/**
* Add properties from a nexus file to
* the workspace run.
* API entry for recursive routine below
*
*
* @param nxfileID :: Nexus file handle to be parsed, just after an NXopengroup
* @param runDetails :: where to add properties
*
*/
void LoadHelper::addNexusFieldsToWsRun(NXhandle nxfileID, API::Run& runDetails)
{
std::string emptyStr; // needed for first call
int datatype;
char nxname[NX_MAXNAMELEN], nxclass[NX_MAXNAMELEN];
// As a workaround against some "not so good" old ILL nexus files (ILLIN5_Vana_095893.nxs for example)
// we begin the parse on the first entry (entry0). This allow to avoid the bogus entries that follows.
NXstatus getnextentry_status = NXgetnextentry(nxfileID, nxname, nxclass, &datatype);
if (getnextentry_status == NX_OK)
{
NXstatus opengroup_status;
if ((opengroup_status = NXopengroup(nxfileID, nxname, nxclass)) == NX_OK)
{
if (std::string(nxname) == "entry0")
{
recurseAndAddNexusFieldsToWsRun(nxfileID, runDetails, emptyStr, emptyStr, 1 /* level */);
}
else
{
g_log.debug() << "Unexpected group name in nexus file : " << nxname << std::endl;
}
NXclosegroup(nxfileID);
}
}
}
/*-------------------------------------------------------------------*/
char *nx_getnextentry(void *handle, char separator){
int status, length, type;
NXhandle hfil;
char *resultBuffer = NULL;
NXname group,nxclass;
hfil = (NXhandle)handle;
status = NXgetnextentry(hfil,group, nxclass,&type);
if(status == NX_OK){
length = 30 + strlen(group) + strlen(nxclass);
/*
This introduces a memory leak. I had hoped, that swig would
kill it for me after use, but I'am afraid, this is not the
case. Unfortately I do not know how to fix the issue.
*/
resultBuffer = (char *)malloc(length*sizeof(char));
if(resultBuffer == NULL){
return NULL;
}
sprintf(resultBuffer,"%s%c%s%c%d",group,separator,nxclass,
separator,type);
return resultBuffer;
} else {
return NULL;
}
}
/* Outputs the contents of a NeXus group */
int NXBdir(NXhandle fileId)
{
int status, dataType, dataRank, dataDimensions[NX_MAXRANK], length;
NXname name, nxclass, nxurl;
if (NXinitgroupdir(fileId) != NX_OK)
return NX_ERROR;
do {
status = NXgetnextentry(fileId, name, nxclass, &dataType);
if (status == NX_ERROR)
break;
if (status == NX_OK) {
if (strncmp(nxclass, "CDF", 3) == 0) {
;
} else if (strcmp(nxclass, "SDS") == 0) {
printf(" NX Data : %s", name);
if (NXopendata(fileId, name) != NX_OK)
return NX_ERROR;
if (NXgetinfo (fileId, &dataRank, dataDimensions, &dataType) != NX_OK)
return NX_ERROR;
if (NXclosedata(fileId) != NX_OK)
return NX_ERROR;
PrintDimensions(dataRank, dataDimensions);
printf(" ");
PrintType(dataType);
printf("\n");
} else {
length = sizeof(nxurl);
if (NXisexternalgroup(fileId, name, nxclass, nxurl, length) == NX_OK) {
printf(" NX external Group: %s (%s), linked to: %s \n",
name, nxclass, nxurl);
} else {
printf(" NX Group : %s (%s)\n", name, nxclass);
if ((status = NXopengroup(fileId, name, nxclass)) != NX_OK) {
return status;
}
PrintGroupAttributes(fileId, name);
if ((status = NXclosegroup(fileId)) != NX_OK) {
return status;
}
}
}
}
} while (status == NX_OK);
return status;
}
/* Searches group for the requested data item */
