Mercurial > hg > minc-tools
changeset 1972:4cf7ce657102
Port changes from 2.0 branch
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--- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,14 @@ +2005-03-16 Bert Vincent <bert@bic.mni.mcgill.ca> + * Port other changes from 2.0 branch - new mincconcat bimodal + threshold calculations, get rid of minc_def.h for all programs. + * Add -dappend and -sappend operations to minc_modify_header on + the 1.X branch + * Add minctoecat to the 1.X branch + +2005-02-15 Bert Vincent <bert@bic.mni.mcgill.ca> + * Add conversions to the branch + * Add simplified interface to the branch + 2004-08-11 Bert Vincent <bert@bic.mni.mcgill.ca> * Fix MI_MAX_IMGDIMS at 100 to avoid netCDF 3.5.1 problem.
--- a/Makefile.am +++ b/Makefile.am @@ -62,7 +62,15 @@ progs/minccalc/node.h \ progs/minccalc/y.tab.h \ progs/mincresample/mincresample.h \ - progs/mincreshape/mincreshape.h + progs/mincreshape/mincreshape.h \ + conversion/ecattominc/ecat_file.h \ + conversion/ecattominc/machine_indep.h \ + conversion/ecattominc/ecat_header_definition.h \ + conversion/minctoecat/ecat_write.h \ + conversion/minctoecat/machine_indep.h \ + conversion/nifti1/nifti1.h \ + conversion/nifti1/nifti1_io.h \ + conversion/nifti1/nifti1_local.h # Libraries which must be built and installed. # @@ -105,7 +113,12 @@ rawtominc \ transformtags \ xfmconcat \ - xfminvert + xfminvert \ + ecattominc \ + minctoecat \ + mnc2nii \ + nii2mnc \ + upet2mnc noinst_PROGRAMS = \ mincexample1 \ @@ -210,6 +223,28 @@ xfminvert_SOURCES = progs/xfm/xfminvert.c +ecattominc_SOURCES = \ + conversion/ecattominc/ecattominc.c \ + conversion/ecattominc/insertblood.c \ + conversion/ecattominc/ecat_file.c \ + conversion/ecattominc/machine_indep.c + +minctoecat_SOURCES = \ + conversion/minctoecat/minctoecat.c \ + conversion/minctoecat/ecat_write.c \ + conversion/minctoecat/machine_indep.c + +nii2mnc_SOURCES = \ + conversion/nifti1/nii2mnc.c \ + conversion/nifti1/nifti1_io.c + +mnc2nii_SOURCES = \ + conversion/nifti1/mnc2nii.c \ + conversion/nifti1/nifti1_io.c + +upet2mnc_SOURCES = \ + conversion/micropet/upet2mnc.c + libminc_la_LDFLAGS = -version-info 1:0:1 libminc_la_SOURCES = \ libsrc/ParseArgv.c \ @@ -293,6 +328,8 @@ progs/rawtominc/rawtominc.man1 \ progs/xfm/transformtags.man1 \ progs/xfm/xfmconcat.man1 \ - progs/xfm/xfminvert.man1 + progs/xfm/xfminvert.man1 \ + conversion/ecattominc/ecattominc.man1 \ + conversion/minctoecat/minctoecat.man1 dist_man3_MANS = libsrc/ParseArgv.man3
--- a/NEWS +++ b/NEWS @@ -1,7 +1,12 @@ - New in Release 1.4 + New in Release 1.4-test ------------------ * New support for Windows +* Added conversion programs for ecat, NIfTI-1/Analyze, and microPET + formats. + +* Added "simplified" MINC programming interface. + New in Release 1.3 ------------------
--- a/configure.in +++ b/configure.in @@ -1,12 +1,12 @@ dnl Process this file with autoconf to produce a configure script. -AC_INIT +AC_INIT(minc, [1.4-test], [bert@bic.mni.mcgill.ca]) AC_CONFIG_SRCDIR([libsrc/minc.h]) AC_CONFIG_AUX_DIR(ac_config_aux) -AM_INIT_AUTOMAKE(minc, 1.4) +AM_INIT_AUTOMAKE AC_CONFIG_HEADERS([config.h]) -AC_REVISION($Revision: 6.14.2.2 $) +AC_REVISION($Revision: 6.14.2.3 $) AC_PROG_INSTALL AC_PROG_LN_S
--- a/libsrc/ParseArgv.c +++ b/libsrc/ParseArgv.c @@ -16,13 +16,17 @@ * * This file has been modified to not rely on tcl, tk or X11. * Based on tkArgv.c from tk2.3 : -static char rcsid[] = "$Header: /private-cvsroot/minc/libsrc/ParseArgv.c,v 6.4.2.1 2004-09-28 20:23:39 bert Exp $ SPRITE (Berkeley)"; +static char rcsid[] = "$Header: /private-cvsroot/minc/libsrc/ParseArgv.c,v 6.4.2.2 2005-03-16 19:02:49 bert Exp $ SPRITE (Berkeley)"; * * Modifications by Peter Neelin (November 27, 1992) */ +#include "config.h" #include "minc_private.h" +#include <stdio.h> +#include <stdlib.h> +#include <string.h> #include <math.h> -#include "ParseArgv.h" +#include <ParseArgv.h> /* * Default table of argument descriptors. These are normally available
--- a/progs/minc_modify_header/minc_modify_header.c +++ b/progs/minc_modify_header/minc_modify_header.c @@ -10,11 +10,8 @@ @CREATED : March 31, 1995 (Peter Neelin) @MODIFIED : * $Log: minc_modify_header.c,v $ - * Revision 6.9 2004-06-11 15:19:34 bert - * Fix attribute append operation - * - * Revision 6.8 2004/05/25 21:33:51 bert - * Add -dappend and -sappend + * Revision 6.7.2.1 2005-03-16 19:02:49 bert + * Port changes from 2.0 branch * * Revision 6.7 2004/02/02 18:27:06 bert * Include config.h @@ -75,7 +72,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/minc_modify_header/minc_modify_header.c,v 6.9 2004-06-11 15:19:34 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/minc_modify_header/minc_modify_header.c,v 6.7.2.1 2005-03-16 19:02:49 bert Exp $"; #endif #include "config.h" @@ -86,7 +83,6 @@ #include <math.h> #include <minc.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #define MINC_EXTENSION ".mnc" @@ -204,7 +200,7 @@ if (created_tempfile) { if (newfile != NULL) { (void) remove(newfile); - FREE(newfile); + free(newfile); } (void) fprintf(stderr, "Cannot edit file \"%s\" in place.\n", filename); @@ -325,8 +321,8 @@ } else if (!done_redef && attribute_exists && (total_length > 0)) { if (total_length > alloc_length) { - if (zeros != NULL) FREE(zeros); - zeros = MALLOC(total_length); + if (zeros != NULL) free(zeros); + zeros = malloc(total_length); alloc_length = total_length; for (ival=0; ival < alloc_length; ival++) zeros[ival] = '\0'; @@ -378,8 +374,8 @@ (void) miclose(mincid); /* Free stuff */ - FREE(newfile); - if (zeros != NULL) FREE(zeros); + free(newfile); + if (zeros != NULL) free(zeros); exit(EXIT_SUCCESS); } @@ -486,7 +482,7 @@ } /* Allocate a list */ - dvalues = MALLOC(sizeof(*dvalues) * num_doubles); + dvalues = malloc(sizeof(*dvalues) * num_doubles); /* Loop over values */ cur = value; @@ -528,11 +524,11 @@ attribute_list_alloc += 10; if (attribute_list == NULL) { attribute_list = - MALLOC(attribute_list_alloc * sizeof(*attribute_list)); + malloc(attribute_list_alloc * sizeof(*attribute_list)); } else { attribute_list = - REALLOC(attribute_list, + realloc(attribute_list, attribute_list_alloc * sizeof(*attribute_list)); } }
--- a/progs/mincaverage/mincaverage.c +++ b/progs/mincaverage/mincaverage.c @@ -10,7 +10,10 @@ @CREATED : April 28, 1995 (Peter Neelin) @MODIFIED : * $Log: mincaverage.c,v $ - * Revision 6.4.2.1 2004-09-28 20:22:12 bert + * Revision 6.4.2.2 2005-03-16 19:02:49 bert + * Port changes from 2.0 branch + * + * Revision 6.4.2.1 2004/09/28 20:22:12 bert * Minor portability fix for Windows * * Revision 6.4 2001/04/24 13:38:42 neelin @@ -68,7 +71,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4.2.1 2004-09-28 20:22:12 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005-03-16 19:02:49 bert Exp $"; #endif #include "config.h" @@ -82,15 +85,10 @@ #include <minc.h> #include <ParseArgv.h> #include <time_stamp.h> -#include <minc_def.h> #include <voxel_loop.h> /* Constants */ -#ifndef public -# define public -#endif - #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -126,30 +124,29 @@ } Norm_Data; /* Function prototypes */ -public int main(int argc, char *argv[]); -public void do_normalization(void *caller_data, long num_voxels, +static void do_normalization(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void find_mincfile_range(int mincid, double *minimum, double *maximum); -public void do_average(void *caller_data, long num_voxels, +static void find_mincfile_range(int mincid, double *minimum, double *maximum); +static void do_average(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void start_average(void *caller_data, long num_voxels, +static void start_average(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void finish_average(void *caller_data, long num_voxels, +static void finish_average(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public int get_double_list(char *dst, char *key, char *nextarg); -public char **read_file_names(char *filelist, int *num_files); +static int get_double_list(char *dst, char *key, char *nextarg); +static char **read_file_names(char *filelist, int *num_files); /* Argument variables */ int clobber = FALSE; @@ -246,7 +243,7 @@ /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { char **infiles, *outfiles[2]; int nfiles, nout; @@ -361,12 +358,12 @@ /* Save the weights */ average_data.num_weights = weights.numvalues; average_data.weights = - MALLOC(sizeof(*average_data.weights) * average_data.num_weights); + malloc(sizeof(*average_data.weights) * average_data.num_weights); for (iweight=0; iweight < average_data.num_weights; iweight++) { average_data.weights[iweight] = weights.values[iweight]; } - FREE(weights.values); + free(weights.values); } /* Check for width weighting */ @@ -414,7 +411,7 @@ (void) ncdiminq(first_mincid, dim[0], NULL, &count); average_data.num_weights = count; average_data.weights = - MALLOC(sizeof(*average_data.weights) * average_data.num_weights); + malloc(sizeof(*average_data.weights) * average_data.num_weights); /* Read in the widths */ start = 0; @@ -478,9 +475,9 @@ /* Do normalization if needed */ average_data.norm_factor = - MALLOC(sizeof(*average_data.norm_factor) * nfiles); + malloc(sizeof(*average_data.norm_factor) * nfiles); if (normalize) { - vol_mean = MALLOC(sizeof(*vol_mean) * nfiles); + vol_mean = malloc(sizeof(*vol_mean) * nfiles); loop_options = create_loop_options(); set_loop_verbose(loop_options, FALSE); set_loop_accumulate(loop_options, TRUE, 0, NULL, NULL); @@ -538,7 +535,7 @@ ifile, average_data.norm_factor[ifile]); } } - FREE(vol_mean); + free(vol_mean); } else { for (ifile=0; ifile < nfiles; ifile++) { @@ -567,8 +564,8 @@ free_loop_options(loop_options); /* Free stuff */ - FREE(average_data.weights); - FREE(average_data.norm_factor); + free(average_data.weights); + free(average_data.norm_factor); exit(EXIT_SUCCESS); } @@ -586,7 +583,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_normalization(void *caller_data, long num_voxels, +static void do_normalization(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -640,7 +637,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void find_mincfile_range(int mincid, double *minimum, double *maximum) +static void find_mincfile_range(int mincid, double *minimum, double *maximum) { int varid; char *varname; @@ -715,7 +712,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_average(void *caller_data, long num_voxels, +static void do_average(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -799,7 +796,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void start_average(void *caller_data, long num_voxels, +static void start_average(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info) @@ -842,7 +839,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void finish_average(void *caller_data, long num_voxels, +static void finish_average(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info) @@ -909,7 +906,7 @@ @CREATED : March 8, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_double_list(char *dst, char *key, char *nextarg) +static int get_double_list(char *dst, char *key, char *nextarg) { #define VECTOR_SEPARATOR ',' @@ -958,11 +955,11 @@ num_alloc += 20; if (double_list == NULL) { double_list = - MALLOC(num_alloc * sizeof(*double_list)); + malloc(num_alloc * sizeof(*double_list)); } else { double_list = - REALLOC(double_list, num_alloc * sizeof(*double_list)); + realloc(double_list, num_alloc * sizeof(*double_list)); } } double_list[num_elements-1] = dvalue; @@ -978,7 +975,7 @@ /* Update the global variables */ double_array->numvalues = num_elements; if (double_array->values != NULL) { - FREE(double_array->values); + free(double_array->values); } double_array->values = double_list; @@ -1000,7 +997,7 @@ @CREATED : March 8, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public char **read_file_names(char *filelist, int *num_files) +static char **read_file_names(char *filelist, int *num_files) { #define FILE_NAME_ALLOC_SIZE 10 char **files; @@ -1024,7 +1021,7 @@ /* Allocate an initial array and NULL-terminate it */ array_size = FILE_NAME_ALLOC_SIZE; - files = MALLOC(sizeof(*files) * array_size); + files = malloc(sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL; @@ -1046,7 +1043,7 @@ /* Make room for names if needed */ while (nfiles >= array_size-1) { array_size += FILE_NAME_ALLOC_SIZE; - files = REALLOC(files, sizeof(*files) * array_size); + files = realloc(files, sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL;
--- a/progs/minccalc/minccalc.c +++ b/progs/minccalc/minccalc.c @@ -19,7 +19,10 @@ This is predominately a rehash of mincmath by Peter Neelin * $Log: minccalc.c,v $ - * Revision 1.8.2.1 2004-06-11 21:36:53 bert + * Revision 1.8.2.2 2005-03-16 19:02:50 bert + * Port changes from 2.0 branch + * + * Revision 1.8.2.1 2004/06/11 21:36:53 bert * Fix for nasty bug which causes lots of bogus zero values to be inserted when minccalc is used with a file with a vector_dimension * * Revision 1.8 2001/05/24 15:08:40 neelin @@ -66,7 +69,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/minccalc/minccalc.c,v 1.8.2.1 2004-06-11 21:36:53 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/minccalc/minccalc.c,v 1.8.2.2 2005-03-16 19:02:50 bert Exp $"; #endif #include <stdlib.h> @@ -81,13 +84,9 @@ #include <ParseArgv.h> #include <voxel_loop.h> #include <time_stamp.h> -#include <minc_def.h> #include "node.h" /* Constants */ -#ifndef public -# define public -#endif #ifndef TRUE # define TRUE 1 @@ -103,14 +102,14 @@ #define DEFAULT_BOOL -1 /* Function prototypes */ -public void do_math(void *caller_data, long num_voxels, +static void do_math(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public char **read_file_names(char *filelist, int *num_files); -public char *read_expression_file(char *filename); -public int get_list_option(char *dst, char *key, int argc, char **argv); +static char **read_file_names(char *filelist, int *num_files); +static char *read_expression_file(char *filename); +static int get_list_option(char *dst, char *key, int argc, char **argv); /* Argument variables */ int Output_list_size = 0; @@ -219,7 +218,7 @@ scalar_t *Output_values; /* Main program */ -public int main(int argc, char *argv[]){ +int main(int argc, char *argv[]){ char **infiles, **outfiles; int nfiles, nout; char *arg_string; @@ -245,7 +244,7 @@ /* Get output file names */ nout = (Output_list == NULL ? 1 : Output_list_size); - outfiles = MALLOC(nout * sizeof(*outfiles)); + outfiles = malloc(nout * sizeof(*outfiles)); if (Output_list == NULL) { outfiles[0] = argv[argc-1]; } @@ -333,7 +332,7 @@ Output_values = NULL; } else { - Output_values = MALLOC(Output_list_size * sizeof(*Output_values)); + Output_values = malloc(Output_list_size * sizeof(*Output_values)); for (i=0; i < Output_list_size; i++) { ident = ident_lookup(Output_list[i].symbol); scalar = new_scalar(eval_width); @@ -371,10 +370,10 @@ /* Clean up */ vector_free(A); sym_leave_scope(rootsym); - if (expr_file != NULL) FREE(expression); - FREE(outfiles); - if (Output_list != NULL) FREE(Output_list); - if (Output_values != NULL) FREE(Output_values); + if (expr_file != NULL) free(expression); + free(outfiles); + if (Output_list != NULL) free(Output_list); + if (Output_values != NULL) free(Output_values); exit(EXIT_SUCCESS); } @@ -390,7 +389,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : Thu Dec 21 17:08:40 EST 2000 (Andrew Janke - rotor@cmr.uq.edu.au) ---------------------------------------------------------------------------- */ -public void do_math(void *caller_data, long num_voxels, +static void do_math(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -479,7 +478,7 @@ @CREATED : March 8, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public char **read_file_names(char *filelist, int *num_files) +static char **read_file_names(char *filelist, int *num_files) { #define FILE_NAME_ALLOC_SIZE 10 char **files; @@ -503,7 +502,7 @@ /* Allocate an initial array and NULL-terminate it */ array_size = FILE_NAME_ALLOC_SIZE; - files = MALLOC(sizeof(*files) * array_size); + files = malloc(sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL; @@ -525,7 +524,7 @@ /* Make room for names if needed */ while (nfiles >= array_size-1) { array_size += FILE_NAME_ALLOC_SIZE; - files = REALLOC(files, sizeof(*files) * array_size); + files = realloc(files, sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL; @@ -563,7 +562,7 @@ @CREATED : May 3, 2001 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public char *read_expression_file(char *filename) +static char *read_expression_file(char *filename) { struct stat statbuf; size_t size; @@ -604,7 +603,7 @@ if (size == 0) size = ALLOC_SIZE; /* Get space */ - expression = MALLOC(size * sizeof(*expression)); + expression = malloc(size * sizeof(*expression)); /* Read the expression */ ichar = 0; @@ -635,7 +634,7 @@ /* Check whether we need more space */ if (ichar >= size-1) { size += ALLOC_SIZE; - expression = REALLOC(expression, size * sizeof(expression)); + expression = realloc(expression, size * sizeof(expression)); } /* Save the character */ @@ -670,7 +669,7 @@ @CREATED : May 3, 2001 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_list_option(char *dst, char *key, int argc, char **argv) +static int get_list_option(char *dst, char *key, int argc, char **argv) /* ARGSUSED */ { enum {OPT_OUTPUT_SYMBOL} option_type; @@ -708,11 +707,11 @@ *list_alloc += 10; if (*list == NULL) { *list = - MALLOC(*list_alloc * entry_size); + malloc(*list_alloc * entry_size); } else { *list = - REALLOC(*list, + realloc(*list, *list_alloc * entry_size); } }
