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633 lines
23 KiB
C
633 lines
23 KiB
C
/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
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*
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* $Id$
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*
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* Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice, this
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* list of conditions and the following disclaimer.
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*
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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/*! \file xdrfile.h
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* \brief Interface to read/write portabile binary files using XDR.
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*
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* This file provides an interface to read & write portably binary files,
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* using XDR - the external data representation standard defined in RFC 1014.
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*
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* There are several advantages to the XDR approach:
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*
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* -# It is portable. And not just portable between big/small integer endian,
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* but truly portable if you have system XDR routines. For example:
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* - It doesn't matter if the character representation is ASCII or EBCDIC.
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* - Some systems are small endian but use big endian order of the two
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* dword in a double precision floating-point variable. The system XDR
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* libraries will read/write this correctly.
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* - Some systems (VAX...) don't use IEEE floating point. Their system
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* XDR libraries will convert to/from this automatically.
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* -# XDR libraries are required for NFS and lots of other network functions.
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* This means there isn't a single Unix-like system that doesn't have them.
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* -# There is NO extra metadata whatsoever, and we write plain XDR files.
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* If you write a float, it will take exactly 4 bytes in the file.
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* (All basic datatypes are 4 bytes, double fp 8 bytes).
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* -# You can read/write the files by calling the system XDR routines directly
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* too - you don't have to use the routines defined in this file.
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* -# It is no problem if your system doesn't have XDR libraries (MS Windows).
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* We have written our own versions of the necessary routines that work if
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* your system uses ASCII for strings and IEEE floating-point. All types
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* of byte and dword endian for integer and floating-point are supported.
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* -# You can use these routines for any type of data, but since we designed
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* them for Gromacs we also provide a special routine to write coordinates
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* with (adjustable) lossy compression. The default precision will give you
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* three decimals guaranteed accuracy, and reduces the filesize to 1/10th
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* of normal binary data.
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*
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* We do not support getting or setting positions in XDR files, since it can
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* break in horrible ways for large (64-bit) files, resulting in silent data
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* corruption. Note that it works great to open/read/write 64-bit files if
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* your system supports it; it is just the random access we cannot trust!
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*
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* We also provide wrapper routines so this module can be used from FORTRAN -
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* see the file xdrfile_fortran.txt in the Gromacs distribution for
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* documentation on the FORTRAN interface!
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*/
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#ifndef _XDRFILE_H_
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#define _XDRFILE_H_
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#ifdef __cplusplus
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extern "C"
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{
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#endif
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/*! \brief Abstract datatype for an portable binary file handle
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*
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* This datatype essentially works just like the standard FILE type in C.
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* The actual contents is hidden in the implementation, so you can only
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* define pointers to it, for use with the xdrfile routines.
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*
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* If you \a really need to see the definition it is in xdrfile.c, but you
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* cannot access elements of the structure outside that file.
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*
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* \warning The implementation is completely different from the C standard
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* library FILE, so don't even think about using an XDRFILE pointer as an
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* argument to a routine that needs a standard FILE pointer.
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*/
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typedef struct XDRFILE XDRFILE;
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enum { exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE,
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exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC,
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exdrNOMEM, exdrENDOFFILE, exdrFILENOTFOUND, exdrNR };
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extern char *exdr_message[exdrNR];
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#define DIM 3
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typedef float matrix[DIM][DIM];
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typedef float rvec[DIM];
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typedef int mybool;
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/*! \brief Open a portable binary file, just like fopen()
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*
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* Use this routine much like calls to the standard library function
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* fopen(). The only difference is that the returned pointer should only
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* be used with routines defined in this header.
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*
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* \param path Full or relative path (including name) of the file
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* \param mode "r" for reading, "w" for writing, "a" for append.
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*
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* \return Pointer to abstract xdr file datatype, or NULL if an error occurs.
