/**
* gwy_data_field_correlate_iteration:
* @state: Correlation iterator.
*
* Performs one iteration of correlation.
*
* An iterator can be created with gwy_data_field_correlate_init().
* When iteration ends, either by finishing or being aborted,
* gwy_data_field_correlate_finalize() must be called to release allocated
* resources.
**/
void
gwy_data_field_correlate_iteration(GwyComputationState *cstate)
{
GwyCorrelationState *state = (GwyCorrelationState*)cstate;
gint xres, yres, kxres, kyres, k, xoff, yoff;
gdouble s, davg, drms;
xres = state->data_field->xres;
yres = state->data_field->yres;
kxres = state->kernel_field->xres;
kyres = state->kernel_field->yres;
xoff = (kxres - 1)/2;
yoff = (kyres - 1)/2;
if (state->cs.state == GWY_COMPUTATION_STATE_INIT) {
gwy_data_field_fill(state->score, -1);
state->kavg = gwy_data_field_get_avg(state->kernel_field);
state->krms = gwy_data_field_get_rms(state->kernel_field);
state->avg = gwy_data_field_duplicate(state->data_field);
state->rms = gwy_data_field_duplicate(state->data_field);
calculate_normalization(state->avg, state->rms, kxres, kyres);
state->cs.state = GWY_COMPUTATION_STATE_ITERATE;
state->cs.fraction = 0.0;
state->i = yoff;
state->j = xoff;
}
else if (state->cs.state == GWY_COMPUTATION_STATE_ITERATE) {
k = state->i*xres + state->j;
davg = state->avg->data[k];
drms = state->rms->data[k];
if (drms && state->krms) {
s = gwy_data_field_get_raw_correlation_score(state->data_field,
state->kernel_field,
state->j - xoff,
state->i - yoff,
0, 0,
kxres, kyres,
davg, state->kavg);
state->score->data[k] = s/(drms*state->krms);
}
else
state->score->data[k] = 0.0;
state->j++;
if (state->j + kxres - xoff > xres) {
state->j = xoff;
state->i++;
if (state->i + kyres - yoff > yres)
state->cs.state = GWY_COMPUTATION_STATE_FINISHED;
}
state->cs.fraction += 1.0/((xres - kxres + 1)*(yres - kyres + 1));
state->cs.fraction = MIN(state->cs.fraction, 1.0);
}
else if (state->cs.state == GWY_COMPUTATION_STATE_FINISHED)
return;
gwy_data_field_invalidate(state->score);
}
static void
mask_extract(GwyContainer *data, GwyRunType run)
{
GwyDataField *dfield;
GwySIUnit *siunit;
gint oldid, newid;
g_return_if_fail(run & MASKOPS_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_MASK_FIELD, &dfield,
GWY_APP_DATA_FIELD_ID, &oldid,
0);
g_return_if_fail(dfield);
dfield = gwy_data_field_duplicate(dfield);
gwy_data_field_clamp(dfield, 0.0, 1.0);
/* Other functions should set the units correctly, but do not trust them */
siunit = gwy_si_unit_new("");
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
newid = gwy_app_data_browser_add_data_field(dfield, data, TRUE);
g_object_unref(dfield);
gwy_app_set_data_field_title(data, newid, _("Mask"));
gwy_app_channel_log_add_proc(data, oldid, newid);
}
static void
plot_correlated(GwyDataField *retfield, gint xsize, gint ysize,
gdouble threshold)
{
GwyDataField *tmp;
gint xres, yres, i, j, col, row, w, h;
const gdouble *data;
tmp = gwy_data_field_duplicate(retfield);
gwy_data_field_clear(retfield);
xres = gwy_data_field_get_xres(retfield);
yres = gwy_data_field_get_yres(retfield);
data = gwy_data_field_get_data_const(tmp);
/* FIXME: this is very inefficient */
for (i = 0; i < yres; i++) {
row = MAX(i - ysize/2, 0);
h = MIN(i + ysize - ysize/2, yres) - row;
for (j = 0; j < xres; j++) {
if (data[i*xres + j] > threshold) {
col = MAX(j - xsize/2, 0);
w = MIN(j + xsize - xsize/2, xres) - col;
gwy_data_field_area_fill(retfield, col, row, w, h, 1.0);
}
}
}
g_object_unref(tmp);
}
static void
presentation_logscale(GwyContainer *data, GwyRunType run)
{
GwyDataField *dfield, *sfield;
GQuark squark;
gdouble *d;
gdouble min, max, m0;
gint xres, yres, i, zeroes, id;
g_return_if_fail(run & PRESENTATIONOPS_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD, &dfield,
GWY_APP_SHOW_FIELD_KEY, &squark,
GWY_APP_SHOW_FIELD, &sfield,
GWY_APP_DATA_FIELD_ID, &id,
0);
g_return_if_fail(dfield && squark);
xres = gwy_data_field_get_xres(dfield);
yres = gwy_data_field_get_yres(dfield);
gwy_app_undo_qcheckpointv(data, 1, &squark);
if (!sfield) {
sfield = gwy_data_field_duplicate(dfield);
gwy_container_set_object(data, squark, sfield);
g_object_unref(sfield);
}
else {
gwy_data_field_resample(sfield, xres, yres, GWY_INTERPOLATION_NONE);
gwy_data_field_copy(dfield, sfield, FALSE);
}
d = gwy_data_field_get_data(sfield);
zeroes = 0;
max = 0;
min = G_MAXDOUBLE;
for (i = 0; i < xres*yres; i++) {
d[i] = ABS(d[i]);
if (G_UNLIKELY(d[i] > max))
max = d[i];
if (d[i] == 0.0)
zeroes++;
else if (G_UNLIKELY(d[i] < min))
min = d[i];
}
if (min == max || zeroes == xres*yres)
return;
if (!zeroes) {
for (i = 0; i < xres*yres; i++)
d[i] = log(d[i]);
}
else {
m0 = log(min) - log(max/min)/512.0;
for (i = 0; i < xres*yres; i++)
d[i] = d[i] ? log(d[i]) : m0;
}
gwy_data_field_data_changed(sfield);
gwy_app_channel_log_add_proc(data, id, id);
}
static void
laplace(GwyContainer *data, GwyRunType run)
{
GwyDataField *dfield, *mfield, *buffer;
GQuark dquark;
gdouble error, cor, maxer, lastfrac, frac, starter;
gint i, id;
gboolean cancelled = FALSE;
g_return_if_fail(run & LAPLACE_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD_KEY, &dquark,
GWY_APP_DATA_FIELD, &dfield,
GWY_APP_MASK_FIELD, &mfield,
GWY_APP_DATA_FIELD_ID, &id,
0);
g_return_if_fail(dfield && dquark && mfield);
maxer = gwy_data_field_get_rms(dfield)/1.0e4;
gwy_app_wait_start(gwy_app_find_window_for_channel(data, id),
_("Laplace interpolation..."));
dfield = gwy_data_field_duplicate(dfield);
buffer = gwy_data_field_new_alike(dfield, TRUE);
gwy_data_field_correct_average(dfield, mfield);
cor = 0.2;
error = 0.0;
lastfrac = 0.0;
starter = 0.0;
for (i = 0; i < 5000; i++) {
gwy_data_field_correct_laplace_iteration(dfield, mfield, buffer,
cor, &error);
if (error < maxer)
break;
if (!i)
starter = error;
frac = log(error/starter)/log(maxer/starter);
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_app_undo_qcheckpointv(data, 1, &dquark);
gwy_container_set_object(data, dquark, dfield);
gwy_app_channel_log_add_proc(data, id, id);
}
g_object_unref(dfield);
g_object_unref(buffer);
}
static GwyDataField*
median_background(gint size,
GwyDataField *dfield)
{
GwyDataField *rfield;
gint *circle;
gdouble *data, *rdata, *buffer;
gint i, j, xres, yres, buflen;
data = gwy_data_field_get_data(dfield);
rfield = gwy_data_field_duplicate(dfield);
xres = gwy_data_field_get_xres(rfield);
yres = gwy_data_field_get_yres(rfield);
rdata = gwy_data_field_get_data(rfield);
buflen = 0;
circle = median_make_circle(size);
for (i = 0; i < 2*size + 1; i++)
buflen += 2*circle[i] + 1;
buffer = g_new(gdouble, buflen);
for (i = 0; i < yres; i++) {
for (j = 0; j < xres; j++) {
gint n, k, from, to;
n = 0;
for (k = MAX(0, i - size); k <= MIN(yres - 1, i + size); k++) {
gdouble *row = data + k*xres;
from = MAX(0, j - circle[k - i + size]);
to = MIN(xres - 1, j + circle[k - i + size]);
memcpy(buffer + n, row + from, (to - from + 1)*sizeof(gdouble));
n += to - from + 1;
}
rdata[i*xres + j] = gwy_math_median(n, buffer);
}
if (i % 10 == 0
&& !gwy_app_wait_set_fraction((gdouble)i/yres)) {
g_free(circle);
g_object_unref(rfield);
return NULL;
}
}
