/*
* Get the phase data from the input data. Allocate the temporary
* memory required and read the input file.
*
* in_format = 0 for 8-byte complex data,
* 1 for 4-byte complex data,
* 2 for 1-byte phase data,
* 3 for 4-byte float phase data
*
* Output: normalized (0 - 1) phase values in array "phase"
*/
void GetPhase(int in_format, FILE *ifp, char *infile, float *phase,
int xsize, int ysize)
{
void *in_data;
if (in_format==0) /* floating-pt real & imaginary parts */
AllocateFloat((float**)(&in_data), 2*xsize*ysize, "input data");
else if (in_format==1) /* short integer real & imaginary parts */
AllocateShort((short**)(&in_data), 2*xsize*ysize, "input data");
else if (in_format==2) /* 1-byte (quantized) phase values */
AllocateByte((unsigned char **)(&in_data), xsize*ysize,
"input data");
else /* floating-pt phase values */
AllocateFloat((float **)(&in_data), xsize*ysize, "input data");
printf("Reading input data...\n");
if (in_format==1) /* short int real and imaginary parts */
ReadShort(ifp, (short *)in_data, 2*xsize*ysize, infile);
else if (in_format==0) /* floating-pt real and imag parts */
ReadFloat(ifp, (float *)in_data, 2*xsize*ysize, infile);
else if (in_format==3) /* floating-pt phase */
ReadFloat(ifp, (float *)in_data, xsize*ysize, infile);
else /* 1-byte quantized phase */
ReadByte(ifp, (unsigned char *)in_data, xsize*ysize, infile);
ExtractPhase(in_format, in_data, phase, xsize, ysize, 1);
free(in_data);
}
main (int argc, char *argv[])
{
int i, j, k, m, n, a, b;
FILE *ifp, *ofp, *mfp;
float *phase; /* array */
float *soln; /* array */
unsigned char *bitflags;
char buffer[200], string[200];
char infile[200], outfile[200];
char maskfile[200], tempstr[200], format[200];
int in_format, debug_flag, dipole_flag;
int xsize, ysize; /* dimensions of arrays */
int NumRes, MaxCutLen;
char use[] = /* define usage statement */
"Usage: prog-name -input file -format fkey -output file\n"
" -xsize x -ysize y [ -mask file -cutlen c -debug yes/no\n"
" -dipole yes/no ]\n"
"where 'fkey' is a keyword designating the input file type\n"
"(key = complex8, complex4, float or byte), 'x' and 'y' are\n"
"the dimensions of the file, mask is an optional byte-file\n"
"of masks for masking out undefined phase values and cutlen\n"
"is the max branchcut length allowed. All files are simple\n"
"raster files, and the output file consists of floating\n"
"point numbers that define the heights of the unwrapped\n"
"surface. If the 'debug' parm is 'yes', then intermediate\n"
"byte-files are saved (residues, branch cuts, etc.) If\n"
"the 'dipole' parm is 'yes', then dipole-residues are\n"
"eliminated before unwrapping.\n";
printf("Phase Unwrapping By Means of Goldstein's Algorithm\n");
/* GET COMMAND LINE PARAMETERS AND CHECK */
CommandLineParm(argc,argv, "-input", StringParm, infile, 1, use);
CommandLineParm(argc,argv, "-format", StringParm, format, 1, use);
CommandLineParm(argc,argv, "-output", StringParm, outfile, 1,use);
CommandLineParm(argc, argv, "-xsize", IntegerParm, &xsize, 1,use);
CommandLineParm(argc, argv, "-ysize", IntegerParm, &ysize, 1,use);
