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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* filename: m-stack.c *
* *
* UTIL C-source: Medical Image Conversion Utility *
* *
* purpose : stack files as specified *
* *
* project : (X)MedCon by Erik Nolf *
* *
* Functions : MdcGetNormSliceSpacing() - Get spacing between slices *
* MdcStackSlices() - Stack single slice image files*
* MdcStackFrames() - Stack multi slice volume files*
* MdcStackFiles() - Main stack routine *
* *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* $Id: m-stack.c,v 1.38 2008/01/23 21:28:36 enlf Exp $
*/
/*
Copyright (C) 1997-2008 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 <stdio.h>
#include <math.h>
#include "medcon.h"
/****************************************************************************
D E F I N E S
****************************************************************************/
static FILEINFO infi, outfi;
static int mdc_nrstack=0;
/****************************************************************************
F U N C T I O N S
****************************************************************************/
float MdcGetNormSliceSpacing(IMG_DATA *id1, IMG_DATA *id2)
{
/* slice_spacing = sqrt( (x2-x1)^2 + (y2-y1)^2 + (z2-z1)^2 ) */
float value, slice_spacing;
float dx, dy, dz;
slice_spacing = id1->slice_spacing;
dx = id1->image_pos_pat[0] - id2->image_pos_pat[0];
dy = id1->image_pos_pat[1] - id2->image_pos_pat[1];
dz = id1->image_pos_pat[2] - id2->image_pos_pat[2];
value = (float)sqrt((double)(dx*dx + dy*dy + dz*dz));
if (fabs(slice_spacing - value) <= MDC_FLT_EPSILON) {
/* insignificant difference, use original header value */
slice_spacing = id1->slice_spacing;
}else{
/* significant, use calculated value from image_pos_pat[] info */
slice_spacing = (float)value;
}
return(slice_spacing);
}
/* tomo : stack single slice image files into one 3D volume file (2D+ -> 3D)*/
/* planar: stack planar slice image files into one single file */
char *MdcStackSlices(void)
{
FILEINFO *ifi, *ofi;
IMG_DATA *id1, *id2;
DYNAMIC_DATA *dd1, *dd2;
Uint32 d, nr_of_images;
int HAS_DYNAMIC_DATA = MDC_NO;
char *msg=NULL;
int *total = mdc_arg_total; /* total arguments of files & conversions */
int *convs = mdc_arg_convs; /* counter for each conversion format */
char **files = mdc_arg_files; /* array of pointers to input filenames */
int i, convert, c;
float time_frame_duration=0.;
ifi = &infi; ofi= &outfi;
/* initialize output FILEINFO */
MdcInitFI(ofi,"stack3d");
nr_of_images = total[MDC_FILES];
if ((ifi->dynnr > 0) && (ifi->dyndata != NULL)) HAS_DYNAMIC_DATA = MDC_YES;
/* read and stack the several single slice files */
for (i=0; i<total[MDC_FILES]; i++) {
/* open file */
if (MdcOpenFile(ifi,files[i]) != MDC_OK) {
MdcCleanUpFI(ofi); return("stack slices : Failure to open file");
}
/* read the file */
if (MdcReadFile(ifi,i,NULL) != MDC_OK) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack slices : Failure to read file");
}
if (i == 0) {
/* copy FILEINFO stuff from 1st image */
MdcCopyFI(ofi,ifi,MDC_NO,MDC_NO);
/* set some specific parameters */
MdcSplitPath(ofi->ipath,ofi->idir,ofi->ifname);
ofi->dim[0] = 3;
ofi->dim[1] = ifi->dim[1];
ofi->dim[2] = ifi->dim[2];
ofi->dim[3] = nr_of_images;
ofi->pixdim[0] = 3.;
ofi->pixdim[1] = ifi->pixdim[1];
ofi->pixdim[2] = ifi->pixdim[2];
if (ofi->planar == MDC_NO) ofi->acquisition_type = MDC_ACQUISITION_TOMO;
