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implement reading/writing HDF5 object references in attribute
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h5writeAttribute(object_to_reference, object, attribute_name) will write
a reference to object_to_reference into attribute_name of object.
Similarly, if attr is an attribute containing an object reference,
H5Aread(attr) will return an H5IdComponent of the referenced object.
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@ilia-kats
ilia-kats committed Sep 10, 2021
1 parent 996bbfb commit d045d45
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Showing 7 changed files with 109 additions and 47 deletions.
6 changes: 5 additions & 1 deletion R/H5A.R
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Expand Up @@ -236,7 +236,11 @@ H5Aread <- function(h5attribute, buf = NULL, bit64conversion) {
stop("install package 'bit64' before using bit64conversion='bit64'")
}

return(.Call("_H5Aread", h5attribute@ID, buf, bit64conv, PACKAGE='rhdf5'))
rval = .Call("_H5Aread", h5attribute@ID, buf, bit64conv, PACKAGE='rhdf5')
if (is(rval, "H5IdComponent"))
rval@native <- h5attribute@native

return(rval)
}

#' Write data to an HDF5 attribute
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1 change: 1 addition & 0 deletions R/h5create.R
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Expand Up @@ -513,6 +513,7 @@ h5createAttribute <- function(obj, attr, dims, maxdims = dims, file,
H5Tset_size(tid, size) # NULL = variable.
tid
},
H5IdComponent=h5constants$H5T["H5T_STD_REF_OBJ"],
{ stop("datatype ",storage.mode," not yet implemented. Try 'double', 'integer', or 'character'.") } )
} else {
stop("Can not create dataset. 'storage.mode' has to be a character.")
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10 changes: 8 additions & 2 deletions R/h5writeAttr.R
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Expand Up @@ -17,7 +17,10 @@
#' @export
h5writeAttribute <- function(attr, h5obj, name, cset=c("ASCII", "UTF8"), variableLengthString=FALSE, asScalar=FALSE) {
h5checktype(h5obj, "object")
res <- UseMethod("h5writeAttribute")
if (is(attr, "H5IdComponent"))
res <- h5writeAttribute.array(attr, h5obj, name, asScalar=TRUE)
else
res <- UseMethod("h5writeAttribute")
invisible(res)
}

Expand Down Expand Up @@ -56,7 +59,10 @@ h5writeAttribute.array <- function(attr, h5obj, name, cset=c("ASCII", "UTF8"), v
if (H5Aexists(h5obj, name)) {
H5Adelete(h5obj, name)
}
h5createAttribute(h5obj, name, dims = dims, storage.mode = storage.mode(attr), size = size, cset=match.arg(cset))
storagemode <- storage.mode(attr)
if (storagemode == "S4" && is(attr, "H5IdComponent"))
storagemode <- "H5IdComponent"
h5createAttribute(h5obj, name, dims = dims, storage.mode = storagemode, size = size, cset=match.arg(cset))
h5attr <- H5Aopen(h5obj, name)

DimMem <- dim(attr)
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117 changes: 77 additions & 40 deletions src/H5A.c
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Expand Up @@ -281,6 +281,25 @@ SEXP H5Aread_helper_STRING(hid_t attr_id, hsize_t n, SEXP Rdim, SEXP _buf, hid_t
return(Rval);
}

SEXP H5Aread_helper_REFERENCE(hid_t attr_id, hsize_t n, SEXP Rdim, SEXP _buf, hid_t dtype_id) {
hobj_ref_t references[n];
herr_t err = H5Aread(attr_id, dtype_id, &references);
if (err < 0) {
error("could not read attribute");
return R_NilValue;
}
if (!H5Tequal(dtype_id, H5T_STD_REF_OBJ)) {
error("Reading references of type %s is not yet implemented", getReferenceType(dtype_id));
return R_NilValue;
}
hid_t obj = H5Rdereference2(attr_id, H5P_DEFAULT, H5R_OBJECT, &references);
SEXP hid = PROTECT(HID_2_STRSXP(obj));
SEXP Rval = PROTECT(R_do_new_object(R_getClassDef("H5IdComponent")));
R_do_slot_assign(Rval, mkString("ID"), hid);
UNPROTECT(2);
return Rval;
}

