path: root/Carpet/CarpetIOHDF5/src/util/hdf5_slicer.cc

 /*@@
   @file      hdf5_slicer.cc
   @date      Fri 17 October 2008
   @author    Thomas Radke
   @desc
              Utility program to extract a 1D line or 2D slice from 3D datasets
              in datafiles generated by CarpetIOHDF5.
   @enddesc
 @@*/

#include <algorithm>
#include <cassert>
#include <iostream>
#include <iomanip>
#include <string>
#include <vector>
#include <cmath>
#include <cstring>
#include <regex.h>

#define H5_USE_16_API 1
#include <hdf5.h>

using namespace std;

/*****************************************************************************
 *************************     Macro Definitions   ***************************
 *****************************************************************************/

// value for an unset parameter
#define PARAMETER_UNSET	-424242.0

// fuzzy factor for comparing dataset timesteps with user-specified value
#define FUZZY_FACTOR	1e-6

// the datatype for the 'start' argument in H5Sselect_hyperslab()
#if (H5_VERS_MAJOR == 1 && \
     (H5_VERS_MINOR < 6 || (H5_VERS_MINOR == 6 && H5_VERS_RELEASE < 4)))
#define h5size_t hssize_t
#else
#define h5size_t hsize_t
#endif

// macro to check the return code of calls to the HDF5 library
#define CHECK_HDF5(fn_call) {                                                 \
          const int _retval = fn_call;                                        \
          if (_retval < 0) {                                                  \
            cerr << "HDF5 call " << #fn_call                                  \
                 << " in file " << __FILE__ << " line " << __LINE__           \
                 << " returned error code " << _retval << endl;               \
          }                                                                   \
        }

// the name of the group containing file metadata
#define METADATA_GROUP "Parameters and Global Attributes"

/*****************************************************************************
 *************************       Global Data         *************************
 *****************************************************************************/

// the slab coordinate as selected by the user
static double slab_coord[3] = {PARAMETER_UNSET, PARAMETER_UNSET, PARAMETER_UNSET};

// flag for outputting data in full 3D
static bool out3D = false;

// the specific timestep selected by the user
static double timestep = PARAMETER_UNSET;

// the regular expression to match against dataset names
static const char* regex = NULL;
static regex_t preg;

// the total number of datasets sliced
static unsigned int slices_extracted = 0;

// whether to print omitted datasets
static bool verbose = false; 

// rank of the output slices
static hsize_t outrank = 0;

// output file id
static hid_t outfile = -1;

/*****************************************************************************
 *************************     Function Prototypes   *************************
 *****************************************************************************/
static herr_t ProcessDataset (hid_t group, const char *name, void *_file);


 /*@@
   @routine    main
   @date       Fri 17 October 2008
   @author     Thomas Radke
   @desc
               Evaluates command line options and opens the input files.
   @enddesc

   @var        argc
   @vdesc      number of command line parameters
   @vtype      int
   @vio        in
   @endvar
   @var        argv
   @vdesc      array of command line parameters
   @vtype      char* const []
   @vio        in
   @endvar
 @@*/
int main (int argc, char *const argv[])
{
  int i;
  bool help = false;
  int num_slab_options = 0;


