static GwyContainer*
dumb_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
gchar *buffer = NULL;
GError *err = NULL;
gsize size;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < MAGIC_SIZE || memcmp(buffer, MAGIC, MAGIC_SIZE) != 0) {
err_FILE_TYPE(error, "Gwyddion dumb dump");
goto fail;
}
container = text_dump_import(buffer, size, filename, error);
fail:
g_free(buffer);
return container;
}
static GHashTable*
hitachi_load_header(const gchar *filename,
gchar **header,
GError **error)
{
gchar *line, *p;
GwyTextHeaderParser parser;
GHashTable *hash = NULL;
gsize size;
GError *err = NULL;
*header = NULL;
if (!g_file_get_contents(filename, header, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
p = *header;
line = gwy_str_next_line(&p);
if (!gwy_strequal(line, MAGIC)) {
err_FILE_TYPE(error, "Hitachi SEM");
g_free(header);
*header = NULL;
return NULL;
}
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
gwy_debug("reading header");
hash = gwy_text_header_parse(p, &parser, NULL, NULL);
gwy_debug("header %p", hash);
return hash;
}
static GwyContainer*
spmlab_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
const gchar *title;
gint type;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
/* 2048 is wrong. moreover it differs for r5 and r4, kasigra uses 5752 for
* r5 */
if (size < 2048) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
if (buffer[0] != '#' || buffer[1] != 'R') {
err_FILE_TYPE(error, "Thermicroscopes SpmLab");
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
switch (buffer[2]) {
case '3':
case '4':
case '5':
case '6':
dfield = read_data_field(buffer, size, buffer[2], &type, error);
break;
default:
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Unknown format version %c."), buffer[2]);
break;
}
gwy_file_abandon_contents(buffer, size, NULL);
if (!dfield)
return NULL;
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
title = gwy_enum_to_string(type,
spmlab_channel_types,
G_N_ELEMENTS(spmlab_channel_types));
if (*title)
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(title));
return container;
}
static GwyContainer*
aist_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
AistContext context;
guchar *buffer = NULL;
const guchar *p;
gsize remaining, size = 0;
GError *err = NULL;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
p = buffer;
remaining = size;
context.container = gwy_container_new();
context.filename = filename;
context.channel_id = 0;
context.graph_id = 0;
read_aist_tree(&p, &remaining, &context);
gwy_file_abandon_contents(buffer, size, NULL);
if ((context.channel_id == 0) && (context.graph_id == 0)) {
g_object_unref(context.container);
context.container = NULL;
err_NO_DATA(error);
}
return context.container;
}
static GwyContainer*
hitachi_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error,
const gchar *name)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
GwyDataField *(*do_load)(const guchar*, guint, GError**);
guint header_size;
if (gwy_strequal(name, "hitachi-afm")) {
do_load = &read_data_field;
header_size = HEADER_SIZE;
}
else if (gwy_strequal(name, "hitachi-afm-old")) {
do_load = &read_data_field_old;
header_size = HEADER_SIZE_OLD;
}
else {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_UNIMPLEMENTED,
_("Hitachi-AFM has not registered file type `%s'."), name);
return NULL;
}
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < header_size + 2) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
dfield = do_load(buffer, size, error);
gwy_file_abandon_contents(buffer, size, NULL);
if (!dfield)
return NULL;
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("Topography"));
gwy_app_channel_check_nonsquare(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
