/usr/include/odindata/data.h is in libodin-dev 1.8.5-2ubuntu1.
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data.h - description
-------------------
begin : Fri Apr 6 2001
copyright : (C) 2001 by Thies Jochimsen & Michael von Mengershausen
email : jochimse@cns.mpg.de mengers@cns.mpg.de
***************************************************************************/
/***************************************************************************
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************/
#ifndef DATA_H
#define DATA_H
#ifndef TJUTILS_CONFIG_H
#define TJUTILS_CONFIG_H
#include <tjutils/config.h>
#endif
#include <tjutils/tjfeedback.h>
#ifdef ODIN_DEBUG
#define BZ_DEBUG
#endif
#include <blitz/blitz.h> // include 1st to overwrite mutex defines
// undef mutex defines
#ifdef BZ_MUTEX_DECLARE
#undef BZ_MUTEX_DECLARE
#endif
#ifdef BZ_MUTEX_INIT
#undef BZ_MUTEX_INIT
#endif
#ifdef BZ_MUTEX_LOCK
#undef BZ_MUTEX_LOCK
#endif
#ifdef BZ_MUTEX_UNLOCK
#undef BZ_MUTEX_UNLOCK
#endif
#ifdef BZ_MUTEX_DESTROY
#undef BZ_MUTEX_DESTROY
#endif
// do not use mutex in Blitz, even if pthread is available
// to get consistent behaviour across all platforms
#define BZ_MUTEX_DECLARE(name)
#define BZ_MUTEX_INIT(name)
#define BZ_MUTEX_LOCK(name)
#define BZ_MUTEX_UNLOCK(name)
#define BZ_MUTEX_DESTROY(name)
#include <blitz/array.h>
#include <blitz/tinyvec-et.h> // to use arithmetics of TinyVectors
using namespace blitz;
#include <tjutils/tjtypes.h>
#include <tjutils/tjprofiler.h>
#include <odinpara/protocol.h>
#include <odindata/converter.h>
#include <odindata/fileio_opts.h>
// some additional macros for complex numbers
BZ_DECLARE_FUNCTION_RET (float2real, STD_complex);
BZ_DECLARE_FUNCTION_RET (float2imag, STD_complex);
BZ_DECLARE_FUNCTION_RET (creal, float)
BZ_DECLARE_FUNCTION_RET (cimag, float)
BZ_DECLARE_FUNCTION_RET (cabs, float)
BZ_DECLARE_FUNCTION_RET (phase, float)
BZ_DECLARE_FUNCTION (logc)
BZ_DECLARE_FUNCTION (expc)
BZ_DECLARE_FUNCTION (conjc)
// Other useful macros
BZ_DECLARE_FUNCTION2(secureDivision)
BZ_DECLARE_FUNCTION (secureInv)
#ifdef STL_REPLACEMENT
BZ_DECLARE_ARRAY_ET_SCALAR_OPS(tjstd_complex)
#endif
/**
* @addtogroup odindata
* @{
*/
///////////////////////////////////////////////////////
struct FileMapHandle {
FileMapHandle() : fd(-1), offset(0), refcount(1) {}
int fd;
LONGEST_INT offset; // in bytes
int refcount;
Mutex mutex; // protect refcount
};
///////////////////////////////////////////////////////
/**
* This template class holds multidimensional data. In addition to functionality
* provided by the Blitz Array class, it offers methods to read/write raw data
* and and other file formats (nifti, vtk, ...) to/from a file.
* In addition, uing a special constructor, the array can be associated with a block
* of data on disk using the UNIX mmap functionality. In this case, any changes made
* to the array will be automatically tranfered to the file. Please note that any
* attempt to resize such an array will most likely cause a segmentation fault.