  // evaluate command line parameters
  for (i = 1; i < argc; i++) {
    if (strcmp (argv[i], "--help") == 0) {
      help = true; break;
    } else if (strcmp (argv[i], "--verbose") == 0) {
      verbose = true;
    } else if (strcmp (argv[i], "--out3d-cube") == 0) {
      outrank = 3;
      out3D = true;
    } else if (strcmp (argv[i], "--timestep") == 0 and i+1 < argc) {
      timestep = atof (argv[++i]);
    } else if (strcmp (argv[i], "--match") == 0 and i+1 < argc) {
      regex = argv[++i];
      if (regcomp (&preg, regex, REG_EXTENDED)) {
        cerr << "Error: invalid regular expression '" << regex << "' given"
             << endl << endl;
        return (-1);
      }
    } else if (strcmp (argv[i], "--out1d-xline-yz") == 0 and i+2 < argc) {
      outrank = 1;
      slab_coord[1] = atof (argv[++i]);
      slab_coord[2] = atof (argv[++i]); num_slab_options++;
    } else if (strcmp (argv[i], "--out1d-yline-xz") == 0 and i+2 < argc) {
      outrank = 1;
      slab_coord[0] = atof (argv[++i]);
      slab_coord[2] = atof (argv[++i]); num_slab_options++;
    } else if (strcmp (argv[i], "--out1d-zline-xy") == 0 and i+2 < argc) {
      outrank = 1;
      slab_coord[0] = atof (argv[++i]);
      slab_coord[1] = atof (argv[++i]); num_slab_options++;
    } else if (strcmp (argv[i], "--out2d-yzplane-x") == 0 and i+1 < argc) {
      outrank = 2;
      slab_coord[0] = atof (argv[++i]); num_slab_options++;
    } else if (strcmp (argv[i], "--out2d-xzplane-y") == 0 and i+1 < argc) {
      outrank = 2;
      slab_coord[1] = atof (argv[++i]); num_slab_options++;
    } else if (strcmp (argv[i], "--out2d-xyplane-z") == 0 and i+1 < argc) {
      outrank = 2;
      slab_coord[2] = atof (argv[++i]); num_slab_options++;
    } else {
      break;
    }
  }

  /* give some help if called with incorrect number of parameters */
  if (help or i >= argc-1 or num_slab_options != (out3D ? 0 : 1)) {
    const string indent (strlen (argv[0]) + 1, ' ');
    cerr << endl << "   ------------------"
         << endl << "   Carpet HDF5 Slicer"
         << endl << "   ------------------" << endl
         << endl
         << "Usage: " << endl
         << argv[0] << " [--help]" << endl
         << indent << "[--match <regex string>]" << endl
         << indent << "[--timestep <cctk_time value>]" << endl
         << indent << "[--verbose]" << endl
         << indent << "<--out1d-line value value> | <--out2d-plane value> | <out3d-cube>" << endl
         << indent << "<hdf5_infiles> <hdf5_outfile>" << endl << endl
         << "  where" << endl
         << "    [--help]                         prints this help" << endl
         << "    [--match <regex string>]         selects HDF5 datasets by their names" << endl
         << "                                     matching a regex string using POSIX" << endl
         << "                                     Extended Regular Expression syntax" << endl
         << "    [--timestep <cctk_time value>]   selects all HDF5 datasets which" << endl
         << "                                     (fuzzily) match the specified time" << endl
         << "    [--verbose]                      lists skipped HDF5 datasets on stderr" << endl
         << endl
         << "  and either <--out1d-line value value> or <--out2d-plane value> or <--out3d-cube>" << endl
         << "  must be specified as in the following:" << endl
         << "    --out1d-xline-yz  <origin_y> <origin_z>" << endl
         << "    --out1d-yline-xz  <origin_x> <origin_z>" << endl
         << "    --out1d-zline-xy  <origin_x> <origin_y>" << endl
         << endl
         << "    --out2d-yzplane-x  <origin_x>" << endl
         << "    --out2d-xzplane-y  <origin_y>" << endl
         << "    --out2d-xyplane-z  <origin_z>" << endl
         << endl
         << "    --out3d-cube" << endl
#if 0
         << "    --out2d-yzplane-xi <origin_xi>" << endl
         << "    --out2d-xzplane-yi <origin_yi>" << endl
         << "    --out2d-xyplane-zi <origin_zi>" << endl
#endif
         << endl
         << "  eg, to extract a 2D xy-plane at z = 0:" << endl
         << "    " << argv[0] << " --out2d-xyplane-z 0 alp.file_*.h5 alp.z=0.h5" << endl
         << endl
         << "  or the same plane but only for datasets of refinement level 0:" << endl
         << "    " << argv[0] << " --match 'ADMBASE::alp it=[0-9]+ tl=0 rl=0' --out2d-xyplane-z 0 alp.file_*.h5 alp.z=0.h5" << endl;
    return (0);
  }