if (!CommandLineParm(argc, argv, "-mask", StringParm, maskfile,
0, use)) strcpy(maskfile, "none");
if (!CommandLineParm(argc, argv, "-cutlen", IntegerParm,
&MaxCutLen, 0, use)) MaxCutLen = 0; /* default defined below */
if (!CommandLineParm(argc, argv, "-debug", StringParm, tempstr,
0, use)) debug_flag = 0;
else debug_flag = Keyword(tempstr, "yes");
if (!CommandLineParm(argc, argv, "-dipole", StringParm, tempstr,
0, use)) dipole_flag=0;
else dipole_flag = Keyword(tempstr, "yes");
if (Keyword(format, "complex8")) in_format = 0;
else if (Keyword(format, "complex4")) in_format = 1;
else if (Keyword(format, "byte")) in_format = 2;
else if (Keyword(format, "float")) in_format = 3;
else {
fprintf(stderr, "Unrecognized format: %s\n", format);
exit(BAD_PARAMETER);
}
printf("Input file = %s\n", infile);
printf("Input file type = %s\n", format);
printf("Output file = %s\n", outfile);
printf("File dimensions = %dx%d (cols x rows).\n", xsize, ysize);
if (Keyword(maskfile, "none")) printf("No mask file.\n");
else printf("Mask file = %s\n", maskfile);
if (dipole_flag) printf("Dipole-residues will be eliminated.\n");
if (debug_flag)
printf("Intermediate files will be saved (i.e. debug on).\n");
/* OPEN FILES, ALLOCATE MEMORY */
OpenFile(&ifp, infile, "r");
OpenFile(&ofp, outfile, "w");
mfp = NULL;
if (!Keyword(maskfile, "none"))
OpenFile(&mfp, maskfile, "r");
AllocateFloat(&phase, xsize*ysize, "phase data");
AllocateFloat(&soln, xsize*ysize, "unwrapped data");
AllocateByte(&bitflags, xsize*ysize, "bitflag data");
/* READ AND PROCESS DATA */
printf("Reading phase data...\n");
GetPhase(in_format, ifp, infile, phase, xsize, ysize);
/* mask data */
printf("Processing mask data...\n");
if (mfp) {
ReadByte(mfp, bitflags, xsize*ysize, maskfile);
}
else {
for (k=0; k<xsize*ysize; k++)
bitflags[k] = 255;
}
for (k=0; k<xsize*ysize; k++)
bitflags[k] = (!bitflags[k]) ? BORDER : 0;
FattenMask(bitflags, BORDER, 1, xsize, ysize);
/* LOCATE AND PROCESS RESIDUES */
/* compute residues and store in bitflags array */
NumRes = Residues(phase, bitflags, POS_RES, NEG_RES,
BORDER, xsize, ysize);
printf("%d Residues\n", NumRes);
if (debug_flag) {
char filename[300];
sprintf(filename, "%s.res", outfile);
SaveByteToImage(bitflags, "residues", filename, xsize, ysize,
1, 1, 0);
}
/* GENERATE BRANCH CUTS */
if (dipole_flag) { /* elimate dipole-residues first */
Dipole(bitflags, xsize, ysize, BRANCH_CUT);
i = Residues(phase, bitflags, 0, 0, BORDER | BRANCH_CUT,
xsize, ysize);
printf("%d Residues are left\n", i);
}
if (MaxCutLen==0) MaxCutLen = (xsize + ysize)/2;
GoldsteinBranchCuts(bitflags, MaxCutLen, NumRes, xsize, ysize,
BRANCH_CUT);
if (debug_flag) {
char filename[300];
sprintf(filename, "%s.brc", outfile);
SaveByteToImage(bitflags, "branch cuts", filename,
xsize, ysize, 1, 1, BRANCH_CUT | BORDER);
}
/* UNWRAP AROUND CUTS */
for (k=0, i=0; i<xsize*ysize; i++)
if (bitflags[i] & BRANCH_CUT) k++;
printf("%d BRANCH CUT PIXELS\n", k);
printf("Unwrapping around branch cuts\n");
k = UnwrapAroundCuts(phase, bitflags, soln, xsize, ysize, AVOID,
