/*!
* \return
* \ingroup WlzTransform
* \brief Gets a 3D section through a byte packed bitmap.
* \param sizeBitData Number of bytes in bitmap.
* \param bitData Bitmap data.
* \param width Bitmap width.
* \param height Bitmap height.
* \param x_offset Horizontal ofset into the bitmap.
* \param y_offset Vertical offset into the bitmap.
* \param x Fixed point x coordinate.
* \param y Fixed point y coordinate.
* \param z Fixed point z coordinate.
* \param theta Angle of rotation about the z-axis
* (radians).
* \param phi Angle between the viewing direction
* and the original z-axis (radians).
* \param distance Perpendicular distance from the
* fixed point to the view plane.
* \param dstErr Destination error pointer, may be NULL.
*/
WlzObject *Wlz3DViewTransformBitmap(
int sizeBitData,
WlzUByte *bitData,
int width,
int height,
int x_offset,
int y_offset,
double x,
double y,
double z,
double theta,
double phi,
double distance,
WlzErrorNum *dstErr)
{
WlzErrorNum errNum=WLZ_ERR_NONE;
WlzObject *rtnObj=NULL;
WlzObject *tmpObj;
WlzIVertex2 arraySizeDat;
WlzIVertex2 arrayOrigin;
WlzThreeDViewStruct *viewStr;
arraySizeDat.vtX = width;
arraySizeDat.vtY = height;
arrayOrigin.vtX = x_offset;
arrayOrigin.vtY = y_offset;
if((tmpObj = WlzAssignObject(WlzFromBArray1D(arraySizeDat, bitData,
arrayOrigin, &errNum), NULL)) != NULL) {
/* make and initialise WlzThreeDViewStruct */
if((viewStr = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum)) != NULL) {
viewStr->fixed.vtX = x;
viewStr->fixed.vtY = y;
viewStr->fixed.vtZ = z;
viewStr->theta = theta * WLZ_M_PI / 180.0;
viewStr->phi = phi * WLZ_M_PI / 180.0;
viewStr->dist = distance;
viewStr->scale = 1.0;
viewStr->view_mode = WLZ_UP_IS_UP_MODE;
viewStr->up.vtX = 0.0;
viewStr->up.vtY = 0.0;
viewStr->up.vtZ = -1.0;
WlzInit3DViewStruct(viewStr, tmpObj);
/* transform the 2D section to 3D */
rtnObj = Wlz3DViewTransformObj(tmpObj, viewStr, &errNum);
/* clean up */
WlzFree3DViewStruct(viewStr);
}
WlzFreeObj(tmpObj);
}
if( dstErr ) {
*dstErr = errNum;
}
return rtnObj;
}
void setup_ref_display_list_cb(
Widget w,
XtPointer client_data,
XtPointer call_data)
{
WlzPlaneDomain *planedmn;
WlzThreeDViewStruct *viewStr;
WlzErrorNum errNum=WLZ_ERR_NONE;
if( globals.obj == NULL || globals.obj->type != WLZ_3D_DOMAINOBJ ||
globals.ref_display_list == 0){
return;
}
/* create a new display list */
glDeleteLists(globals.ref_display_list, 1);
globals.ref_display_list = glGenLists( (GLsizei) 1 );
planedmn = globals.obj->domain.p;
/* create the reference object 3D display DisplayList */
glNewList( globals.ref_display_list, GL_COMPILE );
glBegin(GL_LINES);
glColor3f(1.0, 0.0, 0.0);
glIndexi( (int) HGU_XGetColorPixel(globals.dpy, globals.cmap, 1.0, 0.0, 0.0) );
glVertex3i(planedmn->kol1, planedmn->line1, planedmn->plane1);
glVertex3i(planedmn->lastkl, planedmn->line1, planedmn->plane1);
glVertex3i(planedmn->kol1, planedmn->line1, planedmn->lastpl);
glVertex3i(planedmn->lastkl, planedmn->line1, planedmn->lastpl);
glVertex3i(planedmn->kol1, planedmn->lastln, planedmn->plane1);
glVertex3i(planedmn->lastkl, planedmn->lastln, planedmn->plane1);
glVertex3i(planedmn->kol1, planedmn->lastln, planedmn->lastpl);
glVertex3i(planedmn->lastkl, planedmn->lastln, planedmn->lastpl);
glColor3f(0.0, 1.0, 0.0);
glIndexi( (int) HGU_XGetColorPixel(globals.dpy, globals.cmap, 0.0, 1.0, 0.0) );
glVertex3i(planedmn->kol1, planedmn->line1, planedmn->plane1);
glVertex3i(planedmn->kol1, planedmn->lastln, planedmn->plane1);
glVertex3i(planedmn->kol1, planedmn->line1, planedmn->lastpl);
glVertex3i(planedmn->kol1, planedmn->lastln, planedmn->lastpl);
glVertex3i(planedmn->lastkl, planedmn->line1, planedmn->plane1);
glVertex3i(planedmn->lastkl, planedmn->lastln, planedmn->plane1);
glVertex3i(planedmn->lastkl, planedmn->line1, planedmn->lastpl);
glVertex3i(planedmn->lastkl, planedmn->lastln, planedmn->lastpl);
glColor3f(0.0, 0.0, 1.0);
glIndexi( (int) HGU_XGetColorPixel(globals.dpy, globals.cmap, 0.0, 0.0, 1.0) );
glVertex3i(planedmn->kol1, planedmn->line1, planedmn->plane1);
glVertex3i(planedmn->kol1, planedmn->line1, planedmn->lastpl);
glVertex3i(planedmn->kol1, planedmn->lastln, planedmn->plane1);
glVertex3i(planedmn->kol1, planedmn->lastln, planedmn->lastpl);
glVertex3i(planedmn->lastkl, planedmn->line1, planedmn->plane1);
glVertex3i(planedmn->lastkl, planedmn->line1, planedmn->lastpl);
glVertex3i(planedmn->lastkl, planedmn->lastln, planedmn->plane1);
glVertex3i(planedmn->lastkl, planedmn->lastln, planedmn->lastpl);
glEnd();
if( globals.fb_obj && (globals.fb_obj->type == WLZ_3D_DOMAINOBJ) ){
WlzObject *obj1, *boundobj;
WlzValues values;
int z, step;
/* establish the step size */
planedmn = globals.fb_obj->domain.p;
step = (planedmn->lastkl - planedmn->kol1) / 6;
z = (planedmn->lastln - planedmn->line1) / 6;
step = WLZ_MIN(step, z);
z = (planedmn->lastpl - planedmn->plane1) / 6;
step = WLZ_MIN(step, z);
/* set up const z boundaries */
glColor3f(1.0, 1.0, 1.0);
glIndexi((int) HGU_XGetColorPixel(globals.dpy, globals.cmap, 1.0, 1.0, 1.0));
(void) glLineWidth( (GLfloat) 2.0 );
for(z=planedmn->plane1+step/2; z <= planedmn->lastpl; z += step)
{
values.core = NULL;
obj1 = WlzMakeMain(WLZ_2D_DOMAINOBJ,
planedmn->domains[z - planedmn->plane1],
values, NULL, NULL, NULL);
if( obj1->domain.core != NULL )
{
boundobj = WlzObjToBoundary(obj1, 1, &errNum);
if( boundobj != NULL )
{
MAOpenGLDisplayBoundList(boundobj->domain.b, (float) z );
WlzFreeObj( boundobj );
}
if( errNum != WLZ_ERR_NONE ){
break;
}
}
WlzFreeObj( obj1 );
}
(void) glLineWidth( (GLfloat) 1.0 );
/* set up const y boundaries */
if( errNum == WLZ_ERR_NONE ){
glColor3f(1.0, 1.0, 0.0);
glIndexi((int) HGU_XGetColorPixel(globals.dpy, globals.cmap, 1.0, 1.0, 0.0));
if((viewStr = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum))){
viewStr->theta = WLZ_M_PI / 2.0;
viewStr->phi = WLZ_M_PI / 2.0;
viewStr->dist = planedmn->line1 - step/2;
errNum = WlzInit3DViewStruct(viewStr, globals.fb_obj);
for(z=viewStr->dist+step; (errNum == WLZ_ERR_NONE) && (z <= planedmn->lastln);
z += step)
{
Wlz3DSectionIncrementDistance(viewStr, (double) step);
if((obj1 = WlzGetSectionFromObject(globals.fb_obj, viewStr,
WLZ_INTERPOLATION_NEAREST,
&errNum))){
obj1 = WlzAssignObject(obj1, NULL);
boundobj = WlzObjToBoundary(obj1, 1, &errNum);
if( boundobj != NULL )
{
/* convert boundary coordinates to voxel coordinates */
Wlz3DSectionTransformYBound(boundobj->domain.b, viewStr);
MAOpenGLDisplayYBoundList(boundobj->domain.b, (float) z);
WlzFreeObj( boundobj );
}
WlzFreeObj( obj1 );
}
}
WlzFree3DViewStruct(viewStr);
}
}
/* set up const x boundaries */
if( errNum == WLZ_ERR_NONE ){
glIndexi((int) HGU_XGetColorPixel(globals.dpy, globals.cmap, 1.0, 1.0, 0.0));
glColor3f(1.0, 1.0, 0.0);
if((viewStr = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum))){
viewStr->theta = 0.0;
viewStr->phi = WLZ_M_PI / 2.0;
viewStr->dist = planedmn->kol1 - step/2;
errNum = WlzInit3DViewStruct(viewStr, globals.fb_obj);
for(z=viewStr->dist+step; (errNum == WLZ_ERR_NONE) && (z <= planedmn->lastkl);
z += step)
{
Wlz3DSectionIncrementDistance(viewStr, (double) step);
if((obj1 = WlzGetSectionFromObject(globals.fb_obj, viewStr,
WLZ_INTERPOLATION_NEAREST,
&errNum))){
obj1 = WlzAssignObject(obj1, NULL);
boundobj = WlzObjToBoundary(obj1, 1, &errNum);
if( boundobj != NULL )
{
/* convert boundary coordinates to voxel coordinates */
Wlz3DSectionTransformXBound(boundobj->domain.b, viewStr);
MAOpenGLDisplayXBoundList(boundobj->domain.b, (float) z);
WlzFreeObj( boundobj );
}
WlzFreeObj( obj1 );
}
}
WlzFree3DViewStruct(viewStr);
}
}
}
if( errNum == WLZ_ERR_NONE ){
glIndexi( (int) HGU_XGetColorPixel(globals.dpy, globals.cmap, 1.0, 1.0, 1.0) );
glColor3f(1.0, 1.0, 1.0);
glEndList();
WLZ_VTX_3_SET(globals.bbox_vtx, planedmn->kol1 - 2.0,
planedmn->line1 - 2.0, planedmn->plane1 - 2.0);
WLZ_VTX_3_SET(globals.bbox_size,
planedmn->lastkl - planedmn->kol1 + 4.0,
planedmn->lastln - planedmn->line1 + 4.0,
planedmn->lastpl - planedmn->plane1 + 4.0);
glFogf(GL_FOG_DENSITY, 0.25/globals.bbox_size.vtX);
MAOpenGLDrawScene( globals.canvas );
}
else {
MAPaintReportWlzError(globals.topl, "setup_ref_display_list_cb", errNum);
}
return;
}
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;
}
int main(int argc,
char **argv)
{
FILE *inFile = NULL; /* used to read Woolz object */
FILE *outFile = NULL; /* used to read Woolz object */
int i,j,k=0, m; /* , l1, label[3], individual[4] */
int option;
int TotalN; /* numChar, numChar1, */
/* int outputAutoMeshVTK = 0,
outputAutoMeshWLZ = 0,
outputTransformedMeshWLZ = 0,
outputCutPlaneAndCorrepSurfaceVTK = 0;
*/
/* WARP = 1 */
/* int basisFnPolyOrder = 3; */
int Inumber, num;
int globalCycle;
/* int binObjFlag; */
int centorOfMass = 1;
int numOf2DWlzFiles = 0, numOfSampleBibFiles = 0;
/* int initialn0, endNum0,initialn1, endNum1; */
int BibFileIndex[50];
/* double zConst = 0.; */
/* double mass = 0.0; */
/* char under ='_'; */
/* char ctemp; */
char *inFileStr, *inFileStr1, *outFileStr; /* *inFileStr3, */
char *inFileStrw, *outputBibFilesDir; /* , inFileStrSec[100]; */
char TwoDImageFilesNameList[1000][120];
char TwoDImagePureFilesNameList[1000][70];
char PureBibFilesNameList[700][70];
char SampleBibFilesNameList[100][120];