--- a/progs/mincconcat/mincconcat.c +++ b/progs/mincconcat/mincconcat.c @@ -11,8 +11,8 @@ @CREATED : March 7, 1995 (Peter Neelin) @MODIFIED : * $Log: mincconcat.c,v $ - * Revision 6.9 2004-04-27 15:37:13 bert - * Added -2 flag + * Revision 6.8.2.1 2005-03-16 19:02:50 bert + * Port changes from 2.0 branch * * Revision 6.8 2001/09/18 15:32:39 neelin * Create image variable last to allow big images and to fix compatibility @@ -94,7 +94,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincconcat/mincconcat.c,v 6.9 2004-04-27 15:37:13 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincconcat/mincconcat.c,v 6.8.2.1 2005-03-16 19:02:50 bert Exp $"; #endif #include <stdlib.h> @@ -108,7 +108,6 @@ #include <ParseArgv.h> #include <time_stamp.h> #include <voxel_loop.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE @@ -139,7 +138,7 @@ char *output_file; int num_input_files; char *history; - int cflags; + int clobber; int verbose; nc_type output_datatype; int output_is_signed; @@ -173,27 +172,26 @@ } Sort_Element; /* Function prototypes */ -public int main(int argc, char *argv[]); -public void get_arginfo(int argc, char *argv[], +static void get_arginfo(int argc, char *argv[], int *num_input_files, char ***input_files, Concat_Info *concat_info); -public int get_double_list(char *dst, char *key, char *nextarg); -public void get_concat_dim_name(Concat_Info *concat_info, +static int get_double_list(char *dst, char *key, char *nextarg); +static void get_concat_dim_name(Concat_Info *concat_info, char *first_filename, int *first_mincid); -public void get_input_file_info(void *caller_data, int input_mincid, +static void get_input_file_info(void *caller_data, int input_mincid, int input_curfile, Loop_Info *loop_info); -public int get_image_dimension_id(int input_mincid, char *dimension_name); -public void do_concat(void *caller_data, long num_voxels, +static int get_image_dimension_id(int input_mincid, char *dimension_name); +static void do_concat(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void sort_coords(Concat_Info *concat_info); -public int sort_function(const void *value1, const void *value2); -public void create_concat_file(int inmincid, Concat_Info *concat_info); -private void update_history(int mincid, char *arg_string); -public char **read_file_names(char *filelist, int *num_files); +static void sort_coords(Concat_Info *concat_info); +static int sort_function(const void *value1, const void *value2); +static void create_concat_file(int inmincid, Concat_Info *concat_info); +static void update_history(int mincid, char *arg_string); +static char **read_file_names(char *filelist, int *num_files); /* Globals */ static int Sort_ascending = TRUE; @@ -201,7 +199,7 @@ /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { Concat_Info *concat_info; Loop_Options *loop_options; @@ -211,7 +209,7 @@ double valid_range[2]; /* Allocate the concat_info structure */ - concat_info = MALLOC(sizeof(*concat_info)); + concat_info = malloc(sizeof(*concat_info)); /* Get argument information */ get_arginfo(argc, argv, &num_input_files, &input_files, concat_info); @@ -263,7 +261,7 @@ /* Free stuff */ free_loop_options(loop_options); - FREE(concat_info); + free(concat_info); exit(EXIT_SUCCESS); } @@ -284,16 +282,13 @@ @CREATED : March 11, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_arginfo(int argc, char *argv[], +static void get_arginfo(int argc, char *argv[], int *num_input_files, char ***input_files, Concat_Info *concat_info) { /* Argument variables */ static int clobber = FALSE; -#ifdef MINC2 - static int minc2_format = FALSE; -#endif /* MINC2 defined */ static int verbose = TRUE; static nc_type datatype = MI_ORIGINAL_TYPE; static int is_signed = INT_MIN; @@ -312,11 +307,6 @@ static ArgvInfo argTable[] = { {NULL, ARGV_HELP, (char *) NULL, (char *) NULL, "General options:"}, - -#ifdef MINC2 - {"-2", ARGV_CONSTANT, (char *) TRUE, (char *) &minc2_format, - "Produce a MINC 2.0 format output file"}, -#endif /* MINC2 defined */ {"-clobber", ARGV_CONSTANT, (char *) TRUE, (char *) &clobber, "Overwrite existing file."}, {"-noclobber", ARGV_CONSTANT, (char *) FALSE, (char *) &clobber, @@ -501,17 +491,7 @@ concat_info->output_file = output_file; concat_info->num_input_files = *num_input_files; concat_info->history = history; - if (clobber) { - concat_info->cflags = NC_CLOBBER; - } - else { - concat_info->cflags = NC_NOCLOBBER; - } -#ifdef MINC2 - if (minc2_format) { - concat_info->cflags |= MI2_CREATE_V2; - } -#endif /* MINC2 defined */ + concat_info->clobber = clobber; concat_info->verbose = verbose; concat_info->max_memory_use_in_kb = max_chunk_size_in_kb; concat_info->check_dim_info = check_dim_info; @@ -529,18 +509,18 @@ /* Fill in coordinate info. We allocate space even if coordinates aren't specified just in case we can't get the info from the files. */ - concat_info->num_file_coords = MALLOC(sizeof(int) * (*num_input_files)); - concat_info->file_coords = MALLOC(sizeof(void *) * (*num_input_files)); - concat_info->file_widths = MALLOC(sizeof(void *) * (*num_input_files)); + concat_info->num_file_coords = malloc(sizeof(int) * (*num_input_files)); + concat_info->file_coords = malloc(sizeof(void *) * (*num_input_files)); + concat_info->file_widths = malloc(sizeof(void *) * (*num_input_files)); for (ifile=0; ifile < *num_input_files; ifile++) { concat_info->num_file_coords[ifile] = 1; - concat_info->file_coords[ifile] = MALLOC(sizeof(double)); + concat_info->file_coords[ifile] = malloc(sizeof(double)); concat_info->file_coords[ifile][0] = ((dimension_coords.numvalues > 0) ? dimension_coords.values[ifile] : dimension_start + dimension_step * ifile); if ((dimension_widths.numvalues > 0) || (dimension_width != DBL_MAX)) { - concat_info->file_widths[ifile] = MALLOC(sizeof(double)); + concat_info->file_widths[ifile] = malloc(sizeof(double)); concat_info->file_widths[ifile][0] = ((dimension_widths.numvalues > 0) ? dimension_widths.values[ifile] : dimension_width); @@ -565,7 +545,7 @@ @CREATED : March 8, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_double_list(char *dst, char *key, char *nextarg) +static int get_double_list(char *dst, char *key, char *nextarg) { #define VECTOR_SEPARATOR ',' @@ -614,11 +594,11 @@ num_alloc += 20; if (double_list == NULL) { double_list = - MALLOC(num_alloc * sizeof(*double_list)); + malloc(num_alloc * sizeof(*double_list)); } else { double_list = - REALLOC(double_list, num_alloc * sizeof(*double_list)); + realloc(double_list, num_alloc * sizeof(*double_list)); } } double_list[num_elements-1] = dvalue; @@ -634,7 +614,7 @@ /* Update the global variables */ double_array->numvalues = num_elements; if (double_array->values != NULL) { - FREE(double_array->values); + free(double_array->values); } double_array->values = double_list; @@ -655,7 +635,7 @@ @CREATED : March 16, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_concat_dim_name(Concat_Info *concat_info, +static void get_concat_dim_name(Concat_Info *concat_info, char *first_filename, int *first_mincid) { char *filename; @@ -670,7 +650,7 @@ if (created_tempfile) { (void) remove(filename); } - FREE(filename); + free(filename); *first_mincid = input_mincid; /* Do we have to get the dimension name from the file? */ @@ -725,7 +705,7 @@ @CREATED : March 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_input_file_info(void *caller_data, int input_mincid, +static void get_input_file_info(void *caller_data, int input_mincid, int input_curfile, Loop_Info *loop_info) { Concat_Info *concat_info; @@ -757,9 +737,9 @@ /* Allocate the arrays */ (void) ncdiminq(input_mincid, dimid, dimname, &dimlength); concat_info->num_file_coords[input_curfile] = dimlength; - FREE(concat_info->file_coords[input_curfile]); + free(concat_info->file_coords[input_curfile]); concat_info->file_coords[input_curfile] = - MALLOC(sizeof(double) * dimlength); + malloc(sizeof(double) * dimlength); /* Set defaults */ if (!Sort_sequential || (input_curfile < 1)) { @@ -846,7 +826,7 @@ /* Allocate space for widths */ concat_info->file_widths[input_curfile] = - MALLOC(sizeof(double) * dimlength); + malloc(sizeof(double) * dimlength); /* Loop through indices, getting values */ for (index=0; index < dimlength; index++) { @@ -878,7 +858,7 @@ @CREATED : March 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_image_dimension_id(int input_mincid, char *dimension_name) +static int get_image_dimension_id(int input_mincid, char *dimension_name) { int dimid, ndims, dim[MAX_VAR_DIMS], idim; int found; @@ -923,7 +903,7 @@ @CREATED : March 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_concat(void *caller_data, long num_voxels, +static void do_concat(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -1058,7 +1038,7 @@ @CREATED : March 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void sort_coords(Concat_Info *concat_info) +static void sort_coords(Concat_Info *concat_info) { int ifile; Sort_Element *sort_list; @@ -1069,17 +1049,17 @@ /* Allocate space for the ordering information */ concat_info->file_to_dim_order = - MALLOC(sizeof(void *) * (concat_info->num_input_files)); + malloc(sizeof(void *) * (concat_info->num_input_files)); concat_dimension_length = 0; for (ifile=0; ifile < concat_info->num_input_files; ifile++) { concat_dimension_length += concat_info->num_file_coords[ifile]; concat_info->file_to_dim_order[ifile] = - MALLOC(sizeof(int) * concat_info->num_file_coords[ifile]); + malloc(sizeof(int) * concat_info->num_file_coords[ifile]); } concat_info->concat_dimension_length = concat_dimension_length; /* Set up sorting stuff */ - sort_list = MALLOC(sizeof(Sort_Element) * concat_dimension_length); + sort_list = malloc(sizeof(Sort_Element) * concat_dimension_length); index = 0; for (ifile=0; ifile < concat_info->num_input_files; ifile++) { for (icoord=0; icoord < concat_info->num_file_coords[ifile]; icoord++) { @@ -1154,7 +1134,7 @@ @CREATED : March 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int sort_function(const void *value1, const void *value2) +static int sort_function(const void *value1, const void *value2) { Sort_Element *element1, *element2; int return_value; @@ -1189,7 +1169,7 @@ @CREATED : March 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void create_concat_file(int inmincid, Concat_Info *concat_info) +static void create_concat_file(int inmincid, Concat_Info *concat_info) { int outmincid, outimgid, inimgid, coordid, widthid, invarid; int maxid, minid, icvid; @@ -1202,7 +1182,8 @@ double valid_range[2]; /* Create the file */ - outmincid = micreate(concat_info->output_file, concat_info->cflags); + outmincid = micreate(concat_info->output_file, + (concat_info->clobber ? NC_CLOBBER : NC_NOCLOBBER)); /* Get image variable id for input file */ inimgid = ncvarid(inmincid, MIimage); @@ -1393,7 +1374,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -private void update_history(int mincid, char *arg_string) +static void update_history(int mincid, char *arg_string) { nc_type datatype; int att_length; @@ -1408,7 +1389,7 @@ att_length += strlen(arg_string) + 1; /* Allocate a string and get the old history */ - string = MALLOC(att_length); + string = malloc(att_length); string[0] = '\0'; (void) miattgetstr(mincid, NC_GLOBAL, MIhistory, att_length, string); @@ -1417,7 +1398,7 @@ /* Add the new command and put the new history. */ (void) strcat(string, arg_string); (void) miattputstr(mincid, NC_GLOBAL, MIhistory, string); - FREE(string); + free(string); } @@ -1436,7 +1417,7 @@ @CREATED : March 8, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public char **read_file_names(char *filelist, int *num_files) +static char **read_file_names(char *filelist, int *num_files) { #define FILE_NAME_ALLOC_SIZE 10 char **files; @@ -1460,7 +1441,7 @@ /* Allocate an initial array and NULL-terminate it */ array_size = FILE_NAME_ALLOC_SIZE; - files = MALLOC(sizeof(*files) * array_size); + files = malloc(sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL; @@ -1482,7 +1463,7 @@ /* Make room for names if needed */ while (nfiles >= array_size-1) { array_size += FILE_NAME_ALLOC_SIZE; - files = REALLOC(files, sizeof(*files) * array_size); + files = realloc(files, sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL;
--- a/progs/minccopy/minccopy.c +++ b/progs/minccopy/minccopy.c @@ -11,7 +11,10 @@ @CREATED : May 13, 1993 (Peter Neelin) @MODIFIED : * $Log: minccopy.c,v $ - * Revision 6.1 1999-10-19 14:45:20 neelin + * Revision 6.1.2.1 2005-03-16 19:02:50 bert + * Port changes from 2.0 branch + * + * Revision 6.1 1999/10/19 14:45:20 neelin * Fixed Log subsitutions for CVS * * Revision 6.0 1997/09/12 13:23:34 neelin @@ -51,7 +54,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/minccopy/minccopy.c,v 6.1 1999-10-19 14:45:20 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/minccopy/minccopy.c,v 6.1.2.1 2005-03-16 19:02:50 bert Exp $"; #endif #include <stdlib.h> @@ -59,7 +62,6 @@ #include <string.h> #include <minc.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE @@ -155,7 +157,7 @@ } /* Allocate space */ - data = MALLOC(size); + data = malloc(size); /* Set up image conversion */ if (!copy_pixel_values) { @@ -203,7 +205,7 @@ (void) miicv_free(outicv); (void) miicv_free(inicv); } - FREE(data); + free(data); exit(EXIT_SUCCESS); }
--- a/progs/mincexample/mincexample1.c +++ b/progs/mincexample/mincexample1.c @@ -10,7 +10,10 @@ @CREATED : August 24, 1993 (Peter Neelin) @MODIFIED : * $Log: mincexample1.c,v $ - * Revision 6.4 2001-09-18 15:32:46 neelin + * Revision 6.4.2.1 2005-03-16 19:02:50 bert + * Port changes from 2.0 branch + * + * Revision 6.4 2001/09/18 15:32:46 neelin * Create image variable last to allow big images and to fix compatibility * problems with 2.3 and 3.x. * @@ -72,7 +75,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincexample/mincexample1.c,v 6.4 2001-09-18 15:32:46 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincexample/mincexample1.c,v 6.4.2.1 2005-03-16 19:02:50 bert Exp $"; #endif #include <stdlib.h> @@ -81,22 +84,7 @@ #include <minc.h> #include <time_stamp.h> -/* Include the standard minc definitions for cross-platform compilation - if we are compiling the package, otherwise, just define MALLOC, - FREE, EXIT_SUCCESS and EXIT_FAILURE */ -#ifdef COMPILING_MINC_PACKAGE -# include <minc_def.h> -#else -# define MALLOC(size) ((void *) malloc(size)) -# define FREE(ptr) free(ptr) -# ifndef EXIT_SUCCESS -# define EXIT_SUCCESS 0 -# define EXIT_FAILURE 1 -# endif -#endif - /* Constants */ -#define public #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -126,22 +114,22 @@ } Volume; /* Function prototypes */ -public void load_volume(char *infile, Volume *volume); -public void get_dimension_info(char *infile, int icvid, Volume *volume); -public void setup_icv(int icvid); -public void read_volume_data(int icvid, Volume *volume); -public void save_volume(char *infile, char *outfile, char *arg_string, +static void load_volume(char *infile, Volume *volume); +static void get_dimension_info(char *infile, int icvid, Volume *volume); +static void setup_icv(int icvid); +static void read_volume_data(int icvid, Volume *volume); +static void save_volume(char *infile, char *outfile, char *arg_string, Volume *volume); -public void setup_variables(int inmincid, int mincid, Volume *volume, +static void setup_variables(int inmincid, int mincid, Volume *volume, char *arg_string); -public void setup_image_variables(int inmincid, int mincid, +static void setup_image_variables(int inmincid, int mincid, int ndims, int dim[]); -public void update_history(int mincid, char *arg_string); -public void write_volume_data(int icvid, Volume *volume); +static void update_history(int mincid, char *arg_string); +static void write_volume_data(int icvid, Volume *volume); /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { char *infile, *outfile; Volume volume; @@ -195,7 +183,7 @@ @CREATED : August 22, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void load_volume(char *infile, Volume *volume) +static void load_volume(char *infile, Volume *volume) { int icvid, mincid; @@ -233,7 +221,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_icv(int icvid) +static void setup_icv(int icvid) { /* Set desired type */ (void) miicv_setint(icvid, MI_ICV_TYPE, NC_BYTE); @@ -274,7 +262,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_dimension_info(char *infile, int icvid, Volume *volume) +static void get_dimension_info(char *infile, int icvid, Volume *volume) { int mincid, imgid, varid; int idim, ndims; @@ -354,7 +342,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void read_volume_data(int icvid, Volume *volume) +static void read_volume_data(int icvid, Volume *volume) { long start[MAX_VAR_DIMS], count[MAX_VAR_DIMS]; @@ -365,7 +353,7 @@ count[2] = volume->ncolumns; /* Allocate space for the data */ - volume->data = MALLOC(sizeof(*volume->data) * + volume->data = malloc(sizeof(*volume->data) * volume->ncolumns * volume->nrows * volume->nslices); @@ -394,7 +382,7 @@ @CREATED : August 22, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void save_volume(char *infile, char *outfile, char *arg_string, +static void save_volume(char *infile, char *outfile, char *arg_string, Volume *volume) { int mincid, icvid, inmincid; @@ -449,7 +437,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_variables(int inmincid, int mincid, Volume *volume, +static void setup_variables(int inmincid, int mincid, Volume *volume, char *arg_string) { int dim[MAX_VAR_DIMS], ndims, idim, varid; @@ -534,7 +522,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_image_variables(int inmincid, int mincid, +static void setup_image_variables(int inmincid, int mincid, int ndims, int dim[]) { int imgid, maxid, minid; @@ -580,7 +568,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void update_history(int mincid, char *arg_string) +static void update_history(int mincid, char *arg_string) { nc_type datatype; int att_length; @@ -595,7 +583,7 @@ att_length += strlen(arg_string) + 1; /* Allocate a string and get the old history */ - string = MALLOC(att_length); + string = malloc(att_length); string[0] = '\0'; (void) miattgetstr(mincid, NC_GLOBAL, MIhistory, att_length, string); @@ -604,7 +592,7 @@ /* Add the new command and put the new history. */ (void) strcat(string, arg_string); (void) miattputstr(mincid, NC_GLOBAL, MIhistory, string); - FREE(string); + free(string); } @@ -621,7 +609,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void write_volume_data(int icvid, Volume *volume) +static void write_volume_data(int icvid, Volume *volume) { int mincid; long start[MAX_VAR_DIMS], count[MAX_VAR_DIMS]; @@ -645,7 +633,7 @@ (void) miicv_put(icvid, start, count, volume->data); /* Free space for the data */ - FREE(volume->data); + free(volume->data); }
--- a/progs/mincexample/mincexample2.c +++ b/progs/mincexample/mincexample2.c @@ -12,7 +12,10 @@ @CREATED : March 16, 1994 (Peter Neelin) @MODIFIED : * $Log: mincexample2.c,v $ - * Revision 6.4 2001-09-18 15:32:46 neelin + * Revision 6.4.2.1 2005-03-16 19:02:50 bert + * Port changes from 2.0 branch + * + * Revision 6.4 2001/09/18 15:32:46 neelin * Create image variable last to allow big images and to fix compatibility * problems with 2.3 and 3.x. * @@ -60,7 +63,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincexample/mincexample2.c,v 6.4 2001-09-18 15:32:46 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincexample/mincexample2.c,v 6.4.2.1 2005-03-16 19:02:50 bert Exp $"; #endif #include <stdlib.h> @@ -69,22 +72,7 @@ #include <minc.h> #include <time_stamp.h> -/* Include the standard minc definitions for cross-platform compilation - if we are compiling the package, otherwise, just define MALLOC, - FREE, EXIT_SUCCESS and EXIT_FAILURE */ -#ifdef COMPILING_MINC_PACKAGE -# include <minc_def.h> -#else -# define MALLOC(size) ((void *) malloc(size)) -# define FREE(ptr) free(ptr) -# ifndef EXIT_SUCCESS -# define EXIT_SUCCESS 0 -# define EXIT_FAILURE 1 -# endif -#endif - /* Constants */ -#define public #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -113,29 +101,29 @@ } Volume_Info; /* Function prototypes */ -public int get_volume_info(char *infile, Volume_Info *volume_info); -public void setup_input_icv(int icvid); -public void get_dimension_info(char *infile, int icvid, +static int get_volume_info(char *infile, Volume_Info *volume_info); +static void setup_input_icv(int icvid); +static void get_dimension_info(char *infile, int icvid, Volume_Info *volume_info); -public void close_volume(int icvid); -public void get_volume_slice(int icvid, Volume_Info *volume_info, +static void close_volume(int icvid); +static void get_volume_slice(int icvid, Volume_Info *volume_info, int slice_num, unsigned char *image); -public int save_volume_info(int input_icvid, char *outfile, char *arg_string, +static int save_volume_info(int input_icvid, char *outfile, char *arg_string, Volume_Info *volume_info); -public void setup_output_icv(int icvid); -public void setup_variables(int inmincid, int mincid, +static void setup_output_icv(int icvid); +static void setup_variables(int inmincid, int mincid, Volume_Info *volume_info, char *arg_string); -public void setup_image_variables(int inmincid, int mincid, +static void setup_image_variables(int inmincid, int mincid, int ndims, int dim[]); -public void update_history(int mincid, char *arg_string); -public void save_volume_slice(int icvid, Volume_Info *volume_info, +static void update_history(int mincid, char *arg_string); +static void save_volume_slice(int icvid, Volume_Info *volume_info, int slice_num, unsigned char *image, double slice_min, double slice_max); /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { char *infile, *outfile; Volume_Info volume_info; @@ -181,7 +169,7 @@ &volume_info); /* Loop through slices, copying them */ - image = MALLOC(volume_info.nrows * volume_info.ncolumns * sizeof(*image)); + image = malloc(volume_info.nrows * volume_info.ncolumns * sizeof(*image)); for (islice=0; islice < volume_info.nslices; islice++) { get_volume_slice(input_icvid, &volume_info, islice, image); save_volume_slice(output_icvid, &volume_info, islice, image, @@ -191,7 +179,7 @@ /* Free up image and close files */ close_volume(input_icvid); close_volume(output_icvid); - FREE(image); + free(image); exit(EXIT_SUCCESS); } @@ -208,7 +196,7 @@ @CREATED : August 22, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_volume_info(char *infile, Volume_Info *volume_info) +static int get_volume_info(char *infile, Volume_Info *volume_info) { int icvid, mincid; @@ -244,7 +232,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_input_icv(int icvid) +static void setup_input_icv(int icvid) { /* Set desired type */ (void) miicv_setint(icvid, MI_ICV_TYPE, NC_BYTE); @@ -286,7 +274,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_dimension_info(char *infile, int icvid, +static void get_dimension_info(char *infile, int icvid, Volume_Info *volume_info) { int mincid, imgid, varid; @@ -384,7 +372,7 @@ @CREATED : March 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void close_volume(int icvid) +static void close_volume(int icvid) { int mincid; @@ -414,7 +402,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_volume_slice(int icvid, Volume_Info *volume_info, +static void get_volume_slice(int icvid, Volume_Info *volume_info, int slice_num, unsigned char *image) { long start[MAX_VAR_DIMS], count[MAX_VAR_DIMS]; @@ -461,7 +449,7 @@ @CREATED : August 22, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int save_volume_info(int input_icvid, char *outfile, char *arg_string, +static int save_volume_info(int input_icvid, char *outfile, char *arg_string, Volume_Info *volume_info) { int mincid, icvid, inmincid; @@ -500,7 +488,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_output_icv(int icvid) +static void setup_output_icv(int icvid) { /* Set desired type */ (void) miicv_setint(icvid, MI_ICV_TYPE, NC_BYTE); @@ -530,7 +518,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_variables(int inmincid, int mincid, +static void setup_variables(int inmincid, int mincid, Volume_Info *volume_info, char *arg_string) { @@ -619,7 +607,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_image_variables(int inmincid, int mincid, +static void setup_image_variables(int inmincid, int mincid, int ndims, int dim[]) { int imgid, maxid, minid; @@ -665,7 +653,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void update_history(int mincid, char *arg_string) +static void update_history(int mincid, char *arg_string) { nc_type datatype; int att_length; @@ -680,7 +668,7 @@ att_length += strlen(arg_string) + 1; /* Allocate a string and get the old history */ - string = MALLOC(att_length); + string = malloc(att_length); string[0] = '\0'; (void) miattgetstr(mincid, NC_GLOBAL, MIhistory, att_length, string); @@ -689,7 +677,7 @@ /* Add the new command and put the new history. */ (void) strcat(string, arg_string); (void) miattputstr(mincid, NC_GLOBAL, MIhistory, string); - FREE(string); + free(string); } @@ -711,7 +699,7 @@ @CREATED : August 26, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void save_volume_slice(int icvid, Volume_Info *volume_info, +static void save_volume_slice(int icvid, Volume_Info *volume_info, int slice_num, unsigned char *image, double slice_min, double slice_max) {
--- a/progs/mincexpand/mincexpand.c +++ b/progs/mincexpand/mincexpand.c @@ -10,7 +10,10 @@ @CREATED : January 20, 1995 (Peter Neelin) @MODIFIED : * $Log: mincexpand.c,v $ - * Revision 6.1 1999-10-19 14:45:22 neelin + * Revision 6.1.2.1 2005-03-16 19:02:50 bert + * Port changes from 2.0 branch + * + * Revision 6.1 1999/10/19 14:45:22 neelin * Fixed Log subsitutions for CVS * * Revision 6.0 1997/09/12 13:24:16 neelin @@ -50,7 +53,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincexpand/mincexpand.c,v 6.1 1999-10-19 14:45:22 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincexpand/mincexpand.c,v 6.1.2.1 2005-03-16 19:02:50 bert Exp $"; #endif #include <stdlib.h> @@ -58,7 +61,6 @@ #include <string.h> #include <minc.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE @@ -122,7 +124,7 @@ } /* Free the temporary file name string */ - FREE(newfile); + free(newfile); exit(EXIT_SUCCESS); }
--- a/progs/mincextract/mincextract.c +++ b/progs/mincextract/mincextract.c @@ -10,7 +10,10 @@ @CREATED : June 10, 1993 (Peter Neelin) @MODIFIED : * $Log: mincextract.c,v $ - * Revision 6.4 2003-10-28 20:31:19 bert + * Revision 6.4.2.1 2005-03-16 19:02:50 bert + * Port changes from 2.0 branch + * + * Revision 6.4 2003/10/28 20:31:19 bert * Remove two unused variables * * Revision 6.3 2001/08/16 16:41:35 neelin @@ -85,7 +88,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincextract/mincextract.c,v 6.4 2003-10-28 20:31:19 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincextract/mincextract.c,v 6.4.2.1 2005-03-16 19:02:50 bert Exp $"; #endif #include <stdlib.h> @@ -96,17 +99,12 @@ #include <float.h> #include <ctype.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE # define TRUE 1 # define FALSE 0 #endif -#ifndef public -# define public -# define private static -#endif #define VECTOR_SEPARATOR ',' #define TYPE_ASCII 0 #define TYPE_BYTE 1 @@ -120,7 +118,7 @@ }; /* Function declarations */ -public int get_arg_vector(char *dst, char *key, char *nextArg); +static int get_arg_vector(char *dst, char *key, char *nextArg); /* Variables used for argument parsing */ int arg_odatatype = TYPE_ASCII; @@ -374,7 +372,7 @@ element_size = nctypelen(output_datatype); /* Allocate space */ - data = MALLOC(element_size*nelements); + data = malloc(element_size*nelements); /* Loop over input slices */ @@ -412,7 +410,7 @@ /* Clean up */ (void) miclose(mincid); (void) miicv_free(icvid); - FREE(data); + free(data); exit(EXIT_SUCCESS); } @@ -433,7 +431,7 @@ @CREATED : June 10, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_arg_vector(char *dst, char *key, char *nextArg) +static int get_arg_vector(char *dst, char *key, char *nextArg) /* ARGSUSED */ {
--- a/progs/mincinfo/mincinfo.c +++ b/progs/mincinfo/mincinfo.c @@ -10,7 +10,10 @@ @CREATED : May 19, 1993 (Peter Neelin) @MODIFIED : * $Log: mincinfo.c,v $ - * Revision 6.4 2001-10-31 19:40:21 neelin + * Revision 6.4.2.1 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch + * + * Revision 6.4 2001/10/31 19:40:21 neelin * Fixed bug in printing of sign for default output - this was introduced * in the change to miget_datatype. * @@ -79,7 +82,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincinfo/mincinfo.c,v 6.4 2001-10-31 19:40:21 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincinfo/mincinfo.c,v 6.4.2.1 2005-03-16 19:02:51 bert Exp $"; #endif #include <stdlib.h> @@ -89,10 +92,8 @@ #include <float.h> #include <minc.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ -#define public #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -124,12 +125,11 @@ #define RTN_ERR(code) if ((code) == MI_ERROR) {return MI_ERROR;} /* Function prototypes */ -public int main(int argc, char *argv[]); -public int process_file( char* filename, int header_only ); -public int get_option(char *dst, char *key, char *nextarg); -public int report_error(void); -public int get_attname(int mincid, char *string, int *varid, char *name); -public int print_image_info(char *filename, int mincid); +static int process_file( char* filename, int header_only ); +static int get_option(char *dst, char *key, char *nextarg); +static int report_error(void); +static int get_attname(int mincid, char *string, int *varid, char *name); +static int print_image_info(char *filename, int mincid); /* Variables used for argument parsing */ char *error_string = NULL; Option_type option_list[MAX_NUM_OPTIONS] = {ENDLIST}; @@ -164,7 +164,7 @@ /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { int ioption, ifile, header_only; int ret_value = EXIT_SUCCESS; @@ -224,7 +224,7 @@ @CREATED : April 25, 2000 (Steve Robbins) @MODIFIED : ---------------------------------------------------------------------------- */ -public int process_file( char* filename, int header_only ) +static int process_file( char* filename, int header_only ) { int mincid, varid, dimid; int ndims, dims[MAX_VAR_DIMS]; @@ -330,23 +330,23 @@ row_length = length; } if (datatype==NC_CHAR) { - cdata = MALLOC(var_length*sizeof(char)); + cdata = malloc(var_length*sizeof(char)); CHK_ERR(ncvarget(mincid, varid, start, count, cdata)); for (ival=0; ival<var_length; ival++) { (void) putchar((int) cdata[ival]); if (((ival+1) % row_length) == 0) (void) putchar((int)'\n'); } - FREE(cdata); + free(cdata); } else { - ddata = MALLOC(var_length*sizeof(double)); + ddata = malloc(var_length*sizeof(double)); CHK_ERR(mivarget(mincid, varid, start, count, NC_DOUBLE, NULL, ddata)); for (ival=0; ival<var_length; ival++) { (void) printf("%.20g\n", ddata[ival]); } - FREE(ddata); + free(ddata); } break; case ATTTYPE: @@ -358,21 +358,21 @@ CHK_ERR(get_attname(mincid, string, &varid, name)); CHK_ERR(ncattinq(mincid, varid, name, &datatype, &att_length)); if (datatype == NC_CHAR) { - cdata = MALLOC((att_length+1)*sizeof(char)); + cdata = malloc((att_length+1)*sizeof(char)); if (miattgetstr(mincid, varid, name, att_length+1, cdata)==NULL) {REPORT_ERROR} (void) printf("%s\n", cdata); - FREE(cdata); + free(cdata); } else { - ddata = MALLOC(att_length * sizeof(double)); + ddata = malloc(att_length * sizeof(double)); CHK_ERR(miattget(mincid, varid, name, NC_DOUBLE, att_length, ddata, NULL)); for (iatt=0; iatt<att_length; iatt++) { (void) printf("%.20g ", ddata[iatt]); } (void) printf("\n"); - FREE(ddata); + free(ddata); } break; default: @@ -402,7 +402,7 @@ @CREATED : May 19, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_option(char *dst, char *key, char *nextarg) +static int get_option(char *dst, char *key, char *nextarg) /* ARGSUSED */ { Option_code code; @@ -454,7 +454,7 @@ @CREATED : May 19, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int report_error(void) +static int report_error(void) { if (error_string == NULL) { (void) fprintf(stderr, "Error reading file.\n"); @@ -481,7 +481,7 @@ @CREATED : May 19, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_attname(int mincid, char *string, int *varid, char *name) +static int get_attname(int mincid, char *string, int *varid, char *name) { #define ATT_SEP_CHAR ':' @@ -530,7 +530,7 @@ @CREATED : May 19, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int print_image_info(char *filename, int mincid) +static int print_image_info(char *filename, int mincid) { int imgid, ndims, dim[MAX_VAR_DIMS], varid; nc_type datatype;