int FindData(NXhandle fileId, char *dataName)
{
int status, dataType;
NXname name, nxclass;
NXinitgroupdir(fileId);
do {
status = NXgetnextentry(fileId, name, nxclass, &dataType);
if (status == NX_ERROR)
return NX_ERROR;
if (status == NX_OK) {
if (StrEq(dataName, name)) {
if (!strncmp(nxclass, "SDS", 3)) { /* Data has class "SDS" */
return NX_OK;
} else {
printf("NX_ERROR: %s is not data\n", dataName);
return NX_ERROR;
}
}
}
} while (status != NX_EOD);
printf("NX_ERROR: %s does not exist\n", dataName);
return NX_EOD;
}
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;
}
static char *field_generator(const char *text, int state)
{
struct name_item *item, *t_item;
static struct name_item *names = NULL, *last_item = NULL;
char *res;
int status, dataType;
NXname name, nxclass;
if (!state) {
item = names;
while (item != NULL) {
if (item->name != NULL) {
free(item->name);
item->name = NULL;
}
t_item = item;
item = item->next;
t_item->next = NULL;
free(t_item);
}
last_item = names = NULL;
char matchtext[256], absdir[256], tmppath[256], prefix[256];
prefix[0] = '\0';
char *ptr = rindex(text+1, '/');
if (ptr != NULL) {
strncpy(prefix, text, ptr-text+1);
prefix[ptr-text+1] = '\0';
}
parsepath(text, absdir, matchtext);
/* check if we've got a dir already */
NXMDisableErrorReporting();
strcpy(tmppath, absdir);
strcat(tmppath, "/");
strcat(tmppath, matchtext);
status = NXopengrouppath(the_fileId, tmppath);
if (status == NX_OK) {
strcpy(absdir, tmppath);
strcpy(matchtext, "");
if (strlen(text) > 0 && text[strlen(text)-1] != '/') {
strcpy(prefix, text);
strcat(prefix, "/");
}
} else {
/* if not go into the dir part */
status = NXopengrouppath(the_fileId, absdir);
}
NXMEnableErrorReporting();
if (status == NX_ERROR)
return NULL;
if (NXinitgroupdir(the_fileId) != NX_OK)
return NULL;
do {
status =
NXgetnextentry(the_fileId, name, nxclass, &dataType);
if (status == NX_ERROR)
break;
if (status == NX_OK) {
if (strncmp(nxclass, "CDF", 3) == 0) {
;
} else if (strncmp(name, matchtext, strlen(matchtext)) == 0) {
item = (struct name_item *)
malloc(sizeof(struct name_item));
item->name = (char *)calloc(256, 1);
strcpy(item->name, prefix);
strcat(item->name, name);
if (strcmp(nxclass, "SDS") != 0) {
strcat(item->name, "/");
}
item->next = NULL;
if (last_item == NULL) {
names = item;
} else {
last_item->next = item;
}
last_item = item;
}
}
} while (status == NX_OK);
NXopengrouppath(the_fileId, path);
last_item = names;
}
if (last_item != NULL) {
res = strdup(last_item->name);
last_item = last_item->next;
} else {
res = NULL;
}
return res;
}
/**
* Recursively add properties from a nexus file to
* the workspace run.
*
* @param nxfileID :: Nexus file handle to be parsed, just after an NXopengroup
* @param runDetails :: where to add properties
* @param parent_name :: nexus caller name
* @param parent_class :: nexus caller class
* @param level :: current level in nexus tree
*
*/
void LoadHelper::recurseAndAddNexusFieldsToWsRun(NXhandle nxfileID, API::Run& runDetails,
std::string& parent_name, std::string& parent_class, int level)
{
std::string indent_str(level * 2, ' '); // Two space by indent level
// Link ?
// Attributes ?
