/*-------------------------------------------------------------------------
* subroutine for test_text_dtype(): test_variables().
*-------------------------------------------------------------------------
*/
static int test_variables(void)
{
hid_t dtype;
H5T_class_t type_class;
char* dt_str;
size_t str_len;
TESTING3(" text for variable types");
if((dtype = H5LTtext_to_dtype("H5T_VLEN { H5T_NATIVE_CHAR }\n", H5LT_DDL))<0)
goto out;
if((type_class = H5Tget_class(dtype))<0)
goto out;
if(type_class != H5T_VLEN)
goto out;
if(H5Tis_variable_str(dtype))
goto out;
if(H5Tclose(dtype)<0)
goto out;
if((dtype = H5LTtext_to_dtype("H5T_VLEN { H5T_VLEN { H5T_STD_I32BE } }", H5LT_DDL))<0)
goto out;
if(H5Tis_variable_str(dtype))
goto out;
if(H5LTdtype_to_text(dtype, NULL, H5LT_DDL, &str_len)<0)
goto out;
dt_str = (char*)calloc(str_len, sizeof(char));
if(H5LTdtype_to_text(dtype, dt_str, H5LT_DDL, &str_len)<0)
goto out;
if(strcmp(dt_str, "H5T_VLEN {\n H5T_VLEN {\n H5T_STD_I32BE\n }\n }")) {
printf("dt=\n%s\n", dt_str);
goto out;
}
free(dt_str);
if(H5Tclose(dtype)<0)
goto out;
PASSED();
return 0;
out:
H5_FAILED();
return -1;
}
std::string toString() const
{
if( H5Tis_variable_str(this->type) )
return "VLString";
else
return "String";
}
void write(const hid_attribute_adaptor& attrib, const std::string& value)
{
hid_t attr_type_id = H5CPP_ERR_ON_NEG(H5Aget_type(attrib.id()));
if(H5Tget_class(attr_type_id) != H5T_STRING)
H5CPP_THROW("Attempted to set string value on non-string attribute '"
<< object::get_name(attrib.id()) << '\'');
const char* cstr = value.c_str();
if(H5Tis_variable_str(attr_type_id))
H5CPP_ERR_ON_NEG(H5Awrite(attrib.id(), attr_type_id, &cstr));
else
{
std::size_t attriblen = H5Aget_storage_size(attrib.id());
if(attriblen > value.length())
{
// avoid reading past end of value into unalloc'd mem
std::vector<char> buf(attriblen,'\0');
std::copy(cstr, cstr+value.length(), &buf[0]);
H5CPP_ERR_ON_NEG(H5Awrite(attrib.id(), attr_type_id, &buf[0]));
}
else
H5CPP_ERR_ON_NEG(H5Awrite(attrib.id(), attr_type_id, cstr));
}
}
size_t getSize() const
{
size_t myElements = H5Tget_size(this->type);
/* for variable length string the size is first known after reading
* the actual data or attribute, so we forward HDF5's behaviour */
if( H5Tis_variable_str(this->type) )
return myElements; /* == sizeof(char*) see H5Tget_size description */
else
return sizeof(char) * (myElements - 1); /* just as strlen() */
}
bool hdf5_datatype::is_variable_length_string() const
{
htri_t status = H5Tis_variable_str(get_id());
if(status < 0) {
boost::serialization::throw_exception(
hdf5_archive_exception(
hdf5_archive_exception::hdf5_archive_datatype_access_error
)
);
}
else if(status == 0) {
return false;
}
return true;
}
static CollectionType* genType(hid_t datatype_id)
{
H5T_class_t h5_class = H5Tget_class(datatype_id);
if(h5_class == H5T_STRING)
{
if( H5Tis_variable_str(datatype_id) )
{
return new ColTypeString;
} else
{
size_t size = H5Tget_size(datatype_id);
return new ColTypeString(size);
}
} else
{
return NULL;
}
}
int H5mdfile::H5_write_value(int argc, char **argv, Tcl_Interp *interp)
{
/* Read value from Tcl and write it to dataset array */
// Get array index
int index=0;
if(dataset_rank>=1) index+=atoi(argv[4+dataset_rank-0]);
if(dataset_rank>=2) index+=atoi(argv[4+dataset_rank-1])*dims[dataset_rank-1];else goto label_index;
if(dataset_rank>=3) index+=atoi(argv[4+dataset_rank-2])*dims[dataset_rank-1]*dims[dataset_rank-2];else goto label_index;
if(dataset_rank>=4) index+=atoi(argv[4+dataset_rank-3])*dims[dataset_rank-1]*dims[dataset_rank-2]*dims[dataset_rank-3];else goto label_index;
if(dataset_rank>=5) index+=atoi(argv[4+dataset_rank-4])*dims[dataset_rank-1]*dims[dataset_rank-2]*dims[dataset_rank-3]*dims[dataset_rank-4];else goto label_index;
if(dataset_rank>=6) index+=atoi(argv[4+dataset_rank-5])*dims[dataset_rank-1]*dims[dataset_rank-2]*dims[dataset_rank-3]*dims[dataset_rank-4]*dims[dataset_rank-5];else goto label_index;
if(dataset_rank>=7) index+=atoi(argv[4+dataset_rank-6])*dims[dataset_rank-1]*dims[dataset_rank-2]*dims[dataset_rank-3]*dims[dataset_rank-4]*dims[dataset_rank-5]*dims[dataset_rank-6];else goto label_index;
if(dataset_rank>=8) index+=atoi(argv[4+dataset_rank-7])*dims[dataset_rank-1]*dims[dataset_rank-2]*dims[dataset_rank-3]*dims[dataset_rank-4]*dims[dataset_rank-5]*dims[dataset_rank-6]*dims[dataset_rank-7];else goto label_index;
label_index:
// Write single value from Tcl to dataset array
if(H5Tequal(dataset_type_id, H5T_NATIVE_FLOAT))
{
dset_data_float = static_cast<float*>(dset_data);
dset_data_float[index]=(float)atof(argv[3]);
}
if(H5Tequal(dataset_type_id, H5T_NATIVE_DOUBLE))
{
dset_data_double = static_cast<double*>(dset_data);
dset_data_double[index]=atof(argv[3]);
}
if(H5Tequal(dataset_type_id, H5T_NATIVE_INT))
{
dset_data_int = static_cast<int*>(dset_data);
dset_data_int[index]=atoi(argv[3]);
}
if(H5Tis_variable_str(dataset_type_id)!=0)
{
// dset_data_string = static_cast<h5string*>(dset_data);
// dset_data_chars=static_cast<char *>(dset_data);
dset_data_chars=(char**) dset_data;
