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cavis/libnd4j/include/cnpy/cnpy.cpp

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/*******************************************************************************
* The MIT License
*
* Copyright (c) Carl Rogers, 2011
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
******************************************************************************/
//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 <pointercast.h>
#include <stdexcept>
#include"cnpy.h"
#include <types/types.h>
/**
*
* @return
*/
char cnpy::BigEndianTest() {
unsigned char x[] = {1,0};
short y = *(short*) x;
return y == 1 ? '<' : '>';
}
/**
*
* @param t
* @return
*/
char cnpy::mapType(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 <typename T>
char cnpy::mapType() {
if(std::is_same<float16, T>::value) return 'f';
if(std::is_same<float, T>::value) return 'f';
if(std::is_same<double, T>::value) return 'f';
if(std::is_same<long double, T>::value) return 'f';
if(std::is_same<int, T>::value) return 'i';
if(std::is_same<int8_t, T>::value) return 'i';
if(std::is_same<signed char, T>::value) return 'i';
if(std::is_same<char, T>::value) return 'i';
if(std::is_same<short, T>::value) return 'i';
if(std::is_same<long, T>::value) return 'i';
if(std::is_same<long long, T>::value) return 'i';
if(std::is_same<unsigned char, T>::value) return 'u';
if(std::is_same<unsigned short, T>::value) return 'u';
if(std::is_same<unsigned long, T>::value) return 'u';
if(std::is_same<unsigned long long, T>::value) return 'u';
if(std::is_same<unsigned int, T>::value) return 'u';
if(std::is_same<bool, T>::value) return 'b';
if(std::is_same<std::complex<float>, T>::value) return 'c';
if(std::is_same<std::complex<double>, T>::value) return 'c';
if(std::is_same<std::complex<long double>, T>::value) return 'c';
else return '?';
}
nd4j::DataType cnpy::dataTypeFromHeader(char *data) {
// indices for type & data size
const int st = 10;
const int ti = 22;
const int si = 23;
// read first char to make sure it looks like a header
if (data == nullptr || data[st] != '{')
throw std::runtime_error("cnpy::dataTypeFromHeader() - provided pointer doesn't look like a pointer to numpy header");
const auto t = data[ti];
const auto s = data[si];
switch (t) {
case 'b':
return nd4j::DataType::BOOL;
case 'i':
switch (s) {
case '1': return nd4j::DataType::INT8;
case '2': return nd4j::DataType::INT16;
case '4': return nd4j::DataType::INT32;
case '8': return nd4j::DataType::INT64;
default:
throw std::runtime_error("Only data sizes of [1, 2, 4, 8] are supported for Integer data types import");
}
case 'f':
switch (s) {
case '1': return nd4j::DataType::FLOAT8;
case '2': return nd4j::DataType::HALF;
case '4': return nd4j::DataType::FLOAT32;
case '8': return nd4j::DataType::DOUBLE;
default:
throw std::runtime_error("Only data sizes of [1, 2, 4, 8] are supported for Float data types import");
}
case 'u':
switch (s) {
case '1': return nd4j::DataType::UINT8;
case '2': return nd4j::DataType::UINT16;
case '4': return nd4j::DataType::UINT32;
case '8': return nd4j::DataType::UINT64;
default:
throw std::runtime_error("Only data sizes of [1, 2, 4, 8] are supported for Unsigned data types import");
}
case 'c':
throw std::runtime_error("Import of complex data types isn't supported yet");
default:
throw std::runtime_error("Unknown type marker");
}
}
template <typename T>
std::vector<char>& operator+=(std::vector<char>& lhs, const T rhs) {
//write in little endian
for(char byte = 0; byte < sizeof(T); byte++) {
char val = *((char*)&rhs+byte);
lhs.push_back(val);
}
return lhs;
}
/**
*
* @param lhs
* @param rhs
* @return
*/
template<>
std::vector<char>& operator+=(std::vector<char>& lhs, const std::string rhs) {
lhs.insert(lhs.end(),rhs.begin(),rhs.end());
return lhs;
}
/**
*
* @param lhs
* @param rhs
* @return
*/
template<>
std::vector<char>& 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;
}
/**
* Load the whole file in to memory
* @param path
* @return
*/
char* cnpy::loadFile(const char *path) {
char* buffer = 0;
long length;
FILE * f = fopen (path, "rb"); //was "rb"
if (f) {
fseek (f, 0, SEEK_END);
length = ftell (f);
