mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-06-13 13:27:14 +02:00
changed to have only one virtual file with bunch id, subfnum and data datasets all linked in master file
This commit is contained in:
Dhanya Maliakal
@ -80,17 +80,13 @@ public:
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* @param fnameprefix file name prefix (includes scan and position variables)
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* @param fnum current frame number
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* @param findex file index
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* @param frindexenable frame index enable
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* @param fnum frame number index
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* @returns virtual file name
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*/
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static string CreateVirtualFileName(char* fpath, char* fnameprefix, uint64_t findex, bool frindexenable,
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uint64_t fnum)
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static string CreateVirtualFileName(char* fpath, char* fnameprefix, uint64_t findex)
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{
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ostringstream osfn;
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osfn << fpath << "/" << fnameprefix;
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osfn << "_virtual";
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if (frindexenable) osfn << "_f" << setfill('0') << setw(12) << fnum;
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osfn << "_" << findex;
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osfn << ".h5";
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return osfn.str();
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@ -408,185 +404,198 @@ public:
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}
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/**
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* Create virtual file
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* (in C because H5Pset_virtual doesnt exist yet in C++)
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* @param fd virtual file handle
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* @param virtualfname virtual file name
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* @param virtualDatasetname virtual dataset name
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* @param srcDatasetname source dataset name
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* @param spara1Datasetname source dataset name of parameter 1
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* @param vpara1DatasetName virtual dataset name of parameter 1
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* @param dtype_para1 datatype of parameter 1
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* @param spara1Datasetname source dataset name of parameter 1
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* @param vpara2DatasetName virtual dataset name of parameter 2
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* @param dtype_para2 datatype of parameter 2
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* @param numFiles number of files
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* @param fileNames array of file names
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* @param owenable overwrite enable
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* @param dtype datatype
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* @param srcNDimx source number of objects in x dimension (Number of images)
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* @param srcNDimy source number of objects in y dimension (Number of pixels in y dir)
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* @param srcNDimz source number of objects in z dimension (Number of pixels in x dir)
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* @param dstNDimx destination number of objects in x dimension (Number of images)
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* @param dstNDimy destination number of objects in y dimension (Number of pixels in y dir)
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* @param dstNDimz destination number of objects in z dimension (Number of pixels in x dir)
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* @param masterFileName master file name
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* @param fpath file path
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* @param fnameprefix file name prefix (includes scan and position variables)
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* @param findex file index
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* @param frindexenable frame index enable
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* @param dindex readout index
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* @param numunits number of units per readout. eg. eiger has 2 udp units per readout
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* @param maxFramesPerFile maximum frames per file
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* @param numf number of frames caught
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* @param srcDataseName source dataset name
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* @param srcP1DatasetName source parameter 1 dataset name
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* @param srcP2DatasetName source parameter 2 dataset name
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* @param dataType datatype of data dataset
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* @param p1DataType datatype of parameter 1
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* @param p2DataType datatype of parameter 2
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* @param numDety number of readouts in Y dir
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* @param numDetz number of readouts in Z dir
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* @param nDimy number of objects in y dimension in source file (Number of pixels in y dir)
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* @param nDimz number of objects in z dimension in source file (Number of pixels in x dir)
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* @param version version of software for hdf5 writing
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* @returns 0 for success and 1 for fail
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*/
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static int CreateVirtualDataFile(hid_t& fd, string virtualfname, string virtualDatasetname, string srcDatasetname,