dset_data_chars[index]=strdup(argv[3]);
}
return TCL_OK;
}
H5CompoundData::H5CompoundData(H5Object & _parent, const hsize_t _totalSize, const hsize_t _dataSize, const hsize_t _ndims, const hsize_t * _dims, char * _data, hid_t compoundType, const hsize_t _stride, const size_t _offset, const bool _dataOwner) : H5BasicData<char>(_parent, _totalSize, _dataSize, _ndims, _dims, _data, _stride, _offset, _dataOwner), type(compoundType), cumprod(H5Object::getCumProd(_ndims, dims))
{
nfields = (unsigned int)H5Tget_nmembers(compoundType);
infos = new std::map<std::string, FieldInfo *>();
fieldinfos = new FieldInfo *[nfields];
for (unsigned int i = 0; i < nfields; i++)
{
hid_t mtype = H5Tget_member_type(compoundType, i);
hsize_t size = H5Tget_size(mtype);
char * mname = H5Tget_member_name(compoundType, i);
size_t offs = H5Tget_member_offset(compoundType, i);
FieldInfo * info = 0;
if (H5Tget_class(type) == H5T_STRING && !H5Tis_variable_str(type))
{
// We have a C-string so it is null terminated
size++;
}
info = new FieldInfo(mtype, size, offs, std::string(mname));
(*infos)[std::string(mname)] = info;
fieldinfos[i] = info;
free(mname);
}
}
bool DataType::isVariableString() const {
HTri res = H5Tis_variable_str(hid);
res.check("DataType::isVariableString(): H5Tis_variable_str failed");
return res.result();
}
std::string fast5_get_string_attribute(fast5_file& fh, const std::string& group_name, const std::string& attribute_name)
{
hid_t group, attribute, attribute_type, native_type;
std::string out;
// according to http://hdf-forum.184993.n3.nabble.com/check-if-dataset-exists-td194725.html
// we should use H5Lexists to check for the existence of a group/dataset using an arbitrary path
// HDF5 1.8 returns 0 on the root group, so we explicitly check for it
int ret = group_name == "/" ? 1 : H5Lexists(fh.hdf5_file, group_name.c_str(), H5P_DEFAULT);
if(ret <= 0) {
return "";
}
// Open the group containing the attribute we want
group = H5Gopen(fh.hdf5_file, group_name.c_str(), H5P_DEFAULT);
if(group < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "could not open group %s\n", group_name.c_str());
#endif
goto close_group;
}
// Ensure attribute exists
ret = H5Aexists(group, attribute_name.c_str());
if(ret <= 0) {
goto close_group;
}
// Open the attribute
attribute = H5Aopen(group, attribute_name.c_str(), H5P_DEFAULT);
if(attribute < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "could not open attribute: %s\n", attribute_name.c_str());
#endif
goto close_attr;
}
// Get data type and check it is a fixed-length string
attribute_type = H5Aget_type(attribute);
if(attribute_type < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "failed to get attribute type %s\n", attribute_name.c_str());
#endif
goto close_type;
}
if(H5Tget_class(attribute_type) != H5T_STRING) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "attribute %s is not a string\n", attribute_name.c_str());
#endif
goto close_type;
}
native_type = H5Tget_native_type(attribute_type, H5T_DIR_ASCEND);
if(native_type < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "failed to get native type for %s\n", attribute_name.c_str());
#endif
goto close_native_type;
}
if(H5Tis_variable_str(attribute_type) > 0) {
// variable length string
char* buffer;
ret = H5Aread(attribute, native_type, &buffer);
if(ret < 0) {
fprintf(stderr, "error reading attribute %s\n", attribute_name.c_str());
exit(EXIT_FAILURE);
}
out = buffer;
free(buffer);
buffer = NULL;
} else {
// fixed length string
size_t storage_size;
char* buffer;
// Get the storage size and allocate
storage_size = H5Aget_storage_size(attribute);
buffer = (char*)calloc(storage_size + 1, sizeof(char));
// finally read the attribute
ret = H5Aread(attribute, attribute_type, buffer);
if(ret >= 0) {
out = buffer;
}
// clean up
free(buffer);
}
close_native_type:
H5Tclose(native_type);
close_type:
H5Tclose(attribute_type);
close_attr:
H5Aclose(attribute);
close_group:
H5Gclose(group);
return out;
}
/*-------------------------------------------------------------------------
* Function: h5tools_str_sprint
*
* Purpose: Renders the value pointed to by VP of type TYPE into variable
* length string STR.
*
* Return: A pointer to memory containing the result or NULL on error.
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
* Robb Matzke, 1999-04-26
* Made this function safe from overflow problems by allowing it
* to reallocate the output string.
*
* Robb Matzke, 1999-06-04
* Added support for object references. The new `container'
* argument is the dataset where the reference came from.
*
* Robb Matzke, 1999-06-07
* Added support for printing raw data. If info->raw is non-zero
* then data is printed in hexadecimal format.
*
* Robb Matzke, 2003-01-10
* Binary output format is dd:dd:... instead of 0xdddd... so it
* doesn't look like a hexadecimal integer, and thus users will
* be less likely to complain that HDF5 didn't properly byte
* swap their data during type conversion.
*
* Robb Matzke, LLNL, 2003-06-05
* If TYPE is a variable length string then the pointer to
* the value to pring (VP) is a pointer to a `char*'.
