Exemple #1
0
void SaveISISNexus::dae() {
  NXmakegroup(handle, "dae", "IXdae");
  NXopengroup(handle, "dae", "IXdae");

  saveString("detector_table_file", " ");
  saveString("spectra_table_file", " ");
  saveString("wiring_table_file", " ");

  saveIntOpen("period_index", m_isisRaw->t_pmap, nper);
  NXgetdataID(handle, &period_index_link);
  close();

  NXmakegroup(handle, "time_channels_1", "IXtime_channels");
  NXopengroup(handle, "time_channels_1", "IXtime_channels");

  boost::scoped_array<float> timeChannels(new float[ntc + 1]);
  m_isisRaw->getTimeChannels(timeChannels.get(), ntc + 1);
  saveFloatOpen("time_of_flight", timeChannels.get(), ntc + 1);
  putAttr("axis", 1);
  putAttr("primary", 1);
  putAttr("units", "microseconds");
  NXgetdataID(handle, &time_of_flight_link);
  close();

  saveIntOpen("time_of_flight_raw", m_isisRaw->t_tcb1, ntc + 1);
  putAttr("units", "pulses");
  putAttr("frequency", "32 MHz");
  NXgetdataID(handle, &time_of_flight_raw_link);
  close();

  NXclosegroup(handle); // time_channels_1

  NXclosegroup(handle); // dae
}
Exemple #2
0
/*----------------------------------------------------------------------*/
void *nx_getdataID(void *handle){
  NXhandle hfil;
  int status;
  NXlink *linki;

  linki = (NXlink *)malloc(sizeof(NXlink));
  if(linki == NULL){
    return NULL;
  }

  hfil = (NXhandle)handle;
  status = NXgetdataID(hfil,linki);
  if(status == NX_OK){
    return linki;
  } else {
    free(linki);
    return NULL;
  }
}
Exemple #3
0
int main (int argc, char *argv[])
{
  int i, j, k, n, NXrank, NXdims[32], NXtype, NXlen, entry_status, attr_status;
  float r;
  void *data_buffer;
  unsigned char i1_array[4] = {1, 2, 3, 4};
  short int i2_array[4] = {1000, 2000, 3000, 4000};
  int i4_array[4] = {1000000, 2000000, 3000000, 4000000};
  float r4_array[5][4] =
  {{1., 2., 3., 4.}, {5., 6., 7., 8.}, {9., 10., 11., 12.}, {13., 14., 15., 16.}, {17., 18., 19., 20.}};
  double r8_array[5][4] =
  {{1., 2., 3., 4.}, {5., 6., 7., 8.}, {9., 10., 11., 12.}, {13., 14., 15., 16.}, {17., 18., 19., 20.}};
  int array_dims[2] = {5, 4};
  int unlimited_dims[1] = {NX_UNLIMITED};
  int chunk_size[2]={5,4};
  int slab_start[2], slab_size[2];
  char name[64], char_class[64], char_buffer[128];
  char group_name[64], class_name[64];
  char c1_array[5][4] = {{'a', 'b', 'c' ,'d'}, {'e', 'f', 'g' ,'h'}, 
     {'i', 'j', 'k', 'l'}, {'m', 'n', 'o', 'p'}, {'q', 'r', 's' , 't'}};
  int unlimited_cdims[2] = {NX_UNLIMITED, 4};
  NXhandle fileid, clone_fileid;
  NXlink glink, dlink, blink;
  int comp_array[100][20];
  int dims[2];
  int cdims[2];
  int nx_creation_code;
  char nxFile[80];
  char filename[256];
  int64_t grossezahl[4];
  const char* ch_test_data = "NeXus ><}&{'\\&\" Data";
  char path[512];

  grossezahl[0] = 12;
  grossezahl[2] = 23;
#if HAVE_LONG_LONG_INT
  grossezahl[1] = (int64_t)555555555555LL;
  grossezahl[3] = (int64_t)777777777777LL;
#else
  grossezahl[1] = (int64_t)555555555555;
  grossezahl[3] = (int64_t)777777777777;
#endif /* HAVE_LONG_LONG_INT */

  if(strstr(argv[0],"napi_test-hdf5") != NULL){
    nx_creation_code = NXACC_CREATE5;
    strcpy(nxFile,"NXtest.h5");
  }else if(strstr(argv[0],"napi_test-xml-table") != NULL){
    nx_creation_code = NXACC_CREATEXML | NXACC_TABLE;
    strcpy(nxFile,"NXtest-table.xml");
  }else if(strstr(argv[0],"napi_test-xml") != NULL){
    nx_creation_code = NXACC_CREATEXML;
    strcpy(nxFile,"NXtest.xml");
  } else {
    nx_creation_code = NXACC_CREATE;
    strcpy(nxFile,"NXtest.hdf");
  }

