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Merge pull request #9301 from dkurt:dnn_npy

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Vadim Pisarevsky 2017-09-15 12:42:02 +00:00
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291
modules/dnn/test/cnpy.cpp
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/*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, install,
// copy or use the software.
//
//
// License Agreement
// For Open Source Computer Vision Library
//
// Copyright (C) 2013, OpenCV Foundation, all rights reserved.
// Third party copyrights are property of their respective owners.
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// * Redistribution's of source code must retain the above copyright notice,
// this list of conditions and the following disclaimer.
//
// * Redistribution's in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// * The name of the copyright holders may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// This software is provided by the copyright holders and contributors "as is" and
// any express or implied warranties, including, but not limited to, the implied
// warranties of merchantability and fitness for a particular purpose are disclaimed.
// In no event shall the Intel Corporation or contributors be liable for any direct,
// indirect, incidental, special, exemplary, or consequential damages
// (including, but not limited to, procurement of substitute goods or services;
// loss of use, data, or profits; or business interruption) however caused
// and on any theory of liability, whether in contract, strict liability,
// or tort (including negligence or otherwise) arising in any way out of
// the use of this software, even if advised of the possibility of such damage.
//
//M*/
//Copyright (C) 2011 Carl Rogers
//Released under MIT License
//license available in LICENSE file, or at http://www.opensource.org/licenses/mit-license.php
#include"cnpy.h"
#include<complex>
#include<cstdlib>
#include<algorithm>
#include<cstring>
#include<iomanip>
char cnpy::BigEndianTest() {
union
{
unsigned char x[2];
short y;
};
x[0] = 1;
x[1] = 0;
return y == 1 ? '<' : '>';
}
char cnpy::map_type(const std::type_info& t)
{
if(t == typeid(float) ) return 'f';
if(t == typeid(double) ) return 'f';
if(t == typeid(long double) ) return 'f';
if(t == typeid(int) ) return 'i';
if(t == typeid(char) ) return 'i';
if(t == typeid(short) ) return 'i';
if(t == typeid(long) ) return 'i';
if(t == typeid(long long) ) return 'i';
if(t == typeid(unsigned char) ) return 'u';
if(t == typeid(unsigned short) ) return 'u';
if(t == typeid(unsigned long) ) return 'u';
if(t == typeid(unsigned long long) ) return 'u';
if(t == typeid(unsigned int) ) return 'u';
if(t == typeid(bool) ) return 'b';
if(t == typeid(std::complex<float>) ) return 'c';
if(t == typeid(std::complex<double>) ) return 'c';
if(t == typeid(std::complex<long double>) ) return 'c';
else return '?';
}
template<> std::vector<char>& cnpy::operator+=(std::vector<char>& lhs, const std::string rhs) {
lhs.insert(lhs.end(),rhs.begin(),rhs.end());
return lhs;
}
template<> std::vector<char>& cnpy::operator+=(std::vector<char>& lhs, const char* rhs) {
//write in little endian
size_t len = strlen(rhs);
lhs.reserve(len);
for(size_t byte = 0; byte < len; byte++) {
lhs.push_back(rhs[byte]);
}
return lhs;
}
void cnpy::parse_npy_header(FILE* fp, unsigned int& word_size, unsigned int*& shape, unsigned int& ndims, bool& fortran_order) {
char buffer[256];
size_t res = fread(buffer,sizeof(char),11,fp);
if(res != 11)
throw std::runtime_error("parse_npy_header: failed fread");
std::string header = fgets(buffer,256,fp);
cnpy_assert(header[header.size()-1] == '\n');
size_t loc1, loc2;
//fortran order
loc1 = header.find("fortran_order")+16;
fortran_order = (header.substr(loc1,5) == "True" ? true : false);
//shape
loc1 = header.find("(");
loc2 = header.find(")");
std::string str_shape = header.substr(loc1+1,loc2-loc1-1);
if(str_shape[str_shape.size()-1] == ',') ndims = 1;
else ndims = (unsigned)std::count(str_shape.begin(),str_shape.end(),',')+1;
shape = new unsigned int[ndims];
for(unsigned int i = 0;i < ndims;i++) {
loc1 = str_shape.find(",");
shape[i] = atoi(str_shape.substr(0,loc1).c_str());
str_shape = str_shape.substr(loc1+1);
}
//endian, word size, data type
//byte order code | stands for not applicable.