char SampleBibPureFilesName[100][70];
char SampleBibFilesDir[100];
char TwoDImageFilesDir[100];
char *List2DImageFilesStr, *SampleBibFilesStr;
/* char *cstr; */
/* const char *errMsg; */
/* WlzDVertex2 cMass, cMassS; */
WlzErrorNum errNum = WLZ_ERR_NONE;
/* WlzInterpolationType interp = WLZ_INTERPOLATION_NEAREST; Use the nearest neighbour */
WlzThreeDViewStruct *wlzViewStr, *wlzViewStr1, *wlzViewStrInter;
/* AlcErrno alcErr = ALC_ER_NONE; */
WlzObject *WObjS;/*, *WObj2DS, *WObj2D;*/
/* WlzObjectType wtp = WLZ_3D_DOMAINOBJ; */
/* read the argument list and check for an input file */
static char optList[] = "i:I:f:w:o:d:z:M:m:n:r:R:L:B:h",
opterr = 0;
while( (option = getopt(argc, argv, optList)) != EOF )
{
switch( option )
{
case 'h':
usage(argv[0]);
return(0);
case 'i':
inFileStr = optarg;
/*
outFileStr = optarg;
*/
break;
case 'I':
inFileStr1 = optarg;
break;
case 'L':
List2DImageFilesStr = optarg;
break;
case 'B':
SampleBibFilesStr = optarg;
break;
case 'w':
inFileStrw = optarg;
break;
case 'n':
if(sscanf(optarg, "%d", &num) != 1)
{
printf("read error");
exit(1);
}
break;
case 'o':
outFileStr = optarg;
break;
case 'd':
outputBibFilesDir = optarg;
break;
default:
return(0);
}
}
/* Read 2D Wlz files List */
printf("Read 2D Wlz file list\n");
if((inFile = fopen(List2DImageFilesStr, "r")) == NULL )
{
printf("cannot open the 2D image files list file.\n");
exit(1);
}
i=0;
/* get the number of files */
while(!feof(inFile)){
fscanf(inFile, "%s", *(TwoDImageFilesNameList + i ));
/* printf("%s\n", *(TwoDImageFilesNameList + i ) ); */
i++;
}
fclose(inFile);
inFile = NULL;
numOf2DWlzFiles = i-1;
printf("number of files = %d\n", numOf2DWlzFiles );
/* extract pure wlz filename without directory */
printf("extract pure wlz filename without directory\n");
for(m=0; m<numOf2DWlzFiles; m++)
{
for(i=0; i<sizeof(TwoDImageFilesNameList[m]); i++){
if( TwoDImageFilesNameList[m][i] == (char )NULL )
break;
if( TwoDImageFilesNameList[m][i] == '/' )
k = i;
}
if(k != 0)
k++;
for(j=k; j<i; j++)
{
TwoDImagePureFilesNameList[m][j-k] = TwoDImageFilesNameList[m][j];
PureBibFilesNameList[m][j-k] = TwoDImageFilesNameList[m][j];
}
TwoDImagePureFilesNameList[m][j-k] = (char ) NULL;
PureBibFilesNameList[m][j-k] = (char ) NULL;
PureBibFilesNameList[m][j-k-3] = 'b';
PureBibFilesNameList[m][j-k-2] = 'i';
PureBibFilesNameList[m][j-k-1] = 'b';
/* extract directory */
if(m == 0)
{
for(j=0; j<k; j++)
{
TwoDImageFilesDir[j] = TwoDImageFilesNameList[m][j];
}
TwoDImageFilesDir[j] = (char ) NULL;
printf("I_DIR %s\n",TwoDImageFilesDir );
}
printf("%s\n", TwoDImagePureFilesNameList[m]);
}
/* changeToBibFileNamse */
/*--- Read Sample bib File name list ----*/
if((inFile = fopen(SampleBibFilesStr, "r")) == NULL )
{
printf("cannot open the sample bib files list file.\n");
exit(1);
}
i=0;
while(!feof(inFile)){
fscanf(inFile, "%s", SampleBibFilesNameList[i]);
printf("%s\n", SampleBibFilesNameList[i]);
i++;
}
fclose(inFile);
inFile = NULL;
numOfSampleBibFiles = i-1;
printf("number of files = %d\n", numOfSampleBibFiles );
/* extract pure sample bib filename without directory */
printf("extract pure sample bib filename without directory\n");
for(m=0; m<numOfSampleBibFiles; m++)
{
for(i=0; i<sizeof(SampleBibFilesNameList[m]); i++){
if( SampleBibFilesNameList[m][i] == (char ) NULL )
break;
if( SampleBibFilesNameList[m][i] == '/' )
k = i;
}
if(k != 0)
k++;
for(j=k; j<i; j++)
{
SampleBibPureFilesName[m][j-k] = SampleBibFilesNameList[m][j];
}
SampleBibPureFilesName[m][j-k] = (char ) NULL;
/* extract directory */
if(m == 0)
{
for(j=0; j<k; j++)
{
SampleBibFilesDir[j] = SampleBibFilesNameList[m][j];
}
SampleBibFilesDir[j] = (char) NULL;
printf("B_DIR %s\n",SampleBibFilesDir);
}
printf("%s\n", SampleBibPureFilesName[m]);
}
/*---------- extract the bib File number ----------- */
for(i=0; i<numOfSampleBibFiles; i++)
{
BibFileIndex[i] = -1;
for(m=0; m<numOf2DWlzFiles; m++)
{
/* printf("%s %s\n", PureBibFilesNameList[m], SampleBibPureFilesName[i] ); */
if(strcmp(PureBibFilesNameList[m], SampleBibPureFilesName[i] ) == 0)
{
BibFileIndex[i] = m;
break;
}
}
printf("m = %d\n",BibFileIndex[i]);
}
centorOfMass = 0;
if(centorOfMass)
{
/* read Woolz object */
if((inFile = fopen(inFileStrw, "r")) == NULL )
{
printf("cannot open the input woolz file.\n");
exit(1);
}
if( !(WObjS = WlzReadObj(inFile, &errNum) ) )
{
printf("input Woolz Object Error.\n");
fclose(inFile);
exit(1);
}
fclose(inFile);
inFile = NULL;
}
/* read Section viewer parameters */
centorOfMass = 1;
if(centorOfMass)
{
wlzViewStr = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, NULL);
wlzViewStr1 = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, NULL);
wlzViewStrInter = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, NULL);
}
/* interpolation */
globalCycle = 0;
while(globalCycle < numOfSampleBibFiles - 1)
{
printf("%d\n",globalCycle );
errNum = ReadBibFile(inFile, SampleBibFilesNameList[globalCycle], wlzViewStr );
errNum = ReadBibFile(inFile, SampleBibFilesNameList[globalCycle+1], wlzViewStr1 );
errNum = ReadBibFile(inFile, SampleBibFilesNameList[globalCycle], wlzViewStrInter );
TotalN = BibFileIndex[globalCycle+1] - BibFileIndex[globalCycle];
/* cycle through between sample bib file */
j = BibFileIndex[globalCycle] + 1;
k = BibFileIndex[globalCycle+1];
printf("NNNN: %d %d\n",j,k );
i=j;
while ( i < k )
{
Inumber = i - BibFileIndex[globalCycle];
/* linear interpolations */
errNum = LinearInterpolations(wlzViewStr, wlzViewStr1, wlzViewStrInter, Inumber, TotalN);
/* change the fixed point to (0 0 0) */
errNum = ChangeFixedPoint(wlzViewStrInter, 0., 0., 0.);
/* write Section viewer parameters */
printf("%s\n", PureBibFilesNameList[i]);
errNum = WriteBibFile(outFile, PureBibFilesNameList[i], inFileStrw, TwoDImageFilesNameList[i], wlzViewStrInter);
i++;
}
globalCycle++;
}
/* Now cover the orginal input bib files with new */
globalCycle = 0;
while(globalCycle < numOfSampleBibFiles)
{
i = BibFileIndex[globalCycle];
errNum = ReadBibFile(inFile, SampleBibFilesNameList[globalCycle], wlzViewStr );
errNum = ReadBibFile(inFile, SampleBibFilesNameList[globalCycle], wlzViewStr1 );
errNum = ReadBibFile(inFile, SampleBibFilesNameList[globalCycle], wlzViewStrInter );
errNum = LinearInterpolations(wlzViewStr, wlzViewStr, wlzViewStrInter, 1, 1);
/* change the fixed point to (0 0 0) */
errNum = ChangeFixedPoint(wlzViewStrInter, 0., 0., 0.);
errNum = WriteBibFile(outFile, PureBibFilesNameList[i], inFileStrw, TwoDImageFilesNameList[i], wlzViewStrInter);
globalCycle++;
}
/* */
centorOfMass = 0;
if(centorOfMass)
{
WlzFreeObj(WObjS);
}
centorOfMass = 1;
if(centorOfMass)
{
WlzFree3DViewStruct(wlzViewStr);
WlzFree3DViewStruct(wlzViewStr1);
WlzFree3DViewStruct(wlzViewStrInter);
}
return ( 0 );
}
int main(int argc, char **argv)
{
int tI,
errIdx,
option,
keep2D = 0,
ok = 1,
usage = 0;
WlzDDOVxSzSrc voxSzSrc = WLZDDO_VSS_UNIT;
WlzDVertex2 org;
WlzThreeDViewStruct *view = NULL;
WlzErrorNum errNum = WLZ_ERR_NONE;
WlzObject *dwnObj = NULL,
*refObj = NULL;
FILE *fP = NULL;
char *errMsg0,
*cmdStr = NULL,
*refFileStr = NULL,
*outFileStr,
*inFileStr;
double voxSz[3];
const char *errMsg;
static char optList[] = "a:b:d:E:f:g:m:o:r:s:u:2eh",
outFileStrDef[] = "-",
inFileStrDef[] = "-";
opterr = 0;
errMsg = errMsg0 = "";
org.vtX = org.vtY = 0.0;
inFileStr = inFileStrDef;
outFileStr = outFileStrDef;
voxSz[0] = voxSz[1] = voxSz[2] = 1.0;
if((view = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum)) == NULL)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed to create view structure (%s)\n",
*argv, errMsg);
}
if(ok)
{
view->dist = 0.0;
view->scale = 1.0;
view->ref_obj = NULL;
view->view_mode = WLZ_UP_IS_UP_MODE;
view->phi = view->theta = view->zeta = 0.0;
view->up.vtX = view->up.vtY = 0.0; view->up.vtZ = 1.0;
view->fixed.vtX = view->fixed.vtY = view->fixed.vtZ = 0.0;
while((usage == 0) && ((option = getopt(argc, argv, optList)) != -1))
{
switch(option)
{
case '2':
keep2D = 1;
break;
case 'a':
usage = WlzDrawDomObjScanTriple(optarg,
&(view->phi),
&(view->theta),
&(view->zeta)) < 1;
break;
case 'e':
voxSzSrc = WLZDDO_VSS_OBJ;
break;
case 'E':
voxSzSrc = WLZDDO_VSS_GVN;
usage = WlzDrawDomObjScanTriple(optarg,
&(voxSz[0]),
&(voxSz[1]),
&(voxSz[2])) < 1;
break;
case 'f':
usage = WlzDrawDomObjScanTriple(optarg,
&(view->fixed.vtX),
&(view->fixed.vtY),
&(view->fixed.vtZ)) < 1;
break;
case 'd':
usage = sscanf(optarg, "%lg", &(view->dist)) != 1;
break;
case 'b':
usage = WlzDrawDomObjReadView(optarg, view,
&errMsg0) != WLZ_ERR_NONE;
if(usage)
{
(void )fprintf(stderr,
"%s: failed to read view parameters from file "
"%s (%s)\n",
*argv, optarg, errMsg0);
}
break;
case 'm':
if(WlzStringMatchValue(&tI, optarg,
"up-is-up", WLZ_UP_IS_UP_MODE,
"statue", WLZ_STATUE_MODE,
"absolute", WLZ_ZETA_MODE,
NULL))
{
view->view_mode = (WlzThreeDViewMode )tI;
}
else
{
usage = 1;
}
break;
case 'u':
usage = WlzDrawDomObjScanTriple(optarg,
&(view->up.vtX),
&(view->up.vtY),
&(view->up.vtZ)) < 1;
break;
case 'g':
usage = WlzDrawDomObjScanPair(optarg, &(org.vtX), &(org.vtY)) < 1;
break;
case 'o':
outFileStr = optarg;
break;
case 'r':
refFileStr = optarg;
errNum = WLZ_ERR_READ_EOF;
if((refFileStr == NULL) ||
(*refFileStr == '\0') ||
((fP = (strcmp(refFileStr, "-")?