/* create file */
  if (NXopen (nxFile, nx_creation_code, &fileid) != NX_OK) return 1;
  if (nx_creation_code == NXACC_CREATE5)
  {
    if (NXreopen (fileid, &clone_fileid) != NX_OK) return 1;
  }
  NXsetnumberformat(fileid,NX_FLOAT32,"%9.3f");
  if (NXmakegroup (fileid, "entry", "NXentry") != NX_OK) return 1;
  if (NXopengroup (fileid, "entry", "NXentry") != NX_OK) return 1;
  if(NXputattr(fileid,"hugo","namenlos",strlen("namenlos"), NX_CHAR) != NX_OK) return 1;
  if(NXputattr(fileid,"cucumber","passion",strlen("passion"), NX_CHAR) != NX_OK) return 1;
     NXlen = strlen(ch_test_data);
     if (NXmakedata (fileid, "ch_data", NX_CHAR, 1, &NXlen) != NX_OK) return 1;
     if (NXopendata (fileid, "ch_data") != NX_OK) return 1;
        if (NXputdata (fileid, ch_test_data) != NX_OK) return 1;
     if (NXclosedata (fileid) != NX_OK) return 1;
     if (NXmakedata (fileid, "c1_data", NX_CHAR, 2, array_dims) != NX_OK) return 1;
     if (NXopendata (fileid, "c1_data") != NX_OK) return 1;
        if (NXputdata (fileid, c1_array) != NX_OK) return 1;
     if (NXclosedata (fileid) != NX_OK) return 1;
     if (NXmakedata (fileid, "i1_data", NX_INT8, 1, &array_dims[1]) != NX_OK) return 1;
     if (NXopendata (fileid, "i1_data") != NX_OK) return 1;
        if (NXputdata (fileid, i1_array) != NX_OK) return 1;
     if (NXclosedata (fileid) != NX_OK) return 1;
     if (NXmakedata (fileid, "i2_data", NX_INT16, 1, &array_dims[1]) != NX_OK) return 1;
     if (NXopendata (fileid, "i2_data") != NX_OK) return 1;
        if (NXputdata (fileid, i2_array) != NX_OK) return 1;
     if (NXclosedata (fileid) != NX_OK) return 1;
     if (NXmakedata (fileid, "i4_data", NX_INT32, 1, &array_dims[1]) != NX_OK) return 1;
     if (NXopendata (fileid, "i4_data") != NX_OK) return 1;
        if (NXputdata (fileid, i4_array) != NX_OK) return 1;
     if (NXclosedata (fileid) != NX_OK) return 1;
     if (NXcompmakedata (fileid, "r4_data", NX_FLOAT32, 2, array_dims,NX_COMP_LZW,chunk_size) != NX_OK) return 1;
     if (NXopendata (fileid, "r4_data") != NX_OK) return 1;
        if (NXputdata (fileid, r4_array) != NX_OK) return 1;
     if (NXclosedata (fileid) != NX_OK) return 1;
     if (NXmakedata (fileid, "r8_data", NX_FLOAT64, 2, array_dims) != NX_OK) return 1;
     if (NXopendata (fileid, "r8_data") != NX_OK) return 1;
        slab_start[0] = 4; slab_start[1] = 0; slab_size[0] = 1; slab_size[1] = 4;
        if (NXputslab (fileid, (double*)r8_array + 16, slab_start, slab_size) != NX_OK) return 1;
        slab_start[0] = 0; slab_start[1] = 0; slab_size[0] = 4; slab_size[1] = 4;
        if (NXputslab (fileid, r8_array, slab_start, slab_size) != NX_OK) return 1;
        if (NXputattr (fileid, "ch_attribute", ch_test_data, strlen (ch_test_data), NX_CHAR) != NX_OK) return 1;
        i = 42;
        if (NXputattr (fileid, "i4_attribute", &i, 1, NX_INT32) != NX_OK) return 1;
        r = 3.14159265;
        if (NXputattr (fileid, "r4_attribute", &r, 1, NX_FLOAT32) != NX_OK) return 1;
        if (NXgetdataID (fileid, &dlink) != NX_OK) return 1;
     if (NXclosedata (fileid) != NX_OK) return 1;
     dims[0] = 4;
