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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* filename: m-anlz.c *
* *
* UTIL C-source: Medical Image Conversion Utility *
* *
* purpose : read and write ANALYZE files *
* *
* project : (X)MedCon by Erik Nolf *
* *
* Functions : MdcCheckANLZ() - Check ANALYZE format *
* MdcReadANLZ() - Read ANALYZE file *
* MdcWriteANLZ() - Write ANALYZE file *
* MdcWriteHeaderKey() - Write Header Key to file *
* MdcWriteImageDimension() - Write Image Dimension to file *
* MdcWriteDataHistory() - Write Data History to file *
* MdcWriteImagesData() - Write the images to file *
* MdcGetSpmOpt() - Get specific SPM options *
* *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* $Id: m-anlz.c,v 1.80 2007/05/21 20:16:10 enlf Exp $
*/
/*
Copyright (C) 1997-2007 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>
#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
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include "medcon.h"
/****************************************************************************
D E F I N E S
*****************************************************************************/
static Int8 INIT_SPMOPT = MDC_YES;
static MDC_SPMOPT spmopt;
#define MDC_ALWAYS_SET_4D 1 /* 0/1 disable/enable always set 4 dims */
/****************************************************************************
F U N C T I O N S
*****************************************************************************/
int MdcCheckANLZ(FILEINFO *fi)
{
MDC_ANLZ_HEADER_KEY hk;
int check=2, FORMAT=MDC_FRMT_NONE;
if (fread((char *)&hk,1,MDC_ANLZ_HK_SIZE,fi->ifp) != MDC_ANLZ_HK_SIZE)
return(MDC_BAD_READ);
MDC_FILE_ENDIAN = MDC_HOST_ENDIAN;
while (check--) {
if ( (hk.sizeof_hdr==348 || hk.sizeof_hdr==148 || hk.sizeof_hdr==228 ||
hk.sizeof_hdr==384)
&& (hk.regular == MDC_ANLZ_SIG ) ) {
FORMAT = MDC_FRMT_ANLZ;
break;
}
MDC_FILE_ENDIAN = !MDC_HOST_ENDIAN;
MdcSWAP(hk.sizeof_hdr);
}
return(FORMAT);
}
const char *MdcReadANLZ(FILEINFO *fi)
{
MDC_SPMOPT *opt = &spmopt;
FILE *fp=fi->ifp;
MDC_ANLZ_HEADER_KEY hk;
MDC_ANLZ_IMAGE_DIMS imd;
MDC_ANLZ_DATA_HIST dh;
IMG_DATA *id=NULL;
DYNAMIC_DATA *dd=NULL;
Uint32 bytes, i, plane, f, number;
Uint8 *img8=NULL;
Int8 WAS_COMPRESSED = MDC_NO;
char *origpath=NULL;
const char *err=NULL;
if (MDC_FILE_STDIN == MDC_YES)
return("ANLZ File input from stdin unsupported");
if (MDC_PROGRESS) MdcProgress(MDC_PROGRESS_BEGIN,0.,"Reading Analyze:");
if (MDC_VERBOSE) MdcPrntMesg("ANLZ Reading <%s> ...",fi->ifname);
/* get endian of the file in MDC_FILE_ENDIAN */
i=MdcCheckANLZ(fi); fseek(fp,0,SEEK_SET);
if (i != MDC_FRMT_ANLZ) {
if (MDC_FALLBACK_FRMT == MDC_FRMT_ANLZ) {
/* set host endian to try analyze */
MDC_FILE_ENDIAN = MDC_HOST_ENDIAN;
}else{
/* bail out */
return("ANLZ Endian check failed");
}
}
memset(&hk,0,MDC_ANLZ_HK_SIZE);
memset(&imd,0,MDC_ANLZ_IMD_SIZE);
memset(&dh,0,MDC_ANLZ_DH_SIZE);
/* put some default we use */
fi->reconstructed = MDC_YES;
fi->acquisition_type = MDC_ACQUISITION_TOMO;
dh.orient=(char)0xff;
if (fread((char *)&hk,1,MDC_ANLZ_HK_SIZE,fp) != MDC_ANLZ_HK_SIZE)
return("ANLZ Bad read HeadKey struct");
fi->endian=MDC_FILE_ENDIAN;
MdcSWAP(hk.sizeof_hdr); MdcSWAP(hk.extents); MdcSWAP(hk.session_error);
if (MDC_INFO) {
MdcPrntScrn("\nMDC_ANLZ_HEADER_KEY (%d bytes)\n",MDC_ANLZ_HK_SIZE);
MdcPrintLine('-',MDC_HALF_LENGTH);
MdcPrntScrn("sizeof_hdr : %d\n",hk.sizeof_hdr);
strncpy(mdcbufr,hk.data_type,10); mdcbufr[10]='\0';
MdcPrntScrn("data_type : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,hk.db_name,18); mdcbufr[18]='\0';
