/** Write out an array to the open file. */
void NexusFileIO::NXwritedata( const char * name, int datatype, int rank, int * dims_array, void * data, bool compress) const
{
if (compress)
{
// We'll use the same slab/buffer size as the size of the array
NXcompmakedata(fileID, name, datatype, rank, dims_array, m_nexuscompression, dims_array);
}
else
{
// Write uncompressed.
NXmakedata(fileID, name, datatype, rank, dims_array);
}
NXopendata(fileID, name);
NXputdata(fileID, data );
NXclosedata(fileID);
}
/*--------------------------------------------------------------------*/
int nx_compmakedata(void *ptr, char *name, int rank, int type,
void *dimPtr, void *bufPtr){
int status;
NXhandle hfil;
pNXDS dimData, bufData;
hfil = (NXhandle)ptr;
dimData = (pNXDS)dimPtr;
if(dimData->type != NX_INT32){
NXReportError("ERROR: dimension data not integer");
return 0;
}
bufData = (pNXDS)bufPtr;
status = NXcompmakedata(hfil, name, type, rank,
dimData->u.iPtr, NX_COMP_LZW,bufData->u.iPtr);
if(status == NX_OK){
return 1;
} else {
return 0;
}
}
/** Write out a combined chunk of event data
*
* @param ws :: an EventWorkspace
* @param indices :: array of event list indexes
* @param tofs :: array of TOFs
* @param weights :: array of event weights
* @param errorSquareds :: array of event squared errors
* @param pulsetimes :: array of pulsetimes
* @param compress :: if true, compress the entry
*/
int NexusFileIO::writeNexusProcessedDataEventCombined( const DataObjects::EventWorkspace_const_sptr& ws,
std::vector<int64_t> & indices,
double * tofs, float * weights, float * errorSquareds, int64_t * pulsetimes,
bool compress) const
{
NXopengroup(fileID,"event_workspace","NXdata");
// The array of indices for each event list #
int dims_array[1] = { static_cast<int>(indices.size()) };
if (indices.size() > 0)
{
if (compress)
NXcompmakedata(fileID, "indices", NX_INT64, 1, dims_array, m_nexuscompression, dims_array);
else
NXmakedata(fileID, "indices", NX_INT64, 1, dims_array);
NXopendata(fileID, "indices");
NXputdata(fileID, (void*)(indices.data()) );
std::string yUnits=ws->YUnit();
std::string yUnitLabel=ws->YUnitLabel();
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(yUnits.c_str())), static_cast<int>(yUnits.size()), NX_CHAR);
NXputattr (fileID, "unit_label", reinterpret_cast<void*>(const_cast<char*>(yUnitLabel.c_str())), static_cast<int>(yUnitLabel.size()), NX_CHAR);
NXclosedata(fileID);
}
// Write out each field
dims_array[0] = static_cast<int>(indices.back()); // TODO big truncation error! This is the # of events
if (tofs)
NXwritedata("tof", NX_FLOAT64, 1, dims_array, (void *)(tofs), compress);
if (pulsetimes)
NXwritedata("pulsetime", NX_INT64, 1, dims_array, (void *)(pulsetimes), compress);
if (weights)
NXwritedata("weight", NX_FLOAT32, 1, dims_array, (void *)(weights), compress);
if (errorSquareds)
NXwritedata("error_squared", NX_FLOAT32, 1, dims_array, (void *)(errorSquareds), compress);
// Close up the overall group
NXstatus status=NXclosegroup(fileID);
return((status==NX_ERROR)?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;
}
/** Write out a table Workspace's
*/
int NexusFileIO::writeNexusTableWorkspace( const API::ITableWorkspace_const_sptr& itableworkspace,
const char * group_name) const
{
NXstatus status = 0;
boost::shared_ptr<const TableWorkspace> tableworkspace =
boost::dynamic_pointer_cast<const TableWorkspace>(itableworkspace);
boost::shared_ptr<const PeaksWorkspace> peakworkspace =
boost::dynamic_pointer_cast<const PeaksWorkspace>(itableworkspace);
if ( !tableworkspace && !peakworkspace )