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*
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*/
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XDRFILE *
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xdrfile_open (const char * path,
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const char * mode);
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/*! \brief Close a previously opened portable binary file, just like fclose()
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*
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* Use this routine much like calls to the standard library function
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* fopen(). The only difference is that it is used for an XDRFILE handle
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* instead of a FILE handle.
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*
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* \param xfp Pointer to an abstract XDRFILE datatype
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*
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* \return 0 on success, non-zero on error.
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*/
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int
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xdrfile_close (XDRFILE * xfp);
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/*! \brief Read one or more \a char type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of characters to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of characters read
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*/
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int
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xdrfile_read_char(char * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a characters type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of characters to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of characters written
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*/
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int
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xdrfile_write_char(char * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read one or more \a unsigned \a char type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of unsigned characters to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of unsigned characters read
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*/
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int
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xdrfile_read_uchar(unsigned char * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a unsigned \a characters type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of unsigned characters to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of unsigned characters written
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*/
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int
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xdrfile_write_uchar(unsigned char * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read one or more \a short type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of shorts to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of shorts read
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*/
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int
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xdrfile_read_short(short * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a short type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of shorts to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of shorts written
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*/
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int
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xdrfile_write_short(short * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read one or more \a unsigned \a short type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of unsigned shorts to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of unsigned shorts read
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*/
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int
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xdrfile_read_ushort(unsigned short * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a unsigned \a short type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of unsigned shorts to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of unsigned shorts written
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*/
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int
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xdrfile_write_ushort(unsigned short * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read one or more \a integer type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of integers to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of integers read
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*
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* The integer data type is assumed to be less than or equal to 32 bits.
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*
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* We do not provide any routines for reading/writing 64-bit integers, since
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* - Not all XDR implementations support it
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* - Not all machines have 64-bit integers
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*
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* Split your 64-bit data into two 32-bit integers for portability!
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*/
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int
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xdrfile_read_int(int * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a integer type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of integers to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of integers written
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*
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* The integer data type is assumed to be less than or equal to 32 bits.
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*
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* We do not provide any routines for reading/writing 64-bit integers, since
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* - Not all XDR implementations support it
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* - Not all machines have 64-bit integers
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*
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* Split your 64-bit data into two 32-bit integers for portability!
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*/
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int
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xdrfile_write_int(int * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read one or more \a unsigned \a integers type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of unsigned integers to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of unsigned integers read
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*
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* The integer data type is assumed to be less than or equal to 32 bits.
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*
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* We do not provide any routines for reading/writing 64-bit integers, since
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* - Not all XDR implementations support it
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* - Not all machines have 64-bit integers
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*
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* Split your 64-bit data into two 32-bit integers for portability!
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*/
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int
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xdrfile_read_uint(unsigned int * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a unsigned \a integer type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of unsigned integers to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of unsigned integers written
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*
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* The integer data type is assumed to be less than or equal to 32 bits.
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*
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* We do not provide any routines for reading/writing 64-bit integers, since
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* - Not all XDR implementations support it
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* - Not all machines have 64-bit integers
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*
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* Split your 64-bit data into two 32-bit integers for portability!
