/** * 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; }