diff options
| -rw-r--r-- | CMakeLists.txt | 6 | ||||
| -rw-r--r-- | include/CMakeLists.txt | 1 | ||||
| -rw-r--r-- | include/tng_io.h | 70 | ||||
| -rw-r--r-- | src/compression/CMakeLists.txt | 8 | ||||
| -rw-r--r-- | src/compression/bwlzh.c | 8 | ||||
| -rw-r--r-- | src/compression/coder.c | 138 | ||||
| -rw-r--r-- | src/lib/CMakeLists.txt | 2 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 2 |
8 files changed, 118 insertions, 117 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt index 496a830..f91d747 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,10 +2,10 @@ cmake_minimum_required(VERSION 2.8) set(CMAKE_C_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall") -project(TRAJECTORY) +project(TNG_IO) set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin) set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib) -include_directories(${CMAKE_SOURCE_DIR}/include) +include_directories(${CMAKE_SOURCE_DIR}/include ${CMAKE_SOURCE_DIR}/include/compression) option(BUILD_FORTRAN "Build Fortran compatible library and examples for testing" OFF) @@ -47,4 +47,4 @@ if(BUILD_DOCUMENTATION) SOURCES ${PROJECT_BINARY_DIR}/Doxyfile) # IF you do NOT want the documentation to be generated EVERY time you build the project # then leave out the 'ALL' keyword from the above command. -endif()
\ No newline at end of file +endif() diff --git a/include/CMakeLists.txt b/include/CMakeLists.txt deleted file mode 100644 index 74d02ac..0000000 --- a/include/CMakeLists.txt +++ /dev/null @@ -1 +0,0 @@ -add_subdirectory(compression) diff --git a/include/tng_io.h b/include/tng_io.h index 30aa4fa..9443dd3 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -275,42 +275,52 @@ #ifdef USE_STD_INTTYPES_H #include <inttypes.h> #else -// /* Visual Studio does not contain inttypes.h and stdint.h. Some defines and * typedefs are used from the GNU C Library */ +#ifdef _MSC_VER -#ifndef _STDINT_H -/* This first part is from stdint.h (GNU C Library) */ -#ifndef __int8_t_defined -# define __int8_t_defined -typedef signed char int8_t; -typedef short int int16_t; -typedef int int32_t; -# if __WORDSIZE == 64 -typedef long int int64_t; -# else -#ifdef __GNUC__ -__extension__ -#endif -typedef long long int int64_t; -# endif -#endif +typedef __int32 int32_t; +typedef unsigned __int32 uint32_t; +typedef __int64 int64_t; +typedef unsigned __int64 uint64_t; -typedef unsigned char uint8_t; -typedef unsigned short int uint16_t; -#ifndef __uint32_t_defined -typedef unsigned int uint32_t; -# define __uint32_t_defined -#endif -#if __WORDSIZE == 64 -typedef unsigned long int uint64_t; #else -#ifdef __GNUC__ -__extension__ -#endif -typedef unsigned long long int uint64_t; -#endif +#include <stdint.h> #endif +// + +// #ifndef _STDINT_H +// /* This first part is from stdint.h (GNU C Library) */ +// #ifndef __int8_t_defined +// # define __int8_t_defined +// typedef signed char int8_t; +// typedef short int int16_t; +// typedef int int32_t; +// # if __WORDSIZE == 64 +// typedef long int int64_t; +// # else +// #ifdef __GNUC__ +// __extension__ +// #endif +// typedef long long int int64_t; +// # endif +// #endif +// +// typedef unsigned char uint8_t; +// typedef unsigned short int