Mercurial > hg > minc-tools
changeset 1452:52e8681f7dbf
Moved nd_loop, voxel_loop, ParseArgv and time_stamp to ../../libsrc for
inclusion in the minc library.
| author | neelin <neelin> |
|---|---|
| date | Mon, 14 Jan 2002 21:26:51 +0000 |
| parents | 5f850368deee |
| children | c91b75a015b5 |
| files | progs/Proglib/Makefile progs/Proglib/ParseArgv.c progs/Proglib/ParseArgv.h progs/Proglib/ParseArgv.man3 progs/Proglib/nd_loop.c progs/Proglib/nd_loop.h progs/Proglib/time_stamp.c progs/Proglib/time_stamp.h progs/Proglib/voxel_loop.c progs/Proglib/voxel_loop.h |
| diffstat | 10 files changed, 2 insertions(+), 5101 deletions(-) [+] |
line wrap: on
line diff
--- a/progs/Proglib/Makefile +++ b/progs/Proglib/Makefile @@ -8,9 +8,7 @@ include $(ROOT)/Make_configuration # Object names -OBJS = ParseArgv.o vax_conversions.o time_stamp.o nd_loop.o voxel_loop.o \ - convert_origin_to_start.o -MANPAGES = ParseArgv.3 +OBJS = vax_conversions.o convert_origin_to_start.o CDEFINES = # cpp defines # -------------------------------------------------------------------- @@ -29,9 +27,7 @@ all: build lint -build: $(CC_PROG_LIB) man - -man: $(MANPAGES) +build: $(CC_PROG_LIB) #Dependency on Makefile $(OBJS) $(LINT_OBJS) : Makefile @@ -55,10 +51,6 @@ $(LINT_PROG_LIB) : $(LINT_OBJS) $(LINT) -o $(PROG_LIB) $(LINT_LIBOPTS) $(LINTFLAGS) $(LINT_OBJS) -# how to make man pages -.man3.3: - $(NROFF) $(NROFF_FLAGS) $< > $@ - # Remove all derived files in this directory clean: mostlyclean $(RM) $(RM_FLAGS) $(CC_PROG_LIB) $(LINT_PROG_LIB)
deleted file mode 100644 --- a/progs/Proglib/ParseArgv.c +++ /dev/null @@ -1,420 +0,0 @@ -/* - * ParseArgv.c -- - * - * This file contains a procedure that handles table-based - * argv-argc parsing. - * - * Copyright 1990 Regents of the University of California - * Permission to use, copy, modify, and distribute this - * software and its documentation for any purpose and without - * fee is hereby granted, provided that the above copyright - * notice appear in all copies. The University of California - * makes no representations about the suitability of this - * software for any purpose. It is provided "as is" without - * express or implied warranty. - * - * - * This file has been modified to not rely on tcl, tk or X11. - * Based on tkArgv.c from tk2.3 : -static char rcsid[] = "$Header: /private-cvsroot/minc/progs/Proglib/Attic/ParseArgv.c,v 6.0 1997-09-12 13:23:41 neelin Rel $ SPRITE (Berkeley)"; - * - * Modifications by Peter Neelin (November 27, 1992) - */ - -#include <stdio.h> -#include <stdlib.h> -#include <string.h> -#include <math.h> -#include <ParseArgv.h> - -#define TRUE 1 -#define FALSE 0 - -/* - * Default table of argument descriptors. These are normally available - * in every application. - */ - -static ArgvInfo defaultTable[] = { - {"-help", ARGV_HELP, (char *) NULL, (char *) NULL, - "Print summary of command-line options and abort"}, - {NULL, ARGV_END, (char *) NULL, (char *) NULL, - (char *) NULL} -}; - -/* - * Forward declarations for procedures defined in this file: - */ - -static void PrintUsage _ANSI_ARGS_((ArgvInfo *argTable, int flags)); - -/* - *---------------------------------------------------------------------- - * - * ParseArgv -- - * - * Process an argv array according to a table of expected - * command-line options. See the manual page for more details. - * - * Results: - * The return value is a Boolean value with TRUE indicating an error. - * If an error occurs then an error message is printed on stderr. - * Under normal conditions, both *argcPtr and *argv are modified - * to return the arguments that couldn't be processed here (they - * didn't match the option table, or followed an ARGV_REST - * argument). - * - * Side effects: - * - *---------------------------------------------------------------------- - */ - -int -ParseArgv(argcPtr, argv, argTable, flags) - int *argcPtr; /* Number of arguments in argv. Modified - * to hold # args left in argv at end. */ - char **argv; /* Array of arguments. Modified to hold - * those that couldn't be processed here. */ - ArgvInfo *argTable; /* Array of option descriptions */ - int flags; /* Or'ed combination of various flag bits, - * such as ARGV_NO_DEFAULTS. */ -{ - register ArgvInfo *infoPtr; - /* Pointer to the current entry in the - * table of argument descriptions. */ - ArgvInfo *matchPtr; /* Descriptor that matches current argument. */ - char *curArg; /* Current argument */ - register char c; /* Second character of current arg (used for - * quick check for matching; use 2nd char. - * because first char. will almost always - * be '-'). */ - int srcIndex; /* Location from which to read next argument - * from argv. */ - int dstIndex; /* Index into argv to which next unused - * argument should be copied (never greater - * than srcIndex). */ - int argc; /* # arguments in argv still to process. */ - int length; /* Number of characters in current argument. */ - int nargs; /* Number of following arguments to get. */ - int i; - -/* Macro to optionally print errors */ -#define FPRINTF if (!(flags&ARGV_NO_PRINT)) (void) fprintf - - if (flags & ARGV_DONT_SKIP_FIRST_ARG) { - srcIndex = dstIndex = 0; - argc = *argcPtr; - } else { - srcIndex = dstIndex = 1; - argc = *argcPtr-1; - } - - while (argc > 0) { - curArg = argv[srcIndex]; - srcIndex++; - argc--; - c = curArg[1]; - length = strlen(curArg); - - /* - * Loop throught the argument descriptors searching for one with - * the matching key string. If found, leave a pointer to it in - * matchPtr. - */ - - matchPtr = NULL; - for (i = 0; i < 2; i++) { - if (i == 0) { - infoPtr = argTable; - } else { - infoPtr = defaultTable; - } - for (; infoPtr->type != ARGV_END; infoPtr++) { - if (infoPtr->key == NULL) { - continue; - } - if ((infoPtr->key[1] != c) - || (strncmp(infoPtr->key, curArg, length) != 0)) { - continue; - } - if (infoPtr->key[length] == 0) { - matchPtr = infoPtr; - goto gotMatch; - } - if (flags & ARGV_NO_ABBREV) { - continue; - } - if (matchPtr != NULL) { - FPRINTF(stderr, "ambiguous option \"%s\"\n", curArg); - return TRUE; - } - matchPtr = infoPtr; - } - } - if (matchPtr == NULL) { - - /* - * Unrecognized argument. Just copy it down, unless the caller - * prefers an error to be registered. - */ - - if (flags & ARGV_NO_LEFTOVERS) { - FPRINTF(stderr, "unrecognized argument \"%s\"\n", curArg); - } - argv[dstIndex] = curArg; - dstIndex++; - continue; - } - - /* - * Take the appropriate action based on the option type - */ - gotMatch: - infoPtr = matchPtr; - switch (infoPtr->type) { - case ARGV_CONSTANT: - *((int *) infoPtr->dst) = (int) infoPtr->src; - break; - case ARGV_INT: - nargs = (int) infoPtr->src; - if (nargs<1) nargs=1; - for (i=0; i<nargs; i++) { - if (argc == 0) { - goto missingArg; - } else { - char *endPtr; - - *(((int *) infoPtr->dst)+i) = - strtol(argv[srcIndex], &endPtr, 0); - if ((endPtr == argv[srcIndex]) || (*endPtr != 0)) { - FPRINTF(stderr, - "expected integer argument for \"%s\" but got \"%s\"", - infoPtr->key, argv[srcIndex]); - return TRUE; - } - srcIndex++; - argc--; - } - } - break; - case ARGV_STRING: - nargs = (int) infoPtr->src; - if (nargs<1) nargs=1; - for (i=0; i<nargs; i++) { - if (argc == 0) { - goto missingArg; - } else { - *(((char **)infoPtr->dst)+i) = argv[srcIndex]; - srcIndex++; - argc--; - } - } - break; - case ARGV_REST: - *((int *) infoPtr->dst) = dstIndex; - goto argsDone; - case ARGV_FLOAT: - nargs = (int) infoPtr->src; - if (nargs<1) nargs=1; - for (i=0; i<nargs; i++) { - if (argc == 0) { - goto missingArg; - } else { - char *endPtr; - - *(((double *) infoPtr->dst)+i) = - strtod(argv[srcIndex], &endPtr); - if ((endPtr == argv[srcIndex]) || (*endPtr != 0)) { - FPRINTF(stderr, - "expected floating-point argument for \"%s\" but got\"%s\"\n", - infoPtr->key, argv[srcIndex]); - return TRUE; - } - srcIndex++; - argc--; - } - } - break; - case ARGV_FUNC: { - int (*handlerProc)(); - - handlerProc = (int (*)())infoPtr->src; - - if ((*handlerProc)(infoPtr->dst, infoPtr->key, - argv[srcIndex])) { - srcIndex += 1; - argc -= 1; - } - break; - } - case ARGV_GENFUNC: { - int (*handlerProc)(); - - handlerProc = (int (*)())infoPtr->src; - - argc = (*handlerProc)(infoPtr->dst, infoPtr->key, - argc, argv+srcIndex); - if (argc < 0) { - return TRUE; - } - break; - } - case ARGV_HELP: - PrintUsage (argTable, flags); - return TRUE; - default: - FPRINTF(stderr, "bad argument type %d in ArgvInfo", - infoPtr->type); - return TRUE; - } - } - - /* - * If we broke out of the loop because of an OPT_REST argument, - * copy the remaining arguments down. - */ - - argsDone: - while (argc) { - argv[dstIndex] = argv[srcIndex]; - srcIndex++; - dstIndex++; - argc--; - } - argv[dstIndex] = (char *) NULL; - *argcPtr = dstIndex; - return FALSE; - - missingArg: - FPRINTF(stderr, "\"%s\" option requires an additional argument\n", curArg); - return TRUE; -} - -/* - *---------------------------------------------------------------------- - * - * PrintUsage -- - * - * Generate a help string describing command-line options. - * - * Results: - * Prints on stderr (unless ARGV_NO_PRINT is specified in flags) - * a help string describing all the options in argTable, plus all those - * in the default table unless ARGV_NO_DEFAULTS is - * specified in flags. - * - * Side effects: - * None. - * - *---------------------------------------------------------------------- - */ - -static void -PrintUsage(argTable, flags) - ArgvInfo *argTable; /* Array of command-specific argument - * descriptions. */ - int flags; /* If the ARGV_NO_DEFAULTS bit is set - * in this word, then don't generate - * information for default options. */ -{ - register ArgvInfo *infoPtr; - int width, i, j, numSpaces; -#define NUM_SPACES 20 - static char spaces[] = " "; -/* char tmp[30]; */ - int nargs; - -/* Macro to optionally print errors */ -#define FPRINTF if (!(flags&ARGV_NO_PRINT)) (void) fprintf - - /* - * First, compute the width of the widest option key, so that we - * can make everything line up. - */ - - width = 4; - for (i = 0; i < 2; i++) { - for (infoPtr = i ? defaultTable : argTable; - infoPtr->type != ARGV_END; infoPtr++) { - int length; - if (infoPtr->key == NULL) { - continue; - } - length = strlen(infoPtr->key); - if (length > width) { - width = length; - } - } - } - - FPRINTF(stderr, "Command-specific options:"); - for (i = 0; ; i++) { - for (infoPtr = i ? defaultTable : argTable; - infoPtr->type != ARGV_END; infoPtr++) { - if ((infoPtr->type == ARGV_HELP) && (infoPtr->key == NULL)) { - FPRINTF(stderr, "\n%s", infoPtr->help); - continue; - } - FPRINTF(stderr, "\n %s:", infoPtr->key); - numSpaces = width + 1 - strlen(infoPtr->key); - while (numSpaces > 0) { - if (numSpaces >= NUM_SPACES) { - FPRINTF(stderr, "%s",spaces); - } else { - FPRINTF(stderr, "%s",spaces+NUM_SPACES-numSpaces); - } - numSpaces -= NUM_SPACES; - } - FPRINTF(stderr, "%s",infoPtr->help); - switch (infoPtr->type) { - case ARGV_INT: { - FPRINTF(stderr, "\n\t\tDefault value:"); - nargs = (int) infoPtr->src; - if (nargs<1) nargs=1; - for (j=0; j<nargs; j++) { - FPRINTF(stderr, " %d", *(((int *) infoPtr->dst)+j)); - } - break; - } - case ARGV_FLOAT: { - FPRINTF(stderr, "\n\t\tDefault value:"); - nargs = (int) infoPtr->src; - if (nargs<1) nargs=1; - for (j=0; j<nargs; j++) { - FPRINTF(stderr, " %g", *(((double *) infoPtr->dst)+j)); - } - break; - } - case ARGV_STRING: { - char *string; - - nargs = (int) infoPtr->src; - if (nargs<1) nargs=1; - string = *((char **) infoPtr->dst); - if ((nargs==1) && (string == NULL)) break; - for (j=0; j<nargs; j++) { - string = *(((char **) infoPtr->dst)+j); - if (string != NULL) { - FPRINTF(stderr, " \"%s\"", string); - } - else { - FPRINTF(stderr, " \"%s\"", string); - } - } - - break; - } - default: { - break; - } - } - } - - if ((flags & ARGV_NO_DEFAULTS) || (i > 0)) { - break; - } - FPRINTF(stderr, "\nGeneric options for all commands:"); - } - - FPRINTF(stderr, "\n"); -}
deleted file mode 100644 --- a/progs/Proglib/ParseArgv.h +++ /dev/null @@ -1,83 +0,0 @@ -/* - * ParseArgv.h -- - * - * Declarations for Tk-related things that are visible - * outside of the Tk module itself. - * - * Copyright 1989-1992 Regents of the University of California. - * Permission to use, copy, modify, and distribute this - * software and its documentation for any purpose and without - * fee is hereby granted, provided that the above copyright - * notice appear in all copies. The University of California - * makes no representations about the suitability of this - * software for any purpose. It is provided "as is" without - * express or implied warranty. - * - * This file has been modified to be used only for argv parsing without - * reference to tk, tcl or X11. Base on tk.h from tk2.3 - * $Header: /private-cvsroot/minc/progs/Proglib/Attic/ParseArgv.h,v 6.0 1997-09-12 13:23:41 neelin Rel $ SPRITE (Berkeley) - */ - -/* - * Definitions that allow this header file to be used either with or - * without ANSI C features like function prototypes. - */ - -#undef _ANSI_ARGS_ -#if ((defined(__STDC__) || defined(SABER)) && !defined(NO_PROTOTYPE)) || defined(__cplusplus) -# define _ANSI_ARGS_(x) x -#else -# define _ANSI_ARGS_(x) () -#endif - -/* - * Structure used to specify how to handle argv options. - */ - -typedef struct { - char *key; /* The key string that flags the option in the - * argv array. */ - int type; /* Indicates option type; see below. */ - char *src; /* Value to be used in setting dst; usage - * depends on type. */ - char *dst; /* Address of value to be modified; usage - * depends on type. */ - char *help; /* Documentation message describing this option. */ -} ArgvInfo; - -/* - * Legal values for the type field of a ArgvInfo: see the user - * documentation for details. - */ - -#define ARGV_CONSTANT 15 -#define ARGV_INT 16 -#define ARGV_STRING 17 -#define ARGV_REST 19 -#define ARGV_FLOAT 20 -#define ARGV_FUNC 21 -#define ARGV_GENFUNC 22 -#define ARGV_HELP 23 -#define ARGV_END 27 - -/* - * Flag bits for passing to ParseArgv: - */ - -#define ARGV_NO_DEFAULTS 0x1 -#define ARGV_NO_LEFTOVERS 0x2 -#define ARGV_NO_ABBREV 0x4 -#define ARGV_DONT_SKIP_FIRST_ARG 0x8 -#define ARGV_NO_PRINT 0x16 - - -/* - *-------------------------------------------------------------- - * - * Exported procedures and variables. - * - *-------------------------------------------------------------- - */ -extern int ParseArgv _ANSI_ARGS_((int *argcPtr, char **argv, - ArgvInfo *argTable, int flags)); -
deleted file mode 100644 --- a/progs/Proglib/ParseArgv.man3 +++ /dev/null @@ -1,499 +0,0 @@ -'\" -'\" Copyright 1990-1992 Regents of the University of California -'\" Permission to use, copy, modify, and distribute this -'\" documentation for any purpose and without fee is hereby -'\" granted, provided that this notice appears in all copies. -'\" The University of California makes no representations about -'\" the suitability of this material for any purpose. It is -'\" provided "as is" without express or implied warranty. -'\" -'\" Modified to be used without tk or tcl (Peter Neelin, November 30,1992) -'\" Based on tk 2.3 file : -'\" $Header: /private-cvsroot/minc/progs/Proglib/Attic/ParseArgv.man3,v 6.4 1999-08-17 13:36:19 neelin Exp $ SPRITE (Berkeley) -'\" -.\" The definitions below are for supplemental macros used in Sprite -.\" manual entries. -.\" -.\" .HS name section [date [version]] -.\" Replacement for .TH in other man pages. See below for valid -.\" section names. -.\" -.\" .AP type name in/out [indent] -.\" Start paragraph describing an argument to a library procedure. -.\" type is type of argument (int, etc.), in/out is either "in", "out", -.\" or "in/out" to describe whether procedure reads or modifies arg, -.\" and indent is equivalent to second arg of .IP (shouldn't ever be -.\" needed; use .AS below instead) -.\" -.\" .AS [type [name]] -.\" Give maximum sizes of arguments for setting tab stops. Type and -.\" name are examples of largest possible arguments that will be passed -.\" to .AP later. If args are omitted, default tab stops are used. -.\" -.\" .BS -.\" Start box enclosure. From here until next .BE, everything will be -.\" enclosed in one large box. -.\" -.\" .BE -.\" End of box enclosure. -.\" -.\" .VS -.\" Begin vertical sidebar, for use in marking newly-changed parts -.\" of man pages. -.\" -.\" .VE -.\" End of vertical sidebar. -.\" -.\" .DS -.\" Begin an indented unfilled display. -.\" -.\" .DE -.\" End of indented unfilled display. -.\" -'\" # Heading for Sprite man pages -.de HS -.if '\\$2'cmds' .TH \\$1 1 \\$3 \\$4 -.if '\\$2'lib' .TH \\$1 3 \\$3 \\$4 -.if '\\$2'tcl' .TH \\$1 3 \\$3 \\$4 -.if '\\$2'tk' .TH \\$1 3 \\$3 \\$4 -.if t .wh -1.3i ^B -.nr ^l \\n(.l -.ad b -.. -'\" # Start an argument description -.de AP -.ie !"\\$4"" .TP \\$4 -.el \{\ -. ie !"\\$2"" .TP \\n()Cu -. el .TP 15 -.\} -.ie !"\\$3"" \{\ -.ta \\n()Au \\n()Bu -\&\\$1 \\fI\\$2\\fP (\\$3) -.\".b -.\} -.el \{\ -.br -.ie !"\\$2"" \{\ -\&\\$1 \\fI\\$2\\fP -.\} -.el \{\ -\&\\fI\\$1\\fP -.\} -.\} -.. -'\" # define tabbing values for .AP -.de AS -.nr )A 10n -.if !"\\$1"" .nr )A \\w'\\$1'u+3n -.nr )B \\n()Au+15n -.\" -.if !"\\$2"" .nr )B \\w'\\$2'u+\\n()Au+3n -.nr )C \\n()Bu+\\w'(in/out)'u+2n -.. -'\" # BS - start boxed text -'\" # ^y = starting y location -'\" # ^b = 1 -.de BS -.br -.mk ^y -.nr ^b 1u -.if n .nf -.if n .ti 0 -.if n \l'\\n(.lu\(ul' -.if n .fi -.. -'\" # BE - end boxed text (draw box now) -.de BE -.nf -.ti 0 -.mk ^t -.ie n \l'\\n(^lu\(ul' -.el \{\ -.\" Draw four-sided box normally, but don't draw top of -.\" box if the box started on an earlier page. -.ie !\\n(^b-1 \{\ -\h'-1.5n'\L'|\\n(^yu-1v'\l'\\n(^lu+3n\(ul'\L'\\n(^tu+1v-\\n(^yu'\l'|0u-1.5n\(ul' -.\} -.el \}\ -\h'-1.5n'\L'|\\n(^yu-1v'\h'\\n(^lu+3n'\L'\\n(^tu+1v-\\n(^yu'\l'|0u-1.5n\(ul' -.\} -.\} -.fi -.br -.nr ^b 0 -.. -'\" # VS - start vertical sidebar -'\" # ^Y = starting y location -'\" # ^v = 1 (for troff; for nroff this doesn't matter) -.de VS -.mk ^Y -.ie n 'mc \s12\(br\s0 -.el .nr ^v 1u -.. -'\" # VE - end of vertical sidebar -.de VE -.ie n 'mc -.el \{\ -.ev 2 -.nf -.ti 0 -.mk ^t -\h'|\\n(^lu+3n'\L'|\\n(^Yu-1v\(bv'\v'\\n(^tu+1v-\\n(^Yu'\h'-|\\n(^lu+3n' -.sp -1 -.fi -.ev -.\} -.nr ^v 0 -.. -'\" # Special macro to handle page bottom: finish off current -'\" # box/sidebar if in box/sidebar mode, then invoked standard -'\" # page bottom macro. -.de ^B -.ev 2 -'ti 0 -'nf -.mk ^t -.if \\n(^b \{\ -.\" Draw three-sided box if this is the box's first page, -.\" draw two sides but no top otherwise. -.ie !\\n(^b-1 \h'-1.5n'\L'|\\n(^yu-1v'\l'\\n(^lu+3n\(ul'\L'\\n(^tu+1v-\\n(^yu'\h'|0u'\c -.el \h'-1.5n'\L'|\\n(^yu-1v'\h'\\n(^lu+3n'\L'\\n(^tu+1v-\\n(^yu'\h'|0u'\c -.\} -.if \\n(^v \{\ -.nr ^x \\n(^tu+1v-\\n(^Yu -\kx\h'-\\nxu'\h'|\\n(^lu+3n'\ky\L'-\\n(^xu'\v'\\n(^xu'\h'|0u'\c -.\} -.bp -'fi -.ev -.if \\n(^b \{\ -.mk ^y -.nr ^b 2 -.\} -.if \\n(^v \{\ -.mk ^Y -.