/**************************************************************************** * NCSA HDF * * Scientific Data Technologies * * National Center for Supercomputing Applications * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf/COPYING file. * * * ****************************************************************************/ #include "H5DS.h" #include "H5LT.h" #include /*------------------------------------------------------------------------- * Function: H5DSset_scale * * Purpose: write the standard attributes for a Dimension Scale dataset; * optionally set its name * * Return: Success: SUCCESS, Failure: FAIL * * Programmer: pvn@ncsa.uiuc.edu * * Date: January 04, 2005 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5DSset_scale(hid_t did, char *dimname) { int has_dimlist; /*------------------------------------------------------------------------- * check if the dataset is a dataset wich has references to dimension scales *------------------------------------------------------------------------- */ /* try to find the attribute "DIMENSION_LIST" on the >>data<< dataset */ if ((has_dimlist = H5LT_find_attribute(did,DIMENSION_LIST))<0) return FAIL; if (has_dimlist == 1) return FAIL; /*------------------------------------------------------------------------- * write the standard attributes for a Dimension Scale dataset *------------------------------------------------------------------------- */ if (H5LT_set_attribute_string(did,"CLASS",DIMENSION_SCALE_CLASS)<0) return FAIL; if (dimname!=NULL) { if (H5LT_set_attribute_string(did,"NAME",dimname)<0) return FAIL; } return SUCCESS; } /*------------------------------------------------------------------------- * Function: H5DSattach_scale * * Purpose: attach a DS with DSID to the IDX dimension of the existing * dataset DID * * Return: * Success: SUCCESS: both the DS and the dataset exist * Failure: FAIL: if either one of them does not exist * * Programmer: pvn@ncsa.uiuc.edu * * Date: December 20, 2004 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) { int has_dimlist; int has_reflist; int is_ds; hssize_t nelmts; hid_t sid; /* space ID */ hid_t tid; /* attribute type ID */ hid_t aid; /* attribute ID */ int rank; /* rank of dataset */ hsize_t *dims; /* dimension of the "REFERENCE_LIST" array */ ds_list_t dsl; /* attribute data in the DS pointing to the dataset */ ds_list_t *dsbuf; /* array of attribute data in the DS pointing to the dataset */ hobj_ref_t ref; /* reference to the DS */ hvl_t *buf; /* VL buffer to store in the attribute */ int i, len; /*------------------------------------------------------------------------- * verify that the datasets are valid *------------------------------------------------------------------------- */ /* the dataset cannot be a DS dataset */ if ((H5DSis_scale(did))==1) return FAIL; /*------------------------------------------------------------------------- * The dataset may or may not have the associated DS attribute * First we try to open to see if it is already there; if not, it is created. * If it exists, the array of references is extended to hold the reference * to the new DS *------------------------------------------------------------------------- */ /* get dataset space */ if ((sid = H5Dget_space(did))<0) goto out; /* get rank */ if ((rank=H5Sget_simple_extent_ndims(sid))<0) goto out; /* close dataset space */ if (H5Sclose(sid)<0) goto out; /*------------------------------------------------------------------------- * two references are created: one to the DS, saved in "DIMENSION_LIST" * and one to the dataset, saved in "REFERENCE_LIST" *------------------------------------------------------------------------- */ /* create a reference for the >>DS<< dataset */ if (H5Rcreate(&ref,dsid,".",H5R_OBJECT,-1)<0) goto out; /* create a reference for the >>data<< dataset */ if (H5Rcreate(&dsl.ref,did,".",H5R_OBJECT,-1)<0) goto out; /* try to find the attribute "DIMENSION_LIST" on the >>data<< dataset */ if ((has_dimlist = H5LT_find_attribute(did,DIMENSION_LIST))<0) return FAIL; /*------------------------------------------------------------------------- * it