return container;
}
static GwyContainer*
gwyfile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GObject *object;
GError *err = NULL;
guchar *buffer = NULL;
gsize size = 0;
gsize pos = 0;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < MAGIC_SIZE
|| (memcmp(buffer, MAGIC, MAGIC_SIZE)
&& memcmp(buffer, MAGIC2, MAGIC_SIZE))) {
err_FILE_TYPE(error, "Gwyddion");
gwy_file_abandon_contents(buffer, size, &err);
return NULL;
}
if (!memcmp(buffer, MAGIC, MAGIC_SIZE)) {
object = gwy_container_deserialize_old(buffer + MAGIC_SIZE,
size - MAGIC_SIZE, &pos);
gwyfile_remove_old_data(object);
}
else
object = gwy_serializable_deserialize(buffer + MAGIC_SIZE,
size - MAGIC_SIZE, &pos);
gwy_file_abandon_contents(buffer, size, &err);
if (!object) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Data deserialization failed."));
return NULL;
}
if (!GWY_IS_CONTAINER(object)) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Data deserialization succeeded, but resulted in "
"an unexpected object %s."),
g_type_name(G_TYPE_FROM_INSTANCE(object)));
g_object_unref(object);
return NULL;
}
gwyfile_pack_metadata(GWY_CONTAINER(object));
return GWY_CONTAINER(object);
}
static GwyContainer*
sdfile_load_text(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
SDFile sdfile;
GwyContainer *container = NULL;
gchar *p, *buffer = NULL;
gsize len, size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
len = size;
p = buffer;
if (sdfile_read_header_text(&p, &len, &sdfile, error)) {
if (check_params(&sdfile, len, error))
dfield = sdfile_read_data_text(&sdfile, error);
}
if (!dfield) {
g_free(buffer);
return NULL;
}
sdfile_set_units(&sdfile, dfield);
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("Topography"));
g_free(buffer);
if (sdfile.extras)
g_hash_table_destroy(sdfile.extras);
return container;
}
static GwyContainer*
sdfile_load_bin(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
SDFile sdfile;
GwyContainer *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize len, size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
len = size;
p = buffer;
if (sdfile_read_header_bin(&p, &len, &sdfile, error)) {
if (check_params(&sdfile, len, error))
dfield = sdfile_read_data_bin(&sdfile);
}
gwy_file_abandon_contents(buffer, size, NULL);
if (!dfield)
return NULL;
sdfile_set_units(&sdfile, dfield);
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("Topography"));
return container;
}
static GwyContainer*
int_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta;
GwyDataField *dfield = NULL, *mfield = NULL;
CodeVGridDataType type;
gchar *line, *p, *comment, *end, *buffer = NULL;
const gchar *unit, *title;
gchar **fields = NULL;
gsize size;
GError *err = NULL;
gdouble xreal, yreal;
gint i, xres, yres, no_data_value = 32767;
guint fi;
gdouble scale_size, wavelength, q = 1.0, x_scale = 1.0;
gboolean nearest_neighbour = FALSE;
gdouble *data, *mdata;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
/* Skip comments. */
p = buffer;
for (line = gwy_str_next_line(&p);
line && line[0] == '!';
line = gwy_str_next_line(&p)) {
gwy_debug("comment <%s>", line);
}
if (!line) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
/* The title. */
comment = line;
if (!(line = gwy_str_next_line(&p))) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
gwy_debug("comment <%s>", comment);
fields = split_line_in_place(line);
if (!fields
|| g_strv_length(fields) < 8
|| !gwy_strequal(fields[0], "GRD")
|| !(xres = atoi(fields[1]))
|| !(yres = atoi(fields[2]))
|| !(type = gwy_stramong(fields[3],
"SUR", "WFR", "FIL", "THV", "BIR", "CAO",
NULL))
|| !gwy_strequal(fields[4], "WVL")
|| (!(wavelength = g_ascii_strtod(fields[5], &end))