--- a/progs/minclookup/minclookup.c +++ b/progs/minclookup/minclookup.c @@ -11,7 +11,10 @@ @CREATED : December 6, 1994 (Peter Neelin) @MODIFIED : * $Log: minclookup.c,v $ - * Revision 6.3.2.1 2004-09-28 20:08:14 bert + * Revision 6.3.2.2 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch + * + * Revision 6.3.2.1 2004/09/28 20:08:14 bert * Minor portability fix for Windows * * Revision 6.3 2001/04/24 13:38:43 neelin @@ -66,7 +69,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/minclookup/minclookup.c,v 6.3.2.1 2004-09-28 20:08:14 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/minclookup/minclookup.c,v 6.3.2.2 2005-03-16 19:02:51 bert Exp $"; #endif #include "config.h" @@ -79,13 +82,8 @@ #include <minc.h> #include <ParseArgv.h> #include <time_stamp.h> -#include <minc_def.h> #include <voxel_loop.h> -#ifndef public -# define public -#endif - #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -121,21 +119,21 @@ } Sort_Key; /* Function prototypes */ -public Lookup_Table *read_lookup_table(char *lookup_file, char *lookup_string); -public double *get_values_from_string(char *string, int array_size, +static Lookup_Table *read_lookup_table(char *lookup_file, char *lookup_string); +static double *get_values_from_string(char *string, int array_size, double *array, int *nread); -public double *get_null_value(int vector_length, char *null_value_string); -public void get_full_range(int mincid, double lookup_range[2]); -public void do_lookup(void *caller_data, long num_voxels, +static double *get_null_value(int vector_length, char *null_value_string); +static void get_full_range(int mincid, double lookup_range[2]); +static void do_lookup(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void lookup_in_table(double index, Lookup_Table *lookup_table, +static void lookup_in_table(double index, Lookup_Table *lookup_table, int discrete_values, double null_value[], double output_value[]); -private char *get_next_line(char *line, int linelen, FILE *fp, char **string); -private int sorting_function(const void *value1, const void *value2); +static char *get_next_line(char *line, int linelen, FILE *fp, char **string); +static int sorting_function(const void *value1, const void *value2); /* Lookup tables */ static double gray_lookup_values[] = { @@ -352,10 +350,10 @@ do_lookup, (void *) &lookup_data); /* Free stuff */ - if (lookup_data.null_value != NULL) FREE(lookup_data.null_value); + if (lookup_data.null_value != NULL) free(lookup_data.null_value); if (lookup_data.lookup_table->free_data) { - FREE(lookup_data.lookup_table->table); - FREE(lookup_data.lookup_table); + free(lookup_data.lookup_table->table); + free(lookup_data.lookup_table); } exit(EXIT_SUCCESS); @@ -377,7 +375,7 @@ @CREATED : December 8, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public Lookup_Table *read_lookup_table(char *lookup_filename, +static Lookup_Table *read_lookup_table(char *lookup_filename, char *lookup_string) { Lookup_Table *lookup_table; @@ -424,10 +422,10 @@ row = get_values_from_string(line, 0, NULL, &table_nvalues); if (table_nvalues < 2) { (void) fprintf(stderr, "First line has fewer than 2 values.\n"); - if (row != NULL) FREE(row); + if (row != NULL) free(row); exit(EXIT_FAILURE); } - table = MALLOC(sizeof(*table) * table_nvalues); + table = malloc(sizeof(*table) * table_nvalues); for (ivalue=0; ivalue < table_nvalues; ivalue++) table[ivalue] = row[ivalue]; nentries++; @@ -438,11 +436,11 @@ (void) fprintf(stderr, "Wrong number of values on line %d.\n", nentries+1); - FREE(row); - FREE(table); + free(row); + free(table); exit(EXIT_FAILURE); } - table = REALLOC(table, sizeof(*table) * table_nvalues * (nentries+1)); + table = realloc(table, sizeof(*table) * table_nvalues * (nentries+1)); for (ivalue=0; ivalue < table_nvalues; ivalue++) { table[ivalue + nentries*table_nvalues] = row[ivalue]; } @@ -464,7 +462,7 @@ if (need_sort) { /* Set up sorting table */ - sort_table = MALLOC(sizeof(*sort_table) * nentries); + sort_table = malloc(sizeof(*sort_table) * nentries); for (ientry=0; ientry < nentries; ientry++) { sort_table[ientry].key = table[ientry*table_nvalues]; sort_table[ientry].index = ientry; @@ -475,7 +473,7 @@ sorting_function); /* Copy the table */ - new_table = MALLOC(sizeof(*table) * table_nvalues * nentries); + new_table = malloc(sizeof(*table) * table_nvalues * nentries); for (ientry=0; ientry < nentries; ientry++) { new_offset = ientry * table_nvalues; old_offset = sort_table[ientry].index * table_nvalues; @@ -483,13 +481,13 @@ new_table[new_offset + ivalue] = table[old_offset + ivalue]; } } - FREE(table); + free(table); table = new_table; - FREE(sort_table); + free(sort_table); } /* Allocate space for the lookup table and set initial values */ - lookup_table = MALLOC(sizeof(*lookup_table)); + lookup_table = malloc(sizeof(*lookup_table)); lookup_table->free_data = TRUE; lookup_table->nentries = nentries; lookup_table->vector_length = table_nvalues - 1; @@ -516,7 +514,7 @@ @MODIFIED : ---------------------------------------------------------------------------- */ #define LOOKUP_LINE_SEPARATOR ';' -private char *get_next_line(char *line, int linelen, FILE *fp, char **string) +static char *get_next_line(char *line, int linelen, FILE *fp, char **string) { int count; @@ -568,7 +566,7 @@ @CREATED : December 8, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -private int sorting_function(const void *value1, const void *value2) +static int sorting_function(const void *value1, const void *value2) { Sort_Key *key1, *key2; @@ -606,7 +604,7 @@ @CREATED : December 8, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public double *get_values_from_string(char *string, int array_size, +static double *get_values_from_string(char *string, int array_size, double *array, int *nread) { #define VECTOR_SEPARATOR ',' @@ -639,7 +637,7 @@ if (cur == prev) { *nread = 0; if (array_size <= 0 && array != NULL) { - FREE(array); + free(array); } return NULL; } @@ -650,10 +648,10 @@ if (array_size <= 0) { num_alloc += 1; if (array == NULL) { - array = MALLOC(num_alloc * sizeof(*array)); + array = malloc(num_alloc * sizeof(*array)); } else { - array = REALLOC(array, num_alloc * sizeof(*array)); + array = realloc(array, num_alloc * sizeof(*array)); } } else { @@ -690,7 +688,7 @@ @CREATED : December 8, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public double *get_null_value(int vector_length, char *string) +static double *get_null_value(int vector_length, char *string) { int num_read; double *values; @@ -703,7 +701,7 @@ /* Check the number of values read */ if (num_read != vector_length) { - if (values != NULL) FREE(values); + if (values != NULL) free(values); (void) fprintf(stderr, "Null value does not match lookup table (%d values).\n", num_read); @@ -725,7 +723,7 @@ @CREATED : December 8, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_full_range(int mincid, double range[2]) +static void get_full_range(int mincid, double range[2]) { char *string; int varid; @@ -762,7 +760,7 @@ num_values *= length; } if (num_values > 0) { - values = MALLOC(num_values * sizeof(*values)); + values = malloc(num_values * sizeof(*values)); (void) mivarget(mincid, varid, start, count, NC_DOUBLE, NULL, values); *extreme = values[0]; @@ -770,7 +768,7 @@ if ((values[ivalue] * sign) > (*extreme * sign)) *extreme = values[ivalue]; } - FREE(values); + free(values); } } /* If variable is found */ @@ -802,7 +800,7 @@ @CREATED : December 8, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_lookup(void *caller_data, long num_voxels, +static void do_lookup(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -883,7 +881,7 @@ @CREATED : December 8, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void lookup_in_table(double index, Lookup_Table *lookup_table, +static void lookup_in_table(double index, Lookup_Table *lookup_table, int discrete_values, double null_value[], double output_value[]) {
--- a/progs/mincmakescalar/mincmakescalar.c +++ b/progs/mincmakescalar/mincmakescalar.c @@ -10,7 +10,10 @@ @CREATED : August 7, 1997 (Peter Neelin) @MODIFIED : * $Log: mincmakescalar.c,v $ - * Revision 6.3.2.1 2005-01-25 21:01:52 bert + * Revision 6.3.2.2 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch + * + * Revision 6.3.2.1 2005/01/25 21:01:52 bert * Check for proper placement of vector_dimension * * Revision 6.3 2001/04/24 13:38:43 neelin @@ -40,7 +43,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincmakescalar/mincmakescalar.c,v 6.3.2.1 2005-01-25 21:01:52 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincmakescalar/mincmakescalar.c,v 6.3.2.2 2005-03-16 19:02:51 bert Exp $"; #endif #include <stdlib.h> @@ -52,13 +55,8 @@ #include <minc.h> #include <ParseArgv.h> #include <time_stamp.h> -#include <minc_def.h> #include <voxel_loop.h> -#ifndef public -# define public -#endif - #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -87,13 +85,13 @@ } Program_Data; /* Function prototypes */ -public void do_makescalar(void *caller_data, long num_voxels, +static void do_makescalar(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public int get_double_list(char *dst, char *key, char *nextarg); -public long get_vector_length(int mincid); +static int get_double_list(char *dst, char *key, char *nextarg); +static long get_vector_length(int mincid); /* Argument variables */ int clobber = FALSE; @@ -206,7 +204,7 @@ program_data.conversion_type = conversion_type; program_data.num_coefficients = linear_coefficients.numvalues; program_data.linear_coefficients = - MALLOC(linear_coefficients.numvalues * + malloc(linear_coefficients.numvalues * sizeof(*program_data.linear_coefficients)); for (ivalue=0; ivalue < linear_coefficients.numvalues; ivalue++) { program_data.linear_coefficients[ivalue] = @@ -253,10 +251,10 @@ /* Free stuff */ if (program_data.linear_coefficients != NULL) { - FREE(program_data.linear_coefficients); + free(program_data.linear_coefficients); } if (linear_coefficients.values != NULL) { - FREE(linear_coefficients.values); + free(linear_coefficients.values); } exit(EXIT_SUCCESS); @@ -283,7 +281,7 @@ @CREATED : August 7, 1997 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_makescalar(void *caller_data, long num_voxels, +static void do_makescalar(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -387,7 +385,7 @@ @CREATED : March 8, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_double_list(char *dst, char *key, char *nextarg) +static int get_double_list(char *dst, char *key, char *nextarg) { #define VECTOR_SEPARATOR ',' @@ -436,11 +434,11 @@ num_alloc += 20; if (double_list == NULL) { double_list = - MALLOC(num_alloc * sizeof(*double_list)); + malloc(num_alloc * sizeof(*double_list)); } else { double_list = - REALLOC(double_list, num_alloc * sizeof(*double_list)); + realloc(double_list, num_alloc * sizeof(*double_list)); } } double_list[num_elements-1] = dvalue; @@ -456,7 +454,7 @@ /* Update the global variables */ double_array->numvalues = num_elements; if (double_array->values != NULL) { - FREE(double_array->values); + free(double_array->values); } double_array->values = double_list; @@ -475,7 +473,7 @@ @CREATED : November 30, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public long get_vector_length(int mincid) +static long get_vector_length(int mincid) { int imgid; int ndims;
--- a/progs/mincmakevector/mincmakevector.c +++ b/progs/mincmakevector/mincmakevector.c @@ -11,11 +11,8 @@ @CREATED : August 11, 1997 (Peter Neelin) @MODIFIED : * $Log: mincmakevector.c,v $ - * Revision 6.5 2004-04-30 19:53:30 bert - * Remove unused variable - * - * Revision 6.4 2004/04/27 15:32:15 bert - * Added -2 option + * Revision 6.3.2.1 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch * * Revision 6.3 2001/04/24 13:38:44 neelin * Replaced NC_NAT with MI_ORIGINAL_TYPE. @@ -41,7 +38,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincmakevector/mincmakevector.c,v 6.5 2004-04-30 19:53:30 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincmakevector/mincmakevector.c,v 6.3.2.1 2005-03-16 19:02:51 bert Exp $"; #endif #include <stdlib.h> @@ -53,13 +50,8 @@ #include <minc.h> #include <ParseArgv.h> #include <time_stamp.h> -#include <minc_def.h> #include <voxel_loop.h> -#ifndef public -# define public -#endif - #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -75,19 +67,16 @@ } Program_Data; /* Function prototypes */ -public void do_makevector(void *caller_data, long num_voxels, +static void do_makevector(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public long get_vector_length(int mincid); +static long get_vector_length(int mincid); /* Argument variables */ int clobber = FALSE; int verbose = TRUE; -#ifdef MINC2 -int v2format = FALSE; -#endif /* MINC2 defined */ nc_type datatype = MI_ORIGINAL_TYPE; int is_signed = FALSE; double valid_range[2] = {0.0, 0.0}; @@ -95,10 +84,6 @@ /* Argument table */ ArgvInfo argTable[] = { -#ifdef MINC2 - {"-2", ARGV_CONSTANT, (char *) TRUE, (char *) &v2format, - "Produce a MINC 2.0 format output file."}, -#endif /* MINC2 defined */ {"-clobber", ARGV_CONSTANT, (char *) TRUE, (char *) &clobber, "Overwrite existing file."}, {"-noclobber", ARGV_CONSTANT, (char *) FALSE, (char *) &clobber, @@ -173,9 +158,6 @@ loop_options = create_loop_options(); set_loop_clobber(loop_options, clobber); set_loop_verbose(loop_options, verbose); -#ifdef MINC2 - set_loop_v2format(loop_options, v2format); -#endif /* MINC2 defined */ set_loop_datatype(loop_options, datatype, is_signed, valid_range[0], valid_range[1]); set_loop_output_vector_size(loop_options, num_input_files); @@ -211,16 +193,20 @@ @CREATED : August 11, 1997 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_makevector(void *caller_data, long num_voxels, +static void do_makevector(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info) /* ARGSUSED */ { + Program_Data *program_data; long ivoxel, ovoxel; int current_input_file; + /* Get pointer to lookup info */ + program_data = (Program_Data *) caller_data; + /* Check that values correspond */ if ((input_num_buffers != 1) || (output_num_buffers != 1) || (input_vector_length != 1)) { @@ -255,7 +241,7 @@ @CREATED : November 30, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public long get_vector_length(int mincid) +static long get_vector_length(int mincid) { int imgid; int ndims;
--- a/progs/mincmath/mincmath.c +++ b/progs/mincmath/mincmath.c @@ -10,7 +10,10 @@ @CREATED : April 28, 1995 (Peter Neelin) @MODIFIED : * $Log: mincmath.c,v $ - * Revision 6.5.2.1 2004-09-28 20:07:56 bert + * Revision 6.5.2.2 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch + * + * Revision 6.5.2.1 2004/09/28 20:07:56 bert * Minor portability fix for Windows * * Revision 6.5 2001/04/24 13:38:44 neelin @@ -69,7 +72,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincmath/mincmath.c,v 6.5.2.1 2004-09-28 20:07:56 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincmath/mincmath.c,v 6.5.2.2 2005-03-16 19:02:51 bert Exp $"; #endif #include "config.h" @@ -82,15 +85,10 @@ #include <minc.h> #include <ParseArgv.h> #include <time_stamp.h> -#include <minc_def.h> #include <voxel_loop.h> /* Constants */ -#ifndef public -# define public -#endif - #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -164,28 +162,27 @@ } Math_Data; /* Function prototypes */ -public int main(int argc, char *argv[]); -public void do_math(void *caller_data, long num_voxels, +static void do_math(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void accum_math(void *caller_data, long num_voxels, +static void accum_math(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void start_math(void *caller_data, long num_voxels, +static void start_math(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public void end_math(void *caller_data, long num_voxels, +static void end_math(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info); -public char **read_file_names(char *filelist, int *num_files); +static char **read_file_names(char *filelist, int *num_files); /* Argument variables */ int clobber = FALSE; @@ -350,7 +347,7 @@ /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { char **infiles, **outfiles; int nfiles, nout; @@ -511,7 +508,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_math(void *caller_data, long num_voxels, +static void do_math(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -700,7 +697,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void accum_math(void *caller_data, long num_voxels, +static void accum_math(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -799,7 +796,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void start_math(void *caller_data, long num_voxels, +static void start_math(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info) @@ -851,7 +848,7 @@ @CREATED : April 25, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void end_math(void *caller_data, long num_voxels, +static void end_math(void *caller_data, long num_voxels, int output_num_buffers, int output_vector_length, double *output_data[], Loop_Info *loop_info) @@ -901,7 +898,7 @@ @CREATED : March 8, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public char **read_file_names(char *filelist, int *num_files) +static char **read_file_names(char *filelist, int *num_files) { #define FILE_NAME_ALLOC_SIZE 10 char **files; @@ -925,7 +922,7 @@ /* Allocate an initial array and NULL-terminate it */ array_size = FILE_NAME_ALLOC_SIZE; - files = MALLOC(sizeof(*files) * array_size); + files = malloc(sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL; @@ -947,7 +944,7 @@ /* Make room for names if needed */ while (nfiles >= array_size-1) { array_size += FILE_NAME_ALLOC_SIZE; - files = REALLOC(files, sizeof(*files) * array_size); + files = realloc(files, sizeof(*files) * array_size); if (files == NULL) { (void) fprintf(stderr, "Error allocating memory\n"); return NULL;