if (!MdcGetStructDD(ofi,1)) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack slices : Couldn't alloc output DYNAMIC_DATA structs");
}else{
ofi->dyndata[0].nr_of_slices = nr_of_images;
}
if (!MdcGetStructID(ofi,nr_of_images)) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack slices : Couldn't alloc output ING_DATA structs");
}
/* remember time_frame_duration */
if (HAS_DYNAMIC_DATA == MDC_YES) {
time_frame_duration = ifi->dyndata[0].time_frame_duration;
}
}else{
if (HAS_DYNAMIC_DATA == MDC_YES) {
dd1 = &ofi->dyndata[0];
dd2 = &ifi->dyndata[0];
/* check time_frame_duration differences */
if (time_frame_duration != dd2->time_frame_duration) {
MdcPrntWarn("stack slices : Different image durations found");
}
/* planar = increment total time_frame_duration */
if (ofi->planar == MDC_YES) {
dd1->time_frame_duration += dd2->time_frame_duration;
}
}
}
/* sanity checks */
for (d=3; d < MDC_MAX_DIMS; d++) if (ifi->dim[d] > 1 ) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack slices : Only single slice (one image) files supported");
}
if (ifi->dim[3] == 0) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack slices : File without image found");
}
/* copy IMG_DATA info */
msg = MdcCopyID(&ofi->image[i],&ifi->image[0],MDC_YES);
if (msg != NULL) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
sprintf(mdcbufr,"stack slices : %s",msg); return(mdcbufr);
}
/* small checks for file integrity */
if (i > 0) {
id1 = &ifi->image[0]; /* current slice */
id2 = &ofi->image[i-1]; /* previous slice */
if (ifi->pat_slice_orient != ofi->pat_slice_orient) {
MdcPrntWarn("stack slices : Different 'patient_slice_orient' found");
}
if ((id1->width != id2->width) || (id1->height != id2->height)) {
MdcPrntWarn("stack slices : Different image dimensions found");
}
if (id1->slice_width != id2->slice_width) {
MdcPrntWarn("stack slices : Different slice thickness found");
}
if (id1->slice_spacing != id2->slice_spacing) {
MdcPrntWarn("stack slices : Different slice spacing found");
}
if (id1->type != id2->type) {
MdcPrntWarn("stack slices : Different pixel type found");
}
}
MdcCleanUpFI(ifi);
}
/* check all the images */
msg = MdcImagesPixelFiddle(ofi);
if (msg != NULL) {
MdcCleanUpFI(ofi);
sprintf(mdcbufr,"stack slices : %s",msg); return(mdcbufr);
}
if (ofi->planar == MDC_NO) {
/* check for orthogonal slices */
switch (ofi->pat_slice_orient) {
case MDC_SUPINE_HEADFIRST_SAGITTAL :
case MDC_SUPINE_FEETFIRST_SAGITTAL :
case MDC_PRONE_HEADFIRST_SAGITTAL :
case MDC_PRONE_FEETFIRST_SAGITTAL :
case MDC_SUPINE_HEADFIRST_CORONAL :
case MDC_SUPINE_FEETFIRST_CORONAL :
case MDC_PRONE_HEADFIRST_CORONAL :
case MDC_PRONE_FEETFIRST_CORONAL :
case MDC_SUPINE_HEADFIRST_TRANSAXIAL :
case MDC_SUPINE_FEETFIRST_TRANSAXIAL :
case MDC_PRONE_HEADFIRST_TRANSAXIAL :
case MDC_PRONE_FEETFIRST_TRANSAXIAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_SAGITTAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_SAGITTAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_SAGITTAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_SAGITTAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_CORONAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_CORONAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_CORONAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_CORONAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_TRANSAXIAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_TRANSAXIAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_TRANSAXIAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_TRANSAXIAL : break;
