing vertices and improved comments and docs
Jimbles · Jul 3, 2020 · 12802fd · 12802fd
2 parents 611de4d + 166382c
commit 12802fd
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diff --git a/README.md b/README.md
@@ -19,12 +19,16 @@ This has only been tested on Matlab 2019b with Python 3.8.3
 ```matlab
 P=meshio.read(fname); % .msh .vtk .vtu .stl .obj TetGen ANSYS ...
 
-% P.vtx - verticies
-% P.Cells - structure array for each geometry saved in file
-% P.Cells.tri - Trigangulation connectivity list for this cell
-% P.Cells.type - 'Tetra','Triangle','Line','Vertex'
-
-% all contents can be plotted with
+% P.vtx             - verticies
+% P.Cells           - structure array for each geometry saved in file
+% P.Cells.tri       - Trigangulation connectivity list for this cell
+% P.Cells.type      - 'Tetra','Triangle','Line','Vertex'
+% P.cell_data       - Per element data in cell array
+% P.cell_data_name  - Data names in cell array
+% P.point_data      - Per point data in cell array
+% P.point_data_name - Data names in cell array
+
+% all contents can be plotted using:
 meshio.plot(P);
 ```
 
@@ -39,12 +43,22 @@ dt = delaunayTriangulation(x,y,z);
 dataex=1:size(dt.ConnectivityList,1);
 
 %write to gmsh file with cell data
-meshio.write('example.msh',dt.Points,dt.ConnectivityList,dataex);
+meshio.write('example.msh',dt.Points,dt.ConnectivityList,{dataex},{'Data'});
 ```
 
 This can then be loaded directly into [gmsh](https://gmsh.info/)
+
 ![gmsh](examples/figures/RandEx_gmsh.png)
 
-or into paraview (either by writing to .vtu or using meshio paraview plugin)
+or into paraview (either by writing to .vtu or loading .msh using meshio paraview plugin)
 
 ![paraview](examples/figures/RandEx_paraview.png)
+
+### Convert file
+
+Conversion through `meshio-convert` binary is harder to fit into matlab workflow, so this library can be used too
+
+```matlab
+P=meshio.read('example.msh');
+meshio.structwrite('example.vtu',P);
+```
diff --git a/examples/example1.msh b/examples/example1.msh
diff --git a/examples/examplecell.vtu b/examples/examplecell.vtu
diff --git a/examples/examplecell1.msh b/examples/examplecell1.msh
diff --git a/examples/examplecell2.msh b/examples/examplecell2.msh
diff --git a/examples/examplemulti.vtu b/examples/examplemulti.vtu
diff --git a/examples/examplepoint.vtu b/examples/examplepoint.vtu
diff --git a/examples/examplepoint1.msh b/examples/examplepoint1.msh
diff --git a/examples/examplepoint2.msh b/examples/examplepoint2.msh
diff --git a/examples/examplepointcell.msh b/examples/examplepointcell.msh
diff --git a/examples/examplepointcell.vtu b/examples/examplepointcell.vtu
diff --git a/examples/figures/RandEx_gmsh.png b/examples/figures/RandEx_gmsh.png
diff --git a/examples/figures/RandEx_paraview.png b/examples/figures/RandEx_paraview.png
diff --git a/examples/finger_3D.vtu b/examples/finger_3D.vtu
diff --git a/examples/pyexample.py b/examples/pyexample.py
@@ -33,12 +33,6 @@
 F=meshio.read(inpathmulti)
 meshio.write_points_cells(outpathmultivtu,F.points,F.cells)
 
-fc=F.cells
-fnewcell=[]
-fnewcell.append((fc[1].type,fc[1].data))
-fnewcell.append((fc[2].type,fc[2].data))
-
-meshio.write_points_cells(outpathmultivtu,F.points,fnewcell)
 PP=meshio.read(outpathmultivtu)
 
 

diff --git a/examples/run_examples.m b/examples/run_examples.m
@@ -18,67 +18,80 @@
 pointdataname={'test','teest','tesest'};
 
 %write with no data
-meshio.write('example1.msh',dt.Points,dt.ConnectivityList);
-A=meshio.read('example1.msh');
+meshio.write('testout/example1.msh',dt.Points,dt.ConnectivityList);
