static gboolean
fill_data_fields(SurfFile *surffile,
const guchar *buffer,
GError **error)
{
GwySIUnit *siunit;
gdouble *data;
guint i, j;
surffile->dfield = gwy_data_field_new(surffile->xres,
surffile->yres,
surffile->xres*surffile->dx,
surffile->yres*surffile->dy,
FALSE);
data = gwy_data_field_get_data(surffile->dfield);
switch (surffile->pointsize) {
case 16:
{
const gint16 *row, *d16 = (const gint16*)buffer;
for (i = 0; i < surffile->xres; i++) {
row = d16 + i*surffile->yres;
for (j = 0; j < surffile->yres; j++)
*(data++) = GINT16_FROM_LE(row[j]) * surffile->dz;
}
}
break;
case 32:
{
const gint32 *row, *d32 = (const gint32*)buffer;
for (i = 0; i < surffile->xres; i++) {
row = d32 + i*surffile->yres;
for (j = 0; j < surffile->yres; j++)
*(data++) = GINT32_FROM_LE(row[j]) * surffile->dz;
}
}
break;
default:
err_BPP(error, surffile->pointsize);
return FALSE;
break;
}
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(surffile->dfield, siunit);
g_object_unref(siunit);
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_z(surffile->dfield, siunit);
g_object_unref(siunit);
return TRUE;
}
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 GwyDataField*
read_text_data(const gchar *buffer,
gint text_data_start,
GHashTable *hash,
GError **error)
{
const gchar *p;
gchar *end;
gint xres, yres, i, power10;
gdouble xreal, yreal, zscale, xoff, yoff, zoff;
GwySIUnit *unitxy, *unitz;
GwyDataField *dfield = NULL;
gdouble *d;
unitxy = gwy_si_unit_new(NULL);
unitz = gwy_si_unit_new(NULL);
if (!get_scales(hash, TRUE,
&xres, &yres, &xreal, &yreal, &xoff, &yoff, unitxy,
&zscale, &zoff, unitz, error))
goto fail;
p = g_hash_table_lookup(hash, "DATA Unit");
gwy_si_unit_set_from_string_parse(unitz, p, &power10);
zscale = pow10(power10);
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
gwy_data_field_set_si_unit_z(dfield, unitz);
d = gwy_data_field_get_data(dfield);
p = (const gchar*)buffer + text_data_start;
for (i = 0; i < xres*yres; i++) {
d[i] = zscale*g_ascii_strtod(p, &end) + zoff;
if (end == p) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Cannot parse data values after %d of %d."),
i, xres*yres);
gwy_object_unref(dfield);
goto fail;
}
p = end + (*end == ',');
}
fail:
g_object_unref(unitxy);
g_object_unref(unitz);
return dfield;
}
static GwyDataField*
rhk_sm3_page_to_data_field(const RHKPage *page)
{
GwyDataField *dfield;
GwySIUnit *siunit;
const gchar *unit;
gint xres, yres, i;
const gint32 *pdata;
gdouble *data;
xres = page->x_size;
yres = page->y_size;
dfield = gwy_data_field_new(xres, yres,
xres*fabs(page->x_scale),
yres*fabs(page->y_scale),
FALSE);
data = gwy_data_field_get_data(dfield);
pdata = (const gint32*)page->page_data;
for (i = 0; i < xres*yres; i++)
data[i] = GINT32_FROM_LE(pdata[i])*page->z_scale + page->z_offset;
if (page->strings[RHK_STRING_X_UNITS]
&& page->strings[RHK_STRING_Y_UNITS]) {
if (!gwy_strequal(page->strings[RHK_STRING_X_UNITS],
page->strings[RHK_STRING_Y_UNITS]))
g_warning("X and Y units are different, using X");
unit = page->strings[RHK_STRING_X_UNITS];
}
else if (page->strings[RHK_STRING_X_UNITS])
unit = page->strings[RHK_STRING_X_UNITS];
else if (page->strings[RHK_STRING_Y_UNITS])
unit = page->strings[RHK_STRING_Y_UNITS];
else
unit = "";
siunit = gwy_si_unit_new(unit);
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
if (page->strings[RHK_STRING_Z_UNITS])
unit = page->strings[RHK_STRING_Z_UNITS];
else
unit = "";
/* Fix some silly units */
if (gwy_strequal(unit, "N/sec"))
unit = "s^-1";
siunit = gwy_si_unit_new(unit);
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
return dfield;
}
static void
sdfile_set_units(SDFile *sdfile,
GwyDataField *dfield)
{
GwySIUnit *siunit;
gwy_data_field_multiply(dfield, sdfile->zscale);
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
}
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 void
set_units(GwyDataField *dfield,
const MProFile *mprofile,
const gchar *zunit)
{
GwySIUnit *siunit;
if (mprofile->camera_res)
siunit = gwy_si_unit_new("m");
else
siunit = gwy_si_unit_new("");
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
siunit = gwy_si_unit_new(zunit);
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
}
static gboolean
fill_data_fields(SurfFile *surffile,
const guchar *buffer,
GError **error)
{
gdouble *data;
surffile->dfield = gwy_data_field_new(surffile->xres,
surffile->yres,
surffile->xres*surffile->dx,
surffile->yres*surffile->dy,
FALSE);
data = gwy_data_field_get_data(surffile->dfield);
switch (surffile->pointsize) {
case 16:
gwy_convert_raw_data(buffer, surffile->xres*surffile->yres, 1,
GWY_RAW_DATA_SINT16, GWY_BYTE_ORDER_LITTLE_ENDIAN,
data, surffile->dz, 0.0);
break;
case 32:
gwy_convert_raw_data(buffer, surffile->xres*surffile->yres, 1,
GWY_RAW_DATA_SINT32, GWY_BYTE_ORDER_LITTLE_ENDIAN,
data, surffile->dz, 0.0);
break;
default:
err_BPP(error, surffile->pointsize);
return FALSE;
break;
}
gwy_data_field_set_si_unit_xy(surffile->dfield, surffile->xyunit);
g_object_unref(surffile->xyunit);
gwy_data_field_set_si_unit_z(surffile->dfield, surffile->zunit);
g_object_unref(surffile->zunit);
return TRUE;
}
static GwyDataField*
hash_to_data_field(GHashTable *hash,
GHashTable *scannerlist,
GHashTable *scanlist,
NanoscopeFileType file_type,
gboolean has_version,
guint bufsize,
gchar *buffer,
gint gxres,
gint gyres,
gchar **p,
GError **error)
{
NanoscopeValue *val;
GwyDataField *dfield;
GwySIUnit *unitz, *unitxy;
gchar *s, *end;
gchar un[5];
gint xres, yres, bpp, offset, size, power10;
gdouble xreal, yreal, q;
gdouble *data;
gboolean size_ok, use_global;
if (!require_keys(hash, error, "Samps/line", "Number of lines",
"Scan size", "Data offset", "Data length", NULL))
return NULL;
val = g_hash_table_lookup(hash, "Samps/line");
xres = GWY_ROUND(val->hard_value);
val = g_hash_table_lookup(hash, "Number of lines");
yres = GWY_ROUND(val->hard_value);
val = g_hash_table_lookup(hash, "Bytes/pixel");
bpp = val ? GWY_ROUND(val->hard_value) : 2;
/* scan size */
val = g_hash_table_lookup(hash, "Scan size");
xreal = g_ascii_strtod(val->hard_value_str, &end);
if (errno || *end != ' ') {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Cannot parse `Scan size' field."));
return NULL;
}
gwy_debug("xreal = %g", xreal);
s = end+1;
yreal = g_ascii_strtod(s, &end);
if (errno || *end != ' ') {
/* Old files don't have two numbers here, assume equal dimensions */
yreal = xreal;
end = s;
}
gwy_debug("yreal = %g", yreal);
while (g_ascii_isspace(*end))
end++;
if (sscanf(end, "%4s", un) != 1) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Cannot parse `Scan size' field."));
return NULL;
}
gwy_debug("xy unit: <%s>", un);
unitxy = gwy_si_unit_new_parse(un, &power10);
q = pow10(power10);
xreal *= q;
yreal *= q;
offset = size = 0;
if (file_type == NANOSCOPE_FILE_TYPE_BIN) {
val = g_hash_table_lookup(hash, "Data offset");
offset = GWY_ROUND(val->hard_value);
val = g_hash_table_lookup(hash, "Data length");
size = GWY_ROUND(val->hard_value);
size_ok = FALSE;
use_global = FALSE;
/* Try channel size and local size */
if (!size_ok && size == bpp*xres*yres)
size_ok = TRUE;
if (!size_ok && size == bpp*gxres*gyres) {
size_ok = TRUE;
use_global = TRUE;
}
/* If they don't match exactly, try whether they at least fit inside */
if (!size_ok && size > bpp*MAX(xres*yres, gxres*gyres)) {
size_ok = TRUE;
use_global = (xres*yres < gxres*gyres);
}
if (!size_ok && size > bpp*MIN(xres*yres, gxres*gyres)) {
size_ok = TRUE;
use_global = (xres*yres > gxres*gyres);
}
if (!size_ok) {
err_SIZE_MISMATCH(error, size, bpp*xres*yres);
return NULL;
}
if (use_global) {
if (gxres) {
xreal *= (gdouble)gxres/xres;
xres = gxres;
}
if (gyres) {
yreal *= (gdouble)gyres/yres;
yres = gyres;
}
}
if (offset + size > (gint)bufsize) {
err_SIZE_MISMATCH(error, offset + size, bufsize);
return NULL;
}
}
q = 1.0;
unitz = get_physical_scale(hash, scannerlist, scanlist, has_version,
&q, error);
if (!unitz)
return NULL;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
data = gwy_data_field_get_data(dfield);
switch (file_type) {
case NANOSCOPE_FILE_TYPE_TXT:
if (!read_ascii_data(xres*yres, data, p, bpp, error)) {
g_object_unref(dfield);
return NULL;
}
break;
case NANOSCOPE_FILE_TYPE_BIN:
if (!read_binary_data(xres*yres, data, buffer + offset, bpp, error)) {
g_object_unref(dfield);
return NULL;
}
break;
default:
g_assert_not_reached();
break;
}
gwy_data_field_multiply(dfield, q);
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
gwy_data_field_set_si_unit_z(dfield, unitz);
g_object_unref(unitz);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
g_object_unref(unitxy);
return dfield;
}
static 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 GwyDataField*
sensofar_read_data_field(SensofarDataDesc *data_desc,
GwyDataField **maskfield,
const guchar **p,
gsize size,
GError **error)
{
GwyDataField *dfield, *mfield;
guint xres, yres, i, j, mcount;
GwySIUnit *units = NULL;
gdouble *data, *mdata;
if (maskfield)
*maskfield = NULL;
yres = gwy_get_guint32_le(p);
xres = gwy_get_guint32_le(p);
gwy_debug("Data size: %dx%d", xres, yres);
if (err_SIZE_MISMATCH(error, xres*yres*sizeof(gfloat),
size - 2*sizeof(guint32), FALSE))
return NULL;
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
return NULL;
if (!((data_desc->axes_config.mppx
= fabs(data_desc->axes_config.mppx)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
data_desc->axes_config.mppx = 1.0;
}
if (!((data_desc->axes_config.mppy
= fabs(data_desc->axes_config.mppy)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
data_desc->axes_config.mppy = 1.0;
}
dfield = gwy_data_field_new(xres, yres,
data_desc->axes_config.mppx * xres * Micrometer,
data_desc->axes_config.mppy * yres * Micrometer,
FALSE);
units = gwy_si_unit_new("m"); // values are in um only
gwy_data_field_set_si_unit_xy(dfield, units);
g_object_unref(units);
units = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_z(dfield, units);
g_object_unref(units);
mfield = gwy_data_field_new_alike(dfield, FALSE);
gwy_data_field_fill(mfield, 1.0);
data = gwy_data_field_get_data(dfield);
mdata = gwy_data_field_get_data(mfield);
for (i = 0; i < yres; i++) {
for (j = 0; j < xres; j++) {
gdouble v = gwy_get_gfloat_le(p);
if (v == 1000001.0)
mdata[i*xres + j] = 0.0;
else
data[i*xres + j] = v*Micrometer;
}
}
gwy_debug("Offset: %g %g",
data_desc->axes_config.x_0, data_desc->axes_config.y_0);
//FIXME: offset later, support of offset determined by version?