MdcPrntScrn("db_name : "); MdcPrintStr(mdcbufr);
MdcPrntScrn("extents : %d\n",hk.extents);
MdcPrntScrn("session_error : %hd\n",hk.session_error);
MdcPrntScrn("regular : "); MdcPrintChar(hk.regular);
MdcPrntScrn("\n");
MdcPrntScrn("hkey_un0 : "); MdcPrintChar(hk.hkey_un0);
MdcPrntScrn("\n");
}
if (MDC_INFO) {
MdcPrntScrn("\nIMAGE_DIMENSION (%d bytes)\n",MDC_ANLZ_IMD_SIZE);
MdcPrintLine('-',MDC_HALF_LENGTH);
}
if (fread((char *)&imd,1,MDC_ANLZ_IMD_SIZE,fp)!=MDC_ANLZ_IMD_SIZE)
return("ANLZ Bad read ImageDimensions struct");
for (i=0; i<MDC_ANLZ_MAX_DIMS; i++) {
MdcSWAP(imd.dim[i]); MdcSWAP(imd.pixdim[i]);
}
MdcSWAP(imd.unused1);
MdcSWAP(imd.avw_vox_offset);
MdcSWAP(imd.spm_pix_rescale);
MdcSWAP(imd.funused1); MdcSWAP(imd.funused2);
MdcSWAP(imd.avw_cal_max); MdcSWAP(imd.avw_cal_min);
MdcSWAP(imd.datatype); MdcSWAP(imd.bitpix); MdcSWAP(imd.dim_un0);
MdcSWAP(imd.compressed); MdcSWAP(imd.verified);
MdcSWAP(imd.glmax); MdcSWAP(imd.glmin);
if ((imd.dim[0] < 3) || (imd.dim[0] > (MDC_ANLZ_MAX_DIMS - 1))) {
if (MDC_FALLBACK_FRMT == MDC_FRMT_ANLZ) {
/* force reading, set to an acceptable value */
/* hope unused dims were initialized to zero */
for (i = 3; i < MDC_ANLZ_MAX_DIMS; i++) if (imd.dim[i] <= 0) break;
imd.dim[0] = i-1;
MdcPrntWarn("ANLZ Bad header value in dim[0] dimension");
}else{
/* bail out safely */
return("ANLZ Bad header value in dim[0] dimension");
}
}
if (MDC_INFO) {
for (i=0; i<MDC_ANLZ_MAX_DIMS; i++)
MdcPrntScrn("dim[%d] : %hd\n",i,imd.dim[i]);
strncpy(mdcbufr,imd.avw_vox_units,4); mdcbufr[4]='\0';
MdcPrntScrn("avw_vox_units : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,imd.avw_cal_units,8); mdcbufr[8]='\0';
MdcPrntScrn("avw_cal_units : "); MdcPrintStr(mdcbufr);
MdcPrntScrn("unused1 : %hd\n",imd.unused1);
MdcPrntScrn("datatype : ");
switch (imd.datatype) {
case MDC_ANLZ_DT_UNKNOWN : MdcPrntScrn("Unknown");
break;
case MDC_ANLZ_DT_BINARY : MdcPrntScrn("Binary");
break;
case MDC_ANLZ_DT_UNSIGNED_CHAR: MdcPrntScrn("Unsigned character");
break;
case MDC_ANLZ_DT_SIGNED_SHORT : MdcPrntScrn("Signed short integer");
break;
case MDC_ANLZ_DT_SIGNED_INT : MdcPrntScrn("Signed integer");
break;
case MDC_ANLZ_DT_FLOAT : MdcPrntScrn("Floating point");
break;
case MDC_ANLZ_DT_COMPLEX : MdcPrntScrn("Complex");
break;
case MDC_ANLZ_DT_DOUBLE : MdcPrntScrn("Double precision");
break;
case MDC_ANLZ_DT_RGB : MdcPrntScrn("Coloured RGB");
break;
case MDC_ANLZ_DT_ALL : MdcPrntScrn("All");
break;
default: MdcPrntScrn("Unknown");
}
MdcPrntScrn("\n");
MdcPrntScrn("bitpix : %hd\n",imd.bitpix);
for (i=0; i<MDC_ANLZ_MAX_DIMS; i++) {
MdcPrntScrn("pixdim[%d] : %-6e ",i,imd.pixdim[i]);
if ( i<4 ) MdcPrntScrn("[mm]\n");
else MdcPrntScrn("[ms]\n");
}
MdcPrntScrn("avw_vox_offset : %-6e\n",imd.avw_vox_offset);
MdcPrntScrn("spm_pix_rescale: %-6e\n",imd.spm_pix_rescale);
MdcPrntScrn("funused1 : %-6e\n",imd.funused1);
MdcPrntScrn("funused2 : %-6e\n",imd.funused2);
MdcPrntScrn("avw_cal_max : %-6e\n",imd.avw_cal_max);
MdcPrntScrn("avw_cal_min : %-6e\n",imd.avw_cal_min);
MdcPrntScrn("compressed : %6f\n",imd.compressed);
MdcPrntScrn("verified : %6f\n",imd.verified);
MdcPrntScrn("glmax : %d\n",imd.glmax);
MdcPrntScrn("glmin : %d\n",imd.glmin);
}
if (MDC_INFO) {
MdcPrntScrn("\nMDC_ANLZ_DATA_HISTORY (%d bytes)\n", MDC_ANLZ_DH_SIZE);
MdcPrintLine('-',MDC_HALF_LENGTH);
}
if (fread((char *)&dh,1,MDC_ANLZ_DH_SIZE,fp) != MDC_ANLZ_DH_SIZE) {
MdcPrntWarn("Reading <%s> - ANLZ Truncated header",fi->ifname);
}
memcpy(&opt->origin_x,&dh.originator[0],2); MdcSWAP(opt->origin_x);