\} -.. -'\" # DS - begin display -.de DS -.RS -.nf -.sp -.. -'\" # DE - end display -.de DE -.fi -.RE -.sp .5 -.. -.HS ParseArgv tk -.BS -.SH NAME -ParseArgv \- process command-line options -.SH SYNOPSIS -\fB#include <ParseArgv.h>\fR -.sp -int -.br -\fBParseArgv\fR(\fIargcPtr, argv, argTable, flags\fR) -.SH ARGUMENTS -.AS ArgvInfo *argTable -.AP int argcPtr in/out -Pointer to number of arguments in argv; gets modified to hold -number of unprocessed arguments that remain after the call. -.AP char **argv in/out -Command line arguments passed to main program. Modified to -hold unprocessed arguments that remain after the call. -.AP ArgvInfo *argTable in -Array of argument descriptors, terminated by element with -type ARGV_END. -.AP int flags in -If non-zero, then it specifies one or more flags that control the -parsing of arguments. Different flags may be OR'ed together. -.na -The flags currently defined are ARGV_DONT_SKIP_FIRST_ARG, -ARGV_NO_ABBREV, ARGV_NO_LEFTOVERS, ARGV_NO_DEFAULTS and ARGV_NO_PRINT. -.ad -.BE -.SH DESCRIPTION -.PP -\fBParseArgv\fR processes an array of command-line arguments according -to a table describing the kinds of arguments that are expected. -Each of the arguments in \fIargv\fR is processed in turn: if it matches -one of the entries in \fIargTable\fR, the argument is processed -according to that entry and discarded. The arguments that do not -match anything in \fIargTable\fR are copied down to the beginning -of \fIargv\fR (retaining their original order) and returned to -the caller. At the end of the call -\fBParseArgv\fR sets \fI*argcPtr\fR to hold the number of -arguments that are left in \fIargv\fR, and \fIargv[*argcPtr]\fR -will hold the value NULL. Normally, \fBParseArgv\fR -assumes that \fIargv[0]\fR is a command name, so it is treated like -an argument that doesn't match \fIargTable\fR and returned to the -caller; however, if the ARGV_DONT_SKIP_FIRST_ARG bit is set in -\fIflags\fR then \fIargv[0]\fR will be processed just like the other -elements of \fIargv\fR. -.PP -\fBParseArgv\fR normally returns the value FALSE (0). If an error -occurs while parsing the arguments, then TRUE (1) is returned and -\fBParseArgv\fR will print an error message on stderr. In -the event of an error return, \fI*argvPtr\fR will not have been -modified, but \fIargv\fR could have been partially modified. The -possible causes of errors are explained below. -.PP -The \fIargTable\fR array specifies the kinds of arguments that are -expected; each of its entries has the following structure: -.DS -.ta 2c -\fBtypedef struct\fR { - \fBchar\fR *\fIkey\fR; - \fBint\fR \fItype\fR; - \fBchar\fR *\fIsrc\fR; - \fBchar\fR *\fIdst\fR; - \fBchar\fR *\fIhelp\fR; -\fB} ArgvInfo;\fR -.DE -.LP -The \fIkey\fR field is a string such as ``\-display'' or ``\-bg'' -that is compared with the values in \fIargv\fR. \fIType\fR -indicates how to process an argument that matches \fIkey\fR -(more on this below). \fISrc\fR and \fIdst\fR are additional -values used in processing the argument. Their exact usage -depends on \fItype\fR, but typically \fIsrc\fR indicates -a value and \fIdst\fR indicates where to store the -value. The \fBchar *\fR declarations for \fIsrc\fR and \fIdst\fR -are placeholders: the actual types may be different. Lastly, -\fIhelp\fR is a string giving a brief description -of this option; this string is printed when users ask for help -about command-line options. -.PP -When processing an argument in \fIargv\fR, \fBParseArgv\fR -compares the argument to each of the \fIkey\fR's in \fIargTable\fR. -\fBParseArgv\fR selects the first specifier whose \fIkey\fR matches -the argument exactly, if such a specifier exists. Otherwise -\fBParseArgv\fR selects a specifier for which the argument -is a unique abbreviation. If the argument is a unique abbreviation -for more than one specifier, then an error is returned. If there -is no matching entry in \fIargTable\fR, then the argument is -skipped and returned to the caller. -.PP -Once a matching argument specifier is found, \fBParseArgv\fR -processes the argument according to the \fItype\fR field of the -specifier. The argument that matched \fIkey\fR is called ``the matching -argument'' in the descriptions below. As part of the processing, -\fBParseArgv\fR may also use the next argument in \fIargv\fR -after the matching argument, which is called ``the following -argument''. The legal values for \fItype\fR, and the processing -that they cause, are as follows: -.TP -\fBARGV_END\fR -Marks the end of the table. The last entry in \fIargTable\fR -must have this type; all of its other fields are ignored and it -will never match any arguments. -.TP -\fBARGV_CONSTANT\fR -\fISrc\fR is treated as an integer and \fIdst\fR is treated -as a pointer to an integer. \fISrc\fR is stored at \fI*dst\fR. -The matching argument is discarded. -.TP -\fBARGV_INT\fR -The following argument must contain an -integer string in the format accepted by \fBstrtol\fR (e.g. ``0'' -and ``0x'' prefixes may be used to specify octal or hexadecimal -numbers, respectively). \fIDst\fR is treated as a pointer to an -integer; the following argument is converted to an integer value -and stored at \fI*dst\fR. \fISrc\fR is treated as an integer count: if -its value is greater than 1, then that many arguments are processed and -\fIDst\fR is treated as an array pointer. The matching -and following arguments are discarded from \fIargv\fR. -.TP -\fBARGV_FLOAT\fR -The following argument must contain a floating-point number in -the format accepted by \fBstrtol\fR. -\fIDst\fR is treated as the address of an double-precision -floating point value; the following argument is converted to a -double-precision value and stored at \fI*dst\fR. \fISrc\fR is treated -as an integer count: if its value is greater than 1, then that many -arguments are processed and -\fIDst\fR is treated as an array pointer. The matching -and following arguments are discarded from \fIargv\fR. -.TP -\fBARGV_STRING\fR -In this form, \fIdst\fR is treated as a pointer to a (char *); -\fBParseArgv\fR stores at \fI*dst\fR a pointer to the following -argument, and discards the matching and following arguments from -\fIargv\fR. \fISrc\fR is treated as an integer count: if -its value is greater than 1, then that many arguments are processed and -\fIDst\fR is treated as an array pointer. -.TP -\fBARGV_HELP\fR -When this kind of option is encountered, \fBParseArgv\fR uses the -\fIhelp\fR fields of \fIargTable\fR to format a message describing -all the valid arguments. The message is written on stderr -and \fBParseArgv\fR returns TRUE. When this happens, the -caller normally aborts. If the \fIkey\fR -field of a ARGV_HELP specifier is NULL, then the specifier will -never match any arguments; in this case the specifier simply provides -extra documentation, which will be included when some other -ARGV_HELP entry causes help information to be returned. -.TP -\fBARGV_REST\fR -This option is used by programs or commands that allow the last -several of their options to be the name and/or options for some -other program. If a \fBARGV_REST\fR argument is found, then -\fBParseArgv\fR doesn't process any -of the remaining arguments; it returns them all at -the beginning of \fIargv\fR (along with any other unprocessed arguments). -In addition, \fBParseArgv\fR treats \fIdst\fR as the address of an -integer value, and stores at \fI*dst\fR the index of the first of the -\fBARGV_REST\fR options in the returned \fIargv\fR. This allows the -program to distinguish the \fBARGV_REST\fR options from other -unprocessed options that preceeded the \fBARGV_REST\fR. -.TP -\fBARGV_FUNC\fR -For this kind of argument, \fIsrc\fR is treated as the address of -a procedure, which is invoked to process the following argument. -The procedure should have the following structure: -.DS -.ta 1c 2c 3c 4c 5c 6c -\fBint\fI -func(dst, key, nextArg) - \fBchar\fR *\fIdst\fR; - \fBchar\fR *\fIkey\fR; - \fBchar\fR *\fInextArg\fR; -{ -} -.DE -.IP -The \fIdst\fR and \fIkey\fR parameters will contain the -corresponding fields from the \fIargTable\fR entry, and -\fInextArg\fR will point to the following argument from \fIargv\fR -(or NULL if there aren't any more arguments left in \fIargv\fR). -If \fIfunc\fR uses \fInextArg\fR (so that -\fBParseArgv\fR should discard it), then it should return 1. Otherwise it -should return 0 and \fBTkParseArgv\fR will process the following -argument in the normal fashion. In either event the matching argument -is discarded. -.TP -\fBARGV_GENFUNC\fR -This form provides a more general procedural escape. It treats -\fIsrc\fR as the address of a procedure, and passes that procedure -all of the remaining arguments. The procedure should have the following -form: -.DS -.ta 1c 2c 3c 4c 5c 6c -\fBint\fI -genfunc(dst, key, argc, argv) - \fBchar\fR *\fIdst\fR; - \fBchar\fR *\fIkey\fR; - \fBint\fR \fIargc\fR; - \fBchar\fR **\fIargv\fR; -{ -} -.DE -.IP -The \fIdst\fR and \fIkey\fR parameters will contain the -corresponding fields from the \fIargTable\fR entry. -\fIArgc\fR and \fIargv\fR refer to all of the options after the -matching one. \fIGenfunc\fR should behave in a fashion similar -to \fBParseArgv\fR: parse as many of the remaining arguments as it can, -then return any that are left by compacting them to the beginning of -\fIargv\fR (starting at \fIargv\fR[0]). \fIGenfunc\fR -should return a count of how many arguments are left in \fIargv\fR; -\fBParseArgv\fR will process them. If \fIgenfunc\fR encounters -an error then it should print an error message on stderr, -and return -1; when this happens -\fBParseArgv\fR will abort its processing and return TRUE. - -.SH "FLAGS" -.IP \fBARGV_DONT_SKIP_FIRST_ARG\fR -\fBParseArgv\fR normally treats \fIargv[0]\fR as a program -or command name, and returns it to the caller just as if it -hadn't matched \fIargTable\fR. If this flag is given, then -\fIargv[0]\fR is not given special treatment. -.IP \fBARGV_NO_ABBREV\fR -Normally, \fBParseArgv\fR accepts unique abbreviations for -\fIkey\fR values in \fIargTable\fR. If this flag is given then -only exact matches will be acceptable. -.IP \fBARGV_NO_LEFTOVERS\fR -Normally, \fBParseArgv\fR returns unrecognized arguments to the -caller. If this bit is set in \fIflags\fR then \fBParseArgv\fR -will return an error if it encounters any argument that doesn't -match \fIargTable\fR. The only exception to this rule is \fIargv[0]\fR, -which will be returned to the caller with no errors as -long as ARGV_DONT_SKIP_FIRST_ARG isn't specified. -.IP \fBARGV_NO_DEFAULTS\fR -Normally, \fBParseArgv\fR searches an internal table of -standard argument specifiers in addition to \fIargTable\fR. If -this bit is set in \fIflags\fR, then \fBParseArgv\fR will -use only \fIargTable\fR and not its default table. -.IP \fBARGV_NO_PRINT\fR -Normally, \fBParseArgv\fR prints error message on stderr. If -this bit is set in \fIflags\fR, then \fBParseArgv\fR will -not print any error messages. - -.SH EXAMPLE -.PP -Here is an example definition of an \fIargTable\fR and -some sample command lines that use the options. Note the effect -on \fIargc\fR and \fIargv\fR; arguments processed by \fBParseArgv\fR -are eliminated from \fIargv\fR, and \fIargc\fR -is updated to reflect reduced number of arguments. -.DS L -\fC/* - * Define and set default values for globals. - */ -int debugFlag = 0; -int numReps = 100; -char defaultFileName[] = "out"; -char *fileName = defaultFileName; -Boolean exec = FALSE; - -/* - * Define option descriptions. - */ -ArgvInfo argTable[] = { - {"-X", ARGV_CONSTANT, (char *) 1, (char *) &debugFlag, - "Turn on debugging printfs"}, - {"-N", ARGV_INT, (char *) NULL, (char *) &numReps, - "Number of repetitions"}, - {"-of", ARGV_STRING, (char *) NULL, (char *) &fileName, - "Name of file for output"}, - {"x", ARGV_REST, (char *) NULL, (char *) &exec, - "File to exec, followed by any arguments (must be last argument)."}, - {(char *) NULL, ARGV_END, (char *) NULL, (char *) NULL, - (char *) NULL} -}; - -main(argc, argv) - int argc; - char *argv[]; -{ - \&... - - if (ParseArgv(&argc, argv, argTable, 0)) { - exit(1); - } - - /* - * Remainder of the program. - */ -}\fR -.DE -.PP -Note that default values can be assigned to variables named in -\fIargTable\fR: the variables will only be overwritten if the -particular arguments are present in \fIargv\fR. -Here are some example command lines and their effects. -.DS -\fCprog -N 200 infile # just sets the numReps variable to 200 -prog -of out200 infile # sets fileName to reference "out200" -prog -XN 10 infile # sets the debug flag, also sets numReps\fR -.DE -In all of the above examples, \fIargc\fR will be set by \fBParseArgv\fR to 2, -\fIargv\fR[0] will be ``prog'', \fIargv\fR[1] will be ``infile'', -and \fIargv\fR[2] will be NULL. - -.SH KEYWORDS -arguments, command line, options
deleted file mode 100644 --- a/progs/Proglib/nd_loop.c +++ /dev/null @@ -1,164 +0,0 @@ -/* ----------------------------- MNI Header ----------------------------------- -@NAME : nd_loop.c -@DESCRIPTION: File containing routines for doing n-dimensional looping -@METHOD : -@GLOBALS : -@CREATED : March 10, 1994 (Peter Neelin) -@MODIFIED : - * $Log: nd_loop.c,v $ - * Revision 6.1 1999-10-19 14:45:13 neelin - * Fixed Log subsitutions for CVS - * - * Revision 6.0 1997/09/12 13:23:41 neelin - * Release of minc version 0.6 - * - * Revision 5.0 1997/08/21 13:24:41 neelin - * Release of minc version 0.5 - * - * Revision 4.0 1997/05/07 20:00:50 neelin - * Release of minc version 0.4 - * - * Revision 3.0 1995/05/15 19:31:35 neelin - * Release of minc version 0.3 - * - * Revision 1.3 1995/02/08 19:31:47 neelin - * Moved ARGSUSED statements for irix 5 lint. - * - * Revision 1.2 1994/12/02 09:19:59 neelin - * Added comments to clarify use of routines. - * - * Revision 1.1 94/12/02 08:40:12 neelin - * Initial revision - * -@COPYRIGHT : - Copyright 1994 Peter Neelin, McConnell Brain Imaging Centre, - Montreal Neurological Institute, McGill University. - Permission to use, copy, modify, and distribute this - software and its documentation for any purpose and without - fee is hereby granted, provided that the above copyright - notice appear in all copies. The author and McGill University - make no representations about the suitability of this - software for any purpose. It is provided "as is" without - express or implied warranty. ----------------------------------------------------------------------------- */ - -#ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/Proglib/Attic/nd_loop.c,v 6.1 1999-10-19 14:45:13 neelin Exp $"; -#endif - -#include <stdlib.h> -#include <stdio.h> - -/* Constant definition */ -#define public - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : nd_begin_looping -@INPUT : start - vector of indices specifying starting subscript - for each dimension - ndims - number of dimensions in vector -@OUTPUT : current - vector of indices giving current subscript -@RETURNS : (none) -@DESCRIPTION: Sets up current variable for looping -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : October 28, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void nd_begin_looping(long start[], long current[], int ndims) -{ - int idim; - - for (idim=0; idim < ndims; idim++) { - current[idim] = start[idim]; - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : nd_end_of_loop -@INPUT : current - vector of indices giving current subscript - end - vector of indices specifying last subscripts plus one - ndims - number of dimensions in vector -@OUTPUT : (none) -@RETURNS : TRUE if end of loop. -@DESCRIPTION: Tests for end of a multi-dimensional loop. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 10, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public int nd_end_of_loop(long current[], long end[], int ndims) - /* ARGSUSED */ -{ - return (current[0] >= end[0]); -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : nd_update_current_count -@INPUT : current - vector of indices giving current subscript - increment - vector of indices specifying increment - for each dimension - end - vector of indices specifying last subscripts plus one - ndims - number of dimensions in vector -@OUTPUT : current_count - vector of indices giving count for current - position -@RETURNS : (none) -@DESCRIPTION: Sets the count so that we don't go past end -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : October 28, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void nd_update_current_count(long current[], - long increment[], long end[], - long current_count[], - int ndims) -{ - int idim; - - for (idim=0; idim < ndims; idim++) { - current_count[idim] = increment[idim]; - if ((current[idim] + current_count[idim]) > end[idim]) { - current_count[idim] = end[idim] - current[idim]; - } - } - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : nd_increment_loop -@INPUT : current - vector of indices giving current subscript - start - vector of indices specifying starting subscript - for each dimension - increment - vector of indices specifying increment - for each dimension - end - vector of indices specifying last subscripts plus one - ndims - number of dimensions in vector -@OUTPUT : current - vector of indices giving new subscript -@RETURNS : (none) -@DESCRIPTION: Does incrementing for multi-dimensional loop -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 10, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void nd_increment_loop(long current[], - long start[], long increment[], long end[], - int ndims) -{ - int idim; - - idim = ndims-1; - current[idim] += increment[idim]; - while ( (idim>0) && (current[idim] >= end[idim])) { - current[idim] = start[idim]; - idim--; - current[idim] += increment[idim]; - } - -} -
deleted file mode 100644 --- a/progs/Proglib/nd_loop.h +++ /dev/null @@ -1,66 +0,0 @@ -/* ----------------------------- MNI Header ----------------------------------- -@NAME : nd_loop.h -@DESCRIPTION: Header file for nd_loop.c -@METHOD : Use these routines in the following way: - - Set start, end and increment vectors to define looping; - - nd_begin_looping(start, current, ndims); - while (!nd_end_of_loop(current, end, ndims)) { - nd_update_current_count(current, increment, end, - current_count, ndims); - - Use current and current_count to work on hyperslab; - - nd_increment_loop(current, start, increment, end, ndims); - } - -@GLOBALS : -@CREATED : December 2, 1994 (Peter Neelin) -@MODIFIED : - * $Log: nd_loop.h,v $ - * Revision 6.1 1999-10-19 14:45:14 neelin - * Fixed Log subsitutions for CVS - * - * Revision 6.0 1997/09/12 13:23:41 neelin - * Release of minc version 0.6 - * - * Revision 5.0 1997/08/21 13:24:41 neelin - * Release of minc version 0.5 - * - * Revision 4.0 1997/05/07 20:00:50 neelin - * Release of minc version 0.4 - * - * Revision 3.0 1995/05/15 19:31:35 neelin - * Release of minc version 0.3 - * - * Revision 1.3 1994/12/02 09:40:37 neelin - * Fixed arguments to nd_end_of_loop. - * - * Revision 1.2 94/12/02 09:20:17 neelin - * Added comments to clarify use of routines. - * - * Revision 1.1 94/12/02 08:40:31 neelin - * Initial revision - * -@COPYRIGHT : - Copyright 1994 Peter Neelin, McConnell Brain Imaging Centre, - Montreal Neurological Institute, McGill University. - Permission to use, copy, modify, and distribute this - software and its documentation for any purpose and without - fee is hereby granted, provided that the above copyright - notice appear in all copies. The author and McGill University - make no representations about the suitability of this - software for any purpose. It is provided "as is" without - express or implied warranty. ----------------------------------------------------------------------------- */ - -public void nd_begin_looping(long start[], long current[], int ndims); -public int nd_end_of_loop(long current[], long end[], int ndims); -public void nd_update_current_count(long current[], - long increment[], long end[], - long current_count[], - int ndims); -public void nd_increment_loop(long current[], - long start[], long increment[], long end[], - int ndims);
