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Test: cnpy integration.
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@s-trinh
s-trinh committed Sep 27, 2023
1 parent c449424 commit fb4c560
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253 changes: 253 additions & 0 deletions modules/core/include/visp3/core/vpIoTools.h
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Expand Up @@ -47,6 +47,8 @@
#include <stdlib.h>
#include <string>
#include <vector>
#include <numeric>
#include <zlib.h>
#include <visp3/core/vpColor.h>

/*!
Expand Down Expand Up @@ -256,4 +258,255 @@ class VISP_EXPORT vpIoTools
static int mkdir_p(const std::string &path, int mode);
#endif
};

// TODO:
// Copyright (C) 2011 Carl Rogers
// Released under MIT License
// license available in LICENSE file, or at http://www.opensource.org/licenses/mit-license.php
namespace visp
{
namespace cnpy {
struct NpyArray {
NpyArray(const std::vector<size_t>& _shape, size_t _word_size, bool _fortran_order) :
shape(_shape), word_size(_word_size), fortran_order(_fortran_order)
{
num_vals = 1;
for(size_t i = 0;i < shape.size();i++) num_vals *= shape[i];
data_holder = std::shared_ptr<std::vector<char>>(
new std::vector<char>(num_vals * word_size));
}

NpyArray() : shape(0), word_size(0), fortran_order(0), num_vals(0) { }

template<typename T>
T* data() {
return reinterpret_cast<T*>(&(*data_holder)[0]);
}

template<typename T>
const T* data() const {
return reinterpret_cast<T*>(&(*data_holder)[0]);
}

template<typename T>
std::vector<T> as_vec() const {
const T* p = data<T>();
return std::vector<T>(p, p+num_vals);
}

size_t num_bytes() const {
return data_holder->size();
}

std::shared_ptr<std::vector<char>> data_holder;
std::vector<size_t> shape;
size_t word_size;
bool fortran_order;
size_t num_vals;
};

using npz_t = std::map<std::string, NpyArray>;

char BigEndianTest();
char map_type(const std::type_info& t);
template<typename T> std::vector<char> create_npy_header(const std::vector<size_t>& shape);
void parse_npy_header(FILE* fp,size_t& word_size, std::vector<size_t>& shape, bool& fortran_order);
void parse_npy_header(unsigned char* buffer,size_t& word_size, std::vector<size_t>& shape, bool& fortran_order);
void parse_zip_footer(FILE* fp, uint16_t& nrecs, size_t& global_header_size, size_t& global_header_offset);
npz_t npz_load(std::string fname);
NpyArray npz_load(std::string fname, std::string varname);
NpyArray npy_load(std::string fname);

template<typename T> std::vector<char>& operator+=(std::vector<char>& lhs, const T rhs) {
//write in little endian
for(size_t byte = 0; byte < sizeof(T); byte++) {
char val = *((char*)&rhs+byte);
lhs.push_back(val);
}
return lhs;
}

template<> std::vector<char>& operator+=(std::vector<char>& lhs, const std::string rhs);
template<> std::vector<char>& operator+=(std::vector<char>& lhs, const char* rhs);


template<typename T> void npy_save(std::string fname, const T* data, const std::vector<size_t> shape, std::string mode = "w") {
FILE* fp = NULL;
std::vector<size_t> true_data_shape; //if appending, the shape of existing + new data

if(mode == "a") fp = fopen(fname.c_str(),"r+b");

if(fp) {
//file exists. we need to append to it. read the header, modify the array size
size_t word_size;
bool fortran_order;
parse_npy_header(fp,word_size,true_data_shape,fortran_order);
assert(!fortran_order);

if(word_size != sizeof(T)) {
std::cout<<"libnpy error: "<<fname<<" has word size "<<word_size<<" but npy_save appending data sized "<<sizeof(T)<<"\n";
assert( word_size == sizeof(T) );
}
if(true_data_shape.size() != shape.size()) {
std::cout<<"libnpy error: npy_save attempting to append misdimensioned data to "<<fname<<"\n";
assert(true_data_shape.size() != shape.size());
}

for(size_t i = 1; i < shape.size(); i++) {
if(shape[i] != true_data_shape[i]) {
std::cout<<"libnpy error: npy_save attempting to append misshaped data to "<<fname<<"\n";
assert(shape[i] == true_data_shape[i]);
}
}
true_data_shape[0] += shape[0];
}
else {
fp = fopen(fname.c_str(),"wb");
true_data_shape = shape;
}

std::vector<char> header = create_npy_header<T>(true_data_shape);
size_t nels = std::accumulate(shape.begin(),shape.end(),1,std::multiplies<size_t>());

fseek(fp,0,SEEK_SET);
fwrite(&header[0],sizeof(char),header.size(),fp);
fseek(fp,0,SEEK_END);
fwrite(data,sizeof(T),nels,fp);
fclose(fp);
}

template<typename T> void npz_save(std::string zipname, std::string fname, const T* data, const std::vector<size_t>& shape, std::string mode = "w")
{
//first, append a .npy to the fname
fname += ".npy";