g_free(circle);
return rfield;
}
/* create a smaller copy of data */
static GwyContainer*
create_preview_data(GwyContainer *data)
{
GwyContainer *preview;
GwyDataField *dfield, *dfield_show;
gint oldid;
gint xres, yres;
gdouble zoomval;
preview = gwy_container_new();
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD, &dfield,
GWY_APP_DATA_FIELD_ID, &oldid,
0);
dfield = gwy_data_field_duplicate(dfield);
dfield_show = gwy_data_field_duplicate(dfield);
xres = gwy_data_field_get_xres(dfield);
yres = gwy_data_field_get_yres(dfield);
zoomval = (gdouble)PREVIEW_SIZE/MAX(xres, yres);
gwy_data_field_resample(dfield, xres*zoomval, yres*zoomval,
GWY_INTERPOLATION_LINEAR);
dfield_show = gwy_data_field_duplicate(dfield);
gwy_container_set_object_by_name(preview, "/0/data", dfield);
g_object_unref(dfield);
gwy_container_set_object_by_name(preview, "/0/show", dfield_show);
g_object_unref(dfield_show);
gwy_app_sync_data_items(data, preview, oldid, 0, FALSE,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_RANGE,
GWY_DATA_ITEM_MASK_COLOR,
0);
return preview;
}
static GwyDataField*
prof_sqrt(GwyDataField *dfield)
{
gint xres, yres, i;
gdouble *data;
dfield = gwy_data_field_duplicate(dfield);
xres = gwy_data_field_get_xres(dfield);
yres = gwy_data_field_get_yres(dfield);
data = gwy_data_field_get_data(dfield);
for (i = 0; i < xres*yres; i++)
data[i] = sqrt(data[i]);
return dfield;
}
static void
tip_update(TipModelControls *controls,
G_GNUC_UNUSED TipModelArgs *args)
{
GwyDataField *vtipfield, *buffer;
buffer = gwy_data_field_duplicate(controls->tip);
gwy_data_field_resample(buffer, controls->vxres, controls->vyres,
GWY_INTERPOLATION_ROUND);
vtipfield = GWY_DATA_FIELD(gwy_container_get_object_by_name(controls->vtip,
"/0/data"));
gwy_data_field_copy(buffer, vtipfield, FALSE);
g_object_unref(buffer);
gwy_data_field_data_changed(vtipfield);
}
static void
presentation_attach_do(const GwyAppDataId *source,
const GwyAppDataId *target)
{
GwyContainer *sourcedata, *targetdata;
GwyDataField *dfield;
GQuark quark;
sourcedata = gwy_app_data_browser_get(source->datano);
targetdata = gwy_app_data_browser_get(target->datano);
quark = gwy_app_get_data_key_for_id(source->id);
dfield = GWY_DATA_FIELD(gwy_container_get_object(sourcedata, quark));
dfield = gwy_data_field_duplicate(dfield);
quark = gwy_app_get_show_key_for_id(target->id);
gwy_app_undo_qcheckpointv(targetdata, 1, &quark);
gwy_container_set_object(targetdata, quark, dfield);
g_object_unref(dfield);
}
static void
presentation_extract(GwyContainer *data, GwyRunType run)
{
GwyDataField *dfield;
GQuark quark;
gint oldid, newid;
g_return_if_fail(run & PRESENTATIONOPS_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD_ID, &oldid,
GWY_APP_SHOW_FIELD_KEY, &quark,
GWY_APP_SHOW_FIELD, &dfield,
0);
g_return_if_fail(dfield && quark);
dfield = gwy_data_field_duplicate(dfield);
newid = gwy_app_data_browser_add_data_field(dfield, data, TRUE);
g_object_unref(dfield);
gwy_app_sync_data_items(data, data, oldid, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
0);
gwy_app_set_data_field_title(data, newid, NULL);
gwy_app_channel_log_add_proc(data, oldid, newid);
}
static void
prepare_stripe_fields(TipBlindControls *controls,
gboolean keep)
{
TipBlindArgs *args = controls->args;
guint i;
if (!args->split_to_stripes) {
free_stripe_results(args);
return;
}
if (!keep || args->nstripes != controls->oldnstripes)
free_stripe_results(args);
if (!args->stripetips) {
args->stripetips = g_new(GwyDataField*, args->nstripes);
args->goodtip = g_new0(gboolean, args->nstripes);
/* This can potentially initialise all the stripe tips from the global
* one which is probably what we want. */
for (i = 0; i < args->nstripes; i++)
args->stripetips[i] = gwy_data_field_duplicate(controls->tip);
}
static GwyContainer*
igor_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta = NULL, *container = NULL;
GwyDataField *dfield = NULL, *maskfield = NULL;
GwyTextHeaderParser parser;
IgorFile igorfile;
IgorWaveHeader5 *wave5;
GError *err = NULL;
guchar *p, *buffer = NULL;
gint xres, yres;
gsize expected_size, size = 0;
gchar *note = NULL;
const gchar *value;
gchar key[64];
guint i, chid;
GQuark quark;
guint nlabels;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
gwy_clear(&igorfile, 1);
if (!igor_read_headers(&igorfile, buffer, size, FALSE, error))
goto fail;
/* Only accept v5 files because older do not support 2D data */
if (igorfile.header.version != 5) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Format version is %d. Only version 5 is supported."),
igorfile.header.version);
goto fail;
}
/* Detect Asylum research files, leave it at generic if not detected. */
if (memcmp(buffer + size-5, "MFP3D", 5) == 0)
igorfile.variant = IGOR_ASYLUM_MPF3D;
else if (memcmp(buffer + size-5, "Force", 5) == 0)
igorfile.variant = IGOR_ASYLUM_FORCE;
gwy_debug("producer variant %u", igorfile.variant);
/* Must have exactly 3 dims: xres, yres, nchannels */
wave5 = &igorfile.wave5;
xres = wave5->n_dim[0];
yres = wave5->n_dim[1];
igorfile.nchannels = wave5->n_dim[2];
if (igorfile.nchannels==0) igorfile.nchannels=1;
if (!xres || !yres || !igorfile.nchannels || wave5->n_dim[3]) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only two-dimensional data are supported."));
goto fail;
}
igorfile.type_size = igor_data_type_size(wave5->type);
if (!igorfile.type_size) {
err_DATA_TYPE(error, wave5->type);
goto fail;
}
if (wave5->npts != xres*yres*igorfile.nchannels) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Number of data points %u does not match resolutions "
"%u×%u×%u."),
wave5->npts, xres, yres, igorfile.nchannels);
goto fail;
}
if (igorfile.header.wfm_size <= igorfile.wave_header_size) {
err_INVALID(error, "wfmSize");
goto fail;
}
expected_size = igorfile.header.wfm_size - igorfile.wave_header_size;
if (expected_size != wave5->npts*igorfile.type_size) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Data size %u does not match "
"the number of data points %u×%u."),
(guint)expected_size, wave5->npts, igorfile.type_size);
}
if (err_SIZE_MISMATCH(error, expected_size + igorfile.headers_size, size,
FALSE))
goto fail;
p = buffer + igorfile.headers_size + expected_size;
gwy_debug("remaning data size: %lu", (gulong)(size - (p - buffer)));
p += igorfile.header.formula_size;
if ((igorfile.variant == IGOR_ASYLUM_FORCE
|| igorfile.variant == IGOR_ASYLUM_MPF3D)
&& igorfile.header.note_size
&& (p - buffer) + igorfile.header.note_size <= size) {
note = g_strndup((const gchar*)p, size);
gwy_clear(&parser, 1);
parser.key_value_separator = ":";
igorfile.meta = gwy_text_header_parse(note, &parser, NULL, NULL);
}
p += igorfile.header.note_size;
/* FIXME: Support extended units for non-Asylum files! */
p += igorfile.header.data_e_units_size;
for (i = 0; i < MAXDIMS; i++)
p += igorfile.header.dim_e_units_size[i];
/* Skip labels of x and y dimension, we don't know what to do with them. */
for (i = 0; i < 2; i++)
p += igorfile.header.dim_labels_size[i];
/* FIXME: The labels are mandatory only in Asylum Research files. */
nlabels = igorfile.header.dim_labels_size[2]/(MAX_WAVE_NAME5+1);
