/**
* gwy_tip_erosion:
* @tip: Tip data.
* @surface: Surface to be eroded.
* @result: Data field where to store dilated surface to.
* @set_fraction: Function that sets fraction to output (or %NULL).
* @set_message: Function that sets message to output (or %NULL).
*
* Performs surface reconstruction (erosion) algorithm published by
* Villarrubia. This function converts all fields into form requested by
* "morph_lib.c" library, that is almost identical with original Villarubia's
* library.
*
* Returns: Reconstructed (eroded) surface, i.e. @result, on success. May
* return %NULL if aborted.
**/
GwyDataField*
gwy_tip_erosion(GwyDataField *tip,
GwyDataField *surface,
GwyDataField *result,
GwySetFractionFunc set_fraction,
GwySetMessageFunc set_message)
{
gdouble **ftip;
gdouble **fsurface;
gdouble **fresult;
GwyDataField *buffertip;
gboolean freetip;
/*if tip and surface have different spacings, make new, resampled tip*/
buffertip = get_right_tip_field(tip, surface, &freetip);
/*invert tip (as necessary by dilation algorithm)*/
gwy_data_field_invert(buffertip, TRUE, TRUE, FALSE);
/*make auxiliary data arrays expected by Villarubia's algorithms*/
ftip = datafield_to_field(buffertip, TRUE);
fsurface = datafield_to_field(surface, FALSE);
fresult = _gwy_morph_lib_derosion(fsurface, surface->yres, surface->xres,
ftip, buffertip->yres, buffertip->xres,
buffertip->yres/2, buffertip->xres/2,
set_fraction, set_message);
/*convert result back from auxiliary array*/
if (fresult) {
gwy_data_field_resample(result, surface->xres, surface->yres,
GWY_INTERPOLATION_NONE);
result = field_to_datafield(fresult, result);
}
else
result = NULL;
/*free auxiliary data arrays*/
_gwy_morph_lib_dfreematrix(ftip, buffertip->xres);
_gwy_morph_lib_dfreematrix(fsurface, surface->xres);
if (fresult)
_gwy_morph_lib_dfreematrix(fresult, result->xres);
if (freetip)
g_object_unref(buffertip);
else
gwy_data_field_invert(buffertip, TRUE, TRUE, FALSE);
return result;
}
static void
rotate_180(GwyContainer *data, GwyRunType run)
{
GwyDataField *dfields[3];
GQuark quarks[3];
gint id;
gint i;
g_return_if_fail(run & BASICOPS_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD, dfields + 0,
GWY_APP_MASK_FIELD, dfields + 1,
GWY_APP_SHOW_FIELD, dfields + 2,
GWY_APP_DATA_FIELD_KEY, quarks + 0,
GWY_APP_MASK_FIELD_KEY, quarks + 1,
GWY_APP_SHOW_FIELD_KEY, quarks + 2,
GWY_APP_DATA_FIELD_ID, &id,
0);
clean_quarks(G_N_ELEMENTS(quarks), quarks, dfields);
gwy_app_undo_qcheckpointv(data, G_N_ELEMENTS(quarks), quarks);
for (i = 0; i < G_N_ELEMENTS(dfields); i++) {
if (dfields[i]) {
gwy_data_field_invert(dfields[i], TRUE, TRUE, FALSE);
gwy_data_field_data_changed(dfields[i]);
}
}
gwy_app_channel_log_add_proc(data, id, id);
}
static void
preview(DepositControls *controls,
DepositArgs *args)
{
GwyDataField *dfield, *lfield, *zlfield, *zdfield;
gint xres, yres, oxres, oyres;
gint add, i, ii, m, k;
gdouble size, width;
gint xdata[10000];
gint ydata[10000];
gdouble disizes[10000];
gdouble rdisizes[10000];
gdouble rx[10000];
gdouble ry[10000];
gdouble rz[10000];
gdouble ax[10000];
gdouble ay[10000];
gdouble az[10000];
gdouble vx[10000];
gdouble vy[10000];
gdouble vz[10000];
gdouble fx[10000];
gdouble fy[10000];
gdouble fz[10000];
gint xpos, ypos, ndata, too_close;
gdouble disize, mdisize;
gdouble xreal, yreal, oxreal, oyreal;
gdouble diff;
gdouble mass = 1;
gint presetval;
gint nloc, maxloc = 1;
gint max = 5000000;
gdouble rxv, ryv, rzv, timestep = 3e-7; //5e-7
deposit_dialog_update_values(controls, args);
dfield = GWY_DATA_FIELD(gwy_container_get_object_by_name(controls->mydata,
"/0/data"));
gwy_container_set_object_by_name(controls->mydata, "/0/data", gwy_data_field_duplicate(controls->old_dfield));
dfield = GWY_DATA_FIELD(gwy_container_get_object_by_name(controls->mydata,
"/0/data"));
if (controls->in_init)
{
gwy_data_field_data_changed(dfield);
while (gtk_events_pending())
gtk_main_iteration();
return;
}
oxres = gwy_data_field_get_xres(dfield);
oyres = gwy_data_field_get_yres(dfield);
oxreal = gwy_data_field_get_xreal(dfield);
oyreal = gwy_data_field_get_yreal(dfield);
diff = oxreal/oxres/10;
size = args->size*5e-9;
// width = args->width*5e-9 + 2*size; //increased manually to fill boundaries
width = 2*size;
add = gwy_data_field_rtoi(dfield, size + width);
mdisize = gwy_data_field_rtoi(dfield, size);
xres = oxres + 2*add;
yres = oyres + 2*add;
xreal = oxreal + 2*(size+width);
yreal = oyreal + 2*(size+width);
// printf("For field of size %g and particle nominak %g, real %g (%g), the final size will change from %d to %d\n",
// gwy_data_field_get_xreal(dfield), args->size, size, disize, oxres, xres);
/*make copy of datafield, with mirrored boundaries*/
lfield = gwy_data_field_new(xres, yres,
gwy_data_field_itor(dfield, xres),
gwy_data_field_jtor(dfield, yres),
TRUE);
gwy_data_field_area_copy(dfield, lfield, 0, 0, oxres, oyres, add, add);
gwy_data_field_invert(dfield, 1, 0, 0);
gwy_data_field_area_copy(dfield, lfield, 0, oyres-add-1, oxres, add, add, 0);
gwy_data_field_area_copy(dfield, lfield, 0, 0, oxres, add, add, yres-add-1);
gwy_data_field_invert(dfield, 1, 0, 0);
gwy_data_field_invert(dfield, 0, 1, 0);
gwy_data_field_area_copy(dfield, lfield, oxres-add-1, 0, add, oyres, 0, add);
