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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* filename: m-getopt.c *
* *
* UTIL C-source: Medical Image Conversion Utility *
* *
* purpose : routines for handling the command-line options *
* *
* project : (X)MedCon by Erik Nolf *
* *
* Functions : MdcPrintGlobalOptions() - Print only global option usage *
* MdcPrintLocalOptions() - Print only local option usage *
* MdcPrintShortInfo() - Print info to get more help *
* MdcPrintUsage() - Print usage of medcon options *
* MdcHandleArgs() - Handle the arguments *
* MdcApplyReadOptions() - Apply read options *
* *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* $Id: m-getopt.c,v 1.147 2013/06/23 21:51:19 enlf Exp $
*/
/*
Copyright (C) 1997-2013 by Erik Nolf
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation; either version 2, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
59 Place - Suite 330, Boston, MA 02111-1307, USA. */
/****************************************************************************
H E A D E R S
****************************************************************************/
#include "m-depend.h"
#include <stdio.h>
#include <ctype.h>
#ifdef HAVE_STDLIB_H
#include <stdlib.h>
#endif
#ifdef HAVE_STRING_H
#include <string.h>
#endif
#ifdef HAVE_STRINGS_H
#ifndef _WIN32
#include <strings.h>
#endif
#endif
#include "medcon.h"
/****************************************************************************
F U N C T I O N S
****************************************************************************/
/* options useful for derived programs */
void MdcPrintGlobalOptions(void)
{
if (XMDC_GUI == MDC_NO) {
MdcPrntScrn("\
\n -c, --convert give list of conversion \"<format>\" strings:\n"
);
MdcPrntScrn("\n");
MdcPrntScrn("\t\t\"ascii\" = %s (.%s)\n",
FrmtString[MDC_FRMT_ASCII],
FrmtExt[MDC_FRMT_ASCII]);
MdcPrntScrn("\t\t\"bin\" = %s (.%s)\n",
FrmtString[MDC_FRMT_RAW],
FrmtExt[MDC_FRMT_RAW]);
#if MDC_INCLUDE_ACR
MdcPrntScrn("\t\t\"acr\" = %s (.%s)\n",
FrmtString[MDC_FRMT_ACR],
FrmtExt[MDC_FRMT_ACR]);
#endif
#if MDC_INCLUDE_ANLZ
MdcPrntScrn("\t\t\"anlz\" = %s (.%s)+(.img)\n",
FrmtString[MDC_FRMT_ANLZ],
FrmtExt[MDC_FRMT_ANLZ]);
#endif
#if MDC_INCLUDE_CONC
MdcPrntScrn("\t\t\"conc\" = %s (.%s)\n",
FrmtString[MDC_FRMT_CONC],
FrmtExt[MDC_FRMT_CONC]);
#endif
#if MDC_INCLUDE_DICM
MdcPrntScrn("\t\t\"dicom\" = %s (.%s)\n",
FrmtString[MDC_FRMT_DICM],
FrmtExt[MDC_FRMT_DICM]);
#endif
#if MDC_INCLUDE_ECAT
MdcPrntScrn("\t\t\"ecat6\" = %s (.%s)\n",
FrmtString[MDC_FRMT_ECAT6],
FrmtExt[MDC_FRMT_ECAT6]);
#if MDC_INCLUDE_TPC
MdcPrntScrn("\t\t\"ecat7\" = %s (.%s)\n",
FrmtString[MDC_FRMT_ECAT7],
FrmtExt[MDC_FRMT_ECAT7]);
#endif
#endif
#if MDC_INCLUDE_GIF
MdcPrntScrn("\t\t\"gif\" = %s (.%s)\n",
FrmtString[MDC_FRMT_GIF],
FrmtExt[MDC_FRMT_GIF]);
#endif
#if MDC_INCLUDE_INTF
MdcPrntScrn("\t\t\"intf\" = %s (.%s)+(.i33)\n",
FrmtString[MDC_FRMT_INTF],
FrmtExt[MDC_FRMT_INTF]);
#endif
#if MDC_INCLUDE_INW
MdcPrntScrn("\t\t\"inw\" = %s (.%s)\n",
FrmtString[MDC_FRMT_INW],
FrmtExt[MDC_FRMT_INW]);
#endif
#if MDC_INCLUDE_NIFTI
MdcPrntScrn("\t\t\"nifti\" = %s (.%s)\n",
FrmtString[MDC_FRMT_NIFTI],
FrmtExt[MDC_FRMT_NIFTI]);
#endif
#if MDC_INCLUDE_PNG
MdcPrntScrn("\t\t\"png\" = %s (.%s)\n",
FrmtString[MDC_FRMT_PNG],
FrmtExt[MDC_FRMT_PNG]);
#endif
}
MdcPrntScrn("\n\
Pixels: [-n] [-nf] [-qs|-qc|-q] [-b8|-b16[.12]] [-big|little]\n\
[-si=<slope>:<intercept>] [-cw=<centre>:<width>]\n\
\n -n, --negatives enable negative pixels\
\n -nf, --norm-over-frames normalize values over each frames\
\n -q, --quantitation quantitation using all factors (-qc)\
\n -qs, --quantification quantification (use one scale factor )\
\n -qc, --calibration calibration (use two scale factors)");
MdcPrntScrn("\
\n -b8, --unsigned-char write unsigned char pixels (8 bits)\
\n -b16, --signed-short write signed short integers (16 bits)\
\n -b16.12 write unsigned shorts, only 12 bits used\
\n -big, --big-endian write files in big endian\
\n -little, --little-endian write files in little endian\
\n -si force slope/intercept rescaling\
\n -cw force specified contrast remapping\
\n");
MdcPrntScrn("\n\
Fallback Read Format: [-fb-none|-fb-anlz|-fb-conc|-fb-ecat|fb-dicom]\n\
\n -fb-none, --without-fallback fallback disabled");
MdcPrntScrn("\
\n -fb-anlz, --fallback-analyze ");
#if MDC_INCLUDE_ANLZ
MdcPrntScrn("fallback on Analyze (SPM)");
#else
MdcPrntScrn("(*unused*)");
#endif
MdcPrntScrn("\
\n -fb-conc, --fallback-concorde ");
#if MDC_INCLUDE_CONC
MdcPrntScrn("fallback on Concorde uPET");
#else
MdcPrntScrn("(*unused*)");
#endif
MdcPrntScrn("\
\n -fb-ecat, --fallback-ecat ");
#if MDC_INCLUDE_ECAT
MdcPrntScrn("fallback on ECAT 6.4");
#else
MdcPrntScrn("(*unused*)");
#endif
MdcPrntScrn("\
\n -fb-dicom, --fallback-dicom ");
#if MDC_INCLUDE_DICM
MdcPrntScrn("fallback on DICOM 3.0");
#else
MdcPrntScrn("(*unused*)");
#endif
MdcPrntScrn("\n\n\
Slices Transform: [-fh -fv] [-rs -cs -cu] [-sqr | -sqr2] [-crop=<X>:<Y>:<W>:<H>]\n\t\t[-pad | -padtl | -padbr]\