default:
MdcPrntWarn("stack slices : Probably file with Non-Orthogonal slices");
}
}
/* correct slice_spacing */
for (i=1; i<nr_of_images; i++) {
id1 = &ofi->image[i];
id2 = &ofi->image[i-1];
id1->slice_spacing=MdcGetNormSliceSpacing(id1,id2);
}
/* and also for the first image */
if (nr_of_images > 1) {
ofi->image[0].slice_spacing = ofi->image[1].slice_spacing;
}
/* if requested, reverse slices */
if (MDC_SORT_REVERSE == MDC_YES) {
msg = MdcSortReverse(ofi);
if (msg != NULL) return(msg);
}
/* write the file */
if (total[MDC_CONVS] > 0) {
/* go through conversion formats */
for (c=1; c<MDC_MAX_FRMTS; c++) {
convert = convs[c];
/* write output format when selected */
while (convert -- > 0) {
if (MdcWriteFile(ofi, c, mdc_nrstack++, NULL) != MDC_OK) {
MdcCleanUpFI(ofi);
return("stack slices : Failure to write file");
}
}
}
}
MdcCleanUpFI(ofi);
return(NULL);
}
/* tomo : stack volumes at different time frames into one 4D file (3D+ -> 4D)*/
/* planar: stack planar dynamic files into one planar dynamic file */
char *MdcStackFrames(void)
{
FILEINFO *ifi, *ofi;
Uint32 d, nr_of_frames, nr_of_images=0;
char *msg = NULL;
int *total = mdc_arg_total; /* total arguments of files & conversions */
int *convs = mdc_arg_convs; /* counter for each conversion format */
char **files = mdc_arg_files; /* array of pointers to input filenames */
int i, j, f, convert, c;
ifi = &infi; ofi = &outfi;
/* initialize output FILEINFO */
MdcInitFI(ofi,"stack4d");
nr_of_frames = total[MDC_FILES];
for (i=0, j=0, f=0; f < total[MDC_FILES]; f++) {
/* open file */
if (MdcOpenFile(ifi,files[f]) != MDC_OK) {
MdcCleanUpFI(ofi);
return("stack frames : Failure to open file");
}
/* read the file */
if (MdcReadFile(ifi,f,NULL) != MDC_OK) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : Failure to read file");
}
MdcCloseFile(ifi->ifp); /* no further need */
/* sanity checks */
for (d=4; d<MDC_MAX_DIMS; d++) if (ifi->dim[d] > 1) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : Only tomo volumes or planar dynamic supported");
}
if ((ifi->dim[3] == 1) && (ifi->planar == MDC_NO)) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : Use option '-stacks' for single slice files");
}
if (ifi->dim[3] == 0) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : File without images found");
}
if (f == 0) {
/* copy FILEINFO stuff from 1st file */
MdcCopyFI(ofi,ifi,MDC_NO,MDC_NO);
/* 4D -> dynamic */
ofi->acquisition_type = MDC_ACQUISITION_DYNAMIC;
/* get appropriate structs */
if (!MdcGetStructDD(ofi,nr_of_frames)) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : Couldn't alloc output DYNAMIC_DATA structs");
}
/* set some specific parameters */
if (ofi->planar == MDC_YES) {
/* planar: asymmetric */
nr_of_images= ifi->number; /* increment */
ofi->dim[0] = 3;
ofi->dim[1] = ifi->dim[1];
ofi->dim[2] = ifi->dim[2];
ofi->dim[3] = nr_of_images;
ofi->pixdim[0] = 3.;
ofi->pixdim[1] = ifi->pixdim[1];
ofi->pixdim[2] = ifi->pixdim[2];
ofi->pixdim[3] = ifi->pixdim[3];
}else{
/* tomo : symmectric */
nr_of_images= ifi->number * nr_of_frames;
ofi->dim[0] = 4;
ofi->dim[1] = ifi->dim[1];
ofi->dim[2] = ifi->dim[2];
ofi->dim[3] = ifi->dim[3];
ofi->dim[4] = nr_of_frames;
ofi->pixdim[0] = 4.;
ofi->pixdim[1] = ifi->pixdim[1];
ofi->pixdim[2] = ifi->pixdim[2];
ofi->pixdim[3] = ifi->pixdim[3];
ofi->pixdim[4] = ofi->dyndata[0].time_frame_duration; /* tomo */