// Classes
NXstatus getnextentry_status; ///< return status
int datatype; ///< NX data type if a dataset, e.g. NX_CHAR, NX_FLOAT32, see napi.h
char nxname[NX_MAXNAMELEN], nxclass[NX_MAXNAMELEN];
nxname[0] = '0';
nxclass[0] = '0';
bool has_entry = true; // follows getnextentry_status
while (has_entry)
{
getnextentry_status = NXgetnextentry(nxfileID, nxname, nxclass, &datatype);
if (getnextentry_status == NX_OK)
{
g_log.debug() << indent_str << parent_name << "." << nxname << " ; " << nxclass << std::endl;
NXstatus opengroup_status;
NXstatus opendata_status;
if ((opengroup_status = NXopengroup(nxfileID, nxname, nxclass)) == NX_OK)
{
// Go down to one level
std::string p_nxname(nxname); //current names can be useful for next level
std::string p_nxclass(nxclass);
recurseAndAddNexusFieldsToWsRun(nxfileID, runDetails, p_nxname, p_nxclass, level + 1);
NXclosegroup(nxfileID);
} // if(NXopengroup
else if ((opendata_status = NXopendata(nxfileID, nxname)) == NX_OK)
{
//dump_attributes(nxfileID, indent_str);
g_log.debug() << indent_str << nxname << " opened." << std::endl;
if (parent_class == "NXData" || parent_class == "NXMonitor" || std::string(nxname) == "data")
{
g_log.debug() << indent_str << "skipping " << parent_class << " (" << nxname << ")"
<< std::endl;
/* nothing */
}
else
{ // create a property
int rank;
int dims[4];
int type;
dims[0] = dims[1] = dims[2] = dims[3] = 0;
std::string property_name = (parent_name.empty() ? nxname : parent_name + "." + nxname);
g_log.debug() << indent_str << "considering property " << property_name << std::endl;
// Get the value
NXgetinfo(nxfileID, &rank, dims, &type);
// Note, we choose to only build properties on small float arrays
// filter logic is below
bool build_small_float_array = false; // default
if ((type == NX_FLOAT32) || (type == NX_FLOAT64))
{
if ((rank == 1) && (dims[0] <= 9))
{
build_small_float_array = true;
}
else
{
g_log.debug() << indent_str << "ignored multi dimension float data on "
<< property_name << std::endl;
}
}
else if (type != NX_CHAR)
{
if ((rank != 1) || (dims[0] != 1) || (dims[1] != 1) || (dims[2] != 1) || (dims[3] != 1))
{
g_log.debug() << indent_str << "ignored multi dimension data on " << property_name
<< std::endl;
}
}
void *dataBuffer;
NXmalloc(&dataBuffer, rank, dims, type);
if (NXgetdata(nxfileID, dataBuffer) != NX_OK)
{
NXfree(&dataBuffer);
throw std::runtime_error("Cannot read data from NeXus file");
}
if (type == NX_CHAR)
{
std::string property_value((const char *) dataBuffer);
if (boost::algorithm::ends_with(property_name, "_time"))
{
// That's a time value! Convert to Mantid standard
property_value = dateTimeInIsoFormat(property_value);
}
runDetails.addProperty(property_name, property_value);
}
else if ((type == NX_FLOAT32) || (type == NX_FLOAT64) || (type == NX_INT16)
|| (type == NX_INT32) || (type == NX_UINT16))
{
// Look for "units"
NXstatus units_status;
char units_sbuf[NX_MAXNAMELEN];
int units_len = NX_MAXNAMELEN;
int units_type = NX_CHAR;
units_status = NXgetattr(nxfileID, const_cast<char*>("units"), (void *) units_sbuf,
&units_len, &units_type);
if (units_status != NX_ERROR)
{
g_log.debug() << indent_str << "[ " << property_name << " has unit " << units_sbuf
<< " ]" << std::endl;
}
if ((type == NX_FLOAT32) || (type == NX_FLOAT64))
{
// Mantid numerical properties are double only.
double property_double_value = 0.0;
// Simple case, one value
if (dims[0] == 1)
{
if (type == NX_FLOAT32)
{
property_double_value = *((float*) dataBuffer);
}
else if (type == NX_FLOAT64)
{
property_double_value = *((double*) dataBuffer);
}
if (units_status != NX_ERROR)
runDetails.addProperty(property_name, property_double_value,
std::string(units_sbuf));
else
runDetails.addProperty(property_name, property_double_value);
}
else if (build_small_float_array)
{
// An array, converted to "name_index", with index < 10 (see test above)
for (int dim_index = 0; dim_index < dims[0]; dim_index++)
{
if (type == NX_FLOAT32)
{
property_double_value = ((float*) dataBuffer)[dim_index];
}
else if (type == NX_FLOAT64)
{
property_double_value = ((double*) dataBuffer)[dim_index];
}
std::string indexed_property_name = property_name + std::string("_")
+ boost::lexical_cast<std::string>(dim_index);
if (units_status != NX_ERROR)
runDetails.addProperty(indexed_property_name, property_double_value,
std::string(units_sbuf));
else
runDetails.addProperty(indexed_property_name, property_double_value);
}
}
}
else
{
// int case
int property_int_value = 0;
if (type == NX_INT16)
{
property_int_value = *((short int*) dataBuffer);
}
else if (type == NX_INT32)
{
property_int_value = *((int*) dataBuffer);
}
else if (type == NX_UINT16)
{
property_int_value = *((short unsigned int*) dataBuffer);
}
if (units_status != NX_ERROR)
runDetails.addProperty(property_name, property_int_value, std::string(units_sbuf));
else
runDetails.addProperty(property_name, property_int_value);
} // if (type==...
