mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-06-12 12:57:13 +02:00
created virtual datasets for bunchid and subframenumber
This commit is contained in:
Dhanya Maliakal
@ -104,13 +104,16 @@ public:
|
||||
* @param ds dataset pointer
|
||||
*/
|
||||
|
||||
static void CloseDataFile(int ind, H5File*& fd, DataSpace*& dp, DataSet*& ds)
|
||||
static void CloseDataFile(int ind, H5File*& fd, DataSpace*& dp, DataSet*& ds,
|
||||
DataSet*& ds_p1, DataSet*& ds_p2)
|
||||
{
|
||||
try {
|
||||
Exception::dontPrint(); //to handle errors
|
||||
if(dp) {delete dp; dp = 0;}
|
||||
if(ds) {delete ds; ds = 0;}
|
||||
if(fd) {delete fd; fd = 0;}
|
||||
if(dp) {delete dp; dp = 0;}
|
||||
if(ds) {delete ds; ds = 0;}
|
||||
if(ds_p1) {delete ds_p1; ds_p1 = 0;}
|
||||
if(ds_p2) {delete ds_p2; ds_p2 = 0;}
|
||||
if(fd) {delete fd; fd = 0;}
|
||||
} catch(Exception error) {
|
||||
cprintf(RED,"Error in closing HDF5 handles\n");
|
||||
error.printError();
|
||||
@ -182,6 +185,34 @@ public:
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Write Parameter Arrays as datasets (to virtual file)
|
||||
*/
|
||||
template <typename P1, typename P2>
|
||||
static int WriteParameterDatasets(int ind, DataSpace* dspace_para, uint64_t fnum,
|
||||
DataSet*& dset_para1, DataType dtype_para1, P1* para1,
|
||||
DataSet*& dset_para2, DataType dtype_para2, P2* para2)
|
||||
{
|
||||
hsize_t count[1] = {1};
|
||||
hsize_t start[1] = {fnum};
|
||||
hsize_t dims2[2] = {1};
|
||||
try{
|
||||
Exception::dontPrint(); //to handle errors
|
||||
dspace_para->selectHyperslab( H5S_SELECT_SET, count, start);
|
||||
DataSpace memspace(H5S_SCALAR);
|
||||
dset_para1->write(para1, dtype_para1, memspace, *dspace_para);
|
||||
dset_para2->write(para2, dtype_para2, memspace, *dspace_para);
|
||||
}
|
||||
catch(Exception error){
|
||||
cprintf(RED,"Error in writing parameters to file in object %d\n",ind);
|
||||
error.printError();
|
||||
return 1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Create master file
|
||||
* @param fname master file name
|
||||
@ -307,12 +338,22 @@ public:
|
||||
* @param dset dataset pointer
|
||||
* @param version version of software for hdf5 writing
|
||||
* @param maxchunkedimages maximum chunked images
|
||||
* @param dspace_para dataspace of parameters
|
||||
* @param para1 parameter 1 name
|
||||
* @param dset_para1 dataset of parameter 1
|
||||
* @param dtype_para1 datatype of parameter 1
|
||||
* @param para2 parameter 2 name
|
||||
* @param dset_para2 dataset of parameter 2
|
||||
* @param dtype_para2 datatype of parameter 2
|
||||
* @returns 0 for success and 1 for fail
|
||||
*/
|
||||
static int CreateDataFile(int ind, bool owenable, string fname, bool frindexenable,
|
||||
uint64_t fnum, uint64_t nDimx, uint32_t nDimy, uint32_t nDimz,
|
||||
DataType dtype, H5File*& fd, DataSpace*& dspace, DataSet*& dset,
|
||||
double version, uint64_t maxchunkedimages)
|
||||
double version, uint64_t maxchunkedimages,
|
||||
DataSpace*& dspace_para,
|
||||
string para1, DataSet*& dset_para1, DataType dtype_para1,
|
||||
string para2, DataSet*& dset_para2, DataType dtype_para2)
|
||||
{
|
||||
try {
|
||||
Exception::dontPrint(); //to handle errors
|
||||
@ -351,6 +392,11 @@ public:
|
||||
}else
|
||||
dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace));
|
||||
|
||||
//create parameter datasets
|
||||
hsize_t dims[1] = {nDimx};
|
||||
dspace_para = new DataSpace (1,dims);