*
* PVN, 28 March 2006
* added H5T_NATIVE_LDOUBLE case
*-------------------------------------------------------------------------
*/
char *
h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t container,
hid_t type, void *vp, h5tools_context_t *ctx)
{
size_t n, offset, size=0, nelmts, start;
char *name;
unsigned char *ucp_vp = (unsigned char *)vp;
char *cp_vp = (char *)vp;
hid_t memb, obj, region;
unsigned nmembs;
static char fmt_llong[8], fmt_ullong[8];
H5T_str_t pad;
/*
* some tempvars to store the value before we append it to the string to
* get rid of the memory alignment problem
*/
unsigned long long tempullong;
long long templlong;
unsigned long tempulong;
long templong;
unsigned int tempuint;
int tempint;
/* Build default formats for long long types */
if (!fmt_llong[0]) {
sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH);
sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH);
}
/* Append value depending on data type */
start = h5tools_str_len(str);
if (info->raw) {
size_t i;
n = H5Tget_size(type);
if (1 == n) {
h5tools_str_append(str, OPT(info->fmt_raw, "0x%02x"), ucp_vp[0]);
}
else {
for (i = 0; i < n; i++) {
if (i)
h5tools_str_append(str, ":");
h5tools_str_append(str, OPT(info->fmt_raw, "%02x"), ucp_vp[i]);
}
}
}
else if (H5Tequal(type, H5T_NATIVE_FLOAT)) {
float tempfloat;
HDmemcpy(&tempfloat, vp, sizeof(float));
h5tools_str_append(str, OPT(info->fmt_float, "%g"), tempfloat);
}
else if (H5Tequal(type, H5T_NATIVE_DOUBLE)) {
double tempdouble;
HDmemcpy(&tempdouble, vp, sizeof(double));
h5tools_str_append(str, OPT(info->fmt_double, "%g"), tempdouble);
#if H5_SIZEOF_LONG_DOUBLE !=0
}
else if (H5Tequal(type, H5T_NATIVE_LDOUBLE)) {
long double templdouble;
HDmemcpy(&templdouble, vp, sizeof(long double));
h5tools_str_append(str, "%Lf", templdouble);
#endif
}
else if (info->ascii && (H5Tequal(type, H5T_NATIVE_SCHAR) ||
H5Tequal(type, H5T_NATIVE_UCHAR))) {
h5tools_print_char(str, info, (char) (*ucp_vp));
}
else if (H5T_STRING == H5Tget_class(type)) {
unsigned int i;
char quote = '\0';
char *s;
quote = '\0';
if (H5Tis_variable_str(type)) {
/* cp_vp is the pointer into the struct where a `char*' is stored. So we have
* to dereference the pointer to get the `char*' to pass to HDstrlen(). */
s = *(char**) cp_vp;
if (s != NULL)
size = HDstrlen(s);
}
else {
s = cp_vp;
size = H5Tget_size(type);
}
pad = H5Tget_strpad(type);
/* Check for NULL pointer for string */
if (s == NULL) {
h5tools_str_append(str, "NULL");
}
else {
for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) {
int j = 1;
/*
* Count how many times the next character repeats. If the
* threshold is zero then that means it can repeat any number
* of times.
*/
if (info->str_repeat > 0)
while (i + j < size && s[i] == s[i + j])
j++;
/*
* Print the opening quote. If the repeat count is high enough to
* warrant printing the number of repeats instead of enumerating
* the characters, then make sure the character to be repeated is
* in it's own quote.
*/
if (info->str_repeat > 0 && j > info->str_repeat) {
if (quote)
h5tools_str_append(str, "%c", quote);
quote = '\'';
h5tools_str_append(str, "%s%c", i ? " " : "", quote);
}
else if (!quote) {
quote = '"';
h5tools_str_append(str, "%s%c", i ? " " : "", quote);
}
/* Print the character */
h5tools_print_char(str, info, s[i]);
/* Print the repeat count */
if (info->str_repeat && j > info->str_repeat) {
#ifdef REPEAT_VERBOSE
h5tools_str_append(str, "%c repeats %d times", quote, j - 1);
#else
h5tools_str_append(str, "%c*%d", quote, j - 1);
#endif /* REPEAT_VERBOSE */
quote = '\0';
i += j - 1;
}
}
if (quote)
h5tools_str_append(str, "%c", quote);
if (i == 0)
/*empty string*/
h5tools_str_append(str, "\"\"");
} /* end else */
}
else if (H5Tequal(type, H5T_NATIVE_INT)) {
HDmemcpy(&tempint, vp, sizeof(int));
#ifdef H5_HAVE_H5DUMP_PACKED_BITS
if(packed_bits_num)
tempint = (tempint >> packed_data_offset) & packed_data_mask;
#endif
h5tools_str_append(str, OPT(info->fmt_int, "%d"), tempint);
}
else if (H5Tequal(type, H5T_NATIVE_UINT)) {
/****************************************************************
**
** test_vlstring_type(): Test VL string type.
** Tests if VL string is treated as string.
**
****************************************************************/
static void test_vlstring_type(void)
{
hid_t fid; /* HDF5 File IDs */
hid_t tid_vlstr;
H5T_cset_t cset;
H5T_str_t pad;
htri_t vl_str; /* Whether string is VL */
herr_t ret;
/* Output message about test being performed */
MESSAGE(5, ("Testing VL String type\n"));
/* Open file */
fid = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fopen");
/* Create a datatype to refer to */
tid_vlstr = H5Tcopy(H5T_C_S1);
CHECK(tid_vlstr, FAIL, "H5Tcopy");
/* Change padding and verify it */
ret = H5Tset_strpad(tid_vlstr, H5T_STR_NULLPAD);
CHECK(ret, FAIL, "H5Tset_strpad");
pad = H5Tget_strpad(tid_vlstr);
VERIFY(pad, H5T_STR_NULLPAD, "H5Tget_strpad");
/* Convert to variable-length string */
ret = H5Tset_size(tid_vlstr, H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
/* Check if datatype is VL string */
ret = H5Tget_class(tid_vlstr);
VERIFY(ret, H5T_STRING, "H5Tget_class");
ret = H5Tis_variable_str(tid_vlstr);
VERIFY(ret, TRUE, "H5Tis_variable_str");
/* Verify that the class detects as a string */
vl_str = H5Tdetect_class(tid_vlstr, H5T_STRING);
CHECK(vl_str, FAIL, "H5Tdetect_class");
VERIFY(vl_str, TRUE, "H5Tdetect_class");
/* Check default character set and padding */
cset = H5Tget_cset(tid_vlstr);
VERIFY(cset, H5T_CSET_ASCII, "H5Tget_cset");
pad = H5Tget_strpad(tid_vlstr);
VERIFY(pad, H5T_STR_NULLPAD, "H5Tget_strpad");
/* Commit variable-length string datatype to storage */
ret = H5Tcommit2(fid, VLSTR_TYPE, tid_vlstr, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Tcommit2");
/* Close datatype */
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
tid_vlstr = H5Topen2(fid, VLSTR_TYPE, H5P_DEFAULT);
CHECK(tid_vlstr, FAIL, "H5Topen2");
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Fclose(fid);
CHECK(ret, FAIL, "H5Fclose");
fid = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fopen");
/* Open the variable-length string datatype just created */
tid_vlstr = H5Topen2(fid, VLSTR_TYPE, H5P_DEFAULT);
CHECK(tid_vlstr, FAIL, "H5Topen2");
/* Verify character set and padding */
cset = H5Tget_cset(tid_vlstr);
VERIFY(cset, H5T_CSET_ASCII, "H5Tget_cset");
pad = H5Tget_strpad(tid_vlstr);
VERIFY(pad, H5T_STR_NULLPAD, "H5Tget_strpad");
/* Close datatype and file */
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Fclose(fid);
CHECK(ret, FAIL, "H5Fclose");
} /* end test_vlstring_type() */
static herr_t HDF5AttrIterate( hid_t hH5ObjID,
const char *pszAttrName,
// TODO(schwehr): void * -> HDF5Dataset *
void *pDS )
{
char **papszTokens = nullptr;
CPLString osKey;
HDF5Dataset *const poDS = static_cast<HDF5Dataset *>(pDS);
// Convert "/" into "_" for the path component
const char *pszPath = poDS->poH5CurrentObject->pszUnderscorePath;
if(pszPath != nullptr && strlen(pszPath) > 0)
{
papszTokens = CSLTokenizeString2(pszPath, "/", CSLT_HONOURSTRINGS);
for( hsize_t i = 0; papszTokens != nullptr && papszTokens[i] != nullptr; ++i )
{
if( i != 0)
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy(papszTokens);
}
// Convert whitespaces into "_" for the attribute name component
papszTokens = CSLTokenizeString2(
pszAttrName, " ", CSLT_STRIPLEADSPACES | CSLT_STRIPENDSPACES);
for( hsize_t i = 0; papszTokens != nullptr && papszTokens[i] != nullptr; ++i )
{
if(!osKey.empty())
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy(papszTokens);
const hid_t hAttrID = H5Aopen_name(hH5ObjID, pszAttrName);
const hid_t hAttrTypeID = H5Aget_type(hAttrID);
const hid_t hAttrNativeType =
H5Tget_native_type(hAttrTypeID, H5T_DIR_DEFAULT);
const hid_t hAttrSpace = H5Aget_space(hAttrID);
if( H5Tget_class(hAttrNativeType) == H5T_VLEN )
return 0;
hsize_t nSize[64] = {};
const unsigned int nAttrDims =
H5Sget_simple_extent_dims(hAttrSpace, nSize, nullptr);
unsigned int nAttrElmts = 1;
for( hsize_t i = 0; i < nAttrDims; i++ )
{
nAttrElmts *= static_cast<int>(nSize[i]);
}
char *szData = nullptr;
hsize_t nAttrSize = 0;
char *szValue = nullptr;
if( H5Tget_class(hAttrNativeType) == H5T_STRING )
{
if ( H5Tis_variable_str(hAttrNativeType) )
{
char **papszStrings =
static_cast<char **>(CPLMalloc(nAttrElmts * sizeof(char *)));
// Read the values.
