mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-04-27 16:50:02 +02:00
slsReceiver: HDF5: unlimited max dimension in x (#numImages), x dim gets incremented by #frames when it gets an extra image, removed virtual_ naming in parameter names, small cased parameter names
This commit is contained in:
parent
40c96b5562
commit
3b6ead7783
@ -185,5 +185,8 @@ class HDF5File : private virtual slsReceiverDefs, public File, public HDF5FileSt
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/** Dataset array for parameters */
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vector <DataSet*> dataset_para;
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/** Number of Images (including extended during acquisition) */
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uint64_t extNumImages;
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};
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#endif
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@ -189,8 +189,8 @@ public:
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/**
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* Write Parameter Arrays as datasets (to virtual file)
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* @param ind self index
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* @param dspace_para dataspace of parametrs
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* @param fnum frame number
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* @param dspace_para parameter dataspace
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* @param fnum current frame number
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* @param dset_para vector or dataset pointers of parameters
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* @param rheader sls_receiver_header pointer
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* @param parameterDataTypes parameter datatypes
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@ -230,6 +230,47 @@ public:
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}
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/**
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* Extend datasets in #images dimension (x dimension)
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* @param ind self index
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* @param dpace data space pointer address
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* @param dset data set pointer
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* @param dspace_para parameter dataspace address pointer
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* @param dset dataset parameter pointer
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* @param initialNumImages initial number of images
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* @returns 0 for success and 1 for fail
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*/
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static int ExtendDataset(int ind, DataSpace*& dspace, DataSet* dset,
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DataSpace*& dspace_para, vector <DataSet*> dset_para,
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uint64_t initialNumImages) {
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try{
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Exception::dontPrint(); //to handle errors
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hsize_t dims[3];
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dspace->getSimpleExtentDims(dims);
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dims[0] += initialNumImages;
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dset->extend(dims);
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delete dspace;
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dspace = new DataSpace(dset->getSpace());
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hsize_t dims_para[1] = {dims[0]};
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for (unsigned int i = 0; i < dset_para.size(); ++i)
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dset_para[i]->extend(dims_para);
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delete dspace_para;
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dspace_para = new DataSpace(dset_para[0]->getSpace());
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}
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catch(Exception error){
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cprintf(RED,"Error in extending dataset in object %d\n",ind);
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error.printError();
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return 1;
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}
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return 0;
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}
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/**
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* Create master file
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* @param fname master file name
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@ -418,7 +459,8 @@ public:
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//dataspace
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hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
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dspace = new DataSpace (3,srcdims);
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hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
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dspace = new DataSpace (3,srcdims,srcdimsmax);
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//dataset name
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@ -432,18 +474,24 @@ public:
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DSetCreatPropList plist;
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int fill_value = -1;
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plist.setFillValue(dtype, &fill_value);
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//chunked dataset if greater than max_chunked_images
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if(nDimx > maxchunkedimages){
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hsize_t chunk_dims[3] ={maxchunkedimages, nDimy, nDimz};
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plist.setChunk(3, chunk_dims);
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}
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// always create chunked dataset as unlimited is only supported with chunked layout
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hsize_t chunk_dims[3] ={maxchunkedimages, nDimy, nDimz};
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plist.setChunk(3, chunk_dims);
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dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace, plist));
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//create parameter datasets
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hsize_t dims[1] = {nDimx};
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dspace_para = new DataSpace (1,dims);
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hsize_t dimsmax[1] = {H5S_UNLIMITED};