*
*/
template <typename T, int N_rank>
class Data : public Array<T,N_rank> {
public:
/**
* Constructs an array with the given dimensionality and initial value
*/
Data(const TinyVector<int,N_rank>& dimvec, const T& val=0) : Array<T,N_rank>(dimvec), fmap(0) {(*this)=val;}
// Variable extent constructors
Data() : fmap(0) {}
Data(int extent1) : Array<T,N_rank>(extent1), fmap(0) {}
Data(int extent1, int extent2) : Array<T,N_rank>(extent1,extent2), fmap(0) {}
Data(int extent1, int extent2,int extent3) : Array<T,N_rank>(extent1,extent2,extent3), fmap(0) {}
Data(int extent1, int extent2,int extent3,int extent4) : Array<T,N_rank>(extent1,extent2,extent3,extent4), fmap(0) {}
Data(int extent1, int extent2,int extent3,int extent4,int extent5) : Array<T,N_rank>(extent1,extent2,extent3,extent4,extent5), fmap(0) {}
Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6) : Array<T,N_rank>(extent1,extent2,extent3,extent4,extent5,extent6), fmap(0) {}
Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7) : Array<T,N_rank>(extent1,extent2,extent3,extent4,extent5,extent6,extent7), fmap(0) {}
Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7,int extent8) : Array<T,N_rank>(extent1,extent2,extent3,extent4,extent5,extent6,extent7,extent8), fmap(0) {}
Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7,int extent8,int extent9) : Array<T,N_rank>(extent1,extent2,extent3,extent4,extent5,extent6,extent7,extent8,extent9), fmap(0) {}
/**
* Maps the given file 'filename' into the newly created array via the the mmap function,
* see the mmap man page for details. The mapping is abolish when the
* array is destroyed (destructor). Other parameters:
* - readonly : If true, file can only be read. If false, the file will be created if it does not exist
* - shape : The extent in each dimension
* - offset : Skip first 'offset' bytes
*/
Data(const STD_string& filename, bool readonly, const TinyVector<int,N_rank>& shape, LONGEST_INT offset=0 );
/**
* Copy constructor
*/
Data(const Data<T,N_rank>& d) : fmap(0) {Data<T,N_rank>::reference(d);}
/**
* Copy constructor from Blitz::Array
*/
Data(const Array<T,N_rank>& a) : Array<T,N_rank>(a), fmap(0) {}
/**
* Constructor from an equivalent tjarray (\ref arrays). If rank of 'a' is smaller, extent will pe padded with 1 at front.
*/
Data(const tjarray<tjvector<T>,T>& a) : fmap(0) { (*this)=a;}
/**
* Constructor from expression template
*/
template<class T_expr>
Data(BZ_ETPARM(_bz_ArrayExpr<T_expr>) expr) : Array<T,N_rank>(expr), fmap(0) {}
/**
* Destructor
*/
~Data();
/**
* Assignment operator
*/
Data<T,N_rank>& operator = (const Data<T,N_rank>& d) {Array<T,N_rank>::operator=(d); return *this;}
/**
* Assignment operator from Blitz::Array
*/
Data<T,N_rank>& operator = (const Array<T,N_rank>& a) {Array<T,N_rank>::operator=(a); return *this;}
/**
* Fills all elements with 'val'
*/
Data<T,N_rank>& operator = (const T& val) {Array<T,N_rank>::operator=(val); return *this;}
/**
* Assignment operator for expression templates
*/
template<class T_expr>
inline Data<T,N_rank>& operator = (BZ_ETPARM(_bz_ArrayExpr<T_expr>) expr) {
typedef _bz_typename T_expr::T_numtype T_numtype;
this->evaluate(expr, _bz_update<T_numtype, _bz_typename T_expr::T_numtype>());
return *this;
}
/**
* Assignment from an equivalent tjarray (\ref arrays). If rank of 'a' is smaller, extent will pe padded with 1 at front.
*/
Data<T,N_rank>& operator = (const tjarray<tjvector<T>,T>& a);
// resolve ambiguities
Array<T,N_rank> operator + (const Data<T,N_rank>& b) const {return Array<T,N_rank>(Array<T,N_rank>(*this)+Array<T,N_rank>(b));}
Array<T,N_rank> operator - (const Data<T,N_rank>& b) const {return Array<T,N_rank>(Array<T,N_rank>(*this)-Array<T,N_rank>(b));}
Array<T,N_rank> operator * (const Data<T,N_rank>& b) const {return Array<T,N_rank>(Array<T,N_rank>(*this)*Array<T,N_rank>(b));}
Array<T,N_rank> operator / (const Data<T,N_rank>& b) const {return Array<T,N_rank>(Array<T,N_rank>(*this)/Array<T,N_rank>(b));}
// resolve ambiguities
Array<T,N_rank> operator + (const T& v) const {return Array<T,N_rank>(Array<T,N_rank>(*this)+v);}
Array<T,N_rank> operator - (const T& v) const {return Array<T,N_rank>(Array<T,N_rank>(*this)-v);}
Array<T,N_rank> operator * (const T& v) const {return Array<T,N_rank>(Array<T,N_rank>(*this)*v);}
Array<T,N_rank> operator / (const T& v) const {return Array<T,N_rank>(Array<T,N_rank>(*this)/v);}
/**
* Reads the array from a raw data file 'filename' of type 'format' which can be one of
* 's8bit, u8bit, s16bit, u16bit, s32bit, u32bit, float or double'.