gwy_data_field_area_copy(dfield, lfield, 0, 0, add, oyres, xres-add-1, add);
gwy_data_field_invert(dfield, 0, 1, 0);
gwy_data_field_invert(dfield, 1, 1, 0);
gwy_data_field_area_copy(dfield, lfield, oxres-add-1, oyres-add-1, add, add, 0, 0);
gwy_data_field_area_copy(dfield, lfield, 0, 0, add, add, xres-add-1, yres-add-1);
gwy_data_field_area_copy(dfield, lfield, oxres-add-1, 0, add, add, 0, yres-add-1);
gwy_data_field_area_copy(dfield, lfield, 0, oyres-add-1, add, add, xres-add-1, 0);
gwy_data_field_invert(dfield, 1, 1, 0);
zlfield = gwy_data_field_duplicate(lfield);
zdfield = gwy_data_field_duplicate(dfield);
/*determine number of spheres necessary for given coverage*/
for (i=0; i<10000; i++)
{
ax[i] = ay[i] = az[i] = vx[i] = vy[i] = vz[i] = 0;
}
srand ( time(NULL) );
ndata = 0;
/* for test only */
/*
disize = mdisize;
xpos = oxres/2 - 2*disize;
ypos = oyres/2;
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = (gdouble)xpos*oxreal/(gdouble)oxres;
ry[ndata] = (gdouble)ypos*oyreal/(gdouble)oyres;
rz[ndata] = 2.0*gwy_data_field_get_val(lfield, xpos, ypos) + rdisizes[ndata];
ndata++;
xpos = oxres/2 + 2*disize;
ypos = oyres/2;
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = (gdouble)xpos*oxreal/(gdouble)oxres;
ry[ndata] = (gdouble)ypos*oyreal/(gdouble)oyres;
rz[ndata] = 2.0*gwy_data_field_get_val(lfield, xpos, ypos) + rdisizes[ndata];
ndata++;
*/
/*end of test*/
i = 0;
presetval = args->coverage*10;
while (ndata < presetval && i<max)
{
//disize = mdisize*(0.8+(double)(rand()%20)/40.0);
disize = mdisize;
xpos = disize+(rand()%(xres-2*(gint)(disize+1))) + 1;
ypos = disize+(rand()%(yres-2*(gint)(disize+1))) + 1;
i++;
{
too_close = 0;
/*sync real to integer positions*/
for (k=0; k<ndata; k++)
{
if (((xpos-xdata[k])*(xpos-xdata[k]) + (ypos-ydata[k])*(ypos-ydata[k]))<(4*disize*disize))
{
too_close = 1;
break;
}
}
if (too_close) continue;
if (ndata>=10000) {
break;
}
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = (gdouble)xpos*oxreal/(gdouble)oxres;
ry[ndata] = (gdouble)ypos*oyreal/(gdouble)oyres;
//printf("surface at %g, particle size %g\n", gwy_data_field_get_val(lfield, xpos, ypos), rdisizes[ndata]);
rz[ndata] = 1.0*gwy_data_field_get_val(lfield, xpos, ypos) + rdisizes[ndata]; //2
ndata++;
}
};
// if (i==max) printf("Maximum reached, only %d particles depositd instead of %d\n", ndata, presetval);
// else printf("%d particles depositd\n", ndata);
/*refresh shown data and integer positions (necessary in md calculation)*/
gwy_data_field_copy(zlfield, lfield, 0);
showit(lfield, zdfield, rdisizes, rx, ry, rz, xdata, ydata, ndata,
oxres, oxreal, oyres, oyreal, add, xres, yres);
gwy_data_field_area_copy(lfield, dfield, add, add, oxres, oyres, 0, 0);
gwy_data_field_data_changed(dfield);
for (i=0; i<(20*args->revise); i++)
{
// printf("###### step %d of %d ##########\n", i, (gint)(20*args->revise));
/*try to add some particles if necessary, do this only for first half of molecular dynamics*/
if (ndata<presetval && i<(10*args->revise)) {
ii = 0;
nloc = 0;
while (ndata < presetval && ii<(max/1000) && nloc<maxloc)
{
disize = mdisize;
xpos = disize+(rand()%(xres-2*(gint)(disize+1))) + 1;
ypos = disize+(rand()%(yres-2*(gint)(disize+1))) + 1;
ii++;
{
too_close = 0;
rxv = ((gdouble)xpos*oxreal/(gdouble)oxres);
ryv = ((gdouble)ypos*oyreal/(gdouble)oyres);
rzv = gwy_data_field_get_val(zlfield, xpos, ypos) + 5*size;
for (k=0; k<ndata; k++)
{
if (((rxv-rx[k])*(rxv-rx[k])
+ (ryv-ry[k])*(ryv-ry[k])
+ (rzv-rz[k])*(rzv-rz[k]))<(4.0*size*size))
{
too_close = 1;
break;
}
}
if (too_close) continue;
if (ndata>=10000) {
// printf("Maximum reached!\n");
break;
}
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = rxv;
ry[ndata] = ryv;
rz[ndata] = rzv;
vz[ndata] = -0.01;
ndata++;
nloc++;
}
};
// if (ii==(max/100)) printf("Maximum reached, only %d particles now present instead of %d\n", ndata, presetval);
// else printf("%d particles now at surface\n", ndata);
}
/*test succesive LJ steps on substrate (no relaxation)*/
for (k=0; k<ndata; k++)
{
fx[k] = fy[k] = fz[k] = 0;
/*calculate forces for all particles on substrate*/
if (gwy_data_field_rtoi(lfield, rx[k])<0
|| gwy_data_field_rtoj(lfield, ry[k])<0
|| gwy_data_field_rtoi(lfield, rx[k])>=xres
|| gwy_data_field_rtoj(lfield, ry[k])>=yres)
continue;
for (m=0; m<ndata; m++)
{
if (m==k) continue;
// printf("(%g %g %g) on (%g %g %g)\n", rx[m], ry[m], rz[m], rx[k], ry[k], rz[k]);
fx[k] -= (get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k]+diff, ry[k], rz[k], gwy_data_field_itor(dfield, disizes[k]))
-get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k]-diff, ry[k], rz[k], gwy_data_field_itor(dfield, disizes[k])))/2/diff;
fy[k] -= (get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k]+diff, rz[k], gwy_data_field_itor(dfield, disizes[k]))
-get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k]-diff, rz[k], gwy_data_field_itor(dfield, disizes[k])))/2/diff;
fz[k] -= (get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k], rz[k]+diff, gwy_data_field_itor(dfield, disizes[k]))
-get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k], rz[k]-diff, gwy_data_field_itor(dfield, disizes[k])))/2/diff;
}