|
||||
dset_para1 = new DataSet(fd->createDataSet(para1.c_str(), dtype_para1, *dspace_para));
|
||||
dset_para2 = new DataSet(fd->createDataSet(para2.c_str(), dtype_para2, *dspace_para));
|
||||
}
|
||||
catch(Exception error){
|
||||
cprintf(RED,"Error in creating HDF5 handles in object %d\n",ind);
|
||||
@ -366,13 +412,19 @@ public:
|
||||
/**
|
||||
* Create virtual file
|
||||
* (in C because H5Pset_virtual doesnt exist yet in C++)
|
||||
* @param fd virtual file handle
|
||||
* @param virtualfname virtual file name
|
||||
* @param virtualDatasetname virtual dataset name
|
||||
* @param srcDatasetname source dataset name
|
||||
* @param spara1Datasetname source dataset name of parameter 1
|
||||
* @param vpara1DatasetName virtual dataset name of parameter 1
|
||||
* @param dtype_para1 datatype of parameter 1
|
||||
* @param spara1Datasetname source dataset name of parameter 1
|
||||
* @param vpara2DatasetName virtual dataset name of parameter 2
|
||||
* @param dtype_para2 datatype of parameter 2
|
||||
* @param numFiles number of files
|
||||
* @param fileNames array of file names
|
||||
* @param owenable overwrite enable
|
||||
* @param fnum current frame number
|
||||
* @param dtype datatype
|
||||
* @param srcNDimx source number of objects in x dimension (Number of images)
|
||||
* @param srcNDimy source number of objects in y dimension (Number of pixels in y dir)
|
||||
@ -384,115 +436,222 @@ public:
|
||||
* @returns 0 for success and 1 for fail
|
||||
*/
|
||||
static int CreateVirtualDataFile(hid_t& fd, string virtualfname, string virtualDatasetname, string srcDatasetname,
|
||||
int numFiles, string fileNames[], bool owenable, uint64_t fnum, hid_t dtype,
|
||||
string spara1DatasetName, string vpara1DatasetName, hid_t dtype_para1,
|
||||
string spara2DatasetName, string vpara2DatasetName, hid_t dtype_para2,
|
||||
int numFiles, string fileNames[], bool owenable, hid_t dtype,
|
||||
uint64_t srcNDimx, uint32_t srcNDimy, uint32_t srcNDimz,
|
||||
uint64_t dstNDimx, uint32_t dstNDimy, uint32_t dstNDimz, double version)
|
||||
{
|
||||
|
||||
//file
|
||||
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
|
||||
if (dfal >= 0) {
|
||||
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) >= 0) {
|
||||
if(!owenable) fd = H5Fcreate( virtualfname.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, dfal);
|
||||
else fd = H5Fcreate( virtualfname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
|
||||
if (fd >= 0) {
|
||||
if (dfal < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating file access property for virtual file ") + virtualfname + string("\n"));
|
||||
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
|
||||
return CloseFileOnError(fd, string("Error in setting strong file close degree for virtual file ") + virtualfname + string("\n"));
|
||||
if(!owenable)
|
||||
fd = H5Fcreate( virtualfname.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, dfal);
|
||||
else
|
||||
fd = H5Fcreate( virtualfname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
|
||||
if (fd < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//attributes - version
|
||||
hid_t dataspace_attr = H5Screate (H5S_SCALAR);
|
||||
if (dataspace_attr >= 0) {
|
||||
hid_t attrid = H5Acreate2 (fd, "version", H5T_NATIVE_DOUBLE, dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
|
||||
if (attrid >= 0) {
|
||||
double attr_data = version;
|
||||