//not sure when this applies except for byte array
loc1 = header.find("descr")+9;
bool littleEndian = (header[loc1] == '<' || header[loc1] == '|' ? true : false);
cnpy_assert(littleEndian);
//char type = header[loc1+1];
//assert(type == map_type(T));
std::string str_ws = header.substr(loc1+2);
loc2 = str_ws.find("'");
word_size = atoi(str_ws.substr(0,loc2).c_str());
}
void cnpy::parse_zip_footer(FILE* fp, unsigned short& nrecs, unsigned int& global_header_size, unsigned int& global_header_offset)
{
std::vector<char> footer(22);
fseek(fp,-22,SEEK_END);
size_t res = fread(&footer[0],sizeof(char),22,fp);
if(res != 22)
throw std::runtime_error("parse_zip_footer: failed fread");
unsigned short disk_no, disk_start, nrecs_on_disk, comment_len;
disk_no = *(unsigned short*) &footer[4];
disk_start = *(unsigned short*) &footer[6];
nrecs_on_disk = *(unsigned short*) &footer[8];
nrecs = *(unsigned short*) &footer[10];
global_header_size = *(unsigned int*) &footer[12];
global_header_offset = *(unsigned int*) &footer[16];
comment_len = *(unsigned short*) &footer[20];
cnpy_assert(disk_no == 0);
cnpy_assert(disk_start == 0);
cnpy_assert(nrecs_on_disk == nrecs);
cnpy_assert(comment_len == 0);
}
cnpy::NpyArray load_the_npy_file(FILE* fp) {
unsigned int* shape;
unsigned int ndims, word_size;
bool fortran_order;
cnpy::parse_npy_header(fp,word_size,shape,ndims,fortran_order);
unsigned long long size = 1; //long long so no overflow when multiplying by word_size
for(unsigned int i = 0;i < ndims;i++) size *= shape[i];
cnpy::NpyArray arr;
arr.word_size = word_size;
arr.shape = std::vector<unsigned int>(shape,shape+ndims);
delete[] shape;
arr.data = new char[size*word_size];
arr.fortran_order = fortran_order;
size_t nread = fread(arr.data,word_size,size,fp);
if(nread != size)
throw std::runtime_error("load_the_npy_file: failed fread");
return arr;
}
cnpy::npz_t cnpy::npz_load(std::string fname) {
FILE* fp = fopen(fname.c_str(),"rb");
if(!fp) printf("npz_load: Error! Unable to open file %s!\n",fname.c_str());
cnpy_assert(fp);
cnpy::npz_t arrays;
while(1) {
std::vector<char> local_header(30);
size_t headerres = fread(&local_header[0],sizeof(char),30,fp);
if(headerres != 30)
throw std::runtime_error("npz_load: failed fread");
//if we've reached the global header, stop reading
if(local_header[2] != 0x03 || local_header[3] != 0x04) break;
//read in the variable name
unsigned short name_len = *(unsigned short*) &local_header[26];
std::string varname(name_len,' ');
size_t vname_res = fread(&varname[0],sizeof(char),name_len,fp);
if(vname_res != name_len)
throw std::runtime_error("npz_load: failed fread");
//erase the lagging .npy
varname.erase(varname.end()-4,varname.end());
//read in the extra field
unsigned short extra_field_len = *(unsigned short*) &local_header[28];
if(extra_field_len > 0) {
std::vector<char> buff(extra_field_len);
size_t efield_res = fread(&buff[0],sizeof(char),extra_field_len,fp);
if(efield_res != extra_field_len)
throw std::runtime_error("npz_load: failed fread");
}
arrays[varname] = load_the_npy_file(fp);
}
fclose(fp);
return arrays;
}
cnpy::NpyArray cnpy::npz_load(std::string fname, std::string varname) {
FILE* fp = fopen(fname.c_str(),"rb");
if(!fp) {
throw std::runtime_error("npz_load: Error! Unable to open file " + fname + "!\n");
}
while(1) {
std::vector<char> local_header(30);
size_t header_res = fread(&local_header[0],sizeof(char),30,fp);
if(header_res != 30)
throw std::runtime_error("npz_load: failed fread");
//if we've reached the global header, stop reading
if(local_header[2] != 0x03 || local_header[3] != 0x04) break;
//read in the variable name
unsigned short name_len = *(unsigned short*) &local_header[26];
std::string vname(name_len,' ');
size_t vname_res = fread(&vname[0],sizeof(char),name_len,fp);
if(vname_res != name_len)
throw std::runtime_error("npz_load: failed fread");
vname.erase(vname.end()-4,vname.end()); //erase the lagging .npy
//read in the extra field
unsigned short extra_field_len = *(unsigned short*) &local_header[28];
fseek(fp,extra_field_len,SEEK_CUR); //skip past the extra field
if(vname == varname) {
NpyArray array = load_the_npy_file(fp);
fclose(fp);
return array;
}
else {
//skip past the data
unsigned int size = *(unsigned int*) &local_header[22];