\n -fh, --flip-horizontal flip images horizontally (along x-axis)\
\n -fv, --flip-vertical flip images vertically (along y-axis)\
\n -sqr, --make-square make square images (largest dimension)\
\n -sqr2, --make-square-two make square images (nearest power)");
MdcPrntScrn("\
\n -crop, --crop-images crop image dimensions\
\n -rs, --reverse-slices reverse slices sequence\
\n -cs, --cine-sorting apply cine sorting\
\n -cu, --cine-undo undo cine sorting\
\n -pad, --pad-around padding symmetrical around image\
\n -padtl, --pad-top-left padding before first row and column\
\n -padbr, --pad-bottom-right padding after last row and column (default)\
\n");
MdcPrntScrn("\n\
Color Remap: [-24 | -8 [-g -dith -mh|-mr|-mi|-mc|-lut <file>]]\n\
\n -24, --true-color color mode of 24 bits RGB triplets\
\n -8, --indexed-color color mode of 8 bits indexed colormap\
\n -dith, --dither-color apply dithering on color reduction\n\
\n -g, --make-gray remap images to grayscale");
MdcPrntScrn("\
\n -mh, --map-hotmetal load colormap hotmetal\
\n -mr, --map-rainbow load colormap rainbow\
\n -mi, --map-inverted load colormap gray inverted\
\n -mc, --map-combined load colormap combined (gray/rainbow)\
\n -lut, --load-lut load specified LUT colormap\
\n");
MdcPrntScrn("\n\
Extras: [-alias -noprefix -preacq -preser -uin]\
\n [[-splits | -splitf] | [-stacks | -stackf]]\n\
\n -alias, --alias-naming output name based on patient/study id's\
\n -noprefix, --without-prefix output name without default prefix\
\n -preacq, --prefix-acquisition use acquisition number as filename prefix\
\n -preser, --prefix-series use series number as filename prefix\
\n -uin, --use-institution-name override default name of institution");
MdcPrntScrn("\n\
\n -split3d, --split-slices split single image slices in separate files\
\n -split4d, --split-frames split volume time frames in separate files\
\n -stack3d, --stack-slices stack single image slices into one 3D file\
\n -stack4d, --stack-frames stack volume time frames into one 4D file\
\n");
#if MDC_INCLUDE_ECAT
MdcPrntScrn("\n\
Format Ecat/Matrix: [-byframe]\n\
\n -byframe, --sort-by-frame sort ECAT images by frame (not anatomical)\
\n");
/*MdcWaitForEnter(0);*/
#endif
#if MDC_INCLUDE_ANLZ
MdcPrntScrn("\n\
Format Analyze: [-spm -optspm]\n\
\n -spm, --analyze-spm use analyze format for SPM software\
\n");
if (XMDC_GUI == MDC_NO) {
MdcPrntScrn("\
\n -optspm, --options-spm ask for SPM related options\
\n");
}
#endif
#if (MDC_INCLUDE_DICM || MDC_INCLUDE_ACR)
MdcPrntScrn("\n\
Format DICOM:\n\
\n a) general: [-cw=<center>:<width>]\n\
[-contrast] [-gap] [-implicit] [-nometa]\n\
\n -contrast, --enable-contrast enable support for contrast changes\
\n -gap, --spacing-true-gap slice spacing is true gap or overlap");
MdcPrntScrn("\
\n -implicit, --write-implicit output file as implicit little endian\
\n -nometa, --write-without-meta output file without (part 10) meta header\
\n -cw force window center/width contrast");
MdcPrntScrn("\n\
\n b) mosaic: [-mosaic | -fmosaic=<W>x<H>x<N> [-interl] [-mfixv]]\n\
\n -mosaic, --enable-mosaic enable mosaic by \"detected\" stamps layout\
\n -fmosaic, --force-mosaic force mosaic by predefined stamps layout\
\n -mfixv, --mosaic-fix-voxel rescale voxel sizes by mosaic factor\
\n -interl, --mosaic-interlaced consider mosaic stamp slices as interlaced\
\n");
#endif
#if MDC_INCLUDE_GIF
MdcPrntScrn("\n\
\nFormat Gif89a: [-optgif]\n");
if (XMDC_GUI == MDC_NO) {
MdcPrntScrn("\
\n -optgif, --options-gif ask for GIF related options\
\n");
}else{
MdcPrntScrn("\
\n <none>\
\n");
}
#endif
#if MDC_INCLUDE_INTF
MdcPrntScrn("\
\nFormat InterFile: [-skip1 -nopath -one]\n\
\n -skip1, --skip-preview-slice skip first preview slice\
\n -nopath, --ignore-path ignore path in \'name of data file\' key\
\n -one, --single-file write header and image to same file\
\n");
#endif
if (XMDC_GUI == MDC_YES) MdcPrntScrn("\n");
}
/* options for MedCon in particular */
void MdcPrintLocalOptions(void)
{
MdcPrntScrn("\n\n\
Patient/Slice/Study: [-anon|-ident] [-vifi]\n\
\n -anon, --anonymous make patient/study anonymous\
\n -ident, --identify ask for patient/study information\
\n -vifi, --edit-fileinfo edit internal entries (images/slice/origent)\
\n");
MdcPrntScrn("\n\
Reslicing: [-tra|-sag|-cor]\n\
\n -tra, --tranverse reslice images transverse\
\n -sag, --sagittal reslice images sagittal\
\n -cor, --coronal reslice images coronal\
\n");
MdcPrntScrn("\n\
Debug/Mode: [-d -v -db -hackacr -ean]\n\
\n -d, --debug give debug information (printout FI)\
\n -s, --silent force silent mode, suppress all messages\
\n -v, --verbose run in verbose mode\
\n -db, --database print database info\
\n -ean, --echo-alias-name echo alias name on screen\
\n");
#if MDC_INCLUDE_ACR
MdcPrntScrn("\
\n -hackacr, --hack-acrtags try to locate and interpret acr tags in file\
\n");
#endif
MdcPrntScrn("\n");
}
void MdcPrintShortInfo(void)
{
if (XMDC_GUI == MDC_YES) {
MdcPrntScrn("\nGUI X Window System");
}else{
MdcPrntScrn("\nCLI");