&& end == fields[5])) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
gwy_debug("type %u (%s)", type, fields[3]);
gwy_debug("xres %d, yres %d", xres, yres);
gwy_debug("wavelength %g", wavelength);
fi = 6;
if (gwy_strequal(fields[fi], "NNB")) {
nearest_neighbour = TRUE;
fi++;
}
gwy_debug("nearest_neighbour %d", nearest_neighbour);
if (!fields[fi] || !gwy_strequal(fields[fi], "SSZ")) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
fi++;
if (!(scale_size = g_ascii_strtod(fields[fi], &end)) && end == fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
gwy_debug("scale_size %g", scale_size);
if (!scale_size) {
g_warning("Zero SSZ, fixing to 1.0");
scale_size = 1.0;
}
fi++;
if (fields[fi] && gwy_strequal(fields[fi], "NDA")) {
fi++;
if (!fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
no_data_value = atoi(fields[fi]);
fi++;
}
gwy_debug("no_data_value %d", no_data_value);
if (fields[fi] && gwy_strequal(fields[fi], "XSC")) {
fi++;
if (!fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
if (!(x_scale = g_ascii_strtod(fields[fi], &end))
&& end == fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
fi++;
}
gwy_debug("x_scale %g", x_scale);
if (!x_scale) {
g_warning("Zero XSC, fixing to 1.0");
x_scale = 1.0;
}
/* There may be more stuff but we do not know anything about it. */
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
goto fail;
yreal = 1.0;
xreal = x_scale*yreal;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, TRUE);
if (type == CODEV_INT_SURFACE_DEFORMATION) {
q = 1e-6*wavelength/scale_size;
unit = "m";
title = "Surface";
}
else if (type == CODEV_INT_WAVEFRONT_DEFORMATION) {
q = 1e-6*wavelength/scale_size;
unit = "m";
title = "Wavefront";
}
else {
g_warning("Don't know how to convert this grid data type to physical "
"units.");
title = fields[3];
}
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), unit);
mfield = gwy_data_field_new_alike(dfield, TRUE);
data = gwy_data_field_get_data(dfield);
mdata = gwy_data_field_get_data(mfield);
for (i = 0; i < xres*yres; i++, p = end) {
gint value = strtol(p, &end, 10);
if (value != no_data_value && (type != CODEV_INT_INTENSITY_FILTER
|| value >= 0)) {
mdata[i] = 1.0;
data[i] = q*value;
}
}
if (!gwy_app_channel_remove_bad_data(dfield, mfield))
gwy_object_unref(mfield);
container = gwy_container_new();
/*
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
from F. Riguet : apparently no flip is needed (the raw data import module
gives the correct orientation without further flipping)
*/
gwy_container_set_object(container, gwy_app_get_data_key_for_id(0), dfield);
g_object_unref(dfield);
gwy_app_channel_check_nonsquare(container, 0);
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(title));
if (mfield) {
/*
gwy_data_field_invert(mfield, FALSE, TRUE, FALSE);
*/
gwy_container_set_object(container, gwy_app_get_mask_key_for_id(0),
mfield);
g_object_unref(mfield);
}
meta = gwy_container_new();
gwy_container_set_string_by_name(meta, "Comment", g_strdup(comment));
gwy_container_set_string_by_name(meta, "Interpolation",
g_strdup(nearest_neighbour
? "NNB" : "Linear"));
gwy_container_set_string_by_name(meta, "Wavelength",
g_strdup_printf("%g μm", wavelength));
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
g_free(fields);
g_free(buffer);
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 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;
}
static GwyContainer*
surffile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
SurfFile surffile;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize expected_size, size = 0;
GError *err = NULL;
gchar signature[12];
gdouble max, min;
gint add = 0;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