}
/* malloc all IMG_DATA structs */
if (!MdcGetStructID(ofi,nr_of_images)) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : Couldn't alloc output IMG_DATA structs");
}
}else{
if (ofi->planar == MDC_YES) {
nr_of_images += ifi->number;
ofi->dim[3] = nr_of_images;
/* malloc IMG_DATA structs current frame */
if (!MdcGetStructID(ofi,nr_of_images)) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : Couldn't alloc planar IMG_DATA structs");
}
}
/* copy DYNAMIC_DATA struct when available */
/* f=0 already copied at initial MdcCopyFI() */
if ((ifi->dynnr > 0) && (ifi->dyndata != NULL)) {
MdcCopyDD(&ofi->dyndata[f],&ifi->dyndata[0]);
}
/* suspectable differences */
if (ifi->pat_slice_orient != ofi->pat_slice_orient) {
MdcPrntWarn("stack frames : Different 'patient_slice_orient' found");
}
if (ifi->planar != ofi->planar) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
return("stack frames : wrongful mixture of tomo and planar frames");
}
}
for (i=0; i<ifi->dim[3]; i++, j++) {
/* copy IMG_DATA info */
msg = MdcCopyID(&ofi->image[j],&ifi->image[i],MDC_YES);
if (msg != NULL) {
MdcCleanUpFI(ofi); MdcCleanUpFI(ifi);
sprintf(mdcbufr,"stack frames : %s",msg); return(mdcbufr);
}
}
MdcCleanUpFI(ifi);
}
/* check all the images */
msg = MdcImagesPixelFiddle(ofi);
if (msg != NULL) {
MdcCleanUpFI(ofi);
sprintf(mdcbufr,"stack frames : %s",msg); return(mdcbufr);
}
if (ofi->planar == MDC_NO) {
/* check for orthogonal slices */
switch (ofi->pat_slice_orient) {
case MDC_SUPINE_HEADFIRST_SAGITTAL :
case MDC_SUPINE_FEETFIRST_SAGITTAL :
case MDC_PRONE_HEADFIRST_SAGITTAL :
case MDC_PRONE_FEETFIRST_SAGITTAL :
case MDC_SUPINE_HEADFIRST_CORONAL :
case MDC_SUPINE_FEETFIRST_CORONAL :
case MDC_PRONE_HEADFIRST_CORONAL :
case MDC_PRONE_FEETFIRST_CORONAL :
case MDC_SUPINE_HEADFIRST_TRANSAXIAL :
case MDC_SUPINE_FEETFIRST_TRANSAXIAL :
case MDC_PRONE_HEADFIRST_TRANSAXIAL :
case MDC_PRONE_FEETFIRST_TRANSAXIAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_SAGITTAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_SAGITTAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_SAGITTAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_SAGITTAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_CORONAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_CORONAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_CORONAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_CORONAL :
case MDC_DECUBITUS_RIGHT_HEADFIRST_TRANSAXIAL :
case MDC_DECUBITUS_RIGHT_FEETFIRST_TRANSAXIAL :
case MDC_DECUBITUS_LEFT_HEADFIRST_TRANSAXIAL :
case MDC_DECUBITUS_LEFT_FEETFIRST_TRANSAXIAL : break;
default:
MdcPrntWarn("stack frames : Probably file with Non-Orthogonal slices");
}
}
/* write the file */
if (total[MDC_CONVS] > 0) {
/* go through conversion formats */
for (c=1; c<MDC_MAX_FRMTS; c++) {
convert = convs[c];
/* write output format when selected */
while (convert -- > 0) {
if (MdcWriteFile(ofi, c, mdc_nrstack++, NULL) != MDC_OK) {
MdcCleanUpFI(ofi);
return("stack frames : Failure to write file");
}
}
}
}
MdcCleanUpFI(ofi);
return(NULL);
}
char *MdcStackFiles(Int8 stack)
{
char *msg=NULL;
if (MDC_CONVERT != MDC_YES)
return("In order to stack specify an output format");
if (mdc_arg_total[MDC_FILES] == 1)
return("In order to stack at least two files are required");
switch (stack) {
case MDC_STACK_SLICES: msg = MdcStackSlices();
break;
case MDC_STACK_FRAMES: msg = MdcStackFrames();
break;
}
return(msg);
}
|