deleted file mode 100644 --- a/progs/Proglib/time_stamp.c +++ /dev/null @@ -1,109 +0,0 @@ -/* ----------------------------- MNI Header ----------------------------------- -@NAME : time_stamp.c -@DESCRIPTION: File containing routine to create a time stamp string. -@METHOD : -@CREATED : February 1, 1993 (Peter Neelin) -@MODIFIED : - * $Log: time_stamp.c,v $ - * Revision 6.2 1999-10-19 15:57:18 neelin - * Fixed log message containing log substitution - * - * Revision 6.1 1999/10/19 14:45:14 neelin - * Fixed Log subsitutions for CVS - * - * Revision 6.0 1997/09/12 13:23:41 neelin - * Release of minc version 0.6 - * - * Revision 5.0 1997/08/21 13:24:41 neelin - * Release of minc version 0.5 - * - * Revision 4.0 1997/05/07 20:00:50 neelin - * Release of minc version 0.4 - * - * Revision 3.0 1995/05/15 19:31:35 neelin - * Release of minc version 0.3 - * - * Revision 2.0 1994/09/28 10:34:30 neelin - * Release of minc version 0.2 - * - * Revision 1.4 94/09/28 10:34:20 neelin - * Pre-release - * - * Revision 1.3 93/08/04 13:03:56 neelin - * Added RCS Log to keep track of modifications in source - * -@COPYRIGHT : - Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre, - Montreal Neurological Institute, McGill University. - Permission to use, copy, modify, and distribute this - software and its documentation for any purpose and without - fee is hereby granted, provided that the above copyright - notice appear in all copies. The author and McGill University - make no representations about the suitability of this - software for any purpose. It is provided "as is" without - express or implied warranty. ----------------------------------------------------------------------------- */ -#include <stdlib.h> -#include <string.h> -#include <time.h> - -#include <time_stamp.h> - -#ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/Proglib/Attic/time_stamp.c,v 6.2 1999-10-19 15:57:18 neelin Exp $"; -#endif - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : time_stamp -@INPUT : argc - number of arguments - argv - list of arguments -@OUTPUT : -@RETURNS : pointer to string containing time stamp. -@DESCRIPTION: Function to produce a time stamp string for a program. - Returns a string of the form "date > command". The command - is simply the concatenation of argv elements. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : February 1, 1993 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -char *time_stamp(int argc, char *argv[]) -{ - char *str, *the_time; - int length, i, last; - static char separator[]={">>>"}; - time_t timer; - - /* Get the time, overwriting newline */ - timer = time(NULL); - the_time = ctime(&timer); - - /* Get the total length of the string and allocate space */ - length=strlen(the_time) + strlen(separator) + 2; - for(i=0; i<argc; i++) { - length += strlen(argv[i]) + 1; - } - str = malloc(length); - - /* Copy the time and separator */ - (void) strcpy(str, the_time); - str[strlen(str)-1]='\0'; - (void) strcat(str, separator); - - /* Copy the program name and arguments */ - for (i=0; i<argc; i++) { - last = strlen(str); - str[last]=' '; - str[last+1]='\0'; - (void) strcat(str, argv[i]); - } - - /* Add a terminating newline */ - last = strlen(str); - str[last]='\n'; - str[last+1]='\0'; - - - return str; -}
deleted file mode 100644 --- a/progs/Proglib/time_stamp.h +++ /dev/null @@ -1,48 +0,0 @@ -/* ----------------------------- MNI Header ----------------------------------- -@NAME : time_stamp.h -@DESCRIPTION: Header file for time_stamp.c -@GLOBALS : -@CREATED : February 1, 1993 (Peter Neelin) -@MODIFIED : - * $Log: time_stamp.h,v $ - * Revision 6.2 1999-10-19 15:57:18 neelin - * Fixed log message containing log substitution - * - * Revision 6.1 1999/10/19 14:45:14 neelin - * Fixed Log subsitutions for CVS - * - * Revision 6.0 1997/09/12 13:23:41 neelin - * Release of minc version 0.6 - * - * Revision 5.0 1997/08/21 13:24:41 neelin - * Release of minc version 0.5 - * - * Revision 4.0 1997/05/07 20:00:50 neelin - * Release of minc version 0.4 - * - * Revision 3.0 1995/05/15 19:31:35 neelin - * Release of minc version 0.3 - * - * Revision 2.0 1994/09/28 10:34:31 neelin - * Release of minc version 0.2 - * - * Revision 1.4 94/09/28 10:34:20 neelin - * Pre-release - * - * Revision 1.3 93/08/04 13:04:00 neelin - * Added RCS Log to keep track of modifications in source - * -@COPYRIGHT : - Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre, - Montreal Neurological Institute, McGill University. - Permission to use, copy, modify, and distribute this - software and its documentation for any purpose and without - fee is hereby granted, provided that the above copyright - notice appear in all copies. The author and McGill University - make no representations about the suitability of this - software for any purpose. It is provided "as is" without - express or implied warranty. ----------------------------------------------------------------------------- */ - -char *time_stamp(int argc, char *argv[]); -
deleted file mode 100644 --- a/progs/Proglib/voxel_loop.c +++ /dev/null @@ -1,3411 +0,0 @@ -/* ----------------------------- MNI Header ----------------------------------- -@NAME : voxel_loop.c -@DESCRIPTION: Routines to loop through a file doing an operation on a single - voxel. -@METHOD : -@GLOBALS : -@CREATED : January 10, 1994 (Peter Neelin) -@MODIFIED : - * $Log: voxel_loop.c,v $ - * Revision 6.9 2002-01-14 20:02:39 neelin - * Force the input buffers to have a minimum size so that large images do - * not force excessive reading of the input file. - * - * Revision 6.8 2001/11/28 18:39:16 neelin - * Added get_info_vxoel_index to allow users to get the full multi-dimensional - * file index of the current voxel. - * Modifications to allow arg_string to be NULL. - * - * Revision 6.7 2001/09/18 15:32:27 neelin - * Create image variable last to allow big images and to fix compatibility - * problems with 2.3 and 3.x. - * - * Revision 6.6 2001/08/16 16:41:32 neelin - * Added library functions to handle reading of datatype, sign and valid range, - * plus writing of valid range and setting of default ranges. These functions - * properly handle differences between valid_range type and image type. Such - * difference can cause valid data to appear as invalid when double to float - * conversion causes rounding in the wrong direction (out of range). - * Modified voxel_loop, volume_io and programs to use these functions. - * - * Revision 6.5 2001/08/16 13:32:27 neelin - * Partial fix for valid_range of different type from image (problems - * arising from double to float conversion/rounding). NOT COMPLETE. - * - * Revision 6.4 2001/04/24 13:38:40 neelin - * Replaced NC_NAT with MI_ORIGINAL_TYPE. - * - * Revision 6.3 2001/04/17 18:40:15 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. - * A few fixes to the configure script. - * - * Revision 6.2 2000/09/19 14:36:05 neelin - * Added ability for caller to specify functions for allocating and freeing - * voxel buffers used in loop. This is particularly useful for embedding - * the voxel_loop code in other programs, such as Python, which manage memory - * in their own way. - * - * Revision 6.1 1999/10/19 14:45:15 neelin - * Fixed Log subsitutions for CVS - * - * Revision 6.0 1997/09/12 13:23:41 neelin - * Release of minc version 0.6 - * - * Revision 5.0 1997/08/21 13:24:41 neelin - * Release of minc version 0.5 - * - * Revision 4.2 1997/06/20 13:58:35 neelin - * Fixed bug: when doing accumulation with no output file and with - * 4D input (or more), had problem setting input start vector. This broke - * mincconcat for 4D input files. - * - * Revision 4.1 1997/05/22 12:41:40 neelin - * Loosened up checking of start coordinates so that we look at error - * relative to the total extent of the volume (nelements*step) instead of - * relative to start value (which may be close to zero). - * - * Revision 4.0 1997/05/07 20:00:50 neelin - * Release of minc version 0.4 - * - * Revision 3.0 1995/05/15 19:31:35 neelin - * Release of minc version 0.3 - * - * Revision 1.6 1995/05/11 12:31:29 neelin - * Removed error messages from ncattdel. - * - * Revision 1.5 1995/05/02 16:05:32 neelin - * Fixed bug in handling more than 30 files (needed to detach from icv). - * Added more checking of dimensions. - * Fixed bug in allocation of space for global max/min. - * - * Revision 1.4 1995/05/01 20:04:50 neelin - * Fixed memory leak - not freeing global_minimum/maximum. - * - * Revision 1.3 1995/03/21 15:33:07 neelin - * Changed call to voxel_function to always use proper vector length and - * set num_voxels to the number of voxels, not multiplying by vector length. - * - * Revision 1.2 1995/03/21 14:06:39 neelin - * Improved interface and added lots of functionality (much for the benefit - * of mincconcat). - * - * Revision 1.1 94/12/14 10:17:19 neelin - * Initial revision - * -@COPYRIGHT : - Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre, - Montreal Neurological Institute, McGill University. - Permission to use, copy, modify, and distribute this - software and its documentation for any purpose and without - fee is hereby granted, provided that the above copyright - notice appear in all copies. The author and McGill University - make no representations about the suitability of this - software for any purpose. It is provided "as is" without - express or implied warranty. ----------------------------------------------------------------------------- */ - -#ifndef lint -static char rcsid[]="$Header: /private-cvsroot/minc/progs/Proglib/Attic/voxel_loop.c,v 6.9 2002-01-14 20:02:39 neelin Exp $"; -#endif - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> -#include <float.h> -#include <minc.h> -#include <minc_def.h> -#include <voxel_loop.h> -#include <nd_loop.h> - -#ifndef TRUE -# define TRUE 1 -# define FALSE 0 -#endif - -/* Minimum number of voxels to put in a buffer. If this is too small, - then for large images excessive reading can result. If it is - too large, then for large images too much memory will be used. */ -#define MIN_VOXELS_IN_BUFFER 1024 - -/* Default ncopts values for error handling */ -#define NC_OPTS_VAL NC_VERBOSE | NC_FATAL - -/* Epsilon for coordinate comparisons */ -#define COORD_EPSILON FLT_EPSILON * 10.0 - -/* Macros */ -#define ABS(x) ( ((x) > (0)) ? (x) : (-(x))) - -/* Typedefs */ -typedef struct Loopfile_Info Loopfile_Info; - -/* Structure definitions */ -struct Loop_Info { - int current_file; - int current_index; - long start[MAX_VAR_DIMS]; - long count[MAX_VAR_DIMS]; - long dimvoxels[MAX_VAR_DIMS]; /* Number of voxels skipped by a step - of one in each dimension */ - Loopfile_Info *loopfile_info; -}; - -struct Loop_Options { - int verbose; - int clobber; - nc_type datatype; - int is_signed; - double valid_range[2]; - int max_open_files; - int check_all_input_dim_info; - int convert_input_to_scalar; - int output_vector_size; /* 0 = same as input size */ - int input_mincid; - long total_copy_space; - char *loop_dimension; - int num_all_inputs; - VoxelInputFileFunction input_file_function; - VoxelOutputFileFunction output_file_function; - int copy_all_header_info; - int do_accumulate; - int num_extra_buffers; - VoxelStartFunction start_function; - VoxelFinishFunction finish_function; - VoxelFunction voxel_function; - void *caller_data; - Loop_Info *loop_info; - int is_floating_type; - AllocateBufferFunction allocate_buffer_function; -}; - -struct Loopfile_Info { - int clobber_output; - int num_input_files; - int num_output_files; - char **input_files; - char **output_files; - int input_all_open; - int output_all_open; - int *input_mincid; - int *output_mincid; - int *input_icvid; - int *output_icvid; - int current_input_file_number; - int current_output_file_number; - int headers_only; - int want_headers_only; - int sequential_access; - int can_open_all_input; -}; - -/* Function prototypes */ -private int get_loop_dim_size(int inmincid, Loop_Options *loop_options); -private void translate_input_coords(int inmincid, - long chunk_cur[], long input_cur[], - long chunk_curcount[], - long input_curcount[], - int *loop_dim_index, - Loop_Options *loop_options); -private void check_input_files(Loop_Options *loop_options, - Loopfile_Info *loopfile_info); -private int input_image_varinq(int mincid, int imgid, char *name, - nc_type *datatype, int *ndims, int dim[], - int *natts, Loop_Options *loop_options); -private void get_dim_info(int mincid, int *ndims, long size[], - char dimname[][MAX_NC_NAME], - double start[], double step[], - double dircos[][3], int is_regular[], - Loop_Options *loop_options); -private void setup_output_files(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - char *arg_string); -private long get_vector_length(int mincid, Loop_Options *loop_options); -private void setup_variables(int inmincid, int outmincid, - int output_curfile, - char *arg_string, Loop_Options *loop_options); -private void update_history(int mincid, char *arg_string); -private void setup_icvs(Loop_Options *loop_options, - Loopfile_Info *loopfile_info); -private void do_voxel_loop(Loop_Options *loop_options, - Loopfile_Info *loopfile_info); -private void setup_looping(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int *ndims, - long block_start[], long block_end[], - long block_incr[], long *block_num_voxels, - long chunk_incr[], long *chunk_num_voxels); -private void initialize_file_and_index(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int do_loop, - int *ifile, int *dim_index, - int *dummy_index); -private int finish_file_and_index(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int do_loop, - int ifile, int dim_index, - int dummy_index); -private void increment_file_and_index(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int do_loop, - int *ifile, int *dim_index, - int *dummy_index); -private Loopfile_Info *initialize_loopfile_info(int num_input_files, - char *input_files[], - int num_output_files, - char *output_files[], - Loop_Options *loop_options); -private void cleanup_loopfile_info(Loopfile_Info *loopfile_info); -private int get_input_numfiles(Loopfile_Info *loopfile_info); -private int get_output_numfiles(Loopfile_Info *loopfile_info); -private char *get_input_filename(Loopfile_Info *loopfile_info, int file_num); -private char *get_output_filename(Loopfile_Info *loopfile_info, int file_num); -private void set_input_headers_only(Loopfile_Info *loopfile_info, - int headers_only); -private void set_input_sequential(Loopfile_Info *loopfile_info, - int sequential_access); -private int get_input_mincid(Loopfile_Info *loopfile_info, - int file_num); -private int get_output_mincid(Loopfile_Info *loopfile_info, - int file_num); -private int create_output_file(Loopfile_Info *loopfile_info, - int file_num); -private int get_input_icvid(Loopfile_Info *loopfile_info, - int file_num); -private int get_output_icvid(Loopfile_Info *loopfile_info, - int file_num); -private int create_input_icvid(Loopfile_Info *loopfile_info, - int file_num); -private int create_output_icvid(Loopfile_Info *loopfile_info, - int file_num); -private Loop_Info *create_loop_info(void); -private void initialize_loop_info(Loop_Info *loop_info); -private void free_loop_info(Loop_Info *loop_info); -private void set_info_shape(Loop_Info *loop_info, long start[], long count[]); -private void set_info_current_file(Loop_Info *loop_info, int current_file); -private void set_info_current_index(Loop_Info *loop_info, int current_index); -private void set_info_loopfile_info(Loop_Info *loop_info, - Loopfile_Info *loopfile_info); - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : voxel_loop -@INPUT : num_input_files - number of input files. - input_files - array of names of input files. - num_output_files - number of output files. - output_files - array of names of output files. - arg_string - string for history. - loop_options - pointer to structure containing loop options. - voxel_function - user function to process a group of voxels. - See description in header file. - caller_data - data that will be passed to voxel_function -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to loop through the voxels of a file and call a function - to operate on each voxel. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 10, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void voxel_loop(int num_input_files, char *input_files[], - int num_output_files, char *output_files[], - char *arg_string, - Loop_Options *loop_options, - VoxelFunction voxel_function, void *caller_data) -{ - Loopfile_Info *loopfile_info; - int need_to_free_loop_options; - int old_ncopts; - - /* Save ncopts and set it to default value */ - old_ncopts = ncopts; - ncopts = NC_OPTS_VAL; - - /* Check that there is at least one input file */ - if (num_input_files < 1) { - (void) fprintf(stderr, "There must be at least one input file.\n"); - exit(EXIT_FAILURE); - } - if (num_output_files < 0) { - (void) fprintf(stderr, "Negative number of output files!\n"); - exit(EXIT_FAILURE); - } - - /* Initialize loop options if needed */ - need_to_free_loop_options = FALSE; - if (loop_options == NULL) { - loop_options = create_loop_options(); - need_to_free_loop_options = TRUE; - } - loop_options->voxel_function = voxel_function; - loop_options->caller_data = caller_data; - - /* Make sure that Loop_Info structure is initialized */ - initialize_loop_info(loop_options->loop_info); - - /* Initialize looping info */ - loopfile_info = initialize_loopfile_info(num_input_files, input_files, - num_output_files, output_files, - loop_options); - - /* Check that input files match */ - set_input_headers_only(loopfile_info, TRUE); - check_input_files(loop_options, loopfile_info); - set_input_headers_only(loopfile_info, FALSE); - - /* Set up variables in output file */ - setup_output_files(loop_options, loopfile_info, arg_string); - - /* Setup icv's */ - setup_icvs(loop_options, loopfile_info); - - /* Loop through the voxels */ - do_voxel_loop(loop_options, loopfile_info); - - /* Clean up looping info */ - cleanup_loopfile_info(loopfile_info); - - /* Free loop options if needed */ - if (need_to_free_loop_options) { - free_loop_options(loop_options); - } - - /* Restore ncopts */ - ncopts = old_ncopts; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_loop_dim_size -@INPUT : inmincid - input minc id - loop_options - Options for loops -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to get the size of the looping dimension for the given - input file -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 24, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int get_loop_dim_size(int inmincid, Loop_Options *loop_options) -{ - int dimid; - long dim_length; - int ndims, dim[MAX_VAR_DIMS]; - int found; - int idim; - - /* Look for dimension */ - dimid = MI_ERROR; - if (loop_options->loop_dimension != NULL) { - ncopts = 0; - dimid = ncdimid(inmincid, loop_options->loop_dimension); - ncopts = NC_OPTS_VAL; - } - if (dimid == MI_ERROR) return 1; - (void) ncdiminq(inmincid, dimid, NULL, &dim_length); - - /* Get image variable info */ - (void) ncvarinq(inmincid, ncvarid(inmincid, MIimage), NULL, NULL, - &ndims, dim, NULL); - - /* Check to see if the dimension subscripts the image */ - found = FALSE; - for (idim=0; idim < ndims; idim++) { - if (dimid == dim[idim]) found = TRUE; - } - - /* Return appropriate value */ - if (found) - return dim_length; - else - return 1; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : translate_input_coords -@INPUT : inmincid - input minc id - chunk_cur - start for current chunk - chunk_curcount - count for current chunk - loop_options - Options for loops -@OUTPUT : input_cur - start for input file - input_curcount - count for input file - loop_dim_index - index in input_cur for looping dimension -@RETURNS : (nothing) -@DESCRIPTION: Routine to translate the input hyperslab coords from those - excluding the looping dimension to ones appropriate for the - input file. Also returns the index (offset in input_cur) for - the looping dimension (so that the caller can modify this - index). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 24, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void translate_input_coords(int inmincid, - long chunk_cur[], long input_cur[], - long chunk_curcount[], - long input_curcount[], - int *loop_dim_index, - Loop_Options *loop_options) -{ - int dimid; - int ndims, dim[MAX_VAR_DIMS]; - int idim, jdim; - - /* Look for dimension */ - dimid = MI_ERROR; - if (loop_options->loop_dimension != NULL) { - ncopts = 0; - dimid = ncdimid(inmincid, loop_options->loop_dimension); - ncopts = NC_OPTS_VAL; - } - - /* Get image variable info */ - (void) ncvarinq(inmincid, ncvarid(inmincid, MIimage), NULL, NULL, - &ndims, dim, NULL); - - /* Copy the hyperslab coordinates and get the index */ - *loop_dim_index = ndims; - jdim = 0; - for (idim=0; idim < ndims; idim++) { - if (dimid != dim[idim]) { - input_cur[idim] = chunk_cur[jdim]; - input_curcount[idim] = chunk_curcount[jdim]; - jdim++; - } - else { - input_cur[idim] = 0; - input_curcount[idim] = 1; - *loop_dim_index = idim; - } - } - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : check_input_files -@INPUT : loop_options - Options for loops - loopfile_info - Information describing looping stuff and files -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to check input files for consistency. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void check_input_files(Loop_Options *loop_options, - Loopfile_Info *loopfile_info) -{ - int ifile, idim, jdim; - int first_ndims, ndims; - int input_mincid; - long first_size[MAX_VAR_DIMS], size[MAX_VAR_DIMS]; - char first_dimname[MAX_VAR_DIMS][MAX_NC_NAME]; - char dimname[MAX_VAR_DIMS][MAX_NC_NAME]; - double extent; - double first_start[MAX_VAR_DIMS], start[MAX_VAR_DIMS]; - double first_step[MAX_VAR_DIMS], step[MAX_VAR_DIMS]; - double start_diff, step_diff; - double first_dircos[MAX_VAR_DIMS][3], dircos[MAX_VAR_DIMS][3]; - double dircos_diff, dircos_cumdiff; - int first_is_regular[MAX_VAR_DIMS], is_regular[MAX_VAR_DIMS]; - - /* Keep track of number of inputs (files and looping dimension) */ - loop_options->num_all_inputs = 0; - - /* Loop over files. For the first file, we only get the dimension info, - we don't check it. */ - for (ifile = 0; ifile < get_input_numfiles(loopfile_info); ifile++) { - - /* Get mincid */ - input_mincid = get_input_mincid(loopfile_info, ifile); - - /* Add up number of inputs */ - loop_options->num_all_inputs += - get_loop_dim_size(input_mincid, loop_options); - - /* Get dimension information for this file */ - if (ifile == 0) { - get_dim_info(input_mincid, &first_ndims, first_size, first_dimname, - first_start, first_step, first_dircos, - first_is_regular, loop_options); - } - else { - get_dim_info(input_mincid, &ndims, size, dimname, start, step, - dircos, is_regular, loop_options); - - /* Check number of dimensions */ - if (ndims != first_ndims) { - (void) fprintf(stderr, - "Files %s and %s have different numbers of dimensions\n", - get_input_filename(loopfile_info,ifile), - get_input_filename(loopfile_info,0)); - exit(EXIT_FAILURE); - } - - /* Loop over dimensions */ - for (idim = 0; idim < first_ndims; idim++) { - - /* Check dimension sizes */ - if (size[idim] != first_size[idim]) { - (void) fprintf(stderr, - "Files %s and %s have different sizes of dimensions\n", - get_input_filename(loopfile_info,ifile), - get_input_filename(loopfile_info,0)); - exit(EXIT_FAILURE); - } - - /* Check optional dimension stuff */ - if (loop_options->check_all_input_dim_info) { - - /* Check names */ - if (strcmp(dimname[idim], first_dimname[idim]) != 0) { - (void) fprintf(stderr, - "Files %s and %s have different dimension names\n", - get_input_filename(loopfile_info,ifile), - get_input_filename(loopfile_info,0)); - exit(EXIT_FAILURE); - } - - /* Check coordinates */ - start_diff = start[idim] - first_start[idim]; - extent = ((double) first_size[idim]) * first_step[idim]; - if (extent != 0.0) start_diff /= extent; - step_diff = step[idim] - first_step[idim]; - if (first_step[idim] != 0.0) step_diff /= first_step[idim]; - dircos_cumdiff = 0.0; - for (jdim=0; jdim < 3; jdim++) { - dircos_diff = first_dircos[idim][jdim] - dircos[idim][jdim]; - if (first_dircos[idim][jdim] != 0.0) - dircos_diff /= first_dircos[idim][jdim]; - dircos_cumdiff += ABS(dircos_diff); - } - if (ABS(start_diff) > COORD_EPSILON) { - (void) fprintf(stderr, - "Files %s and %s have different start coordinates (%s)\n", - get_input_filename(loopfile_info,ifile), - get_input_filename(loopfile_info,0), - first_dimname[idim]); - exit(EXIT_FAILURE); - } - if (ABS(step_diff) > COORD_EPSILON) { - (void) fprintf(stderr, - "Files %s and %s have different step coordinates (%s)\n", - get_input_filename(loopfile_info,ifile), - get_input_filename(loopfile_info,0), - first_dimname[idim]); - exit(EXIT_FAILURE); - } - if (dircos_cumdiff > COORD_EPSILON) { - (void) fprintf(stderr, - "Files %s and %s have different direction cosines (%s)\n", - get_input_filename(loopfile_info,ifile), - get_input_filename(loopfile_info,0), - first_dimname[idim]); - exit(EXIT_FAILURE); - } - if (first_is_regular[idim] != is_regular[idim]) { - (void) fprintf(stderr, - "Files %s and %s have different coordinate spacings (%s)\n", - get_input_filename(loopfile_info,ifile), - get_input_filename(loopfile_info,0), - first_dimname[idim]); - exit(EXIT_FAILURE); - } - - } /* If check all dimension info */ - - } /* End of loop over dimensions */ - - } /* End of if ifile == 0 else */ - - /* Call the user's function if needed */ - if (loop_options->input_file_function != NULL) { - set_info_current_file(loop_options->loop_info, ifile); - set_info_loopfile_info(loop_options->loop_info, loopfile_info); - loop_options->input_file_function(loop_options->caller_data, - input_mincid, ifile, - loop_options->loop_info); - set_info_loopfile_info(loop_options->loop_info, NULL); - } - - } /* End of loop over files */ -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : input_image_varinq -@INPUT : mincid - Minc id of file - imgid - id of image variable - loop_options - structure containing looping options -@OUTPUT : name - name of variable - datatype - type of variable - ndims - number of dimensions - dim - array of dimension ids - natts - number of attributes -@RETURNS : MI_ERROR if an error occurs -@DESCRIPTION: Routine to call ncvarinq for the image variable, suppressing - the dimension specified in loop_options. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 20, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int input_image_varinq(int mincid, int imgid, char *name, - nc_type *datatype, int *ndims, int dim[], - int *natts, Loop_Options *loop_options) -{ - int dimid; - int old_ncopts; - int idim, jdim; - int status; - int nimgdims; - char dimname[MAX_NC_NAME]; - - /* Get loop dimension id */ - dimid = MI_ERROR; - if (loop_options->loop_dimension != NULL) { - old_ncopts = ncopts; ncopts = 0; - dimid = ncdimid(mincid, loop_options->loop_dimension); - ncopts = old_ncopts; - } - - /* Call ncvarinq. If there is no loop dim, or an error occurred, then - return. */ - status = ncvarinq(mincid, imgid, name, datatype, ndims, dim, natts); - if ((dimid == MI_ERROR) || (status == MI_ERROR)) - return status; - - /* Get number of image dimensions */ - nimgdims = 2; - if (*ndims > 0) { - (void) ncdiminq(mincid, dim[*ndims-1], dimname, NULL); - if (strcmp(dimname, MIvector_dimension) == 0) - nimgdims++; - } - - /* Look for the loop dimension */ - jdim = 0; - for (idim=0; idim < *ndims; idim++) { - if (dim[idim] != dimid) { - dim[jdim] = dim[idim]; - jdim++; - } - else if (idim >= *ndims-nimgdims) { - (void) fprintf(stderr, - "Don't use an image dimension as a loop dimension.\n"); - exit(EXIT_FAILURE); - } - } - - /* Save number of dimensions */ - *ndims = jdim; - - return status; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_dim_info -@INPUT : mincid - Minc id of file -@OUTPUT : ndims - number of dimensions - size - array of sizes of dimensions - dimname - array of dimension names - start - array of starts for dimensions - step - array of steps for dimensions - dircos - array of direction cosines - is_regular - array of flags indicating whether dimension is - regularly spaced or not - loop_options - looping options -@RETURNS : (nothing) -@DESCRIPTION: Routine to get dimension information for a file. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void get_dim_info(int mincid, int *ndims, long size[], - char dimname[][MAX_NC_NAME], - double start[], double step[], - double dircos[][3], int is_regular[], - Loop_Options *loop_options) -{ - int imgid, varid; - int idim, jdim; - int dim[MAX_VAR_DIMS]; - int att_length; - char string[MAX_NC_NAME]; - char *thename; - int old_ncopts; - enum {XAXIS, YAXIS, ZAXIS, OAXIS} dimtype; - static double default_dircos[][3] = { - 1.0, 0.0, 0.0, - 0.0, 1.0, 0.0, - 0.0, 0.0, 1.0, - 0.0, 0.0, 0.0 - }; - char regstring[MI_MAX_ATTSTR_LEN]; - - /* Get image variable info */ - imgid = ncvarid(mincid, MIimage); - (void) input_image_varinq(mincid, imgid, NULL, NULL, ndims, dim, NULL, - loop_options); - - /* Loop through dimensions */ - for (idim=0; idim < *ndims; idim++) { - if (dimname == NULL) thename = string; - else thename = dimname[idim]; - (void) ncdiminq(mincid, dim[idim], thename, &size[idim]); - - /* Set default coordinate info */ - if (start != NULL) start[idim] = 0.0; - if (step != NULL) step[idim] = 1.0; - if (dircos != NULL) { - if ((strcmp(thename, MIxspace) == 0) || - (strcmp(thename, MIxfrequency) == 0)) - dimtype = XAXIS; - else if ((strcmp(thename, MIyspace) == 0) || - (strcmp(thename, MIyfrequency) == 0)) - dimtype = YAXIS; - else if ((strcmp(thename, MIzspace) == 0) || - (strcmp(thename, MIzfrequency) == 0)) - dimtype = ZAXIS; - else - dimtype = OAXIS; - for (jdim=0; jdim < 3; jdim++) - dircos[idim][jdim] = default_dircos[dimtype][jdim]; - } - if (is_regular != NULL) - is_regular[idim] = TRUE; - - /* Get the coordinate info */ - old_ncopts = ncopts; ncopts = 0; - varid = ncvarid(mincid, thename); - if (varid != MI_ERROR) { - if (start != NULL) - (void) miattget1(mincid, varid, MIstart, NC_DOUBLE, &start[idim]); - if (step != NULL) - (void) miattget1(mincid, varid, MIstep, NC_DOUBLE, &step[idim]); - if (dircos != NULL) - (void) miattget(mincid, varid, MIdirection_cosines, NC_DOUBLE, - 3, dircos[idim], &att_length); - if (is_regular != NULL) { - if (miattgetstr(mincid, varid, MIspacing, - sizeof(regstring), regstring) != NULL) { - if (strcmp(regstring, MI_REGULAR) == 0) - is_regular[idim] = TRUE; - else if (strcmp(regstring, MI_IRREGULAR) == 0) - is_regular[idim] = FALSE; - } - } - } - ncopts = old_ncopts; - } - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : setup_output_files -@INPUT : loop_options - Options controlling looping - loopfile_info - Looping information - arg_string - string for history -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to setup the the output files -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void setup_output_files(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - char *arg_string) -{ - int inmincid, outmincid; - int ifile; - - /* Get mincid for first input file */ - inmincid = get_input_mincid(loopfile_info, 0); - - /* Create output files */ - for (ifile=0; ifile < get_output_numfiles(loopfile_info); ifile++) { - outmincid = create_output_file(loopfile_info, ifile); - setup_variables(inmincid, outmincid, ifile, arg_string, loop_options); - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_vector_length -@INPUT : mincid - minc file id - loop_options - looping options (if NULL, uses ncvarinq) -@OUTPUT : (none) -@RETURNS : Length of vector dimension or zero if no such dimension. -@DESCRIPTION: Routine to get the length of the vector dimension in a minc file. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private long get_vector_length(int mincid, Loop_Options *loop_options) -{ - int imgid; - int ndims; - int dim[MAX_VAR_DIMS]; - char dimname[MAX_NC_NAME]; - long vector_length; - - /* Get image variable id */ - imgid = ncvarid(mincid, MIimage); - - /* Get the image dimension info */ - if (loop_options != NULL) { - (void) input_image_varinq(mincid, imgid, NULL, NULL, &ndims, dim, NULL, - loop_options); - } - else { - (void) ncvarinq(mincid, imgid, NULL, NULL, &ndims, dim, NULL); - } - - /* Check for vector dimension */ - (void) ncdiminq(mincid, dim[ndims-1], dimname, &vector_length); - if ((strcmp(dimname, MIvector_dimension) != 0) || (ndims <= 2)) { - vector_length = 0; - } - - return vector_length; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : setup_variables -@INPUT : inmincid - input minc file id - outmincid - output minc file id - output_curfile - current output file number (counting from zero) - arg_string - string for history - loop_options - options controlling loop behaviour -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to setup the variables in the output file. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 10, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void setup_variables(int inmincid, int outmincid, - int output_curfile, - char *arg_string, Loop_Options *loop_options) -{ - int inimgid, outimgid, maxid, minid, varid; - int indim[MAX_VAR_DIMS], outdim[MAX_VAR_DIMS]; - nc_type datatype; - int idim, odim, ivar, in_ndims, out_ndims, in_nimgdims, out_nimgdims; - char dimname[MAX_NC_NAME]; - int nvars, varlist[MAX_VAR_DIMS*2]; - long dimlength; - int input_vector_length; - int changing_vector_dim; - double valid_range[2]; - - /* Get image variable id for input file */ - inimgid = ncvarid(inmincid, MIimage); - - /* Get the list of dimensions subscripting the image variable */ - (void) input_image_varinq(inmincid, inimgid, NULL, &datatype, - &in_ndims, indim, NULL, loop_options); - - /* Get the length of the input vector dimension */ - input_vector_length = get_vector_length(inmincid, loop_options); - if (loop_options->convert_input_to_scalar && (input_vector_length > 0)) { - input_vector_length = 0; - in_ndims--; - } - - /* Get the number of image dimensions in the input file */ - in_nimgdims = (input_vector_length == 0 ? 2 : 3); - - /* Are we changing the length of the vector dimension (or removing it?). - For an output vector size of 1, we don't want an output vector - dimension. */ - changing_vector_dim = - ((loop_options->output_vector_size != 0) && - (loop_options->output_vector_size != input_vector_length)); - if (loop_options->output_vector_size == 1) - changing_vector_dim = (input_vector_length != 0); - - /* Work out number of output dimensions and image dimensions */ - out_ndims = in_ndims; - out_nimgdims = in_nimgdims; - if (changing_vector_dim && (input_vector_length == 0)) { - out_ndims++; - out_nimgdims++; - } - else if (changing_vector_dim && (loop_options->output_vector_size <= 1)) { - out_ndims--; - out_nimgdims--; - } - - /* Set up the output minc file */ - - /* Loop, creating output dimensions */ - odim = 0; - nvars = 0; - for (idim=0; idim < in_ndims; idim++) { - - /* Check for a change in vector dimension length */ - if ((idim != in_ndims-1) || (input_vector_length == 0) || - !changing_vector_dim) { - - /* Copy the dimension */ - (void) ncdiminq(inmincid, indim[idim], dimname, &dimlength); - outdim[odim] = ncdimdef(outmincid, dimname, dimlength); - - /* Copy the dimension variables if we are not copying the - whole header */ - if (!loop_options->copy_all_header_info) { - ncopts = 0; - for (ivar=0; ivar < 2; ivar++) { - if (ivar == 1) - (void) strcat(dimname, "_width"); - varlist[nvars] = ncvarid(inmincid, dimname); - if (varlist[nvars] != MI_ERROR) { - (void) micopy_var_def(inmincid, varlist[nvars], outmincid); - nvars++; - } - } - ncopts = NC_OPTS_VAL; - } - - odim++; - } - } - - /* Create the output vector dimension if needed */ - if (changing_vector_dim && (loop_options->output_vector_size > 1)) { - outdim[odim] = ncdimdef(outmincid, MIvector_dimension, - (long) loop_options->output_vector_size); - } - - /* Copy other variables in file, if appropriate */ - if (loop_options->copy_all_header_info) { - nvars = 0; - ncopts = 0; - varlist[nvars] = inimgid; - if (varlist[nvars] != MI_ERROR) nvars++; - varlist[nvars] = ncvarid(inmincid, MIimagemax); - if (varlist[nvars] != MI_ERROR) nvars++; - varlist[nvars] = ncvarid(inmincid, MIimagemin); - if (varlist[nvars] != MI_ERROR) nvars++; - if (loop_options->loop_dimension != NULL) { - (void) strcpy(dimname, loop_options->loop_dimension); - varlist[nvars] = ncvarid(inmincid, dimname); - if (varlist[nvars] != MI_ERROR) nvars++; - (void) strcat(dimname, "_width"); - varlist[nvars] = ncvarid(inmincid, dimname); - if (varlist[nvars] != MI_ERROR) nvars++; - } - (void) micopy_all_var_defs(inmincid, outmincid, - nvars, varlist); - ncopts = NC_OPTS_VAL; - } - - /* Add the time stamp to the history */ - update_history(outmincid, arg_string); - - /* Call the user's function if needed */ - if (loop_options->output_file_function != NULL) { - set_info_current_file(loop_options->loop_info, 0); - loop_options->output_file_function(loop_options->caller_data, - outmincid, output_curfile, - loop_options->loop_info); - } - - /* Create the image-min/max variables */ - maxid = micreate_std_variable(outmincid, MIimagemax, NC_DOUBLE, - out_ndims-out_nimgdims, outdim); - minid = micreate_std_variable(outmincid, MIimagemin, NC_DOUBLE, - out_ndims-out_nimgdims, outdim); - ncopts = 0; - (void) micopy_all_atts(inmincid, ncvarid(inmincid, MIimagemax), - outmincid, maxid); - (void) micopy_all_atts(inmincid, ncvarid(inmincid, MIimagemin), - outmincid, minid); - ncopts = NC_OPTS_VAL; - - /* Create the image variable */ - if (loop_options->datatype != MI_ORIGINAL_TYPE) { - datatype = loop_options->datatype; - } - loop_options->is_floating_type = - ((datatype == NC_FLOAT) || (datatype == NC_DOUBLE)); - outimgid = micreate_std_variable(outmincid, MIimage, datatype, - out_ndims, outdim); - (void) micopy_all_atts(inmincid, inimgid, outmincid, outimgid); - if (loop_options->is_floating_type) { - ncopts = 0; - (void) ncattdel(outmincid, outimgid, MIsigntype); - ncopts = NC_OPTS_VAL; - valid_range[0] = 0; - valid_range[1] = 1; - (void) miset_valid_range(outmincid, outimgid, valid_range); - } - else if (loop_options->datatype != MI_ORIGINAL_TYPE) { - if (loop_options->is_signed) - (void) miattputstr(outmincid, outimgid, MIsigntype, MI_SIGNED); - else - (void) miattputstr(outmincid, outimgid, MIsigntype, MI_UNSIGNED); - if ((loop_options->valid_range[1] > loop_options->valid_range[0])) { - (void) miset_valid_range(outmincid, outimgid, - loop_options->valid_range); - } - else { - ncopts = 0; - (void) ncattdel(outmincid, outimgid, MIvalid_range); - ncopts = NC_OPTS_VAL; - } - } - (void) miattputstr(outmincid, outimgid, MIcomplete, MI_FALSE); - - /* Put the file in data mode */ - (void) ncsetfill(outmincid, NC_NOFILL); - (void) ncendef(outmincid); - - /* Copy over variable values */ - ncopts = 0; - if (loop_options->copy_all_header_info) { - (void) micopy_all_var_values(inmincid, outmincid, nvars, varlist); - } - else { - for (ivar=0; ivar < nvars; ivar++) { - (void) ncvarinq(inmincid, varlist[ivar], dimname, NULL, NULL, - NULL, NULL); - varid = ncvarid(outmincid, dimname); - if (varid != MI_ERROR) { - (void) micopy_var_values(inmincid, varlist[ivar], - outmincid, varid); - } - } - } - ncopts = NC_OPTS_VAL; - - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : update_history -@INPUT : mincid - id of output minc file - arg_string - string giving list of arguments -@OUTPUT : (nothing) -@RETURNS : (nothing) -@DESCRIPTION: Routine to update the history global variable in the output - minc file -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : August 26, 1993 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void update_history(int mincid, char *arg_string) -{ - nc_type datatype; - int att_length; - char *string; - - if (arg_string == NULL) return; - - /* Get the history attribute length */ - ncopts=0; - if ((ncattinq(mincid, NC_GLOBAL, MIhistory, &datatype, - &att_length) == MI_ERROR) || - (datatype != NC_CHAR)) - att_length = 0; - att_length += strlen(arg_string) + 1; - - /* Allocate a string and get the old history */ - string = MALLOC(att_length); - string[0] = '\0'; - (void) miattgetstr(mincid, NC_GLOBAL, MIhistory, att_length, - string); - ncopts = NC_OPTS_VAL; - - /* Add the new command and put the new history. */ - (void) strcat(string, arg_string); - (void) miattputstr(mincid, NC_GLOBAL, MIhistory, string); - FREE(string); - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : setup_icvs -@INPUT : loop_options - loop option info - loopfile_info - looping information -@OUTPUT : (nothing) -@RETURNS : (nothing) -@DESCRIPTION: Routine to set up the input and output icv's. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void setup_icvs(Loop_Options *loop_options, - Loopfile_Info *loopfile_info) -{ - int ifile; - int icvid; - - /* Loop through input icv's, setting their values. Attaching is - done by get_input_icvid. */ - for (ifile=0; ifile < get_input_numfiles(loopfile_info); ifile++) { - icvid = create_input_icvid(loopfile_info, ifile); - (void) miicv_setint(icvid, MI_ICV_TYPE, NC_DOUBLE); - (void) miicv_setint(icvid, MI_ICV_DO_NORM, TRUE); - (void) miicv_setint(icvid, MI_ICV_USER_NORM, TRUE); - (void) miicv_setint(icvid, MI_ICV_DO_FILLVALUE, TRUE); - if (loop_options->convert_input_to_scalar) { - (void) miicv_setint(icvid, MI_ICV_DO_DIM_CONV, TRUE); - (void) miicv_setint(icvid, MI_ICV_DO_SCALAR, TRUE); - (void) miicv_setint(icvid, MI_ICV_XDIM_DIR, MI_ICV_ANYDIR); - (void) miicv_setint(icvid, MI_ICV_YDIM_DIR, MI_ICV_ANYDIR); - (void) miicv_setint(icvid, MI_ICV_ZDIM_DIR, MI_ICV_ANYDIR); - (void) miicv_setint(icvid, MI_ICV_KEEP_ASPECT, FALSE); - } - } - - /* Loop through output icv's, setting their values. Attaching is - done by get_input_icvid. */ - for (ifile=0; ifile < get_output_numfiles(loopfile_info); ifile++) { - icvid = create_output_icvid(loopfile_info, ifile); - (void) miicv_setint(icvid, MI_ICV_TYPE, NC_DOUBLE); - (void) miicv_setint(icvid, MI_ICV_DO_NORM, TRUE); - (void) miicv_setint(icvid, MI_ICV_USER_NORM, TRUE); - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : do_voxel_loop -@INPUT : loop_options - user options for looping - loopfile_info - information on files used in loop -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to loop through the voxels and do something to each one -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 10, 1994 (Peter Neelin) -@MODIFIED : November 30, 1994 (P.N.) ----------------------------------------------------------------------------- */ -private void do_voxel_loop(Loop_Options *loop_options, - Loopfile_Info *loopfile_info) -{ - long block_start[MAX_VAR_DIMS], block_end[MAX_VAR_DIMS]; - long block_incr[MAX_VAR_DIMS]; - long block_cur[MAX_VAR_DIMS], block_curcount[MAX_VAR_DIMS]; - long chunk_start[MAX_VAR_DIMS], chunk_end[MAX_VAR_DIMS]; - long chunk_incr[MAX_VAR_DIMS]; - long chunk_cur[MAX_VAR_DIMS], chunk_curcount[MAX_VAR_DIMS]; - long input_cur[MAX_VAR_DIMS], input_curcount[MAX_VAR_DIMS]; - long firstfile_cur[MAX_VAR_DIMS], firstfile_curcount[MAX_VAR_DIMS]; - double **input_buffers, **output_buffers, **extra_buffers; - double **results_buffers; - long chunk_num_voxels, block_num_voxels, ivox; - int outmincid, imgid, maxid, minid; - double *data, minimum, maximum, valid_range[2]; - double *global_minimum, *global_maximum; - int ifile, ofile, ibuff, ndims, idim; - int num_output_files; - int num_input_buffers, num_output_buffers, num_extra_buffers; - int input_vector_length, output_vector_length; - int modify_vector_count; - int current_input; - int input_icvid, input_mincid; - int loop_dim_index; - int dim_index; - int outer_file_loop; - int dummy_index; - int input_curfile; - nc_type file_datatype; - - /* Get number of files, buffers, etc. */ - num_output_files = get_output_numfiles(loopfile_info); - num_input_buffers = (loop_options->do_accumulate ? 1 : - loop_options->num_all_inputs); - num_extra_buffers = loop_options->num_extra_buffers; - num_output_buffers = num_output_files + num_extra_buffers; - input_vector_length = - get_vector_length(get_input_mincid(loopfile_info, 0), loop_options); - if ((input_vector_length == 0) || (loop_options->convert_input_to_scalar)) - input_vector_length = 1; - if (num_output_files > 0) { - output_vector_length = - get_vector_length(get_output_mincid(loopfile_info, 0), NULL); - if (output_vector_length == 0) output_vector_length = 1; - } - else - output_vector_length = 1; - modify_vector_count = (input_vector_length != output_vector_length); - - /* Initialize all of the counters to reasonable values */ - (void) miset_coords(MAX_VAR_DIMS, 0, block_start); - (void) miset_coords(MAX_VAR_DIMS, 0, block_end); - (void) miset_coords(MAX_VAR_DIMS, 0, block_incr); - (void) miset_coords(MAX_VAR_DIMS, 0, block_cur); - (void) miset_coords(MAX_VAR_DIMS, 0, block_curcount); - (void) miset_coords(MAX_VAR_DIMS, 0, chunk_start); - (void) miset_coords(MAX_VAR_DIMS, 0, chunk_end); - (void) miset_coords(MAX_VAR_DIMS, 0, chunk_incr); - (void) miset_coords(MAX_VAR_DIMS, 0, chunk_cur); - (void) miset_coords(MAX_VAR_DIMS, 0, chunk_curcount); - (void) miset_coords(MAX_VAR_DIMS, 0, input_cur); - (void) miset_coords(MAX_VAR_DIMS, 0, input_curcount); - (void) miset_coords(MAX_VAR_DIMS, 0, firstfile_cur); - (void) miset_coords(MAX_VAR_DIMS, 0, firstfile_curcount); - - /* Get block and chunk looping information */ - setup_looping(loop_options, loopfile_info, &ndims, - block_start, block_end, - block_incr, &block_num_voxels, - chunk_incr, &chunk_num_voxels); - - /* Allocate space for buffers */ - - if (loop_options->allocate_buffer_function != NULL) { - loop_options->allocate_buffer_function - (loop_options->caller_data, TRUE, - num_input_buffers, chunk_num_voxels, input_vector_length, - &input_buffers, - num_output_files, block_num_voxels, output_vector_length, - &output_buffers, - num_extra_buffers, chunk_num_voxels, output_vector_length, - &extra_buffers, - loop_options->loop_info); - - } - else { - - /* Allocate input buffers */ - input_buffers = MALLOC(sizeof(*input_buffers) * num_input_buffers); - for (ibuff=0; ibuff < num_input_buffers; ibuff++) { - input_buffers[ibuff] = MALLOC(sizeof(double) * chunk_num_voxels * - input_vector_length); - } - - /* Allocate output buffers */ - if (num_output_files > 0) { - output_buffers = MALLOC(sizeof(*output_buffers) * num_output_files); - for (ibuff=0; ibuff < num_output_files; ibuff++) { - output_buffers[ibuff] = MALLOC(sizeof(double) * block_num_voxels * - output_vector_length); - } - } - - /* Allocate extra buffers */ - if (num_extra_buffers > 0) { - extra_buffers = MALLOC(sizeof(*extra_buffers) * num_extra_buffers); - for (ibuff=0; ibuff < num_extra_buffers; ibuff++) { - extra_buffers[ibuff] = MALLOC(sizeof(double) * chunk_num_voxels * - output_vector_length); - } - } - - } - - /* Set up the results pointers */ - if (num_output_buffers > 0) { - results_buffers = MALLOC(sizeof(*results_buffers) * num_output_buffers); - for (ibuff=0; ibuff < num_output_buffers; ibuff++) { - if (ibuff < num_output_files) { - results_buffers[ibuff] = output_buffers[ibuff]; - } - else { - results_buffers[ibuff] = extra_buffers[ibuff-num_output_files]; - } - } - } - - /* Initialize global min and max */ - if (num_output_files > 0) { - global_minimum = MALLOC(num_output_files * sizeof(double)); - global_maximum = MALLOC(num_output_files * sizeof(double)); - for (ofile=0; ofile < num_output_files; ofile++) { - global_minimum[ofile] = DBL_MAX; - global_maximum[ofile] = -DBL_MAX; - } - } - else { - global_minimum = NULL; - global_maximum = NULL; - } - - /* Initialize loop info - just to be safe */ - initialize_loop_info(loop_options->loop_info); - - /* Print log message */ - if (loop_options->verbose) { - (void) fprintf(stderr, "Processing:"); - (void) fflush(stderr); - } - - /* Outer loop over files, if appropriate */ - outer_file_loop = (loop_options->do_accumulate && - (num_output_buffers <= 0)); - for (initialize_file_and_index(loop_options, loopfile_info, - outer_file_loop, &ifile, &dim_index, - &dummy_index); - finish_file_and_index(loop_options, loopfile_info, - outer_file_loop, ifile, dim_index, - dummy_index); - increment_file_and_index(loop_options, loopfile_info, - outer_file_loop, &ifile, &dim_index, - &dummy_index)) { - - /* Loop through blocks (image-max/min do not vary over blocks) */ - - nd_begin_looping(block_start, block_cur, ndims); - - while (!nd_end_of_loop(block_cur, block_end, ndims)) { - - nd_update_current_count(block_cur, block_incr, block_end, - block_curcount, ndims); - - /* Set results_buffers to beginning of output buffers */ - for (ofile=0; ofile < num_output_files; ofile++) { - results_buffers[ofile] = output_buffers[ofile]; - } - - /* Loop through chunks (space for input buffers) */ - for (idim=0; idim < ndims; idim++) { - chunk_start[idim] = block_cur[idim]; - chunk_end[idim] = block_cur[idim] + block_curcount[idim]; - } - - nd_begin_looping(chunk_start, chunk_cur, ndims); - - while (!nd_end_of_loop(chunk_cur, chunk_end, ndims)) { - - nd_update_current_count(chunk_cur, chunk_incr, chunk_end, - chunk_curcount, ndims); - - /* Print log message */ - if (loop_options->verbose) { - (void) fprintf(stderr, "."); - (void) fflush(stderr); - } - - /* Calculate number of voxels in a chunk */ - chunk_num_voxels = 1; - for (idim=0; idim < ndims; idim++) - chunk_num_voxels *= chunk_curcount[idim]; - chunk_num_voxels /= input_vector_length; - - /* Translate start and count for file and save in loop_info */ - if (outer_file_loop) - input_curfile = ifile; - else - input_curfile = 0; - input_mincid = get_input_mincid(loopfile_info, input_curfile); - translate_input_coords(input_mincid, chunk_cur, firstfile_cur, - chunk_curcount, firstfile_curcount, - &loop_dim_index, loop_options); - - /* Save start and count and file and index in loop_info */ - set_info_shape(loop_options->loop_info, - firstfile_cur, firstfile_curcount); - set_info_current_file(loop_options->loop_info, 0); - set_info_current_index(loop_options->loop_info, 0); - - /* Initialize results buffers if necessary */ - if (loop_options->do_accumulate) { - if (loop_options->start_function != NULL) { - loop_options->start_function - (loop_options->caller_data, - chunk_num_voxels, - num_output_buffers, - output_vector_length, - results_buffers, - loop_options->loop_info); - } - } - - /* Get the input buffers and accumulate them if needed */ - current_input = 0; - for (initialize_file_and_index(loop_options, loopfile_info, - !outer_file_loop, &ifile, - &dim_index, &dummy_index); - finish_file_and_index(loop_options, loopfile_info, - !outer_file_loop, ifile, - dim_index, dummy_index); - increment_file_and_index(loop_options, loopfile_info, - !outer_file_loop, &ifile, - &dim_index, &dummy_index)) { - - /* Get input icvid and mincid and translate coords for file. - We need to do this each time in case we have an outer - file loop. */ - input_icvid = get_input_icvid(loopfile_info, ifile); - (void) miicv_inqint(input_icvid, MI_ICV_CDFID, - &input_mincid); - translate_input_coords(input_mincid, chunk_cur, input_cur, - chunk_curcount, input_curcount, - &loop_dim_index, loop_options); - - - /* Read buffer */ - ibuff = (loop_options->do_accumulate ? 0 : current_input); - input_cur[loop_dim_index] = dim_index; - (void) miicv_get(input_icvid, - input_cur, input_curcount, - input_buffers[ibuff]); - if (loop_options->do_accumulate) { - set_info_shape(loop_options->loop_info, - input_cur, input_curcount); - set_info_current_file(loop_options->loop_info, ifile); - set_info_current_index(loop_options->loop_info, dim_index); - set_info_loopfile_info(loop_options->loop_info, - loopfile_info); - loop_options->voxel_function(loop_options->caller_data, - chunk_num_voxels, - num_input_buffers, - input_vector_length, - input_buffers, - num_output_buffers, - output_vector_length, - results_buffers, - loop_options->loop_info); - set_info_loopfile_info(loop_options->loop_info, NULL); - } - - current_input++; - - } /* Inner loop over files and dimension index */ - - /* Do something with the buffers or finish accumulation */ - set_info_shape(loop_options->loop_info, - firstfile_cur, firstfile_curcount); - set_info_current_file(loop_options->loop_info, 0); - set_info_current_index(loop_options->loop_info, 0); - if (loop_options->do_accumulate) { - if (loop_options->finish_function != NULL) { - loop_options->finish_function(loop_options->caller_data, - chunk_num_voxels, - num_output_buffers, - output_vector_length, - results_buffers, - loop_options->loop_info); - } - } - else { - loop_options->voxel_function(loop_options->caller_data, - chunk_num_voxels, - num_input_buffers, - input_vector_length, - input_buffers, - num_output_buffers, - output_vector_length, - results_buffers, - loop_options->loop_info); - } - - /* Increment results_buffers through output buffers */ - for (ofile=0; ofile < num_output_files; ofile++) { - results_buffers[ofile] += - chunk_num_voxels * output_vector_length; - } - - nd_increment_loop(chunk_cur, chunk_start, chunk_incr, - chunk_end, ndims); - - } /* End of loop through chunks */ - - /* Write out output buffers */ - - for (ofile=0; ofile < num_output_files; ofile++) { - outmincid = get_output_mincid(loopfile_info, ofile); - maxid = ncvarid(outmincid, MIimagemax); - minid = ncvarid(outmincid, MIimagemin); - data = output_buffers[ofile]; - - /* Find the max and min */ - minimum = DBL_MAX; - maximum = -DBL_MAX; - for (ivox=0; ivox < block_num_voxels*output_vector_length; - ivox++) { - if (data[ivox] != -DBL_MAX) { - if (data[ivox] < minimum) minimum = data[ivox]; - if (data[ivox] > maximum) maximum = data[ivox]; - } - } - if ((minimum == DBL_MAX) && (maximum == -DBL_MAX)) { - minimum = 0.0; - maximum = 0.0; - } - - /* Save global min and max */ - if (minimum < global_minimum[ofile]) - global_minimum[ofile] = minimum; - if (maximum > global_maximum[ofile]) - global_maximum[ofile] = maximum; - - /* Write out the max and min */ - (void) mivarput1(outmincid, maxid, block_cur, - NC_DOUBLE, NULL, &maximum); - (void) mivarput1(outmincid, minid, block_cur, - NC_DOUBLE, NULL, &minimum); - - /* Write out the values */ - if (modify_vector_count) - block_curcount[ndims-1] = output_vector_length; - (void) miicv_put(get_output_icvid(loopfile_info, ofile), - block_cur, block_curcount, data); - } /* End of loop through output files */ - - nd_increment_loop(block_cur, block_start, block_incr, - block_end, ndims); - - } /* End of loop through chunks */ - - } /* End of outer loop through files and dimension indices */ - - /* Data has been completely written */ - for (ofile=0; ofile < num_output_files; ofile++) { - outmincid = get_output_mincid(loopfile_info, ofile); - imgid = ncvarid(outmincid, MIimage); - (void) miattputstr(outmincid, imgid, MIcomplete, MI_TRUE); - if (loop_options->is_floating_type) { - if ((global_minimum[ofile] == DBL_MAX) && - (global_maximum[ofile] == -DBL_MAX)) { - global_minimum[ofile] = 0.0; - global_maximum[ofile] = 0.0; - } - valid_range[0] = global_minimum[ofile]; - valid_range[1] = global_maximum[ofile]; - - /* Force truncation of valid_range to match float image */ - if ((ncvarinq(outmincid, imgid, NULL, &file_datatype, NULL, NULL, - NULL) != MI_ERROR) && (file_datatype == NC_FLOAT)) { - valid_range[0] = (float) valid_range[0]; - valid_range[1] = (float) valid_range[1]; - } - - (void) miset_valid_range(outmincid, imgid, valid_range); - - } - } - - /* Print log message */ - if (loop_options->verbose) { - (void) fprintf(stderr, "Done\n"); - (void) fflush(stderr); - } - - /* Free results pointer array, but not its buffers, since these - were allocate as output_buffers and extra_buffers */ - if (num_output_buffers > 0) { - FREE(results_buffers); - } - - /* Free the buffers */ - if (loop_options->allocate_buffer_function != NULL) { - loop_options->allocate_buffer_function - (loop_options->caller_data, FALSE, - num_input_buffers, chunk_num_voxels, input_vector_length, - &input_buffers, - num_output_files, block_num_voxels, output_vector_length, - &output_buffers, - num_extra_buffers, chunk_num_voxels, output_vector_length, - &extra_buffers, - loop_options->loop_info); - } - else { - - /* Free input buffers */ - for (ibuff=0; ibuff < num_input_buffers; ibuff++) { - FREE(input_buffers[ibuff]); - } - FREE(input_buffers); - - /* Free output buffers */ - if (num_output_files > 0) { - for (ibuff=0; ibuff < num_output_files; ibuff++) { - FREE(output_buffers[ibuff]); - } - FREE(output_buffers); - } - - /* Free extra buffers */ - if (num_extra_buffers > 0) { - for (ibuff=0; ibuff < num_extra_buffers; ibuff++) { - FREE(extra_buffers[ibuff]); - } - FREE(extra_buffers); - } - - } - - /* Free max and min arrays */ - if (num_output_files > 0) { - FREE(global_minimum); - FREE(global_maximum); - } - - return; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : setup_looping -@INPUT : loop_options - users options controlling looping - loopfile_info - information on files -@OUTPUT : ndims - number of dimensions - block_start - vector specifying start of block - block_end - end of block - block_incr - increment for stepping through blocks - block_num_voxels - number of voxels in block - chunk_incr - increment for stepping through chunks - chunk_num_voxels - number of voxels in chunk -@RETURNS : (nothing) -@DESCRIPTION: Routine to set up vectors giving blocks and chunks through - which we will loop. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 2, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void setup_looping(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int *ndims, - long block_start[], long block_end[], - long block_incr[], long *block_num_voxels, - long chunk_incr[], long *chunk_num_voxels) -{ - int inmincid; - int total_ndims, scalar_ndims, idim; - int input_vector_length, output_vector_length; - int num_input_buffers; - int vector_data; - int nimgdims; - long size[MAX_VAR_DIMS]; - long max_voxels_in_buffer; - - /* Get input mincid */ - inmincid = get_input_mincid(loopfile_info, 0); - - /* Get number of dimensions and their sizes */ - get_dim_info(inmincid, &total_ndims, size, NULL, NULL, NULL, NULL, NULL, - loop_options); - - /* Get vector lengths */ - input_vector_length = get_vector_length(inmincid, loop_options); - if (get_output_numfiles(loopfile_info) > 0) - output_vector_length = - get_vector_length(get_output_mincid(loopfile_info, 0), NULL); - else - output_vector_length = 0; - - /* Check for vector data and whether we are adding a dimension */ - vector_data = ((input_vector_length > 0) || (output_vector_length > 0)); - if ((input_vector_length == 0) && (output_vector_length > 0)) { - total_ndims++; - size[total_ndims-1] = 1; - } - scalar_ndims = (vector_data ? total_ndims - 1 : total_ndims); - - /* Get number of image dimensions */ - nimgdims = (vector_data ? 3 : 2); - - /* Set vector lengths properly */ - if (input_vector_length <= 0) input_vector_length = 1; - if (output_vector_length <= 0) output_vector_length = 1; - - /* Set vectors */ - *block_num_voxels = 1; - for (idim=0; idim < total_ndims; idim++) { - block_start[idim] = 0; - block_end[idim] = size[idim]; - if (idim < total_ndims - nimgdims) - block_incr[idim] = 1; - else - block_incr[idim] = size[idim]; - *block_num_voxels *= block_incr[idim]; - chunk_incr[idim] = 1; - } - if (vector_data) { - *block_num_voxels /= input_vector_length; - idim = total_ndims-1; - chunk_incr[idim] = block_incr[idim]; - } - - /* Figure out chunk size. Enforce a minimum chunk size. */ - *chunk_num_voxels = 1; - num_input_buffers = (loop_options->do_accumulate ? 