  // check that the output doesn't exist already
  const char *const outfilename = argv[argc-1];
  H5E_BEGIN_TRY {
    if (H5Fis_hdf5(outfilename) >= 0) {
      cerr << "The designated output file '" << outfilename
           << "' must not exist beforehand." << endl
           << "Please remove it before continuing !" << endl << endl;
      return (-1);
    }
  } H5E_END_TRY;

  // create the output file
  cout << endl << "  creating output file '" << outfilename << "'" << endl;
  H5E_BEGIN_TRY {
    outfile = H5Fcreate (outfilename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
  } H5E_END_TRY;
  if (outfile < 0) {
    cerr << "Could not create output file '" << outfilename << "'" << endl;
    return (-1);
  }

  // browse though input file(s)
  for (; i < argc-1; i++) {
    hid_t file;

    H5E_BEGIN_TRY {
      file = H5Fopen (argv[i], H5F_ACC_RDONLY, H5P_DEFAULT);
    } H5E_END_TRY;

    if (file < 0) {
      cerr << "Could not open input file '" << argv[i] << "'" << endl << endl;
      continue;
    }

    cout << "  iterating through input file '" << argv[i] << "'..." << endl;
    CHECK_HDF5 (H5Giterate (file, "/", NULL, ProcessDataset, &file));

    // close file
    if (file >= 0) {
      CHECK_HDF5 (H5Fclose (file));
    }
  }

  if (slices_extracted == 0) {
    cerr << endl << "No matching datasets were found for the selected "
                    "slice parameters." << endl << endl;
  }

  // close output file
  CHECK_HDF5 (H5Fclose (outfile));

  cout << endl << "Done." << endl << endl;

  return (0);
}


 /*@@
   @routine    ProcessDataset
   @date       Fri 17 October 2008
   @author     Thomas Radke
   @desc
               The worker routine which is called by H5Giterate().
               It checks whether the current HDF5 object is a dataset matching
               the user's slab criteria.
   @enddesc

   @var        group
   @vdesc      HDF5 object to start the iteration
   @vtype      hid_t
   @vio        in
   @endvar
   @var        datasetname
   @vdesc      name of the object at the current iteration
   @vtype      const char *
   @vio        in
   @endvar
   @var        _file
   @vdesc      pointer to the descriptor of the currently opened file
   @vtype      void *
   @vio        in
   @endvar
@@*/
static herr_t ProcessDataset (hid_t group, const char *datasetname, void *_file)
{
  // we are interested in datasets only - skip anything else
  H5G_stat_t object_info;
  CHECK_HDF5 (H5Gget_objinfo (group, datasetname, 0, &object_info));
  if (object_info.type != H5G_DATASET) {
    return (0);
  }

  hid_t dataset, datatype, attr;
  CHECK_HDF5 (dataset   = H5Dopen (group, datasetname));

  // check the dataset's datatype - make sure it is either integer or real
  CHECK_HDF5 (datatype  = H5Dget_type (dataset));
  H5T_class_t typeclass;
  CHECK_HDF5 (typeclass = H5Tget_class (datatype));

  // read the timestep and variable name
  CHECK_HDF5 (attr = H5Aopen_name (dataset, "time"));
  double time;
  CHECK_HDF5 (H5Aread (attr, H5T_NATIVE_DOUBLE, &time));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (attr = H5Aopen_name (dataset, "name"));
  hid_t stringdatatype;
  CHECK_HDF5 (stringdatatype = H5Aget_type (attr));
  string varname(H5Tget_size (stringdatatype) + 1, 0);
  CHECK_HDF5 (H5Aread (attr, stringdatatype, &varname[0]));
  CHECK_HDF5 (H5Aclose (attr));