fopen(refFileStr, "r"): stdin)) == NULL) ||
((refObj = WlzAssignObject(
WlzReadObj(fP, &errNum), NULL)) == NULL) ||
(errNum != WLZ_ERR_NONE))
{
usage = 1;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed to read 3D reference object from %s (%s)\n",
*argv, refFileStr, errMsg);
}
if(fP)
{
if(strcmp(refFileStr, "-"))
{
(void )fclose(fP);
}
fP = NULL;
}
break;
case 's':
if((cmdStr = AlcStrDup(optarg)) == NULL)
{
usage = 1;
errNum = WLZ_ERR_MEM_ALLOC;
}
break;
case 'h':
default:
usage = 1;
ok = 0;
break;
}
}
if((usage == 0) && (cmdStr == NULL))
{
if((optind == argc))
{
inFileStr = inFileStrDef;
}
else if(optind + 1 == argc )
{
inFileStr = *(argv + optind);
}
else
{
usage = 1;
}
if(usage == 0)
{
cmdStr = WlzDrawDomObjReadStr(inFileStr, &errNum);
}
}
ok = usage == 0;
}
if(ok)
{
switch(voxSzSrc)
{
case WLZDDO_VSS_UNIT:
view->voxelRescaleFlg = 0;
view->voxelSize[0] = 1.0f;
view->voxelSize[1] = 1.0f;
view->voxelSize[2] = 1.0f;
break;
case WLZDDO_VSS_GVN:
view->voxelRescaleFlg = 1;
view->voxelSize[0] = (float )WLZ_CLAMP(voxSz[0], FLT_MIN, FLT_MAX);
view->voxelSize[1] = (float )WLZ_CLAMP(voxSz[1], FLT_MIN, FLT_MAX);
view->voxelSize[2] = (float )WLZ_CLAMP(voxSz[2], FLT_MIN, FLT_MAX);
break;
case WLZDDO_VSS_OBJ:
/* Handled below. */
break;
}
}
if(ok && refObj)
{
WlzObject *sObj = NULL;
WlzThreeDViewStruct *v = NULL;
v = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum);
if(errNum == WLZ_ERR_NONE)
{
v->type = view->type;
v->fixed = view->fixed;
v->theta = view->theta;
v->phi = view->phi;
v->zeta = view->zeta;
v->dist = view->dist;
v->scale = view->scale;
if(voxSzSrc == WLZDDO_VSS_OBJ)
{
view->voxelRescaleFlg = 1;
if((refObj->type == WLZ_3D_DOMAINOBJ) &&
(refObj->domain.core != NULL) &&
(refObj->domain.core->type == WLZ_PLANEDOMAIN_DOMAIN))
{
view->voxelSize[0] = refObj->domain.p->voxel_size[0];
view->voxelSize[1] = refObj->domain.p->voxel_size[1];
view->voxelSize[2] = refObj->domain.p->voxel_size[2];
}
}
v->voxelRescaleFlg = view->voxelRescaleFlg;
v->voxelSize[0] = view->voxelSize[0];
v->voxelSize[1] = view->voxelSize[1];
v->voxelSize[2] = view->voxelSize[2];
v->interp = view->interp;
v->view_mode = view->view_mode;
v->up = view->up;
v->fixed_2 = view->fixed_2;
v->fixed_line_angle = view->fixed_line_angle;
errNum = WlzInit3DViewStruct(v, refObj);
}
if(errNum == WLZ_ERR_NONE)
{
sObj = WlzGetSectionFromObject(refObj, v, WLZ_INTERPOLATION_NEAREST,
&errNum);
}
if(errNum == WLZ_ERR_NONE)
{
if((sObj->type != WLZ_2D_DOMAINOBJ) || (sObj->domain.core == NULL))
{
errNum = WLZ_ERR_DOMAIN_DATA;
}
else
{
org.vtX += sObj->domain.i->kol1;
org.vtY += sObj->domain.i->line1;
}
}
(void )WlzFree3DViewStruct(v);
(void )WlzFreeObj(sObj);
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed find offset from reference object (%s).\n",
*argv, errMsg);
}
}
if(ok)
{
dwnObj = WlzDrawDomainObj(org, view, keep2D, cmdStr, &errIdx, &errNum);
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed to draw object in command prior to string\n"
"position %d (%s)\n",
*argv, errIdx, errMsg);
}
}
if(ok)
{
errNum = WLZ_ERR_WRITE_EOF;
if((fP = (strcmp(outFileStr, "-")? fopen(outFileStr, "w"):
stdout)) == NULL)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed to open output file (%s).\n",
*argv, errMsg);
}
else
{
if((errNum = WlzWriteObj(fP, dwnObj)) != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: Failed to write output object (%s).\n",
argv[0], errMsg);
}
}
if(fP && strcmp(outFileStr, "-"))
{
fclose(fP);
}
}
AlcFree(cmdStr);
(void )WlzFreeObj(refObj);
(void )WlzFree3DViewStruct(view);
(void )WlzFreeObj(dwnObj);
if(usage)
{
(void )fprintf(stderr,
"Usage: %s%s%s%sExample: %s%s",
*argv,
" [-2] [-a<pitch,yaw,roll>]\n"
" [-f <fx,fy,fz>]\n"
" [-d <dist> [-b <view bib file>]\n"
" [-m <mode>] [-u<ux,uy,uz>]\n"
" [-e] [-E<vx,vy,vz>]\n"
" [-g <ox,oy,oz>] [-h] [-o<output>]\n"
" [-r <ref object>]\n"
" [-s <cmd str>] [<cmd str file>>]\n"
"Version: ",
WlzVersion(),
"\n"
"Options:\n"
" -2 Ignore the view struct and keep as a 2D object.\n"
" -a Viewing angles: pitch (phi), yaw (theta) and roll (zeta),\n"
" default 0.0,0.0,0.0.\n"
" -f Fixed point position, default 0.0,0.0,0.0.\n"
" -d Distance parameter, default 0.0.\n"
" -b Bib file with view parameters, e.g. saved from MAPaint.\n"
" -m Viewing mode, one of: up-is-up, statue or absolute, default\n"
" is up-is-up.\n"
" -u Up vector, default 0.0,0.0,1.0.\n"
" -e Use object voxel size, default is voxel size 1.0,1.0,1.0.\n"
" -E Use supplied voxel size rather than the object voxel size,\n"
" default 1.0,1.0,1.0.\n"
" -g Origin of the drawing with respect to the 2D Woolz object\n"
" cut using the view transform, default 0.0,0.0.\n"
" -r Reference object. If given this is must be a 3D spatial domain\n"
" object. The object is used to determine an additional offset\n"
" for the origin of the 2D plane with respect to the section in 3D\n"
" (i.e. it is added to any offset given using the -g option).\n"
" -s Drawing command string.\n"
" -h Help, prints this usage message.\n"
" -o Output file name.\n"
"Reads drawing commands from either a string given on the command line,\n"
"a file given on the command line or the standard input (in this order\n"
"of precidence). The drawing commands are used to create a drawn\n"
"section which is placed into 3D using the view transform.\n"
"\n"
"The command string must have the following syntax:\n"
" <command string> = <init command>[<command>]+<end command>\n"
" <init command> = <ident>:<version>;\n"
" <end command> = END:;\n"
" <ident> = WLZ_DRAW_DOMAIN\n"
" <version> = 1\n"
" <command> = <command name>:[<parameter>[,<parameter>]*];\n"
" <command name> = PEN | LINE | CIRCLE\n"
"In addition to the init and end commands, the following\n"
"drawing commands are recognised:\n"
" CIRCLE:<action>:<radius>,<x>,<y>;\n"
" LINE:<action>:<width>,<x>,<y>,<x>,<y>;\n"
" PEN:<action>,<width>,<x>,<y>[,<x>,<y>]*;\n"
"Where:\n"
" <action> = DRAW | ERASE\n"
"The circle command draws or erases a filled circle which is specified\n"
"by it's radius and centre parameters.\n"
"The line command draws a rectangle using the given width and end\n"
"coordinates of the mid-line.\n"
"The pen command draws a polyline which is composed of a series of\n"
"rectangular segments, with each segment ending in a semi-circular cap.\n"
"The parameters of the pen command are the width and line segment end\n"
"point coordinates.\n"
"All widths, radii and coordinates may be in any floating point format\n"
"recognised by scanf(3).\n"
"Other commands may be present provided they have the same syntax\n"
"described above, but they will be ignored.\n"
"All white space characters are ignored.\n",
*argv,
" -o out.wlz -s 'WLZ_DRAW_DOMAIN:1; CIRCLE:DRAW,100,200,300; END:;'\n"
"This creates a 3D domain object with a single plane at z = 0\n"
"which has a domain that is a single circle (radius = 100,\n"
"centre = 200,300).\n");
}
return(!ok);
}
int main(int argc, char *argv[])
{
int option,
ok = 1,
usage = 0,
dim = 2,
section = 0,
timer = 0;
double yaw = 0.0,
pitch = 0.0,
roll = 0.0,
dist = 0.0,
scale = 1.0;
WlzPixelV bgdV;
WlzGreyType gType;
WlzDVertex3 up,
fixed;
WlzInterpolationType interp = WLZ_INTERPOLATION_NEAREST;
WlzThreeDViewMode mode = WLZ_UP_IS_UP_MODE;
WlzErrorNum errNum = WLZ_ERR_NONE;
FILE *fP = NULL;
WlzObject *inObj = NULL,
*tlObj = NULL;
char *inFileStr,
*outFileStr,
*secFileStr;
struct timeval times[3];
const char *errMsg;
const size_t tlSz = 4096;
static char optList[] = "hsto:S:",
inFileStrDef[] = "-";
opterr = 0;
outFileStr = NULL;
inFileStr = inFileStrDef;
secFileStr = inFileStrDef;
gType = WLZ_GREY_UBYTE;
bgdV.type = WLZ_GREY_UBYTE;
bgdV.v.ubv = 0;
up.vtX = up.vtY = 0.0; up.vtZ = -1.0;
fixed.vtX = fixed.vtY = fixed.vtZ = 0.0;
while(ok && ((option = getopt(argc, argv, optList)) != -1))
{
switch(option)
{
case 'o':
outFileStr = optarg;
break;
case 's':
section = 1;
break;
case 'S':
secFileStr = optarg;
break;
case 't':
timer = 1;
break;
case 'h': /* FALLTHROUGH */
default:
usage = 1;
break;
}
}
if((usage == 0) && (optind < argc))
{
if((optind + 1) != argc)
{
usage = 1;
}
else
{
inFileStr = *(argv + optind);
}
}
ok = !usage;
if(ok)
{
fP = NULL;
errNum = WLZ_ERR_READ_EOF;
if(((fP = (strcmp(inFileStr, "-")? fopen(inFileStr, "r"):
stdin)) == NULL) ||
((inObj= WlzAssignObject(WlzReadObj(fP, &errNum), NULL)) == NULL))
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: Failed to read object from file %s (%s).\n",
*argv, inFileStr, errMsg);
}
if(fP && strcmp(inFileStr, "-"))
{
(void )fclose(fP);
}
}
if(ok)
{
if(inObj == NULL)
{
errNum = WLZ_ERR_OBJECT_NULL;
}
else if(inObj->domain.core == NULL)
{
errNum = WLZ_ERR_DOMAIN_NULL;
}
else
{
switch(inObj->type)
{
case WLZ_2D_DOMAINOBJ:
dim = 2;
break;
case WLZ_3D_DOMAINOBJ:
dim = 3;
break;
default:
errNum = WLZ_ERR_OBJECT_TYPE;
break;
}
}
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: invalid object read from file %s (%s).\n",