fseek(fp,size,SEEK_CUR);
}
}
fclose(fp);
throw std::runtime_error("npz_load: Error! Variable name " + varname + " not found in " + fname + "!\n");
}
cnpy::NpyArray cnpy::npy_load(std::string fname) {
FILE* fp = fopen(fname.c_str(), "rb");
if(!fp) {
throw std::runtime_error("npy_load: Error! Unable to open file " + fname + "!\n");
}
NpyArray arr = load_the_npy_file(fp);
fclose(fp);
return arr;
}

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modules/dnn/test/cnpy.h
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/*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, install,
// copy or use the software.
//
//
// License Agreement
// For Open Source Computer Vision Library
//
// Copyright (C) 2013, OpenCV Foundation, all rights reserved.
// Third party copyrights are property of their respective owners.
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// * Redistribution's of source code must retain the above copyright notice,
// this list of conditions and the following disclaimer.
//
// * Redistribution's in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// * The name of the copyright holders may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// This software is provided by the copyright holders and contributors "as is" and
// any express or implied warranties, including, but not limited to, the implied
// warranties of merchantability and fitness for a particular purpose are disclaimed.
// In no event shall the Intel Corporation or contributors be liable for any direct,
// indirect, incidental, special, exemplary, or consequential damages
// (including, but not limited to, procurement of substitute goods or services;
// loss of use, data, or profits; or business interruption) however caused
// and on any theory of liability, whether in contract, strict liability,
// or tort (including negligence or otherwise) arising in any way out of
// the use of this software, even if advised of the possibility of such damage.
//
//M*/
//Copyright (C) 2011 Carl Rogers
//Released under MIT License
//license available in LICENSE file, or at http://www.opensource.org/licenses/mit-license.php
#ifndef LIBCNPY_H_
#define LIBCNPY_H_
#include<string>
#include<stdexcept>
#include<sstream>
#include<vector>
#include<cstdio>
#include<typeinfo>
#include<iostream>
#include<cassert>
#include<map>
#if defined(HAVE_ZLIB) && HAVE_ZLIB
#include<zlib.h>
#endif
#ifndef NDEBUG
#define cnpy_assert(expression) assert(expression)
#else
#define cnpy_assert(expression) ((void)(expression))
#endif
namespace cnpy {
struct NpyArray {
char* data;
std::vector<unsigned int> shape;
unsigned int word_size;
bool fortran_order;
void destruct() {delete[] data;}
};
struct npz_t : public std::map<std::string, NpyArray>
{
void destruct()
{
npz_t::iterator it = this->begin();
for(; it != this->end(); ++it) (*it).second.destruct();
}
};
char BigEndianTest();
char map_type(const std::type_info& t);
template<typename T> std::vector<char> create_npy_header(const T* data, const unsigned int* shape, const unsigned int ndims);
void parse_npy_header(FILE* fp,unsigned int& word_size, unsigned int*& shape, unsigned int& ndims, bool& fortran_order);
void parse_zip_footer(FILE* fp, unsigned short& nrecs, unsigned int& global_header_size, unsigned int& 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(char byte = 0; (size_t)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> std::string tostring(T i, int = 0, char = ' ') {
std::stringstream s;
s << i;
return s.str();
}
template<typename T> void npy_save(std::string fname, const T* data, const unsigned int* shape, const unsigned int ndims, std::string mode = "w") {
FILE* fp = NULL;
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
unsigned int word_size, tmp_dims;
unsigned int* tmp_shape = 0;
bool fortran_order;
parse_npy_header(fp,word_size,tmp_shape,tmp_dims,fortran_order);
cnpy_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";
cnpy_assert( word_size == sizeof(T) );
}
if(tmp_dims != ndims) {
std::cout<<"libnpy error: npy_save attempting to append misdimensioned data to "<<fname<<"\n";
cnpy_assert(tmp_dims == ndims);
}
for(unsigned i = 1; i < ndims; i++) {
if(shape[i] != tmp_shape[i]) {
