RefTester(hid_t id) : obj(id) {
if (H5Iis_valid(id)) {
ref = H5Iget_ref(id);
} else {
ref = 0;
}
}
void close(hid_t id, H5I_type_t type)
{
if((id == -1) || (is_constant(type, id)))
return;
if(!H5Iis_valid(id))
H5CPP_THROW("attempted to close bad hdf5 id: " << id);
_close(id, type);
}
void close(hid_t id)
{
if((id == -1) || (is_constant(id)))
return;
if(!H5Iis_valid(id))
H5CPP_THROW("attempted to close bad hdf5 id: " << id);
H5I_type_t t = H5CPP_ERR_ON_NEG(H5Iget_type(id));
_close(id, t);
}
//--------------------------------------------------------------------------
// Function: isValid (static)
///\brief Checks if the given ID is valid.
///\return true if the given identifier is valid, and false, otherwise.
///\par Description
/// A valid ID is one that is in use and has an application
/// reference count of at least 1.
// Programmer Binh-Minh Ribler - Mar 1, 2017
//--------------------------------------------------------------------------
bool IdComponent::isValid(hid_t an_id)
{
// Call C function
htri_t ret_value = H5Iis_valid(an_id);
if (ret_value > 0)
return true;
else if (ret_value == 0)
return false;
else // Raise exception when H5Iis_valid returns a negative value
throw IdComponentException("isValid", "H5Iis_valid failed");
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Iis_valid
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Iis_1valid
(JNIEnv *env, jclass clss, jlong obj_id)
{
htri_t bval = JNI_FALSE;
bval = H5Iis_valid((hid_t)obj_id);
if (bval > 0)
bval = JNI_TRUE;
else if (bval < 0)
h5libraryError(env);
return (jboolean)bval;
} /* end Java_hdf_hdf5lib_H5_H5Iis_1valid */
void TestH5::setUp() {
unsigned int &openMode = open_mode();
if (openMode == H5F_ACC_TRUNC) {
h5file = H5Fcreate("test_h5.h5", openMode, H5P_DEFAULT, H5P_DEFAULT);
} else {
h5file = H5Fopen("test_h5.h5", openMode, H5P_DEFAULT);
}
CPPUNIT_ASSERT(H5Iis_valid(h5file));
hid_t g;
if (openMode == H5F_ACC_TRUNC) {
g = H5Gcreate2(h5file, "h5", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
} else {
g = H5Gopen2(h5file, "h5", H5P_DEFAULT);
}
CPPUNIT_ASSERT(H5Iis_valid(g));
h5group = nix::hdf5::Group(g);
openMode = H5F_ACC_RDWR;
}
// Check for path validity
char AH5_path_valid(hid_t loc_id, const char *path)
{
char *temp;
int i, slashes = 0;
temp = strdup(path);
for (i = (int) strlen(path); i > 0; i--)
{
if (temp[i] == '/')
{
temp[i] = '\0';
slashes++; /* count number of slashes excluding the first one */
}
}
if (strcmp(path, ".") == 0)
{
if (!H5Iis_valid(loc_id))
{
free(temp);
return AH5_FALSE;
}
}
else
{
if(H5Lexists(loc_id, temp, H5P_DEFAULT) != AH5_TRUE)
{
free(temp);
return AH5_FALSE;
}
}
i = 1;
while (slashes > 0)
{
while (temp[i] != '\0')
i++;
temp[i] = '/';
slashes--;
if(H5Lexists(loc_id, temp, H5P_DEFAULT) != AH5_TRUE)
{
free(temp);
return AH5_FALSE;
}
}
free(temp);
return AH5_TRUE;
}
/*----------------------------------------------------------------------------
* Name: h5iis_valid_c
* Purpose: Calls H5Iis_valid
* Inputs: obj_id - object identifier
* Outputs: 0 = false, 1 = true
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Tuesday, August 24, 2004
* Modifications:
*---------------------------------------------------------------------------*/
int_f
h5iis_valid_c(hid_t_f *obj_id, int_f *c_valid)
{
int ret_value;
htri_t c_ret_value;
/*
* Call H5Iis_valid
*/
if ((c_ret_value = H5Iis_valid(*obj_id)) < 0)
HGOTO_DONE(FAIL);
/* Set output & return values */
*c_valid = (int_f)c_ret_value;
ret_value=0;
done:
return ret_value;
}
FileHDF5::FileHDF5(const string &name, FileMode mode, Compression compression, OpenFlags flags) {
if (!fileExists(name)) {
mode = FileMode::Overwrite;
}
this->mode = mode;
this->compr = compression;
//we want hdf5 to keep track of the order in which links were created so that
//the order for indexed based accessors is stable cf. issue #387
H5Object fcpl = H5Pcreate(H5P_FILE_CREATE);