*argv, inFileStr, errMsg);
}
}
if(ok)
{
if(timer)
{
gettimeofday(times + 0, NULL);
}
tlObj = WlzMakeTiledValuesFromObj(inObj, tlSz, 1, gType, bgdV, &errNum);
if(timer)
{
gettimeofday(times + 1, NULL);
timersub(times + 1, times + 0, times + 2);
(void )fprintf(stderr,
"%s: Elapsed time for WlzMakeTiledValuesFromObj() %gs\n",
*argv,
times[2].tv_sec + (0.000001 * times[2].tv_usec));
}
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: Failed to create object with tiled values (%s).\n",
*argv, errMsg);
}
}
if(ok && (outFileStr != NULL))
{
if(((fP = (strcmp(outFileStr, "-")? fopen(outFileStr, "w"):
stdout)) == NULL) ||
((errNum = WlzWriteObj(fP, tlObj)) != WLZ_ERR_NONE))
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: Failed to write tiled object to file %s (%s).\n",
*argv, outFileStr, errMsg);
}
}
if(ok && section && (dim == 3))
{
WlzObject *secObj = NULL;
WlzThreeDViewStruct *view = NULL;
view = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum);
if(errNum == WLZ_ERR_NONE)
{
view->theta = yaw * WLZ_M_PI / 180.0;
view->phi = pitch * WLZ_M_PI / 180.0;
view->zeta = roll * WLZ_M_PI / 180.0;
view->dist = dist;
view->fixed = fixed;
view->up = up;
view->view_mode = mode;
view->scale = scale;
errNum = WlzInit3DViewStruct(view, tlObj);
}
if(errNum == WLZ_ERR_NONE)
{
if(timer)
{
gettimeofday(times + 0, NULL);
}
secObj = WlzGetSubSectionFromObject(tlObj, NULL, view, interp,
NULL, &errNum);
if(timer)
{
gettimeofday(times + 1, NULL);
timersub(times + 1, times + 0, times + 2);
(void )fprintf(stderr,
"%s: Elapsed time for WlzGetSubSectionFromObject() %gs\n",
*argv,
times[2].tv_sec + (0.000001 * times[2].tv_usec));
}
fP = NULL;
errNum = WLZ_ERR_WRITE_EOF;
if(((fP = (strcmp(secFileStr, "-")? fopen(secFileStr, "w"):
stdout)) == NULL) ||
((errNum = WlzWriteObj(fP, secObj)) != WLZ_ERR_NONE))
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: Failed to write section object to file %s (%s).\n",
*argv, secFileStr, errMsg);
}
if(fP && strcmp(secFileStr, "-"))
{
(void )fclose(fP);
}
}
(void )WlzFree3DViewStruct(view);
(void )WlzFreeObj(secObj);
}
(void )WlzFreeObj(tlObj);
(void )WlzFreeObj(inObj);
if(usage)
{
(void )fprintf(stderr,
"Usage: %s%s",
*argv,
" [-o<output object>] [-h] [-o <file>] [-s] [-S <file>] [-t]\n"
" [<input object>]\n"
"Copied the input object to an object with tiled values.\n"
"Options:\n"
" -h Prints this usage information.\n"
" -o Output tiled object.\n"
" -s Cut section from tiled object.\n"
" -S Output file for section object.\n"
" -t Output timing information.\n");
}
return(!ok);
}
int main(int argc,
char **argv)
{
FILE *inFile = NULL; /* used to read Woolz object */
int i,j,k=0, m;
int option;
int startJ;
int cycleI, cycleNext;
double ntnm,nfnm,nsnm;
int numOf2DWlzFiles = 0, numOfBibFiles = 0;
int ok, usage1, idx;
double deltaZ;
double sx=0,sy=0,sz=0, fx=0,fy=100,fz=0, tx=100,ty=0,tz=0;
double Sx=0,Sy=0,Sz=60, Fx=0,Fy=100,Fz=60, Tx=100,Ty=0,Tz=60;
double lengthTS;
char *inFileStr, *inFileStr1, *outFileStr;
char *inFileStrw=NULL, *outputWlzFilesDir=NULL;
char TwoDImageFilesNameList[700][120];
char TwoDImagePureFilesNameList[700][120];
char warpedFilesNameList[700][120];
char BibFilesNameList[700][120];
char TwoDImageFilesDir[120];
char *List2DImageFilesStr= NULL, *ListBibFilesStr= NULL;
WlzVertex vs, vt, vf, vS, vT, vF;
WlzVertex vs1, vt1, vf1, vsp, vtp, vfp, vST;
WlzVertex vsr, vtr, vfr;
WlzVertex ns, nf, nt, nsp, nfp, ntp, nz,nm;
WlzDVertex2 *vtxVec1;
WlzErrorNum errNum = WLZ_ERR_NONE;
WlzThreeDViewStruct *wlzViewStr, *wlzViewStr1;
WlzObject *WObjS;
char *cutStr[3];
double cutVal[3];
/* read the argument list and check for an input file */
static char optList[] = "i:I:w:o:d:s:S:f:F:t:T:M:n:r:R:L:B:h",opterr = 0;
ok = 1;
while( (option = getopt(argc, argv, optList)) != EOF )
{
switch( option )
{
case 'h':
usage(argv[0]);
return(0);
case 'i':
inFileStr = optarg;
/*
outFileStr = optarg;
*/
break;
case 'I':
inFileStr1 = optarg;
break;
case 'L':
List2DImageFilesStr = optarg;
break;
case 'B':
ListBibFilesStr = optarg;
break;
case 'w':
inFileStrw = optarg;
break;
case 'n':
if(sscanf(optarg, "%d", &startJ) != 1)
{
printf("read error");
exit(1);
}
break;
case 's':
case 'f':
case 't':
case 'S':
case 'F':
case 'T':
if(optarg)
{
while(*optarg && isspace(*optarg))
{
++optarg;
}
if(*optarg == ',')
{
cutStr[0] = NULL;
cutStr[1] = strtok(optarg, ",");
cutStr[2] = strtok(optarg, ",");
}
else
{
cutStr[0] = strtok(optarg, ",");
cutStr[1] = strtok(NULL, ",");
cutStr[2] = strtok(NULL, ",");
}
if((cutStr[0] == NULL) && (cutStr[1] == NULL) && (cutStr[2] == NULL) )
{
usage1 = 1;
ok = 0;
}
else
{
idx = 0;
while(ok && (idx < 3))
{
if(cutStr[idx] && (sscanf(cutStr[idx], "%lg",
cutVal + idx) != 1))
{
usage1 = 1;
ok = 0;
}
++idx;
}
}
}
if(ok)
{
switch(option)
{
case 's':
sx = (double) cutVal[0];
sy = (double) cutVal[1];
sz = (double) cutVal[2];
break;
case 'f':
fx = (double) cutVal[0];
fy = (double) cutVal[1];
fz = (double) cutVal[2];
break;
case 't':
tx = (double) cutVal[0];
ty = (double) cutVal[1];
tz = (double) cutVal[2];
break;
case 'S':
Sx = (double) cutVal[0];
Sy = (double) cutVal[1];
Sz = (double) cutVal[2];
break;
case 'F':
Fx = (double) cutVal[0];
Fy = (double) cutVal[1];
Fz = (double) cutVal[2];
break;
case 'T':
Tx = (double) cutVal[0];
Ty = (double) cutVal[1];
Tz = (double) cutVal[2];
break;
}
}
break;
case 'o':
outFileStr = optarg;
break;
case 'd':
outputWlzFilesDir = optarg;
break;
default:
return(0);
}
}
printf("t: %f %f %f\n",tx,ty, tz );
printf("T: %f %f %f\n",Tx,Ty, Tz );
/*------- allocate memory --------*/
if (
((vtxVec1 = (WlzDVertex2 *)AlcCalloc(sizeof(WlzDVertex2), 3)) == NULL)
)
{
errNum = WLZ_ERR_MEM_ALLOC;
}
/* ------Read 2D Wlz files List------- */
printf("Read 2D Wlz file list\n");
if((inFile = fopen(List2DImageFilesStr, "r")) == NULL )
{
printf("cannot open the 2D image files list file.\n");
exit(1);
}
i=0;
/* get the number of files */
while(!feof(inFile)){
fscanf(inFile, "%s", *(TwoDImageFilesNameList + i ));
/* printf("%s\n", *(TwoDImageFilesNameList + i ) ); */
i++;
}
fclose(inFile);
inFile = NULL;
numOf2DWlzFiles = i-1;
printf("number of files = %d\n", numOf2DWlzFiles );
/* extract pure wlz filename without directory */
printf("extract pure wlz filename without directory\n");
for(m=0; m<numOf2DWlzFiles; m++)
{
for(i=0; i<sizeof(TwoDImageFilesNameList[m]); i++){
if( TwoDImageFilesNameList[m][i] == (char) NULL )
break;
if( TwoDImageFilesNameList[m][i] == '/' )
k = i;
}
if(k != 0)
k++;
for(j=k; j<i; j++)
{
TwoDImagePureFilesNameList[m][j-k] = TwoDImageFilesNameList[m][j];
warpedFilesNameList[m][j-k] = TwoDImageFilesNameList[m][j];
}
TwoDImagePureFilesNameList[m][j-k] = ( char ) NULL;
warpedFilesNameList[m][j-k] = ( char ) NULL;
/* extract directory */
if(m == 0)
{
for(j=0; j<k; j++)
{
TwoDImageFilesDir[j] = TwoDImageFilesNameList[m][j];
}
TwoDImageFilesDir[j] = ( char ) NULL;
printf("I_DIR %s\n",TwoDImageFilesDir );
}
printf("%s\n", TwoDImagePureFilesNameList[m]);
}
/*--- Read bib File name list ----*/
if((inFile = fopen(ListBibFilesStr, "r")) == NULL )
{
printf("cannot open the 2D image files list file.\n");
exit(1);
}
i=0;
while(!feof(inFile)){
fscanf(inFile, "%s", BibFilesNameList[i]);
printf("%s\n", BibFilesNameList[i]);
i++;
}
fclose(inFile);
inFile = NULL;
numOfBibFiles = i-1;
printf("number of files bib files = %d\n", numOfBibFiles );
/* check whether the number of bib files is the same as number of Wlz 2D sections */
if(numOfBibFiles != numOf2DWlzFiles )
{
printf("Number of 2D woolz files and number of bib files are different\n");
exit(1);
}
/* get the output file namelist */
i = (int) strlen( (const char *) outputWlzFilesDir);
printf("%d\n", i);
for( j = 0; j < numOfBibFiles; j++)
{
strcpy( warpedFilesNameList[j], (const char *) outputWlzFilesDir );
strcat( warpedFilesNameList[j], "/");
strcat(warpedFilesNameList[j], (const char *) TwoDImagePureFilesNameList[j]);
printf("%s\n", warpedFilesNameList[j] );
}
/* --------read Woolz object--------- */
if((inFile = fopen(inFileStrw, "r")) == NULL )
{
printf("cannot open the input woolz file.\n");
exit(1);
}
if( !(WObjS = WlzReadObj(inFile, &errNum) ) )
{
printf("input Woolz Object Error.\n");
fclose(inFile);
exit(1);
}
fclose(inFile);
inFile = NULL;
/* ------get the fixed S , T and F ready and s, t, f in OPT space------ */
vS.d3.vtX = Sx;
vS.d3.vtY = Sy;
vS.d3.vtZ = Sz;
vT.d3.vtX = Tx;
vT.d3.vtY = Ty;
vT.d3.vtZ = Tz;
vF.d3.vtX = Fx;
vF.d3.vtY = Fy;
vF.d3.vtZ = Fz;
vs.d3.vtX = sx;
vs.d3.vtY = sy;
vs.d3.vtZ = sz;
vt.d3.vtX = tx;
vt.d3.vtY = ty;
vt.d3.vtZ = tz;
vf.d3.vtX = fx;
vf.d3.vtY = fy;
vf.d3.vtZ = fz;
printf("vt: %f %f %f\n",vt.d3.vtX,vt.d3.vtY, vt.d3.vtZ );
printf("vT: %f %f %f\n",vT.d3.vtX,vT.d3.vtY, vT.d3.vtZ );
/* -----get the three directions in OPT space-------
n = 1/(|r2-r1|) { (x2-x1) i + (y2-y1) j + (z2-z1) k }
*/
WLZ_VTX_3_SUB(vST.d3,vS.d3,vs.d3);