return((status==NX_ERROR)?3:0);
//write data entry
status=NXmakegroup(fileID,group_name,"NXdata");
if(status==NX_ERROR)
return(2);
NXopengroup(fileID,group_name,"NXdata");
int nRows = static_cast<int>(itableworkspace->rowCount());
int dims_array[1] = { nRows };
for (size_t i = 0; i < itableworkspace->columnCount(); i++)
{
Column_const_sptr col = itableworkspace->getColumn(i);
std::string str = "column_" + boost::lexical_cast<std::string>(i+1);
if ( col->isType<double>() )
{
double * toNexus = new double[nRows];
for (int ii = 0; ii < nRows; ii++)
toNexus[ii] = col->cell<double>(ii);
NXwritedata(str.c_str(), NX_FLOAT64, 1, dims_array, (void *)(toNexus), false);
delete[] toNexus;
// attributes
NXopendata(fileID, str.c_str());
std::string units = "Not known";
std::string interpret_as = "A double";
NXputattr(fileID, "units", reinterpret_cast<void*>(const_cast<char*>(units.c_str())), static_cast<int>(units.size()), NX_CHAR);
NXputattr(fileID, "interpret_as", reinterpret_cast<void*>(const_cast<char*>(interpret_as.c_str())),
static_cast<int>(interpret_as.size()), NX_CHAR);
NXclosedata(fileID);
}
else if ( col->isType<int>() )
{
int * toNexus = new int[nRows];
for (int ii = 0; ii < nRows; ii++)
toNexus[ii] = col->cell<int>(ii);
NXwritedata(str.c_str(), NX_INT32, 1, dims_array, (void *)(toNexus), false);
delete[] toNexus;
// attributes
NXopendata(fileID, str.c_str());
std::string units = "Not known";
std::string interpret_as = "An integer";
NXputattr(fileID, "units", reinterpret_cast<void*>(const_cast<char*>(units.c_str())), static_cast<int>(units.size()), NX_CHAR);
NXputattr(fileID, "interpret_as", reinterpret_cast<void*>(const_cast<char*>(interpret_as.c_str())),
static_cast<int>(interpret_as.size()), NX_CHAR);
NXclosedata(fileID);
}
else if ( col->isType<std::string>() )
{
// determine max string size
size_t maxStr = 0;
for (int ii = 0; ii < nRows; ii++)
{
if ( col->cell<std::string>(ii).size() > maxStr)
maxStr = col->cell<std::string>(ii).size();
}
int dims_array[2] = { nRows, static_cast<int>(maxStr) };
int asize[2]={1,dims_array[1]};
NXcompmakedata(fileID, str.c_str(), NX_CHAR, 2, dims_array,false,asize);
NXopendata(fileID, str.c_str());
char* toNexus = new char[maxStr*nRows];
for(int ii = 0; ii < nRows; ii++)
{
std::string rowStr = col->cell<std::string>(ii);
for (size_t ic = 0; ic < rowStr.size(); ic++)
toNexus[ii*maxStr+ic] = rowStr[ic];
for (size_t ic = rowStr.size(); ic < static_cast<size_t>(maxStr); ic++)
toNexus[ii*maxStr+ic] = ' ';
}
NXputdata(fileID, (void *)(toNexus));
delete[] toNexus;
// attributes
std::string units = "N/A";
std::string interpret_as = "A string";
NXputattr(fileID, "units", reinterpret_cast<void*>(const_cast<char*>(units.c_str())), static_cast<int>(units.size()), NX_CHAR);
NXputattr(fileID, "interpret_as", reinterpret_cast<void*>(const_cast<char*>(interpret_as.c_str())),
static_cast<int>(interpret_as.size()), NX_CHAR);
NXclosedata(fileID);
}
#define IF_VECTOR_COLUMN(Type, NexusType) \
else if ( col->isType< std::vector<Type> >() ) \
{ \
auto vecCol = boost::dynamic_pointer_cast< const VectorColumn<Type> >(col); \
writeNexusVectorColumn<Type>(vecCol, str, NexusType, #Type); \
}
IF_VECTOR_COLUMN(int,NX_INT32)
IF_VECTOR_COLUMN(double,NX_FLOAT64)
// write out title
NXopendata(fileID, str.c_str());
NXputattr(fileID, "name", reinterpret_cast<void*>(const_cast<char*>(col->name().c_str())), static_cast<int>(col->name().size()), NX_CHAR);
NXclosedata(fileID);
}
status=NXclosegroup(fileID);
return((status==NX_ERROR)?3:0);
}
/** Write out a MatrixWorkspace's data as a 2D matrix.