  // read the dimensions
  hid_t dataspace = -1;
  CHECK_HDF5 (dataspace = H5Dget_space (dataset));
  int ndims;
  ndims = H5Sget_simple_extent_ndims (dataspace);
  hsize_t dims[3];
  int iorigin[3], cctk_nghostzones[3];
  double origin[3], delta[3];
  int itimestep = 0, level = 0;

  bool is_okay = false;
  if (typeclass != H5T_FLOAT and typeclass != H5T_INTEGER) {
    if (verbose) {
      cerr << "skipping dataset '" << datasetname << "':" << endl
           << "  is not of integer or floating-point datatype" << endl;
    }
  } else if (ndims != 3) {
    if (verbose) {
      cerr << "skipping dataset '" << datasetname << "':" << endl
           << "  dataset has " << ndims << " dimensions" << endl;
    }
  } else if (regex && regexec (&preg, datasetname, 0, NULL, 0)) {
    if (verbose) {
      cerr << "skipping dataset '" << datasetname << "':" << endl
           << "  name doesn't match regex" << endl;
    }
  } else if (timestep != PARAMETER_UNSET and
             fabs (timestep - time) > FUZZY_FACTOR) {
    if (verbose) {
      cerr << "skipping dataset '" << datasetname << "':" << endl
           << "  timestep (" << time << ") doesn't match" << endl;
    }
  } else {
    CHECK_HDF5 (attr = H5Aopen_name (dataset, "iorigin"));
    CHECK_HDF5 (H5Aread (attr, H5T_NATIVE_INT, iorigin));
    CHECK_HDF5 (H5Aclose (attr));
    CHECK_HDF5 (attr = H5Aopen_name (dataset, "origin"));
    CHECK_HDF5 (H5Aread (attr, H5T_NATIVE_DOUBLE, origin));
    CHECK_HDF5 (H5Aclose (attr));
    CHECK_HDF5 (attr = H5Aopen_name (dataset, "delta"));
    CHECK_HDF5 (H5Aread (attr, H5T_NATIVE_DOUBLE, delta));
    CHECK_HDF5 (H5Aclose (attr));
    CHECK_HDF5 (attr = H5Aopen_name (dataset, "timestep"));
    CHECK_HDF5 (H5Aread (attr, H5T_NATIVE_INT, &itimestep));
    CHECK_HDF5 (H5Aclose (attr));
    CHECK_HDF5 (attr = H5Aopen_name (dataset, "level"));
    CHECK_HDF5 (H5Aread (attr, H5T_NATIVE_INT, &level));
    CHECK_HDF5 (H5Aclose (attr));
    CHECK_HDF5 (attr = H5Aopen_name (dataset, "cctk_nghostzones"));
    CHECK_HDF5 (H5Aread (attr, H5T_NATIVE_INT, cctk_nghostzones));
    CHECK_HDF5 (H5Aclose (attr));
    CHECK_HDF5 (H5Sget_simple_extent_dims (dataspace, dims, NULL));

    int i;
    is_okay = out3D;
    if (not out3D) {
      for (i = 0; i < 3; i++) {
        if (slab_coord[i] != PARAMETER_UNSET) {
          is_okay = slab_coord[i] >= origin[i] and
                    slab_coord[i] <= origin[i] + (dims[2-i]-1)*delta[i];
          if (not is_okay) break;
        }
      }
    }
    if (not is_okay) {
      if (verbose) {
        cerr << "skipping dataset '" << datasetname << "':" << endl
             << "  slab " << slab_coord[i] << " is out of dataset range ["
             << origin[i] << ", "
             << origin[i] + (dims[2-i]-1)*delta[i] << "]"
             << endl;
      }
    }
  }

  if (not is_okay) {
    CHECK_HDF5 (H5Tclose (stringdatatype));
    CHECK_HDF5 (H5Tclose (datatype));
    CHECK_HDF5 (H5Dclose (dataset));
    return (0);
  }

  slices_extracted++;

  h5size_t slabstart[3] = {0, 0, 0};
  hsize_t slabcount[3] = {dims[0], dims[1], dims[2]};
  hsize_t outslabcount[3];
  double slice_origin[3], slice_delta[3];
  int slice_iorigin[3], slice_cctk_nghostzones[3];
  int j = 0;
  for (int i = 0; i < 3; i++) {
    if (slab_coord[i] != PARAMETER_UNSET) {
      slabstart[2-i] = (h5size_t) ((slab_coord[i] - origin[i]) / delta[i] + 0.5);
      slabcount[2-i] = 1;
    } else {
      outslabcount[outrank-j-1] = dims[2-i];
      slice_origin[j] = origin[i];
      slice_delta[j] = delta[i];
      slice_iorigin[j] = iorigin[i];
      slice_cctk_nghostzones[j] = cctk_nghostzones[i];
      j++;
    }
  }
  assert(j == outrank);