lengthTS = WLZ_VTX_3_LENGTH( vST.d3);
ns.d3.vtX = vST.d3.vtX/ lengthTS;
ns.d3.vtY = vST.d3.vtY/ lengthTS;
ns.d3.vtZ = vST.d3.vtZ/ lengthTS;
WLZ_VTX_3_SUB(vST.d3,vF.d3,vf.d3);
lengthTS = WLZ_VTX_3_LENGTH( vST.d3);
nf.d3.vtX = vST.d3.vtX/ lengthTS;
nf.d3.vtY = vST.d3.vtY/ lengthTS;
nf.d3.vtZ = vST.d3.vtZ/ lengthTS;
WLZ_VTX_3_SUB(vST.d3,vT.d3,vt.d3);
printf("vt: %f %f %f\n",vt.d3.vtX,vt.d3.vtY, vt.d3.vtZ );
printf("vT: %f %f %f\n",vT.d3.vtX,vT.d3.vtY, vT.d3.vtZ );
lengthTS = WLZ_VTX_3_LENGTH( vST.d3);
printf("Length: %f\n",lengthTS);
nt.d3.vtX = vST.d3.vtX/ lengthTS;
nt.d3.vtY = vST.d3.vtY/ lengthTS;
nt.d3.vtZ = vST.d3.vtZ/ lengthTS;
/*
---- get the three points in the master plane ( startJ plane ) ----
*/
/* allocate memory and give default values for viewer strcuture */
wlzViewStr = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, NULL);
wlzViewStr1 = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, NULL);
/* set up */
cycleI = startJ;
/* read Section viewer parameters */
errNum = ReadBibFile(inFile, (char *) BibFilesNameList[cycleI], wlzViewStr );
if(errNum != WLZ_ERR_NONE)
{
printf("Read or parse bib file err.\n");
exit(1);
}
inFile = NULL;
WlzInit3DViewStruct(wlzViewStr, WObjS);
/* -------- get the corresponding three directions in Main view space -------
(It is also the stack up space
nsp = Tm ns,
nfp = Tm nf,
ntp = Tm nt;
*/
errNum = Wlz3DSectionTransformVtxR(wlzViewStr, ns.d3, &nsp.d3 );
if(errNum != WLZ_ERR_NONE)
{
printf("can not get the direction in stack up space for ns err.\n");
exit(1);
}
errNum = Wlz3DSectionTransformVtxR(wlzViewStr, nf.d3, &nfp.d3 );
if(errNum != WLZ_ERR_NONE)
{
printf("can not get the direction in stack up space for nf err.\n");
exit(1);
}
errNum = Wlz3DSectionTransformVtxR(wlzViewStr, nt.d3, &ntp.d3 );
if(errNum != WLZ_ERR_NONE)
{
printf("can not get the direction in stack up space for np err.\n");
exit(1);
}
/* --- get the main plane direction in OPT space --- */
/* it can got by inverse transform from stack up viewer space to
OPT space */
/* in stack up space or master plane sapce */
nz.d3.vtX = 0.0;
nz.d3.vtY = 0.0;
nz.d3.vtZ = 1.0;
/* nm = Tm^-1 nz (inverse transform used here ) nm is in OPT space */
errNum = Wlz3DSectionTransformInvVtxR(wlzViewStr, nz.d3, &nm.d3 );
if(errNum != WLZ_ERR_NONE)
{
printf("can not get the main plane direction in OPT space err.\n");
printf("Which means your three straight line has to be rechosen\n");
exit(1);
}
/* get the nt dot nm, etc */
ntnm = WLZ_VTX_3_DOT(nt.d3, nm.d3);
nfnm = WLZ_VTX_3_DOT(nf.d3, nm.d3);
nsnm = WLZ_VTX_3_DOT(ns.d3, nm.d3);
ntnm = nm.d3.vtX * nt.d3.vtX + nm.d3.vtY * nt.d3.vtY + nm.d3.vtZ * nt.d3.vtZ;
if( ( ( ntnm == 0 ) || ( nfnm == 0 ) ) ||( nsnm == 0 ) )
{
printf("At least one of your three strait lines are parallel to the main plane err.\n");
printf("Which means your three straight line has to be rechosen or chose another plane\n");
printf("as main plane\n");
exit(1);
}
/* get crossed point in this plane p_{i} then project to viewer space */
errNum = WlzGetCorssPoint(vs, ns, &vsr, wlzViewStr);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
errNum = WlzGetCorssPoint(vt, nt, &vtr, wlzViewStr);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
errNum = WlzGetCorssPoint(vf, nf, &vfr, wlzViewStr);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
/* use this 3 point as refernce */
/* --------Get Tie-points -------- */
/* get the target points for this plane in stack up space */
(vtxVec1 )->vtX = vsr.d3.vtX;
(vtxVec1 )->vtY = vsr.d3.vtY;
(vtxVec1 + 1)->vtX = vtr.d3.vtX;
(vtxVec1 + 1)->vtY = vtr.d3.vtY;
(vtxVec1 + 2)->vtX = vfr.d3.vtX;
(vtxVec1 + 2)->vtY = vfr.d3.vtY;
/* get the source point */
/* get ( sx' sy' sz' )_i */
printf("%f %f\n", sx, sy);
vsp.d3.vtX = vsr.d3.vtX;
vsp.d3.vtY = vsr.d3.vtY;
vsp.d3.vtZ = vsr.d3.vtZ;
/* get ( tx' ty' tz' )_i */
printf("%f %f\n", tx, ty);
vtp.d3.vtX = vtr.d3.vtX;
vtp.d3.vtY = vtr.d3.vtY;
vtp.d3.vtZ = vtr.d3.vtZ;
/* get ( fx' fy' fz' )_i */
printf("%f %f\n", fx, fy);
vfp.d3.vtX = vfr.d3.vtX;
vfp.d3.vtY = vfr.d3.vtY;
vfp.d3.vtZ = vfr.d3.vtZ;
/* ------ output the affine transformed Wlz ------*/
errNum = outputTheWarpedWlz( vsp,
vtp,
vfp,
vtxVec1,
TwoDImageFilesNameList[cycleI],
warpedFilesNameList[cycleI]
);
while(cycleI < numOfBibFiles - 1)
{
cycleNext = cycleI + 1;
errNum = ReadBibFile(inFile, (char *) BibFilesNameList[cycleNext], wlzViewStr1 );
WlzInit3DViewStruct(wlzViewStr1, WObjS);
/* ------ get Tie - points -------*/
/* get crossed point in this plane p_{i} then project to viewer space */
errNum = WlzGetCorssPoint(vs, ns, &vs1, wlzViewStr1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
errNum = WlzGetCorssPoint(vt, nt, &vt1, wlzViewStr1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
errNum = WlzGetCorssPoint(vf, nf, &vf1, wlzViewStr1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
/* get the source points */
/* get ( sx' sy' sz' )_i */
/* printf("%f %f\n", sx, sy); */
vsp.d3.vtX = vs1.d3.vtX;
vsp.d3.vtY = vs1.d3.vtY;
vsp.d3.vtZ = vs1.d3.vtZ;
/* get ( tx' ty' tz' )_i */
/* printf("%f %f\n", tx, ty); */
vtp.d3.vtX = vt1.d3.vtX;
vtp.d3.vtY = vt1.d3.vtY;
vtp.d3.vtZ = vt1.d3.vtZ;
/* get ( fx' fy' fz' )_i */
/* printf("%f %f\n", fx, fy); */
vfp.d3.vtX = vf1.d3.vtX;
vfp.d3.vtY = vf1.d3.vtY;
vfp.d3.vtZ = vf1.d3.vtZ;
/* get the target points */
/* find the target points by keep the same direction in
stack up space and the OPT space.The following are in stack up space */
deltaZ = (double) ( cycleNext - startJ );
errNum = WlzGetDxDy( nsp, deltaZ, &vs1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not get Dx Dy err.\n");
exit(1);
}
errNum = WlzGetDxDy( nfp, deltaZ, &vf1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not get Dx Dy err.\n");
exit(1);
}
errNum = WlzGetDxDy( ntp, deltaZ, &vt1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not get Dx Dy err.\n");
exit(1);
}
(vtxVec1 )->vtX = vsr.d3.vtX + vs1.d3.vtX;
(vtxVec1 )->vtY = vsr.d3.vtY + vs1.d3.vtY;
(vtxVec1 + 1)->vtX = vtr.d3.vtX + vt1.d3.vtX;
(vtxVec1 + 1)->vtY = vtr.d3.vtY + vt1.d3.vtY;
(vtxVec1 + 2)->vtX = vfr.d3.vtX + vf1.d3.vtX;
(vtxVec1 + 2)->vtY = vfr.d3.vtY + vf1.d3.vtY;
/* ------ output the affine transformed Wlz ------*/
printf("----------- %d\n",cycleI);
/* out put the source and target for checking */
errNum = outputTheWarpedWlz( vsp,
vtp,
vfp,
vtxVec1,
TwoDImageFilesNameList[cycleNext],
warpedFilesNameList[cycleNext]
);
/* track from s_i' to s_{i+1}' */
/* scale = |T - S |/|t - s| */
cycleI++;
}
cycleI = startJ;
while( cycleI > 0 )
{
cycleNext = cycleI - 1;
errNum = ReadBibFile(inFile, (char *) BibFilesNameList[cycleNext], wlzViewStr1 );
WlzInit3DViewStruct(wlzViewStr1, WObjS);
/* ------ get Tie - points -------*/
/* get crossed point in this plane p_{i} then project to viewer space */
errNum = WlzGetCorssPoint(vs, ns, &vs1, wlzViewStr1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
errNum = WlzGetCorssPoint(vt, nt, &vt1, wlzViewStr1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
errNum = WlzGetCorssPoint(vf, nf, &vf1, wlzViewStr1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not find crossed point err.\n");
exit(1);
}
/* get the source points */
/* get ( sx' sy' sz' )_i */
printf("%f %f\n", sx, sy);
vsp.d3.vtX = vs1.d3.vtX;
vsp.d3.vtY = vs1.d3.vtY;
vsp.d3.vtZ = vs1.d3.vtZ;
/* get ( tx' ty' tz' )_i */
printf("%f %f\n", tx, ty);
vtp.d3.vtX = vt1.d3.vtX;
vtp.d3.vtY = vt1.d3.vtY;
vtp.d3.vtZ = vt1.d3.vtZ;
/* get ( fx' fy' fz' )_i */
printf("%f %f\n", fx, fy);
vfp.d3.vtX = vf1.d3.vtX;
vfp.d3.vtY = vf1.d3.vtY;
vfp.d3.vtZ = vf1.d3.vtZ;
/* get the target points */
/* find the target points by keep the same direction in
stack up space and the OPT space.The following are in stack up space */
deltaZ = (double) ( cycleNext - startJ );
errNum = WlzGetDxDy( nsp, deltaZ, &vs1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not get Dx Dy err.\n");
exit(1);
}
errNum = WlzGetDxDy( nfp, deltaZ, &vf1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not get Dx Dy err.\n");
exit(1);
}
errNum = WlzGetDxDy( ntp, deltaZ, &vt1);
if(errNum != WLZ_ERR_NONE)
{
printf("can not get Dx Dy err.\n");
exit(1);
}
/* target points */
(vtxVec1 )->vtX = vsr.d3.vtX + vs1.d3.vtX;
(vtxVec1 )->vtY = vsr.d3.vtY + vs1.d3.vtY;
(vtxVec1 + 1)->vtX = vtr.d3.vtX + vt1.d3.vtX;
(vtxVec1 + 1)->vtY = vtr.d3.vtY + vt1.d3.vtY;
(vtxVec1 + 2)->vtX = vfr.d3.vtX + vf1.d3.vtX;
(vtxVec1 + 2)->vtY = vfr.d3.vtY + vf1.d3.vtY;
/* ------ output the affine transformed Wlz ------*/
errNum = outputTheWarpedWlz( vsp,
vtp,
vfp,
vtxVec1,
TwoDImageFilesNameList[cycleNext],
warpedFilesNameList[cycleNext]
);
/* track from s_i' to s_{i+1}' */
/* scale = |T - S |/|t - s| */
cycleI--;
}
AlcFree(vtxVec1 );
/* */
WlzFree3DViewStruct(wlzViewStr);
WlzFree3DViewStruct(wlzViewStr1);
return ( 0 );
}
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;
}
/*!