H5Aread(hAttrID, hAttrNativeType, papszStrings);
// Concatenate all values as one string separated by a space.
CPLString osVal = papszStrings[0];
for( hsize_t i = 1; i < nAttrElmts; i++ )
{
osVal += " ";
osVal += papszStrings[i];
}
szValue = static_cast<char *>(CPLMalloc(osVal.length() + 1));
strcpy(szValue, osVal.c_str());
H5Dvlen_reclaim(hAttrNativeType, hAttrSpace, H5P_DEFAULT,
papszStrings);
CPLFree(papszStrings);
}
else
{
nAttrSize = H5Aget_storage_size(hAttrID);
szValue = static_cast<char *>(CPLMalloc((size_t)(nAttrSize + 1)));
H5Aread(hAttrID, hAttrNativeType, szValue);
szValue[nAttrSize] = '\0';
}
}
else
{
const size_t nDataLen = 8192;
void *buf = nullptr;
if( nAttrElmts > 0 )
{
buf = CPLMalloc(nAttrElmts * H5Tget_size(hAttrNativeType));
szData = static_cast<char *>(CPLMalloc(nDataLen));
szValue = static_cast<char *>(CPLMalloc(MAX_METADATA_LEN));
szData[0] = '\0';
szValue[0] = '\0';
H5Aread(hAttrID, hAttrNativeType, buf);
}
if( H5Tequal(H5T_NATIVE_CHAR, hAttrNativeType ) ||
H5Tequal(H5T_NATIVE_SCHAR, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%c ", static_cast<char *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_UCHAR, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%c", static_cast<char *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_SHORT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%d ", static_cast<short *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_USHORT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%ud ",
static_cast<unsigned short *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_INT, hAttrNativeType) )
{
for( hsize_t i=0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%d ", static_cast<int *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_UINT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%ud ",
static_cast<unsigned int *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_LONG, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
snprintf(szData, nDataLen, "%ld ", static_cast<long *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_ULONG, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ ) {
snprintf(szData, nDataLen, "%lu ",
static_cast<unsigned long *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_FLOAT, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
CPLsnprintf(szData, nDataLen, "%.8g ",
static_cast<float *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
else if( H5Tequal(H5T_NATIVE_DOUBLE, hAttrNativeType) )
{
for( hsize_t i = 0; i < nAttrElmts; i++ )
{
CPLsnprintf(szData, nDataLen, "%.15g ",
static_cast<double *>(buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError(CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated");
}
}
CPLFree(buf);
}
H5Sclose(hAttrSpace);
H5Tclose(hAttrNativeType);
H5Tclose(hAttrTypeID);
H5Aclose(hAttrID);
poDS->papszMetadata = CSLSetNameValue(poDS->papszMetadata, osKey, szValue);
CPLFree(szData);
CPLFree(szValue);
return 0;
}
herr_t HDF5AttrIterate( hid_t hH5ObjID,
const char *pszAttrName,
void *pDS )
{
hid_t hAttrID;
hid_t hAttrTypeID;
hid_t hAttrNativeType;
hid_t hAttrSpace;
char *szData = NULL;
hsize_t nSize[64];
unsigned int nAttrElmts;
hsize_t nAttrSize;
hsize_t i;
void *buf = NULL;
unsigned int nAttrDims;
char **papszTokens;
HDF5Dataset *poDS;
CPLString osKey;
char *szValue = NULL;
poDS = (HDF5Dataset *) pDS;
// Convert "/" into "_" for the path component
const char* pszPath = poDS->poH5CurrentObject->pszUnderscorePath;
if(pszPath != NULL && strlen(pszPath) > 0)
{
papszTokens = CSLTokenizeString2( pszPath, "/", CSLT_HONOURSTRINGS );
for( i = 0; papszTokens != NULL && papszTokens[i] != NULL; ++i )
{
if( i != 0)
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy( papszTokens );
}
// Convert whitespaces into "_" for the attribute name component
papszTokens = CSLTokenizeString2( pszAttrName, " ",
CSLT_STRIPLEADSPACES | CSLT_STRIPENDSPACES );
for( i = 0; papszTokens != NULL && papszTokens[i] != NULL; ++i )
{
if(!osKey.empty())
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy( papszTokens );
hAttrID = H5Aopen_name( hH5ObjID, pszAttrName );
hAttrTypeID = H5Aget_type( hAttrID );
hAttrNativeType = H5Tget_native_type( hAttrTypeID, H5T_DIR_DEFAULT );
hAttrSpace = H5Aget_space( hAttrID );
nAttrDims = H5Sget_simple_extent_dims( hAttrSpace, nSize, NULL );
nAttrElmts = 1;
for( i=0; i < nAttrDims; i++ ) {
nAttrElmts *= (int) nSize[i];
}
if( H5Tget_class( hAttrNativeType ) == H5T_STRING )
{
if ( H5Tis_variable_str(hAttrNativeType) )
{
char** papszStrings;
papszStrings = (char**) CPLMalloc( nAttrElmts * sizeof(char*) );
// Read the values
H5Aread( hAttrID, hAttrNativeType, papszStrings );
// Concatenate all values as one string (separated by a space)
CPLString osVal = papszStrings[0];
for( i=1; i < nAttrElmts; i++ ) {
osVal += " ";
osVal += papszStrings[i];
}
szValue = (char*) CPLMalloc(osVal.length() + 1);
strcpy( szValue, osVal.c_str() );
H5Dvlen_reclaim( hAttrNativeType, hAttrSpace, H5P_DEFAULT,
papszStrings );
CPLFree( papszStrings );
}
else
{
nAttrSize = H5Aget_storage_size( hAttrID );