std::cout<<"libnpy error: npy_save attempting to append misshaped data to "<<fname<<"\n";
cnpy_assert(shape[i] == tmp_shape[i]);
}
}
tmp_shape[0] += shape[0];
fseek(fp,0,SEEK_SET);
std::vector<char> header = create_npy_header(data,tmp_shape,ndims);
fwrite(&header[0],sizeof(char),header.size(),fp);
fseek(fp,0,SEEK_END);
delete[] tmp_shape;
}
else {
fp = fopen(fname.c_str(),"wb");
std::vector<char> header = create_npy_header(data,shape,ndims);
fwrite(&header[0],sizeof(char),header.size(),fp);
}
unsigned int nels = 1;
for(unsigned i = 0;i < ndims;i++) nels *= shape[i];
fwrite(data,sizeof(T),nels,fp);
fclose(fp);
}
template<typename T> void npz_save(std::string zipname, std::string fname, const T* data, const unsigned int* shape, const unsigned int ndims, std::string mode = "w")
{
//first, append a .npy to the fname
fname += ".npy";
//now, on with the show
FILE* fp = NULL;
unsigned short nrecs = 0;
unsigned int 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
unsigned int 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(data,shape,ndims);
unsigned long nels = 1;
for (unsigned m=0; m<ndims; m++ ) nels *= shape[m];
int nbytes = nels*sizeof(T) + npy_header.size();
//get the CRC of the data to be added
#if defined(HAVE_ZLIB) && HAVE_ZLIB
unsigned int crc = crc32(0L,(unsigned char*)&npy_header[0],npy_header.size());
crc = crc32(crc,(unsigned char*)data,nels*sizeof(T));
#else
unsigned int crc = 0;
#endif
//build the local header
std::vector<char> local_header;
local_header += "PK"; //first part of sig
local_header += (unsigned short) 0x0403; //second part of sig
local_header += (unsigned short) 20; //min version to extract
local_header += (unsigned short) 0; //general purpose bit flag
local_header += (unsigned short) 0; //compression method
local_header += (unsigned short) 0; //file last mod time
local_header += (unsigned short) 0; //file last mod date
local_header += (unsigned int) crc; //crc
local_header += (unsigned int) nbytes; //compressed size
local_header += (unsigned int) nbytes; //uncompressed size
local_header += (unsigned short) fname.size(); //fname length
local_header += (unsigned short) 0; //extra field length
local_header += fname;
//build global header
global_header += "PK"; //first part of sig
global_header += (unsigned short) 0x0201; //second part of sig
global_header += (unsigned short) 20; //version made by
global_header.insert(global_header.end(),local_header.begin()+4,local_header.begin()+30);
global_header += (unsigned short) 0; //file comment length
global_header += (unsigned short) 0; //disk number where file starts
global_header += (unsigned short) 0; //internal file attributes
global_header += (unsigned int) 0; //external file attributes
global_header += (unsigned int) 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 += (unsigned short) 0x0605; //second part of sig
footer += (unsigned short) 0; //number of this disk
footer += (unsigned short) 0; //disk where footer starts
footer += (unsigned short) (nrecs+1); //number of records on this disk
footer += (unsigned short) (nrecs+1); //total number of records
footer += (unsigned int) global_header.size(); //nbytes of global headers
footer += (unsigned int) (global_header_offset + nbytes + local_header.size()); //offset of start of global headers, since global header now starts after newly written array
footer += (unsigned short) 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> std::vector<char> create_npy_header(const T*, const unsigned int* shape, const unsigned int ndims) {
std::vector<char> dict;
dict += "{'descr': '";
dict += BigEndianTest();
dict += map_type(typeid(T));
dict += tostring(sizeof(T));
dict += "', 'fortran_order': False, 'shape': (";
dict += tostring(shape[0]);
for(unsigned i = 1;i < ndims;i++) {
dict += ", ";
dict += tostring(shape[i]);
}
if(ndims == 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 += (unsigned char) 0x93;
header += "NUMPY";
header += (char) 0x01; //major version of numpy format
header += (char) 0x00; //minor version of numpy format
header += (unsigned short) dict.size();
header.insert(header.end(),dict.begin(),dict.end());
return header;
}
}
#endif

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// This file is part of OpenCV project.