* \return projection object
* \ingroup WlzTransform
* \brief Use the view transform to define a projection from
* 3D to 2D. Currently only the domain is projected as
* an opaque shadow.
* This is old code temporarily kept for compatibility.
* \param obj source 3D object
* \param viewStr view structure defining the projection
* \param intFunc grey-value summation function
* \param intFuncData data to be passed to the integration function
* \param dstErr error return
*/
WlzObject *WlzGetProjectionFromObject(
WlzObject *obj,
WlzThreeDViewStruct *viewStr,
Wlz3DProjectionIntFn intFunc,
void *intFuncData,
WlzErrorNum *dstErr)
{
WlzObject *rtnObj=NULL,
*obj1;
WlzThreeDViewStruct *viewStr1=NULL;
WlzDomain domain;
WlzValues values;
WlzGreyType srcGType = WLZ_GREY_UBYTE,
dstGType = WLZ_GREY_UBYTE;
WlzPixelV pixval;
WlzPixelP pixptr;
WlzIntervalWSpace iwsp;
WlzGreyWSpace gwsp;
WlzGreyValueWSpace *gVWSp = NULL;
WlzDVertex3 vtx, vtx1;
double x, y, z;
double *s_to_x=NULL;
double *s_to_y=NULL;
double *s_to_z=NULL;
int k, xp, yp, s, sp;
int length = 0, size = 0, occupiedFlg;
WlzErrorNum errNum=WLZ_ERR_NONE;
/* check inputs */
if( obj == NULL ){
errNum = WLZ_ERR_OBJECT_NULL;
}
else if( obj->type != WLZ_3D_DOMAINOBJ ){
errNum = WLZ_ERR_OBJECT_TYPE;
}
else if( obj->domain.core == NULL ){
errNum = WLZ_ERR_DOMAIN_NULL;
}
else if( obj->domain.core->type != WLZ_PLANEDOMAIN_DOMAIN ){
errNum = WLZ_ERR_DOMAIN_TYPE;
}
if( (errNum == WLZ_ERR_NONE) && (viewStr == NULL) ){
errNum = WLZ_ERR_OBJECT_NULL;
}
/* create new view transform */
if( errNum == WLZ_ERR_NONE ){
if((viewStr1 = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum)) != NULL){
/* need to worry about fixed line mode here sometime */
viewStr1->fixed = viewStr->fixed;
viewStr1->theta = viewStr->theta;
viewStr1->phi = viewStr->phi;
viewStr1->zeta = viewStr->zeta;
viewStr1->dist = viewStr->dist;
viewStr1->scale = viewStr->scale;
viewStr1->voxelSize[0] = viewStr->voxelSize[0];
viewStr1->voxelSize[1] = viewStr->voxelSize[1];
viewStr1->voxelSize[2] = viewStr->voxelSize[2];
viewStr1->voxelRescaleFlg = viewStr->voxelRescaleFlg;
viewStr1->interp = viewStr->interp;
viewStr1->view_mode = viewStr->view_mode;
viewStr1->up = viewStr->up;
/* now intialize it */
/* could optimise by setting fixed point to object centre */
if( (errNum = WlzInit3DViewStruct(viewStr1, obj)) != WLZ_ERR_NONE ){
WlzFree3DViewStruct(viewStr1);
viewStr1 = NULL;
}
}
}
/* set up orthogonal line parameters & luts */
if( errNum == WLZ_ERR_NONE ){
length = WLZ_NINT(viewStr1->maxvals.vtZ) -
WLZ_NINT(viewStr1->minvals.vtZ) + 1;
s_to_x = (double *) AlcMalloc(sizeof(double) * length );
s_to_y = (double *) AlcMalloc(sizeof(double) * length );
s_to_z = (double *) AlcMalloc(sizeof(double) * length );
/* transform a perpendicular vector */
vtx.vtX = 0.0;
vtx.vtY = 0.0;
vtx.vtZ = 1.0;
Wlz3DSectionTransformInvVtx(&vtx, viewStr1);
vtx1.vtX = 0.0;
vtx1.vtY = 0.0;
vtx1.vtZ = 0.0;
Wlz3DSectionTransformInvVtx(&vtx1, viewStr1);
vtx.vtX -= vtx1.vtX;
vtx.vtY -= vtx1.vtY;
vtx.vtZ -= vtx1.vtZ;
/* assign lut values */
s = (int )(WLZ_NINT(viewStr1->minvals.vtZ) - viewStr1->dist);
for(sp=0; sp < length; sp++, s++){
s_to_x[sp] = s * vtx.vtX;
s_to_y[sp] = s * vtx.vtY;
s_to_z[sp] = s * vtx.vtZ;
}
}
/* if there is an integration function then allocate space for
the grey-level array */
if( (errNum == WLZ_ERR_NONE) && (intFunc) ){
srcGType = WlzGreyTypeFromObj(obj, &errNum);
switch( srcGType ){
case WLZ_GREY_LONG:
size = sizeof(WlzLong)*length;
break;
case WLZ_GREY_INT:
size = sizeof(int)*length;
break;
case WLZ_GREY_SHORT:
size = sizeof(short)*length;
break;
case WLZ_GREY_UBYTE:
size = sizeof(WlzUByte)*length;
break;
case WLZ_GREY_FLOAT:
size = sizeof(float)*length;
break;
case WLZ_GREY_DOUBLE:
size = sizeof(double)*length;
break;
case WLZ_GREY_RGBA:
size = sizeof(int)*length;
break;
default:
errNum = WLZ_ERR_GREY_TYPE;
break;
}
if( (pixptr.p.inp = (int *) AlcMalloc(size)) == NULL ){
errNum = WLZ_ERR_MEM_ALLOC;
}
pixptr.type = srcGType;
/* set up the grey-value workspace for random access */
gVWSp = WlzGreyValueMakeWSp(obj, &errNum);
}
/* create rectangular projection image */
if( errNum == WLZ_ERR_NONE ){
if((domain.i = WlzMakeIntervalDomain(WLZ_INTERVALDOMAIN_RECT,
WLZ_NINT(viewStr1->minvals.vtY),
WLZ_NINT(viewStr1->maxvals.vtY),
WLZ_NINT(viewStr1->minvals.vtX),
WLZ_NINT(viewStr1->maxvals.vtX),
&errNum)) != NULL){
values.core = NULL;
if((rtnObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, domain, values, NULL, NULL,
&errNum)) != NULL){
/* note the grey-values required are determined by the integration
function. Here we use WlzUByte and reset later if needed */
dstGType = WLZ_GREY_UBYTE;
pixval.type = WLZ_GREY_UBYTE;
pixval.v.ubv = (WlzUByte )0;
if((values.v = WlzNewValueTb(rtnObj,
WlzGreyTableType(WLZ_GREY_TAB_RECT,
dstGType, NULL),
pixval, &errNum)) != NULL){
rtnObj->values = WlzAssignValues(values, &errNum);
}
else {
WlzFreeObj(rtnObj);
rtnObj = NULL;
}
}
else {
WlzFreeDomain(domain);
domain.core = NULL;
}
}
}
/* scan image setting values */
if( errNum == WLZ_ERR_NONE ){
errNum = WlzInitGreyScan(rtnObj, &iwsp, &gwsp);
}
if( errNum == WLZ_ERR_NONE ){
while( (errNum = WlzNextGreyInterval(&iwsp)) == WLZ_ERR_NONE ){
yp = iwsp.linpos - WLZ_NINT(viewStr1->minvals.vtY);
for(k=iwsp.lftpos; k <= iwsp.rgtpos; k++){
xp = k - WLZ_NINT(viewStr1->minvals.vtX);
vtx.vtX = viewStr1->xp_to_x[xp] + viewStr1->yp_to_x[yp];
vtx.vtY = viewStr1->xp_to_y[xp] + viewStr1->yp_to_y[yp];
vtx.vtZ = viewStr1->xp_to_z[xp] + viewStr1->yp_to_z[yp];
/* get the projection values */
/* if no function then just check for occupancy */
if( intFunc == NULL ){
occupiedFlg = 0;
sp = (int )(viewStr1->dist - WLZ_NINT(viewStr1->minvals.vtZ));
for(; !occupiedFlg && (sp < length); sp++){
x = vtx.vtX + s_to_x[sp];
y = vtx.vtY + s_to_y[sp];
z = vtx.vtZ + s_to_z[sp];
if( WlzInsideDomain(obj, z, y, x, &errNum) ){
occupiedFlg = 1;
}
}
sp = (int )(viewStr1->dist - WLZ_NINT(viewStr1->minvals.vtZ) - 1);
for(; !occupiedFlg && (sp >= 0); sp--){
x = vtx.vtX + s_to_x[sp];
y = vtx.vtY + s_to_y[sp];
z = vtx.vtZ + s_to_z[sp];
if( WlzInsideDomain(obj, z, y, x, &errNum) ){
occupiedFlg = 1;
}
}
/* set the integrated value - only WlzUByte at the moment */
*(gwsp.u_grintptr.ubp) = (WlzUByte )occupiedFlg;
gwsp.u_grintptr.ubp++;
}
/* use integration function */
else {
/* set array of pixel values */
for(sp=0; sp < length; sp++){
x = vtx.vtX + s_to_x[sp];
y = vtx.vtY + s_to_y[sp];
z = vtx.vtZ + s_to_z[sp];
WlzGreyValueGet(gVWSp, WLZ_NINT(z), WLZ_NINT(y),
WLZ_NINT(x));
switch( srcGType ){
case WLZ_GREY_LONG:
pixptr.p.lnp[sp] = gVWSp->gVal[0].lnv;
break;
case WLZ_GREY_INT:
pixptr.p.inp[sp] = gVWSp->gVal[0].inv;
break;
case WLZ_GREY_SHORT:
pixptr.p.shp[sp] = gVWSp->gVal[0].shv;
break;
case WLZ_GREY_UBYTE:
pixptr.p.ubp[sp] = gVWSp->gVal[0].ubv;
break;
case WLZ_GREY_FLOAT:
pixptr.p.flp[sp] = gVWSp->gVal[0].flv;
break;
case WLZ_GREY_DOUBLE:
pixptr.p.dbp[sp] = gVWSp->gVal[0].dbv;
break;
case WLZ_GREY_RGBA:
pixptr.p.rgbp[sp] = gVWSp->gVal[0].rgbv;
break;
default:
errNum = WLZ_ERR_GREY_TYPE;
break;
}
}
/* call integration function and seet value */
intFunc(pixptr, length, (int )(viewStr1->dist -
WLZ_NINT(viewStr1->minvals.vtZ)),
intFuncData, &errNum);
}
}
}
(void )WlzEndGreyScan(&iwsp, &gwsp);
if(errNum == WLZ_ERR_EOO) /* Reset error from end of intervals */
{
errNum = WLZ_ERR_NONE;
}
/* if no integration function then threshold - binary only */
if( intFunc == NULL ){
pixval.v.ubv = 1;
rtnObj = WlzAssignObject(rtnObj, NULL);
if((obj1 = WlzThreshold(rtnObj, pixval, WLZ_THRESH_HIGH,
&errNum)) != NULL){
WlzFreeObj(rtnObj);
values.core = NULL;
rtnObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, obj1->domain, values, NULL, NULL,
&errNum);
WlzFreeObj(obj1);
}
else {
WlzFreeObj(rtnObj);
rtnObj = NULL;
}
}
}
/* clear space */
if( viewStr1 ){
errNum = WlzFree3DViewStruct(viewStr1);
}
if( s_to_x ){
AlcFree( s_to_x );
}
if( s_to_y ){
AlcFree( s_to_y );
}
if( s_to_z ){
AlcFree( s_to_z );
}
/* check error and return */
if( dstErr ){
*dstErr = errNum;
}
return rtnObj;
}
/*!