fx[k] -= (integrate_lj_substrate(zlfield, rx[k]+diff, ry[k], rz[k], rdisizes[k])
- integrate_lj_substrate(zlfield, rx[k]-diff, ry[k], rz[k], rdisizes[k]))/2/diff;
fy[k] -= (integrate_lj_substrate(zlfield, rx[k], ry[k]-diff, rz[k], rdisizes[k])
- integrate_lj_substrate(zlfield, rx[k], ry[k]+diff, rz[k], rdisizes[k]))/2/diff;
fz[k] -= (integrate_lj_substrate(zlfield, rx[k], ry[k], rz[k]+diff, rdisizes[k])
- integrate_lj_substrate(zlfield, rx[k], ry[k], rz[k]-diff, rdisizes[k]))/2/diff;
}
for (k=0; k<ndata; k++)
{
if (gwy_data_field_rtoi(lfield, rx[k])<0
|| gwy_data_field_rtoj(lfield, ry[k])<0
|| gwy_data_field_rtoi(lfield, rx[k])>=xres
|| gwy_data_field_rtoj(lfield, ry[k])>=yres)
continue;
/*move all particles*/
rx[k] += vx[k]*timestep + 0.5*ax[k]*timestep*timestep;
vx[k] += 0.5*ax[k]*timestep;
ax[k] = fx[k]/mass;
vx[k] += 0.5*ax[k]*timestep;
vx[k] *= 0.9;
if (fabs(vx[k])>0.01) vx[k] = 0; //0.2
ry[k] += vy[k]*timestep + 0.5*ay[k]*timestep*timestep;
vy[k] += 0.5*ay[k]*timestep;
ay[k] = fy[k]/mass;
vy[k] += 0.5*ay[k]*timestep;
vy[k] *= 0.9;
if (fabs(vy[k])>0.01) vy[k] = 0; //0.2
rz[k] += vz[k]*timestep + 0.5*az[k]*timestep*timestep;
vz[k] += 0.5*az[k]*timestep;
az[k] = fz[k]/mass;
vz[k] += 0.5*az[k]*timestep;
vz[k] *= 0.9;
if (fabs(vz[k])>0.01) vz[k] = 0;
if (rx[k]<=gwy_data_field_itor(dfield, disizes[k])) rx[k] = gwy_data_field_itor(dfield, disizes[k]);
if (ry[k]<=gwy_data_field_itor(dfield, disizes[k])) ry[k] = gwy_data_field_itor(dfield, disizes[k]);
if (rx[k]>=(xreal-gwy_data_field_itor(dfield, disizes[k]))) rx[k] = xreal-gwy_data_field_itor(dfield, disizes[k]);
if (ry[k]>=(yreal-gwy_data_field_itor(dfield, disizes[k]))) ry[k] = yreal-gwy_data_field_itor(dfield, disizes[k]);
}
gwy_data_field_copy(zlfield, lfield, 0);
showit(lfield, zdfield, rdisizes, rx, ry, rz, xdata, ydata, ndata,
oxres, oxreal, oyres, oyreal, add, xres, yres);
gwy_data_field_area_copy(lfield, dfield, add, add, oxres, oyres, 0, 0);
gwy_data_field_data_changed(dfield);
while (gtk_events_pending())
gtk_main_iteration();
}
gwy_data_field_area_copy(lfield, dfield, add, add, oxres, oyres, 0, 0);
gwy_data_field_data_changed(dfield);
args->computed = TRUE;
gwy_object_unref(lfield);
gwy_object_unref(zlfield);
gwy_object_unref(zdfield);
}
static GwyContainer*
surffile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
SurfFile surffile;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize expected_size, size = 0;
GError *err = NULL;
gchar signature[12];
gdouble max, min;
gint add = 0;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
g_clear_error(&err);
return NULL;
}
if (size < SURF_HEADER_SIZE + 2) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
p = buffer;
get_CHARARRAY(signature, &p);
if (strncmp(signature, "DIGITAL SURF", 12) != 0) {
err_FILE_TYPE(error, "Surf");
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
surffile.format = gwy_get_guint16_le(&p);
surffile.nobjects = gwy_get_guint16_le(&p);
surffile.version = gwy_get_guint16_le(&p);
surffile.type = gwy_get_guint16_le(&p);
get_CHARS0(surffile.object_name, &p, 30);
get_CHARS0(surffile.operator_name, &p, 30);
surffile.material_code = gwy_get_guint16_le(&p);
surffile.acquisition = gwy_get_guint16_le(&p);
surffile.range = gwy_get_guint16_le(&p);
surffile.special_points = gwy_get_guint16_le(&p);
surffile.absolute = gwy_get_guint16_le(&p);
/*reserved*/
p += 8;
surffile.pointsize = gwy_get_guint16_le(&p);
surffile.zmin = gwy_get_gint32_le(&p);
surffile.zmax = gwy_get_gint32_le(&p);
surffile.xres = gwy_get_gint32_le(&p);
surffile.yres = gwy_get_gint32_le(&p);
surffile.nofpoints = gwy_get_guint32_le(&p);
surffile.dx = gwy_get_gfloat_le(&p);
surffile.dy = gwy_get_gfloat_le(&p);
surffile.dz = gwy_get_gfloat_le(&p);
get_CHARS0(surffile.xaxis, &p, 16);
get_CHARS0(surffile.yaxis, &p, 16);
get_CHARS0(surffile.zaxis, &p, 16);
get_CHARS0(surffile.dx_unit, &p, 16);
get_CHARS0(surffile.dy_unit, &p, 16);
get_CHARS0(surffile.dz_unit, &p, 16);
get_CHARS0(surffile.xlength_unit, &p, 16);
get_CHARS0(surffile.ylength_unit, &p, 16);
get_CHARS0(surffile.zlength_unit, &p, 16);
surffile.xunit_ratio = gwy_get_gfloat_le(&p);
surffile.yunit_ratio = gwy_get_gfloat_le(&p);
surffile.zunit_ratio = gwy_get_gfloat_le(&p);
surffile.imprint = gwy_get_guint16_le(&p);
surffile.inversion = gwy_get_guint16_le(&p);
surffile.leveling = gwy_get_guint16_le(&p);
p += 12;
surffile.seconds = gwy_get_guint16_le(&p);
surffile.minutes = gwy_get_guint16_le(&p);
surffile.hours = gwy_get_guint16_le(&p);
surffile.day = gwy_get_guint16_le(&p);
surffile.month = gwy_get_guint16_le(&p);
surffile.year = gwy_get_guint16_le(&p);
surffile.measurement_duration = gwy_get_guint16_le(&p);
surffile.comment_size = gwy_get_guint16_le(&p);
surffile.private_size = gwy_get_guint16_le(&p);
get_CHARARRAY(surffile.client_zone, &p);
surffile.XOffset = gwy_get_gfloat_le(&p);
surffile.YOffset = gwy_get_gfloat_le(&p);
surffile.ZOffset = gwy_get_gfloat_le(&p);
gwy_debug("fileformat: %d, n_of_objects: %d, "
"version: %d, object_type: %d",
surffile.format, surffile.nobjects,
surffile.version, surffile.type);
gwy_debug("object name: <%s>", surffile.object_name);
gwy_debug("operator name: <%s>", surffile.operator_name);
gwy_debug("material code: %d, acquisition type: %d",