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dspace_para = new DataSpace (1,dims,dimsmax);
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// always create chunked dataset as unlimited is only supported with chunked layout
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DSetCreatPropList paralist;
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hsize_t chunkpara_dims[3] ={maxchunkedimages};
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paralist.setChunk(1, chunkpara_dims);
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for (unsigned int i = 0; i < parameterNames.size(); ++i){
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DataSet* ds = new DataSet(fd->createDataSet(parameterNames[i], parameterDataTypes[i], *dspace_para));
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DataSet* ds = new DataSet(fd->createDataSet(parameterNames[i],
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parameterDataTypes[i], *dspace_para, paralist));
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dset_para.push_back(ds);
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}
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}
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@ -499,52 +547,77 @@ public:
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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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in creating file access property for virtual file ")
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+ 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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in setting strong file close degree for virtual file ")
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+ 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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in creating dataspace for attribute in virtual file ")
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+ 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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in creating attribute in virtual file ")
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+ 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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in writing attribute in virtual file ")
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+ 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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in closing attribute in virtual file ")
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+ virtualFileName + string("\n"));
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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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in creating virtual dataspace in virtual file ")
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+ virtualFileName + string("\n"));
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hsize_t vdsdims_para[2] = {numf, (unsigned int) 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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return CloseFileOnError(fd,
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string("Error in creating virtual dataspace (parameters) in virtual file ")
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+ 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 ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in creating file creation properties in virtual file ")
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+ virtualFileName + string("\n"));
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int fill_value = -1;
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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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return CloseFileOnError(fd,
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string("Error in creating fill value in virtual file ")
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+ virtualFileName + string("\n"));
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hid_t dcpl_para[parameterNames.size()];
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for (unsigned int i = 0; i < parameterNames.size(); ++i) {
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dcpl_para[i] = H5Pcreate (H5P_DATASET_CREATE);
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if (dcpl_para[i] < 0)
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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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return CloseFileOnError(fd,
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string("Error in creating file creation properties (parameters) in virtual file ")
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+ virtualFileName + string("\n"));
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if (H5Pset_fill_value (dcpl_para[i], GetDataTypeinC(parameterDataTypes[i]), &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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return CloseFileOnError(fd,
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string("Error in creating fill value (parameters) in virtual file ")
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+ virtualFileName + string("\n"));
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}
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//hyperslab
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@ -554,7 +627,8 @@ public:
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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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uint64_t nDimx = ((numf - framesSaved) > maxFramesPerFile)
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? 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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@ -568,7 +642,8 @@ public:
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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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if (H5Sselect_hyperslab (vdsDataspace_para, H5S_SELECT_SET,
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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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@ -594,23 +669,31 @@ public:
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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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hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
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hid_t srcDataspace = H5Screate_simple(3, srcdims, srcdimsmax);
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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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return CloseFileOnError(fd,
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string("Error in creating source dataspace in virtual file ")
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+ 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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hsize_t srcdimsmax_para[1] = {H5S_UNLIMITED};
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hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, srcdimsmax_para);