     if (nx_creation_code != NXACC_CREATE)
     {
       if (NXmakedata (fileid, "grosse_zahl", NX_INT64, 1,dims) == NX_OK) {
         if (NXopendata (fileid, "grosse_zahl") != NX_OK) return 1;
         if (NXputdata (fileid, grossezahl) != NX_OK) return 1;
         if (NXclosedata (fileid) != NX_OK) return 1;  
       }
     }
     if (NXmakegroup (fileid, "data", "NXdata") != NX_OK) return 1;
     if (NXopengroup (fileid, "data", "NXdata") != NX_OK) return 1;
        if (NXmakelink (fileid, &dlink) != NX_OK) return 1;
        dims[0] = 100;
        dims[1] = 20;
        for(i = 0; i < 100; i++)
            {
            for(j = 0; j < 20; j++)
               {
                 comp_array[i][j] = i;
               }
            }
        cdims[0] = 20;
        cdims[1] = 20;
        if (NXcompmakedata (fileid, "comp_data", NX_INT32, 2, dims, NX_COMP_LZW, cdims) != NX_OK) return 1;
        if (NXopendata (fileid, "comp_data") != NX_OK) return 1;
           if (NXputdata (fileid, comp_array) != NX_OK) return 1;
        if (NXclosedata (fileid) != NX_OK) return 1;  
        if (NXflush (&fileid) != NX_OK) return 1;
	if (NXmakedata (fileid, "flush_data", NX_INT32, 1, unlimited_dims) != NX_OK) return 1;
	slab_size[0] = 1;
	for (i = 0; i < 7; i++)
	    {
	      slab_start[0] = i;
	      if (NXopendata (fileid, "flush_data") != NX_OK) return 1;
	        if (NXputslab (fileid, &i, slab_start, slab_size) != NX_OK) return 1;
		if (NXflush (&fileid) != NX_OK) return 1;
	}
     if (NXclosegroup (fileid) != NX_OK) return 1;
     if (NXmakegroup (fileid, "sample", "NXsample") != NX_OK) return 1;
     if (NXopengroup (fileid, "sample", "NXsample") != NX_OK) return 1;
        NXlen = 12;
        if (NXmakedata (fileid, "ch_data", NX_CHAR, 1, &NXlen) != NX_OK) return 1;
        if (NXopendata (fileid, "ch_data") != NX_OK) return 1;
           if (NXputdata (fileid, "NeXus sample") != NX_OK) return 1;
        if (NXclosedata (fileid) != NX_OK) return 1;
        if (NXgetgroupID (fileid, &glink) != NX_OK) return 1;
        if (( nx_creation_code & NXACC_CREATEXML) == 0 ) {
            if (NXmakedata (fileid, "cdata_unlimited", NX_CHAR, 2, unlimited_cdims) != NX_OK) return 1;
	    if (NXopendata (fileid, "cdata_unlimited") != NX_OK) return 1;
	    slab_size[0] = 1;
	    slab_size[1] = 4;
	    slab_start[1] = 0;
            for (i = 0; i < 5; i++)
            {
	       slab_start[0] = i;
               if (NXputslab (fileid, &(c1_array[i][0]), slab_start, slab_size) != NX_OK) return 1;
            }
            if (NXclosedata (fileid) != NX_OK) return 1;
        }
     if (NXclosegroup (fileid) != NX_OK) return 1;
  if (NXclosegroup (fileid) != NX_OK) return 1;
  if (NXmakegroup (fileid, "link", "NXentry") != NX_OK) return 1;
  if (NXopengroup (fileid, "link", "NXentry") != NX_OK) return 1;
     if (NXmakelink (fileid, &glink) != NX_OK) return 1;
     if (NXmakenamedlink (fileid,"renLinkGroup", &glink) != NX_OK) return 1;
     if (NXmakenamedlink (fileid, "renLinkData", &dlink) != NX_OK) return 1;
  if (NXclosegroup (fileid) != NX_OK) return 1;
  if (NXclose (&fileid) != NX_OK) return 1;

