static void
fix_scales(EZDSection *section,
gint idx,
GwyContainer *container)
{
GwyDataField *dfield;
GwySIUnit *siunit;
gchar key[40];
gint power10;
gdouble r;
g_snprintf(key, sizeof(key), "/%d/data", idx);
dfield = GWY_DATA_FIELD(gwy_container_get_object_by_name(container, key));
/* Fix value scale */
siunit = gwy_si_unit_new_parse(section->zrange.unit, &power10);
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
r = pow10(power10);
gwy_data_field_multiply(dfield, r*section->zrange.range);
gwy_data_field_add(dfield, r*section->zrange.min);
/* Fix lateral scale */
siunit = gwy_si_unit_new_parse(section->xrange.unit, &power10);
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
gwy_data_field_set_xreal(dfield, pow10(power10)*section->xrange.range);
siunit = gwy_si_unit_new_parse(section->yrange.unit, &power10);
gwy_data_field_set_yreal(dfield, pow10(power10)*section->yrange.range);
g_object_unref(siunit);
/* Some metadata */
if (section->zrange.name) {
const gchar *s;
switch (section->direction) {
case SCAN_FORWARD:
s = " forward";
break;
case SCAN_BACKWARD:
s = " backward";
break;
default:
s = "";
break;
}
g_snprintf(key, sizeof(key), "/%d/data/title", idx);
gwy_container_set_string_by_name(container, key,
g_strdup_printf("%s%s",
section->zrange.name,
s));
}
}
static void
update_range_lables(GtkWidget *from, GtkWidget *to, GtkWidget *unit,
gdouble min, gdouble max, const gchar *unitstring)
{
GwySIValueFormat *vf;
GwySIUnit *siunit;
gint power10;
gchar *s;
siunit = gwy_si_unit_new_parse(unitstring, &power10);
min *= pow10(power10);
max *= pow10(power10);
vf = gwy_si_unit_get_format_with_digits(siunit, GWY_SI_UNIT_FORMAT_VFMARKUP,
MAX(fabs(min), fabs(max)), 3,
NULL);
s = g_strdup_printf("%.*f", vf->precision, min/vf->magnitude);
gtk_label_set_markup(GTK_LABEL(from), s);
g_free(s);
s = g_strdup_printf("%.*f", vf->precision, max/vf->magnitude);
gtk_label_set_markup(GTK_LABEL(to), s);
g_free(s);
gtk_label_set_markup(GTK_LABEL(unit), vf->units);
gwy_si_unit_value_format_free(vf);
g_object_unref(siunit);
}
static GwySIUnit*
read_real_size(const NetCDF *cdffile,
const gchar *name,
gdouble *real,
gint *power10)
{
const NetCDFVar *var;
const NetCDFAttr *attr;
GwySIUnit *siunit;
const guchar *p;
gchar *s;
*real = 1.0;
*power10 = 0;
if (!(var = cdffile_get_var(cdffile, name)))
return NULL;
/*
* Warning: Madness ahead.
*
* Older GXSM files contain "AA" in "unit", that makes sense, as the units
* are Angstroems.
*
* Newer GXSM files contain "nm" in "unit" though, in spite of the units
* being still Angstroems. They seem to contain the real units in
* "var_unit". The info field reads:
*
* This number is alwalys stored in Angstroem. Unit is used for user
* display only.
*
* In addition they invented yet another Angstroem abbreviation: Ang.
*/
attr = cdffile_get_attr(var->attrs, var->nattrs, "var_unit");
if (!attr || attr->type != NC_CHAR) {
attr = cdffile_get_attr(var->attrs, var->nattrs, "unit");
if (!attr || attr->type != NC_CHAR)
return NULL;
}
if (!attr->nelems)
s = NULL;
else
s = g_strndup(attr->values, attr->nelems);
siunit = gwy_si_unit_new_parse(s, power10);
g_free(s);
p = (const guchar*)(cdffile->buffer + var->begin);
if (var->type == NC_DOUBLE)
*real = gwy_get_gdouble_be(&p);
else if (var->type == NC_FLOAT)
*real = gwy_get_gfloat_be(&p);
else
g_warning("Size is not a floating point number");
return siunit;
}
/* Lateral units are a weird thing but they contain the actual units in
* bracket somewhere. If there are no brackes, try to interpret the entire
* string as units -- I've been told this is the right thing. */
static GwySIUnit*
extract_units(const gchar *label,
gdouble *q)
{
GwySIUnit *unit;
gint power10;
const gchar *s;
gchar *t;
if ((s = strchr(label, '['))) {
t = g_strdup(s + 1);
if (strchr(t, ']'))
*strchr(t, ']') = '\0';
unit = gwy_si_unit_new_parse(t, &power10);
g_free(t);
}
else
unit = gwy_si_unit_new_parse(label, &power10);
*q = pow10(power10);
return unit;
}
static void
oldmda_read_params(MDAXMLParams *par, OldMDAFile *mdafile)
{
MDAAxis axis;
mdafile->zres = par->res;
mdafile->xdata = par->xdata;
axis = g_array_index(par->axes, MDAAxis, 0);
if (axis.unitname)
mdafile->siunitz = gwy_si_unit_new(axis.unitname);
else
mdafile->siunitz = gwy_si_unit_new("");
axis = g_array_index(par->axes, MDAAxis, 1);
if (axis.unitname)
mdafile->siunitx = gwy_si_unit_new_parse(axis.unitname,
&mdafile->power10x);
else
mdafile->siunitx = gwy_si_unit_new("");
mdafile->xres = axis.maxindex - axis.minindex + 1;
if (mdafile->xres < 1)
mdafile->xres = 1;
if (axis.scale <= 0.0)
axis.scale = 1.0;
mdafile->xreal = axis.scale * mdafile->xres
* pow(10.0, mdafile->power10x);
axis = g_array_index(par->axes, MDAAxis, 2);
if (axis.unitname)
mdafile->siunity = gwy_si_unit_new_parse(axis.unitname,
&mdafile->power10y);
else
mdafile->siunity = gwy_si_unit_new("");
mdafile->yres = axis.maxindex - axis.minindex + 1;
if (mdafile->yres < 1)
mdafile->yres = 1;
if (axis.scale <= 0.0)
axis.scale = 1.0;
mdafile->yreal = axis.scale * mdafile->yres
* pow(10.0, mdafile->power10y);
}
static GObject*
gwy_si_unit_duplicate_real(GObject *object)
{
GwySIUnit *si_unit, *duplicate;
g_return_val_if_fail(GWY_IS_SI_UNIT(object), NULL);
si_unit = GWY_SI_UNIT(object);
duplicate = gwy_si_unit_new_parse("", NULL);
duplicate->power10 = si_unit->power10;
g_array_append_vals(duplicate->units,
si_unit->units->data, si_unit->units->len);
return (GObject*)duplicate;
}
static void
set_combo_from_unit(GtkWidget *combo,
const gchar *str,
gint basepower)
{
GwySIUnit *unit;
gint power10;
unit = gwy_si_unit_new_parse(str, &power10);
power10 += basepower;
gwy_combo_box_metric_unit_set_unit(GTK_COMBO_BOX(combo),
power10 - 6, power10 + 6, unit);
g_object_unref(unit);
}
static SensolyticsChannel*
create_fields(GHashTable *hash,
/* Can we obtain any useful information from this? */
G_GNUC_UNUSED gchar *line,
gint ndata,
const Dimensions *dimensions)
{
SensolyticsChannel *channels;
GString *str;
const gchar *value;
GwySIUnit *unit;
gint i, power10;
str = g_string_new(NULL);
channels = g_new0(SensolyticsChannel, ndata+1);
for (i = 0; i < ndata; i++) {
channels[i].dfield = gwy_data_field_new(dimensions->xres,
dimensions->yres,
dimensions->xreal,
dimensions->yreal,
FALSE);
channels[i].data = gwy_data_field_get_data(channels[i].dfield);