surffile.material_code, surffile.acquisition);
gwy_debug("range type: %d, special points: %d, absolute: %d",
surffile.range,
surffile.special_points, (gint)surffile.absolute);
gwy_debug("data point size: %d", surffile.pointsize);
gwy_debug("zmin: %d, zmax: %d", surffile.zmin, surffile.zmax);
gwy_debug("xres: %d, yres: %d (xres*yres = %d)",
surffile.xres, surffile.yres, (surffile.xres*surffile.yres));
gwy_debug("total number of points: %d", surffile.nofpoints);
gwy_debug("dx: %g, dy: %g, dz: %g",
surffile.dx, surffile.dy, surffile.dz);
gwy_debug("X axis name: %16s", surffile.xaxis);
gwy_debug("Y axis name: %16s", surffile.yaxis);
gwy_debug("Z axis name: %16s", surffile.zaxis);
gwy_debug("dx unit: %16s", surffile.dx_unit);
gwy_debug("dy unit: %16s", surffile.dy_unit);
gwy_debug("dz unit: %16s", surffile.dz_unit);
gwy_debug("X axis unit: %16s", surffile.xlength_unit);
gwy_debug("Y axis unit: %16s", surffile.ylength_unit);
gwy_debug("Z axis unit: %16s", surffile.zlength_unit);
gwy_debug("xunit_ratio: %g, yunit_ratio: %g, zunit_ratio: %g",
surffile.xunit_ratio, surffile.yunit_ratio, surffile.zunit_ratio);
gwy_debug("imprint: %d, inversion: %d, leveling: %d",
surffile.imprint, surffile.inversion, surffile.leveling);
gwy_debug("Time: %d:%d:%d, Date: %d.%d.%d",
surffile.hours, surffile.minutes, surffile.seconds,
surffile.day, surffile.month, surffile.year);
gwy_debug("private zone size: %d, comment size %d",
surffile.private_size, surffile.comment_size);
expected_size = (SURF_HEADER_SIZE
+ surffile.pointsize/8*surffile.xres*surffile.yres);
if (expected_size != size) {
gwy_debug("Size mismatch!");
if (size > expected_size) add = size - expected_size; /*TODO correct this !*/
else {
err_SIZE_MISMATCH(error, expected_size, size);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
}
p = buffer + SURF_HEADER_SIZE + add;
if (!fill_data_fields(&surffile, p, error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
if (!surffile.absolute) {
max = gwy_data_field_get_max(surffile.dfield);
min = gwy_data_field_get_min(surffile.dfield);
gwy_data_field_add(surffile.dfield, -min);
gwy_data_field_multiply(surffile.dfield,
(surffile.zmax - surffile.zmin)/(max-min));
}
switch (surffile.inversion) {
case SURF_INV_Z:
gwy_data_field_invert(surffile.dfield, FALSE, FALSE, TRUE);
break;
case SURF_FLIP_Z:
gwy_data_field_invert(surffile.dfield, FALSE, TRUE, TRUE);
break;
case SURF_FLOP_Z:
gwy_data_field_invert(surffile.dfield, TRUE, FALSE, TRUE);
break;
default:
break;
}
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", surffile.dfield);
g_object_unref(surffile.dfield);
meta = surffile_get_metadata(&surffile);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_app_channel_check_nonsquare(container, 0);
return container;
}
static GwyContainer*
surffile_load(const gchar *filename)
{
SurfFile surffile;
GObject *object = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize size = 0;
gsize estsize;
GError *err = NULL;
gchar signature[12];
gdouble max, min;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
g_warning("Cannot read file %s", filename);
g_clear_error(&err);
return NULL;
}
p = buffer;
get_CHARARRAY(signature, &p);
if (strncmp(signature, "DIGITAL SURF", 12) != 0) {
g_warning("File %s is not a Surf file", filename);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
if (size < 500) {
g_warning("File %s is too short to be Surf file", filename);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
surffile.format = get_WORD_LE(&p);
surffile.nobjects = get_WORD_LE(&p);
surffile.version = get_WORD_LE(&p);
surffile.type = get_WORD_LE(&p);
get_CHARS0(surffile.object_name, &p, 30);
get_CHARS0(surffile.operator_name, &p, 30);
surffile.material_code = get_WORD_LE(&p);
surffile.acquisition = get_WORD_LE(&p);
surffile.range = get_WORD_LE(&p);
surffile.special_points = get_WORD_LE(&p);
surffile.absolute = get_WORD_LE(&p);
/*reserved*/
p += 8;
surffile.pointsize = get_WORD_LE(&p);
surffile.zmin = get_DWORD(&p);
surffile.zmax = get_DWORD(&p);
surffile.xres = get_DWORD(&p);
surffile.yres = get_DWORD(&p);
surffile.nofpoints = get_DWORD(&p);
//surffile.xres = 200; surffile.yres = 200;
surffile.dx = get_FLOAT_LE(&p);
surffile.dy = get_FLOAT_LE(&p);
surffile.dz = get_FLOAT_LE(&p);
get_CHARS0(surffile.xaxis, &p, 16);
get_CHARS0(surffile.yaxis, &p, 16);
get_CHARS0(surffile.zaxis, &p, 16);
get_CHARS0(surffile.dx_unit, &p, 16);
get_CHARS0(surffile.dy_unit, &p, 16);
get_CHARS0(surffile.dz_unit, &p, 16);
get_CHARS0(surffile.xlength_unit, &p, 16);
get_CHARS0(surffile.ylength_unit, &p, 16);
get_CHARS0(surffile.zlength_unit, &p, 16);
surffile.xunit_ratio = get_FLOAT_LE(&p);
surffile.yunit_ratio = get_FLOAT_LE(&p);
surffile.zunit_ratio = get_FLOAT_LE(&p);
surffile.imprint = get_WORD_LE(&p);
surffile.inversion = get_WORD_LE(&p);
surffile.leveling = get_WORD_LE(&p);
p += 12;
surffile.seconds = get_WORD_LE(&p);
surffile.minutes = get_WORD_LE(&p);
surffile.hours = get_WORD_LE(&p);
surffile.day = get_WORD_LE(&p);
surffile.month = get_WORD_LE(&p);
surffile.year = get_WORD_LE(&p);
surffile.measurement_duration = get_WORD_LE(&p);
surffile.comment_size = get_WORD_LE(&p);
surffile.private_size = get_WORD_LE(&p);
get_CHARARRAY(surffile.client_zone, &p);
