CSV to HDF5
Public domain CSV example file obtained from this link The CSV library is Fast C++ CSV Parser
C++/C representation
arbitrary pod struct can be represented in HDF5 format, one easy representation of strings is character array. An alternative --often better performing --representation would be to factor out strings from numerical data, then save them in separate datasets.
#ifndef CSV2H5_H
#define CSV2H5_H
/*define C++ representation as POD struct*/
struct input_t {
long MasterRecordNumber;
unsigned int Hour;
double Latitude;
double Longitude;
char ReportedLocation[20]; // character arrays are supported
};
#endif
Reading the CSV is rather easy thanks to Fast C++ CSV Parser, a single header file csv.h is attached to the project. Not only fast and simple but also elegantly allows to specify specific columns marked as ncols: N_COLS
io::CSVReader<N_COLS> in("input.csv"); // number of cols may be less, than total columns in a row, we're to read only 5
in.read_header(io::ignore_extra_column, "Master Record Number", "Hour", "Reported_Location","Latitude","Longitude");
[...]
while(in.read_row(row.MasterRecordNumber, row.Hour, ptr, row.Latitude, row.Longitude)){
[...]
The HDF5 part is matching in simplicity:
h5::fd_t fd = h5::create("output.h5",H5F_ACC_TRUNC);
h5::pt_t pt = h5::create<input_t>(fd, "monroe-county-crash-data2003-to-2015.csv",
h5::max_dims{H5S_UNLIMITED}, h5::chunk{1024} | h5::gzip{9} ); // compression, chunked, unlimited size
[...]
while(...){
h5::append(pt, row); // append operator uses internal buffers to cache and convert row insertions to block/chunk operations
}
[...]
The TU translation unit is scanned with LLVM based h5cpp compiler and the necessary hdf5 specific type descriptors are produced:
#ifndef H5CPP_GUARD_mzMuQ
#define H5CPP_GUARD_mzMuQ
namespace h5{
//template specialization of input_t to create HDF5 COMPOUND type
template<> hid_t inline register_struct<input_t>(){
//hsize_t at_00_[] ={20}; hid_t at_00 = H5Tarray_create(H5T_STRING,20,at_00_);
hid_t at_00 = H5Tcopy (H5T_C_S1); H5Tset_size(at_00, 20);
hid_t ct_00 = H5Tcreate(H5T_COMPOUND, sizeof (input_t));
H5Tinsert(ct_00, "MasterRecordNumber", HOFFSET(input_t,MasterRecordNumber),H5T_NATIVE_LONG);
H5Tinsert(ct_00, "Hour", HOFFSET(input_t,Hour),H5T_NATIVE_UINT);
H5Tinsert(ct_00, "Latitude", HOFFSET(input_t,Latitude),H5T_NATIVE_DOUBLE);
H5Tinsert(ct_00, "Longitude", HOFFSET(input_t,Longitude),H5T_NATIVE_DOUBLE);
H5Tinsert(ct_00, "ReportedLocation", HOFFSET(input_t,ReportedLocation),at_00);
//closing all hid_t allocations to prevent resource leakage
H5Tclose(at_00);
//if not used with h5cpp framework, but as a standalone code generator then
//the returned 'hid_t ct_00' must be closed: H5Tclose(ct_00);
return ct_00;
};
}
H5CPP_REGISTER_STRUCT(input_t);
#endif
The entire project can be downloaded from this link but for completeness here is the source file:
/* Copyright (c) 2020 vargaconsulting, Toronto,ON Canada
* Author: Varga, Steven <steven@vargaconsulting.ca>
*/
#include "csv.h"
// data structure include file: `struct.h` must precede 'generated.h' as the latter contains dependencies
// from previous
#include "struct.h"
#include <h5cpp/core> // has handle + type descriptors
// sandwiched: as `h5cpp/io` depends on `henerated.h` which needs `h5cpp/core`
#include "generated.h" // uses type descriptors
#include <h5cpp/io> // uses generated.h + core
int main(){
// create HDF5 container
h5::fd_t fd = h5::create("output.h5",H5F_ACC_TRUNC);
// create dataset
// chunk size is unrealistically small, usually you would set this such that ~= 1MB or an ethernet jumbo frame size
h5::ds_t ds = h5::create<input_t>(fd, "simple approach/dataset.csv",
h5::max_dims{H5S_UNLIMITED}, h5::chunk{10} | h5::gzip{9} );
// `h5::ds_t` handle is seamlessly cast to `h5::pt_t` packet table handle, this could have been done in single step
// but we need `h5::ds_t` handle to add attributes
h5::pt_t pt = ds;
// attributes may be added to `h5::ds_t` handle
ds["data set"] = "monroe-county-crash-data2003-to-2015.csv";
ds["cvs parser"] = "https://github.com/ben-strasser/fast-cpp-csv-parser"; // thank you!
constexpr unsigned N_COLS = 5;
io::CSVReader<N_COLS> in("input.csv"); // number of cols may be less, than total columns in a row, we're to read only 5
in.read_header(io::ignore_extra_column, "Master Record Number", "Hour", "Reported_Location","Latitude","Longitude");
input_t row; // buffer to read line by line
char* ptr; // indirection, as `read_row` doesn't take array directly
while(in.read_row(row.MasterRecordNumber, row.Hour, ptr, row.Latitude, row.Longitude)){
strncpy(row.ReportedLocation, ptr, STR_ARRAY_SIZE); // defined in struct.h
h5::append(pt, row);
std::cout << std::string(ptr) << "\n";
}
// RAII closes all allocated resources
}
the output of h5dump -pH output.h5
HDF5 "output.h5" {
GROUP "/" {
GROUP "simple approach" {
DATASET "dataset.csv" {
DATATYPE H5T_COMPOUND {
H5T_STD_I64LE "MasterRecordNumber";
H5T_STD_U32LE "Hour";
H5T_IEEE_F64LE "Latitude";
H5T_IEEE_F64LE "Longitude";
H5T_ARRAY { [20] H5T_STD_I8LE } "ReportedLocation";
}
DATASPACE SIMPLE { ( 199 ) / ( H5S_UNLIMITED ) }
STORAGE_LAYOUT {
CHUNKED ( 10 )
SIZE 7347 (1.517:1 COMPRESSION)
}
FILTERS {
COMPRESSION DEFLATE { LEVEL 9 }
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_INCR
}
ATTRIBUTE "cvs parser" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "data set" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
}
}
}
}