g_clear_error(&err);
return NULL;
}
if (size < SURF_HEADER_SIZE + 2) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
p = buffer;
get_CHARARRAY(signature, &p);
if (strncmp(signature, "DIGITAL SURF", 12) != 0) {
err_FILE_TYPE(error, "Surf");
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
surffile.format = gwy_get_guint16_le(&p);
surffile.nobjects = gwy_get_guint16_le(&p);
surffile.version = gwy_get_guint16_le(&p);
surffile.type = gwy_get_guint16_le(&p);
get_CHARS0(surffile.object_name, &p, 30);
get_CHARS0(surffile.operator_name, &p, 30);
surffile.material_code = gwy_get_guint16_le(&p);
surffile.acquisition = gwy_get_guint16_le(&p);
surffile.range = gwy_get_guint16_le(&p);
surffile.special_points = gwy_get_guint16_le(&p);
surffile.absolute = gwy_get_guint16_le(&p);
/*reserved*/
p += 8;
surffile.pointsize = gwy_get_guint16_le(&p);
surffile.zmin = gwy_get_gint32_le(&p);
surffile.zmax = gwy_get_gint32_le(&p);
surffile.xres = gwy_get_gint32_le(&p);
surffile.yres = gwy_get_gint32_le(&p);
surffile.nofpoints = gwy_get_guint32_le(&p);
surffile.dx = gwy_get_gfloat_le(&p);
surffile.dy = gwy_get_gfloat_le(&p);
surffile.dz = gwy_get_gfloat_le(&p);
get_CHARS0(surffile.xaxis, &p, 16);
get_CHARS0(surffile.yaxis, &p, 16);
get_CHARS0(surffile.zaxis, &p, 16);
get_CHARS0(surffile.dx_unit, &p, 16);
get_CHARS0(surffile.dy_unit, &p, 16);
get_CHARS0(surffile.dz_unit, &p, 16);
get_CHARS0(surffile.xlength_unit, &p, 16);
get_CHARS0(surffile.ylength_unit, &p, 16);
get_CHARS0(surffile.zlength_unit, &p, 16);
surffile.xunit_ratio = gwy_get_gfloat_le(&p);
surffile.yunit_ratio = gwy_get_gfloat_le(&p);
surffile.zunit_ratio = gwy_get_gfloat_le(&p);
surffile.imprint = gwy_get_guint16_le(&p);
surffile.inversion = gwy_get_guint16_le(&p);
surffile.leveling = gwy_get_guint16_le(&p);
p += 12;
surffile.seconds = gwy_get_guint16_le(&p);
surffile.minutes = gwy_get_guint16_le(&p);
surffile.hours = gwy_get_guint16_le(&p);
surffile.day = gwy_get_guint16_le(&p);
surffile.month = gwy_get_guint16_le(&p);
surffile.year = gwy_get_guint16_le(&p);
surffile.measurement_duration = gwy_get_guint16_le(&p);
surffile.comment_size = gwy_get_guint16_le(&p);
surffile.private_size = gwy_get_guint16_le(&p);
get_CHARARRAY(surffile.client_zone, &p);
surffile.XOffset = gwy_get_gfloat_le(&p);
surffile.YOffset = gwy_get_gfloat_le(&p);
surffile.ZOffset = gwy_get_gfloat_le(&p);
gwy_debug("fileformat: %d, n_of_objects: %d, "
"version: %d, object_type: %d",
surffile.format, surffile.nobjects,
surffile.version, surffile.type);
gwy_debug("object name: <%s>", surffile.object_name);
gwy_debug("operator name: <%s>", surffile.operator_name);
gwy_debug("material code: %d, acquisition type: %d",
surffile.material_code, surffile.acquisition);
gwy_debug("range type: %d, special points: %d, absolute: %d",
surffile.range,
surffile.special_points, (gint)surffile.absolute);
gwy_debug("data point size: %d", surffile.pointsize);
gwy_debug("zmin: %d, zmax: %d", surffile.zmin, surffile.zmax);
gwy_debug("xres: %d, yres: %d (xres*yres = %d)",
surffile.xres, surffile.yres, (surffile.xres*surffile.yres));
gwy_debug("total number of points: %d", surffile.nofpoints);
gwy_debug("dx: %g, dy: %g, dz: %g",
surffile.dx, surffile.dy, surffile.dz);
gwy_debug("X axis name: %16s", surffile.xaxis);
gwy_debug("Y axis name: %16s", surffile.yaxis);
gwy_debug("Z axis name: %16s", surffile.zaxis);
gwy_debug("dx unit: %16s", surffile.dx_unit);
gwy_debug("dy unit: %16s", surffile.dy_unit);
gwy_debug("dz unit: %16s", surffile.dz_unit);
gwy_debug("X axis unit: %16s", surffile.xlength_unit);
gwy_debug("Y axis unit: %16s", surffile.ylength_unit);
gwy_debug("Z axis unit: %16s", surffile.zlength_unit);
gwy_debug("xunit_ratio: %g, yunit_ratio: %g, zunit_ratio: %g",