  if ( (argc >= 2) && !strcmp(argv[1], "-q") )
  {
     return 0;	/* create only */
  }
  /*
    read test
  */
  if (NXopen (nxFile, NXACC_RDWR,&fileid) != NX_OK) return 1;
  if(NXinquirefile(fileid,filename,256) != NX_OK){
    return 1;
  }
  printf("NXinquirefile found: %s\n", relativePathOf(filename));
  NXgetattrinfo (fileid, &i);
  if (i > 0) {
     printf ("Number of global attributes: %d\n", i);
  }
  do { 
     attr_status = NXgetnextattr (fileid, name, NXdims, &NXtype);
     if (attr_status == NX_ERROR) return 1;
     if (attr_status == NX_OK) {
        switch (NXtype) {
           case NX_CHAR:
              NXlen = sizeof (char_buffer);
              if (NXgetattr (fileid, name, char_buffer, &NXlen, &NXtype) 
		  != NX_OK) return 1;
		if ( strcmp(name, "file_time") &&
		     strcmp(name, "HDF_version") &&
		     strcmp(name, "HDF5_Version") &&
		     strcmp(name, "XML_version") )
		{
                 printf ("   %s = %s\n", name, char_buffer);
		}
              break;
        }
     }
  } while (attr_status == NX_OK);
  if (NXopengroup (fileid, "entry", "NXentry") != NX_OK) return 1;
  NXgetattrinfo(fileid,&i);
  printf("Number of group attributes: %d\n", i);
  if(NXgetpath(fileid,path,512) != NX_OK)return 1;
  printf("NXentry path %s\n", path);
  do { 
     attr_status = NXgetnextattr (fileid, name, NXdims, &NXtype);
     if (attr_status == NX_ERROR) return 1;
     if (attr_status == NX_OK) {
        switch (NXtype) {
           case NX_CHAR:
              NXlen = sizeof (char_buffer);
              if (NXgetattr (fileid, name, char_buffer, &NXlen, &NXtype) 
		  != NX_OK) return 1;
                 printf ("   %s = %s\n", name, char_buffer);
        }
     }
  } while (attr_status == NX_OK);
  if (NXgetgroupinfo (fileid, &i, group_name, class_name) != NX_OK) return 1;
     printf ("Group: %s(%s) contains %d items\n", group_name, class_name, i);
  do {
     entry_status = NXgetnextentry (fileid, name, char_class, &NXtype);
     if (entry_status == NX_ERROR) return 1;
     if (strcmp(char_class,"SDS") != 0) {
        if (entry_status != NX_EOD) {
           printf ("   Subgroup: %s(%s)\n", name, char_class);
           entry_status = NX_OK;
        }
     } else {
        if (entry_status == NX_OK) {
           if (NXopendata (fileid, name) != NX_OK) return 1;
	    if(NXgetpath(fileid,path,512) != NX_OK)return 1;
	    printf("Data path %s\n", path);
	    if (NXgetinfo (fileid, &NXrank, NXdims, &NXtype) != NX_OK) return 1;
                 printf ("   %s(%d)", name, NXtype);
              if (NXmalloc ((void **) &data_buffer, NXrank, NXdims, NXtype) != NX_OK) return 1;
	      n = 1;
              for(k=0; k<NXrank; k++)
	      {
                  n *= NXdims[k];
              }
              if (NXtype == NX_CHAR) {
                 if (NXgetdata (fileid, data_buffer) != NX_OK) return 1;
                    print_data (" = ", data_buffer, NXtype, n);
              } else if (NXtype != NX_FLOAT32 && NXtype != NX_FLOAT64) {
                 if (NXgetdata (fileid, data_buffer) != NX_OK) return 1;
                    print_data (" = ", data_buffer, NXtype, n);
              } else {
                 slab_start[0] = 0;
                 slab_start[1] = 0;
                 slab_size[0] = 1;
                 slab_size[1] = 4;
                 if (NXgetslab (fileid, data_buffer, slab_start, slab_size) != NX_OK) return 1;
                    print_data ("\n      ", data_buffer, NXtype, 4);
                 slab_start[0] = 1;
                 if (NXgetslab (fileid, data_buffer, slab_start, slab_size) != NX_OK) return 1;
                    print_data ("      ", data_buffer, NXtype, 4);
                 slab_start[0] = 2;
                 if (NXgetslab (fileid, data_buffer, slab_start, slab_size) != NX_OK) return 1;
                    print_data ("      ", data_buffer, NXtype, 4);
                 slab_start[0] = 3;
                 if (NXgetslab (fileid, data_buffer, slab_start, slab_size) != NX_OK) return 1;
                    print_data ("      ", data_buffer, NXtype, 4);
                 slab_start[0] = 4;
                 if (NXgetslab (fileid, data_buffer, slab_start, slab_size) != NX_OK) return 1;
                    print_data ("      ", data_buffer, NXtype, 4);
                 if (NXgetattrinfo (fileid, &i) != NX_OK) return 1;
                 if (i > 0) {
                    printf ("      Number of attributes : %d\n", i);
                 }
                 do {
                    attr_status = NXgetnextattr (fileid, name, NXdims, &NXtype);
                    if (attr_status == NX_ERROR) return 1;
                    if (attr_status == NX_OK) {
                       switch (NXtype) {
                          case NX_INT32:
                             NXlen = 1;
                             if (NXgetattr (fileid, name, &i, &NXlen, &NXtype) != NX_OK) return 1;
                                printf ("         %s : %d\n", name, i);
                             break;
                          case NX_FLOAT32:
                             NXlen = 1;
                             if (NXgetattr (fileid, name, &r, &NXlen, &NXtype) != NX_OK) return 1;
                                printf ("         %s : %f\n", name, r);
                             break;
                          case NX_CHAR:
                             NXlen = sizeof (char_buffer);
                             if (NXgetattr (fileid, name, char_buffer, &NXlen, &NXtype) != NX_OK) return 1;
                                printf ("         %s : %s\n", name, char_buffer);
                             break;
                       }
                    } 
                 } while (attr_status == NX_OK);
              }
           if (NXclosedata (fileid) != NX_OK) return 1;
           if (NXfree ((void **) &data_buffer) != NX_OK) return 1;
        }
     }
  } while (entry_status == NX_OK);
  if (NXclosegroup (fileid) != NX_OK) return 1;
/*
 * check links
 */
  if (NXopengroup (fileid, "entry", "NXentry") != NX_OK) return 1;
    if (NXopengroup (fileid, "sample", "NXsample") != NX_OK) return 1;
      if (NXgetgroupID (fileid, &glink) != NX_OK) return 1;
    if (NXclosegroup (fileid) != NX_OK) return 1;
    if (NXopengroup (fileid, "data", "NXdata") != NX_OK) return 1;
      if (NXopendata (fileid, "r8_data") != NX_OK) return 1;
        if (NXgetdataID (fileid, &dlink) != NX_OK) return 1;
      if (NXclosedata (fileid) != NX_OK) return 1;
    if (NXclosegroup (fileid) != NX_OK) return 1;
    if (NXopendata (fileid, "r8_data") != NX_OK) return 1;
      if (NXgetdataID (fileid, &blink) != NX_OK) return 1;
    if (NXclosedata (fileid) != NX_OK) return 1;
    if (NXsameID(fileid, &dlink, &blink) != NX_OK)
    {
         printf ("Link check FAILED (r8_data)\n");
         printf ("original data\n");
	 NXIprintlink(fileid, &dlink);
         printf ("linked data\n");
	 NXIprintlink(fileid, &blink);
	 return 1;
    }
  if (NXclosegroup (fileid) != NX_OK) return 1;