if (H5Awrite (attrid, H5T_NATIVE_DOUBLE, &attr_data) >= 0) {
|
||||
if (H5Aclose (attrid) >= 0) {
|
||||
|
||||
//dataspace
|
||||
hsize_t vdsdims[3] = {dstNDimx, dstNDimy, dstNDimz};
|
||||
hid_t vdsDataspace = H5Screate_simple(3, vdsdims ,NULL);
|
||||
if (vdsDataspace >= 0) {
|
||||
hsize_t srcdims[3] = {srcNDimx, srcNDimy, srcNDimz};
|
||||
hid_t srcDataspace = H5Screate_simple(3, srcdims, NULL);
|
||||
if (srcDataspace >= 0) {
|
||||
//attributes - version
|
||||
hid_t dataspace_attr = H5Screate (H5S_SCALAR);
|
||||
if (dataspace_attr < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating dataspace for attribute in virtual file ") + virtualfname + string("\n"));
|
||||
hid_t attrid = H5Acreate2 (fd, "version", H5T_NATIVE_DOUBLE, dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
|
||||
if (attrid < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating attribute in virtual file ") + virtualfname + string("\n"));
|
||||
double attr_data = version;
|
||||
if (H5Awrite (attrid, H5T_NATIVE_DOUBLE, &attr_data) < 0)
|
||||
return CloseFileOnError(fd, string("Error in writing attribute in virtual file ") + virtualfname + string("\n"));
|
||||
if (H5Aclose (attrid) < 0)
|
||||
return CloseFileOnError(fd, string("Error in closing attribute in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//fill values
|
||||
hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
|
||||
if (dcpl >= 0) {
|
||||
int fill_value = -1;
|
||||
if (H5Pset_fill_value (dcpl, dtype, &fill_value) >= 0) {
|
||||
|
||||
//hyperslab
|
||||
hsize_t offset[3]={0,0,0},count[3]={srcNDimx,srcNDimy, srcNDimz};
|
||||
bool error = false;
|
||||
for (int i = 0; i < numFiles; i++) {
|
||||
//cout<<"("<<offset[0]<<","<<offset[1]<<","<<offset[2]<<")"<<endl;
|
||||
if (H5Sselect_hyperslab (vdsDataspace, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) {
|
||||
cprintf(RED,"could not select hyperslab\n");
|
||||
error = true;
|
||||
break;
|
||||
}
|
||||
if (H5Pset_virtual(dcpl, vdsDataspace, fileNames[i].c_str(), srcDatasetname.c_str(), srcDataspace) < 0) {
|
||||
cprintf(RED,"could not set mapping\n");
|
||||
error = true;
|
||||
break;
|
||||
}
|
||||
offset[2] += srcNDimz;
|
||||
if(offset[2] >= dstNDimz){
|
||||
offset[2] = 0;
|
||||
offset[1] += srcNDimy;
|
||||
}
|
||||
}
|
||||
if (!error) {
|
||||
|
||||
//dataset
|
||||
hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetname.c_str(), dtype, vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
||||
if (vdsdataset >= 0){
|
||||
//**data dataset**
|
||||
//dataspace
|
||||
hsize_t vdsdims[3] = {dstNDimx, dstNDimy, dstNDimz};
|
||||
hid_t vdsDataspace = H5Screate_simple(3, vdsdims ,NULL);
|
||||
if (vdsDataspace < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating virtual dataspace in virtual file ") + virtualfname + string("\n"));
|
||||
hsize_t srcdims[3] = {srcNDimx, srcNDimy, srcNDimz};
|
||||
hid_t srcDataspace = H5Screate_simple(3, srcdims, NULL);
|
||||
if (srcDataspace < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating source dataspace in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
H5Sclose(vdsDataspace);vdsDataspace = 0;
|
||||
H5Sclose(srcDataspace);srcDataspace = 0;
|
||||
H5Dclose(vdsdataset);vdsdataset = 0;
|
||||
H5Fclose(fd);fd = 0;
|
||||
return 0;
|
||||
//fill values
|
||||
hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
|
||||