fseek (f, 0, SEEK_SET);
buffer = (char*) malloc ((length+ 1) * sizeof(char));
// just getting rid of compiler warning
Nd4jLong fps = 0;
if (buffer) {
fps += fread (buffer, sizeof(char), length, f);
}
fclose (f);
}
buffer[length] = '\0';
return buffer;
}
/**
* Parse the numpy header from
* the given file
* based on the pointers passed in
* @param fp the file to parse from
* @param wordSize the size of
* the individual elements
* @param shape
* @param ndims
* @param fortranOrder
*/
void cnpy::parseNpyHeaderStr(std::string header,
unsigned int &wordSize,
unsigned int *&shape,
unsigned int &ndims,
bool &fortranOrder) {
int loc1, loc2;
//fortran order
loc1 = header.find("fortran_order") + 16;
fortranOrder = (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 = 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);
assert(littleEndian);
//char type = header[loc1+1];
//assert(type == map_type(T));
std::string str_ws = header.substr(loc1 + 2);
loc2 = str_ws.find("'");
wordSize = atoi(str_ws.substr(0,loc2).c_str());
}
/**
*
*
*
*
* @param fp the file to open
* @param wordSize the size of each element in the array
* @param shape the pointer to where the shape is stored
* @param ndims the number of dimensions for the array
* @param fortranOrder
*/
void cnpy::parseNpyHeader(FILE *fp,
unsigned int &wordSize,
unsigned int *&shape,
unsigned int &ndims,
bool &fortranOrder) {
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);
assert(header[header.size() - 1] == '\n');
cnpy::parseNpyHeaderStr(header,
wordSize,
shape,
ndims,
fortranOrder);
}
/**
*
* @param fp
* @param nrecs
* @param global_header_size
* @param global_header_offset
*/
void cnpy::parseZipFooter(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];
assert(disk_no == 0);
assert(disk_start == 0);
assert(nrecs_on_disk == nrecs);
assert(comment_len == 0);
}
/**
* Load the numpy array from the given file.
* @param fp the file to load
* @return the loaded array
*/
cnpy::NpyArray cnpy::loadNpyFromFile(FILE *fp) {
unsigned int *shape;
unsigned int ndims, wordSize;
bool fortranOrder;
cnpy::parseNpyHeader(fp,wordSize,shape,ndims,fortranOrder);
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.wordSize = wordSize;
arr.shape = std::vector<unsigned int>(shape,shape + ndims);
arr.data = new char[size * wordSize];
arr.fortranOrder = fortranOrder;
size_t nread = fread(arr.data,wordSize,size,fp);
if(nread != size)
throw std::runtime_error("load_the_npy_file: failed fread");
return arr;
}
/**
*
* @param data
* @return
*/
cnpy::NpyArray cnpy::loadNpyFromPointer(char *data) {
//move the pointer forward by 11 imitating
//the seek in loading directly from a file
return cnpy::loadNpyFromHeader(data);
}
/**
*
* @param data
* @return
*/
cnpy::NpyArray cnpy::loadNpyFromHeader(char *data) {
// check for magic header
if (data == nullptr)
throw std::runtime_error("NULL pointer doesn't look like a NumPy header");
if (data[0] == (char) 0x93) {
std::vector<char> exp({(char) 0x93, 'N', 'U', 'M', 'P', 'Y', (char) 0x01});
std::vector<char> hdr(data, data+7);
if (hdr != exp)
throw std::runtime_error("Pointer doesn't look like a NumPy header");
} else
throw std::runtime_error("Pointer doesn't look like a NumPy header");
//move passed magic
data += 11;
unsigned int *shape;
unsigned int ndims, wordSize;
bool fortranOrder;
cnpy::parseNpyHeaderStr(std::string(data),
wordSize,
shape,
ndims,
fortranOrder);
//the "real" data starts after the \n
char currChar = data[0];
int count = 0;
while(currChar != '\n') {
data++;
currChar = data[0];
count++;
}
//move pass the \n
data++;
count++;
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];
char *cursor = data;
cnpy::NpyArray arr;
arr.wordSize = wordSize;
arr.shape = std::vector<unsigned int>(shape,shape + ndims);
delete[] shape;
arr.data = cursor;
arr.fortranOrder = fortranOrder;
return arr;
}
/**
* Load the numpy z archive
* @param fp FILE pointer
* @return the arrays
*/
cnpy::npz_t cnpy::npzLoad(FILE* 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
for (int e = 0; e < 4; e++)
varname.pop_back();
//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] = loadNpyFromFile(fp);
}
return arrays;
}
/**
* Load the numpy z archive