  if (NXopengroup (fileid, "link", "NXentry") != NX_OK) return 1;
    if (NXopengroup (fileid, "sample", "NXsample") != NX_OK) return 1;
    if(NXgetpath(fileid,path,512) != NX_OK)return 1;
    printf("Group path %s\n", path);
      if (NXgetgroupID (fileid, &blink) != NX_OK) return 1;
        if (NXsameID(fileid, &glink, &blink) != NX_OK)
	{
             printf ("Link check FAILED (sample)\n");
             printf ("original group\n");
	     NXIprintlink(fileid, &glink);
             printf ("linked group\n");
	     NXIprintlink(fileid, &blink);
	     return 1;
	}
      if (NXclosegroup (fileid) != NX_OK) return 1;

    if (NXopengroup (fileid, "renLinkGroup", "NXsample") != NX_OK) return 1;
      if (NXgetgroupID (fileid, &blink) != NX_OK) return 1;
        if (NXsameID(fileid, &glink, &blink) != NX_OK)
	{
             printf ("Link check FAILED (renLinkGroup)\n");
             printf ("original group\n");
	     NXIprintlink(fileid, &glink);
             printf ("linked group\n");
	     NXIprintlink(fileid, &blink);
	     return 1;
	}
      if (NXclosegroup (fileid) != NX_OK) return 1;