if (dcpl < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating file creation properties in virtual file ") + virtualfname + string("\n"));
|
||||
int fill_value = -1;
|
||||
if (H5Pset_fill_value (dcpl, dtype, &fill_value) < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating fill value in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
} else cprintf(RED, "could not create virtual dataset in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not map files in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not fill values in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not create dcpl in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not create source dataspace in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not create virtual dataspace in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not close attribute in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not write attribute in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not create attribute in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not create dataspace for attribute in virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not create virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not set strong file close degree for virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not create dfal for virtual file %s\n", virtualfname.c_str());
|
||||
|
||||
H5Fclose(fd);
|
||||
fd = 0;
|
||||
return 1;
|
||||
//hyperslab
|
||||
hsize_t offset[3]={0, 0, 0},
|
||||
count[3]={srcNDimx, srcNDimy, srcNDimz};
|
||||
bool error = false;
|
||||
for (int i = 0; i < numFiles; i++) {
|
||||
if (H5Sselect_hyperslab (vdsDataspace, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) {
|
||||
cprintf(RED,"could not select hyperslab\n");
|
||||
error = true;
|
||||
break;
|
||||
}
|
||||
if (H5Pset_virtual(dcpl, vdsDataspace, fileNames[i].c_str(), srcDatasetname.c_str(), srcDataspace) < 0) {
|
||||
cprintf(RED,"could not set mapping\n");
|
||||
error = true;
|
||||
break;
|
||||
}
|
||||
offset[2] += srcNDimz;
|
||||
if (offset[2] >= dstNDimz) {
|
||||
offset[2] = 0;
|
||||
offset[1] += srcNDimy;
|
||||
}
|
||||
}
|
||||
if (error)
|
||||
return CloseFileOnError(fd, string("Error in mapping files in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//dataset
|
||||
hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetname.c_str(), dtype, vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
||||
if (vdsdataset < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating virutal dataset in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//close
|
||||
H5Sclose(vdsDataspace);
|
||||
H5Sclose(srcDataspace);
|
||||
H5Dclose(vdsdataset);
|
||||
|
||||
|
||||
|
||||
//**paramter datasets**
|
||||
//dataspace
|
||||
hsize_t vdsdims_para[2] = {dstNDimx, numFiles};
|
||||
hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, NULL);
|
||||
if (vdsDataspace_para < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating virtual dataspace (parameters) in virtual file ") + virtualfname + string("\n"));
|
||||
hsize_t srcdims_para[1] = {srcNDimx};
|
||||
hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, NULL);
|
||||
if (srcDataspace_para < 0)
|
||||
return CloseFileOnError(fd, string("Error in creating source dataspace (parameters) in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//fill values
|
||||
hid_t dcpl1 = H5Pcreate (H5P_DATASET_CREATE);
|
||||
hid_t dcpl2 = H5Pcreate (H5P_DATASET_CREATE);
|
