int main(int argc,
char **argv)
{
FILE *inFile1=NULL, *inFile2=NULL;
char optList[] = "AR123f:F:iIx:y:z:s:a:b:u:v:w:hV";
int option;
int trans1RelFlg=0, trans2RelFlg=0, trans3DFlg=0, outputRelFlg=0;
int invertFlg=0, inverseFlg=0, threeDFlg=0;
WlzAffineTransform *cmdLineTrans=NULL;
double tx, ty, tz, scale, theta, phi, alpha, psi, xsi;
int verboseFlg=0;
RecSectionList recSecList1, recSecList2;
RecSectionList *secList1=&recSecList1, *secList2=&recSecList2;
HGUDlpListItem *listItem, *listItem1;
RecSection *sec, *sec1;
char *errMsg = NULL;
RecError errFlg = REC_ERR_NONE;
int numSec1, numSec2;
WlzErrorNum errNum=WLZ_ERR_NONE;
WlzObject *transformsObj1, *transformsObj2;
int p, i, ip;
WlzAffineTransform *newTransform, *tmpTrans, *tmp1Trans, *reconTrans;
/* default transform */
tx = 0.0;
ty = 0.0;
tx = 0.0;
scale = 1.0;
theta = 0.0;
phi = 0.0;
alpha = 0.0;
psi = 0.0;
xsi = 0.0;
/* parse the command line */
opterr = 0;
while( (option = getopt(argc, argv, optList)) != EOF ){
switch( option ){
case 'A':
outputRelFlg = 0;
break;
case 'R':
outputRelFlg = 1;
break;
case '1':
trans1RelFlg = 1;
break;
case '2':
trans2RelFlg = 1;
break;
case '3':
trans3DFlg = 1;
break;
case 'f':
if( (optarg != NULL) && (strlen(optarg) > 0) ){
if( (inFile1 = fopen(optarg, "r")) == NULL ){
fprintf(stderr, "%s: failed to open input file %s\n",
argv[0], optarg);
usage(argv[0]);
return 1;
}
}
else {
usage(argv[0]);
return 1;
}
break;
case 'F':
if( (optarg != NULL) && (strlen(optarg) > 0) ){
if( (inFile2 = fopen(optarg, "r")) == NULL ){
fprintf(stderr, "%s: failed to open input file %s\n",
argv[0], optarg);
usage(argv[0]);
return 1;
}
}
else {
usage(argv[0]);
return 1;
}
break;
case 'i':
invertFlg = 1;
break;
case 'I':
inverseFlg = 1;
break;
case 'a':
if(sscanf(optarg, "%lg", &theta) != 1)
{
usage(argv[0]);
return 1;
}
break;
case 'b':
if(sscanf(optarg, "%lg", &phi) != 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", &alpha) != 1)
{
usage(argv[0]);
return 1;
}
break;
case 'v':
if(sscanf(optarg, "%lg", &psi) != 1)
{
usage(argv[0]);
return 1;
}
break;
case 'w':
if(sscanf(optarg, "%lg", &xsi) != 1)
{
usage(argv[0]);
return 1;
}
break;
case 'x':
if(sscanf(optarg, "%lg", &tx) != 1)
{
usage(argv[0]);
return 1;
}
break;
case 'y':
if(sscanf(optarg, "%lg", &ty) != 1)
{
usage(argv[0]);
return 1;
}
break;
case 'z':
if(sscanf(optarg, "%lg", &tz) != 1)
{
usage(argv[0]);
return 1;
}
break;
case 'V':
verboseFlg = 1;
break;
case 'h':
default:
usage(argv[0]);
return 1;
}
}
/* create the command line transform */
if( threeDFlg ){
cmdLineTrans = WlzAffineTransformFromPrimVal(WLZ_TRANSFORM_3D_AFFINE,
tx, ty, tz, scale, theta, phi,
alpha, psi, xsi,
invertFlg, &errNum);
}
else {
cmdLineTrans = WlzAffineTransformFromPrimVal(WLZ_TRANSFORM_2D_AFFINE,
tx, ty, tz, scale, theta, phi,
alpha, psi, xsi,
invertFlg, &errNum);
}
/* check for files on the command line */
if( (inFile1 == NULL) && (optind < argc) ){
if( (inFile1 = fopen(*(argv+optind), "r")) == NULL ){
fprintf(stderr, "%s: can't open file %s\n", argv[0], *(argv+optind));
usage(argv[0]);
return 1;
}
optind++;
}
if( (inFile2 == NULL) && (optind < argc) ){
if( (inFile2 = fopen(*(argv+optind), "r")) == NULL ){
fprintf(stderr, "%s: can't open file %s\n", argv[0], *(argv+optind));
usage(argv[0]);
return 1;
}
optind++;
}