}
MdcPrntScrn(" Medical Image Conversion Utility\n");
MdcPrntScrn("(X)MedCon %s\n",MdcGetLibShortVersion());
MdcPrntScrn("Copyright (C) 1997-2013 by Erik Nolf\n\n");
if (XMDC_GUI == MDC_YES) {
MdcPrntScrn("Try \'xmedcon --help\' for more information.\n\n");
}else{
MdcPrntScrn("Try \'medcon --help\' for more information.\n\n");
#ifdef _WIN32
fflush(NULL); MdcWaitForEnter(-1);
#endif
}
}
void MdcPrintUsage(char *pgrname)
{
/* allow usage info to stdout */
/* |more only catches stdout */
MDC_FILE_STDOUT = MDC_NO;
if (pgrname == NULL) {
/* usage for MedCon in particular */
MdcPrintShortInfo();
MdcPrntScrn("\nUsage:\n\n");
MdcPrntScrn(" medcon [options] -f <files> ...\n");
MdcPrntScrn("\n");
MdcPrntScrn("Flags:\n\n");
MdcPrntScrn(" -f, --file, --files file or list of files to handle\n");
MdcPrntScrn("\n");
MdcPrntScrn("General: [-i -e -r -w] [-p -pa|-c <format> ...] ");
MdcPrntScrn("[-o <basename>]\n");
MdcPrntScrn("\n");
MdcPrntScrn(" -e, --extract extract images from file\n");
MdcPrntScrn(" -i, --interactive read raw files after user input\n");
MdcPrntScrn(" -o, --output-name output name set from command-line\n");
MdcPrntScrn(" -p, --print-values print values of specified pixels\n");
MdcPrntScrn(" -pa, --print-all-values print all values without asking\n");
MdcPrntScrn(" -r, --rename-file rename file after user input\n");
MdcPrntScrn(" -w, --overwrite-files always overwrite files\n");
MdcPrintGlobalOptions();
MdcPrintLocalOptions();
}else{
/* usage for any derived program */
MdcPrntScrn("\nUsage:\n\n");
MdcPrntScrn(" %s [options] -f <file> ...\n",pgrname);
if (XMDC_GUI == MDC_NO) {
MdcPrntScrn("\n");
MdcPrntScrn("Options: General: [-c <format> ...] [-o <basename>]\n");
}
MdcPrintGlobalOptions();
}
exit(0);
}
int MdcHandleArgs(FILEINFO *fi, int argc, char *argv[], int MAXFILES)
{
int a,ARG=-1, DO_STDIN=MDC_NO;
char **files = mdc_arg_files;
int *convs = mdc_arg_convs;
int *total = mdc_arg_total;
char *pset = NULL;
MdcExtractInputStruct *input = &mdcextractinput;
/* limit number of files */
if (MAXFILES > MDC_MAX_FILES || MAXFILES <= 0) MAXFILES = MDC_MAX_FILES;
fi->map = MDC_MAP_GRAY; /* default color map */
if ( argc == 1 ) return(MDC_BAD_CODE);
/* initialize some stuff */
files[0]=NULL;
memset(convs,0,sizeof(int)*MDC_MAX_FRMTS);
memset(total,0,sizeof(int)*2);
mdcbufr[0]='\0';
for (a=1; a<argc; a++) {
if ( (strcasecmp(argv[a],"-h") == 0) ||
(strcasecmp(argv[a],"--help") == 0) ) return(MDC_BAD_CODE);
if ( (strcasecmp(argv[a],"-c") == 0) ||
(strcasecmp(argv[a],"--convert") == 0) ) { /* begin list of convs */
if (XMDC_GUI == MDC_NO) {
MDC_INFO=MDC_NO; MDC_CONVERT=MDC_YES; ARG=MDC_ARG_CONV;
}
continue;
}else if ( (strcasecmp(argv[a],"-i") == 0) ||
(strcasecmp(argv[a],"--interactive") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_INTERACTIVE=MDC_YES;
}
continue;
}else if ( (strcasecmp(argv[a],"-e") == 0) ||
(strcasecmp(argv[a],"--extract") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_EXTRACT=MDC_YES; ARG = MDC_ARG_EXTRACT;
input->INTERACTIVE = MDC_YES; input->list[0]='\0';
}
continue;
}else if ( (strcasecmp(argv[a],"-db") == 0) ||
(strcasecmp(argv[a],"--database") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_INFO_DB = MDC_YES; MDC_INFO = MDC_NO;
}
continue;
}else if ( (strcasecmp(argv[a],"-alias") == 0) ||
(strcasecmp(argv[a],"--alias-naming") == 0) ) {
MDC_ALIAS_NAME = MDC_YES;
continue;
}else if ( (strcasecmp(argv[a],"-ean") == 0) ||
(strcasecmp(argv[a],"--echo-alias-name") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_ECHO_ALIAS = MDC_YES;
MDC_INFO = MDC_NO;
if (MDC_BLOCK_MESSAGES == MDC_NO) MDC_BLOCK_MESSAGES = MDC_LEVEL_WARN;
}
continue;
}else if ( (strcasecmp(argv[a],"-noprefix") == 0) ||
(strcasecmp(argv[a],"--without-prefix") == 0) ) {
MDC_PREFIX_DISABLED = MDC_YES;
continue;
}else if ( (strcasecmp(argv[a],"-preacq") == 0) ||
(strcasecmp(argv[a],"--prefix-acquisition") == 0) ) {
MDC_PREFIX_ACQ = MDC_YES;
continue;
}else if ( (strcasecmp(argv[a],"-preser") == 0) ||
(strcasecmp(argv[a],"--prefix-series") == 0) ) {
MDC_PREFIX_SER = MDC_YES;
continue;
}else if ( (strcasecmp(argv[a],"-uin") == 0) ||
(strcasecmp(argv[a],"--use-institution-name") == 0) ) {
a+=1;
if (a < argc) MdcStringCopy(MDC_INSTITUTION,argv[a],strlen(argv[a]));
continue;
}else if ( (strcasecmp(argv[a],"-splits") == 0) ||
(strcasecmp(argv[a],"-split3d") == 0) ||
(strcasecmp(argv[a],"-split3D") == 0) ||
(strcasecmp(argv[a],"--split-slices") == 0) ) {
MDC_FILE_SPLIT = MDC_SPLIT_PER_SLICE;
continue;
}else if ( (strcasecmp(argv[a],"-splitf") == 0) ||
(strcasecmp(argv[a],"-split4d") == 0) ||
(strcasecmp(argv[a],"-split4D") == 0) ||
(strcasecmp(argv[a],"--split-frames") == 0) ) {
MDC_FILE_SPLIT = MDC_SPLIT_PER_FRAME;
continue;
}else if ( (strcasecmp(argv[a],"-stacks") == 0) ||
(strcasecmp(argv[a],"-stack3d") == 0) ||
(strcasecmp(argv[a],"-stack3D") == 0) ||
(strcasecmp(argv[a],"--stack-slices") == 0) ) {
MDC_FILE_STACK = MDC_STACK_SLICES;
continue;
}else if ( (strcasecmp(argv[a],"-stackf") == 0) ||