uint16_t; +// #ifndef __uint32_t_defined +// typedef unsigned int uint32_t; +// # define __uint32_t_defined +// #endif +// #if __WORDSIZE == 64 +// typedef unsigned long int uint64_t; +// #else +// #ifdef __GNUC__ +// __extension__ +// #endif +// typedef unsigned long long int uint64_t; +// #endif +// #endif /* This is from inttypes.h (GNU C Library) */ /* The ISO C99 standard specifies that these macros must only be diff --git a/src/compression/CMakeLists.txt b/src/compression/CMakeLists.txt index 605dac7..91155e0 100644 --- a/src/compression/CMakeLists.txt +++ b/src/compression/CMakeLists.txt @@ -1,10 +1,4 @@ -set(COMP_INC_DIR ${CMAKE_SOURCE_DIR}/include/compression) - -include_directories(${COMP_INC_DIR}) - -set(HEADER_FILES ${COMP_INC_DIR}/bwlzh.h ${COMP_INC_DIR}/bwt.h ${COMP_INC_DIR}/coder.h ${COMP_INC_DIR}/dict.h ${COMP_INC_DIR}/fixpoint.h ${COMP_INC_DIR}/huffman.h ${COMP_INC_DIR}/lz77.h ${COMP_INC_DIR}/merge_sort.h ${COMP_INC_DIR}/mtf.h ${COMP_INC_DIR}/my64bit.h ${COMP_INC_DIR}/rle.h ${COMP_INC_DIR}/tng_compress.h ${COMP_INC_DIR}/vals16.h ${COMP_INC_DIR}/warnmalloc.h ${COMP_INC_DIR}/widemuldiv.h) - -add_library(tng_compress SHARED bwlzh.c bwt.c coder.c dict.c fixpoint.c huffman.c huffmem.c lz77.c merge_sort.c mtf.c rle.c tng_compress.c vals16.c warnmalloc.c widemuldiv.c xtc2.c xtc3.c) +add_library(tng_compress bwlzh.c bwt.c coder.c dict.c fixpoint.c huffman.c huffmem.c lz77.c merge_sort.c mtf.c rle.c tng_compress.c vals16.c warnmalloc.c widemuldiv.c xtc2.c xtc3.c) if(UNIX) target_link_libraries(tng_compress m) endif() diff --git a/src/compression/bwlzh.c b/src/compression/bwlzh.c index e5eb499..88bee37 100644 --- a/src/compression/bwlzh.c +++ b/src/compression/bwlzh.c @@ -81,9 +81,6 @@ static void bwlzh_compress_gen(unsigned int *vals, int nvals, int huffdatalen; int nhufflen[N_HUFFMAN_ALGO]; int huffalgo; -#ifndef PARTIAL_MTF - int ndict; -#endif int bwt_index; unsigned int *bwt=NULL; #ifdef PARTIAL_MTF3 @@ -213,6 +210,7 @@ static void bwlzh_compress_gen(unsigned int *vals, int nvals, #ifdef PARTIAL_MTF Ptngc_comp_conv_to_mtf_partial(bwt,nvals16,mtf); #else + int ndict; Ptngc_comp_canonical_dict(dict,&ndict); Ptngc_comp_conv_to_mtf(bwt,nvals16, dict,ndict,mtf); @@ -496,9 +494,6 @@ static void bwlzh_decompress_gen(unsigned char *input, int nvals, { unsigned int *vals16; int nvals16; -#ifndef PARTIAL_MTF - int ndict; -#endif int bwt_index; unsigned int *bwt=NULL; unsigned int *mtf=NULL; @@ -748,6 +743,7 @@ static void bwlzh_decompress_gen(unsigned char *input, int nvals, #ifdef PARTIAL_MTF Ptngc_comp_conv_from_mtf_partial(mtf,nvals16,bwt); #else + int ndict; Ptngc_comp_canonical_dict(dict,&ndict); Ptngc_comp_conv_from_mtf(mtf,nvals16,dict,ndict,bwt); #endif diff --git a/src/compression/coder.c b/src/compression/coder.c index be46c17..270e4d3 100644 --- a/src/compression/coder.c +++ b/src/compression/coder.c @@ -34,20 +34,20 @@ struct coder *Ptngc_coder_init(void) { - struct coder *coder=warnmalloc(sizeof *coder); - coder->pack_temporary_bits=0; - return coder; + struct coder *coder_inst=warnmalloc(sizeof *coder_inst); + coder_inst->pack_temporary_bits=0; + return coder_inst; } -void Ptngc_coder_deinit(struct coder *coder) +void Ptngc_coder_deinit(struct