--- a/progs/mincresample/mincresample.c +++ b/progs/mincresample/mincresample.c @@ -11,14 +11,8 @@ @CREATED : February 8, 1993 (Peter Neelin) @MODIFIED : * $Log: mincresample.c,v $ - * Revision 6.15 2004-04-30 19:53:40 bert - * Remove unused variable - * - * Revision 6.14 2004/04/30 18:52:49 bert - * Remove some unused variables - * - * Revision 6.13 2004/04/27 15:31:20 bert - * Added -2 option + * Revision 6.12.2.1 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch * * Revision 6.12 2003/09/18 15:01:33 bert * Removed unnecessary brackets from initializer @@ -171,7 +165,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincresample/mincresample.c,v 6.15 2004-04-30 19:53:40 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005-03-16 19:02:51 bert Exp $"; #endif #include <stdlib.h> @@ -184,7 +178,6 @@ #include <ParseArgv.h> #include <time_stamp.h> #include <volume_io.h> -#include <minc_def.h> #include <convert_origin_to_start.h> #include "mincresample.h" @@ -199,7 +192,7 @@ /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { VVolume in_vol_struct, out_vol_struct; VVolume *in_vol = &in_vol_struct, *out_vol = &out_vol_struct; @@ -236,7 +229,7 @@ @CREATED : February 8, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_arginfo(int argc, char *argv[], +static void get_arginfo(int argc, char *argv[], Program_Flags *program_flags, VVolume *in_vol, VVolume *out_vol, General_transform *transformation) @@ -271,16 +264,10 @@ {NULL, NULL, NULL}, /* Pointers to coordinate arrays */ {"", "", ""}, /* units */ {"", "", ""} /* spacetype */ - }, - FALSE /* MINC 2.0 format? */ + } }; static ArgvInfo argTable[] = { -#ifdef MINC2 - {"-2", ARGV_CONSTANT, (char *) TRUE, - (char *) &args.v2format, - "Produce a MINC 2.0 format output file."}, -#endif /* MINC2 defined */ {"-clobber", ARGV_CONSTANT, (char *) TRUE, (char *) &args.clobber, "Overwrite existing file."}, @@ -430,15 +417,14 @@ /* Other variables */ int idim, index; - int out_vindex; /* Volume indices (0, 1 or 2) */ - int out_findex; /* File indices (0 to ndims-1) */ + int in_vindex, out_vindex; /* Volume indices (0, 1 or 2) */ + int in_findex, out_findex; /* File indices (0 to ndims-1) */ long size, total_size; char *infile, *outfile; File_Info *fp; char *tm_stamp, *pname; Volume_Definition input_volume_def, transformed_volume_def; General_transform input_transformation; - int cflags; /* Initialize the transformation to identity */ create_linear_transform(&input_transformation, NULL); @@ -491,7 +477,7 @@ delete_general_transform(&input_transformation); /* Check input file for default argument information */ - in_vol->file = MALLOC(sizeof(File_Info)); + in_vol->file = malloc(sizeof(File_Info)); get_file_info(infile, FALSE, &input_volume_def, in_vol->file); transform_volume_def((transform_input_sampling ? &args.transform_info : NULL), @@ -521,15 +507,15 @@ } /* Save the voxel_to_world transformation information */ - in_vol->voxel_to_world = MALLOC(sizeof(General_transform)); - in_vol->world_to_voxel = MALLOC(sizeof(General_transform)); + in_vol->voxel_to_world = malloc(sizeof(General_transform)); + in_vol->world_to_voxel = malloc(sizeof(General_transform)); get_voxel_to_world_transf(&input_volume_def, in_vol->voxel_to_world); create_inverse_general_transform(in_vol->voxel_to_world, in_vol->world_to_voxel); /* Get input volume data information */ in_vol->slice = NULL; - in_vol->volume = MALLOC(sizeof(Volume_Data)); + in_vol->volume = malloc(sizeof(Volume_Data)); in_vol->volume->datatype = in_vol->file->datatype; in_vol->volume->is_signed = in_vol->file->is_signed; in_vol->volume->vrange[0] = in_vol->file->vrange[0]; @@ -575,14 +561,14 @@ total_size *= size; in_vol->volume->size[index] = size; } - in_vol->volume->data = MALLOC((size_t) total_size * + in_vol->volume->data = malloc((size_t) total_size * nctypelen(in_vol->volume->datatype)); /* Get space for slice scale and offset */ in_vol->volume->scale = - MALLOC(sizeof(double) * in_vol->volume->size[SLC_AXIS]); + malloc(sizeof(double) * in_vol->volume->size[SLC_AXIS]); in_vol->volume->offset = - MALLOC(sizeof(double) * in_vol->volume->size[SLC_AXIS]); + malloc(sizeof(double) * in_vol->volume->size[SLC_AXIS]); /* Save the program flags */ *program_flags = args.flags; @@ -594,7 +580,7 @@ /* Explicitly force output files to have regular spacing */ for (idim=0; idim < WORLD_NDIMS; idim++) { if (args.volume_def.coords[idim] != NULL) { - FREE(args.volume_def.coords[idim]); + free(args.volume_def.coords[idim]); args.volume_def.coords[idim] = NULL; } } @@ -622,7 +608,7 @@ } /* Set up the file description for the output file */ - out_vol->file = MALLOC(sizeof(File_Info)); + out_vol->file = malloc(sizeof(File_Info)); out_vol->file->ndims = in_vol->file->ndims; out_vol->file->datatype = args.datatype; out_vol->file->is_signed = args.is_signed; @@ -636,14 +622,16 @@ /* Get space for output slice */ out_vol->volume = NULL; - out_vol->slice = MALLOC(sizeof(Slice_Data)); + out_vol->slice = malloc(sizeof(Slice_Data)); /* Loop through list of axes, getting size of volume and slice */ total_size = 1; for (idim=0; idim < WORLD_NDIMS; idim++) { /* Get the index for input and output volumes */ + in_vindex = in_vol->file->axes[idim]; /* 0, 1 or 2 */ out_vindex = args.volume_def.axes[idim]; /* 0, 1 or 2 */ + in_findex = in_vol->file->indices[in_vindex]; /* 0 to ndims-1 */ out_findex = in_vol->file->indices[out_vindex]; /* 0 to ndims-1 */ size = args.volume_def.nelements[idim]; @@ -659,33 +647,22 @@ total_size *= size; } } - out_vol->slice->data = MALLOC((size_t) total_size * sizeof(double)); + out_vol->slice->data = malloc((size_t) total_size * sizeof(double)); /* Create the output file */ - if (args.clobber) { - cflags = NC_CLOBBER; - } - else { - cflags = NC_NOCLOBBER; - } -#ifdef MINC2 - if (args.v2format) { - cflags |= MI2_CREATE_V2; - } -#endif /* MINC2 defined */ - create_output_file(outfile, cflags, &args.volume_def, + create_output_file(outfile, args.clobber, &args.volume_def, in_vol->file, out_vol->file, tm_stamp, &args.transform_info); /* Save the voxel_to_world transformation information */ - out_vol->voxel_to_world = MALLOC(sizeof(General_transform)); - out_vol->world_to_voxel = MALLOC(sizeof(General_transform)); + out_vol->voxel_to_world = malloc(sizeof(General_transform)); + out_vol->world_to_voxel = malloc(sizeof(General_transform)); get_voxel_to_world_transf(&args.volume_def, out_vol->voxel_to_world); create_inverse_general_transform(out_vol->voxel_to_world, out_vol->world_to_voxel); /* Free the time stamp */ - FREE(tm_stamp); + free(tm_stamp); } @@ -704,7 +681,7 @@ @CREATED : August 5, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void check_imageminmax(File_Info *fp, Volume_Data *volume) +static void check_imageminmax(File_Info *fp, Volume_Data *volume) { int ndims, idim, dim[MAX_VAR_DIMS], imgdim[MAX_VAR_DIMS]; int ivar, varid; @@ -767,16 +744,17 @@ @CREATED : February 9, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_file_info(char *filename, int initialized_volume_def, +static void get_file_info(char *filename, int initialized_volume_def, Volume_Definition *volume_def, File_Info *file_info) { - int dim[MAX_VAR_DIMS], dimid; + int dim[MAX_VAR_DIMS], dimid, status, length; int axis_counter, idim, jdim, cur_axis; int varndims, vardim[MAX_VAR_DIMS]; long varstart, varcount, dimlength; char attstr[MI_MAX_ATTSTR_LEN]; char dimname[MAX_NC_NAME]; + double vrange[2]; enum {UNKNOWN, REGULAR, IRREGULAR} coord_spacing; /* Open the minc file */ @@ -817,7 +795,7 @@ volume_def->dircos[idim][jdim] = 0.0; } if (initialized_volume_def && (volume_def->coords[idim] != NULL)) { - FREE(volume_def->coords[idim]); + free(volume_def->coords[idim]); } volume_def->coords[idim] = NULL; (void) strcpy(volume_def->units[idim], "mm"); @@ -910,14 +888,14 @@ coord_spacing = REGULAR; } if (coord_spacing == IRREGULAR) { - volume_def->coords[cur_axis] = MALLOC(sizeof(double) * dimlength); + volume_def->coords[cur_axis] = malloc(sizeof(double) * dimlength); varstart = 0; varcount = dimlength; if (mivarget(file_info->mincid, dimid, &varstart, &varcount, NC_DOUBLE, MI_SIGNED, volume_def->coords[cur_axis]) == MI_ERROR) { ncopts = NC_VERBOSE | NC_FATAL; - FREE(volume_def->coords[cur_axis]); + free(volume_def->coords[cur_axis]); volume_def->coords[cur_axis] = NULL; continue; } @@ -960,7 +938,7 @@ @CREATED : November 7, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_args_volume_def(Volume_Definition *input_volume_def, +static void get_args_volume_def(Volume_Definition *input_volume_def, Volume_Definition *args_volume_def) { int idim, jdim; @@ -1008,7 +986,7 @@ @CREATED : November 7, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void transform_volume_def(Transform_Info *transform_info, +static void transform_volume_def(Transform_Info *transform_info, Volume_Definition *input_volume_def, Volume_Definition *transformed_volume_def) { @@ -1112,7 +1090,7 @@ @CREATED : November 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int is_zero_vector(double vector[]) +static int is_zero_vector(double vector[]) { return ((vector[0] == 0.0) && (vector[1] == 0.0) && @@ -1131,7 +1109,7 @@ @CREATED : November 9, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void normalize_vector(double vector[]) +static void normalize_vector(double vector[]) { int idim; double magnitude; @@ -1153,7 +1131,8 @@ /* ----------------------------- MNI Header ----------------------------------- @NAME : create_output_file @INPUT : filename - name of file to create - cflags - flag creation flags + clobber - flag indicating whether any existing file should be + overwritten volume_def - description of volume in_file - description of input file out_file - description of output file @@ -1169,7 +1148,7 @@ @CREATED : February 9, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void create_output_file(char *filename, int cflags, +static void create_output_file(char *filename, int clobber, Volume_Definition *volume_def, File_Info *in_file, File_Info *out_file, @@ -1208,7 +1187,8 @@ ncopts = NC_VERBOSE | NC_FATAL; /* Create the file */ - out_file->mincid = micreate(filename, cflags); + out_file->mincid = micreate(filename, + (clobber ? NC_CLOBBER : NC_NOCLOBBER)); /* Copy all other variable definitions */ (void) micopy_all_var_defs(in_file->mincid, out_file->mincid, @@ -1221,14 +1201,14 @@ (datatype != NC_CHAR)) att_length = 0; att_length += strlen(tm_stamp) + 1; - string = MALLOC(att_length); + string = malloc(att_length); string[0] = '\0'; (void) miattgetstr(out_file->mincid, NC_GLOBAL, MIhistory, att_length, string); ncopts=NC_VERBOSE | NC_FATAL; (void) strcat(string, tm_stamp); (void) miattputstr(out_file->mincid, NC_GLOBAL, MIhistory, string); - FREE(string); + free(string); /* Get the dimension ids from the input file */ (void) ncvarinq(in_file->mincid, in_file->imgid, NULL, NULL, @@ -1273,7 +1253,7 @@ size, then we must rename it */ if (is_volume_dimension && dim_exists && (out_file->nelements[out_index] != in_file->nelements[in_index])) { - string = MALLOC(MAX_NC_NAME); + string = malloc(MAX_NC_NAME); ncopts = 0; idim = 0; do { @@ -1282,7 +1262,7 @@ } while (ncdimid(out_file->mincid, string) != MI_ERROR); ncopts = NC_VERBOSE | NC_FATAL; (void) ncdimrename(out_file->mincid, out_dims[out_index], string); - FREE(string); + free(string); out_dims[out_index] = ncdimdef(out_file->mincid, dimname, out_file->nelements[out_index]); } @@ -1369,7 +1349,7 @@ } /* Look for an unused transformation attribute */ - string = MALLOC(MI_MAX_ATTSTR_LEN); + string = malloc(MI_MAX_ATTSTR_LEN); itrans = 0; do { (void) sprintf(string, "transformation%d-filename", itrans); @@ -1392,7 +1372,7 @@ (void) miattputstr(out_file->mincid, varid, string, MI_TRUE); } - FREE(string); + free(string); } /* If transform specified on command line */ @@ -1445,7 +1425,7 @@ @CREATED : February 9, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_voxel_to_world_transf(Volume_Definition *volume_def, +static void get_voxel_to_world_transf(Volume_Definition *volume_def, General_transform *voxel_to_world) { int idim, jdim, cur_dim, vol_axis; @@ -1488,7 +1468,7 @@ /* If we have an irregularly spaced dimension, then create the appropriate transform */ if (irregular) { - irreg_transf_data = MALLOC(sizeof(*irreg_transf_data)); + irreg_transf_data = malloc(sizeof(*irreg_transf_data)); /* Loop through the axes */ for (idim=0; idim < WORLD_NDIMS; idim++) { @@ -1508,7 +1488,7 @@ dimlength = volume_def->nelements[idim]; irreg_transf_data->nelements[vol_axis] = dimlength; irreg_transf_data->coords[vol_axis] = - MALLOC(sizeof(double) * dimlength); + malloc(sizeof(double) * dimlength); /* Normalize the coordinates to give first coord 0 and last coord n-1 (so that we can concat with the linear @@ -1529,7 +1509,7 @@ sizeof(*irreg_transf_data), irregular_transform_function, irregular_inverse_transform_function); - FREE(irreg_transf_data); + free(irreg_transf_data); /* Concatenate the linear transform with the irregular transform */ copy_general_transform(voxel_to_world, &linear_transf); @@ -1556,7 +1536,7 @@ @CREATED : November 4, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void irregular_transform_function(void *user_data, +static void irregular_transform_function(void *user_data, Real x, Real y, Real z, @@ -1618,7 +1598,7 @@ @CREATED : November 4, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void irregular_inverse_transform_function(void *user_data, +static void irregular_inverse_transform_function(void *user_data, Real x, Real y, Real z, @@ -1712,7 +1692,7 @@ @MODIFIED : February 10, 1993 (Peter Neelin) - ripped off from MINC code ---------------------------------------------------------------------------- */ -public double get_default_range(char *what, nc_type datatype, int is_signed) +static double get_default_range(char *what, nc_type datatype, int is_signed) { double limit; @@ -1753,7 +1733,7 @@ @CREATED : February 15, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void finish_up(VVolume *in_vol, VVolume *out_vol) +static void finish_up(VVolume *in_vol, VVolume *out_vol) { File_Info *in_file, *out_file; @@ -1792,7 +1772,7 @@ @CREATED : February 15, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_transformation(char *dst, char *key, char *nextArg) +static int get_transformation(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Transform_Info *transform_info; @@ -1838,14 +1818,14 @@ /* Read in the file for later use */ if (transform_info->file_contents == NULL) { - transform_info->file_contents = MALLOC(TRANSFORM_BUFFER_INCREMENT); + transform_info->file_contents = malloc(TRANSFORM_BUFFER_INCREMENT); transform_info->buffer_length = TRANSFORM_BUFFER_INCREMENT; } for (index = 0; (ch=getc(fp)) != EOF; index++) { if (index >= transform_info->buffer_length-1) { transform_info->buffer_length += TRANSFORM_BUFFER_INCREMENT; transform_info->file_contents = - REALLOC(transform_info->file_contents, + realloc(transform_info->file_contents, transform_info->buffer_length); } transform_info->file_contents[index] = (char) ch; @@ -1886,7 +1866,7 @@ @CREATED : February 15, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_model_file(char *dst, char *key, char *nextArg) +static int get_model_file(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Volume_Definition *volume_def; @@ -1931,7 +1911,7 @@ @CREATED : November 14, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int set_standard_sampling(char *dst, char *key, char *nextArg) +static int set_standard_sampling(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Volume_Definition *volume_def; @@ -1967,7 +1947,7 @@ @CREATED : December 12, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int set_spacetype(char *dst, char *key, char *nextArg) +static int set_spacetype(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Volume_Definition *volume_def; @@ -2024,7 +2004,7 @@ @CREATED : December 12, 1995 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int set_units(char *dst, char *key, char *nextArg) +static int set_units(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Volume_Definition *volume_def; @@ -2067,7 +2047,7 @@ @CREATED : February 15, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_axis_order(char *dst, char *key, char *nextArg) +static int get_axis_order(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Volume_Definition *volume_def; @@ -2109,7 +2089,7 @@ @CREATED : February 15, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_fillvalue(char *dst, char *key, char *nextArg) +static int get_fillvalue(char *dst, char *key, char *nextArg) /* ARGSUSED */ { double *dptr;