  hid_t slabspace;
  CHECK_HDF5 (slabspace = H5Screate_simple (3, slabcount, NULL));
  CHECK_HDF5 (H5Sselect_hyperslab (dataspace, H5S_SELECT_SET,
                                   slabstart, NULL, slabcount, NULL));
  const hssize_t npoints = H5Sget_select_npoints (dataspace);
  // make sure the vector allocates at least one element
  char *data = new char[(npoints + 1) * H5Tget_size(datatype)];
  CHECK_HDF5 (H5Dread (dataset, datatype, slabspace, dataspace, H5P_DEFAULT,
                       data));
  CHECK_HDF5 (H5Dclose (dataset));
  CHECK_HDF5 (H5Sclose (slabspace));
  CHECK_HDF5 (H5Sclose (dataspace));

  CHECK_HDF5 (dataspace = H5Screate_simple (outrank, outslabcount, NULL));
  CHECK_HDF5 (dataset = H5Dcreate (outfile, datasetname,
                                   datatype, dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Dwrite (dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                        data));
  delete[] data;
  CHECK_HDF5 (H5Tclose (datatype));
  CHECK_HDF5 (H5Sclose (dataspace));

  // write global attributes (only on the first time through)
  static bool first_time_through = true;
  if (first_time_through) {
    hid_t metadata_group;
    CHECK_HDF5 (metadata_group = H5Gcreate(outfile, METADATA_GROUP, 0));
    CHECK_HDF5 (dataspace = H5Screate(H5S_SCALAR));
    CHECK_HDF5 (attr = H5Acreate(metadata_group, "nioprocs", H5T_NATIVE_INT,
                                 dataspace, H5P_DEFAULT));
    const int nioprocs = 1;
    CHECK_HDF5 (H5Awrite(attr, H5T_NATIVE_INT, &nioprocs));
    CHECK_HDF5 (H5Aclose(attr));
    CHECK_HDF5 (H5Sclose(dataspace));
    CHECK_HDF5 (H5Gclose(metadata_group));
    first_time_through = false;
  }
  
  // write basic dataset attributes
  CHECK_HDF5 (dataspace = H5Screate_simple (1, &outrank, NULL));
  CHECK_HDF5 (attr = H5Acreate (dataset, "origin", H5T_NATIVE_DOUBLE,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, H5T_NATIVE_DOUBLE, slice_origin));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (attr = H5Acreate (dataset, "delta", H5T_NATIVE_DOUBLE,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, H5T_NATIVE_DOUBLE, slice_delta));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (attr = H5Acreate (dataset, "iorigin", H5T_NATIVE_INT,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, H5T_NATIVE_INT, slice_iorigin));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (attr = H5Acreate (dataset, "cctk_nghostzones", H5T_NATIVE_INT,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, H5T_NATIVE_INT, slice_cctk_nghostzones));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (H5Sclose (dataspace));
  CHECK_HDF5 (dataspace = H5Screate (H5S_SCALAR));
  CHECK_HDF5 (attr = H5Acreate (dataset, "time", H5T_NATIVE_DOUBLE,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, H5T_NATIVE_DOUBLE, &time));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (attr = H5Acreate (dataset, "timestep", H5T_NATIVE_INT,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, H5T_NATIVE_INT, &itimestep));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (attr = H5Acreate (dataset, "level", H5T_NATIVE_INT,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, H5T_NATIVE_INT, &level));
  CHECK_HDF5 (H5Aclose (attr));
  CHECK_HDF5 (attr = H5Acreate (dataset, "name", stringdatatype,
                                dataspace, H5P_DEFAULT));
  CHECK_HDF5 (H5Awrite (attr, stringdatatype, varname.c_str()));
  CHECK_HDF5 (H5Tclose (stringdatatype));
  CHECK_HDF5 (H5Sclose (dataspace));
  CHECK_HDF5 (H5Dclose (dataset));

  return 0;
}