static GwySpectra*
omicron_read_cs_data(OmicronFile *ofile,
OmicronSpectroChannel *channel,
GError **error)
{
GError *err = NULL;
GwyDataLine *dline;
GwySIUnit *siunit = NULL, *coord_unit = NULL;
GwySpectra *spectra = NULL;
GPtrArray *spectrum = NULL;
gchar *filename;
gdouble *data, x, y;
gdouble *coords = NULL;
gchar *buffer;
gdouble scale;
guint i, j;
gint power10 = 0;
gint ncurves = 0;
gchar* line;
filename = omicron_fix_file_name(ofile->filename, channel->filename, error);
if (!filename)
return NULL;
gwy_debug("Succeeded with <%s>", filename);
if (!g_file_get_contents(filename, &buffer, NULL , &err)) {
g_free(filename);
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
g_free(filename);
scale = channel->resolution; /* can also be extracted from min&max
raw and phys settings */
while ((line = gwy_str_next_line(&buffer))) {
if (strstr(line, ";n_curves")) {
/* Find number of curves this should appear first in file */
ncurves = g_ascii_strtod(strchr(line, ':')+1, NULL);
}
if (strstr(line, "BEGIN COORD")) {
/* Read in cordinates Spectroscopy Curves */
i = 0;
coord_unit = gwy_si_unit_new_parse("nm", &power10);
while ((line = gwy_str_next_line(&buffer))) {
gchar *val2;
if (strstr(line, "END")) {
if (i != ncurves) {
gwy_debug("Less coords than ncurves");
}
break;
}
if (i == ncurves) {
g_critical("More coords than ncurves.");
break;
}
if (!coords) {
if (!(coords = g_new0(gdouble, ncurves*2))) {
gwy_debug("Failed to allocate mem: coords");
return NULL;
}
}
val2 = line+16;
x = g_ascii_strtod(line, &val2) * pow10(power10);
y = g_ascii_strtod(val2, NULL) * pow10(power10);
gwy_debug("Coord %i: x:%g y:%g", i, x, y);
coords[2*i] = x;
coords[2*i+1] = y;
i++;
}
/* i is set to 0 and used as a counter for the dline */
i = 0;
}
if (strstr(line, "BEGIN") && !strstr(line, "COORD")) {
/* Read spectroscopy points */
dline = gwy_data_line_new(channel->npoints,
channel->end - channel->start,
FALSE);
gwy_data_line_set_offset(dline, (channel->start));
data = gwy_data_line_get_data(dline);
j = 0;
while ((line = gwy_str_next_line(&buffer))) {
gchar *val2;
if (strstr(line, "END") || j >= channel->npoints)
break;
val2 = line+13;
x = g_ascii_strtod(line, &val2);
y = g_ascii_strtod(val2, NULL)*scale;
data[j] = y;
j++;
}
/* Set Units for the parameter (x) axis */
if ((channel->param[0] == 'V') || (channel->param[0] == 'E')) {
siunit = gwy_si_unit_new("V");
power10 = 0;
}
else if (channel->param[0] == 'I')
siunit = gwy_si_unit_new_parse("nA", &power10);
else if (channel->param[0] == 'Z')
siunit = gwy_si_unit_new_parse("nm", &power10);
else {
gwy_debug("Parameter unit not recognised");
}
if (siunit) {
gwy_data_line_set_si_unit_x(dline, siunit);
g_object_unref(siunit);
}
if (power10) {
gdouble offset = 0;
gdouble realsize = 0;
offset = gwy_data_line_get_offset(dline)*pow10(power10);
realsize = gwy_data_line_get_real(dline)*pow10(power10);
gwy_data_line_set_offset(dline, offset);
gwy_data_line_set_real(dline, realsize);
}
/* Set Units for the Value (y) Axis */
siunit = gwy_si_unit_new_parse(channel->units, &power10);
gwy_data_line_set_si_unit_y(dline, siunit);
g_object_unref(siunit);
if (power10)
gwy_data_line_multiply(dline, pow10(power10));
if (!spectrum)
spectrum = g_ptr_array_sized_new(ncurves);
g_ptr_array_add(spectrum, dline);
}
}
if (!spectrum)
spectrum = g_ptr_array_new();
if (spectrum->len < ncurves) {
gwy_debug("Less actual spectra than ncurves");
ncurves = spectrum->len;
}
if (spectrum->len > ncurves) {
gwy_debug("More actual spectra than ncurves, "
"remaining pos will be set at (0.0,0.0)");
coords = g_renew(gdouble, coords, spectrum->len*2);
if (!coords) {
g_critical("Could not reallocate mem for coords.");
return NULL;
}
while (spectrum->len > ncurves) {
coords[ncurves*2] = 0.0;
coords[ncurves*2+1] = 0.0;
ncurves++;
}
}
spectra = gwy_spectra_new();
if (coord_unit) {
gwy_spectra_set_si_unit_xy(spectra, coord_unit);
g_object_unref(coord_unit);
}
for (i = 0; i < ncurves; i++) {
dline = g_ptr_array_index(spectrum, i);
gwy_spectra_add_spectrum(spectra, dline,
coords[i*2], ofile->yreal - coords[i*2+1]);
g_object_unref(dline);
}
g_ptr_array_free(spectrum, TRUE);
g_free(coords);
g_free(buffer);
return spectra;
}
static GwySpectra*
rhkspm32_read_spectra(RHKPage *rhkpage)
{
guint i, j;
gdouble *data;
GwySIUnit *siunit = NULL;
GwyDataLine *dline;
GwySpectra *spectra = NULL;
GPtrArray *spectrum = NULL;
// i'm leaving this alone, though it probably doesn't make sense,
// and i should just create graphs straight away - but in case of
// future use, i'll just convert the data later to graphs
// xres stores number of data points per spectra,
// yres stores the number of spectra
// reading data
gwy_debug("rhk-spm32: %d spectra in this page\n", rhkpage->yres);
for (i = 0; i < rhkpage->yres; i++) {
dline = gwy_data_line_new(rhkpage->xres, rhkpage->x.scale, FALSE);
gwy_data_line_set_offset(dline, (rhkpage->x.offset));
data = gwy_data_line_get_data(dline);
// store line data in physical units - which are the z values, not y
if ((rhkpage->data_type) == RHK_DATA_INT16) {
const guint16 *p = (const guint16*)(rhkpage->buffer
+ rhkpage->data_offset);
for (j = 0; j < rhkpage->xres; j++) {
data[j] = GINT16_FROM_LE(p[i*(rhkpage->xres) + j])
*(rhkpage->z.scale)+(rhkpage->z.offset);
}
}
else if ((rhkpage->data_type) == RHK_DATA_SINGLE) {
const guchar *p = (const guchar*)(rhkpage->buffer
+ rhkpage->data_offset);
for (j = 0; j < rhkpage->xres; j++) {
data[j] = gwy_get_gfloat_le(&p)*rhkpage->z.scale
+ rhkpage->z.offset;
}
}
siunit = gwy_si_unit_new(rhkpage->x.units);
gwy_data_line_set_si_unit_x(dline, siunit);
g_object_unref(siunit);
// the y units (and data) for a 1D graph are stored in Z in the rhk
// spm32 format!