    if(NXopendata(fileid,"renLinkData") != NX_OK) return 1;
      if(NXgetdataID(fileid,&blink) != NX_OK) return 1;
        if (NXsameID(fileid, &dlink, &blink) != NX_OK)
	{
             printf ("Link check FAILED (renLinkData)\n");
             printf ("original group\n");
	     NXIprintlink(fileid, &glink);
             printf ("linked group\n");
	     NXIprintlink(fileid, &blink);
	     return 1;
	}
    if(NXclosedata(fileid) != NX_OK) return 1;	
  if (NXclosegroup (fileid) != NX_OK) return 1;
  printf ("Link check OK\n");

  /*
    tests for NXopenpath
  */
  if(NXopenpath(fileid,"/entry/data/comp_data") != NX_OK){
    printf("Failure on NXopenpath\n");
    return 0;
  }
  if(NXopenpath(fileid,"/entry/data/comp_data") != NX_OK){
    printf("Failure on NXopenpath\n");
    return 0;
  }
  if(NXopenpath(fileid,"../r8_data") != NX_OK){
    printf("Failure on NXopenpath\n");
    return 0;
  }
  if(NXopengrouppath(fileid,"/entry/data/comp_data") != NX_OK){
    printf("Failure on NXopengrouppath\n");
    return 0;
  }
  if(NXopenpath(fileid,"/entry/data/r8_data") != NX_OK){
    printf("Failure on NXopenpath\n");
    return 0;
  }
  printf("NXopenpath checks OK\n");

  if (NXclose (&fileid) != NX_OK) return 1;

  printf("before load path tests\n");
  if(testLoadPath() != 0) return 1;

  printf("before external link tests\n");
  if(testExternal(argv[0]) != 0) {
    return 1;
  }

  printf("all ok - done\n");
  return 0;
}
Exemple #4
0
void SaveISISNexus::detector_1() {
  NXmakegroup(handle, "detector_1", "NXdata");
  NXopengroup(handle, "detector_1", "NXdata");

  for (int i = 0; i < nmon; ++i) {
    int si = int(std::distance(
        m_isisRaw->spec,
        std::find(m_isisRaw->spec, m_isisRaw->spec + nsp, m_isisRaw->mdet[i])));
    monitor_index[si] = i;
  }

  // write counts
  int dim[3];
  dim[0] = nper;
  dim[1] = nsp - nmon;
  dim[2] = ntc;
  NXmakedata(handle, "counts", NX_INT32, 3, dim);
  NXopendata(handle, "counts");
  putAttr("units", "counts");
  putAttr("signal", 1);
  putAttr("axes", "period_index,spectrum_index,time_of_flight");

  int size[] = {1, 1, ntc};
  int index = 0;
  for (int p = 0; p < nper; ++p) {
    int ispec = 0;
    m_isisRaw->skipData(rawFile, index++);
    for (int si = 0; si < nsp; ++si) {
      if (monitor_index.find(si) != monitor_index.end()) {
        m_isisRaw->readData(rawFile, index);
        monitorData.insert(monitorData.end(), m_isisRaw->dat1 + 1,
                           m_isisRaw->dat1 + ntc + 1);
      } else {
        m_isisRaw->readData(rawFile, index);
        int start[] = {p, ispec, 0};
        NXputslab(handle, m_isisRaw->dat1 + 1, start, size);
        ++ispec;
      }
      ++index;
    }
  }
  NXgetdataID(handle, &counts_link);
  NXclosedata(handle);

  NXmakelink(handle, &period_index_link);

  std::vector<int> spec_minus_monitors(nsp - nmon);
  std::generate(spec_minus_monitors.begin(), spec_minus_monitors.end(),
                getWithoutMonitors<int>(this, m_isisRaw->spec));
  saveIntOpen("spectrum_index", &spec_minus_monitors[0], nsp - nmon);
  NXgetdataID(handle, &spectrum_index_link);
  close();