coder *coder_inst) { - free(coder); + free(coder_inst); } -TNG_INLINE void Ptngc_out8bits(struct coder *coder, unsigned char **output) +TNG_INLINE void Ptngc_out8bits(struct coder *coder_inst, unsigned char **output) { - int pack_temporary_bits=coder->pack_temporary_bits; - unsigned int pack_temporary=coder->pack_temporary; + int pack_temporary_bits=coder_inst->pack_temporary_bits; + unsigned int pack_temporary=coder_inst->pack_temporary; while (pack_temporary_bits>=8) { unsigned int mask=~(0xFFU<<(pack_temporary_bits-8)); @@ -57,40 +57,40 @@ TNG_INLINE void Ptngc_out8bits(struct coder *coder, unsigned char **output) pack_temporary_bits-=8; pack_temporary&=mask; } - coder->pack_temporary_bits=pack_temporary_bits; - coder->pack_temporary=pack_temporary; + coder_inst->pack_temporary_bits=pack_temporary_bits; + coder_inst->pack_temporary=pack_temporary; } -void Ptngc_write_pattern(struct coder *coder,unsigned int pattern, int nbits, unsigned char **output) +void Ptngc_write_pattern(struct coder *coder_inst,unsigned int pattern, int nbits, unsigned char **output) { unsigned int mask1,mask2; mask1=1; mask2=1<<(nbits-1); - coder->pack_temporary<<=nbits; /* Make room for new data. */ - coder->pack_temporary_bits+=nbits; + coder_inst->pack_temporary<<=nbits; /* Make room for new data. */ + coder_inst->pack_temporary_bits+=nbits; while (nbits) { if (pattern & mask1) - coder->pack_temporary|=mask2; + coder_inst->pack_temporary|=mask2; nbits--; mask1<<=1; mask2>>=1; } - Ptngc_out8bits(coder,output); + Ptngc_out8bits(coder_inst,output); } /* Write up to 24 bits */ -TNG_INLINE void Ptngc_writebits(struct coder *coder,unsigned int value,int nbits, unsigned char **output_ptr) +TNG_INLINE void Ptngc_writebits(struct coder *coder_inst,unsigned int value,int nbits, unsigned char **output_ptr) { /* Make room for the bits. */ - coder->pack_temporary<<=nbits; - coder->pack_temporary_bits+=nbits; - coder->pack_temporary|=value; - Ptngc_out8bits(coder,output_ptr); + coder_inst->pack_temporary<<=nbits; + coder_inst->pack_temporary_bits+=nbits; + coder_inst->pack_temporary|=value; + Ptngc_out8bits(coder_inst,output_ptr); } /* Write up to 32 bits */ -void Ptngc_write32bits(struct coder *coder,unsigned int value,int nbits, unsigned char **output_ptr) +void Ptngc_write32bits(struct coder *coder_inst,unsigned int value,int nbits, unsigned char **output_ptr) { unsigned int mask; if (nbits>=8) @@ -100,19 +100,19 @@ void Ptngc_write32bits(struct coder *coder,unsigned int value,int nbits, unsigne while (nbits>8) { /* Make room for the bits. */ - coder->pack_temporary<<=8; - coder->pack_temporary_bits+=8; - coder->pack_temporary|=(value&mask)>>(nbits-8); - Ptngc_out8bits(coder,output_ptr); + coder_inst->pack_temporary<<=8; + coder_inst->pack_temporary_bits+=8; + coder_inst->pack_temporary|=(value&mask)>>(nbits-8); + Ptngc_out8bits(coder_inst,output_ptr); nbits-=8; mask>>=8; } if (nbits) - Ptngc_writebits(coder,value&mask,nbits,output_ptr); + Ptngc_writebits(coder_inst,value&mask,nbits,output_ptr); } /* Write "arbitrary" number of bits */ -void Ptngc_writemanybits(struct coder *coder,unsigned char *value,int nbits, unsigned char **output_ptr) +void Ptngc_writemanybits(struct coder *coder_inst,unsigned char *value,int nbits, unsigned char **output_ptr) { int vptr=0; while (nbits>=24) @@ -120,23 +120,23 @@ void Ptngc_writemanybits(struct coder *coder,unsigned char *value,int nbits, uns unsigned int v=((((unsigned int)value[vptr])<<16)| (((unsigned int)value[vptr+1])<<8)| (((unsigned int)value[vptr+2]))); - Ptngc_writebits(coder,v,24,output_ptr); + Ptngc_writebits(coder_inst,v,24,output_ptr); vptr+=3; nbits-=24; } while (nbits>=8) { - Ptngc_writebits(coder,(unsigned int)value[vptr],8,output_ptr); + Ptngc_writebits(coder_inst,(unsigned int)value[vptr],8,output_ptr); vptr++; nbits-=8; } if (nbits) { - Ptngc_writebits(coder,(unsigned int)value[vptr],nbits,output_ptr); + Ptngc_writebits(coder_inst,(unsigned int)value[vptr],nbits,output_ptr); } } -static int write_stop_bit_code(struct coder *coder, unsigned int s,unsigned int coding_parameter, unsigned char **output) +static int write_stop_bit_code(struct coder *coder_inst, unsigned int s,unsigned int coding_parameter, unsigned char **output) { do { unsigned int extract=~(0xffffffffU<<coding_parameter); @@ -145,12 +145,12 @@ static int write_stop_bit_code(struct coder *coder, unsigned int s,unsigned int if (s) { this|=1U; - coder->stat_overflow++; + coder_inst->stat_overflow++; } - coder->pack_temporary<<=(coding_parameter+1); - coder->pack_temporary_bits+=coding_parameter+1; - coder->pack_temporary|=this; - Ptngc_out8bits(coder,output); + coder_inst->pack_temporary<<=(coding_parameter+1); + coder_inst->pack_temporary_bits+=coding_parameter+1; + coder_inst->pack_temporary|=this; + Ptngc_out8bits(coder_inst,output); if (s) { coding_parameter>>=1; @@ -158,11 +158,11 @@ static int write_stop_bit_code(struct coder *coder, unsigned int s,unsigned int coding_parameter=1; } } while (s); - coder->stat_numval++; + coder_inst->stat_numval++; return 0; } -static int pack_stopbits_item(struct coder *coder,int item, unsigned char **output, int coding_parameter) +static int pack_stopbits_item(struct coder *coder_inst,int item, unsigned char **output, int coding_parameter) { /* Find this symbol in table. */ int s=0; @@ -170,11 +170,11 @@ static int pack_stopbits_item(struct coder *coder,int item, unsigned char **outp s=1+(item-1)*2; else if (item<0) s=2+(-item-1)*2; - return write_stop_bit_code(coder,s,coding_parameter,output); + return write_stop_bit_code(coder_inst,s,coding_parameter,output); return 0; } -static int pack_triplet(struct coder *coder,unsigned int *s, unsigned char **output, int coding_parameter, +static int pack_triplet(struct coder *coder_inst,unsigned int *s, unsigned char **output, int coding_parameter, unsigned int max_base, int maxbits) { /* Determine base for this triplet. */ @@ -199,23 +199,23 @@ static int pack_triplet(struct coder *coder,unsigned int *s, unsigned char **out jbase=3; } /* 2 bits selects the base */ - coder->pack_temporary<<=2; - coder->pack_temporary_bits+=2; - coder->pack_temporary|=jbase; - Ptngc_out8bits(coder,output); + coder_inst->pack_temporary<<=2; + coder_inst->pack_temporary_bits+=2; + coder_inst->pack_temporary|=jbase; + Ptngc_out8bits(coder_inst,output); for (i=0; i<3; i++) - Ptngc_write32bits(coder,s[i],bits_per_value,output); + Ptngc_write32bits(coder_inst,s[i],bits_per_value,output); return 