(strcasecmp(argv[a],"-stack4d") == 0) ||
(strcasecmp(argv[a],"-stack4D") == 0) ||
(strcasecmp(argv[a],"--stack-frames") == 0) ) {
MDC_FILE_STACK = MDC_STACK_FRAMES;
continue;
}else if ( (strcasecmp(argv[a],"-anon") == 0) ||
(strcasecmp(argv[a],"--anonymous") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_PATIENT_ANON = MDC_YES;
}
continue;
}else if ( (strcasecmp(argv[a],"-ident") == 0) ||
(strcasecmp(argv[a],"--identify") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_PATIENT_IDENT = MDC_YES;
}
continue;
}else if ( (strcasecmp(argv[a],"-o") == 0) ||
(strcasecmp(argv[a],"--output-name") == 0) ) {
a+=1;
if ((XMDC_GUI == MDC_NO) && (a < argc)) mdcbasename = argv[a];
continue;
}else if ( (strcasecmp(argv[a],"-p") == 0) ||
(strcasecmp(argv[a],"--print-values") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_PIXELS=MDC_YES; MDC_INFO=MDC_NO;
MDC_NEGATIVE=MDC_YES; MDC_CALIBRATE=MDC_YES;
}
continue;
}else if ( (strcasecmp(argv[a],"-pa") == 0) ||
(strcasecmp(argv[a],"--print-all-values") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_PIXELS=MDC_YES; MDC_INFO=MDC_NO;
MDC_NEGATIVE=MDC_YES; MDC_CALIBRATE=MDC_YES;
MDC_PIXELS_PRINT_ALL=MDC_YES;
}
continue;
}else if ( (strcasecmp(argv[a],"-r") == 0) ||
(strcasecmp(argv[a],"--rename-file") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_RENAME = MDC_YES;
}
continue;
}else if ( (strcasecmp(argv[a],"-w") == 0) ||
(strcasecmp(argv[a],"--overwrite-files") == 0) ) {
if (XMDC_GUI == MDC_NO) {
MDC_FILE_OVERWRITE = MDC_YES;
}
continue;
}else if ( (strcasecmp(argv[a],"-f") == 0) ||
(strcasecmp(argv[a],"--file") == 0) ||
(strcasecmp(argv[a],"--files") == 0)) {/* begin list of files */
ARG=MDC_ARG_FILE; continue;
}else if ( (strcasecmp(argv[a],"-n") == 0) ||
(strcasecmp(argv[a],"--negatives") == 0) ) {
MDC_NEGATIVE=MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-q") == 0) ||
(strcasecmp(argv[a],"--quantitation") == 0)) {
MDC_CALIBRATE=MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-qs") == 0) ||
(strcasecmp(argv[a],"--quantification") == 0) ) {
MDC_QUANTIFY=MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-qc") == 0) ||
(strcasecmp(argv[a],"--calibration") == 0) ) {
MDC_CALIBRATE=MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-24") == 0) ||
(strcasecmp(argv[a],"--true-color") == 0) ) {
MDC_COLOR_MODE = MDC_COLOR_RGB; continue;
}else if ( (strcasecmp(argv[a],"-8") == 0) ||
(strcasecmp(argv[a],"--indexed-color") == 0) ) {
MDC_COLOR_MODE = MDC_COLOR_INDEXED; continue;
}else if ( (strcasecmp(argv[a],"-mr") == 0) ||
(strcasecmp(argv[a],"--map-rainbow") == 0) ) {
MDC_COLOR_MAP = MDC_MAP_RAINBOW; MDC_MAKE_GRAY = MDC_YES;
MDC_COLOR_MODE = MDC_COLOR_INDEXED; continue;
}else if ( (strcasecmp(argv[a],"-mc") == 0) ||
(strcasecmp(argv[a],"--map-combined") == 0) ) {
MDC_COLOR_MAP = MDC_MAP_COMBINED; MDC_MAKE_GRAY = MDC_YES;
MDC_COLOR_MODE = MDC_COLOR_INDEXED; continue;
}else if ( (strcasecmp(argv[a],"-mh") == 0) ||
(strcasecmp(argv[a],"--map-hotmetal") == 0) ) {
MDC_COLOR_MAP = MDC_MAP_HOTMETAL; MDC_MAKE_GRAY = MDC_YES;
MDC_COLOR_MODE = MDC_COLOR_INDEXED; continue;
}else if ( (strcasecmp(argv[a],"-mi") == 0) ||
(strcasecmp(argv[a],"--map-inverted") == 0) ) {
MDC_COLOR_MAP = MDC_MAP_INVERTED; MDC_MAKE_GRAY = MDC_YES;
MDC_COLOR_MODE = MDC_COLOR_INDEXED; continue;
}else if ( (strcasecmp(argv[a],"-g") == 0) ||
(strcasecmp(argv[a],"--make-gray") == 0) ) {
MDC_COLOR_MAP = MDC_MAP_GRAY; MDC_MAKE_GRAY = MDC_YES;
MDC_COLOR_MODE = MDC_COLOR_INDEXED; continue;
}else if ( (strcasecmp(argv[a],"-dith") == 0) ||
(strcasecmp(argv[a],"--dither-color") == 0) ) {
MDC_DITHER_COLOR = MDC_YES;
MDC_COLOR_MODE = MDC_COLOR_INDEXED; continue;
}else if ( (strcasecmp(argv[a],"-lut") == 0) ||
(strcasecmp(argv[a],"--load-lut") == 0) ) {
a+=1;
if ((a < argc) && (MdcLoadLUT(argv[a]) == MDC_YES)) {
MDC_COLOR_MAP = MDC_MAP_LOADED; MDC_MAKE_GRAY = MDC_YES;
MDC_COLOR_MODE = MDC_COLOR_INDEXED;
}
continue;
#if MDC_INCLUDE_GIF
}else if ( (strcasecmp(argv[a],"-optgif") == 0) ||
(strcasecmp(argv[a],"--options-gif") == 0) ) {
MDC_GIF_OPTIONS = MDC_YES; continue;
#endif
#if MDC_INCLUDE_ACR
}else if ( (strcasecmp(argv[a],"-hackacr") == 0) ||
(strcasecmp(argv[a],"--hack-acrtags") == 0) ) {
MDC_HACK_ACR = MDC_YES; continue;
#endif
#if MDC_INCLUDE_ANLZ
}else if ( (strcasecmp(argv[a],"-spm") == 0) ||
(strcasecmp(argv[a],"--analyze-spm") == 0) ) {
MDC_ANLZ_SPM = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-optspm") == 0) ||
(strcasecmp(argv[a],"--options-spm") == 0) ) {
MDC_ANLZ_OPTIONS = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-fb-anlz") == 0) ||
(strcasecmp(argv[a],"--fallback-analyze") == 0) ) {
MDC_FALLBACK_FRMT = MDC_FRMT_ANLZ; continue;
#endif
#if MDC_INCLUDE_CONC
}else if ( (strcasecmp(argv[a],"-fb-conc") == 0) ||
(strcasecmp(argv[a],"--fallback-concorde") == 0) ) {
MDC_FALLBACK_FRMT = MDC_FRMT_CONC; continue;
#endif
#if MDC_INCLUDE_ECAT
}else if ( (strcasecmp(argv[a],"-fb-ecat") == 0) ||
(strcasecmp(argv[a],"--fallback-ecat") == 0) ) {