/* SEXP H5Dread_helper_COMPOUND(hid_t dataset_id, hid_t file_space_id, hid_t mem_space_id, hsize_t n, SEXP Rdim, SEXP _buf, */
/* hid_t dtype_id, hid_t cpdType, int cpdNField, char ** cpdField, int compoundAsDataFrame ) { */
/* hid_t mem_type_id = -1; */
Expand Down Expand Up @@ -361,14 +380,16 @@ SEXP H5Aread_helper(hid_t attr_id, hsize_t n, SEXP Rdim, SEXP _buf, int bit64con
case H5T_STRING: {
Rval = H5Aread_helper_STRING(attr_id, n, Rdim, _buf, dtype_id);
} break;
case H5T_REFERENCE: {
Rval = H5Aread_helper_REFERENCE(attr_id, n, Rdim, _buf, dtype_id);
} break;
case H5T_COMPOUND:
/* { */
/* Rval = H5Aread_helper_COMPOUND(attr_id, n, Rdim, _buf, dtype_id); */
/* } break; */
case H5T_TIME:
case H5T_BITFIELD:
case H5T_OPAQUE:
case H5T_REFERENCE:
case H5T_ENUM:
case H5T_VLEN:
case H5T_ARRAY:
Expand Down Expand Up @@ -447,57 +468,73 @@ SEXP _H5Aread( SEXP _attr_id, SEXP _buf, SEXP _bit64conversion ) {

/* herr_t H5Awrite(hid_t attr_id, hid_t mem_type_id, const void *buf ) */
SEXP _H5Awrite( SEXP _attr_id, SEXP _buf) {
hid_t attr_id = STRSXP_2_HID( _attr_id );
hid_t mem_type_id;
hid_t attr_id = STRSXP_2_HID( _attr_id );
hid_t mem_type_id;

const void * buf;
if (TYPEOF(_buf) == INTSXP) {
mem_type_id = H5T_NATIVE_INT;
buf = INTEGER(_buf);
} else {
if (TYPEOF(_buf) == REALSXP) {
mem_type_id = H5T_NATIVE_DOUBLE;
buf = REAL(_buf);
} else {
if (TYPEOF(_buf) == STRSXP) {
const void * buf;
static const char* classname[] = {"H5IdComponent", ""};
if (TYPEOF(_buf) == INTSXP) {
mem_type_id = H5T_NATIVE_INT;
buf = INTEGER(_buf);
} else if (TYPEOF(_buf) == REALSXP) {
mem_type_id = H5T_NATIVE_DOUBLE;
buf = REAL(_buf);
} else if (TYPEOF(_buf) == STRSXP) {
mem_type_id = H5Aget_type(attr_id);
size_t stsize;
if (H5Tis_variable_str(mem_type_id)) {
const char ** strbuf = (const char **)R_alloc(LENGTH(_buf),sizeof(const char*));
for (int i=0; i < LENGTH(_buf); i++) {
const char ** strbuf = (const char **)R_alloc(LENGTH(_buf),sizeof(const char*));
for (int i=0; i < LENGTH(_buf); i++) {
strbuf[i] = CHAR(STRING_ELT(_buf,i));
}
buf = strbuf;
}
buf = strbuf;
} else {
stsize = H5Tget_size( mem_type_id );
char * strbuf = (char *)R_alloc(LENGTH(_buf),stsize);
int z=0;
int j;
for (int i=0; i < LENGTH(_buf); i++) {
stsize = H5Tget_size( mem_type_id );
char * strbuf = (char *)R_alloc(LENGTH(_buf),stsize);
int z=0;
int j;
for (int i=0; i < LENGTH(_buf); i++) {
for (j=0; (j < LENGTH(STRING_ELT(_buf,i))) & (j < (stsize-1)); j++) {
strbuf[z++] = CHAR(STRING_ELT(_buf,i))[j];
strbuf[z++] = CHAR(STRING_ELT(_buf,i))[j];
}
for (; j < stsize; j++) {
strbuf[z++] = '\0';
strbuf[z++] = '\0';
}
}
buf = strbuf;
}
buf = strbuf;
}
} else {
mem_type_id = -1;
warning("Writing of this type of attribute data not supported.");
SEXP Rval = R_NilValue;
return Rval;
}
} else if (TYPEOF(_buf) == S4SXP && R_check_class_etc(_buf, classname) >= 0) {
SEXP _obj_id = R_do_slot(_buf, mkString("ID"));
hid_t obj_id = STRSXP_2_HID(_obj_id);
ssize_t namelength = H5Iget_name(obj_id, NULL, 0);
if (namelength > 0) {
char *name = R_alloc(sizeof(char), namelength + 1);
namelength = H5Iget_name(obj_id, name, namelength + 1);
hobj_ref_t *ref = (hobj_ref_t*)R_alloc(sizeof(hobj_ref_t), 1);
herr_t err = H5Rcreate(ref, obj_id, name, H5R_OBJECT, -1);
if (err < 0) {
error("Could not create reference to object.");
return R_NilValue;
}
mem_type_id = H5T_STD_REF_OBJ;
buf = ref;
} else {
error("Object has no name, cannot create a reference");
return R_NilValue;
}
} else {
error("Writing of this type of attribute data not supported.");
SEXP Rval = R_NilValue;
return Rval;
}
}
herr_t herr = 3;
herr = H5Awrite(attr_id, mem_type_id, buf );
SEXP Rval;
PROTECT(Rval = allocVector(INTSXP, 1));
INTEGER(Rval)[0] = herr;
UNPROTECT(1);
return Rval;