* No resizing is performed prior to reading. Skip the first 'offset' bytes.
* - Return value: 0 if succesful, otherwise -1
*/
int read(const STD_string& format,const STD_string& filename, LONGEST_INT offset=0);
/**
* Reads the array from a raw data file 'filename' of type 'T2'.
* No resizing is performed prior to reading. Skip the first 'offset' bytes.
* - Return value: 0 if succesful, otherwise -1
*/
template<typename T2>
int read(const STD_string& filename, LONGEST_INT offset=0);
/**
* Writes the array to a raw data file 'filename' of type 'format' which can be one of
* 's8bit, u8bit, s16bit, u16bit, s32bit, u32bit, float or double'.
* - Return value: 0 if succesful, otherwise -1
*/
int write(const STD_string& format,const STD_string& filename, autoscaleOption scaleopt=autoscale) const;
/**
* Writes the array to a raw data file 'filename' of type 'T2'.
* - Return value: 0 if succesful, otherwise -1
*/
template<typename T2>
int write(const STD_string& filename, autoscaleOption scaleopt=autoscale) const;
/**
* Writes the array to a raw data file 'filename' of type the same type as the array is.
*The mode specifies whether an already existing file is overwritten, or the data is appended.
* - Return value: 0 if succesful, otherwise -1
*/
int write(const STD_string& filename, fopenMode mode=overwriteMode) const;
/**
* Writes the array as a formatted ASCII file to
* 'filename', one value per line. If 'pre' is
* of the same size as this, its values are
* inserted before the value on each line,
* and the values of 'post' are inserted after
* the values of this array on each line.
* Return value is -1 if an error occurs.
*/
int write_asc_file(const STD_string& filename, const Array<T,N_rank>& pre=defaultArray, const Array<T,N_rank>& post=defaultArray) const;
/**
* reads in white-space separated data from ASCII file, no resizing is performed prior to reading
* Return value is -1 if an error occurs.
*/
int read_asc_file(const STD_string& filename);
/**
* Writes data set to file 'filename' in the format automatically detected by the given file extension.
* Extra options can be given by 'opts' and protocol settings can be overwritten by 'prot'.
* Returns number of slices, or -1 if it fails.
*/
int autowrite(const STD_string& filename, const FileWriteOpts& opts=FileWriteOpts(), const Protocol* prot=0) const;
/**
* Reads data set from file 'filename' assuming the format automatically detected by the given file extension.
* Extra options can be given by 'opts' and protocol settings will be stored in 'prot'.
* The progress meter 'progmeter' can be optionally specified to monitor the progress of the operation.
* Returns number of slices sucessfully read, or -1 if it fails.
*/
int autoread(const STD_string& filename, const FileReadOpts& opts=FileReadOpts(), Protocol* prot=0, ProgressMeter* progmeter=0);
/**
* Returns true if the array is associated with a file on disk
*/
bool is_filemapped() const {return fmap;}
/**
* Exports this array into an equivalent tjarray (\ref arrays)
*/
operator tjarray<tjvector<T>,T> () const;
/**
* Creates an index vector according to a linear index for the whole array
* by taking the shape into account.
*/
TinyVector<int, N_rank> create_index(unsigned long index) const;
/**
* Creates a linear index from an index vector
*/
unsigned long create_linear_index(const TinyVector<int, N_rank>& indexvec) const;
/**
* Shift the data by 'shift' pixels in dimension 'shift_dim'. The
* data is shifted cyclically, i.e. the values which are shifted
* out at one edge of the array will be shifted in on the other edge.
*/
void shift(unsigned int shift_dim, int shift);
/**
* Interpolate (or extrapolate) the data in the array to the new shape.
* The interpolation is performed dimension-by-dimension using the GSL spline interpolation
* routines.
* Add extra shift 'subpixel_shift' in units of pixels on the destination grid if 'subpixel_shift' is non-null.
* if 'left_to_right' is set to true, interpolation starts at the most left
* dimension, i.e. at those with the highest index, down to the lowest index.
* If set to false, interpolation is performed vice versa.