||||
if ((dcpl1 < 0) || (dcpl2 < 0))
|
||||
return CloseFileOnError(fd, string("Error in creating file creation properties (parameters) in virtual file ") + virtualfname + string("\n"));
|
||||
fill_value = -1;
|
||||
if ((H5Pset_fill_value (dcpl1, dtype_para1, &fill_value) < 0) || (H5Pset_fill_value (dcpl2, dtype_para2, &fill_value) < 0))
|
||||
return CloseFileOnError(fd, string("Error in creating fill value (parameters) in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//hyperslab
|
||||
hsize_t offset_para[2] = {0,0},
|
||||
count_para[2] = {dstNDimx,1};
|
||||
error = false;
|
||||
for (int i = 0; i < numFiles; i++) {
|
||||
//cout<<"("<<offset[0]<<","<<offset[1]<<","<<offset[2]<<")"<<endl;
|
||||
if (H5Sselect_hyperslab (vdsDataspace_para, H5S_SELECT_SET, offset_para, NULL, count_para, NULL) < 0) {
|
||||
cprintf(RED,"could not select hyperslab\n");
|
||||
error = true;
|
||||
break;
|
||||
}
|
||||
if (H5Pset_virtual(dcpl1, vdsDataspace_para, fileNames[i].c_str(), spara1DatasetName.c_str(), srcDataspace_para) < 0) {
|
||||
cprintf(RED,"could not set mapping for paramter 1\n");
|
||||
error = true;
|
||||
break;
|
||||
}
|
||||
if (H5Pset_virtual(dcpl2, vdsDataspace_para, fileNames[i].c_str(), spara2DatasetName.c_str(), srcDataspace_para) < 0) {
|
||||
cprintf(RED,"could not set mapping for paramter 2\n");
|
||||
error = true;
|
||||
break;
|
||||
}
|
||||
offset_para[1] ++;
|
||||
}
|
||||
if (error)
|
||||
return CloseFileOnError(fd, string("Error in mapping files (parameters) in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//dataset
|
||||
hid_t vdsdataset1 = H5Dcreate2 (fd, vpara1DatasetName.c_str(), dtype_para1, vdsDataspace_para, H5P_DEFAULT, dcpl1, H5P_DEFAULT);
|
||||
hid_t vdsdataset2 = H5Dcreate2 (fd, vpara2DatasetName.c_str(), dtype_para2, vdsDataspace_para, H5P_DEFAULT, dcpl2, H5P_DEFAULT);
|
||||
if ((vdsdataset1 < 0) && (vdsdataset1 < 0))
|
||||
return CloseFileOnError(fd, string("Error in creating virutal dataset (parameters) in virtual file ") + virtualfname + string("\n"));
|
||||
|
||||
//close
|
||||
H5Sclose(vdsDataspace_para);
|
||||
H5Sclose(srcDataspace_para);
|
||||
H5Dclose(vdsdataset1);
|
||||
H5Dclose(vdsdataset2);
|
||||
|
||||
H5Fclose(fd); fd = 0;
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Copy file to another file (mainly to view virutal files in hdfviewer)
|
||||
* @param dataType data type
|
||||
* @param owenable overwrite enable
|
||||
* @param oldFileName file name including path of file to copy
|
||||
* @param oldDatasetName dataset name to copy
|
||||
* @param newFileName file name including path of file to copy to
|
||||
* @param newDatasetName dataset name to copy to
|
||||
* @param rank rank
|
||||
* @param nDimx Number of objects in x dimension
|
||||
* @param nDimy Number of objects in y dimension
|
||||
* @param nDimz Number of objects in z dimension
|
||||
* @param dataType data type
|
||||
* @returns 0 for success and 1 for fail
|
||||
*/
|
||||
template <typename T>
|
||||
static int CopyVirtualFile(bool owenable, string oldFileName, string oldDatasetName,
|
||||
string newFileName, string newDatasetName,
|
||||
uint64_t nDimx, uint32_t nDimy, uint32_t nDimz, T datatype)
|
||||
static int CopyVirtualFile(T datatype, bool owenable, string oldFileName, string oldDatasetName,
|
||||
string newFileName, string newDatasetName, int rank,
|
||||
uint64_t nDimx, uint32_t nDimy, uint32_t nDimz=0)
|