//gwy_data_field_set_xoffset(d, pow10(power10)*data_desc.axes_config.x_0);
//gwy_data_field_set_yoffset(d, pow10(power10)*data_desc.axes_config.y_0);
mcount = gwy_app_channel_remove_bad_data(dfield, mfield);
if (maskfield && mcount)
*maskfield = mfield;
else
g_object_unref(mfield);
return dfield;
}
static GwyContainer*
ecs_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
gchar *s = NULL, *s2 = NULL;
GwySIUnit *siunit;
const guchar *p;
gdouble *data, *row;
guint xres, yres, i, j;
gdouble xreal, q;
const gint16 *pdata;
guchar c;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
g_clear_error(&err);
return NULL;
}
if (size < HEADER_SIZE + 2) {
err_TOO_SHORT(error);
goto fail;
}
p = buffer + ECS_RESOLUTION;
xres = gwy_get_guint16_le(&p);
yres = gwy_get_guint16_le(&p);
gwy_debug("xres: %u, yres: %u", xres, yres);
if (size != HEADER_SIZE + 2*xres*yres) {
err_SIZE_MISMATCH(error, HEADER_SIZE + 2*xres*yres, size);
goto fail;
}
/* Scan size */
p = buffer + ECS_SCAN_SIZE;
s = get_PASCAL_STRING(&p, HEADER_SIZE - ECS_SCAN_SIZE);
if (!s) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Scan size header field overlaps with data."));
goto fail;
}
gwy_debug("Scan size str: <%s>", s);
if (!g_str_has_prefix(s, "Scan Size: ")) {
err_FILE_TYPE(error, "ECS");
goto fail;
}
if (sscanf(s + strlen("Scan Size: "), "%lf %lf%c", &xreal, &q, &c)
!= 3) {
err_INVALID(error, "Scan Size");
goto fail;
}
g_free(s);
s = NULL;
gwy_debug("xreal: %g q: %g unit: %s",
xreal, q, c == 0x8f ? "Angstrom" : "Nanometer");
if (c == 0x8f) {
xreal *= 1e-10;
q *= 1e-10;
}
else {
xreal *= 1e-9;
q *= 1e-9;
}
q /= 65536.0;
/* This does not make much sense when xres != yres, but it is what
* Snomputz does. */
dfield = gwy_data_field_new(xres, yres, xreal, xreal, FALSE);
data = gwy_data_field_get_data(dfield);
pdata = (const gint16*)(buffer + HEADER_SIZE);
for (i = 0; i < yres; i++) {
row = data + (yres-1 - i)*xres;
for (j = 0; j < xres; j++)
row[j] = GINT16_TO_LE(pdata[i*xres + j])*q;
}
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
/* Channel title */
p = buffer + ECS_CHANNEL;
s = get_PASCAL_STRING(&p, HEADER_SIZE - ECS_CHANNEL);
if (!s || !*s)
s = g_strdup("Topography");
gwy_container_set_string_by_name(container, "/0/data/title", s);
s = NULL;
meta = gwy_container_new();
/* Date & time */
p = buffer + ECS_DATE;
s = get_PASCAL_STRING(&p, HEADER_SIZE - ECS_DATE);
if (s) {
p = buffer + ECS_TIME;
s2 = get_PASCAL_STRING(&p, HEADER_SIZE - ECS_TIME);
if (s2) {
gwy_container_set_string_by_name(meta, "Date",
g_strconcat(s, " ", s2, NULL));
g_free(s2);
s2 = NULL;
}
g_free(s);
s = NULL;
}
/* Channel title */
p = buffer + ECS_CHANNEL;
s = get_PASCAL_STRING(&p, HEADER_SIZE - ECS_CHANNEL);
if (s && *s) {
gwy_container_set_string_by_name(meta, "Comment", s);
s = NULL;
}
if (gwy_container_get_n_items(meta))
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
fail:
g_free(s);
g_free(s2);
gwy_object_unref(dfield);
gwy_file_abandon_contents(buffer, size, NULL);
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 GwyContainer*
gxsm_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
static const gchar *dimensions[] = { "time", "value", "dimy", "dimx" };
GwyContainer *data = NULL;
GwyDataField *dfield;
GwySIUnit *siunit;
NetCDF cdffile;
const NetCDFDim *dim;
const NetCDFVar *var;
const NetCDFAttr *attr;
gdouble real;
gint i, power10;
if (!cdffile_load(&cdffile, filename, error))
return NULL;
if (cdffile.nrecs) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("NetCDF records are not supported."));
goto gxsm_load_fail;
}
/* Look for variable "H" or "FloatField". This seems to be how GXSM calls
* data. */
if (!(var = cdffile_get_var(&cdffile, "H"))
&& !(var = cdffile_get_var(&cdffile, "FloatField"))) {
err_NO_DATA(error);
goto gxsm_load_fail;
}
/* Check the dimensions. We only know how to handle time=1 and value=1. */
for (i = 0; i < var->ndims; i++) {
dim = cdffile.dims + var->dimids[i];
if (!gwy_strequal(dim->name, dimensions[i])
|| (i < 2 && dim->length != 1)) {
/* XXX */
err_NO_DATA(error);
goto gxsm_load_fail;
}
}
if (err_DIMENSION(error, cdffile.dims[var->dimids[3]].length)
|| err_DIMENSION(error, cdffile.dims[var->dimids[2]].length))
goto gxsm_load_fail;
dfield = read_data_field((const guchar*)(cdffile.buffer + var->begin),
cdffile.dims[var->dimids[3]].length,
cdffile.dims[var->dimids[2]].length,
var->type);
if ((siunit = read_real_size(&cdffile, "rangex", &real, &power10))) {
/* Use negated positive conditions to catch NaNs */
if (!((real = fabs(real)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
real = 1.0;
}
gwy_data_field_set_xreal(dfield, real*pow10(power10));
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
}
if ((siunit = read_real_size(&cdffile, "rangey", &real, &power10))) {
/* Use negated positive conditions to catch NaNs */
if (!((real = fabs(real)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
real = 1.0;
}
gwy_data_field_set_yreal(dfield, real*pow10(power10));
/* must be the same gwy_data_field_set_si_unit_xy(dfield, siunit); */
g_object_unref(siunit);
}
if ((siunit = read_real_size(&cdffile, "rangez", &real, &power10))) {
/* rangez seems to be some bogus value, take only units */
gwy_data_field_set_si_unit_z(dfield, siunit);
gwy_data_field_multiply(dfield, pow10(power10));
g_object_unref(siunit);
}
if ((siunit = read_real_size(&cdffile, "dz", &real, &power10))) {
/* on the other hand the units seem to be bogus here, take the range */
gwy_data_field_multiply(dfield, real);
g_object_unref(siunit);
}
data = gwy_container_new();
gwy_container_set_object_by_name(data, "/0/data", dfield);
g_object_unref(dfield);
if ((attr = cdffile_get_attr(var->attrs, var->nattrs, "long_name"))
&& attr->type == NC_CHAR
&& attr->nelems) {
gwy_container_set_string_by_name(data, "/0/data/title",
g_strndup(attr->values, attr->nelems));
}
gxsm_load_fail:
gwy_file_abandon_contents(cdffile.buffer, cdffile.size, NULL);
cdffile_free(&cdffile);
return data;
}
static GwyDataField*
read_datafield(const guchar *buffer,
guint size,
const StmprgFile *stmprgfile,
GError **error)
{
gint xres, yres, bpp;
gdouble xreal, yreal, q;
GwyDataField *dfield;
gdouble *data;
GwySIUnit *unit;
bpp = 2; /* words, always */
xres = stmprgfile->mainfield.points;
yres = stmprgfile->mainfield.lines;
xreal = Angstrom * stmprgfile->mainfield.field_x;
yreal = Angstrom * stmprgfile->mainfield.field_y;
q = stmprgfile->mainfield.sol_z * 1.0e-5; /* 5 ?? */
/* resolution of z value in angstrom/bit, 1.0e-10 */
if (err_SIZE_MISMATCH(error, bpp*xres*yres, size, FALSE))
return NULL;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
data = gwy_data_field_get_data(dfield);
if (!read_binary_ubedata(xres * yres, data, buffer, bpp)) {
err_BPP(error, bpp);
g_object_unref(dfield);
return NULL;
}
gwy_data_field_multiply(dfield, q);
unit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, unit);
g_object_unref(unit);
/* Assuming we are reading channel1... */
switch (stmprgfile->control.channel1) {
case STMPRG_CHANNEL_OFF:
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("First channel is switched off."));
return NULL;
case STMPRG_CHANNEL_Z:
unit = gwy_si_unit_new("m");
break;
case STMPRG_CHANNEL_I:
case STMPRG_CHANNEL_I_I0:
case STMPRG_CHANNEL_I0:
unit = gwy_si_unit_new("A");
break;
case STMPRG_CHANNEL_EXT1:
case STMPRG_CHANNEL_EXT2:
case STMPRG_CHANNEL_U0:
unit = gwy_si_unit_new("V");
break;
default:
g_assert_not_reached();
break;
}
gwy_data_field_set_si_unit_z(dfield, unit);
g_object_unref(unit);
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*
plt_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
GwyDataField *dfield = NULL;
GwyTextHeaderParser parser;
GwySIUnit *xunit, *yunit, *zunit;
gchar *p, *value, *buffer = NULL;
GHashTable *hash = NULL;
gsize size;
GError *err = NULL;
G_GNUC_UNUSED gdouble xreal, yreal, zreal;
gint i, xres, yres;
gdouble *data;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
if (strncmp(buffer, MAGIC1, MIN(size, sizeof(MAGIC1)-1))) {
err_FILE_TYPE(error, "Nanosurf PLT");
goto fail;
}
/* Find the first line not starting with '#' */
for (p = buffer; (p - buffer) + 1 < size; p++) {
if ((p[0] == '\n' || p[0] == '\r')
&& (p[1] != '\n' && p[1] != '#')) {
break;
}
}
*p = '\0';
p++;
gwy_clear(&parser, 1);
parser.line_prefix = "#";
parser.key_value_separator = ":";
hash = gwy_text_header_parse(buffer, &parser, NULL, NULL);
if (!require_keys(hash, error,
"Channel", "Lines", "Points",
"XRange", "YRange", "ZRange",
NULL))
goto fail;
xres = atoi(g_hash_table_lookup(hash, "Points"));
yres = atoi(g_hash_table_lookup(hash, "Lines"));
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
goto fail;
value = g_hash_table_lookup(hash, "XRange");
xreal = g_ascii_strtod(value, &value);
xunit = gwy_si_unit_new(value);
value = g_hash_table_lookup(hash, "YRange");
yreal = g_ascii_strtod(value, &value);
yunit = gwy_si_unit_new(value);
value = g_hash_table_lookup(hash, "ZRange");
zreal = g_ascii_strtod(value, &value);
zunit = gwy_si_unit_new(value);
/* 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;
}
if (!gwy_si_unit_equal(xunit, yunit))
g_warning("X and Y units differ, using X");
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_si_unit_xy(dfield, xunit);
gwy_data_field_set_si_unit_z(dfield, zunit);
g_object_unref(xunit);
g_object_unref(yunit);
g_object_unref(zunit);
data = gwy_data_field_get_data(dfield);
value = p;
for (i = 0; i < xres*yres; i++) {
data[i] = g_ascii_strtod(value, &p);
value = p;
}
container = gwy_container_new();
gwy_container_set_object(container, gwy_app_get_data_key_for_id(0), dfield);
g_object_unref(dfield);
if ((value = g_hash_table_lookup(hash, "Channel")))
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:
g_free(buffer);
g_hash_table_destroy(hash);
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*
pni_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
static const GwyEnum titles[] = {
{ "Height", DATA_TYPE_HGT, },
{ "Sens", DATA_TYPE_SEN, },
{ "Dem", DATA_TYPE_DEM, },
{ "Error", DATA_TYPE_ERR, },
{ "L-R", DATA_TYPE_L_R, },
};
GwyContainer *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
const guchar *p;
gint i, xres, yres;
PNIDataType data_type;
PNIValueType value_type;
PNIDirection direction;
gdouble xreal, yreal, zscale;
gdouble *data;
const gint16 *d16;
GwySIUnit *siunit;
const gchar *title;
gchar *s;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < DATA_START + 2) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
p = buffer + DATA_HEADER_START + RESOLUTION_OFFSET;
xres = gwy_get_guint32_le(&p);
yres = gwy_get_guint32_le(&p);
gwy_debug("%d %d", xres, yres);
if (err_DIMENSION(error, xres)
|| err_DIMENSION(error, yres)
|| err_SIZE_MISMATCH(error, DATA_START + 2*xres*yres, size, TRUE)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
p = buffer + DATA_HEADER_START;
data_type = p[DATA_TYPE_OFFSET];
value_type = p[VALUE_TYPE_OFFSET];
direction = p[DIRECTION_OFFSET];
p = buffer + DATA_HEADER_START + REAL_SIZE_OFFSET;
xreal = gwy_get_gfloat_le(&p);
yreal = gwy_get_gfloat_le(&p);
/* 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;
}
xreal *= Micrometer;
yreal *= Micrometer;
p = buffer + DATA_HEADER_START + VALUE_SCALE_OFFSET;
zscale = gwy_get_gfloat_le(&p);
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
data = gwy_data_field_get_data(dfield);
d16 = (const gint16*)(buffer + DATA_START);
for (i = 0; i < xres*yres; i++)
data[i] = zscale*GINT16_FROM_LE(d16[i])/65536.0;
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);
switch (value_type) {
case VALUE_TYPE_NM:
siunit = gwy_si_unit_new("m");
gwy_data_field_multiply(dfield, Nanometer);
break;
case VALUE_TYPE_MV:
siunit = gwy_si_unit_new("V");
gwy_data_field_multiply(dfield, Milivolt);
break;
default:
g_warning("Value type %d is unknown", value_type);
siunit = gwy_si_unit_new(NULL);
break;
}
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
title = gwy_enum_to_string(data_type, titles, G_N_ELEMENTS(titles));
if (title) {
s = g_strdup_printf("%s (%s)",
title,
direction ? "Forward" : "Backward");
gwy_container_set_string_by_name(container, "/0/data/title", s);
}
else
g_warning("Data type %d is unknown", data_type);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
return container;
}
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*
read_binary_data(const gchar *buffer,
gsize size,
GHashTable *hash,
GError **error)
{
ShimadzuDataType data_type;
gint xres, yres, i;
guint expected;
gdouble xreal, yreal, zscale, xoff, yoff, zoff;
GwySIUnit *unitxy, *unitz;
GwyDataField *dfield = NULL;
gdouble *d;
const gchar *s;
if (!(s = g_hash_table_lookup(hash, "DataType"))) {
err_MISSING_FIELD(error, "DataType");
return NULL;
}
if (g_ascii_strcasecmp(s, "short") == 0)
data_type = SHIMADZU_SHORT;
else if (g_ascii_strcasecmp(s, "float") == 0)
data_type = SHIMADZU_FLOAT;
else {
err_UNSUPPORTED(error, "DataType");
return NULL;
}
unitxy = gwy_si_unit_new(NULL);
unitz = gwy_si_unit_new(NULL);
if (!get_scales(hash, FALSE,
&xres, &yres, &xreal, &yreal, &xoff, &yoff, unitxy,
&zscale, &zoff, unitz, error))
goto fail;
expected = data_type*xres*yres + HEADER_SIZE;
if (err_SIZE_MISMATCH(error, expected, size, FALSE))
goto fail;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
gwy_data_field_set_si_unit_z(dfield, unitz);
d = gwy_data_field_get_data(dfield);
if (data_type == SHIMADZU_SHORT) {
const gint16 *d16 = (const gint16*)(buffer + HEADER_SIZE);
for (i = 0; i < xres*yres; i++)
d[i] = zscale*GUINT16_FROM_LE(d16[i]) + zoff;
}
else if (data_type == SHIMADZU_FLOAT) {
const guchar *p = buffer + HEADER_SIZE;
for (i = 0; i < xres*yres; i++)
d[i] = zscale*gwy_get_gfloat_le(&p) + zoff;
}
else {
g_assert_not_reached();
}
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
fail:
g_object_unref(unitxy);
g_object_unref(unitz);
return dfield;
}
static GwyDataField*
read_data_field_old(const guchar *buffer,
guint size,
GError **error)
{
gint xres, yres, n, i, j, vx, vy;
G_GNUC_UNUSED gint vz;
gdouble xscale, yscale, zscale, xreal, yreal, q;
G_GNUC_UNUSED gdouble xunit, yunit, zunit;
GwyDataField *dfield;
GwySIUnit *siunit;
gdouble *data, *row;
const gint16 *pdata;
const guchar *p;
p = buffer + RES_OFFSET_OLD;
xres = gwy_get_guint16_le(&p);
yres = gwy_get_guint16_le(&p);
gwy_debug("xres: %d, yres: %d", xres, yres);
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
return NULL;
n = xres*yres;
if (err_SIZE_MISMATCH(error, 2*n + HEADER_SIZE_OLD, size, TRUE))
return NULL;
p = buffer + SCALE_OFFSET_OLD;
xscale = gwy_get_gdouble_le(&p);
yscale = gwy_get_gdouble_le(&p);
zscale = gwy_get_gdouble_le(&p);
p = buffer + UNIT_OFFSET_OLD;
xunit = gwy_get_gdouble_le(&p);
yunit = gwy_get_gdouble_le(&p);
zunit = gwy_get_gdouble_le(&p);
p = buffer + SPEED_OFFSET_OLD;
vx = gwy_get_guint32_le(&p);
vy = gwy_get_guint32_le(&p);
vz = gwy_get_guint32_le(&p);
xreal = xscale * vx;
yreal = yscale * vy;
q = zscale;
gwy_debug("xreal: %g, yreal: %g, zscale: %g", xreal, yreal, q);
/* 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);
data = gwy_data_field_get_data(dfield);
pdata = (const gint16*)(buffer + HEADER_SIZE_OLD);
for (i = 0; i < yres; i++) {
row = data + i*xres;
for (j = 0; j < xres; j++)
row[j] = GUINT16_FROM_LE(pdata[i*xres + j])*q;
}
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
return dfield;
}
static GwyContainer*
text_dump_import(gchar *buffer,
gsize size,
const gchar *filename,
GError **error)
{
gchar *val, *key, *pos, *line, *title;
GwyContainer *data;
GwyDataField *dfield;
gdouble xreal, yreal;
gint xres, yres, id;
GwySIUnit *uxy, *uz;
const guchar *s;
gdouble *d;
gsize n;
data = gwy_container_new();
pos = buffer;
while ((line = gwy_str_next_line(&pos)) && *line) {
val = strchr(line, '=');
if (!val || *line != '/') {
g_warning("Garbage key: %s", line);
continue;
}
if ((gsize)(val - buffer) + 1 > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached when value was expected."));
goto fail;
}
*val = '\0';
val++;
if (!gwy_strequal(val, "[") || !pos || *pos != '[') {
gwy_debug("<%s>=<%s>", line, val);
if (*val)
gwy_container_set_string_by_name(data, line, g_strdup(val));
else
gwy_container_remove_by_name(data, line);
continue;
}
g_assert(pos && *pos == '[');
pos++;
dfield = NULL;
gwy_container_gis_object_by_name(data, line, &dfield);
id = 0;
sscanf(line, "/%d", &id);
/* get datafield parameters from already read values, failing back
* to values of original data field */
key = g_strconcat(line, "/xres", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
xres = atoi(s);
else if (dfield)
xres = gwy_data_field_get_xres(dfield);
else {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing data field width."));
goto fail;
}
g_free(key);
key = g_strconcat(line, "/yres", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
yres = atoi(s);
else if (dfield)
yres = gwy_data_field_get_yres(dfield);
else {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing data field height."));
goto fail;
}
g_free(key);
key = g_strconcat(line, "/xreal", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
xreal = g_ascii_strtod(s, NULL);
else if (dfield)
xreal = gwy_data_field_get_xreal(dfield);
else {
g_warning("Missing real data field width.");
xreal = 1.0; /* 0 could cause troubles */
}
g_free(key);
key = g_strconcat(line, "/yreal", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