surffile.xunit_ratio, surffile.yunit_ratio, surffile.zunit_ratio);
gwy_debug("imprint: %d, inversion: %d, leveling: %d",
surffile.imprint, surffile.inversion, surffile.leveling);
gwy_debug("Time: %d:%d:%d, Date: %d.%d.%d",
surffile.hours, surffile.minutes, surffile.seconds,
surffile.day, surffile.month, surffile.year);
gwy_debug("private zone size: %d, comment size %d",
surffile.private_size, surffile.comment_size);
expected_size = (SURF_HEADER_SIZE
+ surffile.pointsize/8*surffile.xres*surffile.yres);
if (expected_size != size) {
gwy_debug("Size mismatch!");
if (size > expected_size) add = size - expected_size; /*TODO correct this !*/
else {
err_SIZE_MISMATCH(error, expected_size, size);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
}
p = buffer + SURF_HEADER_SIZE + add;
if (!fill_data_fields(&surffile, p, error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
if (!surffile.absolute) {
max = gwy_data_field_get_max(surffile.dfield);
min = gwy_data_field_get_min(surffile.dfield);
gwy_data_field_add(surffile.dfield, -min);
gwy_data_field_multiply(surffile.dfield,
(surffile.zmax - surffile.zmin)/(max-min));
}
switch (surffile.inversion) {
case SURF_INV_Z:
gwy_data_field_invert(surffile.dfield, FALSE, FALSE, TRUE);
break;
case SURF_FLIP_Z:
gwy_data_field_invert(surffile.dfield, FALSE, TRUE, TRUE);
break;
case SURF_FLOP_Z:
gwy_data_field_invert(surffile.dfield, TRUE, FALSE, TRUE);
break;
default:
break;
}
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", surffile.dfield);
g_object_unref(surffile.dfield);
meta = surffile_get_metadata(&surffile);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_app_channel_check_nonsquare(container, 0);
return container;
}
static GwyContainer*
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*
pt3file_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
PicoHarpFile pt3file;
GwyContainer *meta, *container = NULL;
GwyDataField *dfield = NULL;
GwyGraphModel *gmodel = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize header_len, size = 0;
GError *err = NULL;
LineTrigger *linetriggers = NULL;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
gwy_clear(&pt3file, 1);
if (!(header_len = pt3file_read_header(buffer, size, &pt3file, error)))
goto fail;
if (err_SIZE_MISMATCH
(error, header_len + pt3file.number_of_records*sizeof(guint32), size,
FALSE))
goto fail;
if (pt3file.measurement_mode != 3) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("T2 measurement mode is not implemented."));
goto fail;
}
if (pt3file.imaging.common.instrument != PICO_HARP_PIE710
&& pt3file.imaging.common.instrument != PICO_HARP_KDT180) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only PI E710 and KDT180-100-Im imaging formats are "
"implemented."));
goto fail;
}
/* Scan the records and find the line triggers */
p = buffer + header_len;
if (!(linetriggers = pt3file_scan_line_triggers(&pt3file, p, error)))
goto fail;
container = gwy_container_new();
dfield = pt3file_extract_counts(&pt3file, linetriggers, p);
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("Photon count"));
meta = pt3file_get_metadata(&pt3file);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
gmodel = pt3file_extract_decay(&pt3file, p);
gwy_container_set_object_by_name(container, "/0/graph/graph/1", gmodel);
g_object_unref(gmodel);
fail:
g_free(linetriggers);
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static GwyContainer*
rhk_sm4_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
RHKFile rhkfile;
RHKObject *obj, o;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
const guchar *p;
GString *key = NULL;
guint i, imageid = 0, graphid = 0;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