*/
void congrid(const TinyVector<int,N_rank>& newshape, const TinyVector<float,N_rank>* subpixel_shift=0, bool left_to_right=false);
/**
* Converts the array to type 'T2', with dimensionality 'N_rank2' and stores the result in 'dst'.
* The scaling strategy can be specified by 'scaleopt'.
* 'dst' will be unique, i.e. no other references to the array exist.
* In addition to changing 'dst', a reference to the same array is returned for convenience.
*/
template<typename T2, int N_rank2> Data<T2,N_rank2>& convert_to(Data<T2,N_rank2>& dst, autoscaleOption scaleopt=autoscale) const;
// specialization which uses reference if type/rank are same and scale/offset==0.0 to reduce memory usage
Data<T,N_rank>& convert_to(Data<T,N_rank>& dst, autoscaleOption scaleopt=autoscale) const;
/**
* Makes array unique and continuous and returns pointer to data
*/
T* c_array();
// Reimplemented Blitz::Array functions
void reference(const Data<T,N_rank>& d);
// dummy objects used for default arguments
static Array<T,N_rank> defaultArray;
private:
void interpolate1dim(unsigned int dim, int newsize, float subpixel_shift);
void detach_fmap();
FileMapHandle* fmap;
};
template <typename T, int N_rank>
Array<T,N_rank> Data<T,N_rank>::defaultArray;
/** @}
*/
///////////////////////////////////////////////////////////////////////////////
#ifdef STREAM_REPLACEMENT
template<typename T, int N_rank>
inline STD_ostream& operator << (STD_ostream& s,const Array<T,N_rank>&) {return s;}
template<typename T, int N_rank>
inline STD_ostream& operator << (STD_ostream& s,const TinyVector<T,N_rank>&) { return s;}
inline STD_ostream& operator << (STD_ostream& s,const Range&) { return s;}
#endif
///////////////////////////////////////////////////////////////////////////////
/*
* Create n-dim index from linear 'index' for a given 'shape'
*/
template<int N_rank>
TinyVector<int,N_rank> index2extent(const TinyVector<int,N_rank>& shape, unsigned int index) {
TinyVector<int,N_rank> result;
unsigned int temp=index;
for(int i=N_rank-1;i>=0;i--){
result(i)=temp%shape(i);
temp=temp/shape(i);
}
return result;
}
///////////////////////////////////////////////////////////////////////////////
// leave this function outside of class Data, otherwise it screws up
// when using optimization
template<typename T, int N_rank, typename T2>
void convert_from_ptr(Data<T,N_rank>& dst, const T2* src, const TinyVector<int, N_rank>& shape, autoscaleOption scaleopt=autoscale) {
Log<OdinData> odinlog("Data","convert_from_ptr");
int dstsize=product(shape);
int srcsize=dstsize*Converter::get_elements((T)0)/Converter::get_elements((T2)0);
ODINLOG(odinlog,normalDebug) << "dstsize/srcsize=" << dstsize << "/" << srcsize << STD_endl;
dst.resize(shape);
Converter::convert_array(src, dst.c_array(), srcsize, dstsize, scaleopt);
}
// specialization in case the type is the same
template<typename T, int N_rank>
void convert_from_ptr(Data<T,N_rank>& dst, const T* src, const TinyVector<int, N_rank>& shape) {
dst.reference(Array<T,N_rank>((T*)src, shape, duplicateData));
}
////////////////////////////////////////////////////////////////////////////
template <typename T, int N_rank>
Data<T,N_rank>::Data(const STD_string& filename, bool readonly, const TinyVector<int,N_rank>& shape, LONGEST_INT offset ) : fmap(new FileMapHandle) {
T* ptr=(T*)filemap(filename, (LONGEST_INT)product(shape)*sizeof(T), offset, readonly, fmap->fd);
if(ptr && (fmap->fd)>=0) { // only negative file descriptor indicates filemap failure
Array<T,N_rank>::reference(Array<T,N_rank>(ptr, shape, neverDeleteData));
fmap->offset=offset;
} else {
delete fmap;
fmap=0;
}
}
////////////////////////////////////////////////////////////////////////////
template <typename T, int N_rank>
void Data<T,N_rank>::detach_fmap() {
Log<OdinData> odinlog("Data","detach_fmap");