||||
{
|
||||
|
||||
T *data_out = (T*)malloc(sizeof(T)*(nDimx*nDimy*nDimz));
|
||||
T *data_out;
|
||||
switch (rank) {
|
||||
case 2:
|
||||
data_out = (T*)malloc(sizeof(T)*(nDimx*nDimy));
|
||||
break;
|
||||
case 3:
|
||||
data_out = (T*)malloc(sizeof(T)*(nDimx*nDimy*nDimz));
|
||||
break;
|
||||
default:
|
||||
cprintf(RED,"invalid rank. Options: 2 or 3\n");
|
||||
return 0;
|
||||
}
|
||||
if (datatype == PredType::STD_U16LE) {
|
||||
printf("datatype:16\n");
|
||||
} else if (datatype == PredType::STD_U32LE) {
|
||||
printf("datatype:32\n");
|
||||
} else if (datatype == PredType::STD_U64LE) {
|
||||
printf("datatype:64\n");
|
||||
} else if (datatype == PredType::STD_U8LE) {
|
||||
printf("datatype:8\n");
|
||||
} else {
|
||||
cprintf(RED, "unknown datatype\n");
|
||||
return 1;
|
||||
}
|
||||
printf("owenable:%d\n"
|
||||
"oldFileName:%s\n"
|
||||
"oldDatasetName:%s\n"
|
||||
"newFileName:%s\n"
|
||||
"newDatasetName:%s\n"
|
||||
"rank:%d\n"
|
||||
"nDimx:%llu\n"
|
||||
"nDimy:%u\n"
|
||||
"nDimz:%u\n",
|
||||
owenable?1:0,
|
||||
oldFileName.c_str(),
|
||||
oldDatasetName.c_str(),
|
||||
newFileName.c_str(),
|
||||
newDatasetName.c_str(),
|
||||
rank,
|
||||
(long long unsigned int)nDimx,
|
||||
nDimy,
|
||||
nDimz);
|
||||
|
||||
H5File* oldfd;
|
||||
H5File* newfd;
|
||||
@ -512,8 +671,14 @@ public:
|
||||
else
|
||||
newfd = new H5File( newFileName.c_str(), H5F_ACC_TRUNC, NULL, fapl );
|
||||
//dataspace and dataset
|
||||
hsize_t dims[3] = {nDimx, nDimy, nDimz};
|
||||
DataSpace* newDataspace = new DataSpace (3,dims);
|
||||
DataSpace* newDataspace;
|
||||
if (rank == 3) {
|
||||
hsize_t dims[3] = {nDimx, nDimy, nDimz};
|
||||
newDataspace = new DataSpace (3,dims);
|
||||
} else if (rank == 2) {
|
||||
hsize_t dims[2] = {nDimx, nDimy};
|
||||
newDataspace = new DataSpace (2,dims);
|
||||
}
|
||||
DataSet* newDataset = new DataSet( newfd->createDataSet(newDatasetName.c_str(), datatype, *newDataspace));
|
||||
//write and close
|
||||
newDataset->write(data_out,datatype);
|
||||
@ -537,46 +702,90 @@ public:
|
||||
/**
|
||||
* Link the Virtual File in the Master File
|
||||
* In C because H5Lcreate_external exists only in C
|
||||
* @param masterFileName master file name
|
||||
* @param virtualfname virtual file name
|
||||
* @param virtualDatasetname virtual dataset name
|
||||
* @param masterFileName master file name
|
||||
* @returns 0 for success and 1 for fail
|
||||
*/
|
||||
int LinkVirtualInMaster(string virtualfname, string virtualDatasetname, string masterFileName) {
|
||||
int LinkVirtualInMaster(string masterFileName, string virtualfname, string virtualDatasetname,
|
||||
string virtualpara1DatasetName, string virtualpara2DatasetName) {
|
||||
char linkname[100];
|
||||
sprintf(linkname, "/entry/data/%s",virtualDatasetname.c_str());
|
||||
hid_t mfd=-1, vfd=-1, vdset=-1;
|
||||
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
|
||||
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) >= 0) {
|
||||
mfd = H5Fopen( masterFileName.c_str(), H5F_ACC_RDWR, dfal);
|
||||
if (mfd >= 0) {
|
||||
vfd = H5Fopen( virtualfname.c_str(), H5F_ACC_RDWR, dfal);
|
||||
if (vfd >= 0) {
|
||||
vdset = H5Dopen2( vfd, virtualDatasetname.c_str(), H5P_DEFAULT);
|
||||
if (vdset >= 0) {
|
||||
if(H5Lcreate_external( virtualfname.c_str(), virtualDatasetname.c_str(),
|
||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) >= 0) {
|
||||
H5Dclose(vdset);
|