does not exist. we create the attribute and its reference data *------------------------------------------------------------------------- */ if (has_dimlist == 0) { /* create one entry array */ dims = (hsize_t*) malloc (1 * sizeof (hsize_t)); if (dims == NULL) goto out; dims[0] = rank; /* space for the attribute */ if ((sid = H5Screate_simple(1,dims,NULL))<0) goto out; /* create the type for the attribute "DIMENSION_LIST" */ if ((tid = H5Tvlen_create(H5T_STD_REF_OBJ))<0) goto out; /* create the attribute */ if ((aid = H5Acreate(did,DIMENSION_LIST,tid,sid,H5P_DEFAULT))<0) goto out; /* allocate and initialize the VL */ buf = (hvl_t*)malloc((size_t)rank * sizeof(hvl_t)); if (buf == NULL) goto out; for(i=0; i 0 ) { buf[i].len++; len = buf[i].len; buf[i].p = realloc( buf[i].p, len * sizeof(hobj_ref_t)); ((hobj_ref_t *)buf[i].p)[ len-1 ] = ref; } else { /* store the REF information in the index of the dataset that has the DS */ buf[idx].len = 1; buf[idx].p = malloc( 1 * sizeof(hobj_ref_t)); ((hobj_ref_t *)buf[idx].p)[0] = ref; } } } /* write the attribute with the new references */ if (H5Awrite(aid,tid,buf)<0) goto out; /* close */ if (H5Dvlen_reclaim(tid,sid,H5P_DEFAULT,buf)<0) goto out; if (H5Sclose(sid)<0) goto out; if (H5Tclose(tid)<0) goto out; if (H5Aclose(aid)<0) goto out; if (buf) free(buf); } /* has_dimlist */ /*------------------------------------------------------------------------- * save DS info on the >>DS<< dataset *------------------------------------------------------------------------- */ /* try to find the attribute "REFERENCE_LIST" on the >>DS<< dataset */ if ((has_reflist = H5LT_find_attribute(dsid,REFERENCE_LIST))<0) goto out; /*------------------------------------------------------------------------- * it does not exist. we create the attribute and its reference data *------------------------------------------------------------------------- */ if (has_reflist == 0) { /* create one entry array */ dims = (hsize_t*) malloc (1 * sizeof (hsize_t)); if (dims == NULL) goto out; dims[0] = 1; /* space for the attribute */ if ((sid = H5Screate_simple(1,dims,NULL))<0) goto out; /* create the compound datatype for the attribute "REFERENCE_LIST" */ if ((tid = H5Tcreate(H5T_COMPOUND,sizeof(ds_list_t)))<0) goto out; /* insert reference field */ if (H5Tinsert(tid,"dataset",HOFFSET(ds_list_t,ref),H5T_STD_REF_OBJ)<0) goto out; /* insert dimension idx of the dataset field */ if (H5Tinsert(tid,"dimension",HOFFSET(ds_list_t,dim_idx),H5T_NATIVE_INT)<0) goto out; /* create the attribute */ if ((aid = H5Acreate(dsid,REFERENCE_LIST,tid,sid,H5P_DEFAULT))<0) goto out; /* store the IDX information */ dsl.dim_idx = idx; /* write the attribute with the reference */ if (H5Awrite(aid,tid,&dsl)<0) goto out; /* close */ if (H5Sclose(sid)<0) goto out; if (H5Tclose(tid)<0) goto out; if (H5Aclose(aid)<0) goto out; if (dims) free(dims); } /*------------------------------------------------------------------------- * the "REFERENCE_LIST" array already exists, open it and extend it *------------------------------------------------------------------------- */ else if ( has_reflist == 1 ) { if ((aid = H5Aopen_name(dsid,REFERENCE_LIST))<0) goto out; if ((tid = H5Aget_type(aid))<0) goto out; /* get and save the old reference(s) */ if ((sid = H5Aget_space(aid))<0) goto out; if ((nelmts = H5Sget_simple_extent_npoints(sid))<0) goto out; nelmts++; dsbuf = malloc((size_t)nelmts * sizeof(ds_list_t)); if (dsbuf == NULL) goto out; if (H5Aread(aid,tid,dsbuf)<0) goto out; if (H5Sclose(sid)<0) goto out; /* the attribute must be deleted, in order to the new one can reflect the changes*/ if (H5Adelete(dsid,REFERENCE_LIST)<0) goto out; /* store the IDX information (index of the dataset that has the DS) */ dsl.dim_idx = idx; dsbuf[nelmts-1] = dsl; /* create a new data space for the new references array */ if ((sid = H5Screate_simple(1,&nelmts,NULL))<0) goto out; /* create the attribute again with the changes of space */ if ((aid = H5Acreate(dsid,REFERENCE_LIST,tid,sid,H5P_DEFAULT))<0) goto out; /* write the attribute with the new references */ if (H5Awrite(aid,tid,dsbuf)<0) goto out; /* close */ if (H5Sclose(sid)<0) goto out; if (H5Tclose(tid)<0) goto out; if (H5Aclose(aid)<0) goto out; if (dsbuf) free(dsbuf); } /* has_dimlist */ /*------------------------------------------------------------------------- * write the standard attributes for a Dimension Scale dataset *------------------------------------------------------------------------- */ if ((is_ds=H5DSis_scale(dsid))<0) return FAIL; if (is_ds == 0 ) { if (H5LT_set_attribute_string(dsid,"CLASS",DIMENSION_SCALE_CLASS)<0) return FAIL; } return SUCCESS; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Sclose(sid); H5Aclose(aid); H5Tclose(tid); } H5E_END_TRY; return FAIL; } /*------------------------------------------------------------------------- * Function: H5DSdetach_scale * * Purpose: detach a DS with DSID to the IDX dimension of the existing * dataset DID * * Return: * Success: SUCCESS: both the DS and the dataset exist * Failure: FAIL: if either one of them does not exist * * Programmer: pvn@ncsa.uiuc.edu * * Date: December 20, 2004 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) { int has_dimlist; int has_reflist; hssize_t nelmts; hid_t dsid_j; /* DS dataset ID in DIMENSION_LIST */ hid_t sid; /* space ID */ hid_t tid; /* attribute type ID */ hid_t aid; /* attribute ID */ int rank; /* rank of dataset */ ds_list_t *dsbuf; /* array of attribute data in the DS pointing to the dataset */ hobj_ref_t ref; /* reference to the DS */ hvl_t *buf; /* VL buffer to store in the attribute */ unsigned i, j; H5G_stat_t sb1, sb2, sb3, sb4; int found_dset=0, found_ds=0; /*------------------------------------------------------------------------- * check if the dataset is a DS dataset *------------------------------------------------------------------------- */ if ((H5DSis_scale(did))==1) return FAIL; /*------------------------------------------------------------------------- * Find "DIMENSION_LIST" *------------------------------------------------------------------------- */ /* try to find the attribute "DIMENSION_LIST" on the >>data<< dataset */ if ((has_dimlist = H5LT_find_attribute(did,DIMENSION_LIST))<0) goto out; if (has_dimlist == 0) goto out; /* get dataset space */ if ((sid = H5Dget_space(did))<0) goto out; /* get rank */ if ((rank=H5Sget_simple_extent_ndims(sid))<0) goto out; /* close dataset space */ if (H5Sclose(sid)<0) goto out; /*------------------------------------------------------------------------- * open it, and delete the reference *------------------------------------------------------------------------- */ else if ( has_dimlist == 1 ) { if ((aid = H5Aopen_name(did,DIMENSION_LIST))<0) goto out; if ((tid = H5Aget_type(aid))<0) goto out; if ((sid = H5Aget_space(aid))<0) goto out; /* allocate and initialize the VL */ buf = (hvl_t*)malloc((size_t)rank * sizeof(hvl_t)); if (buf == NULL) goto out; /* read */ if (H5Aread(aid,tid,buf)<0) goto out; for(i=0; i<(unsigned int)rank; i++) { if (idx == i ) { /* reset */ if ( buf[i].len > 0 ) { for(j=0; j>DS<< dataset *------------------------------------------------------------------------- */ /* try to find the attribute "REFERENCE_LIST" on the >>DS<< dataset */ if ((has_reflist = H5LT_find_attribute(dsid,REFERENCE_LIST))<0) goto out; /*------------------------------------------------------------------------- * it does not exist *------------------------------------------------------------------------- */ if (has_reflist == 0) goto out; /*------------------------------------------------------------------------- * the "REFERENCE_LIST" array exists, update *------------------------------------------------------------------------- */ else if ( has_reflist == 1 ) { if ((aid = H5Aopen_name(dsid,REFERENCE_LIST))<0) goto out; if ((tid = H5Aget_type(aid))<0) goto out; /* get and save the old reference(s) */ if ((sid = H5Aget_space(aid))<0) goto out; if ((nelmts = H5Sget_simple_extent_npoints(sid))<0) goto out; dsbuf = malloc((size_t)nelmts * sizeof(ds_list_t)); if (dsbuf == NULL) goto out; if (H5Aread(aid,tid,dsbuf)<0) goto out; for(i=0; i>data<< dataset */ if ((has_labels = H5LT_find_attribute(did,DIMENSION_LABELS))<0) return FAIL; /* get dataset space */ if ((sid = H5Dget_space(did))<0) goto out; /* get rank */ if ((rank=H5Sget_simple_extent_ndims(sid))<0) goto out; /* close dataset space */ if (H5Sclose(sid)<0) goto out; /*------------------------------------------------------------------------- * make the attribute and insert label *------------------------------------------------------------------------- */ if (has_labels == 0) { dims[0] = rank; /* space for the attribute */ if ((sid = H5Screate_simple(1,dims,NULL))<0) goto out; /* create the datatype */ if ((tid = H5Tcopy(H5T_C_S1))<0) goto out; if (H5Tset_size(tid,H5T_VARIABLE)<0) goto out; /* create the attribute */ if ((aid = H5Acreate(did,DIMENSION_LABELS,tid,sid,H5P_DEFAULT))<0) goto out; /* allocate and initialize */ buf = (char **)malloc((size_t)rank * sizeof(char *)); if (buf == NULL) goto out; for(i=0; i<(unsigned int)rank; i++) buf[i] = NULL; /* store the label information in the required index */ buf[idx] = label; /* write the attribute with the label */ if (H5Awrite(aid,tid,buf)<0) goto out; /* close */ if (H5Sclose(sid)<0) goto out; if (H5Tclose(tid)<0) goto out; if (H5Aclose(aid)<0) goto out; if (buf) free(buf); } /*------------------------------------------------------------------------- * just insert label *------------------------------------------------------------------------- */ else { if ((aid = H5Aopen_name(did,DIMENSION_LABELS))<0) goto out; if ((tid = H5Aget_type(aid))<0) goto out; if ((sid = H5Aget_space(aid))<0) goto out; /* allocate and initialize */ buf = (char **)malloc((size_t)rank * sizeof(char *)); if (buf == NULL) goto out; /* read */ if (H5Aread(aid,tid,buf)<0) goto out; for(i=0; i<(unsigned int)rank; i++) { if (idx == i ) { /* store the label information in the required index */ buf[idx] = label; } } /* write the attribute with the new references */ if (H5Awrite(aid,tid,buf)<0) goto out; /* close */ if (H5Sclose(sid)<0) goto out; if (H5Tclose(tid)<0) goto out; if (H5Aclose(aid)<0) goto out; if (buf) free(buf); } return SUCCESS; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Sclose(sid); H5Aclose(aid); H5Tclose(tid); } H5E_END_TRY; return FAIL; } /*------------------------------------------------------------------------- * Function: H5DSget_label * * Purpose: get a label for dimension IDX * * Return: Success: SUCCESS, Failure: FAIL * * Programmer: pvn@ncsa.uiuc.edu * * Date: January 11, 2005 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5DSget_label(hid_t did, char *label, unsigned int idx) { int has_labels; hid_t sid; /* space ID */ hid_t tid; /* attribute type ID */ hid_t aid; /* attribute ID */ int rank; /* rank of dataset */ char **buf=NULL; /* buffer to store in the attribute */ unsigned int i; /* try to find the attribute "DIMENSION_LABELS" on the >>data<< dataset */ if ((has_labels = H5LT_find_attribute(did,DIMENSION_LABELS))<0) return FAIL; if (has_labels == 0) return FAIL; /* get dataset space */ if ((sid = H5Dget_space(did))<0) goto out; /* get rank */ if ((rank=H5Sget_simple_extent_ndims(sid))<0) goto out; /* close dataset space */ if (H5Sclose(sid)<0) goto out; /*------------------------------------------------------------------------- * make the attribute and insert label *------------------------------------------------------------------------- */ if (has_labels == 1) { if ((aid = H5Aopen_name(did,DIMENSION_LABELS))<0) goto out; if ((tid = H5Aget_type(aid))<0) goto out; if ((sid = H5Aget_space(aid))<0) goto out; /* allocate and initialize */ buf = (char **)malloc((size_t)rank * sizeof(char *)); if (buf == NULL) goto out; /* read */ if (H5Aread(aid,tid,buf)<0) goto out; for(i=0; i<(unsigned int)rank; i++) { if (idx == i ) { /* store the label information in the required index */ strcpy(label,buf[idx]); } } /* close */ if (H5Sclose(sid)<0) goto out; if (H5Tclose(tid)<0) goto out; if (H5Aclose(aid)<0) goto out; if (buf) free(buf); } return SUCCESS; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Sclose(sid); H5Aclose(aid); H5Tclose(tid); } H5E_END_TRY; return