--- a/progs/mincresample/mincresample.h +++ b/progs/mincresample/mincresample.h @@ -7,8 +7,8 @@ @CREATED : February 8, 1993 (Peter Neelin) @MODIFIED : * $Log: mincresample.h,v $ - * Revision 6.5 2004-04-27 15:31:20 bert - * Added -2 option + * Revision 6.4.2.1 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch * * Revision 6.4 2002/11/06 13:32:23 jason * Fixes to mincresample: setting the interpolation type is now done @@ -244,7 +244,6 @@ enum Interpolant_type interpolant_type; /* Type of interpolation */ Transform_Info transform_info; Volume_Definition volume_def; - int v2format; /* If non-zero, create a MINC 2.0 output */ } Arg_Data; typedef struct { @@ -335,69 +334,69 @@ /* Function prototypes */ -public void get_arginfo(int argc, char *argv[], +static void get_arginfo(int argc, char *argv[], Program_Flags *program_flags, VVolume *in_vol, VVolume *out_vol, General_transform *transformation); -public void check_imageminmax(File_Info *fp, Volume_Data *volume); -public void get_file_info(char *filename, int initialized_volume_def, +static void check_imageminmax(File_Info *fp, Volume_Data *volume); +static void get_file_info(char *filename, int initialized_volume_def, Volume_Definition *volume_def, File_Info *file_info); -public void get_args_volume_def(Volume_Definition *input_volume_def, +static void get_args_volume_def(Volume_Definition *input_volume_def, Volume_Definition *args_volume_def); -public void transform_volume_def(Transform_Info *transform_info, +static void transform_volume_def(Transform_Info *transform_info, Volume_Definition *input_volume_def, Volume_Definition *transformed_volume_def); -public int is_zero_vector(double vector[]); -public void normalize_vector(double vector[]); -public void create_output_file(char *filename, int clobber, +static int is_zero_vector(double vector[]); +static void normalize_vector(double vector[]); +static void create_output_file(char *filename, int clobber, Volume_Definition *volume_def, File_Info *in_file, File_Info *out_file, char *tm_stamp, Transform_Info *transform_info); -public void get_voxel_to_world_transf(Volume_Definition *volume_def, +static void get_voxel_to_world_transf(Volume_Definition *volume_def, General_transform *voxel_to_world); -public void irregular_transform_function(void *user_data, +static void irregular_transform_function(void *user_data, Real x, Real y, Real z, Real *x_trans, Real *y_trans, Real *z_trans); -public void irregular_inverse_transform_function(void *user_data, +static void irregular_inverse_transform_function(void *user_data, Real x, Real y, Real z, Real *x_trans, Real *y_trans, Real *z_trans); -public double get_default_range(char *what, nc_type datatype, int is_signed); -public void finish_up(VVolume *in_vol, VVolume *out_vol); -public int get_transformation(char *dst, char *key, char *nextArg); -public int get_model_file(char *dst, char *key, char *nextArg); -public int set_standard_sampling(char *dst, char *key, char *nextArg); -public int set_spacetype(char *dst, char *key, char *nextArg); -public int set_units(char *dst, char *key, char *nextArg); -public int get_axis_order(char *dst, char *key, char *nextArg); -public int get_fillvalue(char *dst, char *key, char *nextArg); -public void resample_volumes(Program_Flags *program_flags, +static double get_default_range(char *what, nc_type datatype, int is_signed); +static void finish_up(VVolume *in_vol, VVolume *out_vol); +static int get_transformation(char *dst, char *key, char *nextArg); +static int get_model_file(char *dst, char *key, char *nextArg); +static int set_standard_sampling(char *dst, char *key, char *nextArg); +static int set_spacetype(char *dst, char *key, char *nextArg); +static int set_units(char *dst, char *key, char *nextArg); +static int get_axis_order(char *dst, char *key, char *nextArg); +static int get_fillvalue(char *dst, char *key, char *nextArg); +extern void resample_volumes(Program_Flags *program_flags, VVolume *in_vol, VVolume *out_vol, General_transform *transformation); -public void load_volume(File_Info *file, long start[], long count[], +static void load_volume(File_Info *file, long start[], long count[], Volume_Data *volume); -public void get_slice(long slice_num, VVolume *in_vol, VVolume *out_vol, +static void get_slice(long slice_num, VVolume *in_vol, VVolume *out_vol, General_transform *transformation, double *minimum, double *maximum); -public int trilinear_interpolant(Volume_Data *volume, +extern int trilinear_interpolant(Volume_Data *volume, Coord_Vector coord, double *result); -public int tricubic_interpolant(Volume_Data *volume, +extern int tricubic_interpolant(Volume_Data *volume, Coord_Vector coord, double *result); -public int do_Ncubic_interpolation(Volume_Data *volume, +static int do_Ncubic_interpolation(Volume_Data *volume, long index[], int cur_dim, double frac[], double *result); -public int nearest_neighbour_interpolant(Volume_Data *volume, +extern int nearest_neighbour_interpolant(Volume_Data *volume, Coord_Vector coord, double *result); -public void renormalize_slices(Program_Flags *program_flags, VVolume *out_vol, +static void renormalize_slices(Program_Flags *program_flags, VVolume *out_vol, double slice_min[], double slice_max[]);
--- a/progs/mincresample/resample_volumes.c +++ b/progs/mincresample/resample_volumes.c @@ -6,7 +6,10 @@ @CREATED : February 8, 1993 (Peter Neelin) @MODIFIED : * $Log: resample_volumes.c,v $ - * Revision 6.3 2001-08-16 13:32:39 neelin + * Revision 6.3.2.1 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch + * + * Revision 6.3 2001/08/16 13:32:39 neelin * Partial fix for valid_range of different type from image (problems * arising from double to float conversion/rounding). NOT COMPLETE. * @@ -84,7 +87,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincresample/resample_volumes.c,v 6.3 2001-08-16 13:32:39 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincresample/resample_volumes.c,v 6.3.2.1 2005-03-16 19:02:51 bert Exp $"; #endif #include <stdlib.h> @@ -94,7 +97,6 @@ #include <math.h> #include <minc.h> #include <volume_io.h> -#include <minc_def.h> #include "mincresample.h" /* ----------------------------- MNI Header ----------------------------------- @@ -113,9 +115,9 @@ @CREATED : February 8, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void resample_volumes(Program_Flags *program_flags, - VVolume *in_vol, VVolume *out_vol, - General_transform *transformation) +void resample_volumes(Program_Flags *program_flags, + VVolume *in_vol, VVolume *out_vol, + General_transform *transformation) { long in_start[MAX_VAR_DIMS], in_count[MAX_VAR_DIMS], in_end[MAX_VAR_DIMS]; long out_start[MAX_VAR_DIMS], out_count[MAX_VAR_DIMS]; @@ -132,9 +134,9 @@ /* Allocate slice min/max arrays if needed */ if (ofp->do_slice_renormalization) { - slice_min = MALLOC(ofp->images_per_file * ofp->slices_per_image * + slice_min = malloc(ofp->images_per_file * ofp->slices_per_image * sizeof(double)); - slice_max = MALLOC(ofp->images_per_file * ofp->slices_per_image * + slice_max = malloc(ofp->images_per_file * ofp->slices_per_image * sizeof(double)); } @@ -264,8 +266,8 @@ /* Recompute slices and free vectors, if needed */ if (ofp->do_slice_renormalization) { renormalize_slices(program_flags, out_vol, slice_min, slice_max); - FREE(slice_min); - FREE(slice_max); + free(slice_min); + free(slice_max); } } @@ -285,8 +287,8 @@ @CREATED : February 10, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void load_volume(File_Info *file, long start[], long count[], - Volume_Data *volume) +void load_volume(File_Info *file, long start[], long count[], + Volume_Data *volume) { long nread, islice, mm_start[MAX_VAR_DIMS], mm_count[MAX_VAR_DIMS]; int varid, ivar, idim, ndims; @@ -420,9 +422,9 @@ @CREATED : February 8, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_slice(long slice_num, VVolume *in_vol, VVolume *out_vol, - General_transform *transformation, - double *minimum, double *maximum) +void get_slice(long slice_num, VVolume *in_vol, VVolume *out_vol, + General_transform *transformation, + double *minimum, double *maximum) { Slice_Data *slice; Volume_Data *volume; @@ -541,8 +543,8 @@ @CREATED : February 10, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int trilinear_interpolant(Volume_Data *volume, - Coord_Vector coord, double *result) +int trilinear_interpolant(Volume_Data *volume, + Coord_Vector coord, double *result) { long slcind, rowind, colind, slcmax, rowmax, colmax; long slcnext, rownext, colnext; @@ -658,8 +660,8 @@ @CREATED : February 12, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int tricubic_interpolant(Volume_Data *volume, - Coord_Vector coord, double *result) +int tricubic_interpolant(Volume_Data *volume, + Coord_Vector coord, double *result) { long slcind, rowind, colind, slcmax, rowmax, colmax, index[VOL_NDIMS]; double frac[VOL_NDIMS]; @@ -716,9 +718,9 @@ @CREATED : February 12, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int do_Ncubic_interpolation(Volume_Data *volume, - long index[], int cur_dim, - double frac[], double *result) +int do_Ncubic_interpolation(Volume_Data *volume, + long index[], int cur_dim, + double frac[], double *result) { long base_index; double v0, v1, v2, v3, u; @@ -817,8 +819,8 @@ @CREATED : February 12, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int nearest_neighbour_interpolant(Volume_Data *volume, - Coord_Vector coord, double *result) +int nearest_neighbour_interpolant(Volume_Data *volume, + Coord_Vector coord, double *result) { long slcind, rowind, colind, slcmax, rowmax, colmax; @@ -866,7 +868,7 @@ @CREATED : October 29, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void renormalize_slices(Program_Flags *program_flags, VVolume *out_vol, +static void renormalize_slices(Program_Flags *program_flags, VVolume *out_vol, double slice_min[], double slice_max[]) { File_Info *ofp; @@ -899,8 +901,8 @@ } /* Find the max/min for each image */ - image_maximum = MALLOC( sizeof(double) * ofp->images_per_file); - image_minimum = MALLOC( sizeof(double) * ofp->images_per_file); + image_maximum = malloc( sizeof(double) * ofp->images_per_file); + image_minimum = malloc( sizeof(double) * ofp->images_per_file); for (image=0; image < ofp->images_per_file; image++) { image_maximum[image] = -DBL_MAX; image_minimum[image] = DBL_MAX; @@ -996,8 +998,8 @@ } /* Free the image max/min arrays */ - FREE(image_maximum); - FREE(image_minimum); + free(image_maximum); + free(image_minimum); return; }
--- a/progs/mincreshape/copy_data.c +++ b/progs/mincreshape/copy_data.c @@ -6,7 +6,10 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : * $Log: copy_data.c,v $ - * Revision 6.3 2001-04-17 18:40:24 neelin + * Revision 6.3.2.1 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch + * + * Revision 6.3 2001/04/17 18:40:24 neelin * Modifications to work with NetCDF 3.x * In particular, changed NC_LONG to NC_INT (and corresponding longs to ints). * Changed NC_UNSPECIFIED to NC_NAT. @@ -63,7 +66,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincreshape/copy_data.c,v 6.3 2001-04-17 18:40:24 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincreshape/copy_data.c,v 6.3.2.1 2005-03-16 19:02:51 bert Exp $"; #endif #include <stdlib.h> @@ -73,10 +76,11 @@ #include <string.h> #include <math.h> #include <minc.h> -#include <minc_def.h> #include <nd_loop.h> #include "mincreshape.h" +#define ROUND( x ) ((long) ((x) + ( ((x) >= 0) ? 0.5 : (-0.5) ) )) + /* ----------------------------- MNI Header ----------------------------------- @NAME : copy_data @INPUT : reshape_info - information for reshaping volume @@ -90,7 +94,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void copy_data(Reshape_info *reshape_info) +void copy_data(Reshape_info *reshape_info) { int idim, odim, out_ndims; long block_begin[MAX_VAR_DIMS], block_end[MAX_VAR_DIMS]; @@ -123,7 +127,7 @@ for (odim=0; odim < out_ndims; odim++) { total_size *= reshape_info->chunk_count[odim]; } - chunk_data = MALLOC(total_size); + chunk_data = malloc(total_size); /* Get enough space for image-min and max values for a block */ get_num_minmax_values(reshape_info, NULL, block_count, @@ -131,7 +135,7 @@ num_values = ((num_min_values > num_max_values) ? num_min_values : num_max_values); if (num_values > 0) - minmax_buffer = MALLOC(num_values * sizeof(double)); + minmax_buffer = malloc(num_values * sizeof(double)); else minmax_buffer = NULL; @@ -195,11 +199,11 @@ } /* Free the chunk space */ - FREE(chunk_data); + free(chunk_data); /* Free minmax buffer */ if (minmax_buffer != NULL) { - FREE(minmax_buffer); + free(minmax_buffer); } /* Print ending log message */ @@ -231,7 +235,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_num_minmax_values(Reshape_info *reshape_info, +static void get_num_minmax_values(Reshape_info *reshape_info, long *block_start, long *block_count, long *num_min_values, long *num_max_values) { @@ -315,7 +319,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void handle_normalization(Reshape_info *reshape_info, +static void handle_normalization(Reshape_info *reshape_info, long *block_start, long *block_count, double *minmax_buffer, @@ -413,7 +417,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_block_min_and_max(Reshape_info *reshape_info, +static void get_block_min_and_max(Reshape_info *reshape_info, long *block_start, long *block_count, double *minmax_buffer, @@ -519,7 +523,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void truncate_input_vectors(Reshape_info *reshape_info, +static void truncate_input_vectors(Reshape_info *reshape_info, long *input_start, long *input_count) { @@ -565,7 +569,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void translate_output_to_input(Reshape_info *reshape_info, +static void translate_output_to_input(Reshape_info *reshape_info, long *output_start, long *output_count, long *input_start, @@ -611,7 +615,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void translate_input_to_output(Reshape_info *reshape_info, +static void translate_input_to_output(Reshape_info *reshape_info, long *input_start, long *input_count, long *output_start, @@ -654,7 +658,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void copy_the_chunk(Reshape_info *reshape_info, +static void copy_the_chunk(Reshape_info *reshape_info, long chunk_start[], long chunk_count[], void *chunk_data, @@ -772,7 +776,7 @@ @CREATED : October 25, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void convert_value_from_double(double dvalue, +static void convert_value_from_double(double dvalue, nc_type datatype, int is_signed, void *ptr) {