}
else
{
g_log.debug() << indent_str << "unexpected data on " << property_name << std::endl;
} // test on nxdata type
NXfree(&dataBuffer);
dataBuffer = NULL;
} // if (parent_class == "NXData" || parent_class == "NXMonitor") else
NXclosedata(nxfileID);
}
else
{
g_log.debug() << indent_str << "unexpected status (" << opendata_status << ") on " << nxname
<< std::endl;
}
}
else if (getnextentry_status == NX_EOD)
{
g_log.debug() << indent_str << "End of Dir" << std::endl;
has_entry = false; // end of loop
}
else
{
g_log.debug() << indent_str << "unexpected status (" << getnextentry_status << ")"
<< std::endl;
has_entry = false; // end of loop
}
} // while
} // recurseAndAddNexusFieldsToWsRun
/** Get all the Nexus entry types for a file
*
* Try to open named Nexus file and return all entries plus the definition found for each.
* If definition not found, try and return "analysis" field (Muon V1 files)
* Closes file on exit.
*
* @param fileName :: file to open
* @param entryName :: vector that gets filled with strings with entry names
* @param definition :: vector that gets filled with the "definition" or "analysis" string.
* @return count of entries if OK, -1 failed to open file.
*/
int getNexusEntryTypes(const std::string& fileName, std::vector<std::string>& entryName,
std::vector<std::string>& definition )
{
//
//
NXhandle fileH;
NXaccess mode= NXACC_READ;
NXstatus stat=NXopen(fileName.c_str(), mode, &fileH);
if(stat==NX_ERROR) return(-1);
//
entryName.clear();
definition.clear();
char *nxname,*nxclass;
int nxdatatype;
nxname= new char[NX_MAXNAMELEN];
nxclass = new char[NX_MAXNAMELEN];
int rank,dims[2],type;
//
// Loop through all entries looking for the definition section in each (or analysis for MuonV1)
//
std::vector<std::string> entryList;
while( ( stat=NXgetnextentry(fileH,nxname,nxclass,&nxdatatype) ) == NX_OK )
{
std::string nxc(nxclass);
if(nxc.compare("NXentry")==0)
entryList.push_back(nxname);
}
// for each entry found, look for "analysis" or "definition" text data fields and return value plus entry name
for(size_t i=0;i<entryList.size();i++)
{
//
stat=NXopengroup(fileH,entryList[i].c_str(),"NXentry");
// loop through field names in this entry
while( ( stat=NXgetnextentry(fileH,nxname,nxclass,&nxdatatype) ) == NX_OK )
{
std::string nxc(nxclass),nxn(nxname);
// if a data field
if(nxc.compare("SDS")==0)
// if one of the two names we are looking for
if(nxn.compare("definition")==0 || nxn.compare("analysis")==0)
{
NXopendata(fileH,nxname);
stat=NXgetinfo(fileH,&rank,dims,&type);
if(stat==NX_ERROR)
continue;
char* value=new char[dims[0]+1];
stat=NXgetdata(fileH,value);
if(stat==NX_ERROR)
continue;
value[dims[0]]='\0';
// return e.g entryName "analysis"/definition "muonTD"
definition.push_back(value);
entryName.push_back(entryList[i]);
delete[] value;
NXclosegroup(fileH); // close data group, then entry
stat=NXclosegroup(fileH);
break;
}
}
}
stat=NXclose(&fileH);
delete[] nxname;
delete[] nxclass;
return(static_cast<int>(entryName.size()));
}
/** 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;
}