if(fmap) {
fmap->mutex.lock();
(fmap->refcount)--;
ODINLOG(odinlog,normalDebug) << "fd/offset/refcount=" << fmap->fd << "/" << fmap->offset << "/" << fmap->refcount << STD_endl;
if(!(fmap->refcount)) {
fileunmap(fmap->fd, Array<T,N_rank>::data(), (LONGEST_INT)Array<T,N_rank>::size()*sizeof(T), fmap->offset);
fmap->mutex.unlock();
delete fmap;
fmap=0;
}
if(fmap) fmap->mutex.unlock();
}
}
////////////////////////////////////////////////////////////////////////////
template <typename T, int N_rank>
Data<T,N_rank>::~Data() {
detach_fmap();
}
////////////////////////////////////////////////////////////////////////////
template <typename T, int N_rank>
void Data<T,N_rank>::reference(const Data<T,N_rank>& d) {
Log<OdinData> odinlog("Data","reference");
detach_fmap();
fmap=d.fmap;
if(fmap) {
MutexLock lock(fmap->mutex);
(fmap->refcount)++;
ODINLOG(odinlog,normalDebug) << "fmap->refcount=" << fmap->refcount << STD_endl;
}
Array<T,N_rank>::reference(d);
}
////////////////////////////////////////////////////////////////////////////
template <typename T, int N_rank>
Data<T,N_rank>& Data<T,N_rank>::operator = (const tjarray<tjvector<T>,T>& a) {
Log<OdinData> odinlog("Data","=");
if( a.dim() <= N_rank ) {
ndim nn=a.get_extent();
int npad=N_rank-nn.dim();
ODINLOG(odinlog,normalDebug) << "npad=" << npad << STD_endl;
for(int ipad=0; ipad<npad; ipad++) nn.add_dim(1, true); // pad at front
ODINLOG(odinlog,normalDebug) << "nn(pad)" << nn << STD_endl;
TinyVector<int,N_rank> tv;
for(unsigned int i=0; i<N_rank; i++) tv(i)=nn[i];
this->resize(tv);
for(unsigned int i=0;i<a.total();i++) (*this)(create_index(i))=a[i];
} else ODINLOG(odinlog,errorLog) << "dimension mismatch: this=" << N_rank<< " < tjarray=" << a.dim() << STD_endl;
return *this;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
int Data<T,N_rank>::read(const STD_string& format,const STD_string& filename, LONGEST_INT offset) {
Log<OdinData> odinlog("Data","read");
if(format==TypeTraits::type2label((u8bit)0)) return read<u8bit> (filename);
if(format==TypeTraits::type2label((s8bit)0)) return read<s8bit> (filename);
if(format==TypeTraits::type2label((u16bit)0)) return read<u16bit>(filename);
if(format==TypeTraits::type2label((s16bit)0)) return read<s16bit>(filename);
if(format==TypeTraits::type2label((u32bit)0)) return read<u32bit>(filename);
if(format==TypeTraits::type2label((s32bit)0)) return read<s32bit>(filename);
if(format==TypeTraits::type2label((float)0)) return read<float> (filename);
if(format==TypeTraits::type2label((double)0)) return read<double>(filename);
ODINLOG(odinlog,errorLog) << "Unable to read file " << filename << " with data type " << format << STD_endl;
return -1;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
template<typename T2>
int Data<T,N_rank>::read(const STD_string& filename, LONGEST_INT offset) {
Log<OdinData> odinlog("Data","read");
LONGEST_INT fsize=filesize(filename.c_str())-offset;
LONGEST_INT nelements_file=fsize/sizeof(T2);
LONGEST_INT length=product(Array<T,N_rank>::shape());
ODINLOG(odinlog,normalDebug) << "fsize / nelements_file / length = " << fsize << " / " << nelements_file << " / " << length << STD_endl;
if(!length) return 0;
if(nelements_file<length) {
ODINLOG(odinlog,errorLog) << "Size of file " << filename << " to small for reading" << STD_endl;
return -1;
}
STD_string srctype=TypeTraits::type2label((T2)0);
STD_string dsttype=TypeTraits::type2label((T)0);
ODINLOG(odinlog,normalDebug) << "srctype/dsttype=" << srctype << "/" << dsttype << STD_endl;
TinyVector<int,N_rank> fileshape(Array<T,N_rank>::shape());
fileshape(N_rank-1) *= (Converter::get_elements((T)0)/Converter::get_elements((T2)0)); // Adjust extent of last dim for copmlex data
Data<T2,N_rank> filedata(filename, true, fileshape, offset);
filedata.convert_to(*this);