szValue = (char*) CPLMalloc((size_t) (nAttrSize+1));
H5Aread( hAttrID, hAttrNativeType, szValue );
szValue[nAttrSize] = '\0';
}
}
else {
if( nAttrElmts > 0 ) {
buf = (void *) CPLMalloc( nAttrElmts*
H5Tget_size( hAttrNativeType ));
szData = (char*) CPLMalloc( 8192 );
szValue = (char*) CPLMalloc( MAX_METADATA_LEN );
szData[0] = '\0';
szValue[0] ='\0';
H5Aread( hAttrID, hAttrNativeType, buf );
}
if( H5Tequal( H5T_NATIVE_CHAR, hAttrNativeType )
|| H5Tequal( H5T_NATIVE_SCHAR, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c ", ((char *) buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UCHAR, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c", ((char *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_SHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((short *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_USHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned short *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_INT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((int *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UINT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned int *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_LONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((long *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_ULONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((unsigned long *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_FLOAT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
CPLsprintf( szData, "%.8g ", ((float *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_DOUBLE, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
CPLsprintf( szData, "%.15g ", ((double *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
CPLFree( buf );
}
H5Sclose(hAttrSpace);
H5Tclose(hAttrNativeType);
H5Tclose(hAttrTypeID);
H5Aclose( hAttrID );
poDS->papszMetadata = CSLSetNameValue( poDS->papszMetadata, osKey, szValue);
CPLFree( szData );
CPLFree( szValue );
return 0;
}
MatlabObject::MatlabObject (const HDF5::Object& o) {
HDF5::Object object = o;
bool hasEmptyAttribute;
for (;;) {
isOctaveNewFormat_ = object.getType () == H5I_GROUP && object.existsAttribute ("OCTAVE_NEW_FORMAT");
if (!isOctaveNewFormat_) {
hasEmptyAttribute = object.existsAttribute ("MATLAB_empty");
break;
}
HDF5::Group grp = (HDF5::Group) object;
HDF5::DataSet typeDs = (HDF5::DataSet) grp.open ("type", setEFilePrefix ());
ASSERT (typeDs.getSpace ().getSimpleExtentType () == H5S_SCALAR);
HDF5::DataSpace s = HDF5::DataSpace::create (H5S_SCALAR);
HDF5::StringType ty = (HDF5::StringType) typeDs.getDataType ();
ASSERT (!(Exception::check ("H5Tis_variable_str", H5Tis_variable_str (ty.handle ())) != 0));
/*
const char* str = NULL;
HDF5::DataType t = getH5Type<const char*> ();
typeDs.read (&str, t, s, s);
std::string str2 (str);
typeDs.vlenReclaim (&str, t, s);
*/
size_t size = H5Tget_size (ty.handle ());
HDF5::Exception::check ("H5Tget_size", size ? 0 : -1);
std::vector<char> str (size);
typeDs.read (str.data (), ty, s, s);
std::string str2 (str.begin (), str.end ());
size_t pos = str2.find ('\0');
if (pos != std::string::npos)
str2 = str2.substr (0, pos);
if (str2 != "cell") {
hasEmptyAttribute = grp.existsAttribute ("OCTAVE_EMPTY_MATRIX");
object = grp.open ("value", setEFilePrefix ());
octaveType_ = str2;
break;
} else {
HDF5::DataSet dimsDs = (HDF5::DataSet) grp.open ("value/dims", setEFilePrefix ());
HDF5::DataSpace dimsSp = dimsDs.getSpace ();
ASSERT (dimsSp.getSimpleExtentType () == H5S_SIMPLE);
ASSERT (dimsSp.getSimpleExtentNdims () == 1);
hsize_t dim;
dimsSp.getSimpleExtentDims (&dim);
ASSERT (dim == 2);
int64_t dims[2];
dimsDs.read (dims, HDF5::getH5Type<int64_t> (), dimsSp);
ASSERT (dims[0] == 1);
ASSERT (dims[1] == 1);
object = grp.open ("value/_0", setEFilePrefix ());
}
}
H5I_type_t type = object.getType ();
if (type == H5I_DATASET) {
isStruct_ = false;
dataSet_ = (HDF5::DataSet) object;
if (hasEmptyAttribute) {
isEmpty_ = true;
isNullDataSpace_ = false;
HDF5::DataSpace dataSpace = dataSet_.getSpace ();
ASSERT (dataSpace.getSimpleExtentType () == H5S_SIMPLE);
ASSERT (dataSpace.getSimpleExtentNdims () == 1);
hsize_t ndims;
dataSpace.getSimpleExtentDims (&ndims);
ASSERT (ndims > 0);
std::vector<uint64_t> values (Core::checked_cast<size_t> (ndims));
dataSet_.read (values.data (), getH5Type<uint64_t> (), dataSpace);
bool foundZero = false;
for (size_t i = 0; i < ndims; i++)
if (!values[i])
foundZero = true;
ASSERT (foundZero);
size_.resize (Core::checked_cast<size_t> (ndims));
for (size_t i = 0; i < ndims; i++) {
ASSERT (values[i] <= std::numeric_limits<size_t>::max ());
size_[i] = Core::checked_cast<size_t> (values[i]);
}
} else {
dataSpace_ = dataSet_.getSpace ();
H5S_class_t extentType = dataSpace_.getSimpleExtentType ();
//ASSERT (extentType == H5S_SIMPLE || extentType == H5S_NULL);
ASSERT (extentType == H5S_SIMPLE || extentType == H5S_NULL || extentType == H5S_SCALAR);
if (extentType == H5S_SIMPLE) {
isNullDataSpace_ = false;
size_t dim = dataSpace_.getSimpleExtentNdims ();
size_.resize (dim);
std::vector<hsize_t> dims (dim);