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string spara1DatasetName, string vpara1DatasetName, hid_t dtype_para1,
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string spara2DatasetName, string vpara2DatasetName, hid_t dtype_para2,
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int numFiles, string fileNames[], bool owenable, hid_t dtype,
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uint64_t srcNDimx, uint32_t srcNDimy, uint32_t srcNDimz,
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uint64_t dstNDimx, uint32_t dstNDimy, uint32_t dstNDimz, double version)
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static int CreateVirtualDataFile(
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hid_t& fd, string masterFileName,
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char* fpath, char* fnameprefix, uint64_t findex, bool frindexenable,
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int dindex, int numunits,
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uint32_t maxFramesPerFile, uint64_t numf,
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string srcDataseName, string srcP1DatasetName, string srcP2DatasetName,
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DataType dataType, DataType p1DataType, DataType p2DataType,
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int numDety, int numDetz, uint32_t nDimy, uint32_t nDimz,
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double version)
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{
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//virtual names
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string virtualFileName = CreateVirtualFileName(fpath, fnameprefix, findex);
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printf("Virtual File: %s\n", virtualFileName.c_str());
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//file
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hid_t dfal = H5Pcreate (H5P_FILE_ACCESS);
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if (dfal < 0)
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return CloseFileOnError(fd, string("Error in creating file access property for virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in creating file access property for virtual file ") + virtualFileName + string("\n"));
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if (H5Pset_fclose_degree (dfal, H5F_CLOSE_STRONG) < 0)
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return CloseFileOnError(fd, string("Error in setting strong file close degree for virtual file ") + virtualfname + string("\n"));
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if(!owenable)
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fd = H5Fcreate( virtualfname.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, dfal);
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else
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fd = H5Fcreate( virtualfname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
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return CloseFileOnError(fd, string("Error in setting strong file close degree for virtual file ") + virtualFileName + string("\n"));
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fd = H5Fcreate( virtualFileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
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if (fd < 0)
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return CloseFileOnError(fd, string("Error in creating virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in creating virtual file ") + virtualFileName + string("\n"));
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//attributes - version
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hid_t dataspace_attr = H5Screate (H5S_SCALAR);
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if (dataspace_attr < 0)
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return CloseFileOnError(fd, string("Error in creating dataspace for attribute in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in creating dataspace for attribute in virtual file ") + virtualFileName + string("\n"));
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hid_t attrid = H5Acreate2 (fd, "version", H5T_NATIVE_DOUBLE, dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
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if (attrid < 0)
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return CloseFileOnError(fd, string("Error in creating attribute in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in creating attribute in virtual file ") + virtualFileName + string("\n"));
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double attr_data = version;
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if (H5Awrite (attrid, H5T_NATIVE_DOUBLE, &attr_data) < 0)
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return CloseFileOnError(fd, string("Error in writing attribute in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in writing attribute in virtual file ") + virtualFileName + string("\n"));
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if (H5Aclose (attrid) < 0)
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return CloseFileOnError(fd, string("Error in closing attribute in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in closing attribute in virtual file ") + virtualFileName + string("\n"));
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//**data dataset**
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//dataspace
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hsize_t vdsdims[3] = {dstNDimx, dstNDimy, dstNDimz};
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//virtual dataspace
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hsize_t vdsdims[3] = {numf, numDety * nDimy, numDetz * nDimz};
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hid_t vdsDataspace = H5Screate_simple(3, vdsdims ,NULL);
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if (vdsDataspace < 0)
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return CloseFileOnError(fd, string("Error in creating virtual dataspace in virtual file ") + virtualfname + string("\n"));
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hsize_t srcdims[3] = {srcNDimx, srcNDimy, srcNDimz};
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hid_t srcDataspace = H5Screate_simple(3, srcdims, NULL);
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if (srcDataspace < 0)
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return CloseFileOnError(fd, string("Error in creating source dataspace in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in creating virtual dataspace in virtual file ") + virtualFileName + string("\n"));
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hsize_t vdsdims_para[2] = {numf, numDety * numDetz};