* Use writeNexusProcessedDataEvent if writing an EventWorkspace.
*/
int NexusFileIO::writeNexusProcessedData2D( const API::MatrixWorkspace_const_sptr& localworkspace,
const bool& uniformSpectra, const std::vector<int>& spec,
const char * group_name, bool write2Ddata) const
{
NXstatus status;
//write data entry
status=NXmakegroup(fileID,group_name,"NXdata");
if(status==NX_ERROR)
return(2);
NXopengroup(fileID,group_name,"NXdata");
// write workspace data
const size_t nHist=localworkspace->getNumberHistograms();
if(nHist<1)
return(2);
const size_t nSpectBins=localworkspace->readY(0).size();
const size_t nSpect=spec.size();
int dims_array[2] = { static_cast<int>(nSpect),static_cast<int>(nSpectBins) };
// Set the axis labels and values
Mantid::API::Axis *xAxis=localworkspace->getAxis(0);
Mantid::API::Axis *sAxis=localworkspace->getAxis(1);
std::string xLabel,sLabel;
if ( xAxis->isSpectra() ) xLabel = "spectraNumber";
else
{
if ( xAxis->unit() ) xLabel = xAxis->unit()->unitID();
else xLabel = "unknown";
}
if ( sAxis->isSpectra() ) sLabel = "spectraNumber";
else
{
if ( sAxis->unit() ) sLabel = sAxis->unit()->unitID();
else sLabel = "unknown";
}
// Get the values on the vertical axis
std::vector<double> axis2;
if (nSpect < nHist)
for (size_t i=0;i<nSpect;i++)
axis2.push_back((*sAxis)(spec[i]));
else
for (size_t i=0;i<sAxis->length();i++)
axis2.push_back((*sAxis)(i));
int start[2]={0,0};
int asize[2]={1,dims_array[1]};
// -------------- Actually write the 2D data ----------------------------
if (write2Ddata)
{
std::string name="values";
NXcompmakedata(fileID, name.c_str(), NX_FLOAT64, 2, dims_array,m_nexuscompression,asize);
NXopendata(fileID, name.c_str());
for(size_t i=0;i<nSpect;i++)
{
int s = spec[i];
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readY(s)[0]))),start,asize);
start[0]++;
}
if(m_progress != 0) m_progress->reportIncrement(1, "Writing data");
int signal=1;
NXputattr (fileID, "signal", &signal, 1, NX_INT32);
// More properties
const std::string axesNames="axis2,axis1";
NXputattr (fileID, "axes", reinterpret_cast<void*>(const_cast<char*>(axesNames.c_str())), static_cast<int>(axesNames.size()), NX_CHAR);
std::string yUnits=localworkspace->YUnit();
std::string yUnitLabel=localworkspace->YUnitLabel();
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(yUnits.c_str())), static_cast<int>(yUnits.size()), NX_CHAR);
NXputattr (fileID, "unit_label", reinterpret_cast<void*>(const_cast<char*>(yUnitLabel.c_str())), static_cast<int>(yUnitLabel.size()), NX_CHAR);
NXclosedata(fileID);
// error
name="errors";
NXcompmakedata(fileID, name.c_str(), NX_FLOAT64, 2, dims_array,m_nexuscompression,asize);
NXopendata(fileID, name.c_str());
start[0]=0;
for(size_t i=0;i<nSpect;i++)
{
int s = spec[i];
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readE(s)[0]))),start,asize);
start[0]++;
}
if(m_progress != 0) m_progress->reportIncrement(1, "Writing data");
// Fractional area for RebinnedOutput
if (localworkspace->id() == "RebinnedOutput")
{
RebinnedOutput_const_sptr rebin_workspace = boost::dynamic_pointer_cast<const RebinnedOutput>(localworkspace);