dataSpace_.getSimpleExtentDims (dims.data ());
isEmpty_ = false;
for (size_t i = 0; i < dim; i++) {
ASSERT (dims[i] >= std::numeric_limits<size_t>::min () && dims[i] <= std::numeric_limits<size_t>::max ());
size_[dim - 1 - i] = Core::checked_cast<size_t> (dims[i]);
if (!dims[i])
isEmpty_ = true;
}
if (isEmpty_) {
dataSpace_ = HDF5::DataSpace ();
}
} else if (extentType == H5S_SCALAR) {
isNullDataSpace_ = false;
isEmpty_ = false;
//size_.resize (0);
size_.resize (1);
size_[0] = 1;
} else { // H5S_NULL
isEmpty_ = true;
isNullDataSpace_ = true;
size_.resize (1);
size_[0] = 0;
}
}
if (isEmpty_)
dataSet_ = HDF5::DataSet ();
} else if (type == H5I_GROUP) {
isStruct_ = true;
group_ = (HDF5::Group) object;
} else {
ABORT_MSG ("Unknown object type");
}
}
hsize_t diff_attr(hid_t loc1_id,
hid_t loc2_id,
const char *path1,
const char *path2,
diff_opt_t *options)
{
hid_t attr1_id=-1; /* attr ID */
hid_t attr2_id=-1; /* attr ID */
hid_t space1_id=-1; /* space ID */
hid_t space2_id=-1; /* space ID */
hid_t ftype1_id=-1; /* file data type ID */
hid_t ftype2_id=-1; /* file data type ID */
int vstrtype1=0; /* ftype1 is a variable string */
int vstrtype2=0; /* ftype2 is a variable string */
hid_t mtype1_id=-1; /* memory data type ID */
hid_t mtype2_id=-1; /* memory data type ID */
size_t msize1; /* memory size of memory type */
size_t msize2; /* memory size of memory type */
void *buf1=NULL; /* data buffer */
void *buf2=NULL; /* data buffer */
int buf1hasdata=0; /* buffer has data */
int buf2hasdata=0; /* buffer has data */
hsize_t nelmts1; /* number of elements in dataset */
int rank1; /* rank of dataset */
int rank2; /* rank of dataset */
hsize_t dims1[H5S_MAX_RANK];/* dimensions of dataset */
hsize_t dims2[H5S_MAX_RANK];/* dimensions of dataset */
char *name1;
char *name2;
char np1[512];
char np2[512];
unsigned u; /* Local index variable */
hsize_t nfound = 0;
hsize_t nfound_total = 0;
int j;
table_attrs_t * match_list_attrs = NULL;
if( build_match_list_attrs(loc1_id, loc2_id, &match_list_attrs, options) < 0)
goto error;
/* if detect any unique extra attr */
if(match_list_attrs->nattrs_only1 || match_list_attrs->nattrs_only2)
{
/* exit will be 1 */
options->contents = 0;
}
for(u = 0; u < (unsigned)match_list_attrs->nattrs; u++)
{
if( (match_list_attrs->attrs[u].exist[0]) && (match_list_attrs->attrs[u].exist[1]) )
{
name1 = name2 = match_list_attrs->attrs[u].name;
/*--------------
* attribute 1 */
if((attr1_id = H5Aopen(loc1_id, name1, H5P_DEFAULT)) < 0)
goto error;
/*--------------
* attribute 2 */
if((attr2_id = H5Aopen(loc2_id, name2, H5P_DEFAULT)) < 0)
goto error;
/* get the datatypes */
if((ftype1_id = H5Aget_type(attr1_id)) < 0)
goto error;
vstrtype1 = H5Tis_variable_str(ftype1_id);
if((ftype2_id = H5Aget_type(attr2_id)) < 0)
goto error;
vstrtype2 = H5Tis_variable_str(ftype2_id);
/* no compare if either one but not both are variable string type */
if (vstrtype1 != vstrtype2){
if ((options->m_verbose||options->m_list_not_cmp))
parallel_print("Not comparable: one of attribute <%s/%s> or <%s/%s> is of variable length type\n",
path1, name1, path2, name2);
options->not_cmp = 1;
return 0;
}
if((mtype1_id = h5tools_get_native_type(ftype1_id))<0)
goto error;
if((mtype2_id = h5tools_get_native_type(ftype2_id))<0)
goto error;
if((msize1 = H5Tget_size(mtype1_id))==0)
goto error;
if((msize2 = H5Tget_size(mtype2_id))==0)
goto error;
/* get the dataspace */
if((space1_id = H5Aget_space(attr1_id)) < 0)
goto error;
if((space2_id = H5Aget_space(attr2_id)) < 0)
goto error;
/* get dimensions */
if((rank1 = H5Sget_simple_extent_dims(space1_id, dims1, NULL)) < 0)
goto error;
if((rank2 = H5Sget_simple_extent_dims(space2_id, dims2, NULL)) < 0)
goto error;
/*----------------------------------------------------------------------
* check for comparable TYPE and SPACE
*----------------------------------------------------------------------
*/
/* pass dims1 and dims2 for maxdims as well since attribute's maxdims
* are always same */
if( diff_can_type(ftype1_id, ftype2_id, rank1, rank2, dims1, dims2,
dims1, dims2, name1, name2, options, 0) != 1 )
{
if(H5Tclose(ftype1_id) < 0)
goto error;
if(H5Tclose(ftype2_id) < 0)
goto error;
if(H5Sclose(space1_id) < 0)
goto error;
if(H5Sclose(space2_id) < 0)
goto error;
if(H5Aclose(attr1_id) < 0)
goto error;
if(H5Aclose(attr2_id) < 0)
goto error;
if(H5Tclose(mtype1_id) < 0)
goto error;
if(H5Tclose(mtype2_id) < 0)
goto error;
continue;
}
/*-----------------------------------------------------------------
* "upgrade" the smaller memory size
*------------------------------------------------------------------
*/
if (FAIL == match_up_memsize (ftype1_id, ftype2_id,
&mtype1_id, &mtype2_id,
&msize1, &msize2))
goto error;
/*---------------------------------------------------------------------
* read
*----------------------------------------------------------------------
*/
nelmts1 = 1;
for(j = 0; j < rank1; j++)
nelmts1 *= dims1[j];
buf1 = (void *)HDmalloc((size_t)(nelmts1 * msize1));
buf2 = (void *)HDmalloc((size_t)(nelmts1 * msize2));
if(buf1 == NULL || buf2 == NULL){