memcpy(&opt->origin_y,&dh.originator[2],2); MdcSWAP(opt->origin_y);
memcpy(&opt->origin_z,&dh.originator[4],2); MdcSWAP(opt->origin_z);
MdcSWAP(dh.views); MdcSWAP(dh.vols_added);
MdcSWAP(dh.start_field); MdcSWAP(dh.field_skip);
MdcSWAP(dh.omax); MdcSWAP(dh.omin);
MdcSWAP(dh.smax); MdcSWAP(dh.smin);
if (MDC_INFO) {
strncpy(mdcbufr,dh.descrip,80); mdcbufr[80]='\0';
MdcPrntScrn("description : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,dh.aux_file,24); mdcbufr[24]='\0';
MdcPrntScrn("aux_file : "); MdcPrintStr(mdcbufr);
MdcPrntScrn("orient : ");
switch (dh.orient) {
case MDC_ANLZ_TRANS_UNFLIPPED: MdcPrntScrn("transverse unflipped");
break;
case MDC_ANLZ_CORON_UNFLIPPED: MdcPrntScrn("coronal unflipped");
break;
case MDC_ANLZ_SAGIT_UNFLIPPED: MdcPrntScrn("sagittal unflipped");
break;
case MDC_ANLZ_TRANS_FLIPPED : MdcPrntScrn("transverse flipped");
break;
case MDC_ANLZ_CORON_FLIPPED : MdcPrntScrn("coronal flipped");
break;
case MDC_ANLZ_SAGIT_FLIPPED : MdcPrntScrn("sagittal flipped");
break;
default: MdcPrntScrn("Unknown");
}
MdcPrntScrn("\n");
strncpy(mdcbufr,dh.originator,10); mdcbufr[10]='\0';
MdcPrntScrn("originator : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,dh.generated,10); mdcbufr[10]='\0';
MdcPrntScrn("generated : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,dh.scannum,10); mdcbufr[10]='\0';
MdcPrntScrn("scannum : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,dh.patient_id,10); mdcbufr[10]='\0';
MdcPrntScrn("patient_id : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,dh.exp_date,10); mdcbufr[10]='\0';
MdcPrntScrn("exp_date : "); MdcPrintStr(mdcbufr);
strncpy(mdcbufr,dh.exp_time,10); mdcbufr[10]='\0';
MdcPrntScrn("exp_time : "); MdcPrintStr(mdcbufr);
MdcPrntScrn("views : %d\n",dh.views);
MdcPrntScrn("vols_added : %d\n",dh.vols_added);
MdcPrntScrn("start_field : %d\n",dh.start_field);
MdcPrntScrn("omax : %d\n",dh.omax);
MdcPrntScrn("omin : %d\n",dh.omin);
MdcPrntScrn("smax : %d\n",dh.smax);
MdcPrntScrn("smin : %d\n",dh.smin);
}
if (MDC_INFO) {
MdcPrntScrn("\n");
MdcPrintLine('=',MDC_FULL_LENGTH);
MdcPrntScrn("SPM - HEADER INTERPRETATION\n");
MdcPrintLine('-',MDC_HALF_LENGTH);
MdcPrntScrn("image {x} : %hd\n",imd.dim[1]);
MdcPrntScrn("image {y} : %hd\n",imd.dim[2]);
MdcPrntScrn("image {z} : %hd\n",imd.dim[3]);
MdcPrntScrn("voxel {x} : %+e\n",imd.pixdim[1]);
MdcPrntScrn("voxel {y} : %+e\n",imd.pixdim[2]);
MdcPrntScrn("voxel {z} : %+e\n",imd.pixdim[3]);
MdcPrntScrn("scaling : %+e\n",imd.spm_pix_rescale);
MdcPrntScrn("data type : %hd\n",imd.datatype);
MdcPrntScrn("offset : %+e\n",imd.avw_vox_offset);
MdcPrntScrn("origin : %hd %hd %hd\n",opt->origin_x
,opt->origin_y
,opt->origin_z);
MdcPrntScrn("description : "); MdcPrintStr(dh.descrip);
MdcPrintLine('=',MDC_FULL_LENGTH);
}
/* save the offset, valid for AVW / SPM / MRIcro Analyze files */
opt->offset = imd.avw_vox_offset;
/* update our FILEINFO structure */
MdcStringCopy(fi->study_descr,dh.descrip,80);
MdcStringCopy(fi->patient_id,dh.patient_id,10);
MdcStringCopy(fi->study_id,dh.scannum,10);
if (MDC_ECHO_ALIAS == MDC_YES) {
MdcEchoAliasName(fi); return(NULL);
}
memcpy(fi->dim,imd.dim,sizeof(imd.dim));
memcpy(fi->pixdim,imd.pixdim,sizeof(imd.pixdim));
fi->mwidth = (Uint32) imd.dim[1]; fi->mheight = (Uint32) imd.dim[2];
for ( number=1, i=3; i<=imd.dim[0]; i++)
number*=imd.dim[i];
if (number == 0) return("ANLZ No valid images specified");
fi->bits = imd.bitpix;
switch (imd.datatype) {
case MDC_ANLZ_DT_BINARY : fi->type=BIT1; fi->bits=8; break;