gwy_clear(&rhkfile, 1);
if (size < HEADER_SIZE) {
err_TOO_SHORT(error);
goto fail;
}
/* File header */
p = buffer + MAGIC_OFFSET + MAGIC_TOTAL_SIZE;
rhkfile.page_count = gwy_get_guint32_le(&p);
rhkfile.object_count = gwy_get_guint32_le(&p);
rhkfile.object_field_size = gwy_get_guint32_le(&p);
gwy_debug("page_count: %u, object_count: %u, object_field_size: %u",
rhkfile.page_count, rhkfile.object_count,
rhkfile.object_field_size);
if (rhkfile.object_field_size != OBJECT_SIZE)
g_warning("Object field size %u differs from %u",
rhkfile.object_field_size, OBJECT_SIZE);
rhkfile.reserved1 = gwy_get_guint32_le(&p);
rhkfile.reserved2 = gwy_get_guint32_le(&p);
/* Header objects */
if (!(rhkfile.objects = rhk_sm4_read_objects(buffer, p, size,
rhkfile.object_count,
RHK_OBJECT_FILE_HEADER,
error)))
goto fail;
/* Find page index header */
if (!(obj = rhk_sm4_find_object(rhkfile.objects, rhkfile.object_count,
RHK_OBJECT_PAGE_INDEX_HEADER,
RHK_OBJECT_FILE_HEADER, error))
|| !rhk_sm4_read_page_index_header(&rhkfile.page_index_header,
obj, buffer, size, error))
goto fail;
/* There, find the page index array. That's a single object in the object
* list but it contains a page_count-long sequence of page indices. */
rhkfile.page_indices = g_new0(RHKPageIndex,
rhkfile.page_index_header.page_count);
if (!(obj = rhk_sm4_find_object(rhkfile.page_index_header.objects,
rhkfile.page_index_header.object_count,
RHK_OBJECT_PAGE_INDEX_ARRAY,
RHK_OBJECT_PAGE_INDEX_HEADER, error)))
goto fail;
o = *obj;
for (i = 0; i < rhkfile.page_index_header.page_count; i++) {
if (!rhk_sm4_read_page_index(rhkfile.page_indices + i, &o,
buffer, size, error))
goto fail;
/* Carefully move to the next page index */
o.offset += o.size + OBJECT_SIZE*rhkfile.page_indices[i].object_count;
}
container = gwy_container_new();
key = g_string_new(NULL);
/* Read pages */
for (i = 0; i < rhkfile.page_index_header.page_count; i++) {
RHKPageIndex *pi = rhkfile.page_indices + i;
RHKPage *page = &pi->page;
/* Page must contain header */
if (!(obj = rhk_sm4_find_object(pi->objects, pi->object_count,
RHK_OBJECT_PAGE_HEADER,
RHK_OBJECT_PAGE_INDEX, error))
|| !rhk_sm4_read_page_header(page, obj, buffer, size, error))
goto fail;
/* Page must contain data */
if (!(obj = rhk_sm4_find_object(pi->objects, pi->object_count,
RHK_OBJECT_PAGE_DATA,
RHK_OBJECT_PAGE_INDEX, error))
|| !rhk_sm4_read_page_data(page, obj, buffer, error))
goto fail;
/* Page may contain strings */
if (!(obj = rhk_sm4_find_object(page->objects, page->object_count,
RHK_OBJECT_STRING_DATA,
RHK_OBJECT_PAGE_HEADER, NULL))
|| !rhk_sm4_read_string_data(page, obj, pi->page.string_count,
buffer)) {
g_warning("Failed to read string data in page %u", i);
}
/* Read the data */
if (pi->data_type == RHK_DATA_IMAGE) {
GwyDataField *dfield = rhk_sm4_page_to_data_field(page);
GQuark quark = gwy_app_get_data_key_for_id(imageid);
const gchar *scandir, *name;
gchar *title;
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
if ((name = page->strings[RHK_STRING_LABEL])) {
scandir = gwy_enum_to_string(page->scan_dir, scan_directions,
G_N_ELEMENTS(scan_directions));
g_string_assign(key, g_quark_to_string(quark));
g_string_append(key, "/title");
if (scandir && *scandir)
title = g_strdup_printf("%s [%s]", name, scandir);
else
title = g_strdup(name);
gwy_container_set_string_by_name(container, key->str, title);
}
meta = rhk_sm4_get_metadata(pi, page);
g_string_printf(key, "/%u/meta", imageid);
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
imageid++;
}
else if (pi->data_type == RHK_DATA_LINE) {
GwyGraphModel *gmodel;
RHKSpecDriftHeader drift_header;
RHKSpecInfo spec_info;
G_GNUC_UNUSED gboolean have_header = FALSE, have_info = FALSE;