  NXmakelink(handle, &time_of_flight_link);
  NXmakelink(handle, &time_of_flight_raw_link);

  std::vector<float> float_vec(ndet - nmon);
  std::generate(float_vec.begin(), float_vec.end(),
                getWithoutMonitors<float>(this, m_isisRaw->delt));
  saveFloat("delt", &float_vec[0], ndet - nmon);

  saveFloat("source_detector_distance", &m_isisRaw->ivpb.i_sddist, 1);

  // using the same float_vec, size unchanged ndet-nmon
  std::generate(float_vec.begin(), float_vec.end(),
                getWithoutMonitors<float>(this, m_isisRaw->len2));
  saveFloatOpen("distance", &float_vec[0], ndet - nmon);
  putAttr("units", "metre");
  close();

  // using the same float_vec, size unchanged ndet-nmon
  std::generate(float_vec.begin(), float_vec.end(),
                getWithoutMonitors<float>(this, m_isisRaw->tthe));
  saveFloatOpen("polar_angle", &float_vec[0], ndet - nmon);
  putAttr("units", "degree");
  close();

  NXclosegroup(handle);
}
/** Prints the contents of each group as XML tags and values */
int SaveToSNSHistogramNexus::WriteGroup(int is_definition) {
  int status, dataType, dataRank, dataDimensions[NX_MAXRANK];
  NXname name, theClass;
  void *dataBuffer;
  NXlink link;

  do {
    status = NXgetnextentry(inId, name, theClass, &dataType);
    //      std::cout << name << "(" << theClass << ")\n";

    if (status == NX_ERROR)
      return NX_ERROR;
    if (status == NX_OK) {
      if (!strncmp(theClass, "NX", 2)) {
        if (NXopengroup(inId, name, theClass) != NX_OK)
          return NX_ERROR;
        add_path(name);

        if (NXgetgroupID(inId, &link) != NX_OK)
          return NX_ERROR;
        if (!strcmp(current_path, link.targetPath)) {
          // Create a copy of the group
          if (NXmakegroup(outId, name, theClass) != NX_OK)
            return NX_ERROR;
          if (NXopengroup(outId, name, theClass) != NX_OK)
            return NX_ERROR;
          if (WriteAttributes(is_definition) != NX_OK)
            return NX_ERROR;
          if (WriteGroup(is_definition) != NX_OK)
            return NX_ERROR;
          remove_path(name);
        } else {
          remove_path(name);
          strcpy(links_to_make[links_count].from, current_path);
          strcpy(links_to_make[links_count].to, link.targetPath);
          strcpy(links_to_make[links_count].name, name);
          links_count++;
          if (NXclosegroup(inId) != NX_OK)
            return NX_ERROR;
        }
      } else if (!strncmp(theClass, "SDS", 3)) {
        add_path(name);
        if (NXopendata(inId, name) != NX_OK)
          return NX_ERROR;
        if (NXgetdataID(inId, &link) != NX_OK)
          return NX_ERROR;

        std::string data_label(name);

        if (!strcmp(current_path, link.targetPath)) {
          // Look for the bank name
          std::string path(current_path);
          std::string bank;

          size_t a = path.rfind('/');
          if (a != std::string::npos && a > 0) {
            size_t b = path.rfind('/', a - 1);
            if (b != std::string::npos && (b < a) && (a - b - 1) > 0) {
              bank = path.substr(b + 1, a - b - 1);
              // std::cout << current_path << ":bank " << bank << "\n";
            }
          }

          //---------------------------------------------------------------------------------------
          if (data_label == "data" && (bank != "")) {
            if (this->WriteDataGroup(bank, is_definition) != NX_OK)
              return NX_ERROR;
            ;
          }
          //---------------------------------------------------------------------------------------
          else if (data_label == "time_of_flight" && (bank != "")) {
            // Get the original info
            if (NXgetinfo(inId, &dataRank, dataDimensions, &dataType) != NX_OK)
              return NX_ERROR;

            // Get the X bins
            const MantidVec &X = inputWorkspace->readX(0);
            // 1 dimension, with that number of bin boundaries
            dataDimensions[0] = static_cast<int>(X.size());
            // The output TOF axis will be whatever size in the workspace.
            boost::scoped_array<float> tof_data(new float[dataDimensions[0]]);

