/*!
* - Function: WlzEffWriteMeshTransform3DWithoutDisplacementVTK
* - Returns: none
* - Purpose: output the orginal mesh.
* - Parameters:
* -# *fp: pointer pointing to a specific file.
* -# wmt3D: mesh transform.
* - Author: J. Rao, R. Baldock and B. Hill
*/
static WlzErrorNum ReadBibFile(FILE *inFile, char *inFileStr, WlzThreeDViewStruct *wlzViewStr )
{
WlzErrorNum errNum = WLZ_ERR_NONE;
BibFileRecord *bibfileRecord;
BibFileError bibFileErr;
char *errMsg;
if((inFile = fopen(inFileStr, "r")) == NULL )
{
printf("cannot open the input sample bib file.\n");
exit(1);
}
/* read the bibfile */
bibFileErr = BibFileRecordRead(&bibfileRecord, &errMsg, inFile);
while( bibFileErr == BIBFILE_ER_NONE ){
if( !strncmp(bibfileRecord->name, "Wlz3DSectionViewParams", 22) ){
/* allocate memory for wlzViewStr */
WlzEffBibParse3DSectionViewParamsRecord(bibfileRecord, wlzViewStr);
}
BibFileRecordFree(&bibfileRecord);
bibFileErr = BibFileRecordRead(&bibfileRecord, &errMsg, inFile);
}
BibFileRecordFree(&bibfileRecord);
fclose(inFile);
inFile = NULL;
return errNum;
}
int main(int argc,
char **argv)
{
WlzObject *obj = NULL, *nobj = NULL, *subDomain = NULL;
FILE *inFP = NULL, *outFP = NULL, *trFP = NULL, *bibFP = NULL;
char *outFile = NULL, *trFile = NULL, *bibFile = NULL;
char optList[] = "ACLNTa:b:d:f:m:o:r:s:t:u:R:h";
int option;
int i,
j,
iVal,
timer = 0,
voxRescale = 0,
allFlg = 0;
double dist=0.0, pitch=0.0, yaw=0.0, roll=0.0;
double scale=1.0;
WlzDVertex3 fixed={0.0,0.0,0.0};
WlzDVertex3 up={0.0,0.0,-1.0};
WlzThreeDViewStruct *viewStr=NULL;
WlzThreeDViewMode mode=WLZ_UP_IS_UP_MODE;
WlzInterpolationType interp = WLZ_INTERPOLATION_NEAREST;
WlzErrorNum errNum=WLZ_ERR_NONE;
BibFileRecord *bibfileRecord;
BibFileError bibFileErr;
struct timeval times[3];
char *errMsg;
/* additional defaults */
outFile = "-";
bibFile = NULL;
trFile = NULL;
subDomain = NULL;
/* read the argument list and check for an input file */
opterr = 0;
while( (option = getopt(argc, argv, optList)) != EOF ){
switch( option ){
case 'A':
allFlg = 1;
break;
case 'C':
interp = WLZ_INTERPOLATION_CLASSIFY_1;
break;
case 'L':
interp = WLZ_INTERPOLATION_LINEAR;
break;
case 'N':
interp = WLZ_INTERPOLATION_NEAREST;
break;
case 'a':
switch( sscanf(optarg, "%lg,%lg,%lg", &pitch, &yaw, &roll) ){
default:
usage(argv[0]);
return 1;
case 2:
break;
case 3:
mode = WLZ_ZETA_MODE;
break;
}
break;
case 'b':
bibFile = optarg;
break;
case 'd':
if( sscanf(optarg, "%lg", &dist) < 1 ){
usage(argv[0]);
return 1;
}
break;
case 'f':
if( sscanf(optarg, "%lg,%lg,%lg", &(fixed.vtX), &(fixed.vtY),
&(fixed.vtZ)) < 3 ){
usage(argv[0]);
return 1;
}
break;
case 'm':
if( sscanf(optarg, "%d", &iVal) < 1 ){
usage(argv[0]);
return 1;
}
else if( mode != WLZ_ZETA_MODE ){
switch( iVal ){
default:
usage(argv[0]);
return 1;
case 0:
mode = WLZ_UP_IS_UP_MODE;
break;
case 1:
mode = WLZ_STATUE_MODE;
break;
case 2:
mode = WLZ_ZETA_MODE;
break;
}
}
break;
case 'o':
outFile = optarg;
break;
case 'r':