gwy_debug("page_type %u", page->page_type);
gwy_debug("line_type %u", page->line_type);
gwy_debug("page_sizes %u %u", page->x_size, page->y_size);
/* Page may contain drift header */
if ((obj = rhk_sm4_find_object(page->objects, page->object_count,
RHK_OBJECT_SPEC_DRIFT_HEADER,
RHK_OBJECT_PAGE_HEADER, NULL))
&& rhk_sm4_read_drift_header(&drift_header, obj, buffer)) {
gwy_debug("drift_header OK");
have_header = TRUE;
}
if ((obj = rhk_sm4_find_object(page->objects, page->object_count,
RHK_OBJECT_SPEC_DRIFT_DATA,
RHK_OBJECT_PAGE_HEADER, NULL))
&& rhk_sm4_read_spec_info(&spec_info, obj, buffer)) {
gwy_debug("spec_info OK");
have_info = TRUE;
}
/* FIXME: RHK_STRING_PLL_PRO_STATUS may contain interesting
* metadata. But we have not place where to put it. */
if ((gmodel = rhk_sm4_page_to_graph_model(page))) {
graphid++;
gwy_container_set_object(container,
gwy_app_get_graph_key_for_id(graphid),
gmodel);
g_object_unref(gmodel);
}
}
}
if (!imageid && !graphid)
err_NO_DATA(error);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
rhk_sm4_free(&rhkfile);
if (!imageid && !graphid) {
gwy_object_unref(container);
}
if (key)
g_string_free(key, TRUE);
return container;
}
static GwyContainer*
rhk_sm3_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GPtrArray *rhkfile;
RHKPage *rhkpage;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
const guchar *p;
GString *key;
guint i, count;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < HEADER_SIZE) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
rhkfile = g_ptr_array_new();
p = buffer;
count = 0;
gwy_debug("position %04x", p - buffer);
while ((rhkpage = rhk_sm3_read_page(&p, &size, &err))) {
gwy_debug("Page #%u read OK", count);
count++;
rhkpage->pageno = count;
gwy_debug("position %04x", p - buffer);
if (rhkpage->type != RHK_TYPE_IMAGE) {
gwy_debug("Page is not IMAGE, skipping");
rhk_sm3_page_free(rhkpage);
continue;
}
g_ptr_array_add(rhkfile, rhkpage);
}
/* Be tolerant and don't fail when we were able to import at least
* something */
if (!rhkfile->len) {
if (err)
g_propagate_error(error, err);
else
err_NO_DATA(error);
gwy_file_abandon_contents(buffer, size, NULL);
g_ptr_array_free(rhkfile, TRUE);
return NULL;
}
g_clear_error(&err);
container = gwy_container_new();
key = g_string_new("");
for (i = 0; i < rhkfile->len; i++) {
const gchar *cs;
gchar *s;
rhkpage = g_ptr_array_index(rhkfile, i);
dfield = rhk_sm3_page_to_data_field(rhkpage);
g_string_printf(key, "/%d/data", i);
gwy_container_set_object_by_name(container, key->str, dfield);
g_object_unref(dfield);
p = rhkpage->strings[RHK_STRING_LABEL];
cs = gwy_enum_to_string(rhkpage->scan_dir,
scan_directions, G_N_ELEMENTS(scan_directions));
if (p && *p) {
g_string_append(key, "/title");
if (cs)
s = g_strdup_printf("%s [%s]", p, cs);
else
s = g_strdup(p);
gwy_container_set_string_by_name(container, key->str, s);
}
meta = rhk_sm3_get_metadata(rhkpage);
g_string_printf(key, "/%d/meta", i);
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
gwy_app_channel_check_nonsquare(container, i);
}
g_string_free(key, TRUE);
gwy_file_abandon_contents(buffer, size, NULL);
for (i = 0; i < rhkfile->len; i++)
rhk_sm3_page_free(g_ptr_array_index(rhkfile, i));
g_ptr_array_free(rhkfile, TRUE);
return container;
}
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 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*
mif_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
MIFFile mfile;
GwyDataField *dfield;
guint i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (!mif_read_header(buffer, size, &mfile.header, error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
/* TODO: Check file version */
if (!mif_read_image_items(mfile.images, buffer, