int main( int argc, char *argv[])
{
int i;
FILE *fin, *fout;
struct Mod_Model *mod;
int npatch = 0;
int nvalue = 0, nvalue2 = 0;
int ix, iy, iz;
float dx, dy, dz;
float value, maxval = -1.e30;
float value2, maxval2 = -1.e30;
int ob, co, listInd, listStart;
Ipoint *pts;
char format[10] = "%10.4f";
char format2[10] = "%10.4f";
setExitPrefix("ERROR: imod2patch - ");
if (argc != 3){
if (argc != 1)
printf("ERROR: imod2patch - wrong # of arguments\n");
printf("imod2patch usage:\n");
printf("imod2patch imod_model patch_file\n");
exit(1);
}
i = 1;
mod = imodRead(argv[i]);
if (!mod)
exitError("Reading model %s\n", argv[i]);
if (imodBackupFile(argv[++i]))
exitError("Renaming existing output file to %s\n", argv[i]);
fout = fopen(argv[i], "w");
if (!fout)
exitError("Could not open %s\n", argv[i]);
/* Count up patches and values and find max of values */
for (ob = 0; ob < mod->objsize; ob++) {
listInd = 0;
for (co = 0; co < mod->obj[ob].contsize; co++) {
listStart = listInd;
if (mod->obj[ob].cont[co].psize >= 2) {
npatch++;
if (istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE1, &value,
&listInd)) {
maxval = B3DMAX(maxval, value);
nvalue++;
}
listInd = listStart;
if (istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE2, &value2,
&listInd)) {
maxval2 = B3DMAX(maxval2, value2);
nvalue2++;
}
}
}
}
/* If values are greater than one they are probably residuals and only need
2 decimal places */
if (nvalue && maxval > 1.01)
strcpy(format, "%10.2f");
if (nvalue2 && maxval2 > 1.01)
strcpy(format, "%10.2f");
fprintf(fout, "%d edited positions\n", npatch);
for (ob = 0; ob < mod->objsize; ob++) {
listInd = 0;
for (co = 0; co < mod->obj[ob].contsize; co++) {
listStart = listInd;
if (mod->obj[ob].cont[co].psize >= 2) {
pts = mod->obj[ob].cont[co].pts;
ix = pts[0].x + 0.5;
iy = pts[0].y + 0.5;
iz = pts[0].z + 0.5;
dx = (pts[1].x - pts[0].x) / mod->pixsize;
dy = (pts[1].y - pts[0].y) / mod->pixsize;
dz = (pts[1].z - pts[0].z) / mod->pixsize;
if (mod->flags & IMODF_FLIPYZ)
fprintf(fout, "%6d %5d %5d %8.2f %8.2f %8.2f",
ix, iz, iy, dx, dz, dy);
else
fprintf(fout, "%6d %5d %5d %8.2f %8.2f %8.2f",
ix, iy, iz, dx, dy, dz);
if (nvalue) {
value = 0.;
istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE1, &value,
&listInd);
fprintf(fout, format, value);
}
if (nvalue2) {
listInd = listStart;
value2 = 0.;
istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE2, &value2,
&listInd);
fprintf(fout, format2, value2);
}
fprintf(fout, "\n");
}
}
}
fclose(fout);
exit(0);
}
int main(int argc, char *argv[])
{
Imod model;
FILE *fin, *fout;
char *filename = NULL;
int i;
int mode = 0;
int useZscale = 0;
int doflip = 1;
int transopt = 0;
int rotScaleopt = 0;
int toImage = 0, fromImage = 0;
int oneLine = -1;
int toggleFlip = 0;
int flipModel = 0;
float zscale = 1.;
float transScale = 1.;
float rx = 0., ry = 0., rz = 0.;
float transx = 0., transy = 0., transz = 0.;
int multiTrans = 0;
int newNx = 0, newNy = 0, newNz = 0;
char *progname = imodProgName(argv[0]);
Ipoint newCen, tmpPt;
Imat *mat = imodMatNew(3);
Imat *normMat = imodMatNew(3);
IrefImage useRef, *modRefp;
MrcHeader hdata, hdataFirst;
Ipoint unitPt = {1., 1., 1.};
char prefix[100];
sprintf(prefix, "ERROR: %s - ", progname);
setExitPrefix(prefix);
if (argc < 3){
usage(progname);
}
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
switch (argv[i][1]) {
case '2':
filename = argv[++i];
mode += 2;
break;
case '3':
filename = argv[++i];
mode += 3;
break;
case 'S':