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*/
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int
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xdrfile_write_uint(unsigned int * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read one or more \a float type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of floats to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of floats read
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*/
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int
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xdrfile_read_float(float * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a float type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of floats to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of floats written
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*/
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int
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xdrfile_write_float(float * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read one or more \a double type variable(s)
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*
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* \param ptr Pointer to memory where data should be written
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* \param ndata Number of doubles to read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of doubles read
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*/
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int
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xdrfile_read_double(double * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Write one or more \a double type variable(s)
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*
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* \param ptr Pointer to memory where data should be read
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* \param ndata Number of double to write.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of doubles written
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*/
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int
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xdrfile_write_double(double * ptr,
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int ndata,
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XDRFILE * xfp);
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/*! \brief Read a string (array of characters)
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*
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* \param ptr Pointer to memory where data should be written
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* \param maxlen Maximum length of string. If no end-of-string is encountered,
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* one byte less than this is read and end-of-string appended.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of characters read, including end-of-string
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*/
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int
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xdrfile_read_string(char * ptr,
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int maxlen,
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XDRFILE * xfp);
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/*! \brief Write a string (array of characters)
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*
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* \param ptr Pointer to memory where data should be read
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of characters written, including end-of-string
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*/
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int
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xdrfile_write_string(char * ptr,
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XDRFILE * xfp);
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/*! \brief Read raw bytes from file (unknown datatype)
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*
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* \param ptr Pointer to memory where data should be written
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* \param nbytes Number of bytes to read. No conversion whatsoever is done.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of bytes read from file
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*/
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int
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xdrfile_read_opaque(char * ptr,
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int nbytes,
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XDRFILE * xfp);
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/*! \brief Write raw bytes to file (unknown datatype)
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*
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* \param ptr Pointer to memory where data should be read
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* \param nbytes Number of bytes to write. No conversion whatsoever is done.
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* \param xfp Handle to portable binary file, created with xdrfile_open()
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*
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* \return Number of bytes written to file
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*/
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int
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xdrfile_write_opaque(char * ptr,
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int nbytes,
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XDRFILE * xfp);
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/*! \brief Compress coordiates in a float array to XDR file
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*
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* This routine will perform \a lossy compression on the three-dimensional
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* coordinate data data specified and store it in the XDR file.
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*
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* The lossy part of the compression consists of multiplying each
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* coordinate with the precision argument and then rounding to integers.
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* We suggest a default value of 1000.0, which means you are guaranteed
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* three decimals of accuracy. The only limitation is that scaled coordinates
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* must still fit in an integer variable, so if the precision is 1000.0 the
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* coordinate magnitudes must be less than +-2e6.
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*
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* \param ptr Pointer to coordinates to compress (length 3*ncoord)
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* \param ncoord Number of coordinate triplets in data
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* \param precision Scaling factor for lossy compression. If it is <=0,
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* the default value of 1000.0 is used.
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* \param xfp Handle to portably binary file
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*
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* \return Number of coordinate triplets written.
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* IMPORTANT: Check that this is equal to ncoord - if it is
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* negative, an error occured. This should not happen with
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* normal data, but if your coordinates are NaN or very
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* large (>1e6) it is not possible to use the compression.
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*
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* \warning The compression algorithm is not part of the XDR standard,
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* and very complicated, so you will need this xdrfile module
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* to read it later.
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*/
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int
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xdrfile_compress_coord_float(float * ptr,
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int ncoord,
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float precision,
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XDRFILE * xfp);
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/*! \brief Decompress coordiates from XDR file to array of floats
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*
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* This routine will decompress three-dimensional coordinate data previously
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* stored in an XDR file and store it in the specified array of floats.
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*
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* The precision used during the earlier compression is read from the file
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* and returned - you cannot adjust the accuracy at this stage.
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*
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* \param ptr Pointer to coordinates to compress (length>= 3*ncoord)
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* \param ncoord Max number of coordinate triplets to read on input, actual
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* number of coordinate triplets read on return. If this
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* is smaller than the number of coordinates in the frame an
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* error will occur.
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* \param precision The precision used in the previous compression will be
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* written to this variable on return.
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* \param xfp Handle to portably binary file
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*
|
|
* \return Number of coordinate triplets read. If this is negative,
|
|
* an error occured.
|
|
*
|
|
* \warning Since we cannot count on being able to set/get the
|
|
* position of large files (>2Gb), it is not possible to
|
|
* recover from errors by re-reading the frame if the
|
|
* storage area you provided was too small. To avoid this
|
|
* from happening, we recommend that you store the number of
|
|
* coordinates triplet as an integer either in a header or
|
|
* just before the compressed coordinate data, so you can
|
|
* read it first and allocated enough memory.