expected_size = (MAX_WAVE_NAME5 + 1)*(nlabels);
if ((p - buffer) + expected_size > size ) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Cannot read channel labels."));
goto fail;
}
igorfile.titles = read_channel_labels(p, igorfile.nchannels+1, nlabels);
p += igorfile.header.dim_labels_size[2];
if (igorfile.meta) {
igorfile.channel_info = g_new0(AsylumChannelInfo, igorfile.nchannels);
for (i = 0; i < igorfile.nchannels; i++) {
AsylumChannelInfo *chinfo = igorfile.channel_info + i;
const gchar *title = g_ptr_array_index(igorfile.titles, i+1);
if (title) {
chinfo->name = canonicalize_title(title);
g_snprintf(key, sizeof(key), "%sUnit", chinfo->name);
value = g_hash_table_lookup(igorfile.meta, key);
if (value)
chinfo->units = value;
else
chinfo->units = channel_title_to_units(chinfo->name);
}
}
}
container = gwy_container_new();
for (i = chid = 0; i < igorfile.nchannels; i++, chid++) {
const gchar *title = g_ptr_array_index(igorfile.titles, i+1);
const gchar *zunits = NULL;
if (igorfile.channel_info) {
AsylumChannelInfo *chinfo = igorfile.channel_info + i;
zunits = chinfo->units;
meta = igor_get_metadata(&igorfile, i + 1);
}
dfield = igor_read_data_field(&igorfile, buffer, i, zunits, FALSE);
maskfield = gwy_app_channel_mask_of_nans(dfield, TRUE);
quark = gwy_app_get_data_key_for_id(chid);
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
if (maskfield) {
g_snprintf(key, sizeof(key), "/%d/mask", chid);
gwy_container_set_object_by_name(container, key, maskfield);
}
if (meta) {
g_snprintf(key, sizeof(key), "/%d/meta", chid);
gwy_container_set_object_by_name(container, key, meta);
}
if (title) {
g_snprintf(key, sizeof(key), "/%d/data/title", chid);
gwy_container_set_string_by_name(container, key, g_strdup(title));
}
gwy_app_channel_title_fall_back(container,chid);
if (wave5->type & IGOR_COMPLEX) {
chid++;
dfield = igor_read_data_field(&igorfile, buffer, i, zunits, TRUE);
quark = gwy_app_get_data_key_for_id(chid);
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
if (meta) {
g_snprintf(key, sizeof(key), "/%d/meta", chid);
/* container still holds a reference */
g_object_unref(meta);
meta = gwy_container_duplicate(meta);
gwy_container_set_object_by_name(container, key, meta);
}
if (maskfield) {
g_snprintf(key, sizeof(key), "/%d/mask", chid);
/* container still holds a reference */
g_object_unref(maskfield);
maskfield = gwy_data_field_duplicate(maskfield);
gwy_container_set_object_by_name(container, key, maskfield);
}
if (title) {
g_snprintf(key, sizeof(key), "/%d/data/title", chid);
gwy_container_set_string_by_name(container, key, g_strdup(title));
};
gwy_app_channel_title_fall_back(container,chid);
}
gwy_object_unref(meta);
gwy_object_unref(maskfield);
gwy_file_channel_import_log_add(container, chid, NULL, filename);
}
fail:
gwy_file_abandon_contents(buffer, size, NULL);
g_free(note);
if (igorfile.channel_info) {
for (i = 0; i < igorfile.nchannels; i++)
g_free(igorfile.channel_info[i].name);
g_free(igorfile.channel_info);
}
if (igorfile.meta)
g_hash_table_destroy(igorfile.meta);
if (igorfile.titles) {
g_ptr_array_foreach(igorfile.titles, (GFunc)g_free, NULL);
g_ptr_array_free(igorfile.titles, TRUE);
}
return container;
}
static void
gfilter_dialog(GFilterArgs *args,
GwyContainer *data,
GwyDataField *dfield,
GwyDataField *mfield,
gint id,
GQuark mquark)
{
GtkWidget *dialog, *table, *vbox, *hbox, *scwin, *hbox2, *label;
GtkTreeView *treeview;
GtkTreeSelection *selection;
GFilterControls controls;
gint response, row, i;
GwySIUnit *siunit;
GwyPixmapLayer *layer;
controls.args = args;
controls.mask = mfield;
controls.in_init = TRUE;
controls.computed = FALSE;
siunit = gwy_si_unit_new(NULL);
for (i = 0; i < NQUANTITIES; i++) {
controls.vf[i]
= gwy_si_unit_get_format_with_digits(siunit,
GWY_SI_UNIT_FORMAT_VFMARKUP,
1.0, 4, NULL);
}
g_object_unref(siunit);
dialog = gtk_dialog_new_with_buttons(_("Filter Grains"),
NULL, 0, NULL);
gtk_dialog_add_action_widget(GTK_DIALOG(dialog),
gwy_stock_like_button_new(_("_Update"),
GTK_STOCK_EXECUTE),
RESPONSE_PREVIEW);
gtk_dialog_add_button(GTK_DIALOG(dialog),
GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL);
gtk_dialog_add_button(GTK_DIALOG(dialog),
GTK_STOCK_OK, GTK_RESPONSE_OK);
gtk_dialog_set_default_response(GTK_DIALOG(dialog), GTK_RESPONSE_OK);
gtk_dialog_set_response_sensitive(GTK_DIALOG(dialog), RESPONSE_PREVIEW,
!args->update);
gwy_help_add_to_proc_dialog(GTK_DIALOG(dialog), GWY_HELP_DEFAULT);
controls.dialog = dialog;
hbox = gtk_hbox_new(FALSE, 2);
gtk_box_pack_start(GTK_BOX(GTK_DIALOG(dialog)->vbox), hbox, TRUE, TRUE, 4);
vbox = gtk_vbox_new(FALSE, 4);
gtk_box_pack_start(GTK_BOX(hbox), vbox, FALSE, FALSE, 4);
controls.mydata = gwy_container_new();
gwy_container_set_object_by_name(controls.mydata, "/0/data", dfield);
mfield = gwy_data_field_duplicate(mfield);
gwy_container_set_object_by_name(controls.mydata, "/0/mask", mfield);
g_object_unref(mfield);
gwy_app_sync_data_items(data, controls.mydata, id, 0, FALSE,
GWY_DATA_ITEM_PALETTE,
GWY_DATA_ITEM_MASK_COLOR,
GWY_DATA_ITEM_RANGE,
GWY_DATA_ITEM_REAL_SQUARE,
0);
controls.view = gwy_data_view_new(controls.mydata);
layer = gwy_layer_basic_new();
g_object_set(layer,
"data-key", "/0/data",
"gradient-key", "/0/base/palette",
"range-type-key", "/0/base/range-type",
"min-max-key", "/0/base",
NULL);
gwy_data_view_set_data_prefix(GWY_DATA_VIEW(controls.view), "/0/data");
gwy_data_view_set_base_layer(GWY_DATA_VIEW(controls.view), layer);
layer = gwy_layer_mask_new();
gwy_pixmap_layer_set_data_key(layer, "/0/mask");
gwy_layer_mask_set_color_key(GWY_LAYER_MASK(layer), "/0/mask");
gwy_data_view_set_alpha_layer(GWY_DATA_VIEW(controls.view), layer);
gwy_set_data_preview_size(GWY_DATA_VIEW(controls.view), PREVIEW_SIZE);
gtk_box_pack_start(GTK_BOX(vbox), controls.view, FALSE, FALSE, 0);
controls.update = gtk_check_button_new_with_mnemonic(_("I_nstant updates"));
gtk_toggle_button_set_active(GTK_TOGGLE_BUTTON(controls.update),
args->update);
gtk_box_pack_start(GTK_BOX(vbox), controls.update, FALSE, FALSE, 0);
g_signal_connect_swapped(controls.update, "toggled",
G_CALLBACK(update_changed), &controls);
hbox2 = gtk_hbox_new(FALSE, 6);
gtk_box_pack_start(GTK_BOX(vbox), hbox2, FALSE, FALSE, 0);
label = gtk_label_new_with_mnemonic(_("_Mask color:"));
gtk_box_pack_start(GTK_BOX(hbox2), label, FALSE, FALSE, 0);
controls.color_button = gwy_color_button_new();
gwy_color_button_set_use_alpha(GWY_COLOR_BUTTON(controls.color_button),
TRUE);
load_mask_color(controls.color_button,
gwy_data_view_get_data(GWY_DATA_VIEW(controls.view)));
gtk_label_set_mnemonic_widget(GTK_LABEL(label), controls.color_button);
gtk_box_pack_start(GTK_BOX(hbox2), controls.color_button, FALSE, FALSE, 0);
g_signal_connect(controls.color_button, "clicked",
G_CALLBACK(mask_color_changed), &controls);
table = gtk_table_new(10, 4, FALSE);
gtk_table_set_row_spacings(GTK_TABLE(table), 2);
gtk_table_set_col_spacings(GTK_TABLE(table), 6);
gtk_container_set_border_width(GTK_CONTAINER(table), 4);
gtk_box_pack_start(GTK_BOX(hbox), table, TRUE, TRUE, 4);
controls.table = table;
row = 0;
scwin = gtk_scrolled_window_new(NULL, NULL);
gtk_scrolled_window_set_policy(GTK_SCROLLED_WINDOW(scwin),
GTK_POLICY_NEVER, GTK_POLICY_AUTOMATIC);
gtk_table_attach(GTK_TABLE(table), scwin, 0, 4, row, row+1,
GTK_EXPAND | GTK_FILL, GTK_EXPAND | GTK_FILL, 0, 0);
controls.values = gwy_grain_value_tree_view_new(FALSE,
"name", "symbol_markup",
NULL);
treeview = GTK_TREE_VIEW(controls.values);
gtk_widget_set_size_request(scwin, -1, 120);
gtk_tree_view_set_headers_visible(treeview, FALSE);
selection = gtk_tree_view_get_selection(treeview);
gtk_tree_selection_set_mode(selection, GTK_SELECTION_BROWSE);
gwy_grain_value_tree_view_set_same_units(treeview, args->units_equal);
gwy_grain_value_tree_view_set_expanded_groups(treeview, args->expanded);
gtk_container_add(GTK_CONTAINER(scwin), controls.values);
row++;
hbox2 = gtk_hbox_new(FALSE, 0);
for (i = 0; i < NQUANTITIES; i++) {
gchar buf[2];
buf[0] = 'A' + i;
buf[1] = '\0';
controls.set_as[i] = gtk_button_new_with_label(buf);
gtk_box_pack_start(GTK_BOX(hbox2), controls.set_as[i], FALSE, FALSE, 0);
g_object_set_data(G_OBJECT(controls.set_as[i]),
"id", GUINT_TO_POINTER(i));
g_signal_connect_swapped(controls.set_as[i], "clicked",
G_CALLBACK(set_as_clicked), &controls);
}
gwy_table_attach_hscale(table, row++,
_("Set selected as:"), NULL,
GTK_OBJECT(hbox2), GWY_HSCALE_WIDGET_NO_EXPAND);
controls.logical_op
= gwy_enum_combo_box_newl(G_CALLBACK(logical_op_changed), &controls,
args->logical,
"A", GRAIN_LOGICAL_A,
"A ∧ B", GRAIN_LOGICAL_A_AND_B,
"A ∨ B", GRAIN_LOGICAL_A_OR_B,
"A ∧ B ∧ C", GRAIN_LOGICAL_A_AND_B_AND_C,
"A ∨ B ∨ C", GRAIN_LOGICAL_A_OR_B_OR_C,
"(A ∧ B) ∨ C", GRAIN_LOGICAL_A_AND_B_OR_C,
"(A ∨ B) ∧ C", GRAIN_LOGICAL_A_OR_B_AND_C,
NULL);
gwy_table_attach_hscale(table, row++,
_("Keep grains satisfying:"), NULL,
GTK_OBJECT(controls.logical_op),
GWY_HSCALE_WIDGET);
for (i = 0; i < NQUANTITIES; i++) {
gtk_table_set_row_spacing(GTK_TABLE(table), row-1, 8);
controls.header[i] = gtk_label_new(NULL);
gtk_misc_set_alignment(GTK_MISC(controls.header[i]), 0.0, 0.5);
gtk_table_attach(GTK_TABLE(table), controls.header[i],
0, 4, row, row+1, GTK_FILL, 0, 0, 0);
row++;
/* The values are set properly later. */
controls.lower_label[i] = gtk_label_new(_("Lower threshold:"));
gtk_misc_set_alignment(GTK_MISC(controls.lower_label[i]), 0.0, 0.5);
gtk_table_attach(GTK_TABLE(table), controls.lower_label[i],
0, 1, row, row+1, GTK_FILL, 0, 0, 0);
controls.lower[i] = gtk_adjustment_new(0.0, 0.0, 0.0,
1.0, 10.0, 0.0);
g_object_set_data(G_OBJECT(controls.lower[i]), "id",
GUINT_TO_POINTER(i));
g_signal_connect_swapped(controls.lower[i], "value-changed",
G_CALLBACK(threshold_changed), &controls);
controls.lower_scale[i]
= gtk_hscale_new(GTK_ADJUSTMENT(controls.lower[i]));
gtk_scale_set_draw_value(GTK_SCALE(controls.lower_scale[i]), FALSE);
gtk_widget_set_size_request(controls.lower_scale[i],
GWY_HSCALE_WIDTH, -1);
gtk_table_attach(GTK_TABLE(table), controls.lower_scale[i],
1, 2, row, row+1, GTK_EXPAND | GTK_FILL, 0, 0, 0);
controls.lower_entry[i] = gtk_entry_new();
gtk_entry_set_width_chars(GTK_ENTRY(controls.lower_entry[i]), 8);
gtk_table_attach(GTK_TABLE(table), controls.lower_entry[i],
2, 3, row, row+1, GTK_FILL, 0, 0, 0);
gwy_widget_set_activate_on_unfocus(controls.lower_entry[i], TRUE);
g_object_set_data(G_OBJECT(controls.lower_entry[i]), "id",
GUINT_TO_POINTER(i));
g_signal_connect_swapped(controls.lower_entry[i], "activate",
G_CALLBACK(threshold_activated), &controls);
controls.lower_units[i] = gtk_label_new(NULL);
gtk_misc_set_alignment(GTK_MISC(controls.lower_units[i]), 0.0, 0.5);
gtk_table_attach(GTK_TABLE(table), controls.lower_units[i],
3, 4, row, row+1, GTK_FILL, 0, 0, 0);
row++;
controls.upper_label[i] = gtk_label_new(_("Upper threshold:"));
gtk_misc_set_alignment(GTK_MISC(controls.upper_label[i]), 0.0, 0.5);
gtk_table_attach(GTK_TABLE(table), controls.upper_label[i],
0, 1, row, row+1, GTK_FILL, 0, 0, 0);
controls.upper[i] = gtk_adjustment_new(0.0, 0.0, 0.0,
1.0, 10.0, 0.0);
g_object_set_data(G_OBJECT(controls.upper[i]), "id",
GUINT_TO_POINTER(i | IS_UPPER));
g_signal_connect_swapped(controls.upper[i], "value-changed",
G_CALLBACK(threshold_changed), &controls);
controls.upper_scale[i]
= gtk_hscale_new(GTK_ADJUSTMENT(controls.upper[i]));
gtk_scale_set_draw_value(GTK_SCALE(controls.upper_scale[i]), FALSE);
gtk_widget_set_size_request(controls.upper_scale[i],
GWY_HSCALE_WIDTH, -1);
gtk_table_attach(GTK_TABLE(table), controls.upper_scale[i],
1, 2, row, row+1, GTK_EXPAND | GTK_FILL, 0, 0, 0);
controls.upper_entry[i] = gtk_entry_new();
gtk_entry_set_width_chars(GTK_ENTRY(controls.upper_entry[i]), 8);
gtk_table_attach(GTK_TABLE(table), controls.upper_entry[i],
2, 3, row, row+1, GTK_FILL, 0, 0, 0);
gwy_widget_set_activate_on_unfocus(controls.upper_entry[i], TRUE);
g_object_set_data(G_OBJECT(controls.upper_entry[i]), "id",
GUINT_TO_POINTER(i | IS_UPPER));
g_signal_connect_swapped(controls.upper_entry[i], "activate",
G_CALLBACK(threshold_activated), &controls);
controls.upper_units[i] = gtk_label_new(NULL);
gtk_misc_set_alignment(GTK_MISC(controls.upper_units[i]), 0.0, 0.5);
gtk_table_attach(GTK_TABLE(table), controls.upper_units[i],
3, 4, row, row+1, GTK_FILL, 0, 0, 0);
row++;
}
for (i = 0; i < NQUANTITIES; i++) {
GwyInventory *inventory;
GwyGrainValue *gvalue;
inventory = gwy_grain_values();
gvalue = gwy_inventory_get_item(inventory, args->ranges[i].quantity);
set_up_quantity(&controls, gvalue, i);
}
logical_op_changed(GTK_COMBO_BOX(controls.logical_op), &controls);
/* finished initializing, allow instant updates */
controls.in_init = FALSE;
gfilter_invalidate(&controls);
gtk_widget_show_all(dialog);
do {
response = gtk_dialog_run(GTK_DIALOG(dialog));
switch (response) {
case GTK_RESPONSE_CANCEL:
case GTK_RESPONSE_DELETE_EVENT:
args->expanded = gwy_grain_value_tree_view_get_expanded_groups
(GTK_TREE_VIEW(controls.values));
for (i = 0; i < NQUANTITIES; i++)
gwy_si_unit_value_format_free(controls.vf[i]);
gtk_widget_destroy(dialog);
case GTK_RESPONSE_NONE:
g_object_unref(controls.mydata);
gfilter_save_args(gwy_app_settings_get(), args);
return;
break;
case GTK_RESPONSE_OK:
break;
case RESPONSE_PREVIEW:
preview(&controls);
break;
default:
g_assert_not_reached();
break;
}
} while (response != GTK_RESPONSE_OK);
for (i = 0; i < NQUANTITIES; i++)
gwy_si_unit_value_format_free(controls.vf[i]);
args->expanded = gwy_grain_value_tree_view_get_expanded_groups
(GTK_TREE_VIEW(controls.values));
gwy_app_sync_data_items(controls.mydata, data, 0, id, FALSE,
GWY_DATA_ITEM_MASK_COLOR,
0);
gtk_widget_destroy(dialog);
gfilter_save_args(gwy_app_settings_get(), args);
if (controls.computed) {
mfield = gwy_container_get_object_by_name(controls.mydata, "/0/mask");
gwy_app_undo_qcheckpointv(data, 1, &mquark);
gwy_container_set_object(data, mquark, mfield);
g_object_unref(controls.mydata);
}
else {
g_object_unref(controls.mydata);
run_noninteractive(args, data, controls.mask, mquark);
}
gwy_app_channel_log_add_proc(data, id, id);
}
static void
cwt(GwyContainer *data, GwyRunType run)
{
GtkWidget *dialog;
GwyDataField *dfield;
CWTArgs args;
gboolean ok;
gint xsize, ysize;
gint newsize;
gint oldid, newid;
g_return_if_fail(run & CWT_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD, &dfield,
GWY_APP_DATA_FIELD_ID, &oldid,
0);
g_return_if_fail(dfield);
xsize = gwy_data_field_get_xres(dfield);
ysize = gwy_data_field_get_yres(dfield);
if (xsize != ysize) {
dialog = gtk_message_dialog_new
(gwy_app_find_window_for_channel(data, oldid),
GTK_DIALOG_DESTROY_WITH_PARENT,
GTK_MESSAGE_ERROR,
GTK_BUTTONS_OK,
_("%s: Data must be square."), "CWT");
gtk_dialog_run(GTK_DIALOG(dialog));
gtk_widget_destroy(dialog);
return;
}
cwt_load_args(gwy_app_settings_get(), &args);
if (run == GWY_RUN_INTERACTIVE) {
ok = cwt_dialog(&args);
cwt_save_args(gwy_app_settings_get(), &args);
if (!ok)
return;
}
dfield = gwy_data_field_duplicate(dfield);
newsize = gwy_fft_find_nice_size(xsize);
gwy_data_field_resample(dfield, newsize, newsize, args.interp);
gwy_data_field_cwt(dfield,
args.interp,
args.scale,
args.wavelet);
if (args.preserve)
gwy_data_field_resample(dfield, xsize, ysize, args.interp);
newid = gwy_app_data_browser_add_data_field(dfield, data, TRUE);
gwy_app_sync_data_items(data, data, oldid, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_MASK_COLOR,
0);
g_object_unref(dfield);
gwy_app_set_data_field_title(data, newid, _("CWT"));
}
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 void
immerse_do(ImmerseArgs *args)
{
GwyDataField *resampled, *image, *detail, *result;
GwyContainer *data;
gint newid;
gint kxres, kyres;
gint x, y, w, h;
gdouble iavg, davg;
GQuark quark;
data = gwy_app_data_browser_get(args->image.datano);
quark = gwy_app_get_data_key_for_id(args->image.id);
image = GWY_DATA_FIELD(gwy_container_get_object(data, quark));
data = gwy_app_data_browser_get(args->detail.datano);
quark = gwy_app_get_data_key_for_id(args->detail.id);
detail = GWY_DATA_FIELD(gwy_container_get_object(data, quark));
davg = gwy_data_field_get_avg(detail);
kxres = gwy_data_field_get_xres(detail);
kyres = gwy_data_field_get_yres(detail);
switch (args->sampling) {
case GWY_IMMERSE_SAMPLING_DOWN:
result = gwy_data_field_duplicate(image);
x = gwy_data_field_rtoj(image, args->xpos);
y = gwy_data_field_rtoi(image, args->ypos);
w = GWY_ROUND(gwy_data_field_get_xreal(detail)
/gwy_data_field_get_xmeasure(image));
h = GWY_ROUND(gwy_data_field_get_yreal(detail)
/gwy_data_field_get_ymeasure(image));
w = MAX(w, 1);
h = MAX(h, 1);
gwy_debug("w: %d, h: %d", w, h);
resampled = gwy_data_field_new_resampled(detail, w, h,
GWY_INTERPOLATION_LINEAR);
if (args->leveling == GWY_IMMERSE_LEVEL_MEAN) {
iavg = gwy_data_field_area_get_avg(result, NULL, x, y, w, h);
gwy_data_field_add(resampled, iavg - davg);
}
gwy_data_field_area_copy(resampled, result, 0, 0, w, h, x, y);
g_object_unref(resampled);
break;
case GWY_IMMERSE_SAMPLING_UP:
w = GWY_ROUND(gwy_data_field_get_xreal(image)
/gwy_data_field_get_xmeasure(detail));
h = GWY_ROUND(gwy_data_field_get_yreal(image)
/gwy_data_field_get_ymeasure(detail));
gwy_debug("w: %d, h: %d", w, h);
result = gwy_data_field_new_resampled(image, w, h,
GWY_INTERPOLATION_LINEAR);
x = gwy_data_field_rtoj(result, args->xpos);
y = gwy_data_field_rtoi(result, args->ypos);
if (args->leveling == GWY_IMMERSE_LEVEL_MEAN) {
iavg = gwy_data_field_area_get_avg(result, NULL,
x, y, kxres, kyres);
gwy_data_field_area_copy(detail, result, 0, 0, kxres, kyres, x, y);
gwy_data_field_area_add(result, x, y, kxres, kyres, iavg - davg);
}
else
gwy_data_field_area_copy(detail, result, 0, 0, kxres, kyres, x, y);
break;
default:
g_return_if_reached();
break;
}
gwy_app_data_browser_get_current(GWY_APP_CONTAINER, &data, 0);
newid = gwy_app_data_browser_add_data_field(result, data, TRUE);
gwy_app_set_data_field_title(data, newid, _("Immersed detail"));
g_object_unref(result);
gwy_app_channel_log_add_proc(data, args->image.id, newid);
}
/**
* gwy_data_field_correlate:
* @data_field: A data field.
* @kernel_field: Correlation kernel.
* @score: Data field to store correlation scores to.
* @method: Correlation score calculation method.
*
* Computes correlation score for all positions in a data field.
*
* Correlation score is compute for all points in data field @data_field
* and full size of correlation kernel @kernel_field.
*
* The points in @score correspond to centers of kernel. More precisely, the
* point ((@kxres-1)/2, (@kyres-1)/2) in @score corresponds to kernel field
* top left corner coincident with data field top left corner. Points outside
* the area where the kernel field fits into the data field completely are
* set to -1 for %GWY_CORRELATION_NORMAL.
**/
void
gwy_data_field_correlate(GwyDataField *data_field, GwyDataField *kernel_field,
GwyDataField *score, GwyCorrelationType method)
{
gint xres, yres, kxres, kyres, i, j, k, fftxres, fftyres;
GwyDataField *data_in_re, *data_out_re, *data_out_im;
GwyDataField *kernel_in_re, *kernel_out_re, *kernel_out_im;
gdouble norm;
g_return_if_fail(data_field != NULL && kernel_field != NULL);
xres = data_field->xres;
yres = data_field->yres;
kxres = kernel_field->xres;
kyres = kernel_field->yres;
if (kxres <= 0 || kyres <= 0) {
g_warning("Correlation kernel has nonpositive size.");
return;
}
switch (method) {
case GWY_CORRELATION_NORMAL:
gwy_data_field_fill(score, -1);
/*correlation request outside kernel */
if (kxres > xres || kyres > yres) {
return;
}
{
GwyDataField *avg, *rms;
gdouble s, davg, drms, kavg, krms;
gint xoff, yoff;
/* The number of pixels the correlation kernel extends to the
* negative direction */
xoff = (kxres - 1)/2;
yoff = (kyres - 1)/2;
kavg = gwy_data_field_get_avg(kernel_field);
krms = gwy_data_field_get_rms(kernel_field);
avg = gwy_data_field_duplicate(data_field);
rms = gwy_data_field_duplicate(data_field);
calculate_normalization(avg, rms, kxres, kyres);
for (i = yoff; i + kyres - yoff <= yres; i++) {
for (j = xoff; j + kxres - xoff <= xres; j++) {
k = i*xres + j;
davg = avg->data[k];
drms = rms->data[k];
if (!krms || !drms) {
score->data[k] = 0.0;
continue;
}
s = gwy_data_field_get_raw_correlation_score(data_field,
kernel_field,
j - xoff,
i - yoff,
0, 0,
kxres, kyres,
davg, kavg);
score->data[k] = s/(drms*krms);
}
}
g_object_unref(avg);
g_object_unref(rms);
}
break;
case GWY_CORRELATION_FFT:
case GWY_CORRELATION_POC:
fftxres = gwy_fft_find_nice_size(xres);
fftyres = gwy_fft_find_nice_size(yres);
data_in_re = gwy_data_field_new_resampled(data_field,
fftxres, fftyres,
GWY_INTERPOLATION_BILINEAR);
kernel_in_re = gwy_data_field_new_alike(data_field, TRUE);
gwy_data_field_area_copy(kernel_field, kernel_in_re,
0, 0, kernel_field->xres, kernel_field->yres,
kernel_in_re->xres/2 - kernel_field->xres/2,
kernel_in_re->yres/2 - kernel_field->yres/2);
gwy_data_field_resample(kernel_in_re, fftxres, fftyres,
GWY_INTERPOLATION_BILINEAR);
gwy_data_field_resample(score, fftxres, fftyres,
GWY_INTERPOLATION_NONE);
data_out_re = gwy_data_field_new_alike(data_in_re, TRUE);
data_out_im = gwy_data_field_new_alike(data_in_re, TRUE);
kernel_out_re = gwy_data_field_new_alike(data_in_re, TRUE);
kernel_out_im = gwy_data_field_new_alike(data_in_re, TRUE);
gwy_data_field_2dfft(data_in_re, NULL, data_out_re, data_out_im,
GWY_WINDOWING_NONE,
GWY_TRANSFORM_DIRECTION_FORWARD,
GWY_INTERPOLATION_BILINEAR, FALSE, FALSE);