/* now read the transforms, in each case the logic is that
transform 1 is applied then transform 2 then the command line
transform. If transform 1 is a reconstruct bib file then the
output will include the file information. Note in this case
the output transform will be absolute unless specified on the
command line */
/* transform 1 - try to read as a Reconstruct file, on failure
rewind and read as an MAPaint file */
if( inFile1 != NULL ){
errFlg = RecFileSecListRead(secList1, &numSec1, inFile1, &errMsg);
if( errFlg == REC_ERR_NONE ){
/* check transform attribute */
switch( secList1->attributes.trMode ){
case REC_TRMODE_REL:
trans1RelFlg = 1;
break;
case REC_TRMODE_ABS:
trans1RelFlg = 0;
break;
}
transformsObj1 = SecListToTransforms(secList1, trans1RelFlg, &errNum);
}
else {
secList1 = NULL;
rewind(inFile1);
transformsObj1 = ReadMAPaintRealignTransforms(inFile1, &errNum);
}
}
else {
fprintf(stderr, "%s: a file for transform 1 must be defined\n", argv[0]);
usage(argv[0]);
return 1;
}
/* transform 2 - try to read as a Reconstruct file, on failure
rewind and read as an MAPaint file */
if( inFile2 != NULL ){
errFlg = RecFileSecListRead(secList2, &numSec2, inFile2, &errMsg);
if( errFlg == REC_ERR_NONE ){
/* check transform attribute */
switch( secList2->attributes.trMode ){
case REC_TRMODE_REL:
trans2RelFlg = 1;
break;
case REC_TRMODE_ABS:
trans2RelFlg = 0;
break;
}
transformsObj2 = SecListToTransforms(secList2, trans2RelFlg, &errNum);
}
else {
secList2 = NULL;
rewind(inFile2);
transformsObj2 = ReadMAPaintRealignTransforms(inFile2, &errNum);
}
}
else {
transformsObj2 = NULL;
}
/* form the plane by plane product of the transforms,
note the output will be of the planes in transform 1 */
for(p=transformsObj1->domain.p->plane1, i=0;
p <= transformsObj1->domain.p->lastpl; p++, i++){
/* get the existing transform */
if( transformsObj1->domain.p->domains[i].t ){
newTransform =
WlzAssignAffineTransform(transformsObj1->domain.p->domains[i].t,
NULL);
}
else {
newTransform = NULL;
}
/* check for transform 2 */
if(newTransform && transformsObj2 &&
(p >= transformsObj2->domain.p->plane1) &&
(p <= transformsObj2->domain.p->lastpl) &&
(transformsObj2->domain.p->
domains[p-transformsObj2->domain.p->plane1].t)){
tmpTrans =
WlzAffineTransformProduct(newTransform,
transformsObj2->domain.p->
domains[p-transformsObj2->domain.p->plane1].t,
NULL);
WlzFreeAffineTransform(newTransform);
newTransform = tmpTrans;
}
/* apply the command line transform */
if( newTransform && cmdLineTrans ){
tmpTrans = WlzAffineTransformProduct(newTransform, cmdLineTrans, NULL);
WlzFreeAffineTransform(newTransform);
newTransform = tmpTrans;
}
/* put it back into transformsObj1 */
if( transformsObj1->domain.p->domains[i].t ){
WlzFreeAffineTransform(transformsObj1->domain.p->domains[i].t);
}
transformsObj1->domain.p->domains[i].t =
WlzAssignAffineTransform(newTransform, NULL);
}
/* if there is a section list in Reconstruct form
then take out the reconstruct transform */
if( secList1 ){
/* take out the reconstruct transform first */
reconTrans = WlzAffineTransformFromPrimVal
(WLZ_TRANSFORM_2D_AFFINE, 0.0, 0.0, 0.0,
1.0 / secList1->reconstruction.scale.vtX,
0.0, 0.0, 0.0, 0.0, 0.0, 0, NULL);
listItem = HGUDlpListHead(secList1->list);
while( listItem ){
sec = (RecSection *) HGUDlpListEntryGet(secList1->list, listItem);