0; } -void Ptngc_pack_flush(struct coder *coder,unsigned char **output) +void Ptngc_pack_flush(struct coder *coder_inst,unsigned char **output) { /* Zero-fill just enough. */ - if (coder->pack_temporary_bits>0) - Ptngc_write_pattern(coder,0,8-coder->pack_temporary_bits,output); + if (coder_inst->pack_temporary_bits>0) + Ptngc_write_pattern(coder_inst,0,8-coder_inst->pack_temporary_bits,output); } -unsigned char *Ptngc_pack_array(struct coder *coder,int *input, int *length, int coding, int coding_parameter,int natoms, int speed) +unsigned char *Ptngc_pack_array(struct coder *coder_inst,int *input, int *length, int coding, int coding_parameter,int natoms, int speed) { if ((coding==TNG_COMPRESS_ALGO_BWLZH1) || (coding==TNG_COMPRESS_ALGO_BWLZH2)) { @@ -252,7 +252,7 @@ unsigned char *Ptngc_pack_array(struct coder *coder,int *input, int *length, int else if (coding==TNG_COMPRESS_ALGO_POS_XTC3) return Ptngc_pack_array_xtc3(input,length,natoms,speed); else if (coding==TNG_COMPRESS_ALGO_POS_XTC2) - return Ptngc_pack_array_xtc2(coder,input,length); + return Ptngc_pack_array_xtc2(coder_inst,input,length); else { unsigned char *output=NULL; @@ -260,8 +260,8 @@ unsigned char *Ptngc_pack_array(struct coder *coder,int *input, int *length, int int i; int output_length=0; - coder->stat_numval=0; - coder->stat_overflow=0; + coder_inst->stat_numval=0; + coder_inst->stat_overflow=0; /* Allocate enough memory for output */ output=warnmalloc(8* *length*sizeof *output); output_ptr=output; @@ -287,9 +287,9 @@ unsigned char *Ptngc_pack_array(struct coder *coder,int *input, int *length, int intmax=s; } /* Store intmax */ - coder->pack_temporary_bits=32; - coder->pack_temporary=intmax; - Ptngc_out8bits(coder,&output_ptr); + coder_inst->pack_temporary_bits=32; + coder_inst->pack_temporary=intmax; + Ptngc_out8bits(coder_inst,&output_ptr); while (intmax>=max_base) { max_base*=2; @@ -309,7 +309,7 @@ unsigned char *Ptngc_pack_array(struct coder *coder,int *input, int *length, int else if (item<0) s[j]=2+(-item-1)*2; } - if (pack_triplet(coder,s,&output_ptr,coding_parameter,max_base,maxbits)) + if (pack_triplet(coder_inst,s,&output_ptr,coding_parameter,max_base,maxbits)) { free(output); return NULL; @@ -318,21 +318,21 @@ unsigned char *Ptngc_pack_array(struct coder *coder,int *input, int *length, int } else for (i=0; i<*length; i++) - if (pack_stopbits_item(coder,input[i],&output_ptr,coding_parameter)) + if (pack_stopbits_item(coder_inst,input[i],&output_ptr,coding_parameter)) { free(output); return NULL; } - Ptngc_pack_flush(coder,&output_ptr); + Ptngc_pack_flush(coder_inst,&output_ptr); output_length=(int)(output_ptr-output); *length=output_length; return output; } } -static int unpack_array_stop_bits(struct coder *coder,unsigned char *packed,int *output, int length, int coding_parameter) +static int unpack_array_stop_bits(struct coder *coder_inst,unsigned char *packed,int *output, int length, int coding_parameter) { - (void)coder; + (void)coder_inst; int i,j; unsigned int extract_mask=0x80; unsigned char *ptr=packed; @@ -383,9 +383,9 @@ static int unpack_array_stop_bits(struct coder *coder,unsigned char *packed,int return 