FAIL; } /*------------------------------------------------------------------------- * Function: H5DSget_scale_name * * Purpose: get the name of a DS * * Return: Success: SUCCESS, Failure: FAIL * * Programmer: pvn@ncsa.uiuc.edu * * Date: January 04, 2005 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5DSget_scale_name(hid_t did, char *buf) { int has_name; /*------------------------------------------------------------------------- * check if the dataset is a DS dataset *------------------------------------------------------------------------- */ if ((H5DSis_scale(did))<=0) return FAIL; /*------------------------------------------------------------------------- * check if the DS has a name *------------------------------------------------------------------------- */ /* try to find the attribute "NAME" on the >>DS<< dataset */ if ((has_name = H5LT_find_attribute(did,"NAME"))<0) return FAIL; if (has_name == 1) { /* get the attribute */ if (H5LT_get_attribute_disk(did,"NAME",buf)<0) return FAIL; } return SUCCESS; } /*------------------------------------------------------------------------- * Function: H5DSis_scale * * Purpose: check if the dataset DID is a dimension scale * * Return: 1, is, 0, not, FAIL, error * * Programmer: pvn@ncsa.uiuc.edu * * Date: January 04, 2005 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5DSis_scale(hid_t did) { hid_t tid; /* attribute type ID */ hid_t aid; /* attribute ID */ herr_t has_class; /* has the "CLASS" attribute */ herr_t is_ds; /* boolean return value */ char buf[20]; /* try to find the attribute "CLASS" on the dataset */ if ((has_class = H5LT_find_attribute(did,"CLASS"))<0) return FAIL; if (has_class == 0) is_ds = 0; else if (has_class == 1 ) { if ((aid = H5Aopen_name(did,"CLASS"))<0) goto out; if ((tid = H5Aget_type(aid))<0) goto out; if (H5Aread(aid,tid,buf)<0) goto out; if( strcmp(buf,DIMENSION_SCALE_CLASS)==0) is_ds = 1; else is_ds = 0; if (H5Tclose(tid)<0) goto out; if (H5Aclose(aid)<0) goto out; } return is_ds; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Aclose(aid); H5Tclose(tid); } H5E_END_TRY; return FAIL; } /*------------------------------------------------------------------------- * Function: H5DShas_scale * * Purpose: check if the dataset DID has associated * valid dimension scales; valid means the dimension scales exist and they * are as many as the dataset rank * * Return: 1, has, 0, not, FAIL, error * * Programmer: pvn@ncsa.uiuc.edu * * Date: January 04, 2005 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5DShas_scale(hid_t did) { int has_dimlist; /* do we have the "DIMENSION_LIST" attribute */ hid_t sid; /* space ID */ hid_t dsid; /* DS dataset ID */ hid_t dssid; /* DS space ID */ hid_t tid; /* attribute type ID */ hid_t aid; /* attribute ID */ hssize_t dsnelmts; /* size of a dimension scale array */ herr_t has_ds; /* boolean return value */ int rank; /* rank of dataset */ hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ hvl_t *buf; /* VL buffer stored in the attribute */ hobj_ref_t ref; /* reference to the DS */ int i; has_ds = 1; /* get dataset space */ if ((sid = H5Dget_space(did))<0) goto out; /* get rank */ if ((rank=H5Sget_simple_extent_ndims(sid))<0) goto out; /* get dimensions of dataset */ if (H5Sget_simple_extent_dims(sid,dims,NULL)<0) goto out; /* close the dataspace id */ if (H5Sclose(sid)<0) goto out; /* try to find the attribute "DIMENSION_LIST" on the >>data<< dataset */ if ((has_dimlist = H5LT_find_attribute(did,DIMENSION_LIST))<0) goto out; if (has_dimlist == 0) has_ds = 0; else if (has_dimlist == 1 ) { if ((aid = H5Aopen_name(did,DIMENSION_LIST))<0) goto out; if ((tid = H5Aget_type(aid))<0) goto out; if ((sid = H5Aget_space(aid))<0) goto out; /* allocate and initialize the VL */ buf = (hvl_t*)malloc((size_t)rank * sizeof(hvl_t)); if (buf == NULL) goto out; /* read */ if (H5Aread(aid,tid,buf)<0) goto out; /*------------------------------------------------------------------------- * check if we have at least one entry for each dimension *------------------------------------------------------------------------- */ for(i=0; i