if( sec ){
p = sec->index;
i = p - transformsObj1->domain.p->plane1;
if( transformsObj1->domain.p->domains[i].t ){
tmpTrans = WlzAffineTransformProduct
(transformsObj1->domain.p->domains[i].t, reconTrans, NULL);
WlzFreeAffineTransform(transformsObj1->domain.p->domains[i].t);
transformsObj1->domain.p->domains[i].t =
WlzAssignAffineTransform(tmpTrans, NULL);
}
}
listItem = HGUDlpListNext(secList1->list, listItem);
}
}
/* check for relative flag */
if( outputRelFlg ){
/* use the section list if available */
if( secList1 ){
/* sort out the relative transform */
listItem = HGUDlpListTail(secList1->list);
while( listItem != HGUDlpListHead(secList1->list) ){
sec = (RecSection *) HGUDlpListEntryGet(secList1->list, listItem);
if( sec ){
p = sec->index;
i = p - transformsObj1->domain.p->plane1;
if( strncmp(sec->imageFile, "empty", 5) == 0 ){
WlzFreeAffineTransform(transformsObj1->domain.p->domains[i].t);
transformsObj1->domain.p->domains[i].t =
WlzAffineTransformFromPrimVal(WLZ_TRANSFORM_2D_AFFINE,
0.0, 0.0, 0.0, 1.0,
0.0, 0.0, 0.0, 0.0,
0.0, 0, NULL);
}
else {
/* walk backwards to previous non-empty section */
listItem1 = HGUDlpListPrev(secList1->list, listItem);
while( listItem1 != HGUDlpListHead(secList1->list) ){
sec1 = (RecSection *) HGUDlpListEntryGet(secList1->list, listItem1);
if( strncmp(sec1->imageFile, "empty", 5) ){
break;
}
listItem1 = HGUDlpListPrev(secList1->list, listItem1);
}
ip = sec1->index - transformsObj1->domain.p->plane1;
tmpTrans =
WlzAffineTransformInverse(transformsObj1->domain.p->domains[ip].t,
NULL);
tmp1Trans = WlzAffineTransformProduct(
transformsObj1->domain.p->domains[i].t,
tmpTrans, NULL);
checkTrans(tmp1Trans);
WlzFreeAffineTransform(transformsObj1->domain.p->domains[i].t);
WlzFreeAffineTransform(tmpTrans);
transformsObj1->domain.p->domains[i].t = tmp1Trans;
}
}
listItem = HGUDlpListPrev(secList1->list, listItem);
}
}
else {
i = transformsObj1->domain.p->lastpl - transformsObj1->domain.p->plane1;
ip = i;
for(p = transformsObj1->domain.p->lastpl;
p >= transformsObj1->domain.p->plane1; p--, i--){
if( i > ip ){
continue;
}
ip--;
if(transformsObj1->domain.p->domains[i].t){
/* jump over any NULL transforms */
while((ip >= 0) &&
(transformsObj1->domain.p->domains[ip].t == NULL)){
ip--;
}
/* push the transform down the line */
if(ip >= 0){
tmpTrans =
WlzAffineTransformInverse(transformsObj1->domain.p->domains[ip].t,
NULL);
tmp1Trans =
WlzAffineTransformProduct(transformsObj1->domain.p->domains[i].t,
tmpTrans,
NULL);
checkTrans(tmp1Trans);
WlzFreeAffineTransform(transformsObj1->domain.p->domains[i].t);
WlzFreeAffineTransform(tmpTrans);
transformsObj1->domain.p->domains[i].t =
WlzAssignAffineTransform(tmp1Trans, NULL);
}
}
}
}
}
/* if there is a section list one then output in Reconstruct
bibfile format else MAPaint style */
if( secList1 ){
/* set the relative/absolute attribute */
if( outputRelFlg ){
secList1->attributes.trMode = REC_TRMODE_REL;
}
else {
secList1->attributes.trMode = REC_TRMODE_ABS;
}
/* put back the transforms */
listItem = HGUDlpListHead(secList1->list);
while( listItem ){
sec = (RecSection *) HGUDlpListEntryGet(secList1->list, listItem);
p = sec->index;
i = p - transformsObj1->domain.p->plane1;
/* check for NULL transform */
if( transformsObj1->domain.p->domains[i].t == NULL ){
transformsObj1->domain.p->domains[i].t =