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hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, NULL);
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if (vdsDataspace_para < 0)
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return CloseFileOnError(fd, string("Error in creating virtual dataspace (parameters) in virtual file ") + virtualFileName + string("\n"));
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//fill values
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hid_t dcpl = H5Pcreate (H5P_DATASET_CREATE);
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if (dcpl < 0)
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return CloseFileOnError(fd, string("Error in creating file creation properties in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in creating file creation properties in virtual file ") + virtualFileName + string("\n"));
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int fill_value = -1;
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if (H5Pset_fill_value (dcpl, dtype, &fill_value) < 0)
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return CloseFileOnError(fd, string("Error in creating fill value in virtual file ") + virtualfname + string("\n"));
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//hyperslab
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hsize_t offset[3]={0, 0, 0},
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count[3]={srcNDimx, srcNDimy, srcNDimz};
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bool error = false;
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for (int i = 0; i < numFiles; i++) {
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if (H5Sselect_hyperslab (vdsDataspace, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) {
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cprintf(RED,"could not select hyperslab\n");
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error = true;
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break;
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}
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if (H5Pset_virtual(dcpl, vdsDataspace, fileNames[i].c_str(), srcDatasetname.c_str(), srcDataspace) < 0) {
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cprintf(RED,"could not set mapping\n");
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error = true;
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break;
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}
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offset[2] += srcNDimz;
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if (offset[2] >= dstNDimz) {
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offset[2] = 0;
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offset[1] += srcNDimy;
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}
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}
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if (error)
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return CloseFileOnError(fd, string("Error in mapping files in virtual file ") + virtualfname + string("\n"));
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//dataset
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hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetname.c_str(), dtype, vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
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if (vdsdataset < 0)
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return CloseFileOnError(fd, string("Error in creating virutal dataset in virtual file ") + virtualfname + string("\n"));
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//close
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H5Sclose(vdsDataspace);
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H5Sclose(srcDataspace);
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H5Dclose(vdsdataset);
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//**paramter datasets**
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//dataspace
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hsize_t vdsdims_para[2] = {dstNDimx, numFiles};
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hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, NULL);
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if (vdsDataspace_para < 0)
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return CloseFileOnError(fd, string("Error in creating virtual dataspace (parameters) in virtual file ") + virtualfname + string("\n"));
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hsize_t srcdims_para[1] = {srcNDimx};
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hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, NULL);
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if (srcDataspace_para < 0)
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return CloseFileOnError(fd, string("Error in creating source dataspace (parameters) in virtual file ") + virtualfname + string("\n"));
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//fill values
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if (H5Pset_fill_value (dcpl, GetDataTypeinC(dataType), &fill_value) < 0)
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return CloseFileOnError(fd, string("Error in creating fill value in virtual file ") + virtualFileName + string("\n"));
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hid_t dcpl1 = H5Pcreate (H5P_DATASET_CREATE);
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hid_t dcpl2 = H5Pcreate (H5P_DATASET_CREATE);
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if ((dcpl1 < 0) || (dcpl2 < 0))
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return CloseFileOnError(fd, string("Error in creating file creation properties (parameters) in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in creating file creation properties (parameters) in virtual file ") + virtualFileName + string("\n"));
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fill_value = -1;
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if ((H5Pset_fill_value (dcpl1, dtype_para1, &fill_value) < 0) || (H5Pset_fill_value (dcpl2, dtype_para2, &fill_value) < 0))
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return CloseFileOnError(fd, string("Error in creating fill value (parameters) in virtual file ") + virtualfname + string("\n"));
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if ((H5Pset_fill_value (dcpl1, GetDataTypeinC(p1DataType), &fill_value) < 0) ||
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(H5Pset_fill_value (dcpl2, GetDataTypeinC(p2DataType), &fill_value) < 0))
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return CloseFileOnError(fd, string("Error in creating fill value (parameters) in virtual file ") + virtualFileName + string("\n"));