case MDC_ANLZ_DT_UNSIGNED_CHAR: fi->type=BIT8_U; fi->bits=8; break;
case MDC_ANLZ_DT_SIGNED_SHORT : fi->type=BIT16_S; fi->bits=16; break;
case MDC_ANLZ_DT_SIGNED_INT : fi->type=BIT32_S; fi->bits=32; break;
case MDC_ANLZ_DT_FLOAT : fi->type=FLT32; fi->bits=32; break;
case MDC_ANLZ_DT_COMPLEX :
return("ANLZ Datatype `complex' unsupported"); break;
case MDC_ANLZ_DT_DOUBLE : fi->type=FLT64; fi->bits=64; break;
case MDC_ANLZ_DT_RGB : fi->type=COLRGB; fi->bits=24;
fi->map=MDC_MAP_PRESENT; break;
case MDC_ANLZ_DT_ALL :
return("ANLZ Datatype `All' unsupported"); break;
default :
switch (fi->bits) {
case 1: fi->type=BIT1; break;
case 8: fi->type=BIT8_U; break;
case 16: fi->type=BIT16_S; break;
case 32: fi->type=BIT32_S; break; /* could be FLT32 as well */
default: MdcPrntWarn("ANLZ Unknown datatype");
}
}
/* preserve original path */
MdcMergePath(fi->ipath,fi->idir,fi->ifname);
if ((origpath=malloc(strlen(fi->ipath) + 1)) == NULL)
return("ANLZ Couldn't allocate original path");
strcpy(origpath,fi->ipath);
MdcSplitPath(fi->ipath,fi->idir,fi->ifname);
/* read the image file */
MdcCloseFile(fi->ifp);
MdcMergePath(fi->ipath,fi->idir,fi->ifname);
MdcSetExt(fi->ipath,"img");
/* check for compressed image file */
if (MdcFileExists(fi->ipath) == MDC_NO) {
MdcAddCompressionExt(fi->compression,fi->ipath);
if (MdcDecompressFile(fi->ipath) != MDC_OK) {
MdcFree(origpath); return("ANLZ Decompression image file failed");
}
WAS_COMPRESSED = MDC_YES;
}
if ( (fi->ifp=fopen(fi->ipath,"rb")) == NULL ) {
MdcFree(origpath); return("ANLZ Couldn't open image file");
}
if (WAS_COMPRESSED == MDC_YES) {
unlink(fi->ipath);
if (MDC_PROGRESS) MdcProgress(MDC_PROGRESS_BEGIN,0.,"Reading Analyze:");
}
MdcSplitPath(fi->ipath,fi->idir,fi->ifname);
if (MDC_ANLZ_SPM == MDC_YES) {
/* interpret offset value from the header but we keep */
/* our precautions ... badly initialized headers */
long offsetu = (long)opt->offset;
if ((float)offsetu == opt->offset) fseek(fi->ifp,offsetu,SEEK_SET);
}
if (!MdcGetStructID(fi,number)) {
MdcFree(origpath); return("ANLZ Bad malloc IMG_DATA structs");
}
/* attempt to fill in orientation information */
switch (dh.orient) {
/* flipped, what's the meaning of flipped here ? */
case MDC_ANLZ_TRANS_UNFLIPPED:
fi->pat_slice_orient=MDC_SUPINE_HEADFIRST_TRANSAXIAL; break;
case MDC_ANLZ_CORON_UNFLIPPED:
fi->pat_slice_orient=MDC_SUPINE_HEADFIRST_CORONAL; break;
case MDC_ANLZ_SAGIT_UNFLIPPED:
fi->pat_slice_orient=MDC_SUPINE_HEADFIRST_SAGITTAL; break;
case MDC_ANLZ_TRANS_FLIPPED:
fi->pat_slice_orient=MDC_SUPINE_HEADFIRST_TRANSAXIAL; break;
case MDC_ANLZ_CORON_FLIPPED:
fi->pat_slice_orient=MDC_SUPINE_HEADFIRST_CORONAL; break;
case MDC_ANLZ_SAGIT_FLIPPED:
fi->pat_slice_orient=MDC_SUPINE_HEADFIRST_SAGITTAL; break;
}
strcpy(fi->pat_pos,MdcGetStrPatPos(fi->pat_slice_orient));
strcpy(fi->pat_orient,MdcGetStrPatOrient(fi->pat_slice_orient));
for ( i=0; i < fi->number; i++) {
if (MDC_PROGRESS) MdcProgress(MDC_PROGRESS_INCR,1./(float)fi->number,NULL);
plane = i % fi->dim[3];
id = &fi->image[i];
id->width = fi->mwidth;
id->height = fi->mheight;
id->bits = fi->bits;
id->type = fi->type;
if (MDC_ANLZ_SPM) {
/* consider the scaling factor */
if (imd.spm_pix_rescale > 0.0 ) id->quant_scale = imd.spm_pix_rescale;
}
if (fi->pixdim[0] == 3.0 ) {
id->pixel_xsize = fi->pixdim[1];
id->pixel_ysize = fi->pixdim[2];
id->slice_width = fi->pixdim[3];
}else if (fi->pixdim[0] == 4.0 ) {
id->pixel_xsize = fi->pixdim[1];
id->pixel_ysize = fi->pixdim[2];
id->slice_width = fi->pixdim[3];
}else if ( (fi->pixdim[1] > 0.0) &&