return 0;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
int Data<T,N_rank>::write(const STD_string& format, const STD_string& filename, autoscaleOption scaleopt) const {
Log<OdinData> odinlog("Data","write");
if(format==TypeTraits::type2label((u8bit)0)) return write<u8bit> (filename,scaleopt);
if(format==TypeTraits::type2label((s8bit)0)) return write<s8bit> (filename,scaleopt);
if(format==TypeTraits::type2label((u16bit)0)) return write<u16bit>(filename,scaleopt);
if(format==TypeTraits::type2label((s16bit)0)) return write<s16bit>(filename,scaleopt);
if(format==TypeTraits::type2label((u32bit)0)) return write<u32bit>(filename,scaleopt);
if(format==TypeTraits::type2label((s32bit)0)) return write<s32bit>(filename,scaleopt);
if(format==TypeTraits::type2label((float)0)) return write<float> (filename,scaleopt);
if(format==TypeTraits::type2label((double)0)) return write<double>(filename,scaleopt);
ODINLOG(odinlog,errorLog) << "Unable to write file " << filename << " with data type " << format << STD_endl;
return -1;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
int Data<T,N_rank>::write(const STD_string& filename, fopenMode mode) const {
Log<OdinData> odinlog("Data","write");
if(filename=="") return 0;
FILE* file_ptr=FOPEN(filename.c_str(),modestring(mode));
if(file_ptr==NULL) {
ODINLOG(odinlog,errorLog) << "unable to create/open file >" << filename << "< - " << lasterr() << STD_endl;
return -1;
}
Data<T,N_rank> data_copy(*this); // for contig memory
LONGEST_INT nmemb=Array<T,N_rank>::numElements();
LONGEST_INT count=fwrite(data_copy.c_array(),sizeof(T),nmemb,file_ptr);
if(count!=nmemb) {
ODINLOG(odinlog,errorLog) << "unable to fwrite to file >" << filename << "< - " << lasterr() << STD_endl;
return -1;
}
if(file_ptr!=NULL) fclose(file_ptr);
return 0;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
template<typename T2>
int Data<T,N_rank>::write(const STD_string& filename, autoscaleOption scaleopt) const {
Log<OdinData> odinlog("Data","write");
rmfile(filename.c_str()); // remove old file to get new file size with mmap
ODINLOG(odinlog,normalDebug) << "mem(pre): " << Profiler::get_memory_usage() << STD_endl;
Data<T2,N_rank> converted_data; convert_to(converted_data,scaleopt);
ODINLOG(odinlog,normalDebug) << "mem(cnv): " << Profiler::get_memory_usage() << STD_endl;
Data<T2,N_rank> filedata(filename,false,converted_data.shape());
ODINLOG(odinlog,normalDebug) << "mem(map): " << Profiler::get_memory_usage() << STD_endl;
filedata=converted_data;
return 0;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
int Data<T,N_rank>::write_asc_file(const STD_string& filename, const Array<T,N_rank>& pre, const Array<T,N_rank>& post) const {
bool have_pre=false;
bool have_post=false;
Data<T,N_rank> pre_data(pre);
Data<T,N_rank> post_data(post);
int n=Array<T,N_rank>::numElements();
if(pre_data.numElements()==n) have_pre=true;
if(post_data.numElements()==n) have_post=true;
STD_ofstream ofs(filename.c_str());
if(ofs.bad()) return -1;
T val;
for(int i=0; i<n; i++) {
if(have_pre) {
val=pre_data(pre_data.create_index(i));
ofs << val << " ";
}
val=(*this)(create_index(i));
ofs << val;
if(have_post) {
val=post_data(post_data.create_index(i));
ofs << " " << val;
}
ofs << "\n";
}
ofs.close();
return 0;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
int Data<T,N_rank>::read_asc_file(const STD_string& filename) {
STD_ifstream ifs(filename.c_str());
if(ifs.bad()) return -1;
STD_string valstr;
for(int i=0; i<Array<T,N_rank>::numElements(); i++) {
if(ifs.bad()) return -1;
ifs >> valstr;
TypeTraits::string2type(valstr,(*this)(create_index(i)));
}
ifs.close();
return 0;
}
////////////////////////////////////////////////////////////////////////////
// Interface to FileIO functionality
int fileio_autowrite(const Data<float,4>& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol* prot);