name="frac_area";
NXcompmakedata(fileID, name.c_str(), NX_FLOAT64, 2,
dims_array,m_nexuscompression,asize);
NXopendata(fileID, name.c_str());
start[0]=0;
for(size_t i=0;i<nSpect;i++)
{
int s = spec[i];
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(rebin_workspace->readF(s)[0]))),
start, asize);
start[0]++;
}
if(m_progress != 0) m_progress->reportIncrement(1, "Writing data");
}
NXclosedata(fileID);
}
// write X data, as single array or all values if "ragged"
if(uniformSpectra)
{
dims_array[0]=static_cast<int>(localworkspace->readX(0).size());
NXmakedata(fileID, "axis1", NX_FLOAT64, 1, dims_array);
NXopendata(fileID, "axis1");
NXputdata(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readX(0)[0]))));
}
else
{
dims_array[0]=static_cast<int>(nSpect);
dims_array[1]=static_cast<int>(localworkspace->readX(0).size());
NXmakedata(fileID, "axis1", NX_FLOAT64, 2, dims_array);
NXopendata(fileID, "axis1");
start[0]=0; asize[1]=dims_array[1];
for(size_t i=0;i<nSpect;i++)
{
NXputslab(fileID, reinterpret_cast<void*>(const_cast<double*>(&(localworkspace->readX(i)[0]))),start,asize);
start[0]++;
}
}
std::string dist=(localworkspace->isDistribution()) ? "1" : "0";
NXputattr(fileID, "distribution", reinterpret_cast<void*>(const_cast<char*>(dist.c_str())), 2, NX_CHAR);
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(xLabel.c_str())), static_cast<int>(xLabel.size()), NX_CHAR);
auto label = boost::dynamic_pointer_cast<Mantid::Kernel::Units::Label>(xAxis->unit());
if(label)
{
NXputattr (fileID, "caption", reinterpret_cast<void*>(const_cast<char*>(label->caption().c_str())), static_cast<int>(label->caption().size()), NX_CHAR);
auto unitLbl = label->label();
NXputattr (fileID, "label", reinterpret_cast<void*>(const_cast<char*>(unitLbl.ascii().c_str())), static_cast<int>(unitLbl.ascii().size()), NX_CHAR);
}
NXclosedata(fileID);
if ( ! sAxis->isText() )
{
// write axis2, maybe just spectra number
dims_array[0]=static_cast<int>(axis2.size());
NXmakedata(fileID, "axis2", NX_FLOAT64, 1, dims_array);
NXopendata(fileID, "axis2");
NXputdata(fileID, (void*)&(axis2[0]));
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>(sLabel.c_str())), static_cast<int>(sLabel.size()), NX_CHAR);
auto label = boost::dynamic_pointer_cast<Mantid::Kernel::Units::Label>(sAxis->unit());
if(label)
{
NXputattr (fileID, "caption", reinterpret_cast<void*>(const_cast<char*>(label->caption().c_str())), static_cast<int>(label->caption().size()), NX_CHAR);
auto unitLbl = label->label();
NXputattr (fileID, "label", reinterpret_cast<void*>(const_cast<char*>(unitLbl.ascii().c_str())), static_cast<int>(unitLbl.ascii().size()), NX_CHAR);
}
NXclosedata(fileID);
}
else
{
std::string textAxis;
for ( size_t i = 0; i < sAxis->length(); i ++ )
{
std::string label = sAxis->label(i);
textAxis += label + "\n";
}
dims_array[0] = static_cast<int>(textAxis.size());
NXmakedata(fileID, "axis2", NX_CHAR, 2, dims_array);
NXopendata(fileID, "axis2");
NXputdata(fileID, reinterpret_cast<void*>(const_cast<char*>(textAxis.c_str())));