parallel_print( "cannot read into memory\n" );
goto error;
}
if(H5Aread(attr1_id,mtype1_id,buf1) < 0){
parallel_print("Failed reading attribute1 %s/%s\n", path1, name1);
goto error;
}else
buf1hasdata = 1;
if(H5Aread(attr2_id,mtype2_id,buf2) < 0){
parallel_print("Failed reading attribute2 %s/%s\n", path2, name2);
goto error;
}else
buf2hasdata = 1;
/* format output string */
HDsnprintf(np1, sizeof(np1), "%s of <%s>", name1, path1);
HDsnprintf(np2, sizeof(np1), "%s of <%s>", name2, path2);
/*---------------------------------------------------------------------
* array compare
*----------------------------------------------------------------------
*/
/* always print name */
/* verbose (-v) and report (-r) mode */
if(options->m_verbose || options->m_report) {
do_print_attrname("attribute", np1, np2);
nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
options, np1, np2, mtype1_id, attr1_id, attr2_id);
print_found(nfound);
}
/* quiet mode (-q), just count differences */
else if(options->m_quiet) {
nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
options, np1, np2, mtype1_id, attr1_id, attr2_id);
}
/* the rest (-c, none, ...) */
else {
nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
options, np1, np2, mtype1_id, attr1_id, attr2_id);
/* print info if compatible and difference found */
if(nfound) {
do_print_attrname("attribute", np1, np2);
print_found(nfound);
} /* end if */
} /* end else */
/*----------------------------------------------------------------------
* close
*----------------------------------------------------------------------
*/
/* Free buf1 and buf2, check both VLEN-data VLEN-string to reclaim any
* VLEN memory first */
if(TRUE == h5tools_detect_vlen(mtype1_id))
H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
HDfree(buf1);
buf1 = NULL;
if(TRUE == h5tools_detect_vlen(mtype2_id))
H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
HDfree(buf2);
buf2 = NULL;
if(H5Tclose(ftype1_id) < 0)
goto error;
if(H5Tclose(ftype2_id) < 0)
goto error;
if(H5Sclose(space1_id) < 0)
goto error;
if(H5Sclose(space2_id) < 0)
goto error;
if(H5Aclose(attr1_id) < 0)
goto error;
if(H5Aclose(attr2_id) < 0)
goto error;
if(H5Tclose(mtype1_id) < 0)
goto error;
if(H5Tclose(mtype2_id) < 0)
goto error;
nfound_total += nfound;
}
} /* u */
table_attrs_free(match_list_attrs);
return nfound_total;
error:
H5E_BEGIN_TRY {
if(buf1) {
if(buf1hasdata && TRUE == h5tools_detect_vlen(mtype1_id))
H5Dvlen_reclaim(mtype1_id, space1_id, H5P_DEFAULT, buf1);
HDfree(buf1);
} /* end if */
if(buf2) {
if(buf2hasdata && TRUE == h5tools_detect_vlen(mtype2_id))
H5Dvlen_reclaim(mtype2_id, space2_id, H5P_DEFAULT, buf2);
HDfree(buf2);
} /* end if */
table_attrs_free(match_list_attrs);
H5Tclose(ftype1_id);
H5Tclose(ftype2_id);
H5Tclose(mtype1_id);
H5Tclose(mtype2_id);
H5Sclose(space1_id);
H5Sclose(space2_id);
H5Aclose(attr1_id);
H5Aclose(attr2_id);
} H5E_END_TRY;
options->err_stat = 1;
return nfound_total;
}
int hdf5read(char *name, struct descriptor_xd *xd)
{
hid_t obj,type;
H5G_stat_t statbuf;
int item_type;
int idx = 0;
int status = FindItem(name, &obj, &item_type);
if (status & 1)
{
if (item_type == H5G_DATASET) {
int size;
char dtype;
int htype = 42;
int is_signed;
hsize_t ds_dims[64];
hid_t space = H5Dget_space(obj);
int n_ds_dims = H5Sget_simple_extent_dims(space,ds_dims,0);
size_t precision;
H5Sclose(space);
type = H5Dget_type(obj);
switch (H5Tget_class(type))
{
case H5T_COMPOUND:
{
printf("Compound data is not supported, skipping\n");
break;
}
case H5T_INTEGER:
precision = H5Tget_precision(type);
is_signed = (H5Tget_sign(type) != H5T_SGN_NONE);
size = precision/8;
switch (precision)
{
case 8:
dtype = is_signed ? DTYPE_B : DTYPE_BU;
htype = is_signed ? H5T_NATIVE_CHAR : H5T_NATIVE_UCHAR;
break;
case 16:
dtype = is_signed ? DTYPE_W : DTYPE_WU;
htype = is_signed ? H5T_NATIVE_SHORT : H5T_NATIVE_USHORT;
break;
case 32:
dtype = is_signed ? DTYPE_L : DTYPE_LU;
htype = is_signed ? H5T_NATIVE_INT : H5T_NATIVE_UINT;
break;
case 64:
dtype = is_signed ? DTYPE_Q : DTYPE_QU;
htype = is_signed ? H5T_NATIVE_LLONG : H5T_NATIVE_ULLONG;
break;
default:
dtype = 0;
break;
}
PutData(obj, dtype, htype, size, n_ds_dims, ds_dims,0,xd);
break;
case H5T_FLOAT:
precision = H5Tget_precision(type);
size = precision/8;
switch (precision)
{
case 32:
dtype = DTYPE_NATIVE_FLOAT;
htype = H5T_NATIVE_FLOAT;
break;
case 64:
dtype = DTYPE_NATIVE_DOUBLE;
htype = H5T_NATIVE_DOUBLE;
break;
default:
dtype = 0;
break;
}
PutData(obj, dtype, htype, size, n_ds_dims, ds_dims,0,xd);
break;
case H5T_TIME:
printf("dataset is time ---- UNSUPPORTED\n"); break;
case H5T_STRING:
{
int slen = H5Tget_size(type);
hid_t st_id;
if (slen < 0) {
printf("Badly formed string attribute\n");
return;
}
#if H5_VERS_MAJOR>=1&&H5_VERS_MINOR>=6&&H5_VERS_RELEASE>=1
if(H5Tis_variable_str(type)) {
st_id = H5Tcopy (H5T_C_S1);
H5Tset_size(st_id, H5T_VARIABLE);
} else {
#endif
st_id = H5Tcopy (type);
H5Tset_cset(st_id, H5T_CSET_ASCII);
#if H5_VERS_MAJOR>=1&&H5_VERS_MINOR>=6&&H5_VERS_RELEASE>=1
}
#endif
if (H5Tget_size(st_id) > slen) {