unit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(channels[i].dfield, unit);
g_object_unref(unit);
g_string_printf(str, "Channel %d Unit", i+1);
channels[i].q = 1.0;
if ((value = g_hash_table_lookup(hash, str->str))) {
unit = gwy_si_unit_new_parse(value, &power10);
gwy_data_field_set_si_unit_z(channels[i].dfield, unit);
g_object_unref(unit);
channels[i].q = pow10(power10);
}
else
g_warning("Channel %d has no units", i+1);
g_string_printf(str, "Channel %d Name", i+1);
if (!(channels[i].name = g_hash_table_lookup(hash, str->str)))
g_warning("Channel %d has no name", i+1);
}
return channels;
}
static gboolean
parse_scale(gchar **p,
const gchar *name,
double *value,
GwySIUnit **units,
GError **error)
{
gint power10;
gchar *vp, *line;
line = gwy_str_next_line(p);
if (!line) {
err_MISSING_FIELD(error, name);
return FALSE;
}
vp = strchr(line, ':');
if (!vp) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Missing colon in header line."));
return FALSE;
}
*vp = '\0';
vp++;
gwy_debug("<%s> = <%s>", name, vp);
if (!gwy_strequal(line, name)) {
err_MISSING_FIELD(error, name);
return FALSE;
}
*value = g_ascii_strtod(vp, &vp);
*units = gwy_si_unit_new_parse(vp, &power10);
*value *= pow10(power10);
if (!*value) {
g_warning("%s is 0.0, fixing to 1.0", name);
*value = 1.0;
}
return TRUE;
}
static GwyDataField*
omicron_read_data(OmicronFile *ofile,
OmicronTopoChannel *channel,
GError **error)
{
GError *err = NULL;
GwyDataField *dfield;
GwySIUnit *siunit;
gchar *filename;
gdouble *data;
guchar *buffer;
const gint16 *d;
gdouble scale;
gsize size;
guint i, j, n;
gint power10 = 0;
filename = omicron_fix_file_name(ofile->filename, channel->filename, error);
if (!filename)
return NULL;
gwy_debug("Succeeded with <%s>", filename);
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
g_free(filename);
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
g_free(filename);
n = ofile->xres*ofile->yres;
if (err_SIZE_MISMATCH(error, 2*n, size, TRUE)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
scale = (channel->max_phys - channel->min_phys)
/(channel->max_raw - channel->min_raw);
dfield = gwy_data_field_new(ofile->xres, ofile->yres,
ofile->xreal, ofile->yreal,
FALSE);
data = gwy_data_field_get_data(dfield);
d = (const gint16*)buffer;
for (i = 0; i < ofile->yres; i++) {
for (j = 0; j < ofile->xres; j++)
data[(ofile->yres-1 - i)*ofile->xres + j]
= scale*GINT16_FROM_BE(d[i*ofile->xres + j]);
}
gwy_file_abandon_contents(buffer, size, NULL);
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
siunit = gwy_si_unit_new_parse(channel->units, &power10);
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
if (power10)
gwy_data_field_multiply(dfield, pow10(power10));
return dfield;
}
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;
}
/**
* gwy_si_unit_new:
* @unit_string: Unit string (it can be %NULL for an empty unit).
*
* Creates a new SI unit from string representation.
*
* Unit string represents unit with no prefixes
* (e. g. "m", "N", "A", etc.)
*
* Returns: A new SI unit.
**/
GwySIUnit*
gwy_si_unit_new(const char *unit_string)
{
return gwy_si_unit_new_parse(unit_string, NULL);
}
static GwyContainer*
rawxyz_load(const gchar *filename,
GwyRunType mode,
GError **error)
{
GwyContainer *settings, *container = NULL;
GwySurface *surface = NULL;
RawXYZArgs args;
GwySIUnit *unit;
gint power10;
gdouble q;
gchar *buffer = NULL;
gsize size;
GError *err = NULL;
gboolean ok;
guint k;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
surface = read_xyz_points(buffer);
g_free(buffer);
if (!surface->n) {
err_NO_DATA(error);
goto fail;
}
settings = gwy_app_settings_get();
rawxyz_load_args(settings, &args);
if (mode == GWY_RUN_INTERACTIVE) {
ok = rawxyz_dialog(&args, surface);
rawxyz_save_args(settings, &args);
if (!ok) {
err_CANCELLED(error);
goto fail;
}
}
unit = gwy_si_unit_new_parse(args.xy_units, &power10);
if (power10) {
q = pow10(power10);
for (k = 0; k < surface->n; k++) {
surface->data[k].x *= q;
surface->data[k].y *= q;
}
gwy_surface_invalidate(surface);
}
gwy_serializable_clone(G_OBJECT(unit),
G_OBJECT(gwy_surface_get_si_unit_xy(surface)));
unit = gwy_si_unit_new_parse(args.z_units, &power10);
if (power10) {
q = pow10(power10);
for (k = 0; k < surface->n; k++)
surface->data[k].z *= q;
gwy_surface_invalidate(surface);
}
gwy_serializable_clone(G_OBJECT(unit),
G_OBJECT(gwy_surface_get_si_unit_z(surface)));
container = gwy_container_new();
gwy_container_set_object(container, gwy_app_get_surface_key_for_id(0),
surface);
gwy_app_xyz_title_fall_back(container, 0);
gwy_file_xyz_import_log_add(container, 0, NULL, filename);
fail:
g_free(args.xy_units);
g_free(args.z_units);
GWY_OBJECT_UNREF(surface);
return container;
}
static GwySIUnit*
get_physical_scale(GHashTable *hash,
GHashTable *scannerlist,
GHashTable *scanlist,
gboolean has_version,
gdouble *scale,
GError **error)
{
GwySIUnit *siunit, *siunit2;
NanoscopeValue *val, *sval;
gchar *key;
gint q;
/* Very old style scales (files with Version field) */
if (!has_version) {
if (!(val = g_hash_table_lookup(hash, "Z magnify image"))) {
err_MISSING_FIELD(error, "Z magnify image");
return NULL;
}
/* TODO: Luminescence */
siunit = gwy_si_unit_new("m");
/* According to Markus, the units are 1/100 nm, but his scale
* calculation is raw/655.36 [nm]. We have the factor 1/65536 applied
* automatically, that gives 1e-7 [m]. Whatever. */
*scale = 1e-7 * val->hard_value;
return siunit;
}
/* XXX: This is a damned heuristics. For some value types we try to guess
* a different quantity scale to look up. */
if (!(val = g_hash_table_lookup(hash, "@2:Z scale"))) {
if (!(val = g_hash_table_lookup(hash, "Z scale"))) {
err_MISSING_FIELD(error, "Z scale");
return NULL;
}
/* Old style scales */
siunit = gwy_si_unit_new_parse(val->hard_value_units, &q);
*scale = val->hard_value * pow10(q);
if (val->hard_scale)
*scale *= 65536.0/val->hard_scale;
return siunit;
}
key = g_strdup_printf("@%s", val->soft_scale);
if (!(sval = g_hash_table_lookup(scannerlist, key))
&& (!scanlist || !(sval = g_hash_table_lookup(scanlist, key)))) {
g_warning("`%s' not found", key);
g_free(key);
/* XXX */
*scale = val->hard_value;
return gwy_si_unit_new("");
}
*scale = val->hard_value*sval->hard_value;
if (!sval->hard_value_units || !*sval->hard_value_units) {
if (gwy_strequal(val->soft_scale, "Sens. Phase"))