||||
H5Fclose(mfd);
|
||||
H5Fclose(vfd);
|
||||
return 0;
|
||||
cprintf(BLUE,"link created!\n");
|
||||
} else cprintf(RED, "could not create link\n");
|
||||
} else cprintf(RED, "could not open virtual dataset %s\n", virtualDatasetname.c_str());
|
||||
} else cprintf(RED, "could not open virtual file %s\n", virtualfname.c_str());
|
||||
} else cprintf(RED, "could not open master file %s\n", masterFileName.c_str());
|
||||
}else cprintf(RED, "could not set strong file close degree\n");
|
||||
hid_t vfd = 0;
|
||||
|
||||
if(vdset >=0 ) H5Dclose(vdset);
|
||||
if(mfd >=0 ) H5Fclose(mfd);
|
||||
if(vfd >=0 ) H5Fclose(vfd);
|
||||
return 1;
|
||||
hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
|
||||
if (dfal < 0)
|
||||
return CloseFileOnError( vfd, string("Error in creating file access property for link\n"));
|
||||
if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
|
||||
return CloseFileOnError( vfd, string("Error in setting strong file close degree for link\n"));
|
||||
|
||||
//open master file
|
||||
hid_t mfd = H5Fopen( masterFileName.c_str(), H5F_ACC_RDWR, dfal);
|
||||
if (mfd < 0)
|
||||
return CloseFileOnError( vfd, string("Error in opening master file\n"));
|
||||
|
||||
//open virtual file
|
||||
vfd = H5Fopen( virtualfname.c_str(), H5F_ACC_RDWR, dfal);
|
||||
if (vfd < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in opening virtual file\n"));
|
||||
}
|
||||
|
||||
//**data dataset**
|
||||
hid_t vdset = H5Dopen2( vfd, virtualDatasetname.c_str(), H5P_DEFAULT);
|
||||
if (vdset < 0) {
|
||||
H5Fclose(mfd);
|
||||
return CloseFileOnError( vfd, string("Error in opening virtual data dataset\n"));
|
||||
}
|
||||
sprintf(linkname, "/entry/data/%s",virtualDatasetname.c_str());
|
||||
if(H5Lcreate_external( virtualfname.c_str(), virtualDatasetname.c_str(),
|
||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in creating link to data dataset\n"));
|
||||
}
|
||||
H5Dclose(vdset);
|
||||
|
||||
//**paramter datasets**
|
||||
hid_t vdset1 = H5Dopen2( vfd, virtualpara1DatasetName.c_str(), H5P_DEFAULT);
|
||||
hid_t vdset2 = H5Dopen2( vfd, virtualpara2DatasetName.c_str(), H5P_DEFAULT);
|
||||
if ((vdset1 < 0) || (vdset2 < 0)) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in opening virtual parameter dataet to create link\n"));
|
||||
}
|
||||
sprintf(linkname, "/entry/data/%s",virtualpara1DatasetName.c_str());
|
||||
if(H5Lcreate_external( virtualfname.c_str(), virtualpara1DatasetName.c_str(),
|
||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in creating link to virtual parameter 1 dataset\n"));
|
||||
}
|
||||
sprintf(linkname, "/entry/data/%s",virtualpara2DatasetName.c_str());
|
||||
if(H5Lcreate_external( virtualfname.c_str(), virtualpara2DatasetName.c_str(),
|
||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in creating link to virtual parameter 2 dataset\n"));
|
||||
}
|
||||
H5Dclose(vdset1);
|
||||
H5Dclose(vdset2);
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
H5Fclose(vfd); vfd = 0;
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Print Error msg and Close File and called on error
|
||||
* @returns 1 for fail
|
||||
*/
|
||||
static int CloseFileOnError(hid_t& fd, const string msg) {
|
||||
cprintf(RED, "%s", msg.c_str());
|
||||
if(fd > 0) H5Fclose(fd); fd = 0;
|
||||
return 1;
|
||||
}
|
||||
|
||||
|
||||
};
|
||||
|
||||
|
||||
|
||||
|
||||
#endif
|
||||
|
||||
Reference in New Issue
Block a user