yreal = g_ascii_strtod(s, NULL);
else if (dfield)
yreal = gwy_data_field_get_yreal(dfield);
else {
g_warning("Missing real data field height.");
yreal = 1.0; /* 0 could cause troubles */
}
g_free(key);
if (!(xres > 0 && yres > 0 && xreal > 0 && yreal > 0)) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Data field dimensions are not positive numbers."));
goto fail;
}
key = g_strconcat(line, "/unit-xy", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
uxy = gwy_si_unit_new((const gchar*)s);
else if (dfield) {
uxy = gwy_data_field_get_si_unit_xy(dfield);
uxy = gwy_si_unit_duplicate(uxy);
}
else {
g_warning("Missing lateral units.");
uxy = gwy_si_unit_new("m");
}
g_free(key);
key = g_strconcat(line, "/unit-z", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
uz = gwy_si_unit_new((const gchar*)s);
else if (dfield) {
uz = gwy_data_field_get_si_unit_z(dfield);
uz = gwy_si_unit_duplicate(uz);
}
else {
g_warning("Missing value units.");
uz = gwy_si_unit_new("m");
}
g_free(key);
key = g_strconcat(line, "/title", NULL);
title = NULL;
gwy_container_gis_string_by_name(data, key, (const guchar**)&title);
/* We got the contained string but that would disappear. */
title = g_strdup(title);
g_free(key);
n = xres*yres*sizeof(gdouble);
if ((gsize)(pos - buffer) + n + 3 > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached inside a data field."));
goto fail;
}
dfield = GWY_DATA_FIELD(gwy_data_field_new(xres, yres, xreal, yreal,
FALSE));
gwy_data_field_set_si_unit_xy(dfield, GWY_SI_UNIT(uxy));
gwy_object_unref(uxy);
gwy_data_field_set_si_unit_z(dfield, GWY_SI_UNIT(uz));
gwy_object_unref(uz);
d = gwy_data_field_get_data(dfield);
#if (G_BYTE_ORDER == G_LITTLE_ENDIAN)
memcpy(d, pos, n);
#else
gwy_memcpy_byte_swap(pos, (guint8*)d,
sizeof(gdouble), xres*yres, sizeof(gdouble)-1);
#endif
pos += n;
val = gwy_str_next_line(&pos);
if (!gwy_strequal(val, "]]")) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing end of data field marker."));
gwy_object_unref(dfield);
goto fail;
}
gwy_container_remove_by_prefix(data, line);
gwy_container_set_object_by_name(data, line, dfield);
g_object_unref(dfield);
if (title) {
key = g_strconcat(line, "/title", NULL);
gwy_container_set_string_by_name(data, key, title);
g_free(key);
}
gwy_file_channel_import_log_add(data, id, NULL, filename);
}
return data;
fail:
gwy_container_remove_by_prefix(data, NULL);
g_object_unref(data);
return NULL;
}
static gboolean
read_aist_raster(const guchar **p, gsize *size, AistContext *context)
{
AistRaster raster;
GwyDataField *dfield, *mfield;
GwySIUnit *xyunit, *zunit;
gboolean ok = FALSE;
guint i, j, n, len;
const guchar *data;
gchar *s;
gchar key[32];
gdouble *d;
gdouble qxy, qz;
gwy_clear(&raster, 1);
gwy_debug("reading common");
if (!read_aist_common(p, size, &raster.common))
goto fail;
gwy_debug("reading raster");
if (!read_qt_int(p, size, &raster.xres)
|| !read_qt_int(p, size, &raster.yres)
|| !read_qt_double(p, size, &raster.left)
|| !read_qt_double(p, size, &raster.right)
|| !read_qt_double(p, size, &raster.top)
|| !read_qt_double(p, size, &raster.bottom)
|| !read_qt_string(p, size, &raster.xunits)
|| !read_qt_string(p, size, &raster.yunits)
|| !read_qt_string(p, size, &raster.zunits))
goto fail;
if (!read_qt_byte_array(p, size, &len, &data))
goto fail;
n = raster.xres * raster.yres;
if (len != n*sizeof(gdouble))
goto fail;
xyunit = extract_units(raster.xunits, &qxy);
zunit = extract_units(raster.zunits, &qz);
dfield = gwy_data_field_new(raster.xres, raster.yres,
qxy*fabs(raster.right - raster.left),
qxy*fabs(raster.bottom - raster.top),
FALSE);
gwy_data_field_set_si_unit_xy(dfield, xyunit);
gwy_data_field_set_si_unit_z(dfield, zunit);
/* Apparently this is not generally wanted.
gwy_data_field_set_xoffset(dfield, qxy*MIN(raster.left, raster.right));
gwy_data_field_set_yoffset(dfield, qxy*MIN(raster.top, raster.bottom));
*/
g_object_unref(xyunit);
g_object_unref(zunit);
d = gwy_data_field_get_data(dfield);
for (i = 0; i < raster.yres; i++) {
for (j = 0; j < raster.xres; j++) {
d[(raster.yres-1 - i)*raster.xres + j]
= qz*gwy_get_gdouble_le(&data);
}
}
g_snprintf(key, sizeof(key), "/%d/data", context->channel_id);
gwy_container_set_object_by_name(context->container, key, dfield);
g_object_unref(dfield);
gwy_file_channel_import_log_add(context->container, context->channel_id,
NULL, context->filename);
if ((s = strchr(raster.common.name, '[')))
s = g_strchomp(g_strndup(raster.common.name, s - raster.common.name));
else
s = g_strdup(raster.common.name);
g_snprintf(key, sizeof(key), "/%d/data/title", context->channel_id);
gwy_container_set_string_by_name(context->container, key, s);
g_snprintf(key, sizeof(key), "/%d/mask", context->channel_id);
context->channel_id++;
/* At this moment we consider the loading successful. */
ok = TRUE;
/* The mask raster is byte-valued. It contains nonzeroes in points that
* were measured (the opposite of how we normally create masks upon
* import). */
if (read_qt_byte_array(p, size, &len, &data)) {
if (len == raster.xres*raster.yres) {
mfield = make_mask_field(dfield, data);
if (mfield) {
gwy_app_channel_remove_bad_data(dfield, mfield);
gwy_container_set_object_by_name(context->container, key,
mfield);
g_object_unref(mfield);
}
}
/* Here's something called view data. It means the data was processed
* (by whatever means) hence we are not interesed in it. */
read_qt_byte_array(p, size, &len, &data);
}
fail:
free_aist_common(&raster.common);
g_free(raster.xunits);
g_free(raster.yunits);
g_free(raster.zunits);
return ok;
}
static GwyContainer*
burleigh_load(const gchar *filename)
{
GwySIUnit *unit;
GwyContainer *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize size = 0;
GError *err = NULL;
IMGFile imgfile;
GwyDataField *dfield;
gdouble *data;
const gint16 *d;
gdouble scale;
guint i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
g_warning("Cannot get file contents");
g_clear_error(&err);
return NULL;
}
if (size < HEADER_SIZE_MIN + 2) {
g_warning("File is too short");
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
memset(&imgfile, 0, sizeof(imgfile));
p = buffer;
imgfile.version = get_FLOAT(&p);
imgfile.version_int = ROUND(10*imgfile.version);
if (imgfile.version_int == 21) {
d = burleigh_load_v21(&imgfile, buffer, size);
if (!d) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
}
else {
g_warning("File format version %.f is not supported", imgfile.version);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
dfield = GWY_DATA_FIELD(gwy_data_field_new(imgfile.xres, imgfile.yres,
Angstrom*imgfile.xrange,
Angstrom*imgfile.yrange,
FALSE));
data = gwy_data_field_get_data(dfield);
scale = Angstrom * imgfile.z_gain * imgfile.zrange;
for (i = 0; i < imgfile.xres*imgfile.yres; i++)
data[i] = scale * GINT16_FROM_LE(d[i]);
gwy_file_abandon_contents(buffer, size, NULL);
unit = GWY_SI_UNIT(gwy_si_unit_new("m"));
gwy_data_field_set_si_unit_xy(dfield, unit);
g_object_unref(unit);
container = GWY_CONTAINER(gwy_container_new());
switch (imgfile.data_type) {
case BURLEIGH_CURRENT:
unit = GWY_SI_UNIT(gwy_si_unit_new("A"));
gwy_container_set_string_by_name(container, "/filename/title",
g_strdup("Current"));
break;
case BURLEIGH_TOPOGRAPHY:
unit = GWY_SI_UNIT(gwy_si_unit_new("m"));
gwy_container_set_string_by_name(container, "/filename/title",
g_strdup("Topography"));
break;
default:
unit = GWY_SI_UNIT(gwy_si_unit_new("m"));
break;
}
gwy_data_field_set_si_unit_z(dfield, unit);
g_object_unref(unit);
gwy_container_set_object_by_name(container, "/0/data", (GObject*)dfield);
g_object_unref(dfield);
return container;
}
/* FIXME: this function could use some sort of failure indication, if the
* file is damaged and no data field can be loaded, suspicionless caller can
* return empty Container */
static void
tiff_load_channel(TIFF *tiff,
GwyContainer *container, GwyContainer *meta,
gint idx, gint ilen, gint jlen, gdouble ulen, gdouble vlen)
{
GwyDataField *dfield;
GwySIUnit *siunit;
GString *key;
gdouble *data;
guchar *buffer;
gchar *channel;
const gchar *name = NULL;
const gchar *slot = NULL;
const gchar *unit = NULL;
gboolean retrace = FALSE;
gboolean reflect = FALSE;
gdouble mult = 0.0;
gdouble offset = 0.0;
gint num_slots = 0;
gint i, j;
tiff_get_custom_string(tiff, JPK_TIFFTAG_ChannelFancyName, &name);
if (!name)
tiff_get_custom_string(tiff, JPK_TIFFTAG_Channel, &name);
g_return_if_fail(name != NULL);
tiff_get_custom_boolean(tiff, JPK_TIFFTAG_Channel_retrace, &retrace);
channel = g_strdup_printf("%s%s", name, retrace ? " (retrace)" : "");
gwy_debug("channel: %s", channel);
tiff_get_custom_integer(tiff, JPK_TIFFTAG_NrOfSlots, &num_slots);
g_return_if_fail(num_slots > 0);
gwy_debug("num_slots: %d", num_slots);
/* Locate the default slot */
tiff_get_custom_string(tiff, JPK_TIFFTAG_DefaultSlot, &slot);
g_return_if_fail(slot != NULL);
gwy_debug("num_slots: %d, default slot: %s", num_slots, slot);
for (i = 0; i < num_slots; i++) {
const gchar *string;
if (tiff_get_custom_string(tiff, JPK_TIFFTAG_Slot_Name(i), &string)
&& string
&& gwy_strequal(string, slot)) {
tiff_get_custom_string(tiff, JPK_TIFFTAG_Scaling_Type(i), &string);
g_return_if_fail(gwy_strequal(string, "LinearScaling"));
tiff_get_custom_double(tiff, JPK_TIFFTAG_Scaling_Multiply(i),
&mult);
tiff_get_custom_double(tiff, JPK_TIFFTAG_Scaling_Offset(i),
&offset);
gwy_debug("multipler: %g offset: %g", mult, offset);
tiff_get_custom_string(tiff, JPK_TIFFTAG_Encoder_Unit(i), &unit);
break;
}
}
/* Create a new data field */
dfield = gwy_data_field_new(ilen, jlen, ulen, vlen, FALSE);
siunit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
if (unit) {
siunit = gwy_si_unit_new(unit);
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
}
/* Read the scan data */
data = gwy_data_field_get_data(dfield);
buffer = g_new(guchar, TIFFScanlineSize(tiff));
tiff_get_custom_boolean(tiff, JPK_TIFFTAG_Grid_Reflect, &reflect);
if (!reflect)
data += (jlen - 1) * ilen;
for (j = 0; j < jlen; j++) {
const guint16 *src = (const guint16 *)buffer;
gdouble *dest = data;
TIFFReadScanline(tiff, buffer, j, 0);
for (i = 0; i < ilen; i++) {
guint16 s = *src++;
*dest++ = offset + mult * (gdouble)s;
}
if (reflect)
data += ilen;
else
data -= ilen;
}
/* Add the GwyDataField to the container */
key = g_string_new("");
g_string_printf(key, "/%d/data", idx);
gwy_container_set_object_by_name(container, key->str, dfield);
g_object_unref(dfield);
g_string_append(key, "/title");
gwy_container_set_string_by_name(container, key->str, channel);
if (gwy_container_get_n_items(meta)) {
GwyContainer *tmp;
tmp = gwy_container_duplicate(meta);
g_string_printf(key, "/%d/meta", idx);
gwy_container_set_object_by_name(container, key->str, tmp);
g_object_unref(tmp);
}
g_string_free(key, TRUE);
}
static GwyContainer*
burleigh_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwySIUnit *unit;
GwyContainer *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize size = 0;
GError *err = NULL;
IMGFile imgfile;
GwyDataField *dfield;
gdouble *data;
const gint16 *d;
gdouble zoom;
guint i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < HEADER_SIZE_MIN + 2) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
gwy_clear(&imgfile, 1);
p = buffer;
imgfile.version = gwy_get_gfloat_le(&p);
imgfile.version_int = GWY_ROUND(10*imgfile.version);
if (imgfile.version_int == 21) {
d = burleigh_load_v21(&imgfile, buffer, size, error);
if (!d) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
}
else {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File format version %.1f is not supported."),
imgfile.version);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
zoom = burleigh_get_zoom_v21(&imgfile);
if (err_DIMENSION(error, imgfile.xres)
|| err_DIMENSION(error, imgfile.yres)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
dfield = gwy_data_field_new(imgfile.xres, imgfile.yres,
Angstrom*imgfile.xrange/zoom,
Angstrom*imgfile.yrange/zoom,
FALSE);
data = gwy_data_field_get_data(dfield);
for (i = 0; i < imgfile.xres*imgfile.yres; i++)
data[i] = GINT16_FROM_LE(d[i])*imgfile.zrange/4095.0;
gwy_file_abandon_contents(buffer, size, NULL);
unit = gwy_si_unit_new("m");
gwy_data_field_set_si_unit_xy(dfield, unit);
g_object_unref(unit);
container = gwy_container_new();
switch (imgfile.data_type) {
case BURLEIGH_CURRENT:
unit = gwy_si_unit_new("A");
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup("Current"));
gwy_data_field_multiply(dfield, Picoampere);
break;
case BURLEIGH_TOPOGRAPHY:
unit = gwy_si_unit_new("m");
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup("Topography"));
gwy_data_field_multiply(dfield, Angstrom);
break;
default:
unit = gwy_si_unit_new("m");
break;
}
gwy_data_field_set_si_unit_z(dfield, unit);
g_object_unref(unit);
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
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 void
gwy_data_field_facet_distribution(GwyDataField *dfield,
gint kernel_size,
GwyContainer *container)
{
GwyDataField *dtheta, *dphi, *dist;
GwySIUnit *siunit;
gdouble *xd, *yd, *data;
const gdouble *xdc, *ydc;
gdouble q, max;
gint res, hres, i, j, mi, mj, xres, yres;
if (gwy_container_gis_object_by_name(container, "/theta", &dtheta))
g_object_ref(dtheta);
else
dtheta = gwy_data_field_new_alike(dfield, FALSE);
if (gwy_container_gis_object_by_name(container, "/phi", &dphi))
g_object_ref(dphi);
else
dphi = gwy_data_field_new_alike(dfield, FALSE);
compute_slopes(dfield, kernel_size, dtheta, dphi);
xres = gwy_data_field_get_xres(dfield);
yres = gwy_data_field_get_yres(dfield);
xd = gwy_data_field_get_data(dtheta);
yd = gwy_data_field_get_data(dphi);
for (i = xres*yres; i; i--, xd++, yd++) {
gdouble theta, phi;
slopes_to_angles(*xd, *yd, &theta, &phi);
*xd = theta;
*yd = phi;
}
q = gwy_data_field_get_max(dtheta);
q = MIN(q*1.05, G_PI/2.0);
q = G_SQRT2/(2.0*sin(q/2.0));
if (gwy_container_gis_object_by_name(container, "/0/data", &dist)) {
g_object_ref(dist);
gwy_data_field_clear(dist);
gwy_data_field_set_xreal(dist, 2.0*G_SQRT2/q);
gwy_data_field_set_yreal(dist, 2.0*G_SQRT2/q);
}
else {
dist = gwy_data_field_new(FDATA_RES, FDATA_RES,
2.0*G_SQRT2/q, 2.0*G_SQRT2/q,
TRUE);
siunit = gwy_si_unit_new("");
gwy_data_field_set_si_unit_z(dist, siunit);
g_object_unref(siunit);
/* FIXME */
siunit = gwy_si_unit_new("");
gwy_data_field_set_si_unit_xy(dist, siunit);
g_object_unref(siunit);
}
res = FDATA_RES;
hres = (res - 1)/2;
data = gwy_data_field_get_data(dist);
xdc = gwy_data_field_get_data_const(dtheta);
ydc = gwy_data_field_get_data_const(dphi);
for (i = xres*yres; i; i--, xdc++, ydc++) {
gdouble x, y;
gint xx, yy;
angles_to_xy(*xdc, *ydc, &x, &y);
xx = GWY_ROUND(q*x/G_SQRT2*hres) + hres;
yy = GWY_ROUND(q*y/G_SQRT2*hres) + hres;
data[yy*res + xx] += 1.0;
}
/* Find maxima */
mi = mj = hres;
max = 0;
for (i = 1; i+1 < res; i++) {
for (j = 1; j+1 < res; j++) {
gdouble z;
z = data[i*res + j]
+ 0.3*(data[i*res + j - 1]
+ data[i*res + j + 1]
+ data[i*res - res + j]
+ data[i*res + res + j])
+ 0.1*(data[i*res - res + j - 1]
+ data[i*res - res + j + 1]
+ data[i*res + res + j - 1]
+ data[i*res + res + j + 1]);
if (G_UNLIKELY(z > max)) {
max = z;
mi = i;
mj = j;
}
}
}
for (i = res*res; i; i--, data++)
*data = pow(*data, 0.35);
gwy_container_set_double_by_name(container, "/q", q);
{
gdouble x, y, theta, phi;
x = (mj - hres)*G_SQRT2/(q*hres);
y = (mi - hres)*G_SQRT2/(q*hres);
xy_to_angles(x, y, &theta, &phi);
gwy_container_set_double_by_name(container, "/theta0", theta);
gwy_container_set_double_by_name(container, "/phi0", phi);
}
gwy_container_set_object_by_name(container, "/0/data", dist);
g_object_unref(dist);
gwy_container_set_object_by_name(container, "/theta", dtheta);
g_object_unref(dtheta);
gwy_container_set_object_by_name(container, "/phi", dphi);
g_object_unref(dphi);
gwy_container_set_string_by_name(container, "/0/base/palette",
g_strdup(FVIEW_GRADIENT));
gwy_data_field_data_changed(dist);
}
static GwyContainer*
burleigh_exp_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
gchar *buffer = NULL;
BurleighExpHeader header;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield;
gdouble *data;
guint i, n;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < MIN_FILE_SIZE + 2) {
err_TOO_SHORT(error);
g_free(buffer);
return NULL;
}
if (!burleigh_exp_read_header(&header, buffer, error))
goto fail;
n = header.xres * header.yres;
if (header.binary) {
if (header.bpp != 16) {
err_BPP(error, header.bpp);
goto fail;
}
else if (err_SIZE_MISMATCH(error, header.length + 2*n, size, TRUE))
goto fail;
}
dfield = gwy_data_field_new(header.xres, header.yres,
header.xscale, header.yscale,
FALSE);
data = gwy_data_field_get_data(dfield);
if (header.binary) {
const gint16 *d16 = (const gint16*)(buffer + header.length);
for (i = 0; i < n; i++)
data[i] = GINT16_FROM_LE(d16[i]);
}
else {
gchar *p = buffer + header.length;
for (i = 0; i < n; i++)
data[i] = strtol(p, &p, 10);
}
gwy_data_field_multiply(dfield, header.zscale/32768.0);
/* Units references released in free_header() */
gwy_data_field_set_si_unit_xy(dfield, header.xyunits);
gwy_data_field_set_si_unit_z(dfield, header.zunits);
container = gwy_container_new();
gwy_container_set_object(container, gwy_app_get_data_key_for_id(0), dfield);
g_object_unref(dfield);
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
free_header(&header);
g_free(buffer);
return container;
}