--- a/progs/mincreshape/mincreshape.c +++ b/progs/mincreshape/mincreshape.c @@ -13,8 +13,8 @@ @CREATED : March 10, 1994 (Peter Neelin) @MODIFIED : * $Log: mincreshape.c,v $ - * Revision 6.9 2004-04-27 15:30:02 bert - * Add -2 flag + * Revision 6.8.2.1 2005-03-16 19:02:51 bert + * Port changes from 2.0 branch * * Revision 6.8 2001/11/13 14:16:50 neelin * Get correct valid range for conversion from int to float types @@ -92,7 +92,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincreshape/mincreshape.c,v 6.9 2004-04-27 15:30:02 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincreshape/mincreshape.c,v 6.8.2.1 2005-03-16 19:02:51 bert Exp $"; #endif #include <stdlib.h> @@ -105,12 +105,11 @@ #include <minc.h> #include <ParseArgv.h> #include <time_stamp.h> -#include <minc_def.h> #include "mincreshape.h" /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { Reshape_info reshape_info; @@ -123,8 +122,10 @@ /* Close the output file */ (void) miattputstr(reshape_info.outmincid, reshape_info.outimgid, MIcomplete, MI_TRUE); + (void) miclose(reshape_info.outmincid); (void) miclose(reshape_info.inmincid); + exit(EXIT_SUCCESS); } @@ -142,7 +143,7 @@ @CREATED : March 11, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_arginfo(int argc, char *argv[], +static void get_arginfo(int argc, char *argv[], Reshape_info *reshape_info) { @@ -171,10 +172,6 @@ static long hs_count[MAX_VAR_DIMS] = {LONG_MIN}; static double fillvalue = NOFILL; static int max_chunk_size_in_kb = DEFAULT_MAX_CHUNK_SIZE_IN_KB; -#ifdef MINC2 - static int minc2_format = 0; -#endif /* MINC2 defined */ - int cflags; /* File creation flags */ /* Argument table */ static ArgvInfo argTable[] = { @@ -191,10 +188,6 @@ {"-max_chunk_size_in_kb", ARGV_INT, (char *) 0, (char *) &max_chunk_size_in_kb, "Specify the maximum size of the copy buffer (in kbytes)."}, -#ifdef MINC2 - {"-2", ARGV_CONSTANT, (char *) TRUE, (char *)&minc2_format, - "Produce a MINC 2.0 format output file."}, -#endif /* MINC2 defined */ {NULL, ARGV_HELP, (char *) NULL, (char *) NULL, "Image conversion options (pixel type and range):"}, @@ -437,18 +430,8 @@ ncvarid(reshape_info->inmincid, MIimage)); /* Create the output file */ - if (clobber) { - cflags = NC_CLOBBER; - } - else { - cflags = NC_NOCLOBBER; - } -#ifdef MINC2 - if (minc2_format) { - cflags |= MI2_CREATE_V2; - } -#endif /* MINC2 defined */ - reshape_info->outmincid = micreate(outfile, cflags); + reshape_info->outmincid = + micreate(outfile, (clobber ? NC_CLOBBER : NC_NOCLOBBER)); setup_output_file(reshape_info->outmincid, history, reshape_info); return; @@ -468,7 +451,7 @@ @CREATED : March 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_fillvalue(char *dst, char *key, char *nextArg) +static int get_fillvalue(char *dst, char *key, char *nextArg) /* ARGSUSED */ { double *dptr; @@ -503,7 +486,7 @@ @CREATED : March 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_dimsize(char *dst, char *key, char *nextArg) +static int get_dimsize(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Dimsize_list *dimsize_list; @@ -589,7 +572,7 @@ @CREATED : March 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_axis_order(char *dst, char *key, char *nextArg) +static int get_axis_order(char *dst, char *key, char *nextArg) /* ARGSUSED */ { char **axis_order; @@ -680,7 +663,7 @@ @CREATED : March 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_axis_range(char *dst, char *key, char *nextArg) +static int get_axis_range(char *dst, char *key, char *nextArg) /* ARGSUSED */ { Axis_ranges *axis_ranges; @@ -780,7 +763,7 @@ @CREATED : June 10, 1993 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public int get_arg_vector(char *dst, char *key, char *nextArg) +static int get_arg_vector(char *dst, char *key, char *nextArg) /* ARGSUSED */ { @@ -855,7 +838,7 @@ @CREATED : March 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void get_default_datatype(int mincid, nc_type *datatype, int *is_signed, +static void get_default_datatype(int mincid, nc_type *datatype, int *is_signed, double valid_range[2]) { int imgid; @@ -953,7 +936,7 @@ @CREATED : May 18, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_dim_sizes(int icvid, int mincid, Dimsize_list *dimsize_list) +static void setup_dim_sizes(int icvid, int mincid, Dimsize_list *dimsize_list) { int ientry, idim; int imgid, dimid; @@ -1023,7 +1006,7 @@ @CREATED : May 26, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_reshaping_info(int icvid, int mincid, +static void setup_reshaping_info(int icvid, int mincid, int do_norm, double fillvalue, int do_scalar, char *axis_order[], Axis_ranges *axis_ranges, long hs_start[], long hs_count[], @@ -1311,7 +1294,7 @@ @CREATED : June 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void setup_output_file(int mincid, char *history, +static void setup_output_file(int mincid, char *history, Reshape_info *reshape_info) { int output_ndims, output_dim[MAX_VAR_DIMS]; @@ -1439,13 +1422,13 @@ == MI_ERROR) || (datatype != NC_CHAR)) att_length = 0; att_length += strlen(history) + 1; - string = MALLOC(att_length); + string = malloc(att_length); string[0] = '\0'; (void) miattgetstr(mincid, NC_GLOBAL, MIhistory, att_length, string); ncopts = NCOPTS_DEFAULT; (void) strcat(string, history); (void) miattputstr(mincid, NC_GLOBAL, MIhistory, string); - FREE(string); + free(string); /* Get into data mode */ (void) ncsetfill(mincid, NC_NOFILL); @@ -1485,7 +1468,7 @@ @CREATED : June 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void create_dim_var(int outmincid, int outdimid, +static void create_dim_var(int outmincid, int outdimid, int inicvid, int cur_image_dim, int inmincid, long input_start, long input_count) { @@ -1598,7 +1581,7 @@ @CREATED : June 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void copy_dimension_values(int outmincid, int outdimid, int inmincid, +static void copy_dimension_values(int outmincid, int outdimid, int inmincid, long input_start, long input_count) { char dimname[MAX_NC_NAME]; @@ -1637,7 +1620,7 @@ @CREATED : June 16, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void copy_dim_var_values(int outmincid, char *dimname, char *varname, +static void copy_dim_var_values(int outmincid, char *dimname, char *varname, int inmincid, long input_start, long input_count) {
--- a/progs/mincreshape/mincreshape.h +++ b/progs/mincreshape/mincreshape.h @@ -7,7 +7,10 @@ @CREATED : March 11, 1994 (Peter Neelin) @MODIFIED : * $Log: mincreshape.h,v $ - * Revision 6.3 2001-12-06 14:12:45 neelin + * Revision 6.3.2.1 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch + * + * Revision 6.3 2001/12/06 14:12:45 neelin * Trivial change to definition of NCOPTS_DEFAULT. * * Revision 6.2 1999/10/19 14:45:29 neelin @@ -112,66 +115,65 @@ #define MIN( x, y ) ( ((x) <= (y)) ? (x) : (y) ) /* Function prototypes */ -public int main(int argc, char *argv[]); -public void get_arginfo(int argc, char *argv[], +static void get_arginfo(int argc, char *argv[], Reshape_info *reshape_info); -public int get_fillvalue(char *dst, char *key, char *nextArg); -public int get_dimsize(char *dst, char *key, char *nextArg); -public int get_axis_order(char *dst, char *key, char *nextArg); -public int get_axis_range(char *dst, char *key, char *nextArg); -public int get_arg_vector(char *dst, char *key, char *nextArg); -public void get_default_datatype(int mincid, nc_type *datatype, int *is_signed, +static int get_fillvalue(char *dst, char *key, char *nextArg); +static int get_dimsize(char *dst, char *key, char *nextArg); +static int get_axis_order(char *dst, char *key, char *nextArg); +static int get_axis_range(char *dst, char *key, char *nextArg); +static int get_arg_vector(char *dst, char *key, char *nextArg); +static void get_default_datatype(int mincid, nc_type *datatype, int *is_signed, double valid_range[2]); -public void setup_dim_sizes(int icvid, int mincid, Dimsize_list *dimsize_list); -public void setup_reshaping_info(int icvid, int mincid, +static void setup_dim_sizes(int icvid, int mincid, Dimsize_list *dimsize_list); +static void setup_reshaping_info(int icvid, int mincid, int do_norm, double fillvalue, int do_scalar, char *axis_order[], Axis_ranges *axis_ranges, long hs_start[], long hs_count[], int max_chunk_size_in_kb, Reshape_info *reshape_info); -public void setup_output_file(int mincid, char *history, +static void setup_output_file(int mincid, char *history, Reshape_info *reshape_info); -public void create_dim_var(int outmincid, int outdimid, +static void create_dim_var(int outmincid, int outdimid, int inicvid, int cur_image_dim, int inmincid, long input_start, long input_count); -public void copy_dimension_values(int outmincid, int outdimid, int inmincid, +static void copy_dimension_values(int outmincid, int outdimid, int inmincid, long input_start, long input_count); -public void copy_dim_var_values(int outmincid, char *dimname, char *varname, +static void copy_dim_var_values(int outmincid, char *dimname, char *varname, int inmincid, long input_start, long input_count); -public void copy_data(Reshape_info *reshape_info); -public void get_num_minmax_values(Reshape_info *reshape_info, +extern void copy_data(Reshape_info *reshape_info); +static void get_num_minmax_values(Reshape_info *reshape_info, long *block_start, long *block_count, long *num_min_values, long *num_max_values); -public void handle_normalization(Reshape_info *reshape_info, +static void handle_normalization(Reshape_info *reshape_info, long *block_start, long *block_count, double *minmax_buffer, double *fillvalue); -public void get_block_min_and_max(Reshape_info *reshape_info, +static void get_block_min_and_max(Reshape_info *reshape_info, long *block_start, long *block_count, double *minmax_buffer, double *minimum, double *maximum); -public void truncate_input_vectors(Reshape_info *reshape_info, +static void truncate_input_vectors(Reshape_info *reshape_info, long *input_start, long *input_count); -public void translate_output_to_input(Reshape_info *reshape_info, +static void translate_output_to_input(Reshape_info *reshape_info, long *output_start, long *output_count, long *input_start, long *input_count); -public void translate_input_to_output(Reshape_info *reshape_info, +static void translate_input_to_output(Reshape_info *reshape_info, long *input_start, long *input_count, long *output_start, long *output_count); -public void copy_the_chunk(Reshape_info *reshape_info, +static void copy_the_chunk(Reshape_info *reshape_info, long chunk_start[], long chunk_count[], void *chunk_data, double fillvalue); -public void convert_value_from_double(double dvalue, +static void convert_value_from_double(double dvalue, nc_type datatype, int is_signed, void *ptr);
--- a/progs/mincstats/mincstats.c +++ b/progs/mincstats/mincstats.c @@ -5,7 +5,10 @@ * University of Queensland, Australia * * $Log: mincstats.c,v $ - * Revision 1.14.2.2 2004-10-18 15:02:13 bert + * Revision 1.14.2.3 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch + * + * Revision 1.14.2.2 2004/10/18 15:02:13 bert * Ported AJanke's biModalT fix to 1.X branch * * Revision 1.14.2.1 2004/09/28 20:03:40 bert @@ -103,7 +106,6 @@ #include <string.h> #include <ctype.h> #include <ParseArgv.h> -#include <minc_def.h> #include <voxel_loop.h> #ifndef TRUE @@ -207,6 +209,13 @@ static double pctT = 0.0; static int Entropy = FALSE; +/* Alternative methods of calculating the bimodal threshold */ +#define BMT_OTSU 1 /* Otsu algorithm (default) */ +#define BMT_KITTLER 2 /* Kittler-Illingworth algorithm */ +#define BMT_KAPUR 3 /* Kapur et al. algorithm */ +#define BMT_SIMPLE 4 /* Simple mean-of-means, citation unknown */ +static int BMTMethod = BMT_OTSU; + static Double_Array vol_min = { 0, NULL }; static Double_Array vol_max = { 0, NULL }; static Double_Array vol_range = { 0, NULL }; @@ -345,11 +354,368 @@ "<%> threshold at the supplied % of data."}, {"-entropy", ARGV_CONSTANT, (char *)TRUE, (char *)&Entropy, "entropy of the volume."}, + {"-otsu", ARGV_CONSTANT, (char *)BMT_OTSU, (char *)&BMTMethod, + "Use Otsu '97 algorithm for bimodal threshold (default)"}, + {"-kittler", ARGV_CONSTANT, (char *)BMT_KITTLER, (char *)&BMTMethod, + "Use Kittler&Illingworth '86 algorithm for bimodal threshold"}, + {"-kapur", ARGV_CONSTANT, (char *)BMT_KAPUR, (char *)&BMTMethod, + "Use Kapur et al. '85 algorithm for bimodal threshold"}, + {"-simple", ARGV_CONSTANT, (char *)BMT_SIMPLE, (char *)&BMTMethod, + "Use simple mean-of-means algorithm for bimodal threshold"}, {NULL, ARGV_HELP, NULL, NULL, ""}, {NULL, ARGV_END, NULL, NULL, NULL} }; +/* Alternative thresholding algorithm. This is more computationally + * expensive than some of the alternatives, and doesn't seem to do a + * great job. On the other hand it doesn't seem to fail like the + * current algorithm. + */ + +static double +simple_threshold(float *histogram, float *hist_centre, int hist_bins) +{ + double sum1, sum2; + double mean1, mean2; + double testthreshold; + double newthreshold; + int newthreshold_bin; + double count1, count2; + int c; + + /* Start with a guess of the bimodal threshold. + */ + newthreshold = ceil(hist_centre[hist_bins / 2]); + newthreshold_bin = hist_bins / 2; + + for (;;) { + sum1 = 0.0; + sum2 = 0.0; + count1 = 0.0; + count2 = 0.0; + + /* Calculate the mean of the bins on each side of the + * proposed threshold. + */ + for (c = 0; c < newthreshold_bin; c++) { + sum1 += (hist_centre[c] * histogram[c]); + count1 += histogram[c]; + } + + for (c = newthreshold_bin; c < hist_bins; c++) { + sum2 += (hist_centre[c] * histogram[c]); + count2 += histogram[c]; + } + + /* Avoid divide by zero + */ + if (count1 == 0.0 || count2 == 0.0) { + continue; + } + + mean1 = sum1 / count1; + mean2 = sum2 / count2; + + /* The new threshold is the mean of the means. + */ + testthreshold = ceil((mean1 + mean2) / 2); + + /* If the threshold is unchanged, that is our final + * guess. + */ + if (newthreshold == testthreshold) { + break; /* Return result */ + } + else { + /* Adopt the new guess and try again until we converge. + */ + newthreshold = testthreshold; + + for (c = 0; c < hist_bins; c++) { + if (newthreshold == ceil(hist_centre[c])) { + newthreshold_bin = c; + break; + } + } + } + } + return (newthreshold); +} + +/** This copyright applies to the following functions: + * + * otsu_threshold() + * kittler_threshold() + * kapur_threshold() + * + * These functions were extracted from the "xite" package from this + * source. The functions were extensively modified, however, by me + * to generalize the functions for our purposes. Any bugs are + * therefore my responsibility (bert 2004-12-14). + * + * Copyright 1990, Blab, UiO + * Image processing lab, Department of Informatics + * University of Oslo + * E-mail: blab@ifi.uio.no + *________________________________________________________________ + * + * Permission to use, copy, modify and distribute this software and + * its documentation for any purpose and without fee is hereby + * granted, provided that this copyright notice appear in all copies + * and that both that copyright notice and this permission notice + * appear in supporting documentation and that the name of B-lab, + * Department of Informatics or University of Oslo not be used in + * advertising or publicity pertaining to distribution of the software + * without specific, written prior permission. + * + * B-LAB DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, + * INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN + * NO EVENT SHALL B-LAB BE LIABLE FOR ANY SPECIAL, INDIRECT OR + * CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS + * OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, + * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN + * CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + */ + +/* Otsu, N. "A threshold selection method from gray-level histograms", + * IEEE Transactions on Systems, Man, and Cybernetics, vol T-SMC 9, + * No 1, pp 62-66, 1979. + */ +static double +otsu_threshold(float histo[], float hist_centre[], int hist_bins) +{ + double threshold; + double criterion; + double expr_1; /* Temporary for common subexpression */ + int i, k; /* Generic loop counters */ + double *p = malloc(hist_bins * sizeof(double)); + double omega_k; + double sigma_b_k; + double sigma_T; + double mu_T; + double mu_k; + int sum; + int k_low, k_high; + double mu_0, mu_1, mu; + + /* If memory allocation fails, abandon ship!!! */ + if (p == NULL) { + return (0.0); + } + + sum = 0; + for (i = 0; i < hist_bins; i++) + sum += histo[i]; + + for (i = 0; i < hist_bins; i++) + p[i] = histo[i] * 1.0 / sum; + + mu_T = 0.0; + for (i = 0; i < hist_bins; i++) + mu_T += hist_centre[i] * p[i]; + + sigma_T = 0.0; + for (i = 0; i < hist_bins; i++) + sigma_T += (hist_centre[i] - mu_T) * (hist_centre[i] - mu_T) * p[i]; + + /* Ignore outlying zero bins */ + for (k_low = 0; (p[k_low] == 0) && (k_low < hist_bins - 1); k_low++) + ; + + for (k_high = hist_bins - 1; (p[k_high] == 0) && (k_high > 0); k_high--) + ; + + criterion = 0.0; + threshold = hist_centre[hist_bins / 2]; + mu_0 = hist_centre[hist_bins / 2 - 1]; + mu_1 = hist_centre[hist_bins / 2 + 1]; + + omega_k = 0.0; + mu_k = 0.0; + for (k = k_low; k <= k_high ; k++) { + omega_k += p[k]; + mu_k += hist_centre[k] * p[k]; + + expr_1 = (mu_T * omega_k - mu_k); + sigma_b_k = expr_1 * expr_1 / (omega_k * (1 - omega_k)); + if (criterion < sigma_b_k / sigma_T) { + criterion = sigma_b_k / sigma_T; + threshold = hist_centre[k]; + mu_0 = mu_k / omega_k; + mu_1 = (mu_T - mu_k) / (1.0 - omega_k); + } + } + mu = mu_T; + free(p); + return threshold; +} + +/* Kittler, J. & Illingworth J., "Minimum error thresholding", Pattern + * Recognition, vol 19, pp 41-47, 1986. + */ +static double +kittler_threshold (float hist_bin[], float hist_centre[], int hist_size) +{ + double threshold; + double criterion; + int g; + double n; + int T_low, T_high; + double P_1_T, P_2_T, P_tot; + double mu_1_T, mu_2_T; + double sum_gh_1, sum_gh_2, sum_gh_tot; + double sum_ggh_1, sum_ggh_2, sum_ggh_tot; + double sigma_1_T, sigma_2_T; + double J_T; + double mu, mu_1, mu_2; + + criterion = 1e10; + threshold = hist_centre[hist_size / 2 + 1]; + J_T = criterion; + + T_low = 0; + while ((hist_bin[T_low] == 0) && (T_low < hist_size - 1)) { + T_low++; + } + + T_high = hist_size - 1; + while ((hist_bin[T_high] == 0) && (T_high > 0)) { + T_high--; + } + + n = 0; + for (g = T_low; g <= T_high; g++) { + n += hist_bin[g]; + } + + P_1_T = hist_bin[T_low]; + + P_tot = 0; + for (g = T_low; g <= T_high; g++) { + P_tot += hist_bin[g]; + } + + sum_gh_1 = hist_centre[T_low] * hist_bin[T_low]; + + sum_gh_tot = 0.0; + for (g = T_low; g <= T_high; g++) { + sum_gh_tot += hist_centre[g] * hist_bin[g]; + } + + mu = sum_gh_tot * 1.0 / n; + + sum_ggh_1 = hist_centre[T_low] * hist_centre[T_low] * hist_bin[T_low]; + + sum_ggh_tot = 0.0; + for (g = T_low; g <= T_high; g++) { + sum_ggh_tot += hist_centre[g] * hist_centre[g] * hist_bin[g]; + } + + for (g = T_low + 1; g < T_high - 1; g++) { + P_1_T += hist_bin[g]; + P_2_T = P_tot - P_1_T; + + sum_gh_1 += hist_centre[g] * hist_bin[g]; + sum_gh_2 = sum_gh_tot - sum_gh_1; + + mu_1_T = sum_gh_1 / P_1_T; + mu_2_T = sum_gh_2 / P_2_T; + + sum_ggh_1 += hist_centre[g] * hist_centre[g] * hist_bin[g]; + sum_ggh_2 = sum_ggh_tot - sum_ggh_1; + + sigma_1_T = sum_ggh_1 / P_1_T - mu_1_T * mu_1_T; + sigma_2_T = sum_ggh_2 / P_2_T - mu_2_T * mu_2_T; + + /* Equation (15) in the article */ + if ((sigma_1_T != 0.0) && (P_1_T != 0) && + (sigma_2_T != 0.0) && (P_2_T != 0)) { + J_T = 1 + 2 * (P_1_T * log(sigma_1_T) + P_2_T * log(sigma_2_T)) + - 2 * (P_1_T * log(P_1_T) + P_2_T * log(P_2_T) ); + } + + if (criterion > J_T) { + criterion = J_T; + threshold = hist_centre[g]; + mu_1 = mu_1_T; + mu_2 = mu_2_T; + } + } + return threshold; +} + +/* + Kapur, Sahoo & Wong "A new method for Gray-level picture + thresholding using the entropy of the histogram", Computer Vision, + Graphics, and Image Processing, vol 29, pp 273-285, 1985. +*/ + +#define BIN_TINY 1e-6 + +static double +kapur_threshold(float histo[], float hist_centre[], int hist_bins) +{ + double threshold; + double Phi, Phi_max; + int i, k; + double *p = malloc(sizeof(double) * hist_bins); + double *P = malloc(sizeof(double) * hist_bins); + double *H = malloc(sizeof(double) * hist_bins); + double sum; + + sum = 0; + for (i = 0; i < hist_bins; i++) { + sum += histo[i]; + } + + for (i = 0; i < hist_bins; i++) { + p[i] = histo[i] * 1.0 / sum; + } + + P[0] = p[0]; + for (i = 1; i < hist_bins; i++) { + P[i] = P[i - 1] + p[i]; + } + + if (histo[0] == 0) { + H[0] = 0; + } + else { + H[0] = -p[0] * log(p[0]); + } + + for (i = 1; i < hist_bins; i++) { + if (histo[i] == 0) { + H[i] = H[i - 1]; + } + else { + H[i] = H[i - 1] - p[i] * log(p[i]); + } + } + + Phi_max = -10e10; + threshold = hist_centre[hist_bins / 2]; + + for (k = 0; k <= hist_bins - 1; k++) { + + if ((P[k] > BIN_TINY) && (1 - P[k] > BIN_TINY)) { + Phi = log(P[k] * (1 - P[k])) + + H[k] / P[k] + + (H[hist_bins - 1] - H[k]) / (1.0 - P[k]); + + if (Phi_max < Phi) { + Phi_max = Phi; + threshold = hist_centre[k]; + } + } + } + free(p); + free(P); + free(H); + return threshold; +} + int main(int argc, char *argv[]) { char **infiles; @@ -538,9 +904,9 @@ } /* Initialize the stats structure */ - stats_info = MALLOC(num_ranges * sizeof(*stats_info)); + stats_info = malloc(num_ranges * sizeof(*stats_info)); for(irange = 0; irange < num_ranges; irange++) { - stats_info[irange] = MALLOC(num_masks * sizeof(**stats_info)); + stats_info[irange] = malloc(num_masks * sizeof(**stats_info)); for(imask = 0; imask < num_masks; imask++) { stats = &stats_info[irange][imask]; init_stats(stats, hist_bins); @@ -613,9 +979,9 @@ double max_var = 0.0; /* Allocate space for histograms */ - hist_centre = CALLOC(hist_bins, sizeof(float)); - pdf = CALLOC(hist_bins, sizeof(float)); - cdf = CALLOC(hist_bins, sizeof(float)); + hist_centre = calloc(hist_bins, sizeof(float)); + pdf = calloc(hist_bins, sizeof(float)); + cdf = calloc(hist_bins, sizeof(float)); if(hist_centre == NULL || pdf == NULL || cdf == NULL) { (void)fprintf(stderr, "Memory allocation error\n"); exit(EXIT_FAILURE); @@ -647,7 +1013,7 @@ zero_moment += pdf[c]; first_moment += hist_centre[c] * pdf[c]; - if(c > 0) { + if(c > 0 && zero_moment > 0.0 && zero_moment < 1.0) { var = SQR((stats->mean * zero_moment) - first_moment) / (zero_moment * (1 - zero_moment)); @@ -685,6 +1051,32 @@ * pdf[pctt_bin + 1]) * hist_sep; } + switch (BMTMethod) { + case BMT_KITTLER: + stats->biModalT = kittler_threshold(stats->histogram, + hist_centre, + hist_bins); + break; + + case BMT_KAPUR: + stats->biModalT = kapur_threshold(stats->histogram, + hist_centre, + hist_bins); + break; + + case BMT_SIMPLE: + stats->biModalT = simple_threshold(stats->histogram, + hist_centre, + hist_bins); + break; + + default: + stats->biModalT = otsu_threshold(stats->histogram, + hist_centre, + hist_bins); + break; + } + /* output the histogram */ if(hist_file != NULL) { @@ -710,9 +1102,9 @@ } /* Free the space */ - FREE(hist_centre); - FREE(pdf); - FREE(cdf); + free(hist_centre); + free(pdf); + free(cdf); } /* end histogram calculations */ @@ -844,9 +1236,9 @@ for(imask = 0; imask < num_masks; imask++) { free_stats(&stats_info[irange][imask]); } - FREE(stats_info[irange]); + free(stats_info[irange]); } - FREE(stats_info); + free(stats_info); return EXIT_SUCCESS; } @@ -1288,10 +1680,10 @@ if(num_elements > num_alloc) { num_alloc += 20; if(double_list == NULL) { - double_list = MALLOC(num_alloc * sizeof(*double_list)); + double_list = malloc(num_alloc * sizeof(*double_list)); } else { - double_list = REALLOC(double_list, num_alloc * sizeof(*double_list)); + double_list = realloc(double_list, num_alloc * sizeof(*double_list)); } } double_list[num_elements - 1] = dvalue; @@ -1309,7 +1701,7 @@ /* Update the global variables */ double_array->numvalues = num_elements; if(double_array->values != NULL) { - FREE(double_array->values); + free(double_array->values); } double_array->values = double_list; @@ -1378,11 +1770,11 @@ /* Allocate the space */ if(min->numvalues <= 0) { min->numvalues = num_values; - min->values = MALLOC(num_values * sizeof(double)); + min->values = malloc(num_values * sizeof(double)); } if(max->numvalues <= 0) { max->numvalues = num_values; - max->values = MALLOC(num_values * sizeof(double)); + max->values = malloc(num_values * sizeof(double)); } if(min->values == NULL || max->values == NULL) { (void)fprintf(stderr, "Memory allocation error\n"); @@ -1434,7 +1826,7 @@ stats->mask_range[0] = -DBL_MAX; stats->mask_range[1] = DBL_MAX; if(Hist && hist_bins > 0) { - stats->histogram = CALLOC(hist_bins, sizeof(float)); + stats->histogram = calloc(hist_bins, sizeof(float)); if(stats->histogram == NULL) { (void)fprintf(stderr, "Memory allocation error\n"); exit(EXIT_FAILURE); @@ -1475,5 +1867,5 @@ void free_stats(Stats_Info * stats) { if(stats->histogram != NULL) - FREE(stats->histogram); + free(stats->histogram); }
--- a/progs/minctoraw/minctoraw.c +++ b/progs/minctoraw/minctoraw.c @@ -10,7 +10,10 @@ @CREATED : February 11, 1993 (Peter Neelin) @MODIFIED : * $Log: minctoraw.c,v $ - * Revision 6.7 2003-10-28 20:32:09 bert + * Revision 6.7.2.1 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch + * + * Revision 6.7 2003/10/28 20:32:09 bert * Get rid of a few compiler warnings * * Revision 6.6 2001/08/16 16:41:36 neelin @@ -79,7 +82,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/minctoraw/minctoraw.c,v 6.7 2003-10-28 20:32:09 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/minctoraw/minctoraw.c,v 6.7.2.1 2005-03-16 19:02:52 bert Exp $"; #endif #include <stdlib.h> @@ -89,7 +92,6 @@ #include <limits.h> #include <float.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE @@ -228,7 +230,7 @@ } /* Allocate space */ - data = MALLOC(size); + data = malloc(size); /* Loop over input slices */ @@ -257,7 +259,7 @@ /* Clean up */ (void) miclose(mincid); (void) miicv_free(icvid); - FREE(data); + free(data); exit(EXIT_SUCCESS); }
--- a/progs/mincwindow/mincwindow.c +++ b/progs/mincwindow/mincwindow.c @@ -10,8 +10,8 @@ @CREATED : January 10, 1994 (Peter Neelin) @MODIFIED : * $Log: mincwindow.c,v $ - * Revision 6.2 2004-04-27 15:28:39 bert - * Added -2 option + * Revision 6.1.2.1 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch * * Revision 6.1 1999/10/19 14:45:30 neelin * Fixed Log subsitutions for CVS @@ -64,7 +64,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincwindow/mincwindow.c,v 6.2 2004-04-27 15:28:39 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/mincwindow/mincwindow.c,v 6.1.2.1 2005-03-16 19:02:52 bert Exp $"; #endif #include <stdlib.h> @@ -74,13 +74,8 @@ #include <minc.h> #include <ParseArgv.h> #include <time_stamp.h> -#include <minc_def.h> #include <voxel_loop.h> -#ifndef public -# define public -#endif - #ifndef TRUE # define TRUE 1 # define FALSE 0 @@ -95,7 +90,7 @@ } Window_Data; /* Function prototypes */ -public void do_window(void *caller_data, long num_voxels, +static void do_window(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length, @@ -105,16 +100,9 @@ /* Argument variables */ int clobber = FALSE; int verbose = TRUE; -#ifdef MINC2 -int v2format = FALSE; -#endif /* MINC2 defined */ /* Argument table */ ArgvInfo argTable[] = { -#ifdef MINC2 - {"-2", ARGV_CONSTANT, (char *) TRUE, (char *) &v2format, - "Produce a MINC 2.0 format output file."}, -#endif /* MINC2 defined */ {"-clobber", ARGV_CONSTANT, (char *) TRUE, (char *) &clobber, "Overwrite existing file."}, {"-noclobber", ARGV_CONSTANT, (char *) FALSE, (char *) &clobber, @@ -127,7 +115,7 @@ }; /* Main program */ -public int main(int argc, char *argv[]) +int main(int argc, char *argv[]) { char *infile, *outfile; char *arg_string; @@ -177,9 +165,6 @@ loop_options = create_loop_options(); set_loop_verbose(loop_options, verbose); set_loop_clobber(loop_options, clobber); -#ifdef MINC2 - set_loop_v2format(loop_options, v2format); -#endif /* MINC2 defined */ voxel_loop(1, &infile, 1, &outfile, arg_string, loop_options, do_window, (void *) &window_data); @@ -201,7 +186,7 @@ @CREATED : January 11, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -public void do_window(void *caller_data, long num_voxels, +static void do_window(void *caller_data, long num_voxels, int input_num_buffers, int input_vector_length, double *input_data[], int output_num_buffers, int output_vector_length,
--- a/progs/rawtominc/rawtominc.c +++ b/progs/rawtominc/rawtominc.c @@ -11,7 +11,10 @@ @CREATED : September 25, 1992 (Peter Neelin) @MODIFIED : * $Log: rawtominc.c,v $ - * Revision 6.13.2.1 2004-09-28 20:07:30 bert + * Revision 6.13.2.2 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch + * + * Revision 6.13.2.1 2004/09/28 20:07:30 bert * Minor portability fixes for Windows * * Revision 6.13 2004/02/02 18:24:58 bert @@ -143,7 +146,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.13.2.1 2004-09-28 20:07:30 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005-03-16 19:02:52 bert Exp $"; #endif #include "config.h" @@ -162,7 +165,6 @@ #include <ParseArgv.h> #include <time_stamp.h> #include <convert_origin_to_start.h> -#include <minc_def.h> /* Some constants */ @@ -197,11 +199,11 @@ #define STR_EQ(s1,s2) (strcmp(s1,s2)==0) /* Function declarations */ -void parse_args(int argc, char *argv[]); -void usage_error(char *pname); -int get_attribute(char *dst, char *key, char *nextarg); -int get_times(char *dst, char *key, char *nextarg); -int get_axis_order(char *dst, char *key, char *nextArg); +static void parse_args(int argc, char *argv[]); +static void usage_error(char *pname); +static int get_attribute(char *dst, char *key, char *nextarg); +static int get_times(char *dst, char *key, char *nextarg); +static int get_axis_order(char *dst, char *key, char *nextArg); /* Array containing information about signs. It is subscripted by [signtype][type]. Note that the first row should never be used, since @@ -703,7 +705,7 @@ image_pix *= end[ndims-i]; pix_size=nctypelen(datatype); image_size=image_pix*pix_size; - image=MALLOC(image_size); + image=malloc(image_size); /* Loop through the images */ fastdim=ndims-image_dims-1; @@ -882,7 +884,7 @@ } /* Free the memory */ - FREE(image); + free(image); /* Write the valid max and min */ if (do_vrange) { @@ -926,7 +928,7 @@ @CREATED : December 3, 1992 @MODIFIED : ---------------------------------------------------------------------------- */ -void parse_args(int argc, char *argv[]) +static void parse_args(int argc, char *argv[]) { char *ptr; int time_size; @@ -1035,7 +1037,7 @@ @CREATED : September 25, 1992 (Peter Neelin) @MODIFIED : December 2, 1992 (P.N.) ---------------------------------------------------------------------------- */ -void usage_error(char *progname) +static void usage_error(char *progname) { (void) fprintf(stderr, "\nUsage: %s [<options>] <output.mnc> ", progname); @@ -1061,7 +1063,7 @@ @CREATED : May 3, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -int get_attribute(char *dst, char *key, char *nextarg) +static int get_attribute(char *dst, char *key, char *nextarg) /* ARGSUSED */ { int need_string, need_double; @@ -1112,11 +1114,11 @@ attribute_list_alloc += 10; if (attribute_list == NULL) { attribute_list = - MALLOC(attribute_list_alloc * sizeof(*attribute_list)); + malloc(attribute_list_alloc * sizeof(*attribute_list)); } else { attribute_list = - REALLOC(attribute_list, + realloc(attribute_list, attribute_list_alloc * sizeof(*attribute_list)); } } @@ -1157,7 +1159,7 @@ @CREATED : May 3, 1994 (Peter Neelin) @MODIFIED : ---------------------------------------------------------------------------- */ -int get_times(char *dst, char *key, char *nextarg) +static int get_times(char *dst, char *key, char *nextarg) /* ARGSUSED */ { int *num_elements_ptr; @@ -1217,11 +1219,11 @@ num_alloc += 20; if (time_list == NULL) { time_list = - MALLOC(num_alloc * sizeof(*time_list)); + malloc(num_alloc * sizeof(*time_list)); } else { time_list = - REALLOC(time_list, num_alloc * sizeof(*time_list)); + realloc(time_list, num_alloc * sizeof(*time_list)); } } time_list[num_elements-1] = dvalue; @@ -1237,7 +1239,7 @@ /* Update the global variables */ *num_elements_ptr = num_elements; if (*time_list_ptr != NULL) { - FREE(*time_list_ptr); + free(*time_list_ptr); } *time_list_ptr = time_list; @@ -1273,7 +1275,7 @@ #define YXZ_ORIENTATION 5 #define ZXY_ORIENTATION 6 #define STD_ORIENTATION_COUNT 7 -public int get_axis_order(char *dst, char *key, char *nextArg) +static int get_axis_order(char *dst, char *key, char *nextArg) { char **dim_name_array; char *argp;
--- a/progs/xfm/transformtags.c +++ b/progs/xfm/transformtags.c @@ -10,7 +10,10 @@ @CREATED : September 13, 1993 (Peter Neelin) @MODIFIED : * $Log: transformtags.c,v $ - * Revision 6.1 1999-10-19 14:45:31 neelin + * Revision 6.1.2.1 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch + * + * Revision 6.1 1999/10/19 14:45:31 neelin * Fixed Log subsitutions for CVS * * Revision 6.0 1997/09/12 13:23:28 neelin @@ -47,7 +50,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/xfm/transformtags.c,v 6.1 1999-10-19 14:45:31 neelin Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/xfm/transformtags.c,v 6.1.2.1 2005-03-16 19:02:52 bert Exp $"; #endif #include <stdlib.h> @@ -55,7 +58,6 @@ #include <string.h> #include <volume_io.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE
--- a/progs/xfm/xfmconcat.c +++ b/progs/xfm/xfmconcat.c @@ -10,7 +10,10 @@ @CREATED : August 13, 1993 (Peter Neelin) @MODIFIED : * $Log: xfmconcat.c,v $ - * Revision 6.2 2004-02-02 18:24:11 bert + * Revision 6.2.2.1 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch + * + * Revision 6.2 2004/02/02 18:24:11 bert * Call ParseArgv() so that version information will be available * * Revision 6.1 1999/10/19 14:45:32 neelin @@ -60,7 +63,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/xfm/xfmconcat.c,v 6.2 2004-02-02 18:24:11 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/xfm/xfmconcat.c,v 6.2.2.1 2005-03-16 19:02:52 bert Exp $"; #endif #include <stdlib.h> @@ -68,17 +71,12 @@ #include <string.h> #include <volume_io.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE # define TRUE 1 # define FALSE 0 #endif -#ifndef public -# define public -# define private static -#endif /* Argument table */ ArgvInfo argTable[] = {
--- a/progs/xfm/xfminvert.c +++ b/progs/xfm/xfminvert.c @@ -10,7 +10,10 @@ @CREATED : August 13, 1993 (Peter Neelin) @MODIFIED : * $Log: xfminvert.c,v $ - * Revision 6.2 2004-02-02 18:24:11 bert + * Revision 6.2.2.1 2005-03-16 19:02:52 bert + * Port changes from 2.0 branch + * + * Revision 6.2 2004/02/02 18:24:11 bert * Call ParseArgv() so that version information will be available * * Revision 6.1 1999/10/19 14:45:32 neelin @@ -60,7 +63,7 @@ ---------------------------------------------------------------------------- */ #ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/xfm/xfminvert.c,v 6.2 2004-02-02 18:24:11 bert Exp $"; +static char rcsid[]="$Header: /private-cvsroot/minc/progs/xfm/xfminvert.c,v 6.2.2.1 2005-03-16 19:02:52 bert Exp $"; #endif #include <stdlib.h> @@ -68,17 +71,12 @@ #include <string.h> #include <volume_io.h> #include <ParseArgv.h> -#include <minc_def.h> /* Constants */ #ifndef TRUE # define TRUE 1 # define FALSE 0 #endif -#ifndef public -# define public -# define private static -#endif /* Argument table */ ArgvInfo argTable[] = {