/* Fix "/\xfbHz" to "/Hz".
* XXX: It might be still wrong as the strange character might mean
* sqrt. */
if (g_str_has_suffix(rhkpage->z.units, "/\xfbHz")) {
gchar *s = gwy_strkill(g_strdup(rhkpage->z.units), "\xfb");
siunit = gwy_si_unit_new(s);
g_free(s);
}
else
siunit = gwy_si_unit_new(rhkpage->z.units);
gwy_data_line_set_si_unit_y(dline, siunit);
g_object_unref(siunit);
if (!spectrum)
spectrum = g_ptr_array_sized_new(rhkpage->yres);
g_ptr_array_add(spectrum, dline);
}
gwy_debug("rhk-spm32: finished parsing sps data\n");
spectra = gwy_spectra_new();
for (i = 0; i < rhkpage->yres; i++) {
dline = g_ptr_array_index(spectrum, i);
// since RHK spm32 does not record where it took the spectra,
// i'm setting these to zero
gwy_spectra_add_spectrum(spectra, dline, 0, 0);
g_object_unref(dline);
}
gwy_spectra_set_title(spectra, rhkpage->label);
if (spectrum)
g_ptr_array_free(spectrum, TRUE);
return spectra;
}
static GObject*
gwy_spectra_deserialize(const guchar *buffer,
gsize size,
gsize *position)
{
guint32 ncoords = 0, ncurves = 0, nselected = 0;
gdouble *coords = NULL;
guint32 *selected = NULL;
GwySIUnit *si_unit_xy = NULL;
GwyDataLine **curves = NULL;
GwySpectra *spectra;
gchar* title = NULL, *spec_xlabel = NULL, *spec_ylabel = NULL;
guint isize, i;
gwy_debug("");
g_return_val_if_fail(buffer, NULL);
{
GwySerializeSpec spec[] = {
{ 's', "title", &title, NULL, },
{ 'o', "si_unit_xy", &si_unit_xy, NULL, },
{ 'D', "coords", &coords, &ncoords, },
{ 'I', "selected", &selected, &nselected, },
{ 'O', "data", &curves, &ncurves, },
{ 's', "spec_xlabel", &spec_xlabel, NULL, },
{ 's', "spec_ylabel", &spec_ylabel, NULL, },
};
if (!gwy_serialize_unpack_object_struct(buffer, size, position,
GWY_SPECTRA_TYPE_NAME,
G_N_ELEMENTS(spec), spec)) {
for (i = 0; i < ncurves; i++)
gwy_object_unref(curves[i]);
g_free(curves);
g_free(coords);
g_free(selected);
g_free(title);
g_free(spec_xlabel);
g_free(spec_ylabel);
gwy_object_unref(si_unit_xy);
return NULL;
}
}
isize = 8*sizeof(guint32);
if (2*ncurves != ncoords
|| (nselected && (ncurves + isize-1)/isize != nselected)) {
g_critical("Serialized coordinate, data and selection array size "
"mismatch");
for (i = 0; i < ncurves; i++)
gwy_object_unref(curves[i]);
g_free(curves);
g_free(coords);
g_free(selected);
g_free(title);
g_free(spec_xlabel);
g_free(spec_ylabel);
gwy_object_unref(si_unit_xy);
return NULL;
}
spectra = gwy_spectra_new();
g_free(spectra->title);
spectra->title = title;
g_free(spectra->spec_xlabel);
spectra->spec_xlabel = spec_xlabel;
g_free(spectra->spec_ylabel);
spectra->spec_ylabel = spec_ylabel;
/* Preallocate ncurves items */
g_array_set_size(spectra->spectra, ncurves);
g_array_set_size(spectra->spectra, 0);
for (i = 0; i < ncurves; i++) {
GwySpectrum spec;
spec.x = coords[2*i + 0];
spec.y = coords[2*i + 1];
spec.ydata = curves[i];
if (nselected)
spec.selected = !!(selected[i/isize] & (1 << (i % isize)));
else
spec.selected = FALSE;
g_array_append_val(spectra->spectra, spec);
}
g_free(curves);
g_free(coords);
g_free(selected);
if (si_unit_xy) {
gwy_object_unref(spectra->si_unit_xy);
spectra->si_unit_xy = si_unit_xy;
}
return (GObject*)spectra;
}