sscanf(argv[++i], "%f", &transScale);
break;
case 'i':
toImage = 1;
if (NULL == (fin = fopen(argv[++i], "rb")))
exitError("Couldn't open %s", argv[i]);
if (mrc_head_read(fin, &hdata))
exitError("Reading header from %s", argv[i]);
fclose(fin);
break;
case 'I':
fromImage = 1;
if (NULL == (fin = fopen(argv[++i], "rb")))
exitError("Couldn't open %s", argv[i]);
if (mrc_head_read(fin, &hdataFirst))
exitError("Reading header from %s", argv[i]);
fclose(fin);
break;
case 'z':
useZscale = 1;
break;
case 'f':
doflip = 0;
break;
case 'Y':
flipModel = 1;
break;
case 'T':
toggleFlip = 1;
break;
case 'n':
sscanf(argv[++i], "%d%*c%d%*c%d", &newNx, &newNy, &newNz);
break;
case 'l':
oneLine = atoi(argv[++i]);
break;
case 't': /* Translations */
tmpPt.x = tmpPt.y = tmpPt.z = 0.;
transopt = 1;
switch (argv[i][2]) {
case 'x':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-tx%f", &tmpPt.x);
else
sscanf(argv[++i], "%f", &tmpPt.x);
if (transx)
multiTrans = 1;
transx = tmpPt.x;
break;
case 'y':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-ty%f", &tmpPt.y);
else
sscanf(argv[++i], "%f", &tmpPt.y);
if (transy)
multiTrans = 1;
transy = tmpPt.y;
break;
case 'z':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-tz%f", &tmpPt.z);
else
sscanf(argv[++i], "%f", &tmpPt.z);
if (transz)
multiTrans = 1;
transz = tmpPt.z;
break;
default:
exitError("Invalid option %s", argv[i]);
}
imodMatTrans(mat, &tmpPt);
break;
case 's': /* Scaling */
tmpPt.x = tmpPt.y = tmpPt.z = 1.;
transopt = 1;
rotScaleopt = 1;
switch (argv[i][2]) {
case 'x':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-sx%f", &tmpPt.x);
else
sscanf(argv[++i], "%f", &tmpPt.x);
break;
case 'y':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-sy%f", &tmpPt.y);
else
sscanf(argv[++i], "%f", &tmpPt.y);
break;
case 'z':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-sz%f", &tmpPt.z);
else
sscanf(argv[++i], "%f", &tmpPt.z);
break;
default:
exitError("Invalid option %s", argv[i]);
}
imodMatScale(mat, &tmpPt);
tmpPt.x = 1. / tmpPt.x;
tmpPt.y = 1. / tmpPt.y;
tmpPt.z = 1. / tmpPt.z;
imodMatScale(normMat, &tmpPt);
break;
case 'r': /* Rotations */
transopt = 1;
rotScaleopt = 1;
switch (argv[i][2]) {
case 'x':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-rx%f", &rx);
else
sscanf(argv[++i], "%f", &rx);
imodMatRot(mat, (double)rx, b3dX);
imodMatRot(normMat, (double)rx, b3dX);
break;
case 'y':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-ry%f", &ry);
else
sscanf(argv[++i], "%f", &ry);
imodMatRot(mat, (double)ry, b3dY);
imodMatRot(normMat, (double)ry, b3dY);
break;
case 'z':
if (argv[i][3] != 0x00)
sscanf(argv[i], "-rz%f", &rz);
else
sscanf(argv[++i], "%f", &rz);
imodMatRot(mat, (double)rz, b3dZ);
imodMatRot(normMat, (double)rz, b3dZ);
break;
default:
exitError("Invalid option %s", argv[i]);
}
break;
default:
exitError("Invalid option %s", argv[i]);
}
}else{
break;
}
}
if (mode && mode / 2 != 1)
exitError("You cannot enter both -2 and -3");
if (mode && rotScaleopt)
exitError("You cannot enter -r or -s options with -2 and -3");
if (transopt && mode == 2 && oneLine < 1 && transz)
exitError("You cannot enter -tz option with -2 unless transforming with one line");
if (mode && multiTrans)
exitError("You cannot enter -t options more than once with -2 and -3");
if (i != argc - 2) {
printf("ERROR: %s - Command line should end with two non-option "
"arguments\n", progname);
usage(progname);
}
fin = fopen(argv[i], "rb");
if (!fin)