fcpl.check("Could not create file creation plist");
HErr res = H5Pset_link_creation_order(fcpl.h5id(), H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED);
res.check("Unable to create file (H5Pset_link_creation_order failed.)");
unsigned int h5mode = map_file_mode(mode);
bool is_create = !fileExists(name) || h5mode == H5F_ACC_TRUNC;
if (is_create) {
hid = H5Fcreate(name.c_str(), h5mode, fcpl.h5id(), H5P_DEFAULT);
} else {
hid = H5Fopen(name.c_str(), h5mode, H5P_DEFAULT);
}
if (!H5Iis_valid(hid)) {
throw H5Exception("Could not open/create file");
}
openRoot();
if (is_create) {
createHeader();
} else if (!checkHeader(mode) && (flags & OpenFlags::Force) != OpenFlags::Force) {
throw nix::InvalidFile("FileHDF5::open_existing!");
}
metadata = root.openGroup("metadata");
data = root.openGroup("data");
setCreatedAt();
setUpdatedAt();
}
int main(int argc, char *argv[])
{
hid_t fid = -1;
hid_t access_plist = -1;
hid_t create_plist = -1;
hid_t cparm = -1;
hid_t datatype = -1;
hid_t dataspace = -1;
hid_t dataset = -1;
hid_t memspace = -1;
hid_t groupDetector = -1;
int rank = 1;
hsize_t chunk[2] = {10,10};
hsize_t dims[2] = {1,1};
hsize_t elementSize[2] = {1,1};
hsize_t maxdims[2] = {H5S_UNLIMITED,H5S_UNLIMITED};
int ivalue[2];
int fillValue = 0;
/* Open the source file and dataset */
/* All SWMR files need to use the latest file format */
access_plist = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(access_plist, H5F_CLOSE_STRONG);
#if H5_VERSION_GE(1,9,178)
H5Pset_object_flush_cb(access_plist, cFlushCallback, NULL);
#endif
H5Pset_libver_bounds(access_plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
create_plist = H5Pcreate(H5P_FILE_CREATE);
fid = H5Fcreate("test_string_swmr.h5", H5F_ACC_TRUNC, create_plist, access_plist);
/* Data */
rank = 2;
dims[0] = 10;
dims[1] = 10;
dataspace = H5Screate_simple(rank, dims, dims);
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(cparm, rank, chunk);
datatype = H5Tcopy(H5T_NATIVE_INT8);
H5Pset_fill_value(cparm, datatype, &fillValue);
groupDetector = H5Gcreate(fid, "detector", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
access_plist = H5Pcreate(H5P_DATASET_ACCESS);
H5Pset_chunk_cache(access_plist, 503, 100, 1.0);
dataset = H5Dcreate2(groupDetector, "data1",
datatype, dataspace,
H5P_DEFAULT, cparm, access_plist);
ivalue[0] = 1;
ivalue[1] = 1;
writeInt32Attribute(dataset, "NDArrayDimBinning", 2, ivalue);
ivalue[0] = 0;
ivalue[1] = 0;
writeInt32Attribute(dataset, "NDArrayDimOffset", 2, ivalue);
writeInt32Attribute(dataset, "NDArrayDimReverse", 2, ivalue);
ivalue[0] = 2;
writeInt32Attribute(dataset, "NDArrayNumDims", 1, ivalue);
H5Gclose(groupDetector);
dims[0] = 1;
dims[1] = 1;
chunk[0] = 1;
rank = 1;
/* Unique ID */
datatype = H5T_NATIVE_INT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayUniqueId",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayUniqueId");
writeStringAttribute(dataset, "NDAttrDescription", "The unique ID of the NDArray");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* EPICS Timestemp */
datatype = H5T_NATIVE_DOUBLE;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayTimeStamp",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayTimeStamp");
writeStringAttribute(dataset, "NDAttrDescription", "The timestamp of the NDArray as float64");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* EPICS TS sec */
datatype = H5T_NATIVE_UINT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayEpicsTSSec",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayEpicsTSSec");
writeStringAttribute(dataset, "NDAttrDescription", "The NDArray EPICS timestamp seconds past epoch");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* EPICS TS nsec */
datatype = H5T_NATIVE_UINT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "NDArrayEpicsTSnSec",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "NDArrayEpicsTSnSec");
