add conversion scripts

scripts/README.md

@@ -10,7 +10,7 @@ The matrix solution has to be provided in form of a Matlab `mat`-file which has
 * `T`: an `nt x nvelem` element connectivity matrix which contains in each row an element's `nvelem` vertex indices with respect to the numbering induced by `Points`.
 * `P`: an `nt`-size vector containing the element-wise solution values with respect to the numbering induced by `T`.
 
-Is your original solution data available as a VTK file? A helper function `hdf5_to_mat.m` is provided which extracts the required `mat`-file from an HDF5-file, which in turn can be exported from Paraview: select `File` -> `Save Data...` -> `Files of type: Xdmf Data File`, use the produced `h5`-file.
+Is your original solution data available as a VTK file? A helper function `hdf5_to_mat_matrix.m` is provided which extracts the required `mat`-file from an HDF5-file, which in turn can be exported from Paraview: select `File` -> `Save Data...` -> `Files of type: Xdmf Data File`, use the produced `h5`-file. Type `help hdf5_to_mat_matrix` in Matlab for details.
 
 #### 1.2 Performing the comparison
 
@@ -27,6 +27,9 @@ function [relativeMatrixError] = compute_2d_error(coarseFile, referenceFile)
 The fracture solution has to be provided in form of a Matlab `mat`-file which has to contain a Matlab cell array `fracXAndPCell`. Each cell `fracXAndPCell{i}` provides the solution on fracture branch `i` in form of a `(2.nc) x 3` matrix. As 2x3 block `fracXAndPCell{i}(2*e-1:2*e, :)` describes the solution on fracture element `e` in form of `[xStart, yStart, pStart; xEnd yEnd, pEnd]` where 
 `xStart, yStart` / `xEnd, yEnd` indicate the two vertices of the fracture element and `pStart` / `pEnd` the corresponding solution values.
 
+Is your original solution data available as a VTK file? A helper function `hdf5_to_mat_fracture.m` is provided which extracts the required `mat`-file from HDF5-files for the fracture branches, which in turn can be exported from Paraview: Perform a plot-over-line for a fracture branch, select `File` -> `Save Data...` -> `Files of type: Xdmf Data File`, use the produced `h5`-file. Type `help hdf5_to_mat_fracture` in Matlab for details.
+
+
 #### 2.2 Performing the comparison
 
 The function [compute_1d_error](compute_1d_error.m) can be used to calculate a relative L2-error of the fracture solution. It has the signature

scripts/hdf5_to_mat_fracture.m

+function hdf5_to_mat_fracture(basefilename, numfractures, solutionname, outfilename)
+% hdf5_to_mat_fracture Convert a fracture network solution from HDF5 to Matlab format.
+%
+% Signature:
+% hdf5_to_mat_fracture(basefilename, numfractures, solutionname, outfilename)
+%
+% Parameters:
+% basefilename: the base name of the HDF5 files containing the fracture
+%               network solution, the individual files for each fracture
+%               branch are expected to be named 'basefilenameX.h5' where
+%               'X' is the index of the fracture branch
+% numfractures: the number of individual fracture branches (equal to the
+%               number of input files)              
+% solutionname: the name of the solution vector inside the HDF5 file
+% outfilename: the name of the output Matlab .mat-file
+
+fracXAndPCell = cell(numfractures, 1);
+for fracidx = 1:numfractures
+    filename = strcat(basefilename, num2str(fracidx), '.h5');
+    fraccoords = h5read(filename, '/Block_0_t000000/Geometry/Points');
+    fracpressure = h5read(filename, strcat('/Block_0_t000000/Node/', solutionname));
+    fraccoords(:, isnan(fracpressure)) = [];
+    fracpressure(isnan(fracpressure)) = [];
+    numpoints = size(fraccoords, 2);
+    Xp = zeros(2*(numpoints-1), 3);
+    Xp(1:2:end-1, 1:2) = fraccoords(1:2, 1:end-1)';
+    Xp(2:2:end, 1:2) = fraccoords(1:2, 2:end)';
+    Xp(1:2:end-1, 3) = fracpressure(1:end-1);
+    Xp(2:2:end, 3) = fracpressure(2:end)';
+    fracXAndPCell{fracidx} = Xp;
+end
+
+save(outfilename, 'fracXAndPCell');
+fprintf('Wrote file %s.\n', outfilename);
+
+return

scripts/hdf5_to_mat_matrix.m

+function hdf5_to_mat_matrix(infilename, cellwise, solutionname, outfilename)
+% hdf5_to_mat_matrix Convert a matrix solution from HDF5 to Matlab format.
+%
+% Signature:
+% hdf5_to_mat_matrix(infilename, solutionname, outfilename)
+%
+% Parameters:
+% infilename: the name of the HDF5 file containing the matrix solution
+% cellwise: true for a cell-wise solution vector, false for a vertex-wise
+% solutionname: the name of the solution vector inside the HDF5 file
+% outfilename: the name of the output Matlab .mat-file
+
+T = h5read(infilename, '/Block_0_t000000/Topology');
+T = T' + 1;
+Points = h5read(infilename, '/Block_0_t000000/Geometry/Coordinates');
+Points = Points([1 2], :)';
+if cellwise
+  P = h5read(infilename, strcat('/Block_0_t000000/Cell/', solutionname));
+else
+  pvertex = h5read(infilename, strcat('/Block_0_t000000/Node/', solutionname));
+  P = zeros(size(T, 1), 1);
+  factor = 1/size(T, 2);
+  for i = 1:size(T, 2)
+    P = P + factor.*pvertex(T(:, i));
+  end
+end
+
+save(outfilename, 'T', 'P', 'Points');
+fprintf('Wrote file %s.\n', outfilename);
+
+return