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slsReceiver HDF5: unlimited x dimension (#images) by extending by numImages if caught more images, fixed virtual mapping, fixed linking for jungfrau single module (removed virtual_ in all namings

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maliakal_d
2018-07-17 14:07:23 +02:00
parent 6d11faed87
commit 934bc5b9db
8 changed files with 114 additions and 34 deletions
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86
slsReceiverSoftware/include/HDF5FileStatic.h
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@ -187,6 +187,12 @@ public:
/**
* Write Parameter Arrays as datasets (to virtual file)
* @param ind self index
* @param dpace_para parameter dataspace
* @param fnum frame number current
* @param dset_para parameter dataset
* @param header image header
* @returns 0 for success and 1 for fail
*/
static int WriteParameterDatasets(int ind, DataSpace* dspace_para, uint64_t fnum,
DataSet* dset_para[],sls_detector_header* header)
@ -219,6 +225,44 @@ public:
return 0;
}
/**
* Extend datasets in #images dimension (x dimension)
* @param ind self index
* @param dpace data space pointer address
* @param dset data set pointer
* @param dspace_para parameter dataspace address pointer
* @param dset dataset parameter pointer
* @param initialNumImages initial number of images
* @returns 0 for success and 1 for fail
*/
static int ExtendDataset(int ind, DataSpace*& dspace, DataSet* dset,
DataSpace*& dspace_para, DataSet* dset_para[],
uint64_t initialNumImages) {
try{
Exception::dontPrint(); //to handle errors
hsize_t dims[3];
herr_t status_n = dspace->getSimpleExtentDims(dims);
dims[0] += initialNumImages;
dset->extend(dims);
delete dspace;
dspace = new DataSpace(dset->getSpace());
hsize_t dims_para[1] = {dims[0]};
for (int i = 0; i < NumberofParameters; ++i)
dset_para[i]->extend(dims_para);
delete dspace_para;
dspace_para = new DataSpace(dset_para[0]->getSpace());
}
catch(Exception error){
cprintf(RED,"Error in extending dataset in object %d\n",ind);
error.printError();
return 1;
}
return 0;
}
/**
* Create master file
@ -386,7 +430,8 @@ public:
//dataspace
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
dspace = new DataSpace (3,srcdims);
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
dspace = new DataSpace (3,srcdims,srcdimsmax);
//dataset name
ostringstream osfn;
@ -396,19 +441,24 @@ public:
//dataset
//chunked dataset if greater than max_chunked_images
if(nDimx > maxchunkedimages){
DSetCreatPropList plist;
hsize_t chunk_dims[3] ={maxchunkedimages, nDimy, nDimz};
plist.setChunk(3, chunk_dims);
dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace, plist));
}else
dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace));
// always create chunked dataset as unlimited is only supported with chunked layout
DSetCreatPropList plist;
hsize_t chunk_dims[3] ={maxchunkedimages, nDimy, nDimz};
plist.setChunk(3, chunk_dims);
dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace, plist));
//create parameter datasets
hsize_t dims[1] = {nDimx};
dspace_para = new DataSpace (1,dims);
hsize_t dimsmax[1] = {H5S_UNLIMITED};
dspace_para = new DataSpace (1,dims,dimsmax);
// always create chunked dataset as unlimited is only supported with chunked layout
DSetCreatPropList paralist;
hsize_t chunkpara_dims[3] ={maxchunkedimages};
paralist.setChunk(1, chunkpara_dims);
for (int i = 0; i < NumberofParameters; ++i)
dset_para[i] = new DataSet(fd->createDataSet(ParameterNames[i], ParameterDataTypes[i], *dspace_para));
dset_para[i] = new DataSet(fd->createDataSet(ParameterNames[i], ParameterDataTypes[i], *dspace_para, paralist));
}
catch(Exception error){
cprintf(RED,"Error in creating HDF5 handles in object %d\n",ind);
@ -549,11 +599,13 @@ public:
//source dataspace
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
hid_t srcDataspace = H5Screate_simple(3, srcdims, NULL);
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
hid_t srcDataspace = H5Screate_simple(3, srcdims, srcdimsmax);
if (srcDataspace < 0)
return CloseFileOnError(fd, string("Error in creating source dataspace in virtual file ") + virtualFileName + string("\n"));
hsize_t srcdims_para[1] = {nDimx};
hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, NULL);
hsize_t srcdimsmax_para[1] = {H5S_UNLIMITED};
hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, srcdimsmax_para);
if (srcDataspace_para < 0)
return CloseFileOnError(fd, string("Error in creating source dataspace (parameters) in virtual file ") + virtualFileName + string("\n"));
@ -587,7 +639,7 @@ public:
return CloseFileOnError(fd, string("Error in mapping files in virtual file ") + virtualFileName + string("\n"));
//dataset
string virtualDatasetName = string("/virtual_") + srcDataseName;
string virtualDatasetName = /*string("/virtual_") + */srcDataseName;
hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetName.c_str(), GetDataTypeinC(dataType), vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
if (vdsdataset < 0)
return CloseFileOnError(fd, string("Error in creating virutal dataset in virtual file ") + virtualFileName + string("\n"));
@ -596,7 +648,7 @@ public:
//virtual parameter dataset
for (int i = 0; i < NumberofParameters; ++i) {
hid_t vdsdataset_para = H5Dcreate2 (fd,
(string("/virtual_") + string (ParameterNames[i])).c_str(),
(/*string("/virtual_") + */string (ParameterNames[i])).c_str(),
GetDataTypeinC(ParameterDataTypes[i]), vdsDataspace_para, H5P_DEFAULT, dcpl_para[i], H5P_DEFAULT);
if (vdsdataset_para < 0)
return CloseFileOnError(fd, string("Error in creating virutal dataset (parameters) in virtual file ") + virtualFileName + string("\n"));
@ -755,13 +807,13 @@ public:
//**paramter datasets**
for (int i = 0; i < NumberofParameters; ++i){
hid_t vdset_para = H5Dopen2( vfd, (string("/virtual_") + string (ParameterNames[i])).c_str(), H5P_DEFAULT);
hid_t vdset_para = H5Dopen2( vfd, (/*string("/virtual_") + */string (ParameterNames[i])).c_str(), H5P_DEFAULT);
if (vdset_para < 0) {
H5Fclose(mfd); mfd = 0;
return CloseFileOnError( vfd, string("Error in opening virtual parameter dataset to create link\n"));
}
sprintf(linkname, "/entry/data/%s",(string("/virtual_") + string (ParameterNames[i])).c_str());
if(H5Lcreate_external( virtualfname.c_str(), (string("/virtual_") + string (ParameterNames[i])).c_str(),
sprintf(linkname, "/entry/data/%s",(/*string("/virtual_") + */string (ParameterNames[i])).c_str());
if(H5Lcreate_external( virtualfname.c_str(), (/*string("/virtual_") + */string (ParameterNames[i])).c_str(),
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
H5Fclose(mfd); mfd = 0;
return CloseFileOnError( vfd, string("Error in creating link to virtual parameter dataset\n"));