gwy_data_field_2dfft(kernel_in_re, NULL, kernel_out_re, kernel_out_im,
GWY_WINDOWING_NONE,
GWY_TRANSFORM_DIRECTION_FORWARD,
GWY_INTERPOLATION_BILINEAR, FALSE, FALSE);
for (i = 0; i < fftxres*fftyres; i++) {
/*NOTE: now we construct new "complex field" from data
* and kernel fields, just to save memory*/
data_in_re->data[i] = data_out_re->data[i]*kernel_out_re->data[i]
+ data_out_im->data[i]*kernel_out_im->data[i];
kernel_in_re->data[i] = -data_out_re->data[i]*kernel_out_im->data[i]
+ data_out_im->data[i]*kernel_out_re->data[i];
if (method == GWY_CORRELATION_POC) {
norm = hypot(data_in_re->data[i], kernel_in_re->data[i]);
data_in_re->data[i] /= norm;
kernel_in_re->data[i] /= norm;
}
}
gwy_data_field_2dfft(data_in_re, kernel_in_re, score, data_out_im,
GWY_WINDOWING_NONE,
GWY_TRANSFORM_DIRECTION_BACKWARD,
GWY_INTERPOLATION_BILINEAR, FALSE, FALSE);
gwy_data_field_2dfft_humanize(score);
/*TODO compute it and put to score field*/
g_object_unref(data_in_re);
g_object_unref(data_out_re);
g_object_unref(data_out_im);
g_object_unref(kernel_in_re);
g_object_unref(kernel_out_re);
g_object_unref(kernel_out_im);
break;
}
gwy_data_field_invalidate(score);
}
static void
maskcor_do(MaskcorArgs *args)
{
enum { WORK_PER_UPDATE = 50000000 };
GwyDataField *dfield, *kernel, *retfield, *score;
GwyContainer *data, *kerneldata;
GwyComputationState *state;
GQuark quark;
gint newid, work, wpi;
kerneldata = gwy_app_data_browser_get(args->kernel.datano);
quark = gwy_app_get_data_key_for_id(args->kernel.id);
kernel = GWY_DATA_FIELD(gwy_container_get_object(kerneldata, quark));
data = gwy_app_data_browser_get(args->data.datano);
quark = gwy_app_get_data_key_for_id(args->data.id);
dfield = GWY_DATA_FIELD(gwy_container_get_object(data, quark));
retfield = gwy_data_field_new_alike(dfield, FALSE);
/* FIXME */
if (args->method == GWY_CORRELATION_NORMAL) {
gwy_app_wait_start(gwy_app_find_window_for_channel(data, args->data.id),
_("Initializing..."));
state = gwy_data_field_correlate_init(dfield, kernel, retfield);
gwy_app_wait_set_message(_("Correlating..."));
work = 0;
wpi = gwy_data_field_get_xres(kernel)*gwy_data_field_get_yres(kernel);
wpi = MIN(wpi, WORK_PER_UPDATE);
do {
gwy_data_field_correlate_iteration(state);
work += wpi;
if (work > WORK_PER_UPDATE) {
work -= WORK_PER_UPDATE;
if (!gwy_app_wait_set_fraction(state->fraction)) {
gwy_data_field_correlate_finalize(state);
gwy_app_wait_finish();
g_object_unref(retfield);
return;
}
}
} while (state->state != GWY_COMPUTATION_STATE_FINISHED);
gwy_data_field_correlate_finalize(state);
gwy_app_wait_finish();
}
else
gwy_data_field_correlate(dfield, kernel, retfield, args->method);
/* score - do new data with score */
if (args->result == GWY_MASKCOR_SCORE) {
score = gwy_data_field_duplicate(retfield);
newid = gwy_app_data_browser_add_data_field(score, data, TRUE);
gwy_app_sync_data_items(data, data,
args->data.id, newid, FALSE,
GWY_DATA_ITEM_GRADIENT, 0);
gwy_app_set_data_field_title(data, newid,
_("Correlation score"));
g_object_unref(score);
gwy_app_channel_log_add_proc(data, args->data.id, newid);
}
else {
/* add mask */
quark = gwy_app_get_mask_key_for_id(args->data.id);
gwy_app_undo_qcheckpointv(data, 1, &quark);
if (args->result == GWY_MASKCOR_OBJECTS)
plot_correlated(retfield,
gwy_data_field_get_xres(kernel),
gwy_data_field_get_yres(kernel),
args->threshold);
else if (args->result == GWY_MASKCOR_MAXIMA)
gwy_data_field_threshold(retfield, args->threshold, 0.0, 1.0);
gwy_container_set_object(data, quark, retfield);
gwy_app_channel_log_add_proc(data, args->data.id, args->data.id);
}
g_object_unref(retfield);
}
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 void
rotate(GwyContainer *data, GwyRunType run)
{
GwyDataField *dfields[3];
GQuark quark;
gint oldid, newid;
RotateArgs args;
gboolean ok;
g_return_if_fail(run & ROTATE_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_ID, &oldid,
0);
g_return_if_fail(dfields[0]);
rotate_load_args(gwy_app_settings_get(), &args);
if (run == GWY_RUN_INTERACTIVE) {
ok = rotate_dialog(&args, data);
rotate_save_args(gwy_app_settings_get(), &args);
if (!ok)
return;
}
dfields[0] = gwy_data_field_duplicate(dfields[0]);
rotate_datafield(dfields[0], &args);
if (dfields[1]) {
GwyInterpolationType interp = args.interp;
dfields[1] = gwy_data_field_duplicate(dfields[1]);
args.interp = GWY_INTERPOLATION_ROUND;
rotate_datafield(dfields[1], &args);
args.interp = interp;
}
if (dfields[2]) {
dfields[2] = gwy_data_field_duplicate(dfields[2]);
rotate_datafield(dfields[2], &args);
}
newid = gwy_app_data_browser_add_data_field(dfields[0], data, TRUE);
g_object_unref(dfields[0]);
gwy_app_sync_data_items(data, data, oldid, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_RANGE,
GWY_DATA_ITEM_MASK_COLOR,
0);
if (dfields[1]) {
quark = gwy_app_get_mask_key_for_id(newid);
gwy_container_set_object(data, quark, dfields[1]);
g_object_unref(dfields[1]);
}
if (dfields[2]) {
quark = gwy_app_get_show_key_for_id(newid);
gwy_container_set_object(data, quark, dfields[2]);
g_object_unref(dfields[2]);
}
gwy_app_set_data_field_title(data, newid, _("Rotated Data"));
gwy_app_channel_log_add_proc(data, oldid, newid);
}
static void
square_samples(GwyContainer *data, GwyRunType run)
{
GwyDataField *dfield, *dfields[3];
gdouble xreal, yreal, qx, qy;
gint oldid, newid, xres, yres;
GQuark quark;
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_ID, &oldid,
0);
dfield = dfields[0];
xres = gwy_data_field_get_xres(dfield);
yres = gwy_data_field_get_yres(dfield);
xreal = gwy_data_field_get_xreal(dfield);
yreal = gwy_data_field_get_yreal(dfield);
qx = xres/xreal;
qy = yres/yreal;
if (fabs(log(qx/qy)) > 1.0/hypot(xres, yres)) {
/* Resample */
if (qx < qy)
xres = MAX(GWY_ROUND(xreal*qy), 1);
else
yres = MAX(GWY_ROUND(yreal*qx), 1);
dfields[0] = gwy_data_field_new_resampled(dfields[0], xres, yres,
GWY_INTERPOLATION_BSPLINE);
if (dfields[1]) {
dfields[1]
= gwy_data_field_new_resampled(dfields[1], xres, yres,
GWY_INTERPOLATION_ROUND);
}
if (dfields[2]) {
dfields[2]
= gwy_data_field_new_resampled(dfields[2], xres, yres,
GWY_INTERPOLATION_BSPLINE);
}
}
else {
/* Ratios are equal, just duplicate */
dfields[0] = gwy_data_field_duplicate(dfields[0]);
if (dfields[1])
dfields[1] = gwy_data_field_duplicate(dfields[1]);
if (dfields[2])
dfields[2] = gwy_data_field_duplicate(dfields[2]);
}
newid = gwy_app_data_browser_add_data_field(dfields[0], data, TRUE);
g_object_unref(dfields[0]);
gwy_app_sync_data_items(data, data, oldid, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_RANGE,
GWY_DATA_ITEM_MASK_COLOR,
0);
if (dfields[1]) {
quark = gwy_app_get_mask_key_for_id(newid);
gwy_container_set_object(data, quark, dfields[1]);
g_object_unref(dfields[1]);
}
if (dfields[2]) {
quark = gwy_app_get_show_key_for_id(newid);
gwy_container_set_object(data, quark, dfields[2]);
g_object_unref(dfields[2]);
}
gwy_app_channel_log_add_proc(data, oldid, newid);
}
/**
* proc_plugin_proxy_run:
* @data: A data container.
* @run: Run mode.
* @name: Plug-in name (i.e. data processing function) to run.
*
* The plug-in proxy itself, runs plug-in @name on @data.
*
* Returns: Whether it succeeded running the plug-in.