0, NULL);
if (k > 1) printf("%d disconnected pieces.\n", k);
else printf("%d piece\n", k);
printf("\nFinished\n");
PrintMinAndMax(xsize, ysize, soln, "solution");
/* SAVE RESULT */
for (k=0; k<xsize*ysize; k++)
soln[k] *= TWOPI; /* scale output */
printf("Saving unwrapped surface to file '%s'\n", outfile);
WriteFloat(ofp, soln, xsize*ysize, outfile);
free(soln);
free(phase);
free(bitflags);
}
main (int argc, char *argv[])
{
int i, j, k, n;
FILE *ifp, *ofp, *mfp=0, *qfp=0;
float *phase; /* array */
float *soln; /* array */
float *qual_map; /* array */
float *rarray; /* array */
float *zarray; /* array */
float *parray; /* array */
float *dxwts; /* array */
float *dywts; /* array */
unsigned char *bitflags;
double *xcos, *ycos;
char buffer[200], tempstr[200];
char infile[200], outfile[200];
char bmaskfile[200], qualfile[200];
char format[200], modekey[200];
int in_format, debug_flag;
int xsize, ysize; /* dimensions of arrays */
int xsize_actual, ysize_actual, xsize_dct, ysize_dct;
int avoid_code, thresh_flag, fatten, tsize;
int num_iter=DEFAULT_NUM_ITER;
int pcg_iter=DEFAULT_PCG_ITER;
double rmin, rmax, rscale, e0=DEFAULT_E0;
double one_over_twopi = 1.0/TWOPI;
UnwrapMode mode;
char use[] = /* define usage statement */
"Usage: prog-name -input file -format fkey -output file\n"
" -xsize x -ysize y [ -mode mkey -bmask file -corr file\n"
" -tsize size -debug yes/no -iter num -pcg_iter nump\n"
" -e0 e0val -thresh yes/no -fat n ]\n"
"where 'fkey' is a keyword designating the input file type\n"
"(key = complex8, complex4, float or byte), 'x' and 'y' are\n"
"the dimensions of the file, bmask is an optional byte-file\n"
"for masking out undefined phase, corr is an optional byte-\n"
"file of cross-correlation values, tsize is the size of the\n"
"square template for averaging the corr file or quality\n"
"values (default = 1), and 'mkey' is a keyword designating\n"
"the type of quality map. The value of mkey may be\n"
"'min_grad' for Minimum Gradient, 'min_var' for Minimum\n"
"Variance, 'max_corr' for Maximum Correlation, 'max_pseu' for\n"
"Maximum Pseudocorrelation, or 'none' for no quality map.\n"
"All files are simple raster files, and the output file\n"
"is a raster file of elevation values of the unwrapped\n"
"surface. If the 'debug' parm is 'yes', then intermediate\n"
"byte-files are saved. The maximum number of iterations is\n"
"'num', and the number of PCG iterations is 'nump'. The\n"
"normalization parameter is 'e0'. To apply an automatic\n"
"threshold to the quality map, the 'thresh' parm should be\n"
"yes. To thicken the quality mask, the 'fat' parm should be\n"
"the number of pixels by which to fatten it.\n";
printf("Phase Unwrapping by Minimum Lp Norm Algorithm\n");
/* GET COMMAND LINE PARAMETERS AND CHECK */
CommandLineParm(argc,argv, "-input", StringParm, infile, 1, use);
CommandLineParm(argc,argv, "-format", StringParm, format, 1, use);
CommandLineParm(argc,argv, "-output", StringParm, outfile, 1,use);
CommandLineParm(argc,argv, "-xsize", IntegerParm, &xsize, 1, use);