WlzAffineTransformFromPrimVal(WLZ_TRANSFORM_2D_AFFINE,
0.0, 0.0, 0.0, 1.0,
0.0, 0.0, 0.0, 0.0,
0.0, 0, NULL);
}
sec->transform =
transformsObj1->domain.p->domains[i].t;
listItem = HGUDlpListNext(secList1->list, listItem);
}
RecFileSecListWrite(stdout, secList1, numSec1, &errMsg);
}
else {
WriteMAPaintRealignTransforms(stdout, transformsObj1, outputRelFlg);
}
return 0;
}
int main(int argc, char *argv[])
{
int option,
numSec,
absMode = 1,
ok = 1,
usage = 0;
char *inFile,
*outFile;
FILE *fP = NULL;
RecError recErr = REC_ERR_NONE;
RecSectionList *secList = NULL;
char *errMsg;
static char optList[] = "ahro:",
defFile[] = "-",
defErrMsg[] = "none.";
opterr = 0;
errMsg = defErrMsg;
inFile = outFile = defFile;
while((usage == 0) &&
((option = getopt(argc, argv, optList)) != -1))
{
switch(option)
{
case 'a':
absMode = 1;
break;
case 'r':
absMode = 0;
break;
case 'o':
outFile = optarg;
break;
case 'h': /* FALLTHROUGH */
default:
usage = 1;
break;
}
}
if((usage == 0) && (optind < argc))
{
if((optind + 1) != argc)
{
usage = 1;
}
else
{
inFile = *(argv + optind);
}
}
ok = !usage;
/* Read input bibfile. */
if(ok)
{
if((secList = RecSecNewSectionList(&recErr)) == NULL)
{
ok = 0;
(void )fprintf(stderr,
"%s: Failed to memory for allocate section list.\n",
*argv);
}
}
if(ok)
{
if((inFile == NULL) ||
(*inFile == '\0') ||
((fP = (strcmp(inFile, "-")? fopen(inFile, "r"): stdin)) == NULL))
{
ok = 0;
(void )fprintf(stderr,
"%s: Failed to open input file %s\n",
*argv, (inFile)? inFile: "(null)");
}
}
if(ok)
{
if(RecFileSecListRead(secList, &numSec, fP, &errMsg) != REC_ERR_NONE)
{
ok = 0;
(void )fprintf(stderr,
"%s: Failed to read section list from file %s.\n"
"Error message - %s\n",
*argv, inFile, errMsg);
}
}
if(fP && (strcmp(inFile, "-") == 0))
{
(void )fclose(fP);
}
/* Convert transforms. */
if(ok)
{
if(absMode)
{
recErr = RecSecListAbsFromRel(secList);
}
else
{
recErr = RecSecListRelFromAbs(secList);
}
if(recErr != REC_ERR_NONE)
{
ok = 0;
(void )fprintf(stderr,
"%s: Failed to convert the section list from %s to\n"
"%s transforms.\n",
*argv,
(absMode)? "relative": "absolute",
(absMode)? "absolute": "relative");
}
}
/* Write output bibfile. */
if(ok)
{
if((outFile == NULL) ||
(*outFile == '\0') ||
((fP = (strcmp(outFile, "-")? fopen(outFile, "w"): stdout)) == NULL))
{
ok = 0;
(void )fprintf(stderr,
"%s: Failed to open output file %s\n",
*argv, (inFile)? inFile: "(null)");
}
}
if(ok)
{
if(RecFileSecListWrite(fP, secList, numSec, &errMsg) != REC_ERR_NONE)
{
(void )fprintf(stderr,
"%s: Failed to write section list to file %s.\n"
"Error message - %s\n",
*argv, inFile, errMsg);
ok = 0;
}
}
if(fP && (strcmp(outFile, "-") == 0))
{
(void )fclose(fP);
}
if(usage)
{
(void )fprintf(stderr,
"Usage: %s [-a] [-h] [-r] [-o outfile] [<infile>]\n"
"Reads a reconstruction bibfile and writes it to the output file\n"
"with either absolute or relative transforms.\n"
"Version: %s\n"
"Options:\n"
" -a Output bibfile with absolute transforms (%s).\n"
" -h Help - print this usage information.\n"
" -r Output bibfile with relative transforms (%s).\n"
" -o Output file name.\n"
"By default %s reads from it's standard input and\n"
"writes to it's standard output.\n",
*argv,
WlzVersion(),
(absMode != 0)? "set": "not set",
(absMode == 0)? "set": "not set",
*argv);
}
exit(!ok);
}