* \return New object with the rojection.
* \ingroup WlzTransform
* \brief Use the view transform to define a projection from
* 3D to 2D and then project the object onto this plane.
* The object supplied to this function must be a 3D
* spatial domain object (WLZ_3D_DOMAINOBJ) with either
* no values or for integration WLZ_GREY_UBYTE values.
* Integration will assign each output pixel the sum of
* all input voxels mapped via either the domain density
* or the voxel density.
* The integration is controled by the integrate parameter
* with valid values:
* WLZ_PROJECT_INT_MODE_NONE - a "shadow domain" without values
* is computed,
* WLZ_PROJECT_INT_MODE_DOMAIN - the voxels of the domain are
* integrated using
* \f[
p = \frac{1}{255} n d
\f]
* WLZ_PROJECT_INT_MODE_VALUES - the voxel values are integrated
* using
* \f[
p = \frac{1}{255} \sum{l\left[v\right]}.
\f]
* Where
* \f$p\f$ is the projected image value,
* \f$n\f$ is the number of voxels projected for \f$p\f$,
* \f$d\f$ is the density of domain voxels,
* \f$l\f$ is the voxel value density look up table and
* \f$v\f$ is a voxel value.
* \param obj The given object.
* \param vStr Given view structure defining the
* projection plane.
* \param intMod This may take three values:
* WLZ_PROJECT_INT_MODE_NONE,
* WLZ_PROJECT_INT_MODE_DOMAIN or
* WLZ_PROJECT_INT_MODE_VALUES.
* \param denDom Density of domain voxels this value
* is not used unless the integration
* mode is WLZ_PROJECT_INT_MODE_DOMAIN.
* \param denVal Density look up table for object
* voxel density values which must be
* an array of 256 values. This may be
* NULL if the integration mode is not
* WLZ_PROJECT_INT_MODE_VALUES.
* \param depth If greater than zero, the projection
* depth perpendicular to the viewing
* plane.
* \param dstErr Destination error pointer, may be NULL.
*/
WlzObject *WlzProjectObjToPlane(WlzObject *obj,
WlzThreeDViewStruct *vStr,
WlzProjectIntMode intMod,
WlzUByte denDom, WlzUByte *denVal,
double depth, WlzErrorNum *dstErr)
{
int nThr = 1,
itvVal = 0;
WlzIVertex2 prjSz;
WlzIBox2 prjBox = {0};
double pln[4];
WlzObject *bufObj = NULL,
*prjObj = NULL;
WlzThreeDViewStruct *vStr1 = NULL;
double **vMat = NULL;
WlzValues nullVal;
WlzErrorNum errNum = WLZ_ERR_NONE;
WlzAffineTransform *rescaleTr = NULL;
WlzGreyValueWSpace **gVWSp = NULL;
void ***prjAry = NULL;
const double eps = 0.000001;
#ifdef WLZ_DEBUG_PROJECT3D_TIME
struct timeval times[3];
#endif /* WLZ_DEBUG_PROJECT3D_TIME */
nullVal.core = NULL;
if(obj == NULL)
{
errNum = WLZ_ERR_OBJECT_NULL;
}
else if(obj->type != WLZ_3D_DOMAINOBJ)
{
errNum = WLZ_ERR_OBJECT_TYPE;
}
else if(obj->domain.core == NULL)
{
errNum = WLZ_ERR_DOMAIN_NULL;
}
else if(obj->domain.core->type != WLZ_PLANEDOMAIN_DOMAIN)
{
errNum = WLZ_ERR_DOMAIN_TYPE;
}
else if(vStr == NULL)
{
errNum = WLZ_ERR_TRANSFORM_NULL;
}
else if((intMod == WLZ_PROJECT_INT_MODE_VALUES) &&
(obj->values.core == NULL))
{
errNum = WLZ_ERR_VALUES_NULL;
}
#ifdef WLZ_DEBUG_PROJECT3D_TIME
gettimeofday(times + 0, NULL);
#endif /* WLZ_DEBUG_PROJECT3D_TIME */
/* Create new view transform without voxel scaling. The voxel scaling
* is done after the projection. */
if(errNum == WLZ_ERR_NONE)
{
if((vStr1 = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum)) != NULL)
{
vStr1->fixed = vStr->fixed;
vStr1->theta = vStr->theta;
vStr1->phi = vStr->phi;
vStr1->zeta = vStr->zeta;
vStr1->dist = vStr->dist;
vStr1->scale = vStr->scale;
vStr1->voxelSize[0] = 1.0;
vStr1->voxelSize[1] = 1.0;
vStr1->voxelSize[2] = 1.0;
vStr1->voxelRescaleFlg = 0;
vStr1->interp = vStr->interp;
vStr1->view_mode = vStr->view_mode;
vStr1->up = vStr->up;
vStr1->initialised = WLZ_3DVIEWSTRUCT_INIT_NONE;
vMat = vStr1->trans->mat;
errNum = WlzInit3DViewStructAffineTransform(vStr1);
if(errNum == WLZ_ERR_NONE)
{
errNum = Wlz3DViewStructTransformBB(obj, vStr1);
}
if(errNum != WLZ_ERR_NONE)
{
WlzFree3DViewStruct(vStr1);
vStr1 = NULL;
}
}
}
/* Compute bounding box of the projection. */
if(errNum == WLZ_ERR_NONE)
{
prjBox.xMin = WLZ_NINT(vStr1->minvals.vtX);
prjBox.yMin = WLZ_NINT(vStr1->minvals.vtY);
prjBox.xMax = WLZ_NINT(vStr1->maxvals.vtX);
prjBox.yMax = WLZ_NINT(vStr1->maxvals.vtY);
prjSz.vtX = prjBox.xMax - prjBox.xMin + 1;
prjSz.vtY = prjBox.yMax - prjBox.yMin + 1;
}
/* Compute post projection scaling. */
if((errNum == WLZ_ERR_NONE) && (vStr->voxelRescaleFlg != 0))
{
WlzIBox2 sBox;
WlzIVertex2 sSz;
WlzThreeDViewStruct *vStr2;
vStr2 = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum);
if(errNum == WLZ_ERR_NONE)
{
vStr2->fixed = vStr->fixed;
vStr2->theta = vStr->theta;
vStr2->phi = vStr->phi;
vStr2->zeta = vStr->zeta;
vStr2->dist = vStr->dist;
vStr2->scale = vStr->scale;
vStr2->voxelSize[0] = vStr->voxelSize[0];
vStr2->voxelSize[1] = vStr->voxelSize[1];
vStr2->voxelSize[2] = vStr->voxelSize[2];
vStr2->voxelRescaleFlg = vStr->voxelRescaleFlg;
vStr2->interp = vStr->interp;
vStr2->view_mode = vStr->view_mode;
vStr2->up = vStr->up;
vStr2->initialised = WLZ_3DVIEWSTRUCT_INIT_NONE;
errNum = WlzInit3DViewStructAffineTransform(vStr2);
if(errNum == WLZ_ERR_NONE)
{
errNum = Wlz3DViewStructTransformBB(obj, vStr2);
}
if(errNum == WLZ_ERR_NONE)
{
sBox.xMin = WLZ_NINT(vStr2->minvals.vtX);
sBox.yMin = WLZ_NINT(vStr2->minvals.vtY);
sBox.xMax = WLZ_NINT(vStr2->maxvals.vtX);
sBox.yMax = WLZ_NINT(vStr2->maxvals.vtY);
sSz.vtX = sBox.xMax - sBox.xMin + 1;
sSz.vtY = sBox.yMax - sBox.yMin + 1;
rescaleTr = WlzMakeAffineTransform(WLZ_TRANSFORM_2D_AFFINE, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
double **m;
m = rescaleTr->mat;
m[0][0] = (sSz.vtX * eps) / (prjSz.vtX * eps);
m[1][1] = (sSz.vtY * eps) / (prjSz.vtY * eps);
m[0][2] = sBox.xMin - WLZ_NINT(m[0][0] * prjBox.xMin);
m[1][2] = sBox.yMin - WLZ_NINT(m[1][1] * prjBox.yMin);
}
(void )WlzFree3DViewStruct(vStr2);
}
}
/* Compute plane equation, used to clip intervals if depth was given. */
if((errNum == WLZ_ERR_NONE) && (depth > eps))
{
Wlz3DViewGetPlaneEqn(vStr1, pln + 0, pln + 1, pln + 2, pln + 3);
}
/* Create rectangular projection array buffers, one for each thread,
* also if integrating values create a grey value workspace per thread. */
if(errNum == WLZ_ERR_NONE)
{
int idB;
#ifdef _OPENMP
#pragma omp parallel
{
#pragma omp master
{
nThr = omp_get_num_threads();
}
}
#endif
if((prjAry = (void ***)AlcCalloc(nThr, sizeof(void **))) == NULL)
{
errNum = WLZ_ERR_MEM_ALLOC;
}
else
{
if(intMod == WLZ_PROJECT_INT_MODE_NONE)
{
for(idB = 0; idB < nThr; ++idB)
{
if(AlcUnchar2Calloc((WlzUByte ***)&(prjAry[idB]),
prjSz.vtY, prjSz.vtX) != ALC_ER_NONE)
{
errNum = WLZ_ERR_MEM_ALLOC;
break;
}
}
}
else
{
for(idB = 0; idB < nThr; ++idB)
{
if(AlcInt2Calloc((int ***)&(prjAry[idB]),