siunit = gwy_si_unit_new("deg");
else
siunit = gwy_si_unit_new("V");
}
else {
siunit = gwy_si_unit_new_parse(sval->hard_value_units, &q);
siunit2 = gwy_si_unit_new("V");
gwy_si_unit_multiply(siunit, siunit2, siunit);
gwy_debug("Scale1 = %g V/LSB", val->hard_value);
gwy_debug("Scale2 = %g %s", sval->hard_value, sval->hard_value_units);
*scale *= pow10(q);
gwy_debug("Total scale = %g %s/LSB",
*scale, gwy_si_unit_get_string(siunit,
GWY_SI_UNIT_FORMAT_PLAIN));
g_object_unref(siunit2);
}
g_free(key);
return siunit;
}
static GwyContainer*
quesant_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwySIUnit *units = NULL;
gint32 power10;
FileInfo info;
int row, col;
GwyDataField *dfield;
gdouble multiplier;
const guint16 *p;
gdouble *d;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size <= HEADER_SIZE) {
gwy_file_abandon_contents(buffer, size, NULL);
err_TOO_SHORT(error);
return NULL;
}
if (!read_file_info(buffer, size, &info, error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
// create units and datafield
units = gwy_si_unit_new_parse("um", &power10);
dfield = gwy_data_field_new(info.img_res, info.img_res,
info.real_size * pow10(power10),
info.real_size * pow10(power10),
FALSE);
// set units for XY axes
gwy_data_field_set_si_unit_xy(dfield, units);
g_object_unref(units);
// set units for Z axis
units = gwy_si_unit_new_parse("um", &power10);
gwy_data_field_set_si_unit_z(dfield, units);
g_object_unref(units);
multiplier = info.z_scale * pow10(power10);
p = info.image_data;
d = gwy_data_field_get_data(dfield);
// values are stored in unsigned int16 type
for (row = 0; row < info.img_res; row++) {
for (col = 0; col < info.img_res; col++) {
d[row*info.img_res + col] = GUINT16_FROM_LE(*p) * multiplier;
p++;
}
}
// create container
container = gwy_container_new();
// put datafield into container
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static GwyContainer*
csmfile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
GHashTable *hash = NULL;
guchar *d24, *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
guint xres, yres, bmpsize, header_size, maxval, i, j;
gdouble real, zmin, zmax, q, z0;
GwyTextHeaderParser parser;
GwySIUnit *unit = NULL;
gchar *value, *end, *header = NULL;
gdouble *data;
gint power10;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < BMP_HEADER_SIZE) {
err_TOO_SHORT(error);
goto fail;
}
if (!read_bmp_header(buffer, &xres, &yres, &bmpsize)
|| size <= bmpsize) {
err_FILE_TYPE(error, "CSM");
goto fail;
}
header_size = size - bmpsize;
header = g_new(gchar, header_size + 1);
memcpy(header, buffer + bmpsize, header_size);
header[header_size] = '\0';
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
hash = gwy_text_header_parse(header, &parser, NULL, NULL);
/* Do NOT use the fields Image width, Image height from the added footer.
* Even though it is specifically added by Benyuan it can disagree with the
* BMP diemsions and when they disagree the BMP diemsions are apparently
* right. */
if (err_DIMENSION(error, xres))
goto fail;
if (err_DIMENSION(error, yres))
goto fail;
if (!(value = g_hash_table_lookup(hash, "ScanSize"))) {
err_MISSING_FIELD(error, "ScanSize");
goto fail;
}
real = g_ascii_strtod(value, NULL);
/* Use negated positive conditions to catch NaNs */
if (!((real = fabs(real)) > 0)) {
g_warning("Real size is 0.0, fixing to 1.0");
real = 1.0;
}
if (!(value = g_hash_table_lookup(hash, "HeightScale"))) {
err_MISSING_FIELD(error, "HeightScale");
goto fail;
}
zmax = g_ascii_strtod(value, &end);
unit = gwy_si_unit_new_parse(end, &power10);
/* Optional stuff for which we try to fall back. */
if (!(value = g_hash_table_lookup(hash, "StartHeightScale")))
zmin = 0.0;
else
zmin = g_ascii_strtod(value, NULL);
if (!(value = g_hash_table_lookup(hash, "MaxValue")))
maxval = 0xffff;
else
maxval = MAX(atoi(value), 1);
dfield = gwy_data_field_new(xres, yres, real*Nanometre, real*Nanometre,
FALSE);
data = gwy_data_field_get_data(dfield);
d24 = buffer + BMP_HEADER_SIZE;
q = pow10(power10)*(zmax - zmin)/maxval;
z0 = pow10(power10)*zmin;
for (i = 0; i < yres; i++) {
gdouble *row = data + (yres-1 - i)*xres;
for (j = 0; j < xres; j++, row++, d24 += 3)
*row = (d24[0] + 256.0*d24[1])*q + z0;
}
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_data_field_set_si_unit_z(dfield, unit);
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
meta = gwy_container_new();
g_hash_table_foreach(hash, store_meta, meta);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
if ((value = g_hash_table_lookup(hash, "sTitle"))
&& g_utf8_validate(value, -1, NULL)) {
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(value));
}
else
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
GWY_OBJECT_UNREF(unit);
if (header)
g_free(header);
if (hash)
g_hash_table_destroy(hash);
return container;
}
static GwyContainer*
zeiss_load_tiff(const GwyTIFF *tiff, GError **error)
{
GwyContainer *container = NULL, *meta = NULL;
GwyDataField *dfield;
GwySIUnit *siunit;
GwyTIFFImageReader *reader = NULL;
GHashTable *hash = NULL;
gint i, power10;
gchar *value, *end, *comment = NULL;
gdouble *data;
gboolean new_file;
double factor, dx;
/* Comment with parameters is common for all data fields */
if (!gwy_tiff_get_string0(tiff, ZEISS_HEADER_TAG, &comment)) {
err_FILE_TYPE(error, "Carl Zeiss SEM");
goto fail;
}
if (strstr(comment, MAGIC_COMMENT))
new_file = TRUE;
else if (g_str_has_prefix(comment, SOMEWHAT_LESS_MAGIC_COMMENT))
new_file = FALSE;
else {
err_FILE_TYPE(error, "Carl Zeiss SEM");
goto fail;
}
/* Read the comment header. */
if (new_file) {
hash = parse_comment(comment);
if ((value = g_hash_table_lookup(hash, "Image Pixel Size"))) {
gwy_debug("Using dx from Image Pixel Size: %s", value);
}
else if ((value = g_hash_table_lookup(hash, "Pixel Size"))) {
gwy_debug("Using dx from Pixel Size: %s", value);
}
else {
err_MISSING_FIELD(error, "Pixel Size");
goto fail;
}
}
else {
/* The first thing is the pixel size, apparently. */
value = comment + strlen(SOMEWHAT_LESS_MAGIC_COMMENT);
gwy_debug("Using dx from old-style comment: %s", value);
}
dx = g_ascii_strtod(value, &end);
/* Use negated positive conditions to catch NaNs */
if (!((dx = fabs(dx)) > 0)) {
g_warning("Real pixel size is 0.0, fixing to 1.0");
dx = 1.0;
}
if (!new_file)
end = "m";
/* Request a reader, this ensures dimensions and stuff are defined.
* NB: Newer versions store the image as RGB. Not useful here; just
* average the channels. */
if (!(reader = gwy_tiff_get_image_reader(tiff, 0, 3, error)))
goto fail;
siunit = gwy_si_unit_new_parse(end, &power10);
factor = pow10(power10);
dfield = gwy_data_field_new(reader->width, reader->height,
reader->width * factor * dx,
reader->height * factor * dx,
FALSE);
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
data = gwy_data_field_get_data(dfield);
if (reader->samples_per_pixel > 1) {
gdouble *datarow = g_new(gdouble, reader->width);
gint ch, j, spp = reader->samples_per_pixel;
gwy_data_field_clear(dfield);
for (i = 0; i < reader->height; i++) {
for (ch = 0; ch < spp; ch++) {
gwy_tiff_read_image_row(tiff, reader, 0, i, 1.0, 0.0, datarow);
for (j = 0; j < reader->width; j++)
data[i*reader->width + j] += datarow[j];
}
}
g_free(datarow);
gwy_data_field_multiply(dfield, 1.0/spp);
gwy_data_field_invalidate(dfield);
}
else {
for (i = 0; i < reader->height; i++)
gwy_tiff_read_image_row(tiff, reader, 0, i, 1.0, 0.0,
data + i*reader->width);
}
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup("Secondary electron count"));
if (new_file) {
meta = gwy_container_new();
g_hash_table_foreach(hash, add_meta, meta);
if (gwy_container_get_n_items(meta))
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
}
fail:
if (hash)
g_hash_table_destroy(hash);
g_free(comment);
return container;
}
static GwyContainer*
asc_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
GwyDataField *dfield = NULL, *mfield = NULL;
GwyTextHeaderParser parser;
GwySIUnit *unit;
gchar *line, *p, *value, *buffer = NULL;
GHashTable *hash = NULL;
gsize size;
GError *err = NULL;
gdouble xreal, yreal, q;
gint i, xres, yres;
gdouble *data;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
p = buffer;
line = gwy_str_next_line(&p);
if (!gwy_strequal(line, MAGIC_BARE)) {
err_FILE_TYPE(error, "SPIP ASCII data");
goto fail;
}
gwy_clear(&parser, 1);
parser.line_prefix = "#";
parser.key_value_separator = "=";
parser.terminator = "# Start of Data:";
parser.error = &header_error;
parser.end = &header_end;
if (!(hash = gwy_text_header_parse(p, &parser, &p, &err))) {
g_propagate_error(error, err);
goto fail;
}
if (!require_keys(hash, error,
"x-pixels", "y-pixels", "x-length", "y-length",
NULL))
goto fail;
xres = atoi(g_hash_table_lookup(hash, "x-pixels"));
yres = atoi(g_hash_table_lookup(hash, "y-pixels"));
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
goto fail;
xreal = Nanometer * g_ascii_strtod(g_hash_table_lookup(hash, "x-length"),
NULL);
yreal = Nanometer * g_ascii_strtod(g_hash_table_lookup(hash, "y-length"),
NULL);
/* Use negated positive conditions to catch NaNs */
if (!((xreal = fabs(xreal)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
xreal = 1.0;
}
if (!((yreal = fabs(yreal)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
yreal = 1.0;
}
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
unit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, unit);
g_object_unref(unit);
if ((value = g_hash_table_lookup(hash, "z-unit"))) {
gint power10;
unit = gwy_si_unit_new_parse(value, &power10);
gwy_data_field_set_si_unit_z(dfield, unit);
g_object_unref(unit);
q = pow10(power10);
}
else if ((value = g_hash_table_lookup(hash, "Bit2nm"))) {
q = Nanometer * g_ascii_strtod(value, NULL);
unit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_z(dfield, unit);
g_object_unref(unit);
}
else
q = 1.0;
data = gwy_data_field_get_data(dfield);
value = p;
for (i = 0; i < xres*yres; i++) {
data[i] = q*g_ascii_strtod(value, &p);
if (p == value && (!*p || g_ascii_isspace(*p))) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached when reading sample #%d of %d"),
i, xres*yres);
goto fail;
}
if (p == value) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Malformed data encountered when reading sample "
"#%d of %d"),
i, xres*yres);
goto fail;
}
value = p;
}
if ((value = g_hash_table_lookup(hash, "voidpixels")) && atoi(value)) {
mfield = gwy_data_field_new_alike(dfield, FALSE);
data = gwy_data_field_get_data(mfield);
value = p;
for (i = 0; i < xres*yres; i++) {
data[i] = 1.0 - g_ascii_strtod(value, &p);
value = p;
}
if (!gwy_app_channel_remove_bad_data(dfield, mfield))
GWY_OBJECT_UNREF(mfield);
}
container = gwy_container_new();
gwy_container_set_object(container, gwy_app_get_data_key_for_id(0), dfield);
if (mfield) {
gwy_container_set_object(container, gwy_app_get_mask_key_for_id(0),
mfield);
g_object_unref(mfield);
}
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
GWY_OBJECT_UNREF(dfield);
g_free(buffer);
if (hash)
g_hash_table_destroy(hash);
return container;
}
static GwyDataField*
unisoku_read_data_field(const guchar *buffer,
gsize size,
UnisokuFile *ufile,
GError **error)
{
gint i, n, power10;
const gchar *unit;
GwyDataField *dfield;
GwySIUnit *siunit;
gdouble q, pmin, pmax, rmin, rmax;
gdouble *data;
n = ufile->xres * ufile->yres;
if (err_SIZE_MISMATCH(error, n*type_sizes[ufile->data_type], size, FALSE))
return NULL;
dfield = gwy_data_field_new(ufile->xres, ufile->yres,
fabs((ufile->end_x - ufile->start_x)),
fabs((ufile->end_y - ufile->start_y)),
FALSE);
data = gwy_data_field_get_data(dfield);
/* FIXME: what to do when ascii_flag is set? */
switch (ufile->data_type) {
case UNISOKU_UINT8:
for (i = 0; i < n; i++)
data[i] = buffer[i];
break;
case UNISOKU_SINT8:
for (i = 0; i < n; i++)
data[i] = (signed char)buffer[i];
break;
case UNISOKU_UINT16:
{
const guint16 *pdata = (const guint16*)buffer;
for (i = 0; i < n; i++)
data[i] = GUINT16_FROM_LE(pdata[i]);
}
break;
case UNISOKU_SINT16:
{
const gint16 *pdata = (const gint16*)buffer;
for (i = 0; i < n; i++)
data[i] = GINT16_FROM_LE(pdata[i]);
}
break;
case UNISOKU_FLOAT:
for (i = 0; i < n; i++)
data[i] = gwy_get_gfloat_le(&buffer);
break;
default:
g_return_val_if_reached(NULL);
break;
}
unit = ufile->unit_x;
if (!*unit)
unit = "nm";
siunit = gwy_si_unit_new_parse(unit, &power10);
gwy_data_field_set_si_unit_xy(dfield, siunit);
q = pow10((gdouble)power10);
gwy_data_field_set_xreal(dfield, q*gwy_data_field_get_xreal(dfield));
gwy_data_field_set_yreal(dfield, q*gwy_data_field_get_yreal(dfield));
g_object_unref(siunit);
unit = ufile->unit_z;
/* XXX: No fallback yet, just make z unitless */
siunit = gwy_si_unit_new_parse(unit, &power10);
gwy_data_field_set_si_unit_z(dfield, siunit);
q = pow10((gdouble)power10);
pmin = q*ufile->min_z;
pmax = q*ufile->max_z;
rmin = ufile->min_raw_z;
rmax = ufile->max_raw_z;
gwy_data_field_multiply(dfield, (pmax - pmin)/(rmax - rmin));
gwy_data_field_add(dfield, (pmin*rmax - pmax*rmin)/(rmax - rmin));
g_object_unref(siunit);
return dfield;
}
static void
apedax_get_channels_data(unzFile uFile,
guchar *scanXmlContent,
gsize contentSize,
const gchar *filename,
GwyContainer *container,
GwyContainer *meta,
const APEScanSize *scanSize,
GError **error)
{
xmlDocPtr doc = NULL;
xmlNodePtr cur = NULL;
xmlXPathContextPtr context;
xmlXPathObjectPtr pathObj;
xmlNodeSetPtr nodeset;
xmlChar *buffer = NULL;
gchar key[256];
gint i;
gint power10 = 0;
gdouble scaleFactor = 1.0;
GwySIUnit *zUnit;
gchar *zUnitString = NULL;
gchar *binFileName = NULL;
GwyDataField *dfield;
GwyContainer *tmp;
if (scanXmlContent == NULL || contentSize == 0)
return;
gwy_clear(key, sizeof(key));
doc = xmlReadMemory(scanXmlContent,
contentSize,
"scan.xml",
NULL,
0);
if (doc == NULL)
goto fail;
context = xmlXPathNewContext(doc);
if (context == NULL)
goto fail;
pathObj = xmlXPathEvalExpression("/Scan/Channels/Channel", context);
if (pathObj == NULL) {
xmlXPathFreeContext(context);
goto fail;
}
/*There must be at least one channel*/
if (xmlXPathNodeSetIsEmpty(pathObj->nodesetval)) {
xmlXPathFreeObject(pathObj);
xmlXPathFreeContext(context);
err_NO_DATA(error);
return;
}
nodeset = pathObj->nodesetval;
if (nodeset->nodeNr <= 0)
goto fail;
for (i = 0; i < nodeset->nodeNr; i++) {
cur = nodeset->nodeTab[i]->xmlChildrenNode;
while (cur) {
/*Label*/
if (gwy_strequal((gchar*)cur->name, "Label")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
g_snprintf(key, sizeof(key), "/%d/data/title", i);
gwy_container_set_string_by_name(container, key, g_strdup(buffer));
xmlFree(buffer);
}
/*Factor*/
if (gwy_strequal((gchar*)cur->name, "ConversionFactor")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
scaleFactor = g_ascii_strtod((gchar*)buffer, NULL);
xmlFree(buffer);
}
/*Unit*/
if (gwy_strequal((gchar*)cur->name, "DataUnit")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
zUnitString = g_strdup((gchar*)buffer);
zUnit = gwy_si_unit_new_parse(zUnitString, &power10);
xmlFree(buffer);
g_object_unref(zUnit);
}
/*Binary file name*/
if (gwy_strequal((gchar*)cur->name, "BINFile")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
binFileName = g_strdup((gchar*)buffer);
xmlFree(buffer);
}
cur = cur->next;
}
scaleFactor *= pow(10.0, power10);
dfield = apedax_get_data_field(uFile,
binFileName,
scanSize,
zUnitString,
scaleFactor,
error);
if (dfield) {
g_snprintf(key, sizeof(key), "/%d/data", i);
gwy_container_set_object_by_name(container, key, dfield);
g_object_unref(dfield);
gwy_file_channel_import_log_add(container, i, NULL,
filename);
tmp = gwy_container_duplicate(meta);
g_snprintf(key, sizeof(key), "/%d/meta", i);
gwy_container_set_object_by_name(container, key, tmp);
g_object_unref(tmp);
}
}
xmlXPathFreeObject(pathObj);
xmlXPathFreeContext(context);
xmlFreeDoc(doc);
return;
fail:
err_FILE_TYPE(error, FILE_TYPE);
if (doc)
xmlFreeDoc(doc);
return;
}
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 GwyContainer*
surffile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
SurfFile surffile;
gint coef = 0;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize expected_size, size = 0;
GError *err = NULL;
gchar signature[12];
gint add = 0;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(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.dayof = gwy_get_guint16_le(&p);
surffile.measurement_duration = gwy_get_gfloat_le(&p);
p += 10;
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);
if (err_DIMENSION(error, surffile.xres)
|| err_DIMENSION(error, surffile.yres)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
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, TRUE);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
}
/* Use negated positive conditions to catch NaNs */
if (!((surffile.dx = fabs(surffile.dx)) > 0)) {
g_warning("Real x step is 0.0, fixing to 1.0");
surffile.dx = 1.0;
}
if (!((surffile.dy = fabs(surffile.dy)) > 0)) {
g_warning("Real y step is 0.0, fixing to 1.0");
surffile.dy = 1.0;
}
p = buffer + SURF_HEADER_SIZE + add;
/*units*/
coef = 0;
surffile.xyunit = gwy_si_unit_new_parse(surffile.dx_unit, &coef);
surffile.dx *= pow10(coef);
coef = 0;
surffile.xyunit = gwy_si_unit_new_parse(surffile.dy_unit, &coef);
surffile.dy *= pow10(coef);
coef = 0;
surffile.zunit = gwy_si_unit_new_parse (surffile.dz_unit, &coef);
if (!fill_data_fields(&surffile, p, error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
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;
}
gwy_data_field_multiply(surffile.dfield, pow10(coef));
surffile.ZOffset *= pow10(coef);
gwy_data_field_add(surffile.dfield, surffile.ZOffset);
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);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
return container;
}
static GwyDataField*
read_data_field(const guchar *buffer,
guint size,
guchar version,
gchar **title,
gint *direction,
GError **error)
{
enum { MIN_REMAINDER = 2620 };
/* information offsets in different versions, in r5+ relative to data
* start, in order:
* data offset,
* pixel dimensions,
* physical dimensions,
* value multiplier,
* unit string,
* data type, (if zero, use channel title)
* channel title (if zero, use data type)
*/
const guint offsets34[] = {
0x0104, 0x0196, 0x01a2, 0x01b2, 0x01c2, 0x0400, 0x0000
};
const guint offsets56[] = {
0x0104, 0x025c, 0x0268, 0x0288, 0x02a0, 0x0708, 0x0000
};
const guint offsets7[] = {
0x0104, 0x029c, 0x02a8, 0x02c8, 0x02e0, 0x0000, 0x0b90
};
gint xres, yres, doffset, i, power10, type;
gdouble xreal, yreal, q, z0;
GwyDataField *dfield;
GwySIUnit *unitxy, *unitz;
gdouble *data;
const guint *offset;
const guchar *p, *r, *last;
/* get floats in single precision from r4 but double from r5+ */
gdouble (*getflt)(const guchar**);
*title = NULL;
*direction = -1;
if (version == '5' || version == '6' || version == '7') {
/* There are more headers in r5,
* try to find something that looks like #R5. */
last = r = buffer;
while ((p = memchr(r, '#', size - (r - buffer) - MIN_REMAINDER))) {
if (p[1] == 'R' && p[2] == version && p[3] == '.') {
gwy_debug("pos: %ld", (long)(p - buffer));
last = p;
r = p + MIN_REMAINDER-1;
}
else
r = p + 1;
}
offset = (version == '7') ? &offsets7[0] : &offsets56[0];
buffer = last;
getflt = &gwy_get_gdouble_le;
}
else {
offset = &offsets34[0];
getflt = &get_gfloat_le_as_double;
}
p = buffer + *(offset++);
doffset = gwy_get_guint32_le(&p); /* this appears to be the same number
as in the ASCII miniheader -- so get
it here since it's easier */
gwy_debug("data offset = %u", doffset);
p = buffer + *(offset++);
xres = gwy_get_guint32_le(&p);
yres = gwy_get_guint32_le(&p);
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
return NULL;
p = buffer + *(offset++);
xreal = -getflt(&p);
xreal += getflt(&p);
yreal = -getflt(&p);
yreal += getflt(&p);
if (!((xreal = fabs(xreal)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
xreal = 1.0;
}
if (!((yreal = fabs(yreal)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
yreal = 1.0;
}
p = buffer + *(offset++);
q = getflt(&p);
z0 = getflt(&p);
gwy_debug("xreal.raw = %g, yreal.raw = %g, q.raw = %g, z0.raw = %g",
xreal, yreal, q, z0);
p = buffer + *(offset++);
unitz = gwy_si_unit_new_parse(p, &power10);
q *= pow10(power10);
z0 *= pow10(power10);
unitxy = gwy_si_unit_new_parse(p + 10, &power10);
xreal *= pow10(power10);
yreal *= pow10(power10);
gwy_debug("xres = %d, yres = %d, xreal = %g, yreal = %g, q = %g, z0 = %g",
xres, yres, xreal, yreal, q, z0);
gwy_debug("unitxy = %s, unitz = %s", p, p + 10);
if (offset[1]) {
/* We know channel title */
offset++;
p = buffer + *(offset++);
*title = g_strndup(p, size - (p - buffer));
gwy_debug("title = <%s>", *title);
}
else {
/* We know data type */
p = buffer + *(offset++);
type = gwy_get_guint16_le(&p);
*direction = gwy_get_guint16_le(&p);
gwy_debug("type = %d, dir = %d", type, *direction);
offset++;
*title = type_to_title(type);
}
p = buffer + doffset;
if (err_SIZE_MISMATCH(error, 2*xres*yres, size - (p - buffer), FALSE))
return NULL;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
g_object_unref(unitxy);
gwy_data_field_set_si_unit_z(dfield, unitz);
g_object_unref(unitz);
data = gwy_data_field_get_data(dfield);
for (i = 0; i < xres*yres; i++)
data[i] = (p[2*i] + 256.0*p[2*i + 1])*q + z0;
return dfield;
}
static GwyContainer*
lif_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
LIFHeader *header = NULL;
LIFMemBlock *memblock = NULL;
LIFFile *file = NULL;
LIFElement *element = NULL;
LIFDimension *dimension = NULL;
LIFChannel *channel = NULL;
gsize size = 0, memblock_size = 0;
gint64 remaining = 0;
gchar *buffer;
const guchar *p;
GError *err = NULL;
GwyDataField *dfield = NULL;
GwyBrick *brick = NULL;
gdouble *data = NULL;
gint i, j, channelno = 0, volumeno = 0;
gchar *strkey, *lutname;
GMarkupParser parser = {
header_start_element,
header_end_element,
header_parse_text, NULL, NULL
};
GMarkupParseContext *context;
XMLParserData *xmldata;
gint x, xres, xstep, y, yres, ystep, z, zres, zstep, offset, res;
gdouble xreal, yreal, zreal, xoffset, yoffset, zoffset;
gdouble zscale = 1.0, wscale = 1.0;
GwySIUnit *siunitxy = NULL, *siunitz = NULL;
GwySIUnit *siunitx = NULL, *siunity = NULL, *siunitw = NULL;
gint power10xy = 1;
gint power10x = 1, power10y = 1, power10z = 1, power10w = 1;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
if (size < 13) { /* header too short */
err_TOO_SHORT(error);
goto fail;
}
p = buffer;
remaining = size;
header = g_new0(LIFHeader, 1);
header->magic = gwy_get_gint32_le(&p);
gwy_debug("Magic = %d", header->magic);
header->size = gwy_get_guint32_le(&p);
gwy_debug("Size = %d", header->size);
header->testcode = *(p++);
gwy_debug("Testcode = 0x%x", header->testcode);
if (header->testcode != TESTCODE) {
err_FILE_TYPE(error, "Leica LIF");
goto fail;
}
header->xmllen = gwy_get_guint32_le(&p);
gwy_debug("XML length = %d", header->xmllen);
if (size < 13 + header->xmllen * 2) {
err_TOO_SHORT(error);
goto fail;
}
remaining -= 13;
header->xmlheader = g_convert((const gchar*)p, 2 * header->xmllen,
"UTF-8", "UTF-16", NULL, NULL, NULL);
p += header->xmllen * 2;
remaining -= header->xmllen * 2;
// gwy_debug("%s", header->xmlheader);
/* Parse XML header */
xmldata = g_new0(XMLParserData, 1);
xmldata->file = g_new0(LIFFile, 1);
xmldata->file->elements = g_array_new(FALSE, TRUE,
sizeof(LIFElement));
xmldata->elements = g_ptr_array_new();
context = g_markup_parse_context_new(&parser,
G_MARKUP_TREAT_CDATA_AS_TEXT,
(gpointer)xmldata,
NULL);
if (!g_markup_parse_context_parse(context, header->xmlheader, -1, &err)
|| !g_markup_parse_context_end_parse(context, &err)) {
error = &err;
g_clear_error(&err);
}
g_markup_parse_context_free(context);
file = xmldata->file;
file->header = header;
g_ptr_array_free(xmldata->elements, TRUE);
g_free(xmldata);
/* Reading memblocks */
file->memblocks = g_hash_table_new(g_str_hash, g_str_equal);
while (remaining > 0) {
memblock = lif_read_memblock(p, &memblock_size, file->version);
if (!memblock) {
break;
}
remaining -= memblock_size;
if (remaining >= 0) {
gwy_debug("remaining = %" G_GUINT64_FORMAT "", remaining);
p += memblock_size;
g_hash_table_insert(file->memblocks, memblock->memid,
memblock);
}
}
container = gwy_container_new();
for (i = 0; i < file->elements->len; i++) {
element = &g_array_index(file->elements, LIFElement, i);
if ((element->dimensions == NULL)
|| (element->channels == NULL)) {
gwy_debug("Empty element");
continue;
}
gwy_debug("Dimensions = %d channels=%d",
element->dimensions->len,
element->channels->len);
gwy_debug("memid=%s", element->memid);
/* check if we can load this type of data into