(fi->pixdim[2] > 0.0) &&
(fi->pixdim[3] > 0.0) ) { /* we will try it anyway */
/* some don't fill in pixdim[0] */
/* for example PMOD (11-Apr-2000) */
id->pixel_xsize = fi->pixdim[1];
id->pixel_ysize = fi->pixdim[2];
id->slice_width = fi->pixdim[3];
fi->pixdim[0] = 3.0;
}else {
id->pixel_xsize = 1.0;
id->pixel_ysize = 1.0;
id->slice_width = 1.0;
}
id->slice_spacing = id->slice_width;
MdcFillImgPos(fi,i,plane,0.0);
MdcFillImgOrient(fi,i);
bytes = MdcPixels2Bytes(fi->mwidth*fi->mheight*fi->bits);
if ( (id->buf=MdcGetImgBuffer(bytes)) == NULL ) {
MdcFree(img8); MdcFree(origpath); return("ANLZ Bad malloc image buffer");
}
if (img8 != NULL) {
/* image from buffer */
memcpy(id->buf,img8+i*bytes,bytes);
}else{
/* image from file */
if (fread(id->buf,1,bytes,fi->ifp) != bytes ) {
err=MdcHandleTruncated(fi, i+1,MDC_YES);
if (err != NULL) { MdcFree(origpath); return(err); }
}
if (fi->truncated) break;
}
}
MdcFree(img8);
MdcCloseFile(fi->ifp);
/* check some final FILEINFO entries */
if (fi->dim[4] > 1) {
fi->acquisition_type = MDC_ACQUISITION_DYNAMIC;
/* fill in dynamic data struct */
if (!MdcGetStructDD(fi,(unsigned)fi->dim[4]))
return("ANLZ Couldn't malloc DYNAMIC_DATA structs");
for (f=0; f < fi->dynnr; f++) {
dd = &fi->dyndata[f];
dd->nr_of_slices = fi->dim[3];
dd->time_frame_duration = fi->pixdim[4];
dd->time_frame_start = f * dd->time_frame_duration;
}
}
/* restore original filename */
strcpy(fi->ipath,origpath);
MdcSplitPath(fi->ipath,fi->idir,fi->ifname);
MdcFree(origpath);
if (fi->truncated) return("ANLZ Truncated image file");
return NULL;
}
int MdcWriteHeaderKey(FILEINFO *fi)
{
MDC_ANLZ_HEADER_KEY hk;
char *p = NULL;
memset(&hk,0,MDC_ANLZ_HK_SIZE);
hk.sizeof_hdr = MDC_ANLZ_HK_SIZE + MDC_ANLZ_IMD_SIZE + MDC_ANLZ_DH_SIZE;
sprintf(hk.data_type,"dsr");
MdcSplitPath(fi->opath,fi->odir,fi->ofname);
p = strrchr(fi->ofname,'.');
if (p != NULL) *p = '\0'; /* remove extension */
sprintf(hk.db_name,"%.18s",fi->ofname);
if (p != NULL) *p = '.'; /* add extension */
MdcMergePath(fi->opath,fi->odir,fi->ofname);
hk.extents=16384;
hk.session_error=0;
hk.regular='r';
MdcSWAP(hk.sizeof_hdr); MdcSWAP(hk.extents); MdcSWAP(hk.session_error);
fwrite((char *)&hk,1,MDC_ANLZ_HK_SIZE,fi->ofp);
if (ferror(fi->ofp)) return(MDC_NO);
return(MDC_YES);
}
int MdcWriteImageDimension(FILEINFO *fi, MDC_SPMOPT *opt)
{
MDC_ANLZ_IMAGE_DIMS imd;
float glmax, glmin;
int i;
memset(&imd,0,MDC_ANLZ_IMD_SIZE);
strcpy(imd.avw_vox_units,"mm");
for (i=0; i <= fi->dim[0]; i++) imd.dim[i] = fi->dim[i];
for (i=0; i <= fi->pixdim[0]; i++) imd.pixdim[i] = fi->pixdim[i];
#if MDC_ALWAYS_SET_4D
/* set dummy 4th dimension (time) */
if (imd.dim[0] == 3) {
imd.dim[0] = 4;
imd.dim[4] = 1;
}
if (imd.pixdim[0] == 3.) {
imd.pixdim[0] = 4.;
imd.pixdim[4] = 0.;
}
#endif
#ifdef MDC_USE_SLICE_SPACING
if (fi->number > 1) imd.pixdim[3] = fi->image[0].slice_spacing;
#endif
imd.dim[1] = (Int16) fi->mwidth;
imd.dim[2] = (Int16) fi->mheight;
if (fi->map == MDC_MAP_PRESENT) {
/* colored */
imd.datatype = MDC_ANLZ_DT_RGB;
imd.bitpix = 24;
}else{
/* grayscale */
if (MDC_FORCE_INT != MDC_NO) {
switch (MDC_FORCE_INT) {
case BIT8_U : imd.datatype = MDC_ANLZ_DT_UNSIGNED_CHAR;
imd.bitpix = 8;
break;
case BIT16_S: imd.datatype = MDC_ANLZ_DT_SIGNED_SHORT;
imd.bitpix = 16;
break;
default : imd.datatype = MDC_ANLZ_DT_SIGNED_SHORT;
imd.bitpix = 16;
}
}else if (!(MDC_QUANTIFY || MDC_CALIBRATE)) {
if ( fi->diff_type ) {
imd.datatype = MDC_ANLZ_DT_SIGNED_SHORT;
imd.bitpix = 16;
}else{
switch ( fi->type ) {
case BIT8_U:
case BIT8_S: imd.datatype = MDC_ANLZ_DT_UNSIGNED_CHAR;
imd.bitpix = 8;
break;
case BIT16_U:
case BIT16_S: imd.datatype = MDC_ANLZ_DT_SIGNED_SHORT;
imd.bitpix = 16;
break;
#ifdef HAVE_8BYTE_INT
case BIT64_U:
case BIT64_S:
#endif
case BIT32_U:
case BIT32_S: imd.datatype = MDC_ANLZ_DT_SIGNED_INT;
imd.bitpix = 32;
break;
case FLT32: imd.datatype = MDC_ANLZ_DT_FLOAT;
imd.bitpix = 32;
break;
case FLT64: imd.datatype = MDC_ANLZ_DT_DOUBLE;
imd.bitpix = 64;
break;
}
}
}else{
if (MDC_ANLZ_SPM == MDC_YES) { /* BIT16_S with scaling factor */
imd.datatype = MDC_ANLZ_DT_SIGNED_SHORT;
imd.bitpix = 16;
}else{
imd.datatype = MDC_ANLZ_DT_FLOAT;
imd.bitpix = 32;
}
}
}
/* find and set max/min values */
for (i = 0; i < fi->number; i++) {
IMG_DATA *id = &fi->image[i];
if (id->rescaled == MDC_YES) {
if (i == 0) { /* init values */
glmax = id->rescaled_max;
glmin = id->rescaled_min;
}else{ /* get max/min */
glmax = (id->rescaled_max > glmax) ? id->rescaled_max : glmax;
glmin = (id->rescaled_min < glmin) ? id->rescaled_min : glmin;
}
}else{
if (i == 0) { /* init values */
glmax = id->max;
glmin = id->min;
}else{ /* get max/min */
glmax = (id->max > glmax) ? id->max : glmax;
glmin = (id->min < glmin) ? id->min : glmin;
}
}
}
imd.glmax = (Int32) glmax;
imd.glmin = (Int32) glmin;
imd.avw_cal_max = fi->qglmax;
imd.avw_cal_min = fi->qglmin;
/* thinking about SPM */
if (imd.pixdim[0] <= 0.0 || imd.pixdim[0] >= (float)MDC_ANLZ_MAX_DIMS) {
imd.pixdim[0]=3.;
imd.pixdim[1]=1.;
imd.pixdim[2]=1.;
imd.pixdim[3]=1.;
}
if (opt != NULL) imd.avw_vox_offset = opt->offset;
if (MDC_ANLZ_SPM == MDC_YES) { /* the scaling factor */
if (fi->image[0].rescaled)
imd.spm_pix_rescale=(float)fi->image[0].rescaled_fctr;
/* did rescale over all images -> all images same factor */
}else{
imd.spm_pix_rescale=1.;
}
/* swap the data if necessary */
for (i=0; i<MDC_ANLZ_MAX_DIMS; i++) {
MdcSWAP(imd.dim[i]); MdcSWAP(imd.pixdim[i]);
}
MdcSWAP(imd.unused1);
MdcSWAP(imd.avw_vox_offset);
MdcSWAP(imd.spm_pix_rescale);
MdcSWAP(imd.funused1); MdcSWAP(imd.funused2);
MdcSWAP(imd.avw_cal_max); MdcSWAP(imd.avw_cal_min);
MdcSWAP(imd.datatype); MdcSWAP(imd.bitpix);
MdcSWAP(imd.compressed); MdcSWAP(imd.verified);
MdcSWAP(imd.glmax); MdcSWAP(imd.glmin);
fwrite((char *)&imd,1,MDC_ANLZ_IMD_SIZE,fi->ofp);
if (ferror(fi->ofp)) return(MDC_NO);
return(MDC_YES);
}
int MdcWriteDataHistory(FILEINFO *fi, MDC_SPMOPT *opt)
{
MDC_ANLZ_DATA_HIST dh;
memset(&dh,0,MDC_ANLZ_DH_SIZE);
sprintf(dh.descrip,"%.35s",fi->study_descr);
sprintf(dh.scannum,"%.10s",fi->study_id);
sprintf(dh.patient_id,"%.10s",fi->patient_id);
sprintf(dh.generated,"%.10s",MDC_PRGR);
switch (fi->pat_slice_orient) {
case MDC_SUPINE_HEADFIRST_TRANSAXIAL :
case MDC_PRONE_HEADFIRST_TRANSAXIAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_TRANSAXIAL:
case MDC_DECUBITUS_LEFT_HEADFIRST_TRANSAXIAL :
case MDC_SUPINE_FEETFIRST_TRANSAXIAL :
case MDC_PRONE_FEETFIRST_TRANSAXIAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_TRANSAXIAL:
case MDC_DECUBITUS_LEFT_FEETFIRST_TRANSAXIAL :
dh.orient = MDC_ANLZ_TRANS_UNFLIPPED;
break;
case MDC_SUPINE_HEADFIRST_CORONAL :
case MDC_PRONE_HEADFIRST_CORONAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_CORONAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_CORONAL :
case MDC_SUPINE_FEETFIRST_CORONAL :
case MDC_PRONE_FEETFIRST_CORONAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_CORONAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_CORONAL :
dh.orient = MDC_ANLZ_CORON_UNFLIPPED;
break;
case MDC_SUPINE_HEADFIRST_SAGITTAL :
case MDC_PRONE_HEADFIRST_SAGITTAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_SAGITTAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_SAGITTAL :
case MDC_SUPINE_FEETFIRST_SAGITTAL :
case MDC_PRONE_FEETFIRST_SAGITTAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_SAGITTAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_SAGITTAL :
dh.orient = MDC_ANLZ_SAGIT_UNFLIPPED;
break;
}
if (opt != NULL) {
MdcSWAP(opt->origin_x); memcpy(&dh.originator[0],&opt->origin_x,2);
MdcSWAP(opt->origin_y); memcpy(&dh.originator[2],&opt->origin_y,2);
MdcSWAP(opt->origin_z); memcpy(&dh.originator[4],&opt->origin_z,2);
}
fwrite((char *)&dh,1,MDC_ANLZ_DH_SIZE,fi->ofp);
if (ferror(fi->ofp)) return(MDC_NO);
return(MDC_YES);
}
char *MdcWriteImagesData(FILEINFO *fi)
{
double pval;
Uint8 grval;
Uint32 i, FREE;
Uint32 size, n, nr;
Uint16 type;
Uint8 *buf, *maxbuf;
Int8 saved_norm_over_frames=MDC_NORM_OVER_FRAMES;
IMG_DATA *id;
for (i=fi->number; i>0; i-- ) {
if (MDC_PROGRESS) MdcProgress(MDC_PROGRESS_INCR,1./(float)fi->number,NULL);
nr = fi->number - i; /* normal planes */
id = &fi->image[nr];
buf = id->buf; FREE = MDC_NO;
type = id->type;
if (fi->map != MDC_MAP_PRESENT) {
/* grayscale */
if (MDC_FORCE_INT != MDC_NO) {
if (MDC_ANLZ_SPM) MDC_NORM_OVER_FRAMES = MDC_NO;
switch (MDC_FORCE_INT) {
case BIT8_U : buf = MdcGetImgBIT8_U(fi,nr);
type=BIT8_U; FREE=MDC_YES;
break;
case BIT16_S: buf = MdcGetImgBIT16_S(fi,nr);
type=BIT16_S; FREE=MDC_YES;
break;
default : buf = MdcGetImgBIT16_S(fi,nr);
type=BIT16_S; FREE=MDC_YES;
}
if (MDC_ANLZ_SPM) MDC_NORM_OVER_FRAMES = saved_norm_over_frames;
}else if (!(MDC_QUANTIFY || MDC_CALIBRATE)) {
if ( fi->diff_type ) {
switch (id->type) {
case BIT16_S: buf = id->buf;
type = BIT16_S; FREE=MDC_NO;
break;
default : buf = MdcGetImgBIT16_S(fi,nr);
type = BIT16_S; FREE=MDC_YES;
break;
}
}else{
switch (id->type) {
case BIT8_S: buf = MdcGetImgBIT8_U(fi,nr);
type=BIT8_U ; FREE=MDC_YES;
break;
case BIT16_U: buf = MdcGetImgBIT16_S(fi,nr);
type=BIT16_S; FREE=MDC_YES;
break;
case BIT32_U: buf = MdcGetImgBIT32_S(fi,nr);
type=BIT32_S; FREE=MDC_YES;
break;
case BIT64_S:
case BIT64_U: buf = MdcGetImgBIT32_S(fi,nr);
type=BIT32_S; FREE=MDC_YES;
break;
}
}
}else{
if (MDC_ANLZ_SPM == MDC_YES) {
/* using the global scale factor <=> normalize over ALL images! */
/* so all images have the same scale factor */
MDC_NORM_OVER_FRAMES=MDC_NO;
buf = MdcGetImgBIT16_S(fi,nr);
type = BIT16_S; FREE=MDC_YES;
MDC_NORM_OVER_FRAMES=saved_norm_over_frames;
}else{
buf = MdcGetImgFLT32(fi,nr);
type=FLT32; FREE=MDC_YES;
}
}
}
if (buf == NULL) return("ANLZ Bad malloc image buffer");
if (fi->diff_size) {
maxbuf = MdcGetResizedImage(fi, buf, type, nr);
if (maxbuf == NULL) return("ANLZ Bad malloc maxbuf");
if (FREE) MdcFree(buf);
FREE = MDC_YES;
}else{
maxbuf = buf;
}
size = fi->mwidth * fi->mheight * MdcType2Bytes(type);
if (fi->type == COLRGB) {
/* true color */
if (fwrite(maxbuf,1,size,fi->ofp) != size)
return("ANLZ Bad write RGB buffer");
}else{
for (n=0; n < size; n += MdcType2Bytes(type)) {
/* indexed */
pval = MdcGetDoublePixel((Uint8 *)&maxbuf[n],type);
if (fi->map == MDC_MAP_PRESENT) {
/* colored */
grval = (Uint8)pval;
fwrite(&fi->palette[grval * 3 + 0], 1, 1, fi->ofp); /* red */
fwrite(&fi->palette[grval * 3 + 1], 1, 1, fi->ofp); /* green */
fwrite(&fi->palette[grval * 3 + 2], 1, 1, fi->ofp); /* blue */
if (ferror(fi->ofp))
return("ANLZ Bad write colored pixel");
}else{
/* grayscale */
if (!MdcWriteDoublePixel(pval,type,fi->ofp))
return("ANLZ Bad write image pixel");