1 : - loop_options->num_all_inputs); - max_voxels_in_buffer = - (loop_options->total_copy_space/((long) sizeof(double)) - - get_output_numfiles(loopfile_info) * *block_num_voxels * - output_vector_length) / - (num_input_buffers * input_vector_length + - loop_options->num_extra_buffers * output_vector_length); - if (max_voxels_in_buffer < MIN_VOXELS_IN_BUFFER) { - max_voxels_in_buffer = MIN_VOXELS_IN_BUFFER; - } - if (max_voxels_in_buffer > 0) { - for (idim=scalar_ndims-1; idim >= 0; idim--) { - chunk_incr[idim] = max_voxels_in_buffer / *chunk_num_voxels; - if (chunk_incr[idim] > block_incr[idim]) - chunk_incr[idim] = block_incr[idim]; - *chunk_num_voxels *= chunk_incr[idim]; - } - } - - /* Set ndims */ - *ndims = total_ndims; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : initialize_file_and_index -@INPUT : loop_options - users options controlling looping - loopfile_info - information on files - do_loop - TRUE if looping stuff should really be done -@OUTPUT : ifile - file counter - dim_index - dimension index counter - dummy_index - counter used when do_loop is FALSE -@RETURNS : (nothing) -@DESCRIPTION: Routine to initialize the file and index loop. These - three routines allow looping through files and dimension - indices at two levels. If do_loop is TRUE, then normal looping - is done (increment dim_index fastest, then ifile). If do_loop is - FALSE, then only one loop is performed (using dummy_index). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void initialize_file_and_index(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int do_loop, - int *ifile, int *dim_index, - int *dummy_index) - /* ARGSUSED */ -{ - if (do_loop) { - *ifile = 0; - *dim_index = 0; - } - else { - *dummy_index = 0; - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : finish_file_and_index -@INPUT : loop_options - users options controlling looping - loopfile_info - information on files - do_loop - TRUE if looping stuff should really be done - ifile - file counter - dim_index - dimension index counter - dummy_index - counter used when do_loop is FALSE -@RETURNS : TRUE while there are more buffers to process. -@DESCRIPTION: Routine to test for the end of the file and index loop. These - three routines allow looping through files and dimension - indices at two levels. If do_loop is TRUE, then normal looping - is done (increment dim_index fastest, then ifile). If do_loop is - FALSE, then only one loop is performed (using dummy_index). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int finish_file_and_index(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int do_loop, - int ifile, int dim_index, - int dummy_index) - /* ARGSUSED */ -{ - if (do_loop) { - return (ifile < get_input_numfiles(loopfile_info)); - } - else { - return (dummy_index < 1); - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : increment_file_and_index -@INPUT : loop_options - users options controlling looping - loopfile_info - information on files - do_loop - TRUE if looping stuff should really be done -@OUTPUT : ifile - file counter - dim_index - dimension index counter - dummy_index - counter used when do_loop is FALSE -@RETURNS : (nothing) -@DESCRIPTION: Routine to increment the file and index loop. These - three routines allow looping through files and dimension - indices at two levels. If do_loop is TRUE, then normal looping - is done (increment dim_index fastest, then ifile). If do_loop is - FALSE, then only one loop is performed (using dummy_index). - Note that dummy_index is not touched if do_loop is TRUE. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void increment_file_and_index(Loop_Options *loop_options, - Loopfile_Info *loopfile_info, - int do_loop, - int *ifile, int *dim_index, - int *dummy_index) -{ - int input_mincid; - - if (do_loop) { - (*dim_index)++; - input_mincid = get_input_mincid(loopfile_info, *ifile); - if (*dim_index >= get_loop_dim_size(input_mincid, loop_options)) { - *dim_index = 0; - (*ifile)++; - } - } - else { - (*dummy_index)++; - } -} - - -/* ------------ Routines controlling looping over files ------------ */ - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : initialize_loopfile_info -@INPUT : num_input_files - number of input files - input_files - list of input file names - num_output_files - list of output file names - output_files - list of output file names - loop_options - user options for looping -@OUTPUT : (none) -@RETURNS : pointer to Loopfile_Info structure -@DESCRIPTION: Routine to set up looping information for these files. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private Loopfile_Info *initialize_loopfile_info(int num_input_files, - char *input_files[], - int num_output_files, - char *output_files[], - Loop_Options *loop_options) -{ - int num_free_files, num_files, ifile; - Loopfile_Info *loopfile_info; - - /* Allocate structure */ - loopfile_info = MALLOC(sizeof(*loopfile_info)); - - /* Save clobber info */ - loopfile_info->clobber_output = loop_options->clobber; - - /* Save number of input and output files */ - loopfile_info->num_input_files = num_input_files; - loopfile_info->num_output_files = num_output_files; - - /* Save input file names (just copy pointers, not strings) */ - if (num_input_files > 0) { - loopfile_info->input_files = MALLOC(sizeof(char *) * num_input_files); - for (ifile=0; ifile < num_input_files; ifile++) - loopfile_info->input_files[ifile] = input_files[ifile]; - } - else - loopfile_info->input_files = NULL; - - /* Save output file names (just copy pointers, not strings) */ - if (num_output_files > 0) { - loopfile_info->output_files = MALLOC(sizeof(char *) * num_output_files); - for (ifile=0; ifile < num_output_files; ifile++) - loopfile_info->output_files[ifile] = output_files[ifile]; - } - else - loopfile_info->output_files = NULL; - - /* Keep track of number of files that we can open */ - num_free_files = loop_options->max_open_files; - if (num_free_files > MAX_NC_OPEN) num_free_files = MAX_NC_OPEN; - - /* Check to see if we can open output files (we must leave room for one - input file) */ - if (num_output_files < num_free_files-1) { - loopfile_info->output_all_open = TRUE; - num_files = num_output_files; - } - else { - loopfile_info->output_all_open = FALSE; - num_files = 1; - } - num_free_files -= num_files; - loopfile_info->output_mincid = MALLOC( sizeof(int) * num_files); - loopfile_info->output_icvid = MALLOC( sizeof(int) * num_files); - for (ifile=0; ifile < num_files; ifile++) { - loopfile_info->output_mincid[ifile] = MI_ERROR; - loopfile_info->output_icvid[ifile] = MI_ERROR; - } - loopfile_info->current_input_file_number = -1; - - /* Check whether sequential access would be better */ - loopfile_info->sequential_access = - (loop_options->do_accumulate && - ((num_output_files + loop_options->num_extra_buffers) <= 0)); - - /* Check to see if we can open input files */ - if (num_input_files < num_free_files) { - loopfile_info->can_open_all_input = TRUE; - num_files = num_input_files; - } - else { - loopfile_info->can_open_all_input = FALSE; - num_files = 1; - } - num_free_files -= num_files; - loopfile_info->input_mincid = MALLOC( sizeof(int) * num_files); - loopfile_info->input_icvid = MALLOC( sizeof(int) * num_files); - for (ifile=0; ifile < num_files; ifile++) { - loopfile_info->input_mincid[ifile] = MI_ERROR; - loopfile_info->input_icvid[ifile] = MI_ERROR; - } - loopfile_info->current_output_file_number = -1; - - /* Check for an already open input file */ - if (loop_options->input_mincid != MI_ERROR) { - loopfile_info->input_mincid[0] = loop_options->input_mincid; - loopfile_info->current_input_file_number = 0; - } - - /* Check whether we want to open all input files */ - loopfile_info->input_all_open = (! loopfile_info->sequential_access) && - loopfile_info->can_open_all_input; - - /* Set default for expanding compressed files */ - loopfile_info->headers_only = FALSE; - loopfile_info->want_headers_only = FALSE; - - /* Return the loopfile_info structure */ - return loopfile_info; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : cleanup_loopfile_info -@INPUT : loopfile_info - looping information -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to clean up looping information. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void cleanup_loopfile_info(Loopfile_Info *loopfile_info) -{ - int num_files, ifile; - - /* Close input files and free icv's */ - if (loopfile_info->can_open_all_input) - num_files = loopfile_info->num_input_files; - else - num_files = 1; - for (ifile=0; ifile < num_files; ifile++) { - if (loopfile_info->input_icvid[ifile] != MI_ERROR) - (void) miicv_free(loopfile_info->input_icvid[ifile]); - if (loopfile_info->input_mincid[ifile] != MI_ERROR) - (void) miclose(loopfile_info->input_mincid[ifile]); - } - - /* Close output files and free icv's */ - if (loopfile_info->output_all_open) - num_files = loopfile_info->num_output_files; - else - num_files = 1; - for (ifile=0; ifile < num_files; ifile++) { - (void) miicv_free(loopfile_info->output_icvid[ifile]); - (void) miclose(loopfile_info->output_mincid[ifile]); - } - - /* Free input arrays */ - if (loopfile_info->input_files != NULL) - FREE(loopfile_info->input_files); - if (loopfile_info->input_mincid != NULL) - FREE(loopfile_info->input_mincid); - if (loopfile_info->input_icvid != NULL) - FREE(loopfile_info->input_icvid); - - /* Free output arrays */ - if (loopfile_info->output_files != NULL) - FREE(loopfile_info->output_files); - if (loopfile_info->output_mincid != NULL) - FREE(loopfile_info->output_mincid); - if (loopfile_info->output_icvid != NULL) - FREE(loopfile_info->output_icvid); - - /* Free the structure */ - FREE(loopfile_info); -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_input_numfiles -@INPUT : loopfile_info - looping information -@OUTPUT : (none) -@RETURNS : Number of input files -@DESCRIPTION: Routine to get the number of input files. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int get_input_numfiles(Loopfile_Info *loopfile_info) -{ - return loopfile_info->num_input_files; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_output_numfiles -@INPUT : loopfile_info - looping information -@OUTPUT : (none) -@RETURNS : Number of output files -@DESCRIPTION: Routine to get the number of output files. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int get_output_numfiles(Loopfile_Info *loopfile_info) -{ - return loopfile_info->num_output_files; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_input_filename -@INPUT : loopfile_info - looping information - file_num - input file number -@OUTPUT : (none) -@RETURNS : Pointer to string containing input file name for file ifile. -@DESCRIPTION: Routine to get name of an input file. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private char *get_input_filename(Loopfile_Info *loopfile_info, int file_num) -{ - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_input_files)) { - (void) fprintf(stderr, "Bad input file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - return loopfile_info->input_files[file_num]; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_output_filename -@INPUT : loopfile_info - looping information - file_num - output file number -@OUTPUT : (none) -@RETURNS : Pointer to string containing output file name for file ifile. -@DESCRIPTION: Routine to get name of an output file. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private char *get_output_filename(Loopfile_Info *loopfile_info, int file_num) -{ - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_output_files)) { - (void) fprintf(stderr, "Bad output file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - return loopfile_info->output_files[file_num]; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_input_headers_only -@INPUT : loopfile_info - looping information - headers_only - TRUE if we only need input headers, FALSE - if we need the whole file. -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to modify the Loopfile_Info structure so that - in future we get either whole minc files or only the headers. - The change is only made if it makes sense (ie. we are processing - files sequentially). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void set_input_headers_only(Loopfile_Info *loopfile_info, - int headers_only) -{ - int num_files, ifile; - int icvid, mincid; - - /* Change the indication that we want to have headers only */ - loopfile_info->want_headers_only = headers_only; - - /* If headers_only is not changing, don't do anything */ - if ((headers_only && loopfile_info->headers_only) || - (!headers_only && !loopfile_info->headers_only)) { - return; - } - - /* Check to see if it makes sense to change to headers only */ - if (headers_only && loopfile_info->input_all_open) return; - - /* Change the value */ - loopfile_info->headers_only = headers_only; - - /* If we are going to headers_only == FALSE, then loop through icv's and - files, making sure that they are detached and closed (we will need to - re-open them */ - if (!loopfile_info->headers_only) { - num_files = (loopfile_info->can_open_all_input ? - loopfile_info->num_input_files : 1); - for (ifile=0; ifile < num_files; ifile++) { - icvid = loopfile_info->input_icvid[ifile]; - mincid = MI_ERROR; - if (icvid != MI_ERROR) { - (void) miicv_inqint(icvid, MI_ICV_CDFID, &mincid); - if (mincid != MI_ERROR) { - (void) miicv_detach(icvid); - (void) miclose(mincid); - } - } - if ((loopfile_info->input_mincid[ifile] != MI_ERROR) && - (loopfile_info->input_mincid[ifile] != mincid)) { - (void) miclose(loopfile_info->input_mincid[ifile]); - } - loopfile_info->input_mincid[ifile] = MI_ERROR; - } - - } - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_input_sequential -@INPUT : loopfile_info - looping information - sequential_access - TRUE if we want to open only one file at a - time, FALSE otherwise. -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to modify the Loopfile_Info structure so that - files are opened one at a time. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 1, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void set_input_sequential(Loopfile_Info *loopfile_info, - int sequential_access) -{ - int old_input_all_open; - int ifile, num_files; - int mincid, icvid; - int current_input_file_number; - - /* Set flag for sequential access */ - loopfile_info->sequential_access = sequential_access; - - /* Change status of input_all_open */ - old_input_all_open = loopfile_info->input_all_open; - loopfile_info->input_all_open = (! loopfile_info->sequential_access) && - loopfile_info->can_open_all_input; - - /* Check if input_all_open has changed */ - if (!old_input_all_open && loopfile_info->input_all_open) { - current_input_file_number = loopfile_info->current_input_file_number; - if (current_input_file_number >= 0) { - mincid = loopfile_info->input_mincid[0]; - loopfile_info->input_mincid[0] = MI_ERROR; - loopfile_info->input_mincid[current_input_file_number] = mincid; - } - } - else if (old_input_all_open && !loopfile_info->input_all_open) { - if (loopfile_info->can_open_all_input) - num_files = loopfile_info->num_input_files; - else - num_files = 1; - for (ifile=0; ifile < num_files; ifile++) { - icvid = loopfile_info->input_icvid[ifile]; - if (icvid != MI_ERROR) { - (void) miicv_inqint(icvid, MI_ICV_CDFID, &mincid); - (void) miicv_detach(icvid); - if (mincid != MI_ERROR) { - (void) miclose(mincid); - } - } - if ((loopfile_info->input_mincid[ifile] != MI_ERROR) && - (loopfile_info->input_mincid[ifile] != mincid)) - (void) miclose(loopfile_info->input_mincid[ifile]); - loopfile_info->input_mincid[ifile] = MI_ERROR; - } - } - - /* Call set_input_headers_only in case want_headers_only is different - from headers_only */ - set_input_headers_only(loopfile_info, loopfile_info->want_headers_only); - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_input_mincid -@INPUT : loopfile_info - looping information - file_num - input file number -@OUTPUT : (none) -@RETURNS : Id of minc file -@DESCRIPTION: Routine to get the minc id for an input file. The file number - corresponds to the file's position in the input_files list - (counting from zero). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int get_input_mincid(Loopfile_Info *loopfile_info, - int file_num) -{ - int index; - int created_tempfile; - char *filename; - - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_input_files)) { - (void) fprintf(stderr, "Bad input file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - /* Check to see if all files are open or not */ - if (loopfile_info->input_all_open) { - index = file_num; - } - else { - index = 0; - if ((loopfile_info->input_mincid[index] != MI_ERROR) && - (loopfile_info->current_input_file_number != file_num)) { - if (loopfile_info->input_icvid[index] != MI_ERROR) - (void) miicv_detach(loopfile_info->input_icvid[index]); - (void) miclose(loopfile_info->input_mincid[index]); - loopfile_info->input_mincid[index] = MI_ERROR; - } - loopfile_info->current_input_file_number = file_num; - } - - /* Open the file if it hasn't been already */ - if (loopfile_info->input_mincid[index] == MI_ERROR) { - filename = miexpand_file(loopfile_info->input_files[file_num], NULL, - loopfile_info->headers_only, - &created_tempfile); - loopfile_info->input_mincid[index] = miopen(filename, NC_NOWRITE); - if (created_tempfile) { - (void) remove(filename); - } - FREE(filename); - } - - return loopfile_info->input_mincid[index]; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_output_mincid -@INPUT : loopfile_info - looping information - file_num - output file number -@OUTPUT : (none) -@RETURNS : Id of minc file -@DESCRIPTION: Routine to get the minc id for an output file. The file number - corresponds to the file's position in the output_files list - (counting from zero). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int get_output_mincid(Loopfile_Info *loopfile_info, - int file_num) -{ - int index; - - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_output_files)) { - (void) fprintf(stderr, "Bad output file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - /* Check to see if all files are open or not */ - if (loopfile_info->output_all_open) { - index = file_num; - } - else { - index = 0; - if ((loopfile_info->output_mincid[index] != MI_ERROR) && - (loopfile_info->current_output_file_number != file_num)) { - if (loopfile_info->output_icvid[index] != MI_ERROR) - (void) miicv_detach(loopfile_info->output_icvid[index]); - (void) miclose(loopfile_info->output_mincid[index]); - loopfile_info->output_mincid[index] = MI_ERROR; - } - loopfile_info->current_output_file_number = file_num; - } - - /* Open the file if it hasn't been already */ - if (loopfile_info->output_mincid[index] == MI_ERROR) { - loopfile_info->output_mincid[index] = - miopen(loopfile_info->output_files[file_num], NC_WRITE); - } - - return loopfile_info->output_mincid[index]; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : create_output_file -@INPUT : loopfile_info - looping information - file_num - output file number -@OUTPUT : (none) -@RETURNS : Id of minc file -@DESCRIPTION: Routine to create an output file. The file number - corresponds to the file's position in the output_files list - (counting from zero). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int create_output_file(Loopfile_Info *loopfile_info, - int file_num) -{ - int index; - - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_output_files)) { - (void) fprintf(stderr, "Bad output file number %d for create.