int fileio_autoread(Data<float,4>& data, const STD_string& filename, const FileReadOpts& opts, Protocol* prot, ProgressMeter* progmeter);
template<typename T,int N_rank>
int Data<T,N_rank>::autowrite(const STD_string& filename, const FileWriteOpts& opts, const Protocol* prot) const {
Data<float,4> filedata; convert_to(filedata);
return fileio_autowrite(filedata, filename, opts, prot);
}
template<typename T,int N_rank>
int Data<T,N_rank>::autoread(const STD_string& filename, const FileReadOpts& opts, Protocol* prot, ProgressMeter* progmeter) {
Data<float,4> filedata;
int result=fileio_autoread(filedata, filename, opts, prot, progmeter);
if(result>0) filedata.convert_to(*this);
return result;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
Data<T,N_rank>::operator tjarray<tjvector<T>,T> () const {
tjarray<tjvector<T>,T> a;
ndim nn(N_rank);
for(unsigned int i=0; i<N_rank; i++) nn[i]=Array<T,N_rank>::extent(i);
a.redim(nn);
for(unsigned int i=0;i<a.total();i++) a[i]=(*this)(create_index(i));
return a;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
template<typename T2, int N_rank2>
Data<T2,N_rank2>& Data<T,N_rank>::convert_to(Data<T2,N_rank2>& dst, autoscaleOption scaleopt) const {
Log<OdinData> odinlog("Data","convert_to");
TinyVector<int,N_rank2> newshape; newshape=1;
for(int i=0; i<(N_rank-N_rank2+1); i++) { // collapse extra dims into first dim of new shape, including first dim
int srcindex=i;
if(srcindex>=0 && srcindex<N_rank) newshape(0)*=Array<T,N_rank>::extent(srcindex);
}
for(int i=0; i<(N_rank2-1); i++) { // Fill new shape with extents of original dim, except for the first dim
int srcindex=N_rank-N_rank2+1+i;
if(srcindex>=0 && srcindex<N_rank) newshape(1+i)=Array<T,N_rank>::extent(srcindex);
}
// modify last dimension to account for different element sizes
newshape(N_rank2-1)=newshape(N_rank2-1)*Converter::get_elements((T)0)/Converter::get_elements((T2)0);
dst.resize(newshape); // dst will be unique now
Data<T,N_rank> src_copy(*this); // make read/write copy of this
Converter::convert_array(src_copy.c_array(), dst.c_array(), src_copy.numElements(), dst.numElements(), scaleopt);
return dst;
}
// specialization which uses reference if type/rank are same and no scaling is necessary to reduce memory usage
template<typename T,int N_rank>
Data<T,N_rank>& Data<T,N_rank>::convert_to(Data<T,N_rank>& dst, autoscaleOption scaleopt) const {
Log<OdinData> odinlog("Data","convert_to");
if(scaleopt==noscale || !std::numeric_limits<T>::is_integer) {
ODINLOG(odinlog,normalDebug) << "Using reference" << STD_endl;
dst.reference(*this);
} else {
Data<T,N_rank> src_copy(*this); // make read/write copy of this
dst.resize(src_copy.shape()); // dst will be unique now
Converter::convert_array(src_copy.c_array(), dst.c_array(), src_copy.numElements(), dst.numElements(), scaleopt);
}
return dst;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
TinyVector<int, N_rank> Data<T,N_rank>::create_index(unsigned long index) const {
return index2extent<N_rank>(Array<T,N_rank>::shape(), index);
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
unsigned long Data<T,N_rank>::create_linear_index(const TinyVector<int, N_rank>& indexvec) const {
unsigned long totalIndex=0,subsize;
TinyVector<int, N_rank> nn(Array<T,N_rank>::extent());
for(unsigned long i=0;i<N_rank;i++) {
nn(i)=1;
subsize=product(nn);
if(!subsize) subsize=1;
totalIndex+=subsize*indexvec(i);
}
return totalIndex;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
void Data<T,N_rank>::shift(unsigned int shift_dim, int shift) {
Log<OdinData> odinlog("Data","shift");
if(!shift) return;
if( shift_dim >= N_rank ){
ODINLOG(odinlog,errorLog) << "shift dimension(" << shift_dim << ") >= rank of data (" << N_rank << ") !\n";
return;
}