surffile.XOffset = get_FLOAT_LE(&p);
surffile.YOffset = get_FLOAT_LE(&p);
surffile.ZOffset = get_FLOAT_LE(&p);
gwy_debug("fileformat: %d, n_of_objects: %d, version: %d, object_type: %d",
surffile.format, surffile.nobjects, surffile.version, surffile.type);
gwy_debug("object name: %s", surffile.object_name);
gwy_debug("operator name: %s", surffile.operator_name);
gwy_debug("material code: %d, acquisition type: %d", surffile.material_code, surffile.acquisition);
gwy_debug("range type: %d, special points: %d, absolute: %d", surffile.range,
surffile.special_points, (gint)surffile.absolute);
gwy_debug("data point size: %d", surffile.pointsize);
gwy_debug("zmin: %d, zmax: %d", surffile.zmin, surffile.zmax);
gwy_debug("xres: %d, yres: %d (xres*yres = %d)", surffile.xres, surffile.yres, (surffile.xres*surffile.yres));
gwy_debug("total number of points: %d", surffile.nofpoints);
gwy_debug("dx: %g, dy: %g, dz: %g", surffile.dx, surffile.dy, surffile.dz);
gwy_debug("X axis name: %16s", surffile.xaxis);
gwy_debug("Y axis name: %16s", surffile.yaxis);
gwy_debug("Z axis name: %16s", surffile.zaxis);
gwy_debug("dx unit: %16s", surffile.dx_unit);
gwy_debug("dy unit: %16s", surffile.dy_unit);
gwy_debug("dz unit: %16s", surffile.dz_unit);
gwy_debug("X axis unit: %16s", surffile.xlength_unit);
gwy_debug("Y axis unit: %16s", surffile.ylength_unit);
gwy_debug("Z axis unit: %16s", surffile.zlength_unit);
gwy_debug("xunit_ratio: %g, yunit_ratio: %g, zunit_ratio: %g", surffile.xunit_ratio, surffile.yunit_ratio, surffile.zunit_ratio);
gwy_debug("imprint: %d, inversion: %d, leveling: %d", surffile.imprint, surffile.inversion, surffile.leveling);
gwy_debug("Time: %d:%d:%d, Date: %d.%d.%d", surffile.hours, surffile.minutes, surffile.seconds,
surffile.day, surffile.month, surffile.year);
p = buffer + 512;
estsize = 512 + surffile.pointsize*surffile.xres*surffile.yres/8;
if (size < estsize) {
g_warning("File %s is too short to contain Surf data %d %d", filename, (int)size, (int)estsize);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
fill_data_fields(&surffile, p);
gwy_file_abandon_contents(buffer, size, NULL);
if (surffile.absolute == 0)
{
max = gwy_data_field_get_max(surffile.dfield);
min = gwy_data_field_get_min(surffile.dfield);
gwy_data_field_add(surffile.dfield, -min);
gwy_data_field_multiply(surffile.dfield,
(surffile.zmax - surffile.zmin)/(max-min));
}
if (surffile.inversion == 1)
gwy_data_field_invert(surffile.dfield, FALSE, FALSE, TRUE);
if (surffile.inversion == 2)
gwy_data_field_invert(surffile.dfield, FALSE, TRUE, TRUE);
if (surffile.inversion == 3)
gwy_data_field_invert(surffile.dfield, TRUE, FALSE, TRUE);
if (surffile.dfield) {
object = gwy_container_new();
gwy_container_set_object_by_name(GWY_CONTAINER(object), "/0/data",
G_OBJECT(surffile.dfield));
store_metadata(&surffile, GWY_CONTAINER(object));
}
return (GwyContainer*)object;
return NULL;
}
static GwyDataField*
read_binary_data(const gchar *buffer,
gsize size,
GHashTable *hash,
GError **error)
{
ShimadzuDataType data_type;
gint xres, yres, i;
guint expected;
gdouble xreal, yreal, zscale, xoff, yoff, zoff;
GwySIUnit *unitxy, *unitz;
GwyDataField *dfield = NULL;
gdouble *d;
const gchar *s;
if (!(s = g_hash_table_lookup(hash, "DataType"))) {
err_MISSING_FIELD(error, "DataType");
return NULL;
}
if (g_ascii_strcasecmp(s, "short") == 0)
data_type = SHIMADZU_SHORT;
else if (g_ascii_strcasecmp(s, "float") == 0)
data_type = SHIMADZU_FLOAT;
else {
err_UNSUPPORTED(error, "DataType");
return NULL;
}
unitxy = gwy_si_unit_new(NULL);
unitz = gwy_si_unit_new(NULL);
if (!get_scales(hash, FALSE,
&xres, &yres, &xreal, &yreal, &xoff, &yoff, unitxy,
&zscale, &zoff, unitz, error))
goto fail;
expected = data_type*xres*yres + HEADER_SIZE;
if (err_SIZE_MISMATCH(error, expected, size, FALSE))
goto fail;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
gwy_data_field_set_si_unit_z(dfield, unitz);
d = gwy_data_field_get_data(dfield);
if (data_type == SHIMADZU_SHORT) {
const gint16 *d16 = (const gint16*)(buffer + HEADER_SIZE);
for (i = 0; i < xres*yres; i++)
d[i] = zscale*GUINT16_FROM_LE(d16[i]) + zoff;
}
else if (data_type == SHIMADZU_FLOAT) {
const guchar *p = buffer + HEADER_SIZE;
for (i = 0; i < xres*yres; i++)
d[i] = zscale*gwy_get_gfloat_le(&p) + zoff;
}
else {
g_assert_not_reached();
}
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
fail:
g_object_unref(unitxy);
g_object_unref(unitz);
return dfield;
}
static GwyContainer*
sly_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta = NULL;
gchar *buffer = NULL;
GError *err = NULL;
GHashTable *hash = NULL;
gchar *p, *line, *value;
guint expecting_data = 0;
SensolyticsChannel *channels = NULL;
Dimensions dimensions;
gint ndata = 0, i;
if (!g_file_get_contents(filename, &buffer, NULL, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
p = buffer;
line = gwy_str_next_line(&p);
g_strstrip(line);
if (!gwy_strequal(line, MAGIC)) {
err_FILE_TYPE(error, "Sensolytics");
goto fail;
}
hash = g_hash_table_new(g_str_hash, g_str_equal);
for (line = gwy_str_next_line(&p); line; line = gwy_str_next_line(&p)) {
if (!line[0])
continue;
if (expecting_data) {
expecting_data--;
/* The columns are comma-separated and numbers use decimal points.
* Do not tempt the number parsing functions more than necessary
* and fix commas to tab characters. */
g_strdelimit(line, ",", '\t');
/* Ignore X, Y and Z, each is two values */
for (i = 0; i < 6; i++)
g_ascii_strtod(line, &line);
for (i = 0; i < ndata; i++)
channels[i].data[expecting_data]
= channels[i].q * g_ascii_strtod(line, &line);
}
else {
g_strstrip(line);
if (line[0] != '#') {
g_warning("Comment line does not start with #.");
continue;
}
do {
line++;
} while (g_ascii_isspace(*line));
if (g_str_has_prefix(line, "X [")) {
if (channels) {
g_warning("Multiple data headers!?");
continue;
}
if (!read_dimensions(hash, &ndata, &dimensions, error)
|| !(channels = create_fields(hash, line,
ndata, &dimensions)))
goto fail;
expecting_data = dimensions.xres * dimensions.yres;
continue;
}
value = strchr(line, ':');
if (!value) {
if (!gwy_strequal(line, "ArrayScan"))
g_warning("Non-parameter-like line %s", line);
continue;
}
*value = '\0';
g_strchomp(line);
do {
value++;
} while (g_ascii_isspace(*value));
if (gwy_strequal(line, "Warning"))
continue;
gwy_debug("<%s>=<%s>", line, value);
g_hash_table_insert(hash, line, value);
}
}
if (!channels) {
err_NO_DATA(error);
goto fail;
}
container = gwy_container_new();
for (i = 0; i < ndata; i++) {
GQuark key = gwy_app_get_data_key_for_id(i);
gwy_data_field_invert(channels[i].dfield, FALSE, TRUE, FALSE);
gwy_container_set_object(container, key, channels[i].dfield);
gwy_app_channel_check_nonsquare(container, i);
if (channels[i].name) {
gchar *s = g_strconcat(g_quark_to_string(key), "/title", NULL);
gwy_container_set_string_by_name(container, s,
g_strdup(channels[i].name));
g_free(s);
}
else
gwy_app_channel_title_fall_back(container, i);
gwy_file_channel_import_log_add(container, i, NULL, filename);
}
meta = get_meta(hash);
clone_meta(container, meta, ndata);
g_object_unref(meta);
fail:
g_free(buffer);
if (hash)
g_hash_table_destroy(hash);
if (channels) {
for (i = 0; i < ndata; i++)
g_object_unref(channels[i].dfield);
g_free(channels);
}
return container;
}
/**
* gwy_tip_cmap:
* @tip: Tip data.
* @surface: Surface data.
* @result: Data field to store ceratainty map data to.
* @set_fraction: Function that sets fraction to output (or %NULL).
* @set_message: Function that sets message to output (of %NULL).
*
* Performs certainty map algorithm published by Villarrubia. This function
* converts all fields into form requested by "morph_lib.c" library, that is
* almost identical with original Villarubia's library. Result certainty map
* can be used as a mask of points where tip did not directly touch the
* surface.
*
* Returns: Certainty map, i.e. @result, on success. May return %NULL if
* aborted.
**/
GwyDataField*
gwy_tip_cmap(GwyDataField *tip,
GwyDataField *surface,
GwyDataField *result,
GwySetFractionFunc set_fraction,
GwySetMessageFunc set_message)
{
gint **ftip;
gint **fsurface;
gint **rsurface;
gint **fresult;
gint newx, newy;
gdouble tipmin, surfacemin, step;
GwyDataField *buffertip;
gboolean freetip;
newx = surface->xres + tip->xres;
newy = surface->yres + tip->yres;
/*if tip and surface have different spacings, make new, resampled tip*/
buffertip = get_right_tip_field(tip, surface, &freetip);
/*invert tip (as necessary by dilation algorithm)*/
gwy_data_field_invert(buffertip, TRUE, TRUE, FALSE);
/*convert fields to integer arrays*/
tipmin = gwy_data_field_get_min(buffertip);
surfacemin = gwy_data_field_get_min(surface);
step = (gwy_data_field_get_max(surface) - surfacemin)/10000;
ftip = i_datafield_to_field(buffertip, TRUE, tipmin, step);
fsurface = i_datafield_to_largefield(surface, buffertip, surfacemin, step);
/*perform erosion as it is necessary parameter of certainty map algorithm*/
rsurface = _gwy_morph_lib_ierosion(fsurface, newy, newx,
ftip, buffertip->yres, buffertip->xres,
buffertip->yres/2, buffertip->xres/2,
set_fraction, set_message);
if (!rsurface) {
_gwy_morph_lib_ifreematrix(ftip, buffertip->xres);
_gwy_morph_lib_ifreematrix(fsurface, newx);
if (freetip)
g_object_unref(buffertip);
return NULL;
}
/*find certanty map*/
if (rsurface) {
fresult = _gwy_morph_lib_icmap(fsurface, newy, newx,
ftip, buffertip->yres, buffertip->xres,
rsurface,
buffertip->yres/2, buffertip->xres/2,
set_fraction, set_message);
}
else
fresult = NULL;
/*convert result back*/
if (fresult) {
gwy_data_field_resample(result, surface->xres, surface->yres,
GWY_INTERPOLATION_NONE);
result = i_largefield_to_datafield(fresult, result, buffertip,
0.0, 1.0);
}
else
result = NULL;
_gwy_morph_lib_ifreematrix(ftip, buffertip->xres);
_gwy_morph_lib_ifreematrix(fsurface, newx);
_gwy_morph_lib_ifreematrix(rsurface, newx);
if (fresult)
_gwy_morph_lib_ifreematrix(fresult, result->xres);
if (freetip)
g_object_unref(buffertip);
else
gwy_data_field_invert(buffertip, TRUE, TRUE, FALSE);
return result;
}
static GwyDataField*
hash_to_data_field(GHashTable *hash,
GHashTable *scannerlist,
GHashTable *scanlist,
NanoscopeFileType file_type,
gboolean has_version,
guint bufsize,
gchar *buffer,
gint gxres,
gint gyres,
gchar **p,
GError **error)
{
NanoscopeValue *val;
GwyDataField *dfield;
GwySIUnit *unitz, *unitxy;
gchar *s, *end;
gchar un[5];
gint xres, yres, bpp, offset, size, power10;
gdouble xreal, yreal, q;
gdouble *data;
