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adding project files
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@rogersce
rogersce committed Jun 9, 2011
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21 changes: 21 additions & 0 deletions CMakeLists.txt
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CMAKE_MINIMUM_REQUIRED(VERSION 2.6 FATAL_ERROR)
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
endif(COMMAND cmake_policy)

project(CNPY)

set(CMAKE_INSTALL_PREFIX $ENV{HOME})
option(ENABLE_STATIC "Build static (.a) library" ON)

ADD_LIBRARY(cnpy SHARED "cnpy.cpp")
install(TARGETS "cnpy" LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)

if(ENABLE_STATIC)
add_LIBRARY(cnpy-static STATIC "cnpy.cpp")
SET_TARGET_PROPERTIES(cnpy-static PROPERTIES OUTPUT_NAME "cnpy")
install(TARGETS "cnpy-static" ARCHIVE DESTINATION lib)
endif(ENABLE_STATIC)

install(FILES "cnpy.h" DESTINATION include)
install(FILES "mat2npz" "npy2mat" DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
21 changes: 21 additions & 0 deletions LICENSE
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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.
229 changes: 229 additions & 0 deletions cnpy.cpp
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//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() {
unsigned char x[] = {1,0};
short y = *(short*) x;
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
char len = strlen(rhs);
for(char 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) {
char buffer[256];
fread(buffer,sizeof(char),11,fp);
std::string header = fgets(buffer,256,fp);
assert(header[header.size()-1] == '\n');

int loc1, loc2;

//fortran order
loc1 = header.find("fortran_order")+16;
bool fortran_order = (header.substr(loc1,5) == "True" ? true : false);
assert(!fortran_order);

//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(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
loc1 = header.find("descr")+9;
bool littleEndian = (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("'");
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);
fread(&footer[0],sizeof(char),22,fp);

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);
}

cnpy::NpyArray load_the_npy_file(FILE* fp) {
unsigned int* shape;
unsigned int ndims, word_size;
cnpy::parse_npy_header(fp,word_size,shape,ndims);
unsigned int size = 1;
for(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);
arr.data = new char[size*word_size];
int nread = fread(arr.data,word_size,size,fp);
return arr;
}

std::map<std::string,cnpy::NpyArray> 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());
assert(fp);

std::map<std::string,NpyArray> arrays;

while(1) {
std::vector<char> local_header(30);
fread(&local_header[0],sizeof(char),30,fp);

//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,' ');
fread(&varname[0],sizeof(char),name_len,fp);

//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);
fread(&buff[0],sizeof(char),extra_field_len,fp);
}

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) {
printf("npz_load: Error! Unable to open file %s!\n",fname.c_str());
abort();
}

while(1) {
std::vector<char> local_header(30);
fread(&local_header[0],sizeof(char),30,fp);

//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,' ');
fread(&vname[0],sizeof(char),name_len,fp);
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);
printf("npz_load: Error! Variable name %s not found in %s!\n",varname.c_str(),fname.c_str());
abort();
}

cnpy::NpyArray cnpy::npy_load(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());
abort();
}

NpyArray arr = load_the_npy_file(fp);

fclose(fp);
return arr;
}



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