herr_t herr = 3;
herr = H5Awrite(attr_id, mem_type_id, buf );
SEXP Rval;
PROTECT(Rval = allocVector(INTSXP, 1));
INTEGER(Rval)[0] = herr;
UNPROTECT(1);
return Rval;
}

/* ssize_t H5Aget_name(hid_t attr_id, size_t buf_size, char *buf ) */
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10 changes: 6 additions & 4 deletions src/H5constants.c
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Expand Up @@ -97,7 +97,7 @@ SEXP _H5constants( ) {
const char *name_H5S_SELECT[] = { "H5S_SELECT_SET", "H5S_SELECT_OR", "H5S_SELECT_AND", "H5S_SELECT_XOR", "H5S_SELECT_NOTB", "H5S_SELECT_NOTA"};
addVector_int(i++, Rval, groupnames, "H5S_SELECT", 6, const_H5S_SELECT, name_H5S_SELECT);

hid_t const_H5T[79] = { H5T_IEEE_F32BE, H5T_IEEE_F32LE, H5T_IEEE_F64BE, H5T_IEEE_F64LE,
hid_t const_H5T[] = { H5T_IEEE_F32BE, H5T_IEEE_F32LE, H5T_IEEE_F64BE, H5T_IEEE_F64LE,
H5T_STD_I8BE, H5T_STD_I8LE, H5T_STD_I16BE, H5T_STD_I16LE,
H5T_STD_I32BE, H5T_STD_I32LE, H5T_STD_I64BE, H5T_STD_I64LE,
H5T_STD_U8BE, H5T_STD_U8LE, H5T_STD_U16BE, H5T_STD_U16LE,
Expand All @@ -117,7 +117,8 @@ SEXP _H5constants( ) {
H5T_NATIVE_INT32, H5T_NATIVE_UINT32, H5T_NATIVE_INT_LEAST32, H5T_NATIVE_UINT_LEAST32, H5T_NATIVE_INT_FAST32, H5T_NATIVE_UINT_FAST32,
H5T_NATIVE_INT64, H5T_NATIVE_UINT64, H5T_NATIVE_INT_LEAST64, H5T_NATIVE_UINT_LEAST64, H5T_NATIVE_INT_FAST64, H5T_NATIVE_UINT_FAST64,
H5T_NATIVE_DOUBLE,
H5T_C_S1, H5T_FORTRAN_S1 };
H5T_C_S1, H5T_FORTRAN_S1,
H5T_STD_REF_OBJ, H5T_STD_REF_DSETREG };
/* H5T_UNIX_D32BE, H5T_UNIX_D32LE, H5T_UNIX_D64BE, H5T_UNIX_D64LE, */
/* H5T_C_S1, H5T_FORTRAN_S1, */
/* H5T_INTEL_I8, H5T_INTEL_I16, H5T_INTEL_I32, H5T_INTEL_I64, */
Expand Down Expand Up @@ -154,7 +155,8 @@ SEXP _H5constants( ) {
"H5T_NATIVE_INT32", "H5T_NATIVE_UINT32", "H5T_NATIVE_INT_LEAST32", "H5T_NATIVE_UINT_LEAST32", "H5T_NATIVE_INT_FAST32", "H5T_NATIVE_UINT_FAST32",