}
}
}
if (FREE) MdcFree(maxbuf);
if (ferror(fi->ofp)) return("ANLZ Bad writing of images");
}
return NULL;
}
void MdcGetSpmOpt(FILEINFO *fi, MDC_SPMOPT *opt)
{
if (INIT_SPMOPT == MDC_YES) {
opt->origin_x = 0;
opt->origin_y = 0;
opt->origin_z = 0;
opt->offset = 0.;
INIT_SPMOPT = MDC_NO;
}
if (MDC_FILE_STDIN == MDC_YES) return; /* stdin already in use */
MdcPrintLine('-',MDC_FULL_LENGTH);
MdcPrntScrn("\tSPM OPTIONS\t\tORIG FILE: %s\n",fi->ifname);
MdcPrintLine('-',MDC_FULL_LENGTH);
MdcPrntScrn("\n\tThe origin values must be an Int16 value");
MdcPrntScrn("\n\tThere is NO check performed on the input!\n");
MdcPrntScrn("\n\tOrigin X [%d]? ",opt->origin_x);
if (!MdcPutDefault(mdcbufr)) opt->origin_x = (Int16)atoi(mdcbufr);
MdcPrntScrn("\n\tOrigin Y [%d]? ",opt->origin_y);
if (!MdcPutDefault(mdcbufr)) opt->origin_y = (Int16)atoi(mdcbufr);
MdcPrntScrn("\n\tOrigin Z [%d]? ",opt->origin_z);
if (!MdcPutDefault(mdcbufr)) opt->origin_z = (Int16)atoi(mdcbufr);
/* MARK: skip asking about offset */
/* MdcPrntScrn("\n\tOffset [%+e]? ",opt->offset); */
/* if (!MdcPutDefault(mdcbufr)) opt->offset = (float)atof(mdcbufr); */
MdcPrntScrn("\n");
MdcPrintLine('-',MDC_FULL_LENGTH);
}
const char *MdcWriteANLZ(FILEINFO *fi)
{
MDC_SPMOPT *opt = &spmopt;
char tmpfname[MDC_MAX_PATH + 1];
const char *msg;
MDC_FILE_ENDIAN = MDC_WRITE_ENDIAN;
/* user wanted to supply some parameters */
if ((MDC_ANLZ_OPTIONS == MDC_YES) && (XMDC_GUI == MDC_NO)) {
MdcGetSpmOpt(fi,opt);
}else {
/* set default origin to image centre of middle slice */
opt->origin_x = (Int16)((fi->dim[1] + 1)/2);
opt->origin_y = (Int16)((fi->dim[2] + 1)/2);
opt->origin_z = (Int16)((fi->dim[3] + 1)/2);
opt->offset = 0.;
}
/* header and image separate, rescaled stuff very important */
/* so we will write the images first ! */
/* get filename: no longer with truncation */
/* SPM, PMOD etc don't rely on db_name[18]) */
if (XMDC_GUI == MDC_YES) {
strcpy(tmpfname,fi->opath);
}else{
if (MDC_ALIAS_NAME == MDC_YES) {
MdcAliasName(fi,tmpfname);
}else{
strcpy(tmpfname,fi->ifname);
}
MdcDefaultName(fi,MDC_FRMT_ANLZ,fi->ofname,tmpfname);
}
if (MDC_PROGRESS) MdcProgress(MDC_PROGRESS_BEGIN,0.,"Writing Analyze:");
if (MDC_VERBOSE) MdcPrntMesg("ANLZ Writing <%s> & <.img> ...",fi->ofname);
/* writing images */
if (XMDC_GUI == MDC_YES) {
fi->ofname[0]='\0'; MdcNewExt(fi->ofname,tmpfname,"img");
}else{
MdcNewName(fi->ofname,tmpfname,"img");
}
if (MDC_FILE_STDOUT == MDC_YES) {
/* send image data to stdout (1>stdout) */
fi->ofp = stdout;
}else{
if (MdcKeepFile(fi->ofname))
return("ANLZ Image file exists!!");
if ( (fi->ofp=fopen(fi->ofname,"wb")) == NULL )
return ("ANLZ Couldn't open image file");
}
msg = MdcWriteImagesData(fi);
if (msg != NULL) return(msg);
MdcCloseFile(fi->ofp);
/* writing header with rescaled stuff */
if (XMDC_GUI == MDC_YES) {
strcpy(fi->ofname,tmpfname);
}else{
MdcDefaultName(fi,MDC_FRMT_ANLZ,fi->ofname,tmpfname);
}
if (MDC_FILE_STDOUT == MDC_YES) {
/* send header to stderr (2>stderr) */
fi->ofp = stderr;
}else{
if (MdcKeepFile(fi->ofname))
return("ANLZ Header file exists!!");
if ( (fi->ofp=fopen(fi->ofname,"wb")) == NULL )
return("ANLZ Couldn't open header file");
}
if ( !MdcWriteHeaderKey(fi) )
return("ANLZ Bad write HeaderKey struct");
if ( !MdcWriteImageDimension(fi, opt) )
return("ANLZ Bad write ImageDimension struct");
if ( !MdcWriteDataHistory(fi, opt) )
return("ANLZ Bad write DataHistory struct");
MdcCheckQuantitation(fi);
MdcCloseFile(fi->ofp);
return(NULL);
}
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