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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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return CloseFileOnError(fd,
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string("Error in creating source dataspace (parameters) in virtual file ")
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+ virtualFileName + string("\n"));
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//mapping
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if (H5Pset_virtual(dcpl, vdsDataspace, relative_srcFileName.c_str(), srcDatasetName.c_str(), srcDataspace) < 0) {
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if (H5Pset_virtual(dcpl, vdsDataspace, relative_srcFileName.c_str(),
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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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for (unsigned int k = 0; k < parameterNames.size(); ++k) {
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if (H5Pset_virtual(dcpl_para[k], vdsDataspace_para, relative_srcFileName.c_str(), parameterNames[k], srcDataspace_para) < 0) {
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if (H5Pset_virtual(dcpl_para[k], vdsDataspace_para, relative_srcFileName.c_str(),
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parameterNames[k], srcDataspace_para) < 0) {
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cprintf(RED,"could not set mapping for paramter %d\n", k);
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error = true;
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break;
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@ -629,22 +712,30 @@ public:
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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 in virtual file ") + virtualFileName + string("\n"));
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return CloseFileOnError(fd,
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string("Error in mapping files in virtual file ")
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+ virtualFileName + string("\n"));
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//dataset
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string virtualDatasetName = string("/virtual_") + srcDataseName;
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hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetName.c_str(), GetDataTypeinC(dataType), vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
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string virtualDatasetName = srcDataseName;
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hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetName.c_str(),
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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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return CloseFileOnError(fd,
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string("Error in creating virutal dataset in virtual file ")
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+ virtualFileName + string("\n"));
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//virtual parameter dataset
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for (unsigned int i = 0; i < parameterNames.size(); ++i) {
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hid_t vdsdataset_para = H5Dcreate2 (fd,
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(string("/virtual_") + string (parameterNames[i])).c_str(),
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GetDataTypeinC(parameterDataTypes[i]), vdsDataspace_para, H5P_DEFAULT, dcpl_para[i], H5P_DEFAULT);
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parameterNames[i],
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GetDataTypeinC(parameterDataTypes[i]), vdsDataspace_para,
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H5P_DEFAULT, dcpl_para[i], H5P_DEFAULT);
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if (vdsdataset_para < 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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return CloseFileOnError(fd,
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string("Error in creating virutal dataset (parameters) in virtual file ")
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+ virtualFileName + string("\n"));
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}
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//close
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@ -814,14 +905,14 @@ public:
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//**paramter datasets**
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for (unsigned int i = 0; i < parameterNames.size(); ++i){
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hid_t vdset_para = H5Dopen2( vfd, (string("/virtual_") + string (parameterNames[i])).c_str(), H5P_DEFAULT);
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hid_t vdset_para = H5Dopen2( vfd, (string (parameterNames[i])).c_str(), H5P_DEFAULT);
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if (vdset_para < 0) {
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H5Fclose(mfd); mfd = 0;
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return CloseFileOnError( vfd, string("Error in opening virtual parameter dataset to create link\n"));
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}
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sprintf(linkname, "/entry/data/%s",(string("/virtual_") + string (parameterNames[i])).c_str());
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sprintf(linkname, "/entry/data/%s",(string (parameterNames[i])).c_str());
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if(H5Lcreate_external( relative_virtualfname.c_str(), (string("/virtual_") + string (parameterNames[i])).c_str(),
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if(H5Lcreate_external( relative_virtualfname.c_str(), (string (parameterNames[i])).c_str(),
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mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
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H5Fclose(mfd); mfd = 0;
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return CloseFileOnError( vfd, string("Error in creating link to virtual parameter dataset\n"));
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@ -36,7 +36,9 @@ HDF5File::HDF5File(int ind, uint32_t* maxf,
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nPixelsY(ny),
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numFramesInFile(0),
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numActualPacketsInFile(0),
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numFilesinAcquisition(0)
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numFilesinAcquisition(0),
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dataspace_para(0),
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extNumImages(0)
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{
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#ifdef VERBOSE
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PrintMembers();