writeStringAttribute(dataset, "NDAttrDescription", "The NDArray EPICS timestamp nanoseconds");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* Color mode */
datatype = H5T_NATIVE_INT32;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "ColorMode",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "ColorMode");
writeStringAttribute(dataset, "NDAttrDescription", "Color mode");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceDriver");
writeStringAttribute(dataset, "NDAttrSource", "Driver");
/* Camera manufacturer */
datatype = H5Tcopy(H5T_C_S1);
H5Tset_size(datatype, 256);
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(cparm, datatype, &fillValue);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "CameraManufacturer",
datatype, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
memspace = H5Screate_simple(rank, elementSize, NULL);
writeStringAttribute(dataset, "NDAttrName", "CameraManufacturer");
writeStringAttribute(dataset, "NDAttrDescription", "Camera manufacturer");
writeStringAttribute(dataset, "NDAttrSourceType", "NDAttrSourceParam");
writeStringAttribute(dataset, "NDAttrSource", "MANUFACTURER");
/* Performance data */
rank = 2;
dims[0] = 1;
dims[1] = 5;
chunk[1] = 5;
cparm = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(cparm, rank, chunk);
dataspace = H5Screate_simple(rank, dims, maxdims);
dataset = H5Dcreate2(fid, "timestamp",
H5T_NATIVE_DOUBLE, dataspace,
H5P_DEFAULT, cparm, H5P_DEFAULT);
if (!H5Iis_valid(dataset)) {
printf("Error writing performance dataset");
}
H5Sclose(dataspace);
#if H5_VERSION_GE(1,9,178)
H5Fstart_swmr_write(fid);
#endif
H5Fclose(fid);
return 0;
} /* end main */
/* Test the H5Iis_valid function */
static int test_is_valid(void)
{
hid_t dtype; /* datatype id */
int64_t nmembs1; /* number of type memnbers */
int64_t nmembs2;
htri_t tri_ret; /* htri_t return value */
herr_t ret; /* return value */
/* Create a datatype id */
dtype = H5Tcopy(H5T_NATIVE_INT);
CHECK(dtype, FAIL, "H5Tcopy");
if (dtype < 0)
goto out;
/* Check that the ID is valid */
tri_ret = H5Iis_valid(dtype);
VERIFY(tri_ret, TRUE, "H5Iis_valid");
if (tri_ret != TRUE)
goto out;
/* Artificially manipulate the reference counts so app_count is 0, and dtype
* appears to be an internal id. This takes advantage of the fact that
* H5Ipkg is included.
*/
ret = H5I_inc_ref(dtype, FALSE);
CHECK(ret, FAIL, "H5I_inc_ref");
if (ret < 0)
goto out;
ret = H5I_dec_app_ref(dtype);
CHECK(ret, FAIL, "H5I_dec_ref");
if (ret < 0)
goto out;
/* Check that dtype is invalid */
tri_ret = H5Iis_valid(dtype);
VERIFY(tri_ret, FALSE, "H5Iis_valid");
if (tri_ret != FALSE)
goto out;
/* Close dtype and verify that it has been closed */
nmembs1 = H5I_nmembers(H5I_DATATYPE);
CHECK(nmembs1, FAIL, "H5I_nmembers");
if (nmembs1 < 0)
goto out;
ret = H5I_dec_ref(dtype);
CHECK(ret, FAIL, "H5I_dec_ref");
if (ret < 0)
goto out;
nmembs2 = H5I_nmembers(H5I_DATATYPE);
VERIFY(nmembs2, nmembs1 - 1, "H5I_nmembers");
if (nmembs2 != nmembs1 - 1)
goto out;
/* Check that dtype is invalid */
tri_ret = H5Iis_valid(dtype);
VERIFY(tri_ret, FALSE, "H5Iis_valid");
if (tri_ret != FALSE)
goto out;
/* Check that an id of -1 is invalid */
tri_ret = H5Iis_valid((hid_t)-1);
VERIFY(tri_ret, FALSE, "H4Iis_valid");
if (tri_ret != FALSE)
goto out;
return 0;
out:
/* Don't attempt to close dtype as we don't know the exact state of the
* reference counts. Every state in this function will be automatically
* closed at library exit anyways, as internal count is never > 1.
*/
return -1;
}
file::file(h5_object obj) : h5_object(std::move(obj)) {
if (!H5Iis_valid(this->id)) TRIQS_RUNTIME_ERROR << "Invalid input in h5::file constructor from id";
if (H5Iget_type(this->id) != H5I_FILE) TRIQS_RUNTIME_ERROR << "h5::file constructor must take the id of a file ";
}
~group() {
if (H5Iis_valid(_self) > 0) {
H5Gclose(_self);
}
}
