/*!
* Returns a slice with one Z plane of data at Z value [secno] from the file
* described by the @@mrcfiles.html#MrcHeader structure@ [hin].
* The file pointer in [hin] is used. Bytes are swapped if necessary.
* Returns NULL for errors.
*/
Islice *sliceReadFloat(MrcHeader *hin, int secno)
{
Islice *slice;
if (sliceModeIfReal(hin->mode) < 0) {
b3dError(stderr, "ERROR: sliceReadFloat - file mode must be real");
return NULL;
}
slice = sliceCreate(hin->nx, hin->ny, MRC_MODE_FLOAT);
if (!slice)
return NULL;
if (mrcReadFloatSlice(slice->data.f, hin, secno)) {
sliceFree(slice);
return NULL;
}
return slice;
}
//init SliceCache and clear its old contents
//It needs to be called whenever the tomogram it manages changes.
void SliceCache::initCache(const char *fnStack, int dim,
int hyper, int tSize, int &nx, int &ny, int &nz)
{
int dsize, csize;
mDataOffset = 0.;
if (mFpStack)
iiFClose(mFpStack);
if ((mFpStack = iiFOpen(fnStack, "rb")) == 0)
exitError("could not open input file %s", fnStack);
/* read mHeader */
if (mrc_head_read(mFpStack, &mHeader))
exitError("could not read header of input file %s", fnStack);
mSliceMode = sliceModeIfReal(mHeader.mode);
if (mSliceMode < 0)
exitError("File mode is %d; only byte, short, integer allowed\n",
mHeader.mode);
mrc_getdcsize(mHeader.mode, &dsize, &csize);
nx = mHeader.nx;
ny = mHeader.ny;
nz = mHeader.nz;
mPsDim = (dim + 1) * hyper + 1;
if (mFreqCount)
free(mFreqCount);
mFreqCount = (int *)malloc(mPsDim * sizeof(int));
if (mSliceData)
free(mSliceData);
mSliceData = (float *)malloc(nx * ny * dsize);
if (mPsTmp)
free(mPsTmp);
mPsTmp = (double *)malloc(mPsDim * sizeof(double));
if (!mSliceData || !mFreqCount || !mPsTmp)
exitError("Allocating memory for image slice, frequency counts, or mPsTmp");
mCurSlice = -1;
clearAndSetSize(dim, hyper, tSize);
}
int main( int argc, char *argv[] )
{
int i = 0;
FILE *fin, *fout;
struct MRCheader hdata, hout;
struct MRCheader *hptr;
unsigned char *buf;
int bsize, csize, dsize;
int inside = 0;
int ntaper = DEFAULT_TAPER;
int taperEntered = 0;
Islice slice;
int zmin = -1, zmax = -1;
int secofs;
char *progname = imodProgName(argv[0]);
setStandardExitPrefix(progname);
if (argc < 2){
fprintf(stderr,
"%s version %s\n", progname, VERSION_NAME);
imodCopyright();
mrctaper_help(progname);
exit(3);
}
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
switch (argv[i][1]) {
case 'i':
inside = 1;
break;
case 't':
taperEntered = 1;
if (argv[i][2] != 0x00)
sscanf(argv[i], "-t%d", &ntaper);
else
sscanf(argv[++i], "%d", &ntaper);
break;
case 'z':
if (argv[i][2] != 0x00)
sscanf(argv[i], "-z%d%*c%d", &zmin, &zmax);
else
sscanf(argv[++i], "%d%*c%d", &zmin, &zmax);
break;
default:
printf("ERROR: %s - illegal option\n", progname);
mrctaper_help(progname);
exit(1);
break;
}
} else
break;
}
if (i < (argc - 2) || i == argc){
mrctaper_help(progname);
exit(3);
}
if (ntaper < 1 || ntaper > 127)
exitError("Taper must be between 1 and 127.");
if (i < argc - 1)
fin = iiFOpen(argv[i++], "rb");
else
fin = iiFOpen(argv[i++], "rb+");
if (fin == NULL)
exitError("Opening %s.", argv[i - 1]);
if (mrc_head_read(fin, &hdata))
exitError("Can't Read Input File Header.");
if (sliceModeIfReal(hdata.mode) < 0)
exitError("Can operate only on byte, integer and real data.");
if (!taperEntered) {
ntaper = (hdata.nx + hdata.ny) / 200;
ntaper = B3DMIN(127, B3DMAX(DEFAULT_TAPER, ntaper));
printf("Tapering over %d pixels\n", ntaper);
}
if (zmin == -1 && zmax == -1) {
zmin = 0;
zmax = hdata.nz - 1;
} else {
if (zmin < 0)
zmin = 0;
if (zmax >= hdata.nz)
zmax = hdata.nz - 1;
}
if (i < argc) {
fout = iiFOpen(argv[i], "wb");
if (fout == NULL)
exitError("Opening %s.", argv[i]);
hout = hdata;
hout.fp = fout;
/* DNM: eliminate extra header info in the output, and mark it as not swapped */
mrcInitOutputHeader(&hout);
hptr = &hout;
hout.nz = zmax + 1 - zmin;
hout.mz = hout.nz;
hout.zlen = hout.nz;
secofs = zmin;
} else {
if (b3dOutputFileType() == IIFILE_TIFF)
exitError("Cannot write to an existing TIFF file.");
hptr = &hdata;
fout = fin;
secofs = 0;
}
mrc_getdcsize(hdata.mode, &dsize, &csize);
bsize = hdata.nx * hdata.ny;
buf = (unsigned char *)malloc(dsize * csize * bsize);
if (!buf)
exitError("Couldn't get memory for slice.");
sliceInit(&slice, hdata.nx, hdata.ny, hdata.mode, buf);
for (i = zmin; i <= zmax; i++) {
printf("\rDoing section #%4d", i);
fflush(stdout);
if (mrc_read_slice(buf, fin, &hdata, i, 'Z'))
exitError("Reading section %d.", i);
if (sliceTaperAtFill(&slice, ntaper, inside))
exitError("Can't get memory for taper operation.");
if (mrc_write_slice(buf, fout, hptr, i - secofs, 'Z'))
exitError("Writing section %d.", i);
}
puts("\nDone!");
mrc_head_label(hptr, "mrctaper: Image tapered down to fill value at edges");
mrc_head_write(fout, hptr);
iiFClose(fout);
return(0);
}