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@ -45,46 +47,46 @@ HDF5File::HDF5File(int ind, uint32_t* maxf,
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parameterNames.clear();
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parameterDataTypes.clear();
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parameterNames.push_back("Frame Number");
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parameterNames.push_back("frame number");
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parameterDataTypes.push_back(PredType::STD_U64LE);
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parameterNames.push_back("Exp Length/ Sub Exposure Time");
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parameterNames.push_back("exp length or sub exposure time");
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parameterDataTypes.push_back(PredType::STD_U32LE);
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parameterNames.push_back("Packets Caught");
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parameterNames.push_back("packets caught");
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parameterDataTypes.push_back(PredType::STD_U32LE);
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parameterNames.push_back("Bunch Id");
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parameterNames.push_back("bunch id");
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parameterDataTypes.push_back(PredType::STD_U64LE);
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parameterNames.push_back("Time Stamp");
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parameterNames.push_back("timestamp");
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parameterDataTypes.push_back(PredType::STD_U64LE);
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parameterNames.push_back("Mod Id");
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parameterNames.push_back("mod id");
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parameterDataTypes.push_back(PredType::STD_U16LE);
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parameterNames.push_back("X Coord");
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parameterNames.push_back("x Coord");
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parameterDataTypes.push_back(PredType::STD_U16LE);
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parameterNames.push_back("Y Coord");
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parameterNames.push_back("y Coord");
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parameterDataTypes.push_back(PredType::STD_U16LE);
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parameterNames.push_back("Z Coord");
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parameterNames.push_back("z Coord");
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parameterDataTypes.push_back(PredType::STD_U16LE);
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parameterNames.push_back("Debug");
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parameterNames.push_back("debug");
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parameterDataTypes.push_back(PredType::STD_U32LE);
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parameterNames.push_back("Round Robin Number");
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parameterNames.push_back("round robin number");
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parameterDataTypes.push_back(PredType::STD_U16LE);
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parameterNames.push_back("Detector Type");
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parameterNames.push_back("detector type");
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parameterDataTypes.push_back(PredType::STD_U8LE);
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parameterNames.push_back("Detector Header Version");
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parameterNames.push_back("detector header version");
|
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parameterDataTypes.push_back(PredType::STD_U8LE);
|
||||
|
||||
parameterNames.push_back("Packets Caught Bit Mask");
|
||||
parameterNames.push_back("packets caught bit mask");
|
||||
StrType strdatatype(PredType::C_S1, MAX_NUM_PACKETS);
|
||||
parameterDataTypes.push_back(strdatatype);
|
||||
|
||||
@ -141,8 +143,8 @@ int HDF5File::CreateFile(uint64_t fnum) {
|
||||
if(!fnum) UpdateDataType();
|
||||
|
||||
uint64_t framestosave = ((*maxFramesPerFile == 0) ? *numImages : // infinite images
|
||||
(((*numImages - fnum) > (*maxFramesPerFile)) ? // save up to maximum at a time
|
||||
(*maxFramesPerFile) : (*numImages-fnum)));
|
||||
(((extNumImages - fnum) > (*maxFramesPerFile)) ? // save up to maximum at a time
|
||||
(*maxFramesPerFile) : (extNumImages-fnum)));
|
||||
pthread_mutex_lock(&Mutex);
|
||||
if (HDF5FileStatic::CreateDataFile(index, *overWriteEnable, currentFileName, (*numImages > 1),
|
||||
fnum, framestosave, nPixelsY, ((*dynamicRange==4) ? (nPixelsX/2) : nPixelsX),
|
||||
@ -192,6 +194,20 @@ int HDF5File::WriteToFile(char* buffer, int buffersize, uint64_t fnum, uint32_t
|
||||
numFramesInFile++;
|
||||
numActualPacketsInFile += nump;
|
||||
pthread_mutex_lock(&Mutex);
|
||||
|
||||
// extend dataset (when receiver start followed by many status starts (jungfrau)))
|
||||
if (fnum >= extNumImages) {
|
||||
if (HDF5FileStatic::ExtendDataset(index, dataspace, dataset,
|
||||
dataspace_para, dataset_para, *numImages) == OK) {
|
||||
if (!silentMode) {
|
||||
cprintf(BLUE,"%d Extending HDF5 dataset by %llu, Total x Dimension: %llu\n",
|
||||
index, (long long unsigned int)extNumImages,
|
||||
(long long unsigned int)(extNumImages + *numImages));
|
||||
}
|
||||
extNumImages += *numImages;
|
||||
}
|
||||
}
|
||||
|
||||
if (HDF5FileStatic::WriteDataFile(index, buffer + sizeof(sls_receiver_header),
|
||||
// infinite then no need for %maxframesperfile
|
||||
((*maxFramesPerFile == 0) ? fnum : fnum%(*maxFramesPerFile)),
|
||||
@ -220,6 +236,7 @@ int HDF5File::CreateMasterFile(bool en, uint32_t size,
|
||||
//beginning of every acquisition
|
||||
numFramesInFile = 0;
|
||||
numActualPacketsInFile = 0;
|
||||
extNumImages = *numImages;
|
||||
|
||||
if (master && (*detIndex==0)) {
|
||||
virtualfd = 0;
|
||||
|
||||
@ -446,7 +446,7 @@ void UDPBaseImplementation::setFilePath(const char c[]){
|
||||
else
|
||||
FILE_LOG(logERROR) << "FilePath does not exist: " << filePath;
|
||||
}
|
||||
FILE_LOG(logINFO) << "Info: File path: " << filePath;
|
||||
FILE_LOG(logINFO) << "File path: " << filePath;
|
||||
}
|
||||
|
||||
void UDPBaseImplementation::setFileIndex(const uint64_t i){
|
||||
|
||||
@ -542,7 +542,7 @@ void UDPStandardImplementation::stopReceiver(){
|
||||
tot += dataProcessor[i]->GetNumFramesCaught();
|
||||
|
||||
uint64_t missingpackets = numberOfFrames*generalData->packetsPerFrame-listener[i]->GetPacketsCaught();
|
||||
if (missingpackets) {
|
||||
if ((int)missingpackets > 0) {
|
||||
cprintf(RED, "\n[Port %d]\n",udpPortNum[i]);
|
||||
cprintf(RED, "Missing Packets\t\t: %lld\n",(long long int)missingpackets);
|
||||
cprintf(RED, "Complete Frames\t\t: %lld\n",(long long int)dataProcessor[i]->GetNumFramesCaught());
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user