int shift_extent=Array<T,N_rank>::extent(shift_dim);
int abs_shift=abs(shift);
if(shift_extent < abs_shift){
ODINLOG(odinlog,errorLog) << "extent(" << shift_extent << ") less than shift(" << abs_shift << ") !\n";
return;
}
Data<T,N_rank> data_copy(Array<T,N_rank>::copy());
TinyVector<int,N_rank> index;
for(int i=0; i<Array<T,N_rank>::numElements(); i++) {
index=create_index(i);
T val=data_copy(index);
int shiftindex=index(shift_dim)+shift;
if(shiftindex>=shift_extent) shiftindex-=shift_extent;
if(shiftindex<0) shiftindex+=shift_extent;
index(shift_dim)=shiftindex;
(*this)(index)=val;
}
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
void Data<T,N_rank>::congrid(const TinyVector<int,N_rank>& newshape, const TinyVector<float,N_rank>* subpixel_shift, bool left_to_right) {
Log<OdinData> odinlog("Data","congrid");
for(int i=0;i<N_rank;i++) {
ODINLOG(odinlog,normalDebug) << "oldshape/newshape(" << i << ")=" << Array<T,N_rank>::shape()(i) << "/" << newshape(i) << STD_endl;
if(subpixel_shift) {
ODINLOG(odinlog,normalDebug) << "subpixel_shift(" << i << ")=" << (*subpixel_shift)(i) << STD_endl;
}
}
for(int irank=0; irank<N_rank; irank++) {
int dim=irank;
if(!left_to_right) dim=N_rank-1-irank;
float shift=0.0;
if(subpixel_shift) shift=(*subpixel_shift)(dim);
interpolate1dim(dim,newshape(dim),shift);
}
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
void Data<T,N_rank>::interpolate1dim(unsigned int dim, int newsize, float subpixel_shift) {
Log<OdinData> odinlog("Data","interpolate1dim");
ODINLOG(odinlog,normalDebug) << "dim/newsize=" << dim << "/" << newsize << STD_endl;
if(newsize==Array<T,N_rank>::shape()(dim) && subpixel_shift==0.0) {
ODINLOG(odinlog,normalDebug) << "interpolation not required" << STD_endl;
return;
}
if(dim>=N_rank) {
ODINLOG(odinlog,errorLog) << "dim is larger than N_rank" << STD_endl;
return;
}
if(newsize<0) {
ODINLOG(odinlog,errorLog) << "newsize is negative" << STD_endl;
return;
}
Array<T,N_rank> olddata(*this);
olddata.makeUnique();
TinyVector<int,N_rank> oldshape(olddata.shape());
int oldsize=oldshape(dim);
TinyVector<int,N_rank> newshape(oldshape);
newshape(dim)=newsize;
this->resize(newshape);
// This holds the the shape of the subspace which is orthogonal to direction 'dim'
TinyVector<int,N_rank> ortho_shape(oldshape);
ortho_shape(dim)=1;
// The total number of elements in the orthogonal subspace
unsigned long n_ortho=product(ortho_shape);
ODINLOG(odinlog,normalDebug) << "n_ortho=" << n_ortho << STD_endl;
TinyVector<int,N_rank> indexvec;
T* oldoneline=new T[oldsize];
for(unsigned long iortho=0; iortho<n_ortho; iortho++) {
indexvec=index2extent<N_rank>(ortho_shape,iortho);
for(int j=0; j<oldsize; j++) {
indexvec(dim)=j;
oldoneline[j]=olddata(indexvec);
}
T* newoneline=interpolate1D(oldoneline,oldsize,newsize,subpixel_shift);
for(int j=0; j<newsize; j++) {
indexvec(dim)=j;
(*this)(indexvec)=newoneline[j];
}
delete[] newoneline;
}
delete[] oldoneline;
}
////////////////////////////////////////////////////////////////////////////
template<typename T,int N_rank>
T* Data<T,N_rank>::c_array() {
Log<OdinData> odinlog("Data","c_array");
bool need_copying=false;
// check storage order
TinyVector<int,N_rank>ord=Array<T,N_rank>::ordering();
for(int i=0; i<N_rank-1; i++) {
if(ord(i)<ord(i+1)) need_copying=true;
}
// check storage direction
for(int i=0; i<N_rank; i++) {
if(!Array<T,N_rank>::isRankStoredAscending(i)) need_copying=true;
}
// check for slicing
if(!Array<T,N_rank>::isStorageContiguous()) need_copying=true;
if(need_copying) {
ODINLOG(odinlog,normalDebug) << "need_copying" << STD_endl;
Data<T,N_rank> tmp(Array<T,N_rank>::shape());
tmp=(*this); // reference(copy()) would not be enough since it would preserve ordering
reference(tmp);
}
return Array<T,N_rank>::data();
}
#endif
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