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//hyperslab
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hsize_t offset_para[2] = {0,0},
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count_para[2] = {dstNDimx,1};
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error = false;
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for (int i = 0; i < numFiles; i++) {
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//cout<<"("<<offset[0]<<","<<offset[1]<<","<<offset[2]<<")"<<endl;
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if (H5Sselect_hyperslab (vdsDataspace_para, H5S_SELECT_SET, offset_para, NULL, count_para, NULL) < 0) {
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cprintf(RED,"could not select hyperslab\n");
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error = true;
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break;
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int numMajorHyperslab = numf/maxFramesPerFile;
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if (numf%maxFramesPerFile) numMajorHyperslab++;
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bool error = false;
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uint64_t framesSaved = 0;
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for (int j = 0; j < numMajorHyperslab; j++) {
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uint64_t nDimx = ((numf - framesSaved) > maxFramesPerFile) ? maxFramesPerFile : (numf-framesSaved);
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hsize_t offset[3] = {framesSaved, 0, 0};
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hsize_t count[3] = {nDimx, nDimy, nDimz};
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hsize_t offset_para[2] = {framesSaved, 0};
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hsize_t count_para[2] = {nDimx, 1};
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for (int i = 0; i < numDety * numDetz; ++i) {
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//setect hyperslabs
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if (H5Sselect_hyperslab (vdsDataspace, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) {
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cprintf(RED,"could not select hyperslab\n");
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error = true;
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break;
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}
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if (H5Sselect_hyperslab (vdsDataspace_para, H5S_SELECT_SET, offset_para, NULL, count_para, NULL) < 0) {
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cprintf(RED,"could not select hyperslab for parameters\n");
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error = true;
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break;
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}
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//source file name
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string srcFileName = HDF5FileStatic::CreateFileName(fpath, fnameprefix, findex,
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frindexenable, framesSaved, dindex, numunits, i);
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//source dataset name
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ostringstream osfn;
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osfn << "/data";
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if (frindexenable) osfn << "_f" << setfill('0') << setw(12) << framesSaved;
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string srcDatasetName = osfn.str();
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//source dataspace
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hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
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hid_t srcDataspace = H5Screate_simple(3, srcdims, NULL);
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if (srcDataspace < 0)
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return CloseFileOnError(fd, string("Error in creating source dataspace in virtual file ") + virtualFileName + string("\n"));
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hsize_t srcdims_para[1] = {nDimx};
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hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, NULL);
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if (srcDataspace_para < 0)
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return CloseFileOnError(fd, string("Error in creating source dataspace (parameters) in virtual file ") + virtualFileName + string("\n"));
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//mapping
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if (H5Pset_virtual(dcpl, vdsDataspace, srcFileName.c_str(), srcDatasetName.c_str(), srcDataspace) < 0) {
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cprintf(RED,"could not set mapping for paramter 1\n");
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error = true;
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break;
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}
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if (H5Pset_virtual(dcpl1, vdsDataspace_para, srcFileName.c_str(), srcP1DatasetName.c_str(), srcDataspace_para) < 0) {
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cprintf(RED,"could not set mapping for paramter 1\n");
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error = true;
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break;
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}
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if (H5Pset_virtual(dcpl2, vdsDataspace_para, srcFileName.c_str(), srcP2DatasetName.c_str(), srcDataspace_para) < 0) {
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cprintf(RED,"could not set mapping for paramter 2\n");
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error = true;
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break;
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}
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//H5Sclose(srcDataspace);
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//H5Sclose(srcDataspace_para);
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offset[2] += nDimz;
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if (offset[2] >= (numDetz * nDimz)) {
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offset[2] = 0;
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offset[1] += nDimy;
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}
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offset_para[1]++;
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}