MDC_FALLBACK_FRMT = MDC_FRMT_ECAT6; continue;
}else if ( (strcasecmp(argv[a],"-byframe") == 0) ||
(strcasecmp(argv[a],"--sort-by-frame") == 0) ) {
MDC_ECAT6_SORT = MDC_BYFRAME; continue;
#endif
#if MDC_INCLUDE_DICM
}else if ( (strcasecmp(argv[a],"-fb-dicom") == 0) ||
(strcasecmp(argv[a],"--fallback-dicom") == 0) ) {
MDC_FALLBACK_FRMT = MDC_FRMT_DICM; continue;
}else if ( strstr(argv[a],"-si=") != NULL ) {
MDC_FORCE_RESCALE = MDC_YES; MDC_CALIBRATE = MDC_YES;
sscanf(argv[a],"-si=%f:%f",&mdc_si_slope,&mdc_si_intercept);
continue;
}else if ( strstr(argv[a],"-cw=") != NULL ) {
MDC_FORCE_CONTRAST = MDC_YES; MDC_CONTRAST_REMAP = MDC_YES;
sscanf(argv[a],"-cw=%f:%f",&mdc_cw_centre,&mdc_cw_width);
continue;
}else if ( (strcasecmp(argv[a],"-mosaic") == 0) ||
(strcasecmp(argv[a],"--enable-mosaic") == 0) ) {
MDC_DICOM_MOSAIC_ENABLED = MDC_YES;
continue;
}else if ((pset=strstr(argv[a],"-fmosaic=")) != NULL) {
MDC_DICOM_MOSAIC_ENABLED = MDC_YES; MDC_DICOM_MOSAIC_FORCED = MDC_YES;
MdcLowStr(pset);
sscanf(pset,"-fmosaic=%ux%ux%u",&mdc_mosaic_width
,&mdc_mosaic_height
,&mdc_mosaic_number);
continue;
}else if ((pset=strstr(argv[a],"--force-mosaic=")) != NULL) {
MDC_DICOM_MOSAIC_ENABLED = MDC_YES; MDC_DICOM_MOSAIC_FORCED = MDC_YES;
MdcLowStr(pset);
sscanf(pset,"--force-mosaic=%ux%ux%u",&mdc_mosaic_width
,&mdc_mosaic_height
,&mdc_mosaic_number);
continue;
}else if ( (strcasecmp(argv[a],"-mfixv") == 0) ||
(strcasecmp(argv[a],"--mosaic-fix-voxel") == 0) ) {
MDC_DICOM_MOSAIC_FIX_VOXEL = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-interl") == 0) ||
(strcasecmp(argv[a],"--mosaic-interlaced") == 0) ) {
MDC_DICOM_MOSAIC_DO_INTERL = MDC_YES; mdc_mosaic_interlaced = MDC_YES;
continue;
}else if ( (strcasecmp(argv[a],"-gap") == 0) ||
(strcasecmp(argv[a],"--spacing-true-gap") == 0) ) {
MDC_TRUE_GAP = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-contrast") == 0) ||
(strcasecmp(argv[a],"--enable-contrast") == 0) ) {
MDC_CONTRAST_REMAP = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-implicit") == 0) ||
(strcasecmp(argv[a],"--write-implicit") == 0) ) {
MDC_DICOM_WRITE_IMPLICIT = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-nometa") == 0) ||
(strcasecmp(argv[a],"--write-without-meta") == 0) ) {
MDC_DICOM_WRITE_NOMETA = MDC_YES; continue;
#endif
}else if ( (strcasecmp(argv[a],"-fb-none") == 0) ||
(strcasecmp(argv[a],"--without-fallback") == 0) ) {
MDC_FALLBACK_FRMT = MDC_FRMT_NONE; continue;
}else if ( (strcasecmp(argv[a],"-d") == 0) ||
(strcasecmp(argv[a],"--debug") == 0) ) {
MDC_DEBUG = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-nf") == 0) ||
(strcasecmp(argv[a],"--norm-over-frames") == 0) ) {
MDC_NORM_OVER_FRAMES = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-v") == 0) ||
(strcasecmp(argv[a],"--verbose") == 0) ) {
MDC_VERBOSE = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-b8") == 0) ||
(strcasecmp(argv[a],"--unsigned-char") == 0) ) {
MDC_FORCE_INT = BIT8_U; continue;
}else if ( (strcasecmp(argv[a],"-b16") == 0) ||
(strcasecmp(argv[a],"--signed-short") == 0) ) {
MDC_FORCE_INT = BIT16_S; MDC_INT16_BITS_USED=16; continue;
}else if ( strcasecmp(argv[a],"-b16.12") == 0 ) {
MDC_FORCE_INT = BIT16_S; MDC_INT16_BITS_USED=12; continue;
}else if ( strcasecmp(argv[a],"-debuging") == 0 ) { /* undocumented */
MDC_MY_DEBUG = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-vifi") == 0) ||
(strcasecmp(argv[a],"--edit-fileinfo") == 0) ) {
MDC_EDIT_FI = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-big") == 0) ||
(strcasecmp(argv[a],"--big-endian") == 0) ) {
MDC_WRITE_ENDIAN=MDC_BIG_ENDIAN; continue;
}else if ( (strcasecmp(argv[a],"-little") == 0) ||
(strcasecmp(argv[a],"--little-endian") == 0) ) {
MDC_WRITE_ENDIAN=MDC_LITTLE_ENDIAN; continue;
}else if ( (strcasecmp(argv[a],"-skip1") == 0) ||
(strcasecmp(argv[a],"--skip-preview-slice") == 0) ) {
MDC_SKIP_PREVIEW=MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-nopath") == 0) ||
(strcasecmp(argv[a],"--ignore-path") == 0) ) {
MDC_IGNORE_PATH=MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-one") == 0) ||
(strcasecmp(argv[a],"--single-file") == 0) ) {
MDC_SINGLE_FILE=MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-tra") == 0) ||
(strcasecmp(argv[a],"--transverse") == 0) ) {
MDC_RESLICE = MDC_TRANSAXIAL; continue;
}else if ( (strcasecmp(argv[a],"-sag") == 0) ||
(strcasecmp(argv[a],"--sagittal") == 0) ) {
MDC_RESLICE = MDC_SAGITTAL; continue;
}else if ( (strcasecmp(argv[a],"-cor") == 0) ||
(strcasecmp(argv[a],"--coronal") == 0) ) {
MDC_RESLICE = MDC_CORONAL; continue;
}else if ( (strcasecmp(argv[a],"-fh") == 0) ||
(strcasecmp(argv[a],"--flip-horizontal") == 0) ) {
MDC_FLIP_HORIZONTAL = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-fv") == 0) ||
(strcasecmp(argv[a],"--flip-vertical") == 0) ) {
MDC_FLIP_VERTICAL = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-rs") == 0) ||
(strcasecmp(argv[a],"--reverse-slices") == 0) ) {
MDC_SORT_REVERSE = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-cs") == 0) ||