* Gwyddion structures */
res = 0;
if ((element->dimensions->len != 2)
&& (element->dimensions->len != 3)) {
/* check for case ndim == 4 && res == 1 */
for (i = 0; i < element->dimensions->len; i++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, i);
xres = dimension->res;
gwy_debug("dim[%d].res=%d", i, xres);
if (i == 2) {
res = xres;
}
}
if ((element->dimensions->len == 4) && (res == 1)) {
gwy_debug("4D volume");
}
else {
gwy_debug("not loading");
continue;
}
}
memblock = (LIFMemBlock *)g_hash_table_lookup(file->memblocks,
element->memid);
if (!memblock) {
gwy_debug("Failed to locate memblock with key %s",
element->memid);
continue;
}
p = memblock->data;
if (element->dimensions->len == 2) { /* Image */
for (j = 0; j < element->channels->len; j++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, 0);
xres = dimension->res;
xreal = dimension->length;
xoffset = dimension->origin;
xstep = dimension->bytesinc;
siunitxy = gwy_si_unit_new_parse(dimension->unit,
&power10xy);
dimension = &g_array_index(element->dimensions,
LIFDimension, 1);
yres = dimension->res;
yreal = dimension->length;
yoffset = dimension->origin;
ystep = dimension->bytesinc;
if (xreal <= 0.0)
xreal = 1.0;
if (yreal <= 0.0)
yreal = 1.0;
channel = &g_array_index(element->channels,
LIFChannel, j);
offset = channel->bytesinc;
siunitz = gwy_si_unit_new_parse(channel->unit,
&power10z);
zscale = pow10(power10z);
if (offset + (xres - 1) * xstep + (yres - 1)* ystep
> memblock->memsize) {
gwy_debug("Memblock too small");
gwy_debug("%d %" G_GUINT64_FORMAT "",
offset + (xres-1)*xstep + (yres-1)*ystep,
memblock->memsize);
err_SIZE_MISMATCH(error,
memblock->memsize,
offset+(xres-1)*xstep
+(yres-1)*ystep,
FALSE);
goto fail;
}
dfield = gwy_data_field_new(xres, yres,
xreal*pow10(power10xy),
yreal*pow10(power10xy),
TRUE);
gwy_data_field_set_xoffset(dfield,
xoffset*pow10(power10xy));
gwy_data_field_set_yoffset(dfield,
yoffset*pow10(power10xy));
data = gwy_data_field_get_data(dfield);
for (y = 0; y < yres; y++)
for (x = 0; x < xres; x++) {
*(data++) = zscale
* (gdouble)*(p + offset + x*xstep + y*ystep);
}
if (siunitxy) {
gwy_data_field_set_si_unit_xy(dfield, siunitxy);
g_object_unref(siunitxy);
}
if (siunitz) {
gwy_data_field_set_si_unit_z(dfield, siunitz);
g_object_unref(siunitz);
}
strkey = g_strdup_printf("/%d/data", channelno);
gwy_container_set_object_by_name(container,
strkey,
dfield);
g_object_unref(dfield);
g_free(strkey);
if (element->name) {
strkey = g_strdup_printf("/%d/data/title",
channelno);
gwy_container_set_string_by_name(container, strkey,
g_strdup(element->name));
g_free(strkey);
}
if (element->metadata) {
strkey = g_strdup_printf("/%d/meta",
channelno);
gwy_container_set_object_by_name(container,
strkey,
element->metadata);
g_free(strkey);
}
if (channel->lut) {
lutname = NULL;
if (gwy_strequal(channel->lut, "Red"))
lutname = g_strdup_printf("RGB-Red");
else if (gwy_strequal(channel->lut, "Green"))
lutname = g_strdup_printf("RGB-Green");
else if (gwy_strequal(channel->lut, "Blue"))
lutname = g_strdup_printf("RGB-Blue");
else if (gwy_strequal(channel->lut, "Gray"))
lutname = g_strdup_printf("Gray");
if (lutname) {
strkey = g_strdup_printf("/%u/base/palette",
channelno);
gwy_container_set_string_by_name(container,
strkey,
lutname);
g_free(strkey);
}
}
gwy_file_channel_import_log_add(container, channelno,
NULL, filename);
channelno++;
}
}
else if ((element->dimensions->len == 3)
|| ((element->dimensions->len == 4) && (res == 1))) {
/* Volume */
for (j = 0; j < element->channels->len; j++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, 0);
xres = dimension->res;
xreal = dimension->length;
xoffset = dimension->origin;
xstep = dimension->bytesinc;
siunitx = gwy_si_unit_new_parse(dimension->unit,
&power10x);
dimension = &g_array_index(element->dimensions,
LIFDimension, 1);
yres = dimension->res;
yreal = dimension->length;
yoffset = dimension->origin;
ystep = dimension->bytesinc;
siunity = gwy_si_unit_new_parse(dimension->unit,
&power10y);
if (element->dimensions->len == 3) {
dimension = &g_array_index(element->dimensions,
LIFDimension, 2);
}
else {
dimension = &g_array_index(element->dimensions,
LIFDimension, 3);
}
zres = dimension->res;
zreal = dimension->length;
zoffset = dimension->origin;
zstep = dimension->bytesinc;
siunitz = gwy_si_unit_new_parse(dimension->unit,
&power10z);
channel = &g_array_index(element->channels,
LIFChannel, j);
offset = channel->bytesinc;
siunitw = gwy_si_unit_new_parse(channel->unit,
&power10w);
wscale = pow10(power10w);
if (offset
+ (xres-1)*xstep + (yres-1)*ystep + (zres-1)*zstep
> memblock->memsize) {
gwy_debug("Memblock too small");
gwy_debug("%d %" G_GUINT64_FORMAT "",
offset + (xres-1)*xstep
+ (yres-1)*ystep + (zres-1)*zstep,
memblock->memsize);
err_SIZE_MISMATCH(error,
memblock->memsize,
offset + (xres-1)*xstep
+ (yres-1)*ystep + (zres-1)*zstep,
FALSE);
goto fail;
}
brick = gwy_brick_new(xres, yres, zres,
xreal*pow10(power10x),
yreal*pow10(power10y),
zreal*pow10(power10z),
TRUE);
gwy_brick_set_xoffset(brick, xoffset*pow10(power10x));
gwy_brick_set_yoffset(brick, yoffset*pow10(power10y));
gwy_brick_set_zoffset(brick, zoffset*pow10(power10z));
data = gwy_brick_get_data(brick);
for (z = 0; z < zres; z++)
for (y = 0; y < yres; y++)
for (x = 0; x < xres; x++) {
*(data++) = wscale * (gdouble)*(p + offset
+ x*xstep + y*ystep + z*zstep);
}
if (siunitx) {
gwy_brick_set_si_unit_x(brick, siunitx);
g_object_unref(siunitx);
}
if (siunity) {
gwy_brick_set_si_unit_y(brick, siunity);
g_object_unref(siunity);
}
if (siunitz) {
gwy_brick_set_si_unit_z(brick, siunitz);
g_object_unref(siunitz);
}
if (siunitw) {
gwy_brick_set_si_unit_w(brick, siunitw);
g_object_unref(siunitw);
}
strkey = g_strdup_printf("/brick/%d", volumeno);
gwy_container_set_object_by_name(container,
strkey,
brick);
g_free(strkey);
if (element->name) {
strkey = g_strdup_printf("/brick/%d/title",
volumeno);
gwy_container_set_string_by_name(container, strkey,
g_strdup(element->name));
g_free(strkey);
}
if (element->metadata) {
strkey = g_strdup_printf("/brick/%d/meta",
volumeno);