prjSz.vtY, prjSz.vtX) != ALC_ER_NONE)
{
errNum = WLZ_ERR_MEM_ALLOC;
break;
}
}
}
}
if((errNum == WLZ_ERR_NONE) &&
(intMod == WLZ_PROJECT_INT_MODE_VALUES))
{
itvVal = (WlzGreyTableIsTiled(obj->values.core->type) == 0);
if(itvVal == 0)
{
if((gVWSp = AlcCalloc(nThr, sizeof(WlzGreyValueWSpace *))) == NULL)
{
errNum = WLZ_ERR_MEM_ALLOC;
}
else
{
for(idB = 0; idB < nThr; ++idB)
{
gVWSp[idB] = WlzGreyValueMakeWSp(obj, &errNum);
if(gVWSp[idB]->gType != WLZ_GREY_UBYTE)
{
errNum = WLZ_ERR_GREY_TYPE;
break;
}
}
}
}
}
}
/* Scan through the 3D domain setting value in the projection array. */
if(errNum == WLZ_ERR_NONE)
{
int pIdx,
pCnt;
WlzDomain *doms;
WlzValues *vals = NULL;
doms = obj->domain.p->domains;
if(itvVal)
{
vals = obj->values.vox->values;
}
pCnt = obj->domain.p->lastpl - obj->domain.p->plane1 + 1;
#ifdef _OPENMP
#pragma omp parallel for
#endif
for(pIdx = 0; pIdx < pCnt; ++pIdx)
{
int thrId = 0;
if((errNum == WLZ_ERR_NONE) && (doms[pIdx].core != NULL))
{
WlzObject *obj2;
WlzGreyWSpace gWSp;
WlzIntervalWSpace iWSp;
WlzErrorNum errNum2 = WLZ_ERR_NONE;
#ifdef _OPENMP
thrId = omp_get_thread_num();
#endif
obj2 = WlzMakeMain(WLZ_2D_DOMAINOBJ, doms[pIdx],
(vals)? vals[pIdx]: nullVal,
NULL, NULL, &errNum2);
if(errNum2 == WLZ_ERR_NONE)
{
if(itvVal)
{
errNum2 = WlzInitGreyScan(obj2, &iWSp, &gWSp);
}
else
{
errNum2 = WlzInitRasterScan(obj2, &iWSp, WLZ_RASTERDIR_ILIC);
}
}
if(errNum2 == WLZ_ERR_NONE)
{
double plnZ,
vMZX,
vMZY;
WlzIVertex3 p0,
p1;
p0.vtZ = p1.vtZ = obj->domain.p->plane1 + pIdx;
vMZX = (vMat[0][2] * p0.vtZ) + vMat[0][3] - prjBox.xMin;
vMZY = (vMat[1][2] * p0.vtZ) + vMat[1][3] - prjBox.yMin;
plnZ = (pln[2] * p0.vtZ) + pln[3];
while(((itvVal == 0) &&
((errNum2 = WlzNextInterval(&iWSp)) == WLZ_ERR_NONE)) ||
((itvVal != 0) &&
((errNum2 = WlzNextGreyInterval(&iWSp)) == WLZ_ERR_NONE)))
{
int skip = 0;
WlzDVertex2 q0,
q1;
p0.vtX = iWSp.lftpos;
p1.vtX = iWSp.rgtpos;
p0.vtY = p1.vtY = iWSp.linpos;
if(depth > eps)
{
int c;
double d0,
d1,
plnYZ;
/* Clip the 3D line segment p0,p1 using the plane equation. */
plnYZ = (pln[1] * p0.vtY) + plnZ;
d0 = (pln[0] * p0.vtX) + plnYZ;
d1 = (pln[0] * p1.vtX) + plnYZ;
c = ((d1 > depth) << 3) | ((d0 > depth) << 2) |
((d1 < -depth) << 1) | (d0 < -depth);
if(c)
{
if((c == 3) || (c == 12)) /* 00-- or ++00 */
{
/* Both out of range, so don't render. */
skip = 1;
}
else
{
if(fabs(pln[0]) > eps)
{
double plnX;
plnX = -1.0 / pln[0];
if((c & 1) != 0) /* x0x- */
{
p0.vtX = plnX * (plnYZ + depth);
}
else if((c & 4) != 0) /* x+x0 */
{
p0.vtX = plnX * (plnYZ - depth);
}
if((c & 2) != 0) /* 0x-x */
{
p1.vtX = plnX * (plnYZ + depth);
}
else if((c & 8) != 0) /* +x0x */
{
p1.vtX = plnX * (plnYZ - depth);
}
}
}
}
}
if(skip == 0)
{
q0.vtX = (vMat[0][0] * p0.vtX) + (vMat[0][1] * p0.vtY) + vMZX;
q0.vtY = (vMat[1][0] * p0.vtX) + (vMat[1][1] * p0.vtY) + vMZY;
q1.vtX = (vMat[0][0] * p1.vtX) + (vMat[0][1] * p1.vtY) + vMZX;
q1.vtY = (vMat[1][0] * p1.vtX) + (vMat[1][1] * p1.vtY) + vMZY;
switch(intMod)
{
case WLZ_PROJECT_INT_MODE_NONE:
{
WlzIVertex2 u0,
u1;
WLZ_VTX_2_NINT(u0, q0);
WLZ_VTX_2_NINT(u1, q1);
WlzProjectObjLine((WlzUByte **)(prjAry[thrId]), u0, u1);
}
break;
case WLZ_PROJECT_INT_MODE_DOMAIN:
{
int np,
nq;
WlzDVertex3 dq;
WlzIVertex2 u0,
u1;
WLZ_VTX_2_NINT(u0, q0);
WLZ_VTX_2_NINT(u1, q1);
WLZ_VTX_2_SUB(dq, q0, q1);
np = denDom * (iWSp.rgtpos - iWSp.lftpos + 1);
nq = (int )ceil(WLZ_VTX_2_LENGTH(dq) + eps);
WlzProjectObjLineDom((int **)(prjAry[thrId]), np / nq,
u0, u1);
}
break;
case WLZ_PROJECT_INT_MODE_VALUES:
if(itvVal)
{
WlzProjectObjLineVal((int **)(prjAry[thrId]), denVal,
gWSp.u_grintptr.ubp, NULL,
vMat, vMZX, vMZY, p0, p1);
}
else
{
WlzProjectObjLineVal((int **)(prjAry[thrId]), denVal,
NULL, gVWSp[thrId],
vMat, vMZX, vMZY, p0, p1);
}
break;
}
}
}
(void )WlzEndGreyScan(&iWSp, &gWSp);
if(errNum2 == WLZ_ERR_EOO)
{
errNum2 = WLZ_ERR_NONE;
}
}
(void )WlzFreeObj(obj2);
if(errNum2 != WLZ_ERR_NONE)
{
#ifdef _OPENMP
#pragma omp critical
{
#endif
if(errNum == WLZ_ERR_NONE)
{
errNum = errNum2;
}
#ifdef _OPENMP
}
#endif
}
}
}
}
/* Free grey value workspaces if they were created. */
if(gVWSp)
{
int idB;
for(idB = 0; idB < nThr; ++idB)
{
WlzGreyValueFreeWSp(gVWSp[idB]);
}
AlcFree(gVWSp);
}
if(errNum == WLZ_ERR_NONE)
{
int idB;
size_t idC,
bufSz;
WlzGreyP buf0,
buf1;
WlzIVertex2 prjOrg;
prjOrg.vtX = prjBox.xMin;
prjOrg.vtY = prjBox.yMin;
bufSz = prjSz.vtX * prjSz.vtY;
for(idB = 1; idB < nThr; ++idB)
{
if(intMod == WLZ_PROJECT_INT_MODE_NONE)
{
buf0.ubp = ((WlzUByte ***)(prjAry))[0][0],
buf1.ubp = ((WlzUByte ***)(prjAry))[idB][0];
for(idC = 0; idC < bufSz; ++idC)
{
buf0.ubp[idC] += buf1.ubp[idC];
}
}
else
{
buf0.inp = ((int ***)(prjAry))[0][0],
buf1.inp = ((int ***)(prjAry))[idB][0];
for(idC = 0; idC < bufSz; ++idC)
{
buf0.inp[idC] += buf1.inp[idC];
}
}
}
switch(intMod != WLZ_PROJECT_INT_MODE_NONE)
{
buf0.inp = ((int ***)(prjAry))[0][0];
for(idC = 0; idC < bufSz; ++idC)
{
buf0.inp[idC] /= 256;
}
}
if(intMod == WLZ_PROJECT_INT_MODE_NONE)
{
bufObj = WlzAssignObject(
WlzFromArray2D((void **)(prjAry[0]), prjSz, prjOrg,
WLZ_GREY_UBYTE, WLZ_GREY_UBYTE,
0.0, 1.0, 1, 0, &errNum), NULL);
}
else
{
bufObj = WlzAssignObject(
WlzFromArray2D((void **)(prjAry[0]), prjSz, prjOrg,
WLZ_GREY_INT, WLZ_GREY_INT,
0.0, 1.0, 1, 0, &errNum), NULL);
}
}
/* Free the projection array(s). */
if(prjAry)
{
int idB;
for(idB = 0; idB < nThr; ++idB)
{
(void )Alc2Free((prjAry[idB]));
}
AlcFree(prjAry);
}
/* Make return object using threshold. */
if(errNum == WLZ_ERR_NONE)
{
WlzPixelV tV;
WlzObject *tObj = NULL;
tV.type = WLZ_GREY_UBYTE;
tV.v.ubv = 1;
tObj = WlzAssignObject(
WlzThreshold(bufObj, tV, WLZ_THRESH_HIGH, &errNum), NULL);
if(tObj)
{
if(intMod == WLZ_PROJECT_INT_MODE_NONE)
{
prjObj = WlzMakeMain(tObj->type, tObj->domain, nullVal,
NULL, NULL, &errNum);
}
else
{
prjObj = WlzMakeMain(tObj->type, tObj->domain, tObj->values,
NULL, NULL, &errNum);
}
}
(void )WlzFreeObj(tObj);
}
(void )WlzFreeObj(bufObj);
(void )WlzFree3DViewStruct(vStr1);
/* Scale image. */
if(rescaleTr != NULL)
{
if(errNum == WLZ_ERR_NONE)
{
WlzObject *tObj = NULL;
tObj = WlzAffineTransformObj(prjObj, rescaleTr,
WLZ_INTERPOLATION_NEAREST, &errNum);
(void )WlzFreeObj(prjObj);
prjObj = tObj;
}
(void )WlzFreeAffineTransform(rescaleTr);
}
#ifdef WLZ_DEBUG_PROJECT3D_TIME
gettimeofday(times + 1, NULL);
ALC_TIMERSUB(times + 1, times + 0, times + 2);
(void )fprintf(stderr, "WlzGetProjectionFromObject: Elapsed time = %g\n",
times[2].tv_sec + (0.000001 * times[2].tv_usec));
#endif /* WLZ_DEBUG_PROJECT3D_TIME */
if(dstErr)
{
*dstErr = errNum;
}
return(prjObj);
}
/*!
* \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);
}