(strcasecmp(argv[a],"--cine-sorting") == 0) ) {
MDC_SORT_CINE_APPLY = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-cu") == 0) ||
(strcasecmp(argv[a],"--cine-undo") == 0) ) {
MDC_SORT_CINE_UNDO = MDC_YES; continue;
}else if ( (strcasecmp(argv[a],"-sqr") == 0) ||
(strcasecmp(argv[a],"--make-square") == 0) ) {
MDC_MAKE_SQUARE = MDC_TRANSF_SQR1; continue;
}else if ( (strcasecmp(argv[a],"-sqr2") == 0) ||
(strcasecmp(argv[a],"--make-square-two") == 0) ) {
MDC_MAKE_SQUARE = MDC_TRANSF_SQR2; continue;
}else if ( (strcasecmp(argv[a],"-pad") == 0) ||
(strcasecmp(argv[a],"--pad-around") == 0) ) {
MDC_PADDING_MODE = MDC_PAD_AROUND; continue;
}else if ( (strcasecmp(argv[a],"-padtl") == 0) ||
(strcasecmp(argv[a],"--pad-top-left") == 0) ) {
MDC_PADDING_MODE = MDC_PAD_TOP_LEFT; continue;
}else if ( (strcasecmp(argv[a],"-padbr") == 0) ||
(strcasecmp(argv[a],"--pad-bottom-right") == 0) ) {
MDC_PADDING_MODE = MDC_PAD_BOTTOM_RIGHT; continue;
}else if ((pset=strstr(argv[a],"-crop=")) != NULL) {
MDC_CROP_IMAGES = MDC_YES;
MdcLowStr(pset);
sscanf(pset,"-crop=%u:%u:%u:%u",&mdc_crop_xoffset
,&mdc_crop_yoffset
,&mdc_crop_width
,&mdc_crop_height);
continue;
}else if ((pset=strstr(argv[a],"--crop-images=")) != NULL) {
MDC_CROP_IMAGES = MDC_YES;
MdcLowStr(pset);
sscanf(pset,"--crop-images=%u:%u:%u:%u",&mdc_crop_xoffset
,&mdc_crop_yoffset
,&mdc_crop_width
,&mdc_crop_height);
continue;
}else if ( (strcasecmp(argv[a],"-s") == 0) ||
(strcasecmp(argv[a],"--silent") == 0) ) {
MDC_BLOCK_MESSAGES = MDC_LEVEL_ALL; continue;
}
if ( ARG == -1 ) return(MDC_BAD_CODE); /* no '-c' or '-f' */
switch (ARG) {
case MDC_ARG_CONV:
if ( strcasecmp(argv[a],"ascii")== 0) {
convs[MDC_FRMT_ASCII]+=1; total[MDC_CONVS]+=1;
}else
if ( strcasecmp(argv[a],"bin") == 0) {
convs[MDC_FRMT_RAW]+=1; total[MDC_CONVS]+=1;
}else
#if MDC_INCLUDE_ACR
if ( strcasecmp(argv[a],"acr") == 0 ) {
convs[MDC_FRMT_ACR]+=1; total[MDC_CONVS]+=1;
}else
#endif
#if MDC_INCLUDE_GIF
if ( strcasecmp(argv[a],"gif") == 0 ) {
convs[MDC_FRMT_GIF]+=1; total[MDC_CONVS]+=1;
}else
#endif
#if MDC_INCLUDE_INW
if ( strcasecmp(argv[a],"inw") == 0 ) {
convs[MDC_FRMT_INW]+=1; total[MDC_CONVS]+=1;
}else
#endif
#if MDC_INCLUDE_CONC
if ( strcasecmp(argv[a],"conc") == 0 ) {
convs[MDC_FRMT_CONC]+=1; total[MDC_CONVS]+=1;
}else
#endif
#if MDC_INCLUDE_ECAT
if ( strcasecmp(argv[a],"ecat") == 0 ||
strcasecmp(argv[a],"ecat6") == 0 ) {
convs[MDC_FRMT_ECAT6]+=1; total[MDC_CONVS]+=1;
}else
#if MDC_INCLUDE_TPC
if ( strcasecmp(argv[a],"ecat7") == 0 ) {
convs[MDC_FRMT_ECAT7]+=1; total[MDC_CONVS]+=1;
}else
#endif
#endif
#if MDC_INCLUDE_INTF
if ( strcasecmp(argv[a],"intf") == 0 ) {
convs[MDC_FRMT_INTF]+=1; total[MDC_CONVS]+=1;
}else
#endif
#if MDC_INCLUDE_ANLZ
if ( strcasecmp(argv[a],"anlz") == 0 ) {
convs[MDC_FRMT_ANLZ]+=1; total[MDC_CONVS]+=1;
}else
#endif
#if MDC_INCLUDE_DICM
if ( strcasecmp(argv[a],"dicom") == 0) {
convs[MDC_FRMT_DICM]+=1; total[MDC_CONVS]+=1;
}else
#if MDC_INCLUDE_PNG
if ( strcasecmp(argv[a],"png") == 0) {
convs[MDC_FRMT_PNG]+=1; total[MDC_CONVS]+=1;
}else
#endif
#if MDC_INCLUDE_NIFTI
if ( strcasecmp(argv[a],"nifti") == 0) {
convs[MDC_FRMT_NIFTI]+=1; total[MDC_CONVS]+=1;
}else
#endif
#endif
if ( strcasecmp(argv[a],"-") == 0) {
MDC_FILE_STDOUT = MDC_YES;
}else
MdcPrntErr(MDC_BAD_CODE,"Unsupported conversion \"%s\"",argv[a]);
break;
case MDC_ARG_FILE:
if (MDC_FILE_STDIN == MDC_NO) {
/* input from files */
if ( total[MDC_FILES] == MAXFILES)
MdcPrntErr(MDC_OVER_FLOW,"Too many files specified (max=%d)"
,MAXFILES);
else
files[total[MDC_FILES]]=argv[a]; total[MDC_FILES]+=1;
}else{
/* input from stdin */
/* format specification of stdin file so no MdcCheckFrmt() needed */
/* otherwise a seek is needed, thus eleminating pipes support */
#if MDC_INCLUDE_ACR
if ( strcasecmp(argv[a],"acr") == 0 ) {
MdcPrntErr(MDC_NO_CODE,"ACR is unsupported in pipes (seek)");
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_ACR;
}else
#endif
#if MDC_INCLUDE_GIF
if ( strcasecmp(argv[a],"gif") == 0 ) {
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_GIF;
}else
#endif
#if MDC_INCLUDE_INW
if ( strcasecmp(argv[a],"inw") == 0 ) {
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_INW;
}else
#endif
#if MDC_INCLUDE_CONC
if ( strcasecmp(argv[a],"conc") == 0) {
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_CONC;
}else
#endif
#if MDC_INCLUDE_ECAT
if ( strcasecmp(argv[a],"ecat") == 0 ||
strcasecmp(argv[a],"ecat6") == 0 ) {
MdcPrntErr(MDC_NO_CODE,"ECAT6 is unsupported in pipes (seek)");
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_ECAT6;
}else
#if MDC_INCLUDE_TPC
if ( strcasecmp(argv[a],"ecat7") == 0) {
MdcPrntErr(MDC_NO_CODE,"ECAT7 is unsupported in pipes");
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_ECAT7;
}else
#endif
#endif
#if MDC_INCLUDE_INTF
if ( strcasecmp(argv[a],"intf") == 0) {
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_INTF;
}else
#endif
#if MDC_INCLUDE_ANLZ
if ( strcasecmp(argv[a],"anlz") == 0) {
MdcPrntErr(MDC_NO_CODE,"ANLZ is unsupported in pipes (seek)");
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_ANLZ;
}else
#endif
#if MDC_INCLUDE_DICM
if ( strcasecmp(argv[a],"dicom") == 0) {
MdcPrntErr(MDC_NO_CODE,"DICOM is unsupported in pipes (seek)");
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_DICM;
}else
#endif
#if MDC_INCLUDE_PNG
if ( strcasecmp(argv[a],"png") == 0) {
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_PNG;
}else
#endif
#if MDC_INCLUDE_NIFTI
if ( strcasecmp(argv[a],"nifti") == 0) {
DO_STDIN = MDC_YES; MDC_FRMT_INPUT = MDC_FRMT_NIFTI;
}else
#endif
{ DO_STDIN = MDC_NO; MDC_FRMT_INPUT = MDC_FRMT_NONE; }
}
if (strcmp(argv[a],"-") == 0) DO_STDIN = MDC_YES;
if (DO_STDIN == MDC_YES) {
files[0]=argv[a]; total[MDC_FILES] = 1;
DO_STDIN = MDC_NO; MDC_FILE_STDIN = MDC_YES;
}
break;
case MDC_ARG_EXTRACT:
if (isdigit((int)argv[a][0])) {
if (strlen(input->list) + strlen(argv[a]) < MDC_MAX_LIST) {
strcat(input->list,argv[a]); strcat(input->list," ");
}else{
MdcPrntErr(MDC_NO_CODE,"Extraction list too big for buffer");
}
input->INTERACTIVE = MDC_NO;
}else{
ARG = MDC_ARG_FILE;
}
break;
}
}
/* options shown but not available for GUI front-end */
if (XMDC_GUI == MDC_YES) {
if (MDC_FILE_STACK != MDC_NO) {
MdcPrntWarn("Options '-stack' not available to GUI front-end");
}
if ((MDC_GIF_OPTIONS == MDC_YES) || (MDC_ANLZ_OPTIONS == MDC_YES)) {
MdcPrntWarn("Options '-opt***' not available to GUI front-end");
}
}
/* split / stack mutually exclusive */
if ((MDC_FILE_STACK != MDC_NO) && (MDC_FILE_SPLIT != MDC_NO)) {
MdcPrntErr(MDC_NO_CODE,"Options '-stack' and '-split' mutually exclusive");
}
/* stack only in true color */
if ((MDC_FILE_STACK != MDC_NO) && (MDC_COLOR_MODE == MDC_COLOR_INDEXED)) {
MdcPrntErr(MDC_NO_CODE,"Stacking only supported for true color or gray");
}
/* print database info; legacy option, just used within ECAT */
if (MDC_INFO_DB == MDC_YES) {
if (total[MDC_FILES] > 1)
MdcPrntErr(MDC_NO_CODE,"Option '-db' only useful one file at a time");
if (MDC_CONVERT == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Option '-db' useless with '-c' conversion");
}
/* echo alias name; single option allowed */
if (MDC_ECHO_ALIAS == MDC_YES) {
if (total[MDC_FILES] > 1)
MdcPrntErr(MDC_NO_CODE,"Option '-ean' only useful one file at a time");
if (MDC_CONVERT == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Option '-ean' useless with '-c' conversion");
}
/* useless sorting selections */
if ((MDC_SORT_CINE_APPLY == MDC_YES) && (MDC_SORT_CINE_UNDO == MDC_YES)) {
MDC_SORT_CINE_APPLY = MDC_NO; MDC_SORT_CINE_UNDO = MDC_NO;
}
/* in case of alias filenaming, disable other options */
if (MDC_ALIAS_NAME == MDC_YES) {
MDC_RENAME = MDC_NO; mdcbasename = NULL;
}
/* need an image file, except for XMedCon GUI */
if ( (total[MDC_FILES] == 0) && (XMDC_GUI == MDC_NO) )
MdcPrntErr(MDC_NO_CODE,"No files specified");
/* checks related to file writing to stdout */
if (MDC_FILE_STDOUT == MDC_YES) {
if (MDC_VERBOSE == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Option '-v' disallowed with stdout file writing");
if ((total[MDC_FILES] > 1) && (MDC_FILE_STACK == MDC_NO))
MdcPrntErr(MDC_NO_CODE,"Only one file supported when writing to stdout");
if (total[MDC_CONVS] > 1)
MdcPrntErr(MDC_NO_CODE,"Only one format allowed when writing to stdout");
if (MDC_INTERACTIVE == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Interactive read impossible with stdout");
if (MDC_SINGLE_FILE == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Single file output unsupported with stdout");
}
/* checks related to file input from stdin */
if (MDC_FILE_STDIN == MDC_YES) {
if (MDC_HACK_ACR == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Hack ACR from stdin not allowed");
if (MDC_INTERACTIVE == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Interactive read impossible from stdin");
}
/* quantification troubles */
if (MDC_INFO == MDC_YES) {
if (MDC_QUANTIFY == MDC_YES) {
MDC_NEGATIVE=MDC_YES; MDC_CALIBRATE=MDC_NO;
}else{
MDC_NEGATIVE=MDC_YES; MDC_CALIBRATE=MDC_YES;
}
}
if ((MDC_ANLZ_SPM == MDC_YES) && (MDC_QUANTIFY == MDC_NO)
&& (MDC_CALIBRATE == MDC_NO) )
MdcPrntWarn("For SPM scaling you should select a quantification option");
if (MDC_INTERACTIVE == MDC_YES) {
MdcPrntWarn("Enabling negative pixels & disabling quantification");
MDC_NEGATIVE = MDC_YES;
MDC_QUANTIFY = MDC_NO;
MDC_CALIBRATE = MDC_NO;
}
if ( (MDC_PIXELS == MDC_YES) && (MDC_QUANTIFY == MDC_YES) )
MDC_CALIBRATE = MDC_NO;
/* conversion related issues */
if ((MDC_CONVERT == MDC_YES) || (XMDC_GUI == MDC_YES)) {
/* with output file */
if (XMDC_GUI == MDC_NO) {
if ( total[MDC_CONVS] == 0 )
MdcPrntErr(MDC_NO_CODE,"No conversion formats specified");
if (MDC_PIXELS == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Options '-c' & '-p(a)' are mutually exclusive");
}
}else{
/* without output file */
if (MDC_RENAME == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Option '-r' requires '-c' conversion specified");
if (MDC_EXTRACT == MDC_YES)
MdcPrntErr(MDC_NO_CODE,"Option '-e' requires '-c' conversion specified");