//now, on with the show
FILE* fp = NULL;
uint16_t nrecs = 0;
size_t global_header_offset = 0;
std::vector<char> global_header;

if(mode == "a") fp = fopen(zipname.c_str(),"r+b");

if(fp) {
//zip file exists. we need to add a new npy file to it.
//first read the footer. this gives us the offset and size of the global header
//then read and store the global header.
//below, we will write the the new data at the start of the global header then append the global header and footer below it
size_t global_header_size;
parse_zip_footer(fp,nrecs,global_header_size,global_header_offset);
fseek(fp,global_header_offset,SEEK_SET);
global_header.resize(global_header_size);
size_t res = fread(&global_header[0],sizeof(char),global_header_size,fp);
if(res != global_header_size){
throw std::runtime_error("npz_save: header read error while adding to existing zip");
}
fseek(fp,global_header_offset,SEEK_SET);
}
else {
fp = fopen(zipname.c_str(),"wb");
}

std::vector<char> npy_header = create_npy_header<T>(shape);

size_t nels = std::accumulate(shape.begin(),shape.end(),1,std::multiplies<size_t>());
size_t nbytes = nels*sizeof(T) + npy_header.size();

//get the CRC of the data to be added
uint32_t crc = crc32(0L,(uint8_t*)&npy_header[0],npy_header.size());
crc = crc32(crc,(uint8_t*)data,nels*sizeof(T));

//build the local header
std::vector<char> local_header;
local_header += "PK"; //first part of sig
local_header += (uint16_t) 0x0403; //second part of sig
local_header += (uint16_t) 20; //min version to extract
local_header += (uint16_t) 0; //general purpose bit flag
local_header += (uint16_t) 0; //compression method
local_header += (uint16_t) 0; //file last mod time
local_header += (uint16_t) 0; //file last mod date
local_header += (uint32_t) crc; //crc
local_header += (uint32_t) nbytes; //compressed size
local_header += (uint32_t) nbytes; //uncompressed size
local_header += (uint16_t) fname.size(); //fname length
local_header += (uint16_t) 0; //extra field length
local_header += fname;

//build global header
global_header += "PK"; //first part of sig
global_header += (uint16_t) 0x0201; //second part of sig
global_header += (uint16_t) 20; //version made by
global_header.insert(global_header.end(),local_header.begin()+4,local_header.begin()+30);
global_header += (uint16_t) 0; //file comment length
global_header += (uint16_t) 0; //disk number where file starts
global_header += (uint16_t) 0; //internal file attributes
global_header += (uint32_t) 0; //external file attributes
global_header += (uint32_t) global_header_offset; //relative offset of local file header, since it begins where the global header used to begin
global_header += fname;

//build footer
std::vector<char> footer;
footer += "PK"; //first part of sig
footer += (uint16_t) 0x0605; //second part of sig
footer += (uint16_t) 0; //number of this disk
footer += (uint16_t) 0; //disk where footer starts
footer += (uint16_t) (nrecs+1); //number of records on this disk
footer += (uint16_t) (nrecs+1); //total number of records
footer += (uint32_t) global_header.size(); //nbytes of global headers
footer += (uint32_t) (global_header_offset + nbytes + local_header.size()); //offset of start of global headers, since global header now starts after newly written array
footer += (uint16_t) 0; //zip file comment length

//write everything
fwrite(&local_header[0],sizeof(char),local_header.size(),fp);
fwrite(&npy_header[0],sizeof(char),npy_header.size(),fp);
fwrite(data,sizeof(T),nels,fp);
fwrite(&global_header[0],sizeof(char),global_header.size(),fp);
fwrite(&footer[0],sizeof(char),footer.size(),fp);
fclose(fp);
}

template<typename T> void npy_save(std::string fname, const std::vector<T> data, std::string mode = "w") {
std::vector<size_t> shape;
shape.push_back(data.size());
npy_save(fname, &data[0], shape, mode);
}

template<typename T> void npz_save(std::string zipname, std::string fname, const std::vector<T> data, std::string mode = "w") {
std::vector<size_t> shape;
shape.push_back(data.size());
npz_save(zipname, fname, &data[0], shape, mode);
}

template<typename T> std::vector<char> create_npy_header(const std::vector<size_t>& shape) {

std::vector<char> dict;
dict += "{'descr': '";
dict += BigEndianTest();
dict += map_type(typeid(T));
dict += std::to_string(sizeof(T));
dict += "', 'fortran_order': False, 'shape': (";
dict += std::to_string(shape[0]);
for(size_t i = 1;i < shape.size();i++) {
dict += ", ";
dict += std::to_string(shape[i]);
}
if(shape.size() == 1) dict += ",";
dict += "), }";
//pad with spaces so that preamble+dict is modulo 16 bytes. preamble is 10 bytes. dict needs to end with \n
int remainder = 16 - (10 + dict.size()) % 16;
dict.insert(dict.end(),remainder,' ');
dict.back() = '\n';

std::vector<char> header;
header += (char) 0x93;
header += "NUMPY";
header += (char) 0x01; //major version of numpy format
header += (char) 0x00; //minor version of numpy format
header += (uint16_t) dict.size();
header.insert(header.end(),dict.begin(),dict.end());

return header;
}
}
}
#endif
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