+A=meshio.read('testout/example1.msh');
 
 assert(isequal(A.vtx,dt.Points));
 
 
 %write with cell data
-meshio.write('examplecell1.msh',dt.Points,dt.ConnectivityList,celldata(1),celldataname(1));
-B=meshio.read('examplecell1.msh');
+meshio.write('testout/examplecell1.msh',dt.Points,dt.ConnectivityList,celldata(1),celldataname(1));
+B=meshio.read('testout/examplecell1.msh');
 
 assert(isequal(celldata(1),B.cell_data));
 
-meshio.write('examplecell2.msh',dt.Points,dt.ConnectivityList,celldata,celldataname);
-C=meshio.read('examplecell2.msh');
+meshio.write('testout/examplecell2.msh',dt.Points,dt.ConnectivityList,celldata,celldataname);
+C=meshio.read('testout/examplecell2.msh');
 
 assert(isequal(celldata,C.cell_data));
 
 
 % write with point data
-meshio.write('examplepoint1.msh',dt.Points,dt.ConnectivityList,[],[],pointdata(1),pointdataname(1));
-D=meshio.read('examplepoint1.msh');
+meshio.write('testout/examplepoint1.msh',dt.Points,dt.ConnectivityList,[],[],pointdata(1),pointdataname(1));
+D=meshio.read('testout/examplepoint1.msh');
 
 assert(isequal(pointdata(1),D.point_data));
 
-meshio.write('examplepoint2.msh',dt.Points,dt.ConnectivityList,[],[],pointdata,pointdataname);
-E=meshio.read('examplepoint2.msh');
+meshio.write('testout/examplepoint2.msh',dt.Points,dt.ConnectivityList,[],[],pointdata,pointdataname);
+E=meshio.read('testout/examplepoint2.msh');
 
 assert(isequal(pointdata,E.point_data));
 
 %write with both point and cell data
-meshio.write('examplepointcell.msh',dt.Points,dt.ConnectivityList,celldata,celldataname,pointdata,pointdataname);
-F=meshio.read('examplepointcell.msh');
+meshio.write('testout/examplepointcell.msh',dt.Points,dt.ConnectivityList,celldata,celldataname,pointdata,pointdataname);
+F=meshio.read('testout/examplepointcell.msh');
 
 assert(isequal(pointdata,F.point_data) && isequal(celldata,F.cell_data));
 
 %convert file using structwrite
-meshio.structwrite('examplecell.vtu',C);
-meshio.structwrite('examplepoint.vtu',E);
-meshio.structwrite('examplepointcell.vtu',F);
-
+meshio.structwrite('testout/examplecell.vtu',C);
+meshio.structwrite('testout/examplepoint.vtu',E);
+meshio.structwrite('testout/examplepointcell.vtu',F);
 
 %% read gmsh file
 
 % example gmsh file is conversion from .stl file 
 % this contains vertcies, lines, triangles and tetrahedra which are all read
 % order is always vert/line/tri/tetra
-fname=('finger_3D.msh');
+fname=('finger_3D');
 
-P=meshio.read(fname);
+P=meshio.read([fname '.msh']);
 meshio.plot(P);
 
-% extract just the lines/triangles/tetrahedra
+% extract just the tetrahedra
 Ptet=P;
-Ptet.cells=Ptet.cells(23:end);
+Ptet.cells=Ptet.cells(end);
 meshio.plot(Ptet);
 
-meshio.structwrite('examplemulti.vtu',Ptet);
+% write file back to vtu N.B. meshio merges cells of the same type
+meshio.structwrite([fname '.vtu'],P);
+Pvtu=meshio.read([fname '.vtu']);
+%Ptvu only has 4 cells, each for all vertex,line,tri,tetra
+
+% meshio cannot write .msh files with different cell types in at the moment
+% (meshio v 4.0.16). So write each type to a separate file and merge them
+% in gmsh
+
+try
+meshio.structwrite('testout/error.msh',P);
+
+catch
+    fprintf(2,'\n -----------\n meshio can only write 1 cell type (e.g. tetra) to msh file \n -----------\n');
+end
 
 
 %% read vtu and write new data
-fname=('NNexample.vtu');
+fname='NNexample.vtu';
 fnameoutcell='NNexampleNewDataC.vtu';
 fnameoutpoint='NNexampleNewDataP.vtu';
 

diff --git a/examples/testout/.gitignore b/examples/testout/.gitignore
@@ -0,0 +1 @@
+*