"H5T_NATIVE_INT64", "H5T_NATIVE_UINT64", "H5T_NATIVE_INT_LEAST64", "H5T_NATIVE_UINT_LEAST64", "H5T_NATIVE_INT_FAST64", "H5T_NATIVE_UINT_FAST64",
"H5T_NATIVE_DOUBLE",
"H5T_C_S1", "H5T_FORTRAN_S1" };
"H5T_C_S1", "H5T_FORTRAN_S1",
"H5T_STD_REF_OBJ", "H5T_STD_REF_DSETREG" };

/* "H5T_UNIX_D32BE", "H5T_UNIX_D32LE", "H5T_UNIX_D64BE", "H5T_UNIX_D64LE", */
/* "H5T_INTEL_I8", "H5T_INTEL_I16", "H5T_INTEL_I32", "H5T_INTEL_I64", */
Expand All @@ -171,7 +173,7 @@ SEXP _H5constants( ) {
/* "H5T_MIPS_U8", "H5T_MIPS_U16", "H5T_MIPS_U32", "H5T_MIPS_U64", */
/* "H5T_MIPS_F32", "H5T_MIPS_F64" */

addVector_hid(i++, Rval, groupnames, "H5T", 79, const_H5T, name_H5T);
addVector_hid(i++, Rval, groupnames, "H5T", 81, const_H5T, name_H5T);
/* There are more platform specific datatypes */

int const_H5T_CLASS[11] = { H5T_INTEGER, H5T_FLOAT, H5T_TIME, H5T_STRING, H5T_BITFIELD, H5T_OPAQUE, H5T_COMPOUND, H5T_REFERENCE, H5T_ENUM, H5T_VLEN, H5T_ARRAY };
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11 changes: 11 additions & 0 deletions src/printdatatype.c
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Original file line number Diff line number Diff line change
Expand Up @@ -462,6 +462,17 @@ getDatatypeClass(hid_t type) {
return(name);
}

char* getReferenceType(hid_t ref_type) {
char *name = NULL;
if (H5Tequal(ref_type, H5T_STD_REF_DSETREG))
name = "DATASET_REGION";
else if (H5Tequal(ref_type, H5T_STD_REF_OBJ))
name = "OBJECT";
else
name = "unknown";
return name;
}

SEXP _getDatatypeName(SEXP _type) {
hid_t type = STRSXP_2_HID( _type );
SEXP Rval = mkString(getDatatypeName(type));
Expand Down
1 change: 1 addition & 0 deletions src/printdatatype.h
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@

char* getDatatypeName(hid_t type);
char* getDatatypeClass(hid_t type);
char* getReferenceType(hid_t ref_type);

SEXP _getDatatypeName(SEXP _type);
SEXP _getDatatypeClass(SEXP _type);
Expand Down

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