slen = H5Tget_size(st_id);
}
H5Tset_size (st_id, slen);
PutData(obj, DTYPE_T, st_id, slen, n_ds_dims, ds_dims, 0, xd);
}
/* printf("dataset is string\n"); */
/* dtype = DTYPE_T; */
/* htype = H5T_STRING; */
/* PutData(obj, dtype, htype, 0, 0, 0, 1, xd); */
break;
case H5T_BITFIELD:
printf("dataset is bitfield ---- UNSUPPORTED\n"); break;
case H5T_OPAQUE:
printf("dataset is opaque ---- UNSUPPORTED\n"); break;
case H5T_ARRAY:
printf("dataset is array ---- UNSUPPORTED\n"); break;
case H5T_VLEN:
printf("dataset is vlen ---- UNSUPPORTED\n"); break;
}
H5Tclose(type);
}
else {
int size;
char dtype;
int htype = 42;
int is_signed;
hsize_t ds_dims[64];
hid_t space = H5Aget_space(obj);
int n_ds_dims = H5Sget_simple_extent_dims(space,ds_dims,0);
size_t precision;
H5Sclose(space);
type = H5Aget_type(obj);
switch (H5Tget_class(type))
{
case H5T_COMPOUND:
{
printf("Compound data is not supported, skipping\n");
break;
}
case H5T_INTEGER:
precision = H5Tget_precision(type);
is_signed = (H5Tget_sign(type) != H5T_SGN_NONE);
size = precision/8;
switch (precision)
{
case 8:
dtype = is_signed ? DTYPE_B : DTYPE_BU;
htype = is_signed ? H5T_NATIVE_CHAR : H5T_NATIVE_UCHAR;
break;
case 16:
dtype = is_signed ? DTYPE_W : DTYPE_WU;
htype = is_signed ? H5T_NATIVE_SHORT : H5T_NATIVE_USHORT;
break;
case 32:
dtype = is_signed ? DTYPE_L : DTYPE_LU;
htype = is_signed ? H5T_NATIVE_INT : H5T_NATIVE_UINT;
break;
case 64:
dtype = is_signed ? DTYPE_Q : DTYPE_QU;
htype = is_signed ? H5T_NATIVE_LLONG : H5T_NATIVE_ULLONG;
break;
default:
dtype = 0;
break;
}
PutData(obj, dtype, htype, size, n_ds_dims, ds_dims, 1, xd);
break;
case H5T_FLOAT:
precision = H5Tget_precision(type);
size = precision/8;
switch (precision)
{
case 32:
dtype = DTYPE_NATIVE_FLOAT;
htype = H5T_NATIVE_FLOAT;
break;
case 64:
dtype = DTYPE_NATIVE_DOUBLE;
htype = H5T_NATIVE_DOUBLE;
break;
default:
dtype = 0;
break;
}
PutData(obj, dtype, htype, size, n_ds_dims, ds_dims,1, xd);
break;
case H5T_TIME:
printf("dataset is time ---- UNSUPPORTED\n"); break;
case H5T_STRING:
{
int slen = H5Tget_size(type);
hid_t st_id;
if (slen < 0) {
printf("Badly formed string attribute\n");
return;
}
#if H5_VERS_MAJOR>=1&&H5_VERS_MINOR>=6&&H5_VERS_RELEASE>=1
if(H5Tis_variable_str(type)) {
st_id = H5Tcopy (H5T_C_S1);
H5Tset_size(st_id, H5T_VARIABLE);
} else {
#endif
st_id = H5Tcopy (type);
H5Tset_cset(st_id, H5T_CSET_ASCII);
#if H5_VERS_MAJOR>=1&&H5_VERS_MINOR>=6&&H5_VERS_RELEASE>=1
}
#endif
if (H5Tget_size(st_id) > slen) {
slen = H5Tget_size(st_id);
}
H5Tset_size (st_id, slen);
PutData(obj, DTYPE_T, st_id, slen, n_ds_dims, ds_dims, 1, xd);
}
/* dtype = DTYPE_T; */
/* htype = H5T_STRING; */
/* PutData(obj, dtype, htype, 0, 0, 0, 1, xd); */
break;
case H5T_BITFIELD:
printf("dataset is bitfield ---- UNSUPPORTED\n"); break;
case H5T_OPAQUE:
printf("dataset is opaque ---- UNSUPPORTED\n"); break;
case H5T_ARRAY:
printf("dataset is array ---- UNSUPPORTED\n"); break;
case H5T_VLEN:
printf("dataset is vlen ---- UNSUPPORTED\n"); break;
}
H5Tclose(type);
}
}
return status;
}
/*-------------------------------------------------------------------------
* subroutine for test_text_dtype(): test_strings().
*-------------------------------------------------------------------------
*/
static int test_strings(void)
{
hid_t dtype;
size_t str_size;
H5T_str_t str_pad;
H5T_cset_t str_cset;
H5T_class_t type_class;
char* dt_str;
size_t str_len;
TESTING3(" text for string types");
if((dtype = H5LTtext_to_dtype("H5T_STRING { STRSIZE 13; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; }", H5LT_DDL))<0)
goto out;
if((type_class = H5Tget_class(dtype))<0)
goto out;
if(type_class != H5T_STRING)
goto out;
str_size = H5Tget_size(dtype);
if(str_size != 13)
goto out;
str_pad = H5Tget_strpad(dtype);
if(str_pad != H5T_STR_NULLTERM)
goto out;
str_cset = H5Tget_cset(dtype);
if(str_cset != H5T_CSET_ASCII)
goto out;
if(H5LTdtype_to_text(dtype, NULL, H5LT_DDL, &str_len)<0)
goto out;
dt_str = (char*)calloc(str_len, sizeof(char));
if(H5LTdtype_to_text(dtype, dt_str, H5LT_DDL, &str_len)<0)
goto out;
if(strcmp(dt_str, "H5T_STRING {\n STRSIZE 13;\n STRPAD H5T_STR_NULLTERM;\n CSET H5T_CSET_ASCII;\n CTYPE H5T_C_S1;\n }")) {
printf("dt=\n%s\n", dt_str);
goto out;
}
free(dt_str);
if(H5Tclose(dtype)<0)
goto out;
if((dtype = H5LTtext_to_dtype("H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLPAD; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; }", H5LT_DDL))<0)
goto out;
if(!H5Tis_variable_str(dtype))
goto out;
str_pad = H5Tget_strpad(dtype);
if(str_pad != H5T_STR_NULLPAD)
goto out;
str_cset = H5Tget_cset(dtype);
if(str_cset != H5T_CSET_ASCII)
goto out;
if(H5LTdtype_to_text(dtype, NULL, H5LT_DDL, &str_len)<0)
goto out;
dt_str = (char*)calloc(str_len, sizeof(char));
if(H5LTdtype_to_text(dtype, dt_str, H5LT_DDL, &str_len)<0)
goto out;
if(strcmp(dt_str, "H5T_STRING {\n STRSIZE H5T_VARIABLE;\n STRPAD H5T_STR_NULLPAD;\n CSET H5T_CSET_ASCII;\n CTYPE H5T_C_S1;\n }")) {
printf("dt=\n%s\n", dt_str);
goto out;
}
free(dt_str);
if(H5Tclose(dtype)<0)
goto out;
PASSED();
return 0;
out:
H5_FAILED();
return -1;
}