NXputattr (fileID, "units", reinterpret_cast<void*>(const_cast<char*>("TextAxis")), 8, NX_CHAR);
auto label = boost::dynamic_pointer_cast<Mantid::Kernel::Units::Label>(sAxis->unit());
if(label)
{
NXputattr (fileID, "caption", reinterpret_cast<void*>(const_cast<char*>(label->caption().c_str())), static_cast<int>(label->caption().size()), NX_CHAR);
auto unitLbl = label->label();
NXputattr (fileID, "label", reinterpret_cast<void*>(const_cast<char*>(unitLbl.ascii().c_str())), static_cast<int>(unitLbl.ascii().size()), NX_CHAR);
}
NXclosedata(fileID);
}
writeNexusBinMasking(localworkspace);
status=NXclosegroup(fileID);
return((status==NX_ERROR)?3:0);
}
/** 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;
}
/** Write the group labeled "data"
*
* @param bank :: name of the bank
* @param is_definition
* @return error code
*/
int SaveToSNSHistogramNexus::WriteDataGroup(std::string bank,
int is_definition) {
int dataType, dataRank, dataDimensions[NX_MAXRANK];
NXname name;
void *dataBuffer;
if (NXgetinfo(inId, &dataRank, dataDimensions, &dataType) != NX_OK)
return NX_ERROR;
// Get the rectangular detector
IComponent_const_sptr det_comp =
inputWorkspace->getInstrument()->getComponentByName(std::string(bank));
RectangularDetector_const_sptr det =
boost::dynamic_pointer_cast<const RectangularDetector>(det_comp);
if (!det) {
g_log.information()
<< "Detector '" + bank +
"' not found, or it is not a rectangular detector!\n";
// Just copy that then.
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;
} else {
// YES it is a rectangular detector.
// --- Memory requirements ----
size_t memory_required = size_t(det->xpixels() * det->ypixels()) *
size_t(inputWorkspace->blocksize()) * 2 *
sizeof(float);
Kernel::MemoryStats mem;
mem.update();
size_t memory_available = mem.availMem() * 1024;
std::cout << "Memory available: " << memory_available / 1024 << " kb. ";
std::cout << "Memory required: " << memory_required / 1024 << " kb. ";
// Give a 50% margin of error in allocating the memory
memory_available = memory_available / 2;
if (memory_available > static_cast<size_t>(5e9))
memory_available = static_cast<size_t>(5e9);
if (memory_available < memory_required) {
// Compute how large of a slab you can still use.
int x_slab;
x_slab = static_cast<int>(
memory_available /
(det->ypixels() * inputWorkspace->blocksize() * 2 * sizeof(float)));
if (x_slab <= 0)
x_slab = 1;
// Look for a slab size that evenly divides the # of pixels.
while (x_slab > 1) {
if ((det->xpixels() % x_slab) == 0)
break;
x_slab--;
}
std::cout << "Saving in slabs of " << x_slab << " X pixels.\n";
if (this->WriteOutDataOrErrors(det, x_slab, "data", "data_errors", false,
false, is_definition, bank) != NX_OK)
return NX_ERROR;
if (this->WriteOutDataOrErrors(det, x_slab, "errors", "", true, false,
is_definition, bank) != NX_OK)
return NX_ERROR;
} else {
std::cout << "Saving in one block.\n";
if (this->WriteOutDataOrErrors(det, det->xpixels(), "data", "data_errors",
false, true, is_definition, bank) != NX_OK)
return NX_ERROR;
}
}
return NX_OK;
}
/** Utility function to write out the
* data or errors to a field in the group.