|
|
*/
|
|
int
|
|
xdrfile_decompress_coord_float(float * ptr,
|
|
int * ncoord,
|
|
float * precision,
|
|
XDRFILE * xfp);
|
|
|
|
|
|
|
|
|
|
/*! \brief Compress coordiates in a double array to XDR file
|
|
*
|
|
* This routine will perform \a lossy compression on the three-dimensional
|
|
* coordinate data data specified and store it in the XDR file. Double will
|
|
* NOT give you any extra precision since the coordinates are compressed. This
|
|
* routine just avoids allocating a temporary array of floats.
|
|
*
|
|
* The lossy part of the compression consists of multiplying each
|
|
* coordinate with the precision argument and then rounding to integers.
|
|
* We suggest a default value of 1000.0, which means you are guaranteed
|
|
* three decimals of accuracy. The only limitation is that scaled coordinates
|
|
* must still fit in an integer variable, so if the precision is 1000.0 the
|
|
* coordinate magnitudes must be less than +-2e6.
|
|
*
|
|
* \param ptr Pointer to coordinates to compress (length 3*ncoord)
|
|
* \param ncoord Number of coordinate triplets in data
|
|
* \param precision Scaling factor for lossy compression. If it is <=0, the
|
|
* default value of 1000.0 is used.
|
|
* \param xfp Handle to portably binary file
|
|
*
|
|
* \return Number of coordinate triplets written.
|
|
* IMPORTANT: Check that this is equal to ncoord - if it is
|
|
* negative, an error occured. This should not happen with
|
|
* normal data, but if your coordinates are NaN or very
|
|
* large (>1e6) it is not possible to use the compression.
|
|
*
|
|
* \warning The compression algorithm is not part of the XDR standard,
|
|
* and very complicated, so you will need this xdrfile module
|
|
* to read it later.
|
|
*/
|
|
int
|
|
xdrfile_compress_coord_double(double * ptr,
|
|
int ncoord,
|
|
double precision,
|
|
XDRFILE * xfp);
|
|
|
|
|
|
|
|
|
|
/*! \brief Decompress coordiates from XDR file to array of doubles
|
|
*
|
|
* This routine will decompress three-dimensional coordinate data previously
|
|
* stored in an XDR file and store it in the specified array of doubles.
|
|
* Double will NOT give you any extra precision since the coordinates are
|
|
* compressed. This routine just avoids allocating a temporary array of floats.
|
|
*
|
|
* The precision used during the earlier compression is read from the file
|
|
* and returned - you cannot adjust the accuracy at this stage.
|
|
*
|
|
* \param ptr Pointer to coordinates to compress (length>= 3*ncoord)
|
|
* \param ncoord Max number of coordinate triplets to read on input, actual
|
|
* number of coordinate triplets read on return. If this
|
|
* is smaller than the number of coordinates in the frame an
|
|
* error will occur.
|
|
* \param precision The precision used in the previous compression will be
|
|
* written to this variable on return.
|
|
* \param xfp Handle to portably binary file
|
|
*
|
|
* \return Number of coordinate triplets read. If this is negative,
|
|
* an error occured.
|
|
*
|
|
* \warning Since we cannot count on being able to set/get the
|
|
* position of large files (>2Gb), it is not possible to
|
|
* recover from errors by re-reading the frame if the
|
|
* storage area you provided was too small. To avoid this
|
|
* from happening, we recommend that you store the number of
|
|
* coordinates triplet as an integer either in a header or
|
|
* just before the compressed coordinate data, so you can
|
|
* read it first and allocated enough memory.
|
|
*/
|
|
int
|
|
xdrfile_decompress_coord_double(double * ptr,
|
|
int * ncoord,
|
|
double * precision,
|
|
XDRFILE * xfp);
|
|
|
|
|
|
|
|
#ifdef __cplusplus
|
|
}
|
|
#endif
|
|
|
|
#endif /* _XDRFILE_H_ */
|
|
|