**/
static void
proc_plugin_proxy_run(GwyContainer *data,
GwyRunType run,
const gchar *name)
{
ProcPluginInfo *info;
GwyContainer *newdata;
gchar *filename, *buffer = NULL;
GError *err = NULL;
gint exit_status, id, newid;
gsize size = 0;
FILE *fh;
gchar *args[] = { NULL, "run", NULL, NULL, NULL };
GQuark dquark, mquark, squark;
gboolean ok;
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD_KEY, &dquark,
GWY_APP_MASK_FIELD_KEY, &mquark,
GWY_APP_DATA_FIELD_ID, &id,
0);
gwy_debug("called as %s with run mode %d", name, run);
if (!(info = proc_find_plugin(name, run)))
return;
fh = text_dump_export(data, dquark, mquark, &filename, NULL);
g_return_if_fail(fh);
args[0] = info->file;
args[2] = g_strdup(gwy_enum_to_string(run, run_mode_names, -1));
args[3] = decode_glib_encoded_filename(filename);
gwy_debug("%s %s %s %s", args[0], args[1], args[2], args[3]);
ok = g_spawn_sync(NULL, args, NULL, 0, NULL, NULL,
NULL, NULL, &exit_status, &err);
if (!err)
ok &= g_file_get_contents(filename, &buffer, &size, &err);
g_unlink(filename);
fclose(fh);
gwy_debug("ok = %d, exit_status = %d, err = %p", ok, exit_status, err);
ok &= !exit_status;
if (ok && (newdata = text_dump_import(buffer, size, NULL))) {
GwyDataField *dfield;
/* Merge data */
if (gwy_container_gis_object_by_name(newdata, "/0/data", &dfield))
g_object_ref(dfield);
else {
dfield = gwy_container_get_object(data, dquark);
dfield = gwy_data_field_duplicate(dfield);
}
newid = gwy_app_data_browser_add_data_field(dfield, data, TRUE);
/* Merge mask */
if (gwy_container_gis_object_by_name(newdata, "/0/mask", &dfield))
g_object_ref(dfield);
else if (gwy_container_gis_object(data, mquark, &dfield))
dfield = gwy_data_field_duplicate(dfield);
else
dfield = NULL;
if (dfield) {
mquark = gwy_app_get_mask_key_for_id(newid);
gwy_container_set_object(data, mquark, dfield);
g_object_unref(dfield);
}
/* Merge presentation */
if (gwy_container_gis_object_by_name(newdata, "/0/show", &dfield)) {
squark = gwy_app_get_show_key_for_id(newid);
gwy_container_set_object(data, squark, dfield);
}
/* Merge stuff. XXX: This is brutal and incomplete. */
gwy_app_sync_data_items(data, data, id, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_RANGE_TYPE,
GWY_DATA_ITEM_MASK_COLOR,
GWY_DATA_ITEM_REAL_SQUARE,
0);
gwy_app_sync_data_items(newdata, data, 0, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_RANGE_TYPE,
0);
g_object_unref(newdata);
}
else {
g_warning("Cannot run plug-in %s: %s",
info->file,
err ? err->message : "it returned garbage.");
}
g_free(args[3]);
g_free(args[2]);
g_clear_error(&err);
g_free(buffer);
g_free(filename);
}
static void
dwt_denoise(GwyContainer *data, GwyRunType run)
{
GtkWidget *dialog;
GwyDataField *dfield;
GwyDataLine *wtcoefs;
DWTDenoiseArgs args;
gboolean ok;
gint xsize, ysize, newsize;
gint oldid, newid;
g_return_if_fail(run & DWT_DENOISE_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD, &dfield,
GWY_APP_DATA_FIELD_ID, &oldid,
0);
g_return_if_fail(dfield);
xsize = gwy_data_field_get_xres(dfield);
ysize = gwy_data_field_get_yres(dfield);
if (xsize != ysize) {
dialog = gtk_message_dialog_new
(GTK_WINDOW(gwy_app_data_window_get_current()),
GTK_DIALOG_DESTROY_WITH_PARENT,
GTK_MESSAGE_ERROR,
GTK_BUTTONS_OK,
_("%s: Data must be square."), _("DWT Denoise"));
gtk_dialog_run(GTK_DIALOG(dialog));
gtk_widget_destroy(dialog);
return;
}
dwt_denoise_load_args(gwy_app_settings_get(), &args);
if (run == GWY_RUN_INTERACTIVE) {
ok = dwt_denoise_dialog(&args);
dwt_denoise_save_args(gwy_app_settings_get(), &args);
if (!ok)
return;
}
dfield = gwy_data_field_duplicate(dfield);
newsize = gwy_fft_find_nice_size(xsize);
gwy_data_field_add(dfield, -gwy_data_field_get_avg(dfield));
gwy_data_field_resample(dfield, newsize, newsize,
GWY_INTERPOLATION_BILINEAR);
wtcoefs = gwy_data_line_new(10, 10, TRUE);
wtcoefs = gwy_dwt_set_coefficients(wtcoefs, args.wavelet);
gwy_data_field_dwt_denoise(dfield, wtcoefs, TRUE, 20, args.method);
if (args.preserve)
gwy_data_field_resample(dfield, xsize, ysize, args.interp);
newid = gwy_app_data_browser_add_data_field(dfield, data, TRUE);
gwy_app_copy_data_items(data, data, oldid, newid,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_MASK_COLOR,
0);
g_object_unref(dfield);
gwy_app_set_data_field_title(data, newid, _("DWT denoised"));
g_object_unref(wtcoefs);
}
static void
deposit_dialog(DepositArgs *args,
GwyContainer *data,
GwyDataField *dfield,
gint id)
{
GtkWidget *dialog, *table, *hbox, *label, *pivot;
DepositControls controls;
gint response;
GwyPixmapLayer *layer;
gint row, newid;
GwyDataField *rfield;
controls.args = args;
dialog = gtk_dialog_new_with_buttons(_("Deposit spherical particles"), NULL, 0,
NULL);
gtk_dialog_add_action_widget(GTK_DIALOG(dialog),
gwy_stock_like_button_new(_("_Start"),
GTK_STOCK_EXECUTE),
RESPONSE_PREVIEW);
gtk_dialog_add_button(GTK_DIALOG(dialog), _("_Reset"), RESPONSE_RESET);
gtk_dialog_add_button(GTK_DIALOG(dialog),
GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL);
gtk_dialog_add_button(GTK_DIALOG(dialog),
GTK_STOCK_OK, GTK_RESPONSE_OK);
gtk_dialog_set_has_separator(GTK_DIALOG(dialog), FALSE);
gtk_dialog_set_default_response(GTK_DIALOG(dialog), GTK_RESPONSE_OK);
controls.dialog = dialog;
hbox = gtk_hbox_new(FALSE, 2);
gtk_box_pack_start(GTK_BOX(GTK_DIALOG(dialog)->vbox), hbox,
FALSE, FALSE, 4);
controls.mydata = gwy_container_duplicate_by_prefix(data,
"/0/data/",
"/0/base/palette",
"/0/base/range-type",
"/0/base/", NULL);
gwy_container_set_object_by_name(controls.mydata, "/0/data", gwy_data_field_duplicate(dfield));
controls.old_dfield = gwy_data_field_duplicate(dfield);
controls.view = gwy_data_view_new(controls.mydata);
layer = gwy_layer_basic_new();
g_object_set(layer,
"data-key", "/0/data",
"gradient-key", "/0/base/palette",
"range-type-key", "/0/base/range-type",
"min-max-key", "/0/base",
NULL);
gwy_data_view_set_data_prefix(GWY_DATA_VIEW(controls.view), "/0/data");
gwy_data_view_set_base_layer(GWY_DATA_VIEW(controls.view), layer);
gwy_set_data_preview_size(GWY_DATA_VIEW(controls.view), PREVIEW_SIZE);
gtk_box_pack_start(GTK_BOX(hbox), controls.view, FALSE, FALSE, 4);
table = gtk_table_new(10, 4, FALSE);
gtk_table_set_row_spacings(GTK_TABLE(table), 2);
gtk_table_set_col_spacings(GTK_TABLE(table), 6);
gtk_container_set_border_width(GTK_CONTAINER(table), 4);
gtk_box_pack_start(GTK_BOX(hbox), table, TRUE, TRUE, 4);
row = 0;
gtk_table_attach(GTK_TABLE(table), gwy_label_new_header(_("Deposition parameters:")),
0, 3, row, row+1, GTK_EXPAND | GTK_FILL, 0, 0, 0);
row++;
table_attach_threshold(table, &row, _("_Size"),
&controls.size, args->size,
&controls);
pivot = gwy_table_hscale_get_scale(controls.size);
controls.value_size = gtk_label_new(NULL);
gtk_misc_set_alignment(GTK_MISC(controls.value_size), 1.0, 0.5);
gtk_table_attach(GTK_TABLE(table), controls.value_size,
2, 3, row, row+1, GTK_FILL, 0, 0, 0);
g_signal_connect_swapped(controls.size, "value-changed",
G_CALLBACK(update_threshold_size), &controls);
gwy_widget_sync_sensitivity(pivot, controls.value_size);
controls.format_size
= gwy_data_field_get_value_format_z(dfield, GWY_SI_UNIT_FORMAT_VFMARKUP,
NULL);
label = gtk_label_new(NULL);
gtk_misc_set_alignment(GTK_MISC(label), 0.0, 0.5);
gtk_label_set_markup(GTK_LABEL(label), controls.format_size->units);
gtk_table_attach(GTK_TABLE(table), label,
3, 4, row, row+1, GTK_FILL, 0, 0, 0);
gwy_widget_sync_sensitivity(pivot, label);
gtk_table_set_row_spacing(GTK_TABLE(table), row, 8);
row++;
/*
table_attach_threshold(table, &row, _("_Distribution width"),
&controls.width, args->width,
&controls);
pivot = gwy_table_hscale_get_scale(controls.width);
controls.value_width = gtk_label_new(NULL);
gtk_misc_set_alignment(GTK_MISC(controls.value_width), 1.0, 0.5);
gtk_table_attach(GTK_TABLE(table), controls.value_width,
2, 3, row, row+1, GTK_FILL, 0, 0, 0);
g_signal_connect_swapped(controls.width, "value-changed",
G_CALLBACK(update_threshold_width), &controls);
gwy_widget_sync_sensitivity(pivot, controls.value_width);