exitError("Opening input file %s", argv[i]);
imodDefault(&model);
model.file = fin;
if (imodReadFile(&model))
exitError("Reading imod model (%s)", argv[i]);
fclose(fin);
if (imodBackupFile(argv[i + 1]))
exitError("Couldn't create backup file");
fout = fopen(argv[i + 1], "wb");
if (!fout)
exitError("Opening output file %s", argv[i + 1]);
/* Change image reference information */
if (fromImage && imodSetRefImage(&model, &hdataFirst))
exitError("Allocating a IrefImage structure");
/* Do flipping operations first */
if (flipModel)
imodFlipYZ(&model);
if (toggleFlip) {
if (model.flags & IMODF_FLIPYZ)
model.flags &= ~IMODF_FLIPYZ;
else
model.flags |= IMODF_FLIPYZ;
}
/* Do scaling to image reference next */
if (toImage) {
modRefp = model.refImage;
if (modRefp && !(model.flags & IMODF_OTRANS_ORIGIN))
exitError("Model has no image origin information; -i option invalid");
/* get the target transformation */
useRef.ctrans.x = hdata.xorg;
useRef.ctrans.y = hdata.yorg;
useRef.ctrans.z = hdata.zorg;
useRef.crot.x = hdata.tiltangles[3];
useRef.crot.y = hdata.tiltangles[4];
useRef.crot.z = hdata.tiltangles[5];
useRef.cscale = unitPt;
if (hdata.xlen && hdata.mx)
useRef.cscale.x = hdata.xlen/(float)hdata.mx;
if (hdata.ylen && hdata.my)
useRef.cscale.y = hdata.ylen/(float)hdata.my;
if (hdata.zlen && hdata.mz)
useRef.cscale.z = hdata.zlen/(float)hdata.mz;
if (modRefp) {
/* If there is a refImage, scale the data as when reading into 3dmod */
useRef.otrans = modRefp->ctrans;
useRef.orot = modRefp->crot;
useRef.oscale = modRefp->cscale;
imodTransFromRefImage(&model, &useRef, unitPt);
} else {
/* If there is no refImage, do not scale data but assign all the information
just as if reading into 3dmod */
model.refImage = (IrefImage *)malloc (sizeof(IrefImage));
modRefp = model.refImage;
if (!modRefp)
exitError("Allocating a IrefImage structure");
model.flags |= IMODF_OTRANS_ORIGIN;
}
*modRefp = useRef;
modRefp->otrans = useRef.ctrans;
/* Adjust the maxes for this change */
model.xmax = hdata.nx;
model.ymax = hdata.ny;
model.zmax = hdata.nz;
}
/* Use zscale if user indicated it */
if (useZscale && model.zscale > 0.)
zscale = model.zscale;
/* Do flipping if model flipped and user did not turn it off */
if (!(model.flags & IMODF_FLIPYZ))
doflip = 0;
/* Warning every time is too noxious!
if (!newNx)
printf("Assuming transformed images have same size as original "
"images\n (use -n option to specify size of transformed "
"images)\n");
*/
newCen.x = (newNx ? newNx : model.xmax) * 0.5f;
newCen.y = (newNy ? newNy : model.ymax) * 0.5f;
newCen.z = (newNz ? newNz : model.zmax) * 0.5f;
if (filename){
if (filetrans(filename, &model, mode, oneLine, newCen, zscale, doflip, transScale,
transx, transy, transz))
exitError("Transforming model.");
} else if (transopt) {
imodTransModel3D(&model, mat, normMat, newCen, zscale, doflip);
}
model.xmax = newNx ? newNx : model.xmax;
model.ymax = newNy ? newNy : model.ymax;
model.zmax = newNz ? newNz : model.zmax;
imodWrite(&model, fout);
exit(0);
}
int main( int argc, char *argv[])
{
int i, ind, col, maxValType;
FILE *fout;
Imod *mod;
int npatch = 0;
int numValues[MAX_VALUE_COLS], valueIDs[MAX_VALUE_COLS];
int ix, iy, iz;
int colForVal1 = 1;
float dx, dy, dz;
float value, maxVal[MAX_VALUE_COLS];
int ob, co, listInd, listStart, numCols;
Ipoint *pts;
char format[MAX_VALUE_COLS][10];
int colToTypeMap[MAX_VALUE_COLS];
setExitPrefix("ERROR: imod2patch - ");
if (argc < 3){
if (argc != 1)
printf("ERROR: imod2patch - wrong # of arguments\n");