0; } -static int unpack_array_triplet(struct coder *coder,unsigned char *packed,int *output, int length, int coding_parameter) +static int unpack_array_triplet(struct coder *coder_inst,unsigned char *packed,int *output, int length, int coding_parameter) { - (void)coder; + (void)coder_inst; int i,j; unsigned int extract_mask=0x80; unsigned char *ptr=packed; @@ -455,9 +455,9 @@ static int unpack_array_triplet(struct coder *coder,unsigned char *packed,int *o return 0; } -static int unpack_array_bwlzh(struct coder *coder,unsigned char *packed,int *output, int length, int natoms) +static int unpack_array_bwlzh(struct coder *coder_inst,unsigned char *packed,int *output, int length, int natoms) { - (void)coder; + (void)coder_inst; int i,j,k,n=length; unsigned int *pval=warnmalloc(n*sizeof *pval); int nframes=n/natoms/3; @@ -478,19 +478,19 @@ static int unpack_array_bwlzh(struct coder *coder,unsigned char *packed,int *out return 0; } -int Ptngc_unpack_array(struct coder *coder,unsigned char *packed,int *output, int length, int coding, int coding_parameter, int natoms) +int Ptngc_unpack_array(struct coder *coder_inst,unsigned char *packed,int *output, int length, int coding, int coding_parameter, int natoms) { if ((coding==TNG_COMPRESS_ALGO_STOPBIT) || (coding==TNG_COMPRESS_ALGO_VEL_STOPBIT_INTER)) - return unpack_array_stop_bits(coder, packed, output, length, coding_parameter); + return unpack_array_stop_bits(coder_inst, packed, output, length, coding_parameter); else if ((coding==TNG_COMPRESS_ALGO_TRIPLET) || (coding==TNG_COMPRESS_ALGO_POS_TRIPLET_INTRA) || (coding==TNG_COMPRESS_ALGO_POS_TRIPLET_ONETOONE)) - return unpack_array_triplet(coder, packed, output, length, coding_parameter); + return unpack_array_triplet(coder_inst, packed, output, length, coding_parameter); else if (coding==TNG_COMPRESS_ALGO_POS_XTC2) - return Ptngc_unpack_array_xtc2(coder, packed, output, length); + return Ptngc_unpack_array_xtc2(coder_inst, packed, output, length); else if ((coding==TNG_COMPRESS_ALGO_BWLZH1) || (coding==TNG_COMPRESS_ALGO_BWLZH2)) - return unpack_array_bwlzh(coder, packed, output, length,natoms); + return unpack_array_bwlzh(coder_inst, packed, output, length,natoms); else if (coding==TNG_COMPRESS_ALGO_POS_XTC3) return Ptngc_unpack_array_xtc3(packed, output, length,natoms); return 1; diff --git a/src/lib/CMakeLists.txt b/src/lib/CMakeLists.txt index ef59ed5..4e46c4e 100644 --- a/src/lib/CMakeLists.txt +++ b/src/lib/CMakeLists.txt @@ -1,4 +1,4 @@ -add_library(tng_io SHARED tng_io.c md5.c) +add_library(tng_io tng_io.c md5.c) if(HAVE_INTTYPES_H) set_property(TARGET tng_io APPEND PROPERTY COMPILE_DEFINITIONS USE_STD_INTTYPES_H) diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index ecfb4c5..a4fe668 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -4100,6 +4100,7 @@ static tng_function_status tng_gzip_uncompress(tng_trajectory_t tng_data, void *start_pos, unsigned long uncompressed_len) { + (void)tng_data; Bytef *dest; char *temp; unsigned long stat; @@ -4174,6 +4175,7 @@ static tng_function_status tng_allocate_particle_data_mem const int64_t n_particles, const int64_t n_values_per_frame) { + (void)tng_data; void ***values; int64_t i, j, k, size, frame_alloc; |