\n", - file_num); - exit(EXIT_FAILURE); - } - - /* Check to see if all files are open or not */ - if (loopfile_info->output_all_open) { - index = file_num; - } - else { - index = 0; - if ((loopfile_info->output_mincid[index] != MI_ERROR) && - (loopfile_info->current_output_file_number != file_num)) { - (void) miclose(loopfile_info->output_mincid[index]); - loopfile_info->output_mincid[index] = MI_ERROR; - } - loopfile_info->current_output_file_number = file_num; - } - - /* Create the file */ - if (loopfile_info->output_mincid[index] != MI_ERROR) { - (void) fprintf(stderr, "File %s has already been created\n", - loopfile_info->output_files[file_num]); - exit(EXIT_FAILURE); - } - loopfile_info->output_mincid[index] = - micreate(loopfile_info->output_files[file_num], - (loopfile_info->clobber_output ? - NC_CLOBBER : NC_NOCLOBBER)); - - return loopfile_info->output_mincid[index]; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_input_icvid -@INPUT : loopfile_info - looping information - file_num - input file number -@OUTPUT : (none) -@RETURNS : Id of icv for the specified file -@DESCRIPTION: Routine to get the icv id for an input file. The file number - corresponds to the file's position in the input_files list - (counting from zero). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int get_input_icvid(Loopfile_Info *loopfile_info, - int file_num) -{ - int mincid, icv_mincid, icvid; - int index; - - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_input_files)) { - (void) fprintf(stderr, "Bad input file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - /* Check to see if all files are open or not - get the correct index */ - if (loopfile_info->can_open_all_input) { - index = file_num; - } - else { - index = 0; - } - - /* Check to see if the icv is attached to the correct minc file. If - not, re-attach it. */ - icvid = loopfile_info->input_icvid[index]; - mincid = get_input_mincid(loopfile_info, file_num); - if (icvid != MI_ERROR) - (void) miicv_inqint(icvid, MI_ICV_CDFID, &icv_mincid); - else - icv_mincid = MI_ERROR; - if (mincid != icv_mincid) { - (void) miicv_attach(icvid, mincid, ncvarid(mincid, MIimage)); - } - return icvid; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_output_icvid -@INPUT : loopfile_info - looping information - file_num - output file number -@OUTPUT : (none) -@RETURNS : Id of icv for the specified file -@DESCRIPTION: Routine to get the icv id for an output file. The file number - corresponds to the file's position in the output_files list - (counting from zero). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int get_output_icvid(Loopfile_Info *loopfile_info, - int file_num) -{ - int mincid, icv_mincid, icvid; - int index; - - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_output_files)) { - (void) fprintf(stderr, "Bad output file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - /* Check to see if all files are open or not - get the correct index */ - if (loopfile_info->output_all_open) { - index = file_num; - } - else { - index = 0; - } - - /* Check to see if the icv is attached to the correct minc file. If - not, re-attach it. */ - icvid = loopfile_info->output_icvid[index]; - mincid = get_output_mincid(loopfile_info, file_num); - if (icvid != MI_ERROR) - (void) miicv_inqint(icvid, MI_ICV_CDFID, &icv_mincid); - else - icv_mincid = MI_ERROR; - if (mincid != icv_mincid) { - (void) miicv_attach(icvid, mincid, ncvarid(mincid, MIimage)); - } - return icvid; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : create_input_icvid -@INPUT : loopfile_info - looping information - file_num - input file number -@OUTPUT : (none) -@RETURNS : Id of icv for the specified file -@DESCRIPTION: Routine to create the icv id for an input file. The file number - corresponds to the file's position in the input_files list - (counting from zero). If the icv already exists, just - return it. If there are too many files, then only one - icv will be used. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int create_input_icvid(Loopfile_Info *loopfile_info, - int file_num) -{ - int index; - - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_input_files)) { - (void) fprintf(stderr, "Bad input file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - /* Check to see if all files are open or not - get the correct index */ - if (loopfile_info->can_open_all_input) { - index = file_num; - } - else { - index = 0; - } - - /* Check to see if icv exists - if not create it */ - if (loopfile_info->input_icvid[index] == MI_ERROR) { - loopfile_info->input_icvid[index] = miicv_create(); - } - - return loopfile_info->input_icvid[index]; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : create_output_icvid -@INPUT : loopfile_info - looping information - file_num - output file number -@OUTPUT : (none) -@RETURNS : Id of icv for the specified file -@DESCRIPTION: Routine to create the icv id for an output file. The file number - corresponds to the file's position in the output_files list - (counting from zero). If the icv already exists, just - return it. If there are too many files, then only one - icv will be used. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 30, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private int create_output_icvid(Loopfile_Info *loopfile_info, - int file_num) -{ - int index; - - /* Check for bad file_num */ - if ((file_num < 0) || (file_num >= loopfile_info->num_output_files)) { - (void) fprintf(stderr, "Bad output file number %d\n", file_num); - exit(EXIT_FAILURE); - } - - /* Check to see if all files are open or not - get the correct index */ - if (loopfile_info->output_all_open) { - index = file_num; - } - else { - index = 0; - } - - /* Check to see if icv exists - if not create it */ - if (loopfile_info->output_icvid[index] == MI_ERROR) { - loopfile_info->output_icvid[index] = miicv_create(); - } - - return loopfile_info->output_icvid[index]; -} - - -/* ------------ Routines to set loop options ------------ */ - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : create_loop_options -@INPUT : (none) -@OUTPUT : (none) -@RETURNS : Pointer to Loop_Options structure -@DESCRIPTION: Routine to create and initialize the loop options structure. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public Loop_Options *create_loop_options(void) -{ - Loop_Options *loop_options; - - /* Allocate structure */ - loop_options = MALLOC(sizeof(*loop_options)); - - /* Fill in the defaults */ - loop_options->clobber = FALSE; - loop_options->verbose = TRUE; - loop_options->datatype = MI_ORIGINAL_TYPE; - loop_options->is_signed = TRUE; - loop_options->valid_range[0] = 0.0; - loop_options->valid_range[1] = 0.0; - loop_options->max_open_files = MAX_NC_OPEN - 2; - loop_options->check_all_input_dim_info = TRUE; - loop_options->convert_input_to_scalar = FALSE; - loop_options->output_vector_size = 0; - loop_options->input_mincid = MI_ERROR; - loop_options->total_copy_space = 4 * 1024 * 1024; - loop_options->loop_dimension = NULL; - loop_options->num_all_inputs = 0; - loop_options->input_file_function = NULL; - loop_options->output_file_function = NULL; - loop_options->copy_all_header_info = TRUE; - loop_options->do_accumulate = FALSE; - loop_options->num_extra_buffers = 0; - loop_options->start_function = NULL; - loop_options->finish_function = NULL; - loop_options->voxel_function = NULL; - loop_options->caller_data = NULL; - loop_options->loop_info = create_loop_info(); - - loop_options->allocate_buffer_function = NULL; - - /* Return the structure pointer */ - return loop_options; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : free_loop_options -@INPUT : loop_options - pointer to structure to cleanup -@OUTPUT : (none) -@RETURNS : (none) -@DESCRIPTION: Routine to cleanup and free the Loop_Options structure -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void free_loop_options(Loop_Options *loop_options) -{ - free_loop_info(loop_options->loop_info); - if (loop_options->loop_dimension != NULL) - FREE(loop_options->loop_dimension); - FREE(loop_options); -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_clobber -@INPUT : loop_options - user options for looping - verbose - TRUE if output files should be clobbered -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn output clobber on or off -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_clobber(Loop_Options *loop_options, - int clobber) -{ - loop_options->clobber = clobber; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_verbose -@INPUT : loop_options - user options for looping - verbose - TRUE if logging should be done. -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn logging on or off. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_verbose(Loop_Options *loop_options, - int verbose) -{ - loop_options->verbose = verbose; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_datatype -@INPUT : loop_options - user options for looping - datatype - NetCDF datatype for output (MI_ORIGINAL_TYPE means - use input type) - is_signed - TRUE if type is signed - valid_min - valid minimum for type (if valid_min >= valid_max, - then defaults are used) - valid_max - valid maximum for type -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to set the output file datatype, sign and range. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 20, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_datatype(Loop_Options *loop_options, - nc_type datatype, int is_signed, - double valid_min, double valid_max) -{ - loop_options->datatype = datatype; - loop_options->is_signed = is_signed; - loop_options->valid_range[0] = valid_min; - loop_options->valid_range[1] = valid_max; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_max_open_files -@INPUT : loop_options - user options for looping - max_open_files - maximum number of open files allowed (between - 1 and MAX_NC_OPEN) -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to set the maximum number of open minc files. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_max_open_files(Loop_Options *loop_options, - int max_open_files) -{ - if ((max_open_files <= 0) || (max_open_files > MAX_NC_OPEN)) { - (void) fprintf(stderr, - "Bad number of files %d in set_loop_max_open_files\n", - max_open_files); - exit(EXIT_FAILURE); - } - - loop_options->max_open_files = max_open_files; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_check_dim_info -@INPUT : loop_options - user options for looping - check_dim_info - TRUE if all dimension information in input - files should be check, FALSE otherwise -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn dimension info checking on or off. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 16, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_check_dim_info(Loop_Options *loop_options, - int check_dim_info) -{ - loop_options->check_all_input_dim_info = check_dim_info; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_convert_input_to_scalar -@INPUT : loop_options - user options for looping - convert_input_to_scalar - TRUE if input should be converted - to scalar values -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to allow input to be converted to scalar values -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_convert_input_to_scalar(Loop_Options *loop_options, - int convert_input_to_scalar) -{ - loop_options->convert_input_to_scalar = convert_input_to_scalar; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_output_vector_size -@INPUT : loop_options - user options for looping - output_vector_size - length of vector dimension for output. - 0 means keep the size the same as the input. -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn set the length of the vector dimension for - output. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_output_vector_size(Loop_Options *loop_options, - int output_vector_size) -{ - if (output_vector_size < 0) { - (void) fprintf(stderr, - "Bad vector size %d in set_loop_output_vector_size\n", - output_vector_size); - exit(EXIT_FAILURE); - } - loop_options->output_vector_size = output_vector_size; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_first_input_mincid -@INPUT : loop_options - user options for looping - input_mincid - id of first minc file (already opened). -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn allow the user to pass in an already opened minc - file. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_first_input_mincid(Loop_Options *loop_options, - int input_mincid) -{ - loop_options->input_mincid = input_mincid; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_buffer_size -@INPUT : loop_options - user options for looping - buffer_size - maximum amount of buffer space to use (in bytes). -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn set a limit on the amount of buffer space used. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_buffer_size(Loop_Options *loop_options, - long buffer_size) -{ - if (buffer_size <= 0) { - (void) fprintf(stderr, "Bad buffer size %d in set_loop_buffer_size\n", - (int) buffer_size); - } - - loop_options->total_copy_space = buffer_size; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_dimension -@INPUT : loop_options - user options for looping - dimension_name - name of dimension that is treated like a series - of input files. -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to allow a dimension to be treated like a series of - input files (one buffer per dimension element per file). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 24, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_dimension(Loop_Options *loop_options, - char *dimension_name) -{ - if (loop_options->loop_dimension != NULL) - FREE(loop_options->loop_dimension); - - if ((dimension_name == NULL) || ((int)strlen(dimension_name) <= 0)) { - loop_options->loop_dimension = NULL; - } - else { - loop_options->loop_dimension = strdup(dimension_name); - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_input_file_function -@INPUT : loop_options - user options for looping - input_file_function - function to be called for each - input file so that the user can extract any extract - information. -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to allow the user to define a function to be called - for each input file before processing is done. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 20, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_input_file_function - (Loop_Options *loop_options, - VoxelInputFileFunction input_file_function) -{ - loop_options->input_file_function = input_file_function; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_output_file_function -@INPUT : loop_options - user options for looping - output_file_function - function to be called for each - output file so that the user can modify the header (file - is in define mode). -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to allow the user to define a function to be called - for each output file so that things can be added to the header. - The file will be in define mode and should remain that way. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_output_file_function - (Loop_Options *loop_options, - VoxelOutputFileFunction output_file_function) -{ - loop_options->output_file_function = output_file_function; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_copy_all_header -@INPUT : loop_options - user options for looping - copy_all_header - TRUE if all header info should be copied - to output file -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn copying of all header info off. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 13, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_copy_all_header(Loop_Options *loop_options, - int copy_all_header) -{ - loop_options->copy_all_header_info = copy_all_header; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_accumulate -@INPUT : loop_options - user options for looping - do_accumulation - TRUE if accumulating should be done, - FALSE otherwise. - num_extra_buffers - number of extra buffers to allocate. - start_function - function to be called before looping with - all output and extra buffers as arguments. NULL means - don't call any function. - finish_function - function to be called after looping with - all output and extra buffers as arguments. NULL means - don't call any function. -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to turn allow an accumulation mode of looping. Instead - of loading all input files and then calling the voxel routine, - the voxel routine is called after for each input file. The - user can provide a start_function that is called to initialize - the output buffers and a finish_function that is called to - finish calculations. The user can also ask for extra buffers. - These are treated like output buffers (at the end of the list) - but are not written out. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : December 6, 1994 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void set_loop_accumulate(Loop_Options *loop_options, - int do_accumulation, - int num_extra_buffers, - VoxelStartFunction start_function, - VoxelFinishFunction finish_function) -{ - loop_options->do_accumulate = do_accumulation; - - /* Turning off accumulation */ - if (!do_accumulation) { - loop_options->num_extra_buffers = 0; - loop_options->start_function = NULL; - loop_options->finish_function = NULL; - } - - /* Turning on accumulation */ - else { - if (num_extra_buffers < 0) { - (void) fprintf(stderr, - "Bad num_extra_buffers %d in set_loop_accumulate\n", - num_extra_buffers); - exit(EXIT_FAILURE); - } - loop_options->do_accumulate = TRUE; - loop_options->num_extra_buffers = num_extra_buffers; - loop_options->start_function = start_function; - loop_options->finish_function = finish_function; - } - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_loop_allocate_buffer_function -@INPUT : loop_options - user options for looping - allocate_buffer_function - user function that allocates and frees - input_data -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to set the function that allocates and frees input_data -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : Aug 29, 2000 (J. Taylor) -@MODIFIED : Sept. 19, 2000 (P. Neelin) ----------------------------------------------------------------------------- */ -public void set_loop_allocate_buffer_function(Loop_Options *loop_options, - AllocateBufferFunction allocate_buffer_function) - -{ - loop_options->allocate_buffer_function = allocate_buffer_function; -} - -/* ------------ Routines to set and get loop info ------------ */ - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : create_loop_info -@INPUT : (none) -@OUTPUT : (none) -@RETURNS : Pointer to Loop_Info structure -@DESCRIPTION: Routine to create and initialize the loop info structure. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 20, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private Loop_Info *create_loop_info(void) -{ - Loop_Info *loop_info; - - /* Allocate structure */ - loop_info = MALLOC(sizeof(*loop_info)); - - /* Fill in the defaults */ - initialize_loop_info(loop_info); - - /* Return the structure pointer */ - return loop_info; -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : initialize_loop_info -@INPUT : loop_info - pointer to Loop_Info structure -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Routine to initialize the loop info structure. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : February 28, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void initialize_loop_info(Loop_Info *loop_info) -{ - int idim; - - /* Fill in the defaults */ - loop_info->current_file = 0; - loop_info->current_index = 0; - for (idim=0; idim < MAX_VAR_DIMS; idim++) { - loop_info->start[idim] = 0; - loop_info->count[idim] = 0; - } - loop_info->loopfile_info = NULL; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : free_loop_info -@INPUT : loop_info - pointer to structure to cleanup -@OUTPUT : (none) -@RETURNS : (none) -@DESCRIPTION: Routine to cleanup and free the Loop_Info structure -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 20, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void free_loop_info(Loop_Info *loop_info) -{ - FREE(loop_info); -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_info_shape -@INPUT : loop_info - info structure pointer - start - start of hyperslab - count - count of hyperslab -@OUTPUT : (none) -@RETURNS : (none) -@DESCRIPTION: Routine to set the hyperslab shape (start and count) -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 20, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void set_info_shape(Loop_Info *loop_info, long start[], long count[]) -{ - int idim; - long size; - - /* Save the shape of the current chunk */ - for (idim=0; idim < MAX_VAR_DIMS; idim++) { - loop_info->start[idim] = start[idim]; - loop_info->count[idim] = count[idim]; - } - - /* Figure out how many voxels will be skipped by a step of one - in each dimension */ - loop_info->dimvoxels[MAX_VAR_DIMS-1] = 1; - for (idim=MAX_VAR_DIMS-2; idim >= 0; idim--) { - size = loop_info->count[idim+1]; - if (size <= 0) size = 1; - loop_info->dimvoxels[idim] = size * loop_info->dimvoxels[idim+1]; - } - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_info_shape -@INPUT : loop_info - info structure pointer - ndims - number of dimensions to copy (uses MAX_VAR_DIMS - if ndims == 0) -@OUTPUT : start - start of hyperslab - count - count of hyperslab -@RETURNS : (none) -@DESCRIPTION: Routine to get the current hyperslab shape (start and count) -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : January 20, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void get_info_shape(Loop_Info *loop_info, int ndims, - long start[], long count[]) -{ - int idim; - - if ((ndims <= 0) || (ndims > MAX_VAR_DIMS)) - ndims = MAX_VAR_DIMS; - for (idim=0; idim < ndims; idim++) { - start[idim] = loop_info->start[idim]; - count[idim] = loop_info->count[idim]; - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_info_voxel_index -@INPUT : loop_info - info structure pointer - subscript - 1-D voxel index into data buffers of voxel function - ndims - number of dimensions in index array (uses MAX_VAR_DIMS - if ndims == 0) -@OUTPUT : index - multi-dimensional voxel index into file -@RETURNS : (none) -@DESCRIPTION: Routine to get the current voxel index. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : November 28, 2001 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public void get_info_voxel_index(Loop_Info *loop_info, long subscript, - int ndims, long index[]) -{ - int idim; - long this_index; - - /* Check the array size */ - if ((ndims <= 0) || (ndims > MAX_VAR_DIMS)) - ndims = MAX_VAR_DIMS; - - /* Convert the 1-D subscript into a multi-dim index and add it to - the start index of the chunk */ - for (idim=0; idim < ndims; idim++) { - this_index = subscript / loop_info->dimvoxels[idim]; - index[idim] = loop_info->start[idim] + this_index; - subscript -= this_index * loop_info->dimvoxels[idim]; - } -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_info_current_file -@INPUT : loop_info - info structure pointer - current_file - number of current input file (for - accumulation) -@OUTPUT : (none) -@RETURNS : (none) -@DESCRIPTION: Routine to set the current input file number. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : February 28, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void set_info_current_file(Loop_Info *loop_info, int current_file) -{ - - loop_info->current_file = current_file; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_info_current_file -@INPUT : loop_info - info structure pointer -@OUTPUT : (none) -@RETURNS : Number of current input file (for accumulating over files) -@DESCRIPTION: Routine to get the current input file number. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : February 28, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public int get_info_current_file(Loop_Info *loop_info) -{ - - return loop_info->current_file; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_info_current_mincid -@INPUT : loop_info - info structure pointer -@OUTPUT : (none) -@RETURNS : Minc id for current input file (for accumulating over files) -@DESCRIPTION: Routine to get the current input file mincid. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 8, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public int get_info_current_mincid(Loop_Info *loop_info) -{ - - if (loop_info->loopfile_info == NULL) return MI_ERROR; - return get_input_mincid(loop_info->loopfile_info, loop_info->current_file); - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_info_current_index -@INPUT : loop_info - info structure pointer - current_index - number of current dimension index (for - accumulation over files and dimension) -@OUTPUT : (none) -@RETURNS : (none) -@DESCRIPTION: Routine to set the current dimension index. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : February 28, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void set_info_current_index(Loop_Info *loop_info, int current_index) -{ - - loop_info->current_index = current_index; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_info_current_index -@INPUT : loop_info - info structure pointer -@OUTPUT : (none) -@RETURNS : Number of current dimension index (for accumulating over files) -@DESCRIPTION: Routine to get the current dimension index. -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : February 28, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public int get_info_current_index(Loop_Info *loop_info) -{ - - return loop_info->current_index; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : set_info_loopfile_info -@INPUT : loop_info - info structure pointer - loopfile_info - loopfile info structure pointer -@OUTPUT : (none) -@RETURNS : (none) -@DESCRIPTION: Routine to set the loopfile info structure for future queries -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 7, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -private void set_info_loopfile_info(Loop_Info *loop_info, - Loopfile_Info *loopfile_info) -{ - - loop_info->loopfile_info = loopfile_info; - -} - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : get_info_whole_file -@INPUT : loop_info - info structure pointer -@OUTPUT : (none) -@RETURNS : Id of current minc file -@DESCRIPTION: Routine to change minc file handling to get the whole input - file, not just the header (should be called from within the - input_file_function). -@METHOD : -@GLOBALS : -@CALLS : -@CREATED : March 7, 1995 (Peter Neelin) -@MODIFIED : ----------------------------------------------------------------------------- */ -public int get_info_whole_file(Loop_Info *loop_info) -{ - Loopfile_Info *loopfile_info; - - /* Check for NULL pointer */ - if (loop_info->loopfile_info == NULL) return MI_ERROR; - loopfile_info = loop_info->loopfile_info; - - /* Make the input non-sequential (hold the files open if possible), and - ask for whole files */ - set_input_sequential(loopfile_info, FALSE); - set_input_headers_only(loopfile_info, FALSE); - - /* Return the current minc file id */ - if (loop_info->current_file >= 0) - return get_input_mincid(loopfile_info, loop_info->current_file); - else - return MI_ERROR; - -} -
deleted file mode 100644 --- a/progs/Proglib/voxel_loop.h +++ /dev/null @@ -1,291 +0,0 @@ -/* ----------------------------- MNI Header ----------------------------------- -@NAME : voxel_loop.h -@DESCRIPTION: Header file for voxel_loop.c -@GLOBALS : -@CREATED : January 10, 1994 (Peter Neelin) -@MODIFIED : - * $Log: voxel_loop.h,v $ - * Revision 6.3 2001-11-28 18:39:17 neelin - * Added get_info_vxoel_index to allow users to get the full multi-dimensional - * file index of the current voxel. - * Modifications to allow arg_string to be NULL. - * - * Revision 6.2 2000/09/19 14:36:05 neelin - * Added ability for caller to specify functions for allocating and freeing - * voxel buffers used in loop. This is particularly useful for embedding - * the voxel_loop code in other programs, such as Python, which manage memory - * in their own way. - * - * Revision 6.1 1999/10/19 14:45:16 neelin - * Fixed Log subsitutions for CVS - * - * Revision 6.0 1997/09/12 13:23:41 neelin - * Release of minc version 0.6 - * - * Revision 5.0 1997/08/21 13:24:41 neelin - * Release of minc version 0.5 - * - * Revision 4.0 1997/05/07 20:00:50 neelin - * Release of minc version 0.4 - * - * Revision 3.0 1995/05/15 19:31:35 neelin - * Release of minc version 0.3 - * - * Revision 1.3 1995/03/21 15:33:07 neelin - * Changed call to voxel_function to always use proper vector length and - * set num_voxels to the number of voxels, not multiplying by vector length. - * - * Revision 1.2 1995/03/21 14:06:39 neelin - * Improved interface and added lots of functionality (much for the benefit - * of mincconcat). - * - * Revision 1.1 94/12/14 10:18:21 neelin - * Initial revision - * - * Revision 2.0 94/09/28 10:36:28 neelin - * Release of minc version 0.2 - * - * Revision 1.3 94/09/28 10:36:22 neelin - * Pre-release - * - * Revision 1.2 94/01/12 10:19:19 neelin - * Added logging. Turned off filling. Added miclose for files. - * - * Revision 1.1 94/01/11 15:16:09 neelin - * Initial revision - * -@COPYRIGHT : - Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre, - Montreal Neurological Institute, McGill University. - Permission to use, copy, modify, and distribute this - software and its documentation for any purpose and without - fee is hereby granted, provided that the above copyright - notice appear in all copies. The author and McGill University - make no representations about the suitability of this - software for any purpose. It is provided "as is" without - express or implied warranty. ----------------------------------------------------------------------------- */ - -#ifndef public -# define public -#endif -#ifndef private -# define private static -#endif - -/* Includes */ -#include <minc.h> - -/* Incomplete structure typedefs */ - -typedef struct Loop_Info Loop_Info; -typedef struct Loop_Options Loop_Options; - -/* User function typedefs */ - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : VoxelFunction -@INPUT : caller_data - pointer to client data. - num_voxels - number of voxels to process. Note that the - total number of input values is - num_voxels * input_vector_length. - num_input_buffers - number of input buffers to handle - on this call - either total number of input files or 1 - (for accumulating over files). - input_vector_length - length of input vector. - input_data - array of pointers to input buffers (1 for - each input file, unless we are accumulating). - num_output_buffers - number of output buffers to handle - on this call - will be the total number of output files - unless we are accumulating over files (see - set_loop_accumulate). - output_vector_length - length of output vector - == input_vector_length or as set by - set_loop_output_vector_size. - loop_info - pointer that can be passed to functions returning - looping information -@OUTPUT : output_data - array of pointers to output buffers. Set values - to -DBL_MAX to represent illegal, out-of-range values. If - extra buffers are requested by set_loop_accumulate, they will - follow the output buffers. -@RETURNS : (nothing) -@DESCRIPTION: Typedef for function called by voxel_loop to process data. ----------------------------------------------------------------------------- */ -typedef void (*VoxelFunction) - (void *caller_data, long num_voxels, - int num_input_buffers, int input_vector_length, double *input_data[], - int num_output_buffers, int output_vector_length, double *output_data[], - Loop_Info *loop_info); - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : VoxelInputFileFunction -@INPUT : caller_data - pointer to client data. - input_mincid - mincid for current input file - input_curfile - current input file number (count from zero) - loop_info - pointer that can be passed to functions returning - looping information -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Typedef for function called by voxel_loop to get information - for each input file. ----------------------------------------------------------------------------- */ -typedef void (*VoxelInputFileFunction) - (void *caller_data, int input_mincid, int input_curfile, - Loop_Info *loop_info); - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : VoxelOutputFileFunction -@INPUT : caller_data - pointer to client data. - output_mincid - mincid for current output file - output_curfile - current output file number (count from zero) - loop_info - pointer that can be passed to functions returning - looping information -@OUTPUT : (none) -@RETURNS : (nothing) -@DESCRIPTION: Typedef for function called by voxel_loop to modify the header - of an output file (in define mode) ----------------------------------------------------------------------------- */ -typedef void (*VoxelOutputFileFunction) - (void *caller_data, int output_mincid, int output_curfile, - Loop_Info *loop_info); - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : VoxelStartFunction -@INPUT : caller_data - pointer to client data. - num_voxels - number of voxels to process. - output_num_buffers - number of output buffers to handle - on this call - will be the total number of output files - plus the number of extra buffers requested by - set_loop_accumulate. - output_vector_length - length of output vector = 1 or as set - by set_loop_output_vector_size. - loop_info - pointer that can be passed to functions returning - looping information -@OUTPUT : output_data - array of pointers to output buffers. If - extra buffers are requested by set_loop_accumulate, they will - follow the output buffers. -@RETURNS : (nothing) -@DESCRIPTION: Typedef for function called by voxel_loop to initialize data - processing when accumulating over files (specified when calling - set_loop_accumulate). ----------------------------------------------------------------------------- */ -typedef void (*VoxelStartFunction) - (void *caller_data, long num_voxels, - int output_num_buffers, int output_vector_length, double *output_data[], - Loop_Info *loop_info); - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : VoxelFinishFunction -@INPUT : caller_data - pointer to client data. - num_voxels - number of voxels to process. - output_num_buffers - number of output buffers to handle - on this call - will be the total number of output files - plus the number of extra buffers requested by - set_loop_accumulate. - output_vector_length - length of output vector = 1 or as set - by set_loop_output_vector_size. - loop_info - pointer that can be passed to functions returning - looping information -@OUTPUT : output_data - array of pointers to output buffers. If - extra buffers are requested by set_loop_accumulate, they will - follow the output buffers. -@RETURNS : (nothing) -@DESCRIPTION: Typedef for function called by voxel_loop to finish data - processing when accumulating over files (specified when calling - set_loop_accumulate). ----------------------------------------------------------------------------- */ -typedef void (*VoxelFinishFunction) - (void *caller_data, long num_voxels, - int output_num_buffers, int output_vector_length, double *output_data[], - Loop_Info *loop_info); - -/* ----------------------------- MNI Header ----------------------------------- -@NAME : AllocateBufferFunction -@INPUT : caller_data - pointer to client data. - do_allocations - if TRUE, allocate data, if FALSE, free data - num_input_buffers - number of input buffers to allocate - num_input_voxels - number of voxels in each input buffer - input_vector_length - number of values per input voxel - num_output_buffers - number of output buffers to allocate - num_output_voxels - number of voxels in each output buffer - output_vector_length - number of values per output voxel - num_extra_buffers - number of working buffers to allocate - num_extra_voxels - number of voxels in each extra buffer - extra_vector_length - number of values per extra voxel - loop_info - pointer that can be passed to functions returning - looping information - input_buffers, output_buffers, extra_buffers - if do_allocation - is FALSE, then arrays of pointers to buffers that need - to be freed. The pointer arrays should also be freed. -@OUTPUT : input_buffers, output_buffers, extra_buffers - if do_allocation - is TRUE, then these arrays of buffers should be allocated - (both the array of pointers and the buffers). The pointer - array should have length num_xxx_buffers and each buffer - should have length num_xxx_voxels*xxx_vector_length and be - of type double. -@RETURNS : (nothing) -@DESCRIPTION: Typedef for function called by voxel_loop to allocate and - free buffers. ----------------------------------------------------------------------------- */ -typedef void (*AllocateBufferFunction) - (void *caller_data, int do_allocation, - int num_input_buffers, int num_input_voxels, int input_vector_length, - double ***input_buffers, - int num_output_buffers, int num_output_voxels, int output_vector_length, - double ***output_buffers, - int num_extra_buffers, int num_extra_voxels, int extra_vector_length, - double ***extra_buffers, - Loop_Info *loop_info); - -/* Function declarations */ -public void voxel_loop(int num_input_files, char *input_files[], - int num_output_files, char *output_files[], - char *arg_string, - Loop_Options *loop_options, - VoxelFunction voxel_function, void *caller_data); -public Loop_Options *create_loop_options(void); -public void free_loop_options(Loop_Options *loop_options); -public void set_loop_clobber(Loop_Options *loop_options, - int clobber); -public void set_loop_verbose(Loop_Options *loop_options, - int verbose); -public void set_loop_datatype(Loop_Options *loop_options, - nc_type datatype, int is_signed, - double valid_min, double valid_max); -public void set_loop_max_open_files(Loop_Options *loop_options, - int max_open_files); -public void set_loop_check_dim_info(Loop_Options *loop_options, - int check_dim_info); -public void set_loop_convert_input_to_scalar(Loop_Options *loop_options, - int convert_input_to_scalar); -public void set_loop_output_vector_size(Loop_Options *loop_options, - int output_vector_size); -public void set_loop_first_input_mincid(Loop_Options *loop_options, - int input_mincid); -public void set_loop_buffer_size(Loop_Options *loop_options, - long buffer_size); -public void set_loop_dimension(Loop_Options *loop_options, - char *dimension_name); -public void set_loop_input_file_function - (Loop_Options *loop_options, - VoxelInputFileFunction input_file_function); -public void set_loop_output_file_function - (Loop_Options *loop_options, - VoxelOutputFileFunction output_file_function); -public void set_loop_copy_all_header(Loop_Options *loop_options, - int copy_all_header); -public void set_loop_accumulate(Loop_Options *loop_options, - int do_accumulation, - int num_extra_buffers, - VoxelStartFunction start_function, - VoxelFinishFunction finish_function); -public void set_loop_allocate_buffer_function(Loop_Options *loop_options, - AllocateBufferFunction allocate_buffer_function); -public void get_info_shape(Loop_Info *loop_info, int ndims, - long start[], long count[]); -public void get_info_voxel_index(Loop_Info *loop_info, long subscript, - int ndims, long index[]); -public int get_info_current_file(Loop_Info *loop_info); -public int get_info_current_mincid(Loop_Info *loop_info); -public int get_info_current_index(Loop_Info *loop_info); -public int get_info_whole_file(Loop_Info *loop_info);