printf("imod2patch usage:\n");
printf("imod2patch [-v col] imod_model patch_file\n");
exit(1);
}
for (ind = 0; ind < MAX_VALUE_COLS; ind++) {
numValues[ind] = 0;
valueIDs[ind] = 0;
colToTypeMap[ind] = -1;
maxVal[ind] = -1.e37;
}
i = 1;
if (!strcmp(argv[i], "-v")) {
i++;
colForVal1 = atoi(argv[i++]);
}
mod = imodRead(argv[i]);
if (!mod)
exitError("Reading model %s\n", argv[i]);
if (imodBackupFile(argv[++i]))
exitError("Renaming existing output file to %s\n", argv[i]);
fout = fopen(argv[i], "w");
if (!fout)
exitError("Could not open %s\n", argv[i]);
/* Count up patches and values and find max of values */
for (ob = 0; ob < mod->objsize; ob++) {
listInd = 0;
for (co = 0; co < mod->obj[ob].contsize; co++) {
listStart = listInd;
if (mod->obj[ob].cont[co].psize >= 2) {
npatch++;
for (ind = 0; ind < MAX_VALUE_COLS; ind++) {
listInd = listStart;
if (istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE1 + 2 * ind, &value,
&listInd)) {
maxVal[ind] = B3DMAX(maxVal[ind], value);
numValues[ind]++;
}
}
}
}
}
/* printf("numval %d %d %d %f %f %f\n", numValues[0], numValues[1], numValues[2],
maxVal[0], maxVal[1], maxVal[2]); */
/* Get the value ID's if any and convert an entered ID to a type #. Also set format
for output based on maximum value */
maxValType = -1;
numCols = 0;
for (ind = 0; ind < MAX_VALUE_COLS; ind++) {
strcpy(format[ind], "%10.4f");
if (numValues[ind]) {
numCols++;
maxValType = ind;
if (maxVal[ind] > 10.1)
strcpy(format[ind], "%10.2f");
else if (maxVal[ind] > 1.01)
strcpy(format[ind], "%10.3f");
}
}
for (ind = 0; ind < B3DMIN(maxValType + 1, mod->obj[0].extra[IOBJ_EXSIZE - 1]); ind++)
valueIDs[ind] = mod->obj[0].extra[IOBJ_EXSIZE - 2 - ind];
/*printf("# vla ID %d %d %d %d\n", maxValType, valueIDs[0],valueIDs[1],valueIDs[2]);*/
/* Error checks on the column for value 1 */
if (colForVal1 < 1 || colForVal1 > numCols) {
if (numCols)
exitError("The column for general value type must be between 1 and %d", numCols);
exitError("There are no general values stored in the model");
}
colForVal1--;
/* Set up map from column to value type index */
if (numValues[0])
colToTypeMap[colForVal1] = 0;
col = 0;
for (ind = 1; ind <= maxValType; ind++) {
if (numValues[ind]) {
if (!colToTypeMap[col])
col++;
colToTypeMap[col++] = ind;
}
}
/*printf("%d %d %d %d\n", numCols, colToTypeMap[0], colToTypeMap[1], colToTypeMap[2]);*/
/* Output the header line */
fprintf(fout, "%d edited positions", npatch);
if (mod->obj[0].extra[IOBJ_EXSIZE - 1] > 0)
for (col = 0; col < numCols; col++)
fprintf(fout, " %d", valueIDs[colToTypeMap[col]]);
fprintf(fout, "\n");
for (ob = 0; ob < mod->objsize; ob++) {
listInd = 0;
for (co = 0; co < mod->obj[ob].contsize; co++) {
listStart = listInd;
if (mod->obj[ob].cont[co].psize >= 2) {
pts = mod->obj[ob].cont[co].pts;
ix = pts[0].x + 0.5;
iy = pts[0].y + 0.5;
iz = pts[0].z + 0.5;
dx = (pts[1].x - pts[0].x) / mod->pixsize;
dy = (pts[1].y - pts[0].y) / mod->pixsize;
dz = (pts[1].z - pts[0].z) / mod->pixsize;
if (mod->flags & IMODF_FLIPYZ)
fprintf(fout, "%6d %5d %5d %8.2f %8.2f %8.2f",
ix, iz, iy, dx, dz, dy);
else
fprintf(fout, "%6d %5d %5d %8.2f %8.2f %8.2f",
ix, iy, iz, dx, dy, dz);
for (col = 0; col < numCols; col++) {
ind = colToTypeMap[col];
if (numValues[ind]) {
listInd = listStart;
value = 0.;
istoreFindValue(mod->obj[ob].store, co, GEN_STORE_VALUE1 + 2 * ind, &value,
&listInd);
fprintf(fout, format[ind], value);
}
}
fprintf(fout, "\n");
}
}
}
fclose(fout);
exit(0);
}