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if (H5Pset_virtual(dcpl1, vdsDataspace_para, fileNames[i].c_str(), spara1DatasetName.c_str(), srcDataspace_para) < 0) {
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cprintf(RED,"could not set mapping for paramter 1\n");
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error = true;
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break;
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}
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if (H5Pset_virtual(dcpl2, vdsDataspace_para, fileNames[i].c_str(), spara2DatasetName.c_str(), srcDataspace_para) < 0) {
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cprintf(RED,"could not set mapping for paramter 2\n");
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error = true;
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break;
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}
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offset_para[1] ++;
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framesSaved += nDimx;
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}
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if (error)
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return CloseFileOnError(fd, string("Error in mapping files (parameters) in virtual file ") + virtualfname + string("\n"));
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return CloseFileOnError(fd, string("Error in mapping files in virtual file ") + virtualFileName + string("\n"));
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//dataset
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hid_t vdsdataset1 = H5Dcreate2 (fd, vpara1DatasetName.c_str(), dtype_para1, vdsDataspace_para, H5P_DEFAULT, dcpl1, H5P_DEFAULT);
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hid_t vdsdataset2 = H5Dcreate2 (fd, vpara2DatasetName.c_str(), dtype_para2, vdsDataspace_para, H5P_DEFAULT, dcpl2, H5P_DEFAULT);
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if ((vdsdataset1 < 0) && (vdsdataset1 < 0))
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return CloseFileOnError(fd, string("Error in creating virutal dataset (parameters) in virtual file ") + virtualfname + string("\n"));
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string virtualDatasetName = string("/virtual_") + srcDataseName;
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string virutalP1DatasetName = string("/virtual_") + srcP1DatasetName;
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string virutalP2DatasetName = string("/virtual_") + srcP2DatasetName;
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hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetName.c_str(), GetDataTypeinC(dataType), vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
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if (vdsdataset < 0)
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return CloseFileOnError(fd, string("Error in creating virutal dataset in virtual file ") + virtualFileName + string("\n"));
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hid_t vdsdataset1 = H5Dcreate2 (fd, virutalP1DatasetName.c_str(), GetDataTypeinC(p1DataType), vdsDataspace_para, H5P_DEFAULT, dcpl1, H5P_DEFAULT);
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hid_t vdsdataset2 = H5Dcreate2 (fd, virutalP2DatasetName.c_str(), GetDataTypeinC(p2DataType), vdsDataspace_para, H5P_DEFAULT, dcpl2, H5P_DEFAULT);
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if ((vdsdataset1 < 0) || (vdsdataset2 < 0))
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return CloseFileOnError(fd, string("Error in creating virutal dataset (parameters) in virtual file ") + virtualFileName + string("\n"));
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//close
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H5Sclose(vdsDataspace);
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H5Sclose(vdsDataspace_para);
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H5Sclose(srcDataspace_para);
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H5Dclose(vdsdataset);
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H5Dclose(vdsdataset1);
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H5Dclose(vdsdataset2);
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H5Fclose(fd); fd = 0;
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return 0;
|
||||
|
||||
//link
|
||||
return LinkVirtualInMaster(masterFileName, virtualFileName, virtualDatasetName, virutalP1DatasetName, virutalP2DatasetName);
|
||||
}
|
||||
|
||||
|
||||
@ -699,15 +708,19 @@ public:
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* 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 virtualpara1DatasetName virtual dataset name of parameter 1
|
||||
* @param virtualpara2DatasetName virtual dataset name of parameter 1
|
||||
* @returns 0 for success and 1 for fail
|
||||
*/
|
||||
int LinkVirtualInMaster(string masterFileName, string virtualfname, string virtualDatasetname,
|
||||
static int LinkVirtualInMaster(string masterFileName, string virtualfname, string virtualDatasetname,
|
||||
string virtualpara1DatasetName, string virtualpara2DatasetName) {
|
||||
char linkname[100];
|
||||
hid_t vfd = 0;
|
||||
@ -746,10 +759,18 @@ public:
|
||||
|
||||
//**paramter datasets**
|
||||
hid_t vdset1 = H5Dopen2( vfd, virtualpara1DatasetName.c_str(), H5P_DEFAULT);
|
||||
if (vdset1 < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in opening virtual parameter 1 dataet to create link\n"));
|
||||
}
|
||||
hid_t vdset2 = H5Dopen2( vfd, virtualpara2DatasetName.c_str(), H5P_DEFAULT);
|
||||
if (vdset2 < 0) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in opening virtual parameter 2 dataet to create link\n"));
|
||||
}
|
||||
if ((vdset1 < 0) || (vdset2 < 0)) {
|
||||
H5Fclose(mfd); mfd = 0;
|
||||
return CloseFileOnError( vfd, string("Error in opening virtual parameter dataet to create link\n"));
|
||||
return CloseFileOnError( vfd, string("Error in opening either virtual parameter dataet to create link\n"));
|
||||
}
|
||||
sprintf(linkname, "/entry/data/%s",virtualpara1DatasetName.c_str());
|
||||
if(H5Lcreate_external( virtualfname.c_str(), virtualpara1DatasetName.c_str(),
|
||||
@ -783,6 +804,26 @@ public:
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get Data type in C
|
||||
* @param dtype datatype in C++
|
||||
* @returns datatype in C
|
||||
*/
|
||||
static hid_t GetDataTypeinC(DataType dtype) {
|
||||
if (dtype == PredType::STD_U8LE)
|
||||
return H5T_STD_U8LE;
|
||||
else if (dtype == PredType::STD_U16LE)
|
||||
return H5T_STD_U16LE;
|
||||
else if (dtype == PredType::STD_U32LE)
|
||||
return H5T_STD_U32LE;
|
||||
else if (dtype == PredType::STD_U64LE)
|
||||
return H5T_STD_U64LE;
|
||||
else {
|
||||
cprintf(RED, "Invalid Data type\n");
|
||||
return H5T_STD_U64LE;
|
||||
}
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user