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/**
* @file smooth.c
* @author Nathan Baker
* @brief Convolve grid data with various filters
* @version $Id$
*/
/*
* Last update: 08/29/2016 by Leighton Wilson
* Description: Added ability to read in and output binary DX files
*/
#include "apbs.h"
#define IJK(i,j,k) (((k)*(nx)*(ny))+((j)*(nx))+(i))
#define ERRRC 2
typedef enum Smooth_Filter {
SM_GAUSSIAN /**< Gaussian filter */
} Smooth_Filter;
VEMBED(rcsid="$Id$")
int gaussian(Vgrid *grid, double stddev, double bandwidth);
int usage(int rc) {
char *usage = "\n\n\
----------------------------------------------------------------------\n\
This driver program convolves grid data with various filters. It is\n\
invoked as:\n\
smooth <args>\n\n\
where <args> is a list of the following arguments:\n\
REQUIRED GENERAL ARGUMENTS:\n\
--format=<format> where <format> specifies the data format and is one\n\
of the following:\n\
dx (standard OpenDX)\n\
dxbin (binary OpenDX)\n\
--input=<file> where <file> is the input mesh data in the\n\
specified format\n\
--output=<file> where <file> is the output mesh data in the\n\
specified format\n\
--filter=<filter> where <filter> is the filter with which the data\n\
will be convolved and is one of the following:\n\
gaussian (Gaussian filter)\n\
REQUIRED FILTER-SPECIFIC ARGUMENTS:\n\
Gaussian filter:\n\
--stddev=<n> the standard deviation of the filter (in A)\n\
--bandwidth=<n> the bandwith of the filter (in units of stddev)\n\
----------------------------------------------------------------------\n\n";
Vnm_print(2, usage);
exit(rc);
return 0;
}
int main(int argc, char **argv) {
/* *************** VARIABLES ******************* */
int i;
Vgrid *grid = VNULL;
/* Input parameters */
Vdata_Format format; int gotFormat = 0;
char inPath[VMAX_BUFSIZE]; int gotInPath = 0;
char outPath[VMAX_BUFSIZE]; int gotOutPath = 0;
Smooth_Filter filter; int gotFilter = 0;
double stddev; int gotStddev = 0;
double bandwidth; int gotBandwidth = 0;
char *header = "\n\n\
----------------------------------------------------------------------\n\
----------------------------------------------------------------------\n\
\n\n";
/* *************** CHECK INVOCATION ******************* */
Vio_start();
Vnm_redirect(1);
Vnm_print(1, "%s", header);
for (i=1; i<argc; i++) {
Vnm_print(1, "Parsing: %s...\n", argv[i]);
if (strstr(argv[i], "--format") != NULL) {
if (strstr(argv[i], "dxbin") != NULL) {
gotFormat = 1;
format = VDF_DXBIN;
} else if (strstr(argv[i], "dx") != NULL) {
gotFormat = 1;
format = VDF_DX;
} else {
Vnm_print(2, "Error: %s\n", argv[i]);
usage(2);
}
} else if (strstr(argv[i], "--input") != NULL) {
if (sscanf(argv[i], "--input=%s", inPath) == 1) gotInPath = 1;
else {
Vnm_print(2, "Error: %s\n", argv[i]);
usage(2);
}
} else if (strstr(argv[i], "--output") != NULL) {
if (sscanf(argv[i], "--output=%s", outPath) == 1) gotOutPath = 1;
else {
Vnm_print(2, "Error: %s\n", argv[i]);
usage(2);
}
} else if (strstr(argv[i], "--filter") != NULL) {
if (strstr(argv[i], "gaussian") != NULL) {
gotFilter = 1;
filter = SM_GAUSSIAN;
} else {
Vnm_print(2, "Error: %s\n", argv[i]);
usage(2);
}
} else if (strstr(argv[i], "--stddev") != NULL) {
if (sscanf(argv[i], "--stddev=%lf", &stddev) == 1) gotStddev = 1;
else {
Vnm_print(2, "Error: %s\n", argv[i]);
usage(2);
}
} else if (strstr(argv[i], "--bandwidth") != NULL) {
if (sscanf(argv[i], "--bandwidth=%lf", &bandwidth) == 1)
gotBandwidth = 1;
else {
Vnm_print(2, "Error: %s\n", argv[i]);
usage(2);
}
} else {
Vnm_print(2, "Error: %s\n", argv[i]);
usage(2);
}
}
if (!gotFormat) {
Vnm_print(2, "Error: --format not specified!\n");
usage(2);
}
if (!gotInPath) {
Vnm_print(2, "Error: --input not specified!\n");
usage(2);
}
if (!gotOutPath) {
Vnm_print(2, "Error: --output not specified!\n");
usage(2);
}
if (!gotFilter) {
Vnm_print(2, "Error: --filter not specified!\n");
usage(2);
}
if (filter == SM_GAUSSIAN) {
if (!gotStddev) {
Vnm_print(2, "Error: --stddev not specified!\n");
usage(2);
}
if (!gotBandwidth) {
Vnm_print(2, "Error: --bandwidth not specified!\n");
usage(2);
}
}
/* *************** READ DATA ******************* */
Vnm_print(1, "main: Reading data from %s...\n", inPath);
grid = Vgrid_ctor(0, 0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL);
if (format == VDF_DX) {
if (!Vgrid_readDX(grid, "FILE", "ASC", VNULL, inPath)) {
Vnm_print(2, "main: Problem reading standard OpenDX-format grid from %s\n",
inPath);
return ERRRC;
}
} else if (format == VDF_DXBIN) {
if (!Vgrid_readDXBIN(grid, "FILE", "ASC", VNULL, inPath)) {
Vnm_print(2, "main: Problem reading binary OpenDX-format grid from %s\n",
inPath);
return ERRRC;
}
}
/* *************** SMOOTH ******************* */
switch(filter) {
case SM_GAUSSIAN:
Vnm_print(1, "Smoothing data with Gaussian filter...\n");
gaussian(grid, stddev, bandwidth);
break;
default:
Vnm_print(2, "Invalid format (%d)!\n", format);
usage(2);
}
/* *************** READ DATA ******************* */
Vnm_print(1, "main: Writing data to %s...\n", outPath);
if (format == VDF_DX)
Vgrid_writeDX(grid, "FILE", "ASC", VNULL, outPath, "Smoothed data",
VNULL);
else if (format == VDF_DXBIN)
Vgrid_writeDXBIN(grid, "FILE", "ASC", VNULL, outPath, "Smoothed data",
VNULL);
return 0;
}
int gaussian(Vgrid *grid, double stddev, double bandwidth) {
int nx, ny, nz, iband, jband, kband, i, j, k, ii, jj, kk;
int kkmin, jjmin, iimin, kkmax, jjmax, iimax;
double hx, hy, hzed, xmin, ymin, zmin, *newData, *oldData, scal, norm;
double u, ga, dist2;
Vnm_print(1, "Gaussian filter: std. dev. = %g A, bandwidth = %g A.\n",
stddev, bandwidth*stddev);
nx = grid->nx; ny = grid->ny; nz = grid->nz;
hx = grid->hx; hy = grid->hy; hzed = grid->hzed;
xmin = grid->xmin; ymin = grid->ymin; zmin = grid->zmin;
Vnm_print(1, "Grid: %d x %d x %d points\n", nx, ny, nz);
Vnm_print(1, "Grid: %g, %g, %g A spacing\n", hx, hy, hzed);
Vnm_print(1, "Grid: (%g, %g, %g) A origin\n", xmin, ymin, zmin);
/* Convert HALF bandwidth to grid units */
iband = (int)(stddev*bandwidth/hx);
jband = (int)(stddev*bandwidth/hy);
kband = (int)(stddev*bandwidth/hzed);
/* Special handling for iband, jband and kband, they are non-zero positive integers */
if (iband == 0) iband = 1;
if (jband == 0) jband = 1;
if (kband == 0) kband = 1;
Vnm_print(1, "Bandwidth converted to %d x %d x %d grid units.\n",
iband, jband, kband);
Vnm_print(1, "This means any non-zero data within (%g, %g, %g) of the\n",
(iband+1)*hx, (jband+1)*hy, (kband+1)*hzed);
Vnm_print(1, "domain boundary will be convolved differently.\n");
/* Get exponent scaling factor */
scal = 2.0 * stddev * stddev;
VASSERT(scal > 0);
scal = 1.0/scal;
/* Get data */
oldData = grid->data;
newData = Vmem_malloc(VNULL, (nx*ny*nz), sizeof(double));
/* Copy over old data. All but the boundary values will be replaced in the next step so this is more copying than is strictly
necessary... */
for (i=0; i<(nx*ny*nz); i++) newData[i] = oldData[i];
/* Apply filter */
for (k=1; k<(nz-1); k++) {
kkmin = VMAX2(1, (k - kband));
kkmax = VMIN2((nz-1), (k + kband));
for (j=1; j<(ny-1); j++) {
jjmin = VMAX2(1, (j - jband));
jjmax = VMIN2((ny-1), (j + jband));
for (i=1; i<(nx-1); i++) {
iimin = VMAX2(1, (i - iband));
iimax = VMIN2((nx-1), (i + iband));
u = 0;
/* We normalize within the loop to conserve densities */
norm = 0;
for (kk=kkmin; kk<kkmax; kk++) {
for (jj=jjmin; jj<jjmax; jj++) {
for (ii=iimin; ii<iimax; ii++) {
dist2 = VSQR(hx*(i-ii)) + VSQR(hy*(j-jj)) +
VSQR(hzed*(k-kk));
ga = VEXP(-dist2*scal);
u += (ga*oldData[IJK(ii,jj,kk)]);
norm += ga;
} /* ii loop */
} /* jj loop */
} /* kk loop */
if (norm > 0) newData[IJK(i,j,k)] = u/norm;
else newData[IJK(i,j,k)] = 0;
} /* i loop */
} /* j loop */
} /* k loop */
/* Replace data */
for (i=0; i<(nx*ny*nz); i++) grid->data[i] = newData[i];
Vmem_free(VNULL, (nx*ny*nz), sizeof(double), (void **)&newData);
return 0;
}
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