gboolean size_ok, use_global;
if (!require_keys(hash, error, "Samps/line", "Number of lines",
"Scan size", "Data offset", "Data length", NULL))
return NULL;
val = g_hash_table_lookup(hash, "Samps/line");
xres = GWY_ROUND(val->hard_value);
val = g_hash_table_lookup(hash, "Number of lines");
yres = GWY_ROUND(val->hard_value);
val = g_hash_table_lookup(hash, "Bytes/pixel");
bpp = val ? GWY_ROUND(val->hard_value) : 2;
/* scan size */
val = g_hash_table_lookup(hash, "Scan size");
xreal = g_ascii_strtod(val->hard_value_str, &end);
if (errno || *end != ' ') {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Cannot parse `Scan size' field."));
return NULL;
}
gwy_debug("xreal = %g", xreal);
s = end+1;
yreal = g_ascii_strtod(s, &end);
if (errno || *end != ' ') {
/* Old files don't have two numbers here, assume equal dimensions */
yreal = xreal;
end = s;
}
gwy_debug("yreal = %g", yreal);
while (g_ascii_isspace(*end))
end++;
if (sscanf(end, "%4s", un) != 1) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Cannot parse `Scan size' field."));
return NULL;
}
gwy_debug("xy unit: <%s>", un);
unitxy = gwy_si_unit_new_parse(un, &power10);
q = pow10(power10);
xreal *= q;
yreal *= q;
offset = size = 0;
if (file_type == NANOSCOPE_FILE_TYPE_BIN) {
val = g_hash_table_lookup(hash, "Data offset");
offset = GWY_ROUND(val->hard_value);
val = g_hash_table_lookup(hash, "Data length");
size = GWY_ROUND(val->hard_value);
size_ok = FALSE;
use_global = FALSE;
/* Try channel size and local size */
if (!size_ok && size == bpp*xres*yres)
size_ok = TRUE;
if (!size_ok && size == bpp*gxres*gyres) {
size_ok = TRUE;
use_global = TRUE;
}
/* If they don't match exactly, try whether they at least fit inside */
if (!size_ok && size > bpp*MAX(xres*yres, gxres*gyres)) {
size_ok = TRUE;
use_global = (xres*yres < gxres*gyres);
}
if (!size_ok && size > bpp*MIN(xres*yres, gxres*gyres)) {
size_ok = TRUE;
use_global = (xres*yres > gxres*gyres);
}
if (!size_ok) {
err_SIZE_MISMATCH(error, size, bpp*xres*yres);
return NULL;
}
if (use_global) {
if (gxres) {
xreal *= (gdouble)gxres/xres;
xres = gxres;
}
if (gyres) {
yreal *= (gdouble)gyres/yres;
yres = gyres;
}
}
if (offset + size > (gint)bufsize) {
err_SIZE_MISMATCH(error, offset + size, bufsize);
return NULL;
}
}
q = 1.0;
unitz = get_physical_scale(hash, scannerlist, scanlist, has_version,
&q, error);
if (!unitz)
return NULL;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
data = gwy_data_field_get_data(dfield);
switch (file_type) {
case NANOSCOPE_FILE_TYPE_TXT:
if (!read_ascii_data(xres*yres, data, p, bpp, error)) {
g_object_unref(dfield);
return NULL;
}
break;
case NANOSCOPE_FILE_TYPE_BIN:
if (!read_binary_data(xres*yres, data, buffer + offset, bpp, error)) {
g_object_unref(dfield);
return NULL;
}
break;
default:
g_assert_not_reached();
break;
}
gwy_data_field_multiply(dfield, q);
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
gwy_data_field_set_si_unit_z(dfield, unitz);
g_object_unref(unitz);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
g_object_unref(unitxy);
return dfield;
}
static GwyDataField*
igor_read_data_field(const IgorFile *igorfile,
const guchar *buffer,
guint i,
const gchar *zunits,
gboolean imaginary)
{
const IgorWaveHeader5 *wave5;
guint n, xres, yres, skip;
GwyDataField *dfield;
GwySIUnit *unit;
gdouble *data;
const guchar *p;
gint power10;
gdouble q;
wave5 = &igorfile->wave5;
xres = wave5->n_dim[0];
yres = wave5->n_dim[1];
p = buffer + igorfile->headers_size + xres*yres*igorfile->type_size*i;
n = xres*yres;
dfield = gwy_data_field_new(xres, yres,
wave5->sfA[0]*xres, wave5->sfA[1]*yres,
FALSE);
data = gwy_data_field_get_data(dfield);
g_return_val_if_fail(!imaginary || (wave5->type & IGOR_COMPLEX), dfield);
skip = imaginary ? igorfile->type_size/2 : 0;
if (imaginary)
p += skip;
/* TODO: Support extended units */
unit = gwy_data_field_get_si_unit_xy(dfield);
gwy_si_unit_set_from_string_parse(unit, wave5->dim_units[0], &power10);
gwy_data_field_set_xreal(dfield, pow10(power10)*wave5->sfA[0]*xres);
gwy_data_field_set_yreal(dfield, pow10(power10)*wave5->sfA[1]*yres);
unit = gwy_data_field_get_si_unit_z(dfield);
gwy_si_unit_set_from_string_parse(unit, zunits ? zunits : wave5->data_units,
&power10);
q = pow10(power10);
switch ((guint)wave5->type) {
case IGOR_INT8:
{
const gint8 *ps = (const gint8*)buffer;
while (n--) {
*(data++) = *(ps++) * q;
ps += skip;
}
}
break;
case IGOR_INT8 | IGOR_UNSIGNED:
while (n--) {
*(data++) = *(p++) * q;
p += skip;
}
break;
case IGOR_INT16:
while (n--) {
*(data++) = igorfile->get_gint16(&p) * q;
p += skip;
}
break;
case IGOR_INT16 | IGOR_UNSIGNED:
while (n--) {
*(data++) = igorfile->get_guint16(&p) * q;
p += skip;
}
break;
case IGOR_INT32:
while (n--) {
*(data++) = igorfile->get_gint32(&p) * q;
p += skip;
}
break;
case IGOR_INT32 | IGOR_UNSIGNED:
while (n--) {
*(data++) = igorfile->get_guint32(&p) * q;
p += skip;
}
break;
case IGOR_SINGLE:
while (n--) {
*(data++) = igorfile->get_gfloat(&p) * q;
p += skip;
}
break;
case IGOR_DOUBLE:
while (n--) {
*(data++) = igorfile->get_gdouble(&p) * q;
p += skip;
}
break;
default:
g_return_val_if_reached(NULL);
break;
}
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
return dfield;
}
static void