gwy_container_set_object_by_name(container,
strkey,
element->metadata);
g_free(strkey);
}
if (channel->lut) {
lutname = NULL;
if (gwy_strequal(channel->lut, "Red"))
lutname = g_strdup_printf("RGB-Red");
else if (gwy_strequal(channel->lut, "Green"))
lutname = g_strdup_printf("RGB-Green");
else if (gwy_strequal(channel->lut, "Blue"))
lutname = g_strdup_printf("RGB-Blue");
else if (gwy_strequal(channel->lut, "Gray"))
lutname = g_strdup_printf("Gray");
if (lutname) {
strkey = g_strdup_printf("/brick/%d/preview/palette",
volumeno);
gwy_container_set_string_by_name(container,
strkey,
lutname);
g_free(strkey);
}
}
dfield = gwy_data_field_new(xres, yres,
xreal, yreal, FALSE);
gwy_brick_mean_plane(brick, dfield,
0, 0, 0,
xres, yres, -1, FALSE);
strkey = g_strdup_printf("/brick/%d/preview",
volumeno);
gwy_container_set_object_by_name(container,
strkey,
dfield);
g_free(strkey);
g_object_unref(brick);
g_object_unref(dfield);
gwy_file_volume_import_log_add(container, volumeno,
NULL, filename);
volumeno++;
} /* for (channels) */
} /* if (volume) */
}
fail:
/* freeing all stuff */
if (file) {
if (file->memblocks) {
g_hash_table_foreach_remove(file->memblocks,
lif_remove_memblock,
NULL);
g_hash_table_unref(file->memblocks);
}
if (file->elements) {
for (i = 0; i < file->elements->len; i++) {
element = &g_array_index(file->elements, LIFElement, i);
if (element->dimensions) {
for (j = 0; j < element->dimensions->len; j++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, j);
if (dimension->unit)
g_free(dimension->unit);
}
g_array_free(element->dimensions, TRUE);
}
if (element->channels) {
for (j = 0; j < element->channels->len; j++) {
channel = &g_array_index(element->channels,
LIFChannel, j);
if (channel->unit)
g_free(channel->unit);
if (channel->lut)
g_free(channel->lut);
}
g_array_free(element->channels, TRUE);
}
if (element->name)
g_free(element->name);
if (element->memid)
g_free(element->memid);
if (element->metadata)
g_object_unref(element->metadata);
}
g_array_free(file->elements, TRUE);
}
g_free(file);
}
if (header->xmlheader)
g_free(header->xmlheader);
if (header) {
g_free(header);
}
return container;
}
static GwyContainer*
ols_load_tiff(const GwyTIFF *tiff, const gchar *filename, GError **error)
{
const gchar *colour_channels[] = { "Red", "Green", "Blue" };
const gchar *colour_channel_gradients[] = {
"RGB-Red", "RGB-Green", "RGB-Blue"
};
GwyContainer *container = NULL;
GwyDataField *dfield;
GwySIUnit *siunit;
GwyTIFFImageReader *reader = NULL;
GwyTextHeaderParser parser;
GHashTable *hash;
gint i, power10;
gchar *comment = NULL;
const gchar *s1;
GError *err = NULL;
guint spp, ch, id = 0, dir_num = 0;
gdouble *data;
gdouble z_axis = 1.0, xy_axis, factor;
GQuark quark;
GString *key;
/* Comment with parameters is common for all data fields */
if (!gwy_tiff_get_string0(tiff, GWY_TIFFTAG_IMAGE_DESCRIPTION, &comment)
|| !strstr(comment, MAGIC_COMMENT)) {
g_free(comment);
err_FILE_TYPE(error, "OLS");
return NULL;
}
/* Read the comment header. */
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
parser.section_template = "[\x1a]";
parser.endsection_template = "[\x1a End]";
parser.section_accessor = "::";
hash = gwy_text_header_parse(comment, &parser, NULL, NULL);
key = g_string_new(NULL);
for (dir_num = 0; dir_num < gwy_tiff_get_n_dirs(tiff); dir_num++) {
reader = gwy_tiff_image_reader_free(reader);
/* Request a reader, this ensures dimensions and stuff are defined. */
reader = gwy_tiff_get_image_reader(tiff, dir_num, 3, &err);
if (!reader) {
g_warning("Ignoring directory %u: %s", dir_num, err->message);
g_clear_error(&err);
continue;
}
spp = reader->samples_per_pixel;
g_string_printf(key, "Data %u Info::XY Convert Value", dir_num+1);
if (!(s1 = g_hash_table_lookup(hash, key->str))) {
g_warning("Cannot find 'XY Convert Value' for data %u.", dir_num+1);
continue;
}
xy_axis = g_ascii_strtod(s1, NULL);
if (!((xy_axis = fabs(xy_axis)) > 0)) {
g_warning("Real size step is 0.0, fixing to 1.0");
xy_axis = 1.0;
}
g_string_printf(key, "Data %u Info::Z Convert Value", dir_num+1);
if (!(s1 = g_hash_table_lookup(hash, key->str))) {
g_warning("Cannot find 'Z Convert Value' for data %u.", dir_num+1);
continue;
}
z_axis = g_ascii_strtod(s1, NULL);
for (ch = 0; ch < spp; ch++) {
siunit = gwy_si_unit_new_parse("nm", &power10);
factor = pow10(power10);
dfield = gwy_data_field_new(reader->width, reader->height,
reader->width * xy_axis * factor,
reader->height * xy_axis * factor,
FALSE);
// units
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
if (spp == 1) {
if (dir_num == 1)
siunit = gwy_si_unit_new_parse("nm", &power10);
else
siunit = gwy_si_unit_new_parse("1e-6", &power10);
}
else {
siunit = gwy_si_unit_new(NULL);
power10 = 0;
}
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
factor = z_axis * pow10(power10);
data = gwy_data_field_get_data(dfield);
for (i = 0; i < reader->height; i++)
gwy_tiff_read_image_row(tiff, reader, ch, i, factor, 0.0,
data + i*reader->width);
/* add read datafield to container */
if (!container)
container = gwy_container_new();
quark = gwy_app_get_data_key_for_id(id);
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
g_string_printf(key, "%s/title", g_quark_to_string(quark));
if (spp == 1) {
/* Channel 0 is texture */
if (dir_num == 0) {
gwy_container_set_string_by_name(container, key->str,
g_strdup("Texture"));
}
/* Channel 1 is topography */
else if (dir_num == 1) {
g_string_printf(key, "%s/title", g_quark_to_string(quark));
gwy_container_set_string_by_name(container, key->str,
g_strdup("Height"));
}
}
else {
gwy_container_set_string_by_name(container, key->str,
g_strdup(colour_channels[ch]));
g_string_printf(key, "/%d/base/palette", id);
gwy_container_set_string_by_name
(container, key->str,
g_strdup(colour_channel_gradients[ch]));
}
gwy_file_channel_import_log_add(container, id, NULL, filename);
id++;
}
}
g_hash_table_destroy(hash);
g_string_free(key, TRUE);
g_free(comment);
if (reader) {
gwy_tiff_image_reader_free(reader);
reader = NULL;
}
if (!container)
err_NO_DATA(error);
return container;
}