CommandLineParm(argc,argv, "-ysize", IntegerParm, &ysize, 1, use);
if (!CommandLineParm(argc, argv, "-mode", StringParm,
modekey, 0, use)) strcpy(modekey, "none");
if (!CommandLineParm(argc, argv, "-corr", StringParm,
qualfile, 0, use)) strcpy(qualfile, "none");
if (!CommandLineParm(argc, argv, "-tsize", IntegerParm,
&tsize, 0, use)) tsize = 1;
if (!CommandLineParm(argc, argv, "-bmask", StringParm, bmaskfile,
0, use)) strcpy(bmaskfile, "none");
if (!CommandLineParm(argc, argv, "-debug", StringParm, tempstr,
0, use)) debug_flag = 0;
else debug_flag = Keyword(tempstr, "yes");
if (!CommandLineParm(argc, argv, "-thresh", StringParm,
tempstr, 0, use)) thresh_flag = 0;
else thresh_flag = Keyword(tempstr, "yes");
if (!CommandLineParm(argc, argv, "-fat", IntegerParm,
&fatten, 0, use)) fatten = 0;
CommandLineParm(argc, argv, "-iter", IntegerParm, &num_iter,
0, use);
if (num_iter < 0) num_iter = 1;
CommandLineParm(argc, argv, "-pcg_iter", IntegerParm, &pcg_iter,
0, use);
if (pcg_iter < 0) pcg_iter = 1;
CommandLineParm(argc, argv, "-e0", DoubleParm, &e0, 0, use);
if (Keyword(format, "complex8")) in_format = 0;
else if (Keyword(format, "complex4")) in_format = 1;
else if (Keyword(format, "byte")) in_format = 2;
else if (Keyword(format, "float")) in_format = 3;
else {
fprintf(stderr, "Unrecognized format: %s\n", format);
exit(BAD_PARAMETER);
}
printf("Input file = %s\n", infile);
printf("Input file type = %s\n", format);
printf("Output file = %s\n", outfile);
printf("File dimensions = %dx%d (cols x rows).\n", xsize, ysize);
if (Keyword(bmaskfile, "none")) printf("No border mask file.\n");
else printf("Border mask file = %s\n", bmaskfile);
printf("Quality mode = %s\n", modekey);
if (modekey==none) {
printf("No quality map.\n");
strcpy(qualfile, "none");
}
else {
if (Keyword(qualfile, "none")) printf("No correlation file.\n");
else printf("Correlation image file = %s\n", qualfile);
printf("Averaging template size = %d\n", tsize);
if (tsize < 0 || tsize > 30) {
fprintf(stderr, "Illegal size: must be between 0 and 30\n");
exit(BAD_PARAMETER);
}
}
mode = SetQualityMode(modekey, qualfile, 1);
if (mode < 0) exit(BAD_PARAMETER); /* error msg already printed */
/* Increase dimensions to power of two (plus one) */
xsize_actual = xsize;
ysize_actual = ysize;
for (xsize_dct = 1; xsize_dct+1 < xsize_actual; xsize_dct*=2)
;
xsize_dct+=1;
for (ysize_dct = 1; ysize_dct+1 < ysize_actual; ysize_dct*=2)
;
ysize_dct+=1;
if (xsize_dct != xsize_actual || ysize_dct != ysize_actual) {
printf("Dimensions increase from %dx%d to %dx%d for FFT's\n",
xsize_actual, ysize_actual, xsize_dct, ysize_dct);
}
/* OPEN FILES, ALLOCATE MEMORY */
/* note: xsize_dct >= xsize; ysize_dct >= ysize */
xsize = xsize_dct;
ysize = ysize_dct;
AllocateFloat(&phase, xsize*ysize, "phase data");
AllocateFloat(&soln, xsize*ysize, "scratch data");
AllocateFloat(&qual_map, xsize*ysize, "quality map");
AllocateByte(&bitflags, xsize*ysize, "bitflags array");
OpenFile(&ifp, infile, "r");
OpenFile(&ofp, outfile, "w");
if (!Keyword(bmaskfile, "none")) OpenFile(&mfp, bmaskfile, "r");
if (mode==corr_coeffs) OpenFile(&qfp, qualfile, "r");
/* READ AND PROCESS DATA */
xsize = xsize_actual;
ysize = ysize_actual;
printf("Reading input data...\n");
GetPhase(in_format, ifp, infile, phase, xsize, ysize);
if (qfp) {
printf("Reading quality data...\n");
/* borrow the bitflags array temporarily */
ReadByte(qfp, bitflags, xsize*ysize, qualfile);
/* process data and store in quality map array */
AverageByteToFloat(bitflags, qual_map, tsize, xsize, ysize);
}
/* border mask data */
printf("Processing border mask data...\n");
if (mfp) {
ReadByte(mfp, bitflags, xsize*ysize, bmaskfile);
}
else {
for (k=0; k<xsize*ysize; k++)
bitflags[k] = 255;
}
for (k=0; k<xsize*ysize; k++) {
bitflags[k] = (!bitflags[k]) ? BORDER : 0;
}
if (mfp) FattenMask(bitflags, BORDER, 1, xsize, ysize);
GetQualityMap(mode, qual_map, phase, bitflags, BORDER,
tsize, xsize, ysize);
if (thresh_flag) {
HistoAndThresh(qual_map, xsize, ysize, 0.0, 0, 0.0,
bitflags, BORDER);
if (fatten > 0)
FattenQual(qual_map, fatten, xsize, ysize);
}
/* Set border (masked) pixels to 0-wts */
for (k=0; k<xsize*ysize; k++) {
if (bitflags[k] & BORDER) qual_map[k] = 0.0;
}
if (debug_flag) {
char filename[300];
sprintf(filename, "%s.qual", outfile);
SaveFloatToImage(qual_map, "quality", filename, xsize, ysize,
0, 0, 0);
}
/* embed arrays in possibly larger FFT/DCT arrays */
for (j=ysize_dct-1; j>=0; j--) {
for (i=xsize_dct-1; i>=0; i--) {
if (i<xsize_actual && j<ysize_actual)
phase[j*xsize_dct + i] = phase[j*xsize_actual + i];
else phase[j*xsize_dct + i] = 0.0;
}
}
for (j=ysize_dct-1; j>=0; j--) {
for (i=xsize_dct-1; i>=0; i--) {
if (i<xsize_actual && j<ysize_actual)
bitflags[j*xsize_dct + i] = bitflags[j*xsize_actual + i];
else bitflags[j*xsize_dct + i] = BORDER;
}
}
if (qual_map) {
for (j=ysize_dct-1; j>=0; j--) {
for (i=xsize_dct-1; i>=0; i--) {
if (i<xsize_actual && j<ysize_actual)
qual_map[j*xsize_dct + i] = qual_map[j*xsize_actual + i];
else
qual_map[j*xsize_dct + i] = 0.0;
}
}
}
/* Set dimensions to DCT dimensions */
xsize = xsize_dct;
ysize = ysize_dct;
/* Allocate more memory */
AllocateFloat(&rarray, xsize*ysize, "r array data");
AllocateFloat(&zarray, xsize*ysize, "z array data");
AllocateFloat(&parray, xsize*ysize, "p array data");
AllocateFloat(&dxwts, xsize*ysize, "dx weights");
AllocateFloat(&dywts, xsize*ysize, "dy weights");
/* UNWRAP */
for (k=0; k<xsize*ysize; k++) soln[k] = 0.0;
printf("Unwrapping...\n");
LpNormUnwrap(soln, phase, dxwts, dywts, bitflags, qual_map,
rarray, zarray, parray, num_iter, pcg_iter, e0, xsize, ysize);
printf("\nFinished\n");
PrintMinAndMax(xsize, ysize, soln, "solution");
/* restore dimensions to input sizes and save solution*/
xsize = xsize_actual;
ysize = ysize_actual;
for (j=0; j<ysize; j++) {
for (i=0; i<xsize; i++) {
soln[j*xsize + i] = TWOPI*soln[j*xsize_dct + i];
}
}
/* save solution */
printf("Saving unwrapped surface to file '%s'\n", outfile);
WriteFloat(ofp, soln, xsize*ysize, outfile);
free(rarray);
free(zarray);
free(parray);
free(soln);
free(qual_map);
free(bitflags);
free(dxwts);
free(dywts);
}