* @param fname the fully qualified path
* @return the arrays
*/
cnpy::npz_t cnpy::npzLoad(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());
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
for (int e = 0; e < 4; e++)
varname.pop_back();
//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] = loadNpyFromFile(fp);
}
fclose(fp);
return arrays;
}
/**
* Loads a npz (multiple numpy arrays) file
* @param fname the file name
* @param varname
* @return
*/
cnpy::NpyArray cnpy::npzLoad(std::string fname, std::string varname) {
FILE *fp = fopen(fname.c_str(),"rb");
if(!fp) {
printf("npz_load: Error! Unable to open file %s!\n",fname.c_str());
}
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");
//erase the lagging .npy
for (int e = 0; e < 4; e++)
varname.pop_back();
//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 = cnpy::loadNpyFromFile(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);
printf("npz_load: Error! Variable name %s not found in %s!\n",varname.c_str(),fname.c_str());
throw std::runtime_error("Variable wasn't found in file");
}
/**
* Load a numpy array from the given file
* @param fname the fully qualified path for the file
* @return the NpArray for this file
*/
cnpy::NpyArray cnpy::npyLoad(std::string fname) {
FILE* fp = fopen(fname.c_str(), "rb");
if(!fp) {
printf("npy_load: Error! Unable to open file %s!\n",fname.c_str());
}
NpyArray arr = cnpy::loadNpyFromFile(fp);
fclose(fp);
return arr;
}
/**
* Save the numpy array
* @tparam T
* @param fname the file
* @param data the data for the ndarray
* @param shape the shape of the ndarray
* @param ndims the number of dimensions
* for the ndarray
* @param mode the mode for writing
*/
template<typename T>
void cnpy::npy_save(std::string fname,
const T* data,
const unsigned int* shape,
const unsigned int ndims,
std::string mode) {
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;
parseNpyHeader(fp,
word_size,
tmp_shape,
tmp_dims,
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(tmp_dims != ndims) {
std::cout<<"libnpy error: npy_save attempting to append misdimensioned data to "<<fname<<"\n";
assert(tmp_dims == ndims);
}
for(int 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";
assert(shape[i] == tmp_shape[i]);
}
}
tmp_shape[0] += shape[0];
fseek(fp,0,SEEK_SET);
std::vector<char> header = createNpyHeader<T>(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 = createNpyHeader<T>(data,shape,ndims);
fwrite(&header[0],sizeof(char),header.size(),fp);
}
unsigned long long nels = 1;
for(int i = 0;i < ndims;i++) nels *= shape[i];
fwrite(data,sizeof(T),nels,fp);
fclose(fp);
}
/**
*
* @tparam T
* @param data
* @param shape
* @param ndims
* @return
*/
template<typename T>
std::vector<char> cnpy::createNpyHeader(const void *vdata,
const unsigned int *shape,
const unsigned int ndims,
unsigned int wordSize) {
auto data = reinterpret_cast<const T*>(vdata);
std::vector<char> dict;
dict += "{'descr': '";
dict += sizeof(T) > 1 ? BigEndianTest() : '|';
dict += mapType<T>();
dict += tostring(wordSize);
dict += "', 'fortran_order': False, 'shape': (";
if (ndims > 0) {
dict += tostring(shape[0]);
for (int i = 1; i < ndims; i++) {
dict += ", ";
dict += tostring(shape[i]);
}
if (ndims == 1)
dict += ",";
}
// 0D case still requires close
dict += "), }";
//pad with spaces so that preamble+dict is modulo 16 bytes. preamble is 10 bytes. dict needs to end with \n
int remainder = 64 - (10 + dict.size()) % 64;
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 += (unsigned short) dict.size();
header.insert(header.end(),dict.begin(),dict.end());
return header;
}
BUILD_SINGLE_TEMPLATE(template ND4J_EXPORT std::vector<char> cnpy::createNpyHeader, (const void *data, const unsigned int *shape, const unsigned int ndims, unsigned int wordSize), LIBND4J_TYPES);
//template ND4J_EXPORT std::vector<char> cnpy::createNpyHeader<void>(const void *data, const unsigned int *shape, const unsigned int ndims, unsigned int wordSize);
template ND4J_EXPORT void cnpy::npy_save<float>(std::string fname, const float* data, const unsigned int* shape, const unsigned int ndims, std::string mode);
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