controls.format_width
= gwy_data_field_get_value_format_z(dfield, GWY_SI_UNIT_FORMAT_VFMARKUP,
NULL);
label = gtk_label_new(NULL);
gtk_misc_set_alignment(GTK_MISC(label), 0.0, 0.5);
gtk_label_set_markup(GTK_LABEL(label), controls.format_width->units);
gtk_table_attach(GTK_TABLE(table), label,
3, 4, row, row+1, GTK_FILL, 0, 0, 0);
gwy_widget_sync_sensitivity(pivot, label);
gtk_table_set_row_spacing(GTK_TABLE(table), row, 8);
row++;
*/
table_attach_threshold(table, &row, _("_Coverage:"),
&controls.coverage, args->coverage,
&controls);
table_attach_threshold(table, &row, _("_Revise after settle"),
&controls.revise, args->revise,
&controls);
gtk_table_set_row_spacing(GTK_TABLE(table), row-1, 8);
deposit_invalidate(&controls);
update_threshold_size(&controls);
//update_threshold_width(&controls);
/* finished initializing, allow instant updates */
controls.in_init = FALSE;
/* show initial preview if instant updates are on */
gtk_widget_show_all(dialog);
do {
response = gtk_dialog_run(GTK_DIALOG(dialog));
switch (response) {
case GTK_RESPONSE_CANCEL:
case GTK_RESPONSE_DELETE_EVENT:
deposit_dialog_update_values(&controls, args);
gtk_widget_destroy(dialog);
case GTK_RESPONSE_NONE:
g_object_unref(controls.mydata);
gwy_si_unit_value_format_free(controls.format_size);
//gwy_si_unit_value_format_free(controls.format_width);
return;
break;
case GTK_RESPONSE_OK:
break;
case RESPONSE_RESET:
*args = deposit_defaults;
deposit_dialog_update_controls(&controls, args);
controls.in_init = TRUE;
preview(&controls, args);
controls.in_init = FALSE;
break;
case RESPONSE_PREVIEW:
deposit_dialog_update_values(&controls, args);
preview(&controls, args);
break;
default:
g_assert_not_reached();
break;
}
} while (response != GTK_RESPONSE_OK);
deposit_dialog_update_values(&controls, args);
gwy_app_sync_data_items(controls.mydata, data, 0, id, FALSE,
GWY_DATA_ITEM_MASK_COLOR,
0);
gtk_widget_destroy(dialog);
gwy_si_unit_value_format_free(controls.format_size);
//gwy_si_unit_value_format_free(controls.format_width);
if (args->computed) {
rfield = gwy_container_get_object_by_name(controls.mydata, "/0/data");
newid = gwy_app_data_browser_add_data_field(rfield,
data, TRUE);
gwy_app_sync_data_items(data, data,
id, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
GWY_DATA_ITEM_MASK_COLOR,
GWY_DATA_ITEM_REAL_SQUARE,
GWY_DATA_ITEM_SELECTIONS,
0);
gwy_app_set_data_field_title(data, newid, _("Particles"));
g_object_unref(controls.mydata);
}
}
static GwyDataField*
sphrev_vertical(Sphrev1DArgs *args,
GwyDataField *dfield)
{
GwyDataField *rfield;
GwyDataLine *sphere;
gdouble *data, *rdata, *sphdata, *sum, *sum2, *weight, *tmp;
gdouble q;
gint i, j, k, size, xres, yres;
data = gwy_data_field_get_data(dfield);
rfield = gwy_data_field_duplicate(dfield);
xres = gwy_data_field_get_xres(rfield);
yres = gwy_data_field_get_yres(rfield);
rdata = gwy_data_field_get_data(rfield);
q = gwy_data_field_get_rms(dfield)/sqrt(2.0/3.0 - G_PI/16.0);
sphere = sphrev_make_sphere(args->size, gwy_data_field_get_yres(dfield));
/* Scale-freeing.
* Data is normalized to have the same RMS as if it was composed from
* spheres of radius args->radius. Actually we normalize the sphere
* instead, but the effect is the same. */
gwy_data_line_multiply(sphere, -q);
sphdata = gwy_data_line_get_data(sphere);
size = gwy_data_line_get_res(sphere)/2;
sum = g_new(gdouble, 4*yres);
sum2 = sum + yres;
weight = sum + 2*yres;
tmp = sum + 3*yres;
/* Weights for RMS filter. The xresl-proof way is to sum 1's. */
for (j = 0; j < yres; j++)
weight[j] = 1.0;
moving_sums(yres, weight, sum, size);
memcpy(weight, sum, yres*sizeof(gdouble));
for (i = 0; i < xres; i++) {
gdouble *rcol = rdata + i;
gdouble *dcol = data + i;
/* Kill data that stick down too much */
for (j = 0; j < yres; j++)
tmp[j] = dcol[j*xres];
moving_sums(yres, tmp, sum, size);
for (j = 0; j < yres; j++) {
/* transform to avg - 2.5*rms */
sum[j] = sum[j]/weight[j];
sum2[j] = 2.5*sqrt(sum2[j]/weight[j] - sum[j]*sum[j]);
sum[j] -= sum2[j];
}
for (j = 0; j < yres; j++)
tmp[j] = MAX(dcol[j*xres], sum[j]);
/* Find the touching point */
for (j = 0; j < yres; j++) {
gdouble *col = tmp + j;
gint from, to, km;
gdouble min;
from = MAX(0, j-size) - j;
to = MIN(j+size, yres-1) - j;
min = G_MAXDOUBLE;
km = 0;
for (k = from; k <= to; k++) {
if (-(sphdata[size+k] - col[k]) < min) {
min = -(sphdata[size+k] - col[k]);
km = k;
}
}
rcol[j*xres] = min;
}
}
g_free(sum);
g_object_unref(sphere);
return rfield;
}
static void
do_level(GwyContainer *data,
GwyRunType run,
LevelMethod level_type,
const gchar *dialog_title)
{
GwyDataField *dfield;
GwyDataField *mfield;
LevelArgs args;
gdouble c, bx, by;
GQuark quark;
gint id;
g_return_if_fail(run & LEVEL_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD_KEY, &quark,
GWY_APP_DATA_FIELD, &dfield,
GWY_APP_DATA_FIELD_ID, &id,
GWY_APP_MASK_FIELD, &mfield,
0);
g_return_if_fail(dfield && quark);
load_args(gwy_app_settings_get(), &args);
if (run != GWY_RUN_IMMEDIATE && mfield) {
gboolean ok = level_dialog(&args, dialog_title);
save_args(gwy_app_settings_get(), &args);
if (!ok)
return;
}
if (args.masking == GWY_MASK_IGNORE)
mfield = NULL;
if (mfield) {
if (args.masking == GWY_MASK_EXCLUDE) {
mfield = gwy_data_field_duplicate(mfield);
gwy_data_field_multiply(mfield, -1.0);
gwy_data_field_add(mfield, 1.0);
}
else
g_object_ref(mfield);
}
gwy_app_undo_qcheckpoint(data, quark, NULL);
if (mfield)
gwy_data_field_area_fit_plane(dfield, mfield, 0, 0,
gwy_data_field_get_xres(dfield),
gwy_data_field_get_yres(dfield),
&c, &bx, &by);
else
gwy_data_field_fit_plane(dfield, &c, &bx, &by);
switch (level_type) {
case LEVEL_SUBTRACT:
c = -0.5*(bx*gwy_data_field_get_xres(dfield)
+ by*gwy_data_field_get_yres(dfield));
gwy_data_field_plane_level(dfield, c, bx, by);
break;
case LEVEL_ROTATE:
bx = gwy_data_field_rtoj(dfield, bx);
by = gwy_data_field_rtoi(dfield, by);
gwy_data_field_plane_rotate(dfield, atan2(bx, 1), atan2(by, 1),
GWY_INTERPOLATION_LINEAR);
gwy_debug("b = %g, alpha = %g deg, c = %g, beta = %g deg",
bx, 180/G_PI*atan2(bx, 1), by, 180/G_PI*atan2(by, 1));
break;
default:
g_assert_not_reached();
break;
}
gwy_app_channel_log_add_proc(data, id, id);
gwy_data_field_data_changed(dfield);
gwy_object_unref(mfield);
}
static void
run_noninteractive(NoiseSynthArgs *args,
const GwyDimensionArgs *dimsargs,
GwyContainer *data,
GwyDataField *dfield,
gint oldid,
GQuark quark)
{
GwySIUnit *siunit;
gboolean replace = dimsargs->replace && dfield;
gboolean add = dimsargs->add && dfield;
gint newid;
if (args->randomize)
args->seed = g_random_int() & 0x7fffffff;
if (replace) {
/* Always take a reference so that we can always unref. */
g_object_ref(dfield);
gwy_app_undo_qcheckpointv(data, 1, &quark);
if (!add)
gwy_data_field_clear(dfield);
gwy_app_channel_log_add_proc(data, oldid, oldid);
}
else {
if (add)
dfield = gwy_data_field_duplicate(dfield);
else {
gdouble mag = pow10(dimsargs->xypow10) * dimsargs->measure;
dfield = gwy_data_field_new(dimsargs->xres, dimsargs->yres,
mag*dimsargs->xres, mag*dimsargs->yres,
TRUE);
siunit = gwy_data_field_get_si_unit_xy(dfield);
gwy_si_unit_set_from_string(siunit, dimsargs->xyunits);
siunit = gwy_data_field_get_si_unit_z(dfield);
gwy_si_unit_set_from_string(siunit, dimsargs->zunits);
}
}
noise_synth_do(args, dimsargs, dfield);
if (replace)
gwy_data_field_data_changed(dfield);
else {
if (data) {
newid = gwy_app_data_browser_add_data_field(dfield, data, TRUE);
if (oldid != -1)
gwy_app_sync_data_items(data, data, oldid, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
0);
}
else {
newid = 0;
data = gwy_container_new();
gwy_container_set_object(data, gwy_app_get_data_key_for_id(newid),
dfield);
gwy_app_data_browser_add(data);
gwy_app_data_browser_reset_visibility(data,
GWY_VISIBILITY_RESET_SHOW_ALL);
g_object_unref(data);
}
gwy_app_set_data_field_title(data, newid, _("Generated"));
gwy_app_channel_log_add_proc(data, add ? oldid : -1, newid);
}
g_object_unref(dfield);
}