*
* @param det :: rectangular detector being written
* @param x_pixel_slab :: size of a slab to write, in number of X pixels.
*ignored if doBoth
* @param field_name :: "data" field name
* @param errors_field_name :: "errors" field name.
* @param doErrors :: set true if you are writing the errors field this time.
*field_name should be the "errors" field name
* @param doBoth :: do both data and errors at once, no slabbing.
* @param is_definition ::
* @param bank :: name of the bank being written.
* @return error code
*/
int SaveToSNSHistogramNexus::WriteOutDataOrErrors(
Geometry::RectangularDetector_const_sptr det, int x_pixel_slab,
const char *field_name, const char *errors_field_name, bool doErrors,
bool doBoth, int is_definition, std::string bank) {
int dataRank, dataDimensions[NX_MAXRANK];
int slabDimensions[NX_MAXRANK], slabStartIndices[NX_MAXRANK];
dataRank = 3;
// Dimension 0 = the X pixels
dataDimensions[0] = det->xpixels();
// Dimension 1 = the Y pixels
dataDimensions[1] = det->ypixels();
// Dimension 2 = time of flight bins
dataDimensions[2] = static_cast<int>(inputWorkspace->blocksize());
// ---- Determine slab size -----
// Number of pixels to collect in X before slabbing
slabDimensions[0] = x_pixel_slab;
slabDimensions[1] = dataDimensions[1];
slabDimensions[2] = dataDimensions[2];
if (doBoth)
slabDimensions[0] = dataDimensions[0];
std::cout << "RectangularDetector " << det->getName()
<< " being copied. Dimensions : " << dataDimensions[0] << ", "
<< dataDimensions[1] << ", " << dataDimensions[2] << ".\n";
// ----- Open the data field -----------------------
if (m_compress) {
if (NXcompmakedata(outId, field_name, NX_FLOAT32, dataRank, dataDimensions,
NX_COMP_LZW, slabDimensions) != NX_OK)
return NX_ERROR;
} else {
if (NXmakedata(outId, field_name, NX_FLOAT32, dataRank, dataDimensions) !=
NX_OK)
return NX_ERROR;
}
if (NXopendata(outId, field_name) != NX_OK)
return NX_ERROR;
if (WriteAttributes(is_definition) != NX_OK)
return NX_ERROR;
if (!doErrors) {
// Add an attribute called "errors" with value = the name of the data_errors
// field.
NXname attrName = "errors";
std::string attrBuffer = errors_field_name;
if (NXputattr(outId, attrName, attrBuffer.c_str(),
static_cast<int>(attrBuffer.size()), NX_CHAR) != NX_OK)
return NX_ERROR;
}
// ---- Errors field -----
if (doBoth) {
if (NXclosedata(outId) != NX_OK)
return NX_ERROR;
if (m_compress) {
if (NXcompmakedata(outId, errors_field_name, NX_FLOAT32, dataRank,
dataDimensions, NX_COMP_LZW, slabDimensions) != NX_OK)
return NX_ERROR;
} else {
if (NXmakedata(outId, errors_field_name, NX_FLOAT32, dataRank,
dataDimensions) != NX_OK)
return NX_ERROR;
}
if (NXopendata(outId, errors_field_name) != NX_OK)
return NX_ERROR;
// NXlink * link = new NXlink;
// link->linkType = 1; /* SDS data link */
// NXgetdataID(outId, link);
// std::string targetPath = "/entry/" + bank + "/" + errors_field_name;
// strcpy(link->targetPath, targetPath.c_str());
// if (NXmakelink(outId,link) != NX_OK)
// g_log.debug() << "Error while making link to " << targetPath <<
// '\n';
if (WriteAttributes(is_definition) != NX_OK)
return NX_ERROR;
if (NXclosedata(outId) != NX_OK)
return NX_ERROR;
}
double fillTime = 0;
double saveTime = 0;
// Make a buffer of floats will all the counts in that bank.