            // And fill it with the X data
            for (size_t i = 0; i < X.size(); i++)
              tof_data[i] = float(X[i]);

            if (NXcompmakedata(outId, name, dataType, dataRank, dataDimensions,
                               NX_COMP_LZW, dataDimensions) != NX_OK)
              return NX_ERROR;
            if (NXopendata(outId, name) != NX_OK)
              return NX_ERROR;
            if (WriteAttributes(is_definition) != NX_OK)
              return NX_ERROR;
            if (NXputdata(outId, tof_data.get()) != NX_OK)
              return NX_ERROR;
            if (NXclosedata(outId) != NX_OK)
              return NX_ERROR;

          }

          //---------------------------------------------------------------------------------------
          else {
            // Everything else gets copies
            if (NXgetinfo(inId, &dataRank, dataDimensions, &dataType) != NX_OK)
              return NX_ERROR;
            if (NXmalloc(&dataBuffer, dataRank, dataDimensions, dataType) !=
                NX_OK)
              return NX_ERROR;
            if (NXgetdata(inId, dataBuffer) != NX_OK)
              return NX_ERROR;
            if (NXcompmakedata(outId, name, dataType, dataRank, dataDimensions,
                               NX_COMP_LZW, dataDimensions) != NX_OK)
              return NX_ERROR;
            if (NXopendata(outId, name) != NX_OK)
              return NX_ERROR;
            if (WriteAttributes(is_definition) != NX_OK)
              return NX_ERROR;
            if (NXputdata(outId, dataBuffer) != NX_OK)
              return NX_ERROR;
            if (NXfree(&dataBuffer) != NX_OK)
              return NX_ERROR;
            if (NXclosedata(outId) != NX_OK)
              return NX_ERROR;
          }

          remove_path(name);
        } else {
          // Make a link
          remove_path(name);
          strcpy(links_to_make[links_count].from, current_path);
          strcpy(links_to_make[links_count].to, link.targetPath);
          strcpy(links_to_make[links_count].name, name);
          links_count++;
        }
        if (NXclosedata(inId) != NX_OK)
          return NX_ERROR;
      }
    } else if (status == NX_EOD) {
      if (NXclosegroup(inId) != NX_OK)
        return NX_ERROR;
      if (NXclosegroup(outId) != NX_OK)
        return NX_ERROR;
      return NX_OK;
    }
  } while (status == NX_OK);
  return NX_OK;
}
/** Performs the copying from the input to the output file,
 *  while modifying the data and time_of_flight fields.
 */
int SaveToSNSHistogramNexus::copy_file(const char *inFile, int nx_read_access,
                                       const char *outFile,
                                       int nx_write_access) {
  int nx_is_definition = 0;
  links_count = 0;
  current_path[0] = '\0';
  NXlink link;

  /* Open NeXus input file and NeXus output file */
  if (NXopen(inFile, nx_read_access, &inId) != NX_OK) {
    printf("NX_ERROR: Can't open %s\n", inFile);
    return NX_ERROR;
  }

  if (NXopen(outFile, nx_write_access, &outId) != NX_OK) {
    printf("NX_ERROR: Can't open %s\n", outFile);
    return NX_ERROR;
  }

  /* Output global attributes */
  if (WriteAttributes(nx_is_definition) != NX_OK) {
    return NX_ERROR;
  }
  /* Recursively cycle through the groups printing the contents */
  if (WriteGroup(nx_is_definition) != NX_OK) {
    return NX_ERROR;
  }
  /* close input */
  if (NXclose(&inId) != NX_OK) {
    return NX_ERROR;
  }

  // HDF5 only
  {
    /* now create any required links */
    for (int i = 0; i < links_count; i++) {
      if (NXopenpath(outId, links_to_make[i].to) != NX_OK)
        return NX_ERROR;
      if (NXgetdataID(outId, &link) == NX_OK ||
          NXgetgroupID(outId, &link) == NX_OK) {
        if (NXopenpath(outId, links_to_make[i].from) != NX_OK)
          return NX_ERROR;
        char *tstr = strrchr(links_to_make[i].to, '/');
        if (!strcmp(links_to_make[i].name, tstr + 1)) {
          if (NXmakelink(outId, &link) != NX_OK)
            return NX_ERROR;
        } else {
          if (NXmakenamedlink(outId, links_to_make[i].name, &link) != NX_OK)
            return NX_ERROR;
        }
      } else {
        return NX_ERROR;
      }
    }
  }
  /* Close the input and output files */
  if (NXclose(&outId) != NX_OK) {
    return NX_ERROR;
  }
  return NX_OK;
}