level_grains_do(const LevelGrainsArgs *args,
GwyContainer *data, GQuark dquark, gint id,
GwyDataField *dfield, GwyDataField *mfield)
{
GwyDataField *buffer, *background, *invmask;
gdouble error, cor, maxerr, lastfrac, frac, starterr;
gdouble *heights, *bgdata;
gint *grains;
gboolean cancelled = FALSE;
gint i, xres, yres, ngrains;
xres = gwy_data_field_get_xres(mfield);
yres = gwy_data_field_get_yres(mfield);
grains = g_new0(gint, xres*yres);
ngrains = gwy_data_field_number_grains(mfield, grains);
if (!ngrains) {
g_free(grains);
return;
}
heights = g_new(gdouble, ngrains+1);
gwy_data_field_grains_get_values(dfield, heights, ngrains, grains,
args->base);
heights[0] = 0.0;
background = gwy_data_field_new_alike(dfield, FALSE);
bgdata = gwy_data_field_get_data(background);
for (i = 0; i < xres*yres; i++)
bgdata[i] = -heights[grains[i]];
invmask = gwy_data_field_duplicate(mfield);
gwy_data_field_multiply(invmask, -1.0);
gwy_data_field_add(invmask, 1.0);
maxerr = gwy_data_field_get_rms(dfield)/1.0e4;
gwy_app_wait_start(gwy_app_find_window_for_channel(data, id),
_("Laplace interpolation..."));
g_free(heights);
g_free(grains);
buffer = gwy_data_field_new_alike(background, TRUE);
gwy_data_field_correct_average(background, invmask);
cor = 0.2;
error = 0.0;
lastfrac = 0.0;
starterr = 0.0;
for (i = 0; i < 5000; i++) {
gwy_data_field_correct_laplace_iteration(background, invmask, buffer,
cor, &error);
if (error < maxerr)
break;
if (!i)
starterr = error;
frac = log(error/starterr)/log(maxerr/starterr);
if ((i/(gdouble)(5000)) > frac)
frac = i/(gdouble)(5000);
if (lastfrac > frac)
frac = lastfrac;
if (!gwy_app_wait_set_fraction(frac)) {
cancelled = TRUE;
break;
}
lastfrac = frac;
}
gwy_app_wait_finish();
if (!cancelled) {
gwy_data_field_invert(background, FALSE, FALSE, TRUE);
gwy_app_undo_qcheckpointv(data, 1, &dquark);
gwy_data_field_subtract_fields(dfield, dfield, background);
gwy_data_field_data_changed(dfield);
if (args->do_extract) {
gint newid;
newid = gwy_app_data_browser_add_data_field(background, data, TRUE);
gwy_app_sync_data_items(data, data, id, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
0);
gwy_app_set_data_field_title(data, newid, _("Background"));
}
}
g_object_unref(buffer);
g_object_unref(invmask);
g_object_unref(background);
}
static GwyContainer*
fits_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
fitsfile *fptr = NULL;
GwyDataField *field = NULL, *mask;
gint status = 0; /* Must be initialised to zero! */
gint hdutype, naxis, anynull, nkeys, k;
glong res[3]; /* First index is the fast looping one. */
char strvalue[FLEN_VALUE];
gchar *invalid = NULL;
gdouble real, off;
if (fits_open_image(&fptr, filename, READONLY, &status)) {
err_FITS(error, status);
return NULL;
}
if (fits_get_hdu_type(fptr, &hdutype, &status)) {
err_FITS(error, status);
goto fail;
}
gwy_debug("hdutype %d", hdutype);
if (hdutype != IMAGE_HDU) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only two-dimensional images are supported."));
goto fail;
}
if (fits_get_img_dim(fptr, &naxis, &status)) {
err_FITS(error, status);
goto fail;
}
gwy_debug("naxis %d", naxis);
if (naxis != 2 && naxis != 3) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only two-dimensional images are supported."));
goto fail;
}
if (fits_get_img_size(fptr, naxis, res, &status)) {
err_FITS(error, status);
goto fail;
}
if (naxis == 3 && res[2] != 1) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only two-dimensional images are supported."));
goto fail;
}
gwy_debug("xres %ld, yres %ld", res[0], res[1]);
if (err_DIMENSION(error, res[0]) || err_DIMENSION(error, res[1]))
goto fail;
field = gwy_data_field_new(res[0], res[1], res[0], res[1], FALSE);
invalid = g_new(gchar, res[0]*res[1]);
if (fits_read_imgnull(fptr, TDOUBLE, 1, res[0]*res[1],
field->data, invalid, &anynull, &status)) {
err_FITS(error, status);
goto fail;
}
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", field);
/* Failures here are non-fatal. We already have an image. */
if (fits_get_hdrspace(fptr, &nkeys, NULL, &status)) {
g_warning("Cannot get the first hdrspace.");
goto fail;
}
if (!fits_read_key(fptr, TSTRING, "BUINT ", strvalue, NULL, &status)) {
gint power10;
gwy_debug("BUINT = <%s>", strvalue);
gwy_si_unit_set_from_string_parse(gwy_data_field_get_si_unit_z(field),
strvalue, &power10);
if (power10)
gwy_data_field_multiply(field, pow10(power10));
}
status = 0;
if (get_real_and_offset(fptr, 1, res[0], &real, &off)) {
if (real < 0.0) {
off += real;
real = -real;
gwy_data_field_invert(field, FALSE, TRUE, FALSE);
}
gwy_data_field_set_xreal(field, real);
gwy_data_field_set_xoffset(field, off);
}
if (get_real_and_offset(fptr, 2, res[1], &real, &off)) {
if (real < 0.0) {
off += real;
real = -real;
gwy_data_field_invert(field, TRUE, FALSE, FALSE);
}
gwy_data_field_set_yreal(field, real);
gwy_data_field_set_yoffset(field, off);
}
/* Create a mask of invalid data. */
for (k = 0; k < field->xres*field->yres; k++) {
if (invalid[k])
field->data[k] = NAN;
}
if ((mask = gwy_app_channel_mask_of_nans(field, TRUE))) {
gwy_container_set_object_by_name(container, "/0/mask", mask);
g_object_unref(mask);
}
fail:
fits_close_file(fptr, &status);
gwy_object_unref(field);
g_free(invalid);
return container;
}