auto data =
new float[slabDimensions[0] * slabDimensions[1] * slabDimensions[2]];
// Only allocate an array for errors if it is needed
float *errors = nullptr;
if (doBoth)
errors =
new float[slabDimensions[0] * slabDimensions[1] * slabDimensions[2]];
for (int x = 0; x < det->xpixels(); x++) {
// Which slab are we in?
int slabnum = x / x_pixel_slab;
// X index into the slabbed output array
int slabx = x % x_pixel_slab;
Timer tim1;
int ypixels = static_cast<int>(det->ypixels());
PARALLEL_FOR1(inputWorkspace)
for (int y = 0; y < ypixels; y++) {
PARALLEL_START_INTERUPT_REGION
// Get the workspace index for the detector ID at this spot
size_t wi = 0;
try {
wi = map.find(det->getAtXY(x, y)->getID())->second;
} catch (...) {
std::cout << "Error finding " << bank << " x " << x << " y " << y
<< "\n";
}
// Offset into array.
size_t index = size_t(slabx) * size_t(dataDimensions[1]) *
size_t(dataDimensions[2]) +
size_t(y) * size_t(dataDimensions[2]);
const MantidVec &Y = inputWorkspace->readY(wi);
const MantidVec &E = inputWorkspace->readE(wi);
for (size_t i = 0; i < Y.size(); ++i) {
if (doErrors) {
data[i + index] = static_cast<float>(E[i]);
} else {
data[i + index] = static_cast<float>(Y[i]);
if (doBoth) {
errors[i + index] = static_cast<float>(E[i]);
}
}
}
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
fillTime += tim1.elapsed();
// Is this the last pixel in the slab?
if (!doBoth && (x % x_pixel_slab == x_pixel_slab - 1)) {
Timer tim2;
// std::cout << "starting slab " << x << "\n";
// This is where the slab is in the greater data array.
slabStartIndices[0] = slabnum * x_pixel_slab;
slabStartIndices[1] = 0;
slabStartIndices[2] = 0;
if (NXputslab(outId, data, slabStartIndices, slabDimensions) != NX_OK)
return NX_ERROR;
saveTime += tim2.elapsed();
std::ostringstream mess;
mess << det->getName() << ", " << field_name << " slab " << slabnum
<< " of " << det->xpixels() / x_pixel_slab;
this->prog->reportIncrement(x_pixel_slab * det->ypixels(), mess.str());
}
} // X loop
if (doBoth) {
bool returnerror = false;
Timer tim2;
if (NXopendata(outId, field_name) != NX_OK)
returnerror = true;
else if (NXputdata(outId, data) != NX_OK)
returnerror = true;
else if (NXclosedata(outId) != NX_OK)
returnerror = true;
else {
this->prog->reportIncrement(det->xpixels() * det->ypixels() * 1,
det->getName() + " data");
if (NXopendata(outId, errors_field_name) != NX_OK)
returnerror = true;
else if (NXputdata(outId, errors) != NX_OK)
returnerror = true;
else if (NXclosedata(outId) != NX_OK)
returnerror = true;
else {
this->prog->reportIncrement(det->xpixels() * det->ypixels() * 1,
det->getName() + " errors");
saveTime += tim2.elapsed();
}
}
if (returnerror) {
delete[] data;
delete[] errors;
return NX_ERROR;
}
} else {
if (NXclosedata(outId) != NX_OK) {
delete[] data;
return NX_ERROR;
}
}
std::cout << "Filling out " << det->getName() << " took " << fillTime
<< " sec.\n";
std::cout << "Saving " << det->getName() << " took " << saveTime
<< " sec.\n";
delete[] data;
if (doBoth)
delete[] errors;
return NX_OK;
}