}
/* study identification */
if ( (MDC_PATIENT_ANON == MDC_YES) && (MDC_PATIENT_IDENT == MDC_YES) )
MdcPrntErr(MDC_NO_CODE,"Options '-anon' & '-ident' are mutually exclusive");
/* the must do FINAL quantification/calibration check */
if ( (MDC_QUANTIFY == MDC_YES) && (MDC_CALIBRATE == MDC_YES) )
MdcPrntErr(MDC_NO_CODE,"Options '-qs' & '-qc' are mutually exclusive");
/* some checks on mosaic settings */
if ( (MDC_DICOM_MOSAIC_DO_INTERL == MDC_YES) &&
(MDC_DICOM_MOSAIC_FORCED == MDC_NO) )
MdcPrntWarn("Option '-interl' requires mosaic forced");
/* color */
if (MDC_COLOR_MODE == MDC_COLOR_RGB) {
if (MDC_MAKE_GRAY == MDC_YES)
MdcPrntWarn("Option -24 overrides -g option");
if (MDC_DITHER_COLOR == MDC_YES)
MdcPrntWarn("Option -24 overrides -dith option");
}
/* giving an overview of settings */
if (MDC_VERBOSE ) {
if (MDC_WRITE_ENDIAN == MDC_LITTLE_ENDIAN)
MdcPrntMesg("Writing in little endian as default");
else
MdcPrntMesg("Writing in big endian as default");
switch (MDC_FALLBACK_FRMT) {
case MDC_FRMT_ANLZ:
MdcPrntMesg("Read fallback format Analyze (SPM)"); break;
case MDC_FRMT_DICM:
MdcPrntMesg("Read fallback format DICOM 3.0"); break;
case MDC_FRMT_CONC:
MdcPrntMesg("Read fallback format Concorde/uPET"); break;
case MDC_FRMT_ECAT6:
MdcPrntMesg("Read fallback format ECAT 6.4"); break;
}
/* flags */
if (MDC_FILE_OVERWRITE == MDC_YES)
MdcPrntMesg("Files overwrite is ON");
if (MDC_FILE_STDIN == MDC_YES)
MdcPrntMesg("Input from stdin is ON");
if (MDC_FILE_STDOUT == MDC_YES)
MdcPrntMesg("Output to stdout is ON");
if (MDC_QUANTIFY == MDC_YES)
MdcPrntMesg("Quantification is ON (ECAT units=[counts/second/pixel])");
if (MDC_CALIBRATE == MDC_YES)
MdcPrntMesg("Calibration is ON (ECAT units=[uCi/ml])");
if (MDC_NEGATIVE == MDC_YES)
MdcPrntMesg("Negative pixels is ON");
if (MDC_CONTRAST_REMAP == MDC_YES)
MdcPrntMesg("Contrast remapping is ON");
if (MDC_ANLZ_SPM == MDC_YES)
MdcPrntMesg("Analyze for SPM is ON");
if (MDC_DICOM_MOSAIC_ENABLED == MDC_YES)
MdcPrntMesg("Mosaic support is ON");
if (MDC_DICOM_MOSAIC_FORCED == MDC_YES)
MdcPrntMesg("Mosaic forced is ON");
if (MDC_DICOM_MOSAIC_FIX_VOXEL == MDC_YES)
MdcPrntMesg("Mosaic fix voxel is ON");
if (MDC_TRUE_GAP == MDC_YES)
MdcPrntMesg("True gap/overlap is ON");
if (MDC_DICOM_WRITE_IMPLICIT == MDC_YES)
MdcPrntMesg("Dicom implicit is ON");
if (MDC_DICOM_WRITE_NOMETA == MDC_YES)
MdcPrntMesg("Dicom no meta is ON");
if (MDC_NORM_OVER_FRAMES == MDC_YES)
MdcPrntMesg("Norm over frames is ON");
if (MDC_SKIP_PREVIEW == MDC_YES)
MdcPrntMesg("Skip preview slice is ON");
if (MDC_IGNORE_PATH == MDC_YES)
MdcPrntMesg("Ignore path fname is ON");
if (MDC_ALIAS_NAME == MDC_YES)
MdcPrntMesg("Alias file name is ON");
if (MDC_PREFIX_DISABLED == MDC_YES)
MdcPrntMesg("Disable prefix is ON");
if (MDC_FLIP_HORIZONTAL == MDC_YES)
MdcPrntMesg("Flip horizontal is ON");
if (MDC_FLIP_VERTICAL == MDC_YES)
MdcPrntMesg("Flip vertical is ON");
if (MDC_SORT_REVERSE == MDC_YES)
MdcPrntMesg("Sort reverse is ON");
if (MDC_SORT_CINE_APPLY == MDC_YES)
MdcPrntMesg("Sort cine apply is ON");
if (MDC_SORT_CINE_UNDO == MDC_YES)
MdcPrntMesg("Sort cine undo is ON");
if (MDC_MAKE_SQUARE == MDC_TRANSF_SQR1)
MdcPrntMesg("Make square images is ON");
if (MDC_MAKE_SQUARE == MDC_TRANSF_SQR2)
MdcPrntMesg("Make square pwr2 is ON");
if (MDC_FORCE_CONTRAST == MDC_YES)
MdcPrntMesg("DICOM contrast is ON");
if (MDC_FORCE_RESCALE == MDC_YES)
MdcPrntMesg("DICOM rescale is ON");
if (MDC_COLOR_MODE == MDC_COLOR_RGB)
MdcPrntMesg("Color 24 bits RGB is ON");
if (MDC_COLOR_MODE == MDC_COLOR_INDEXED)
MdcPrntMesg("Color 8 bits map is ON");
if (MDC_DITHER_COLOR == MDC_YES)
MdcPrntMesg("Color dithering is ON");
if (MDC_MAKE_GRAY == MDC_YES)
MdcPrntMesg("Color to gray is ON");
if (MDC_FORCE_INT != MDC_NO) {
switch (MDC_FORCE_INT) {
case BIT8_U :
MdcPrntMesg("Writing Uint8 pixs is ON (quantified values lost!)");
break;
case BIT16_S:
MdcPrntMesg("Writing Int16 pixs is ON (quantified values lost!)");
break;
default :
MdcPrntMesg("Writing Int16 pixs is ON (quantified values lost!)");
}
if (MDC_INT16_BITS_USED == 12)
MdcPrntMesg("Using only 12 bits is ON");
}
}
return(MDC_OK);
}
char *MdcApplyReadOptions(FILEINFO *fi)
{
char *msg=NULL;
/* anonymize patient information */
if (MDC_PATIENT_ANON) MdcMakePatAnonymous(fi);
/* ask for patient information */
if (MDC_PATIENT_IDENT) MdcGivePatInformation(fi);
/* edit the FILEINFO structure */
if (MDC_EDIT_FI) {
if ((msg = MdcEditFI(fi)) != NULL) return(msg);
}
/* print FILEINFO structure */
if (MDC_DEBUG) MdcPrintFI(fi);
/* print out pixel requested values */
if (MDC_PIXELS) MdcDisplayPixels(fi);
/* extract some images */
if (MDC_EXTRACT) {
if ((msg = MdcExtractImages(fi)) != NULL) return(msg);
}
/* reslice images as specified */
if (MDC_RESLICE != MDC_NO) {
if ((msg = MdcResliceImages(fi, MDC_RESLICE)) != NULL) return(msg);
}
/* rename base filename */
if (MDC_RENAME) MdcRenameFile(fi->ifname);
return(NULL);
}
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