// It is subject to the license terms in the LICENSE file found in the top-level directory
// of this distribution and at http://opencv.org/license.html.
//
// Copyright (C) 2017, Intel Corporation, all rights reserved.
// Third party copyrights are property of their respective owners.
#include "npy_blob.hpp"
namespace cv
{
static std::string getType(const std::string& header)
{
std::string field = "'descr':";
int idx = header.find(field);
CV_Assert(idx != -1);
int from = header.find('\'', idx + field.size()) + 1;
int to = header.find('\'', from);
return header.substr(from, to - from);
}
static std::string getFortranOrder(const std::string& header)
{
std::string field = "'fortran_order':";
int idx = header.find(field);
CV_Assert(idx != -1);
int from = header.find_last_of(' ', idx + field.size()) + 1;
int to = header.find(',', from);
return header.substr(from, to - from);
}
static std::vector<int> getShape(const std::string& header)
{
std::string field = "'shape':";
int idx = header.find(field);
CV_Assert(idx != -1);
int from = header.find('(', idx + field.size()) + 1;
int to = header.find(')', from);
std::string shapeStr = header.substr(from, to - from);
if (shapeStr.empty())
return std::vector<int>(1, 1);
// Remove all commas.
shapeStr.erase(std::remove(shapeStr.begin(), shapeStr.end(), ','),
shapeStr.end());
std::istringstream ss(shapeStr);
int value;
std::vector<int> shape;
while (ss >> value)
{
shape.push_back(value);
}
return shape;
}
Mat blobFromNPY(const std::string& path)
{
std::ifstream ifs(path.c_str(), std::ios::binary);
CV_Assert(ifs.is_open());
std::string magic(6, '*');
ifs.read(&magic[0], magic.size());
CV_Assert(magic == "\x93NUMPY");
ifs.ignore(1); // Skip major version byte.
ifs.ignore(1); // Skip minor version byte.
uint16_t headerSize;
ifs.read((char*)&headerSize, sizeof(headerSize));
std::string header(headerSize, '*');
ifs.read(&header[0], header.size());
// Extract data type.
CV_Assert(getType(header) == "<f4");
CV_Assert(getFortranOrder(header) == "False");
std::vector<int> shape = getShape(header);
Mat blob(shape, CV_32F);
ifs.read((char*)blob.data, blob.total() * blob.elemSize());
CV_Assert(ifs.gcount() == blob.total() * blob.elemSize());
return blob;
}
} // namespace cv

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/*M///////////////////////////////////////////////////////////////////////////////////////
// This file is part of OpenCV project.
// It is subject to the license terms in the LICENSE file found in the top-level directory
// of this distribution and at http://opencv.org/license.html.
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
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#ifndef __OPENCV_DNN_TEST_NPY_BLOB_HPP__
#define __OPENCV_DNN_TEST_NPY_BLOB_HPP__
#include "test_precomp.hpp"
#include "cnpy.h"
namespace cv
{
inline Mat blobFromNPY(const String &path)
{
cnpy::NpyArray npyBlob = cnpy::npy_load(path.c_str());
Mat blob = Mat((int)npyBlob.shape.size(), (int*)&npyBlob.shape[0], CV_32F, npyBlob.data).clone();
npyBlob.destruct();
return blob;
}
inline void saveBlobToNPY(const Mat &blob, const String &path)
{
cnpy::npy_save(path.c_str(), blob.ptr<float>(), (unsigned*)&blob.size.p[0], blob.dims);
}
// Parse serialized NumPy array by np.save(...)
// Based on specification of .npy data format.
Mat blobFromNPY(const std::string& path);
}