if( sscanf(optarg, "%d", &voxRescale) < 1 ){
usage(argv[0]);
return 1;
}
break;
case 's':
if( sscanf(optarg, "%lg", &scale) < 1 ){
usage(argv[0]);
return 1;
}
break;
case 'u':
if( sscanf(optarg, "%lg,%lg,%lg", &(up.vtX), &(up.vtY),
&(up.vtZ)) < 3 ){
usage(argv[0]);
return 1;
}
break;
case 'R':
if((inFP = fopen(optarg, "rb"))){
if((subDomain = WlzReadObj(inFP, &errNum)) == NULL){
fprintf(stderr, "%s: can't read sub-domain object %s\n", argv[0], optarg);
usage(argv[0]);
return 1;
}
fclose(inFP);
}
else {
fprintf(stderr, "%s: can't open file %s\n", argv[0], optarg);
usage(argv[0]);
return 1;
}
break;
case 'T':
timer = 1;
break;
case 't':
trFile = optarg;
break;
case 'h':
default:
usage(argv[0]);
return 0;
}
}
/* check input file/stream */
inFP = stdin;
if( optind < argc ){
if( (inFP = fopen(*(argv+optind), "rb")) == NULL ){
fprintf(stderr, "%s: can't open file %s\n", argv[0], *(argv+optind));
usage(argv[0]);
return 1;
}
}
/* check output file/stream */
if( allFlg ){
if(strcmp(outFile, "-"))
{
/* strip any file extension */
for(i=0, j=strlen(outFile); i < strlen(outFile); i++){
if( outFile[i] == '.' ){
j = i;
}
}
outFile[j] = '\0';
}
else {
outFile = "plane";
}
}
else {
if(strcmp(outFile, "-"))
{
if((outFP = fopen(outFile, "wb")) == NULL)
{
errNum = WLZ_ERR_WRITE_EOF;
}
}
else
{
outFP = stdout;
}
}
/* create view structure */
if((viewStr = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum)) != NULL){
viewStr->theta = yaw * WLZ_M_PI / 180.0;
viewStr->phi = pitch * WLZ_M_PI / 180.0;
viewStr->zeta = roll * WLZ_M_PI / 180.0;
viewStr->dist = dist;
viewStr->fixed = fixed;
viewStr->up = up;
viewStr->view_mode = mode;
viewStr->scale = scale;
viewStr->voxelRescaleFlg = voxRescale;
}
if((errNum == WLZ_ERR_NONE) && (bibFile != NULL) && (trFile != NULL)) {
fprintf(stderr, "%s: both bibfile and transform file specified.\n",
argv[0]);
}
/* check bibfile - select first section parameters in the file */
if((errNum == WLZ_ERR_NONE) && (bibFile != NULL)){
if((bibFP = fopen(bibFile, "r")) != NULL){
bibFileErr = BibFileRecordRead(&bibfileRecord, &errMsg, bibFP);
while((bibFileErr == BIBFILE_ER_NONE) &&
(strncmp(bibfileRecord->name, "Wlz3DSectionViewParams", 22))){
BibFileRecordFree(&bibfileRecord);
bibFileErr = BibFileRecordRead(&bibfileRecord, &errMsg, bibFP);
}
fclose( bibFP );
if( bibFileErr != BIBFILE_ER_NONE ){
fprintf(stderr, "%s: error reading bibfile: %s\n", argv[0], errMsg);
AlcFree((void *) errMsg);
return 1;
}
WlzEffBibParse3DSectionViewParamsRecord(bibfileRecord, viewStr);
BibFileRecordFree(&bibfileRecord);
}
else {
fprintf(stderr, "%s: can't open parameter bibfile %s\n", argv[0],
bibFile);
return 1;
}
}
if((errNum == WLZ_ERR_NONE) && (trFile != NULL)){
if((trFP = fopen(trFile, "r")) != NULL){
WlzObject *trObj = NULL;
if((trObj = WlzReadObj(trFP, &errNum)) != NULL) {
if(trObj->type != WLZ_3D_VIEW_STRUCT) {
errNum = WLZ_ERR_OBJECT_TYPE;
}
else if (trObj->domain.core == NULL) {
errNum = WLZ_ERR_DOMAIN_NULL;
}
else {
WlzThreeDViewStruct *fViewStr;
fViewStr = trObj->domain.vs3d;
viewStr->theta = fViewStr->theta;
viewStr->phi = fViewStr->phi;
viewStr->zeta = fViewStr->zeta;
viewStr->dist = fViewStr->dist;
viewStr->fixed = fViewStr->fixed;
viewStr->up = fViewStr->up;
viewStr->view_mode = fViewStr->view_mode;
viewStr->scale = fViewStr->scale;
viewStr->voxelRescaleFlg = fViewStr->voxelRescaleFlg;
}
(void )WlzFreeObj(trObj);
}
}
if(errNum != WLZ_ERR_NONE) {
fprintf(stderr,
"%s: error reading section view transform from %s.\n",
argv[0], trFile);
return 1;
}
}
/* read objects and section if possible */
while((errNum == WLZ_ERR_NONE) &&
((obj = WlzReadObj(inFP, &errNum)) != NULL))
{
obj = WlzAssignObject(obj, &errNum);
switch( obj->type )
{
case WLZ_CONTOUR:
case WLZ_3D_DOMAINOBJ:
if(voxRescale && obj->domain.core)
{
viewStr->voxelSize[0] = obj->domain.p->voxel_size[0];
viewStr->voxelSize[1] = obj->domain.p->voxel_size[1];
viewStr->voxelSize[2] = obj->domain.p->voxel_size[2];
}
WlzInit3DViewStruct(viewStr, obj);
if(timer)
{
gettimeofday(times + 0, NULL);
}
if( allFlg ){
/* loop through all possible planes */
for(i=WLZ_NINT(viewStr->minvals.vtZ), j=0;
i <= WLZ_NINT(viewStr->maxvals.vtZ); i++, j++){
viewStr->dist = i;
WlzInit3DViewStruct(viewStr, obj);
nobj = WlzGetSubSectionFromObject(obj, subDomain, viewStr, interp,
NULL, &errNum);
if( nobj != NULL){
char fileBuf[256];
sprintf(fileBuf, "%s%06d.wlz", outFile, j);
if((outFP = fopen(fileBuf, "w")) != NULL){
WlzWriteObj(outFP, nobj);
fclose(outFP);
}
}
else {
return errNum;
}
WlzFreeObj(nobj);
}
}
else {
nobj = WlzGetSubSectionFromObject(obj, subDomain, viewStr, interp,
NULL, &errNum);
if( nobj != NULL){
WlzWriteObj(outFP, nobj);
}
else {
return errNum;
}
WlzFreeObj(nobj);
}
if(timer)
{
gettimeofday(times + 1, NULL);
ALC_TIMERSUB(times + 1, times + 0, times + 2);
(void )fprintf(stderr,
"%s: Elapsed time = %g\n",
*argv,
times[2].tv_sec + (0.000001 * times[2].tv_usec));
}
break;
default:
WlzWriteObj(outFP, obj);
break;
}
WlzFreeObj(obj);
}
if(errNum == WLZ_ERR_READ_EOF)
{
errNum = WLZ_ERR_NONE;
}
if( viewStr ){
WlzFree3DViewStruct(viewStr);
}
if( subDomain ){
WlzFreeObj(subDomain);
}
return errNum;
}
int main(int argc,
char **argv)
{
WlzObject *obj, *nobj;
FILE *inFP, *outFP, *bibFP;
char *outFile, *bibFile;
char optList[] = "a:b:d:f:m:o:s:u:hv";
int option;
int iVal;
double dist=0.0, pitch=0.0, yaw=0.0, roll=0.0;
double scale=1.0;
WlzDVertex3 fixed={0.0,0.0,0.0};
WlzDVertex3 up={0.0,0.0,-1.0};
WlzThreeDViewStruct *viewStr=NULL;
WlzThreeDViewMode mode=WLZ_UP_IS_UP_MODE;
WlzErrorNum errNum=WLZ_ERR_NONE;
BibFileRecord *bibfileRecord;
BibFileError bibFileErr;
int verboseFlg=0;
char *errMsg;
/* additional defaults */
outFile = "-";
bibFile = NULL;
/* read the argument list and check for an input file */
opterr = 0;
while( (option = getopt(argc, argv, optList)) != EOF ){
switch( option ){
case 'a':
switch( sscanf(optarg, "%lg,%lg,%lg", &pitch, &yaw, &roll) ){
default:
usage(argv[0]);
return 1;
case 2:
break;
case 3:
mode = WLZ_ZETA_MODE;
break;
}
break;
case 'b':
bibFile = optarg;
break;
case 'd':
if( sscanf(optarg, "%lg", &dist) < 1 ){
usage(argv[0]);
return 1;
}
break;
case 'f':
if( sscanf(optarg, "%lg,%lg,%lg", &(fixed.vtX), &(fixed.vtY),
&(fixed.vtZ)) < 3 ){
usage(argv[0]);
return 1;
}
break;
case 'm':
if( sscanf(optarg, "%d", &iVal) < 1 ){
usage(argv[0]);
return 1;
}
else if( mode != WLZ_ZETA_MODE ){
switch( iVal ){
default:
usage(argv[0]);
return 1;
case 0:
mode = WLZ_UP_IS_UP_MODE;
break;
case 1:
mode = WLZ_STATUE_MODE;
break;
case 2:
mode = WLZ_ZETA_MODE;
break;
}
}
break;
case 'o':
outFile = optarg;
break;
case 's':
if( sscanf(optarg, "%lg", &scale) < 1 ){
usage(argv[0]);
return 1;
}
break;
case 'u':
if( sscanf(optarg, "%lg,%lg,%lg", &(up.vtX), &(up.vtY),
&(up.vtZ)) < 3 ){
usage(argv[0]);
return 1;
}
break;
case 'h':
default:
usage(argv[0]);
return 0;
case 'v':
verboseFlg = 1;
break;
}
}
/* check input file/stream */
inFP = stdin;
if( optind < argc ){
if( (inFP = fopen(*(argv+optind), "r")) == NULL ){
fprintf(stderr, "%s: can't open file %s\n", argv[0], *(argv+optind));
usage(argv[0]);
return 1;
}
}
/* check output file/stream */
if(strcmp(outFile, "-"))
{
if((outFP = fopen(outFile, "w")) == NULL)
{
errNum = WLZ_ERR_WRITE_EOF;
}
}
else
{
outFP = stdout;
}
/* create view structure */
if((viewStr = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum)) != NULL){
viewStr->theta = yaw * WLZ_M_PI / 180.0;
viewStr->phi = pitch * WLZ_M_PI / 180.0;
viewStr->zeta = roll * WLZ_M_PI / 180.0;
viewStr->dist = dist;
viewStr->fixed = fixed;
viewStr->up = up;
viewStr->view_mode = mode;
viewStr->scale = scale;
}
/* check bibfile - select first section parameters in the file */
if((errNum == WLZ_ERR_NONE) && (bibFile != NULL)){
if((bibFP = fopen(bibFile, "r")) != NULL){
bibFileErr = BibFileRecordRead(&bibfileRecord, &errMsg, bibFP);
while((bibFileErr == BIBFILE_ER_NONE) &&
(strncmp(bibfileRecord->name, "Wlz3DSectionViewParams", 22))){
BibFileRecordFree(&bibfileRecord);
bibFileErr = BibFileRecordRead(&bibfileRecord, &errMsg, bibFP);
}
fclose( bibFP );
if( bibFileErr != BIBFILE_ER_NONE ){
fprintf(stderr, "%s: error reading bibfile: %s\n", argv[0], errMsg);
AlcFree((void *) errMsg);
return 1;
}
WlzEffBibParse3DSectionViewParamsRecord(bibfileRecord, viewStr);
BibFileRecordFree(&bibfileRecord);
}
else {
fprintf(stderr, "%s: can't open parameter bibfile %s\n", argv[0],
bibFile);
return 1;
}
}
/* read objects and section if possible */
while((errNum == WLZ_ERR_NONE) &&
((obj = WlzReadObj(inFP, &errNum)) != NULL))
{
switch( obj->type )
{
case WLZ_3D_DOMAINOBJ:
WlzInit3DViewStruct(viewStr, obj);
nobj = WlzGetProjectionFromObject(obj, viewStr, NULL, NULL, &errNum);
if( nobj != NULL){
WlzWriteObj(outFP, nobj);
}
else {
return errNum;
}
WlzFreeObj(nobj);
break;
default:
WlzWriteObj(outFP, obj);
break;
}
WlzFreeObj(obj);
}
if(errNum == WLZ_ERR_READ_EOF)
{
errNum = WLZ_ERR_NONE;
}
return errNum;
}
/*!
* \return Woolz error code.
* \brief Read the input section parameters file to find the reference
* and source file object file names, read the reference and
* source objects from these files and parse the section view
* parameters.
* \param fP Input section parameters file.
* \param dstView Destination pointer for the 3D view
* transform.
* \param dstRefFileStr Destination pointer for the reference
* object file name. If the reference file
* string is NULL and the reference object
* is not NULL then the reference object
* is assumed valid.
* \param dstRefFileType Destination pointer for the reference
* object file type.
* \param dstRefObj Destination pointer for the reference
* object.
* \param dstSrcFileStr Destination pointer for the source
* object file name. If the source file
* string is NULL and the source object
* is not NULL then the source object is
* assumed valid.
* \param dstSrcFileType Destination pointer for the source
* object file type.
* \param dstsrcObj Destination pointer for the source
* object.
*/
static WlzErrorNum WlzMatchICPPlaneReadSecParam(FILE *fP,
WlzThreeDViewStruct **dstView,
char **dstRefFileStr, WlzEffFormat *dstRefFileType,
WlzObject **dstRefObj,
char **dstSrcFileStr, WlzEffFormat *dstSrcFileType,
WlzObject **dstSrcObj)
{
int idx;
char *fileStr;
WlzEffFormat fileType;
BibFileRecord *bibRec;
BibFileError bibErr = BIBFILE_ER_NONE;
WlzErrorNum errNum = WLZ_ERR_NONE;
*dstView = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum);
if(errNum == WLZ_ERR_NONE)
{
bibErr = BibFileRecordRead(&bibRec, NULL, fP);
}
while((bibErr == BIBFILE_ER_NONE) && (errNum == WLZ_ERR_NONE))
{
if(!strcmp(bibRec->name, "Wlz3DSectionViewParams"))
{
errNum = WlzEffBibParse3DSectionViewParamsRecord(bibRec, *dstView);
}
if(!strcmp(bibRec->name, "MAPaintWarpInputSourceFile"))
{
errNum = WlzEffBibParseFileRecord(bibRec, &idx, &fileStr, &fileType);
if(dstSrcFileStr)
{
*dstSrcFileStr = fileStr;
if(dstSrcFileType)
{
*dstSrcFileType = fileType;
}
if(dstSrcObj)
{
*dstSrcObj = WlzAssignObject(
WlzEffReadObj(NULL, fileStr, fileType,
0, 0, 0, &errNum), NULL);
}
}
}
if(!strcmp(bibRec->name, "MAPaintWarpInputReferenceFile"))
{
errNum = WlzEffBibParseFileRecord(bibRec, &idx, &fileStr, &fileType);
if(dstRefFileStr)
{
*dstRefFileStr = fileStr;
if(dstRefFileType)
{
*dstRefFileType = fileType;
}
if(dstRefObj)
{
*dstRefObj = WlzAssignObject(
WlzEffReadObj(NULL, fileStr, fileType,
0, 0, 0, &errNum), NULL);
}
}
}
BibFileRecordFree(&bibRec);
bibErr = BibFileRecordRead(&bibRec, NULL, fP);
if((errNum == WLZ_ERR_NONE) && (bibErr != BIBFILE_ER_NONE))
{
if(bibErr != BIBFILE_ER_EOF)
{
errNum = WLZ_ERR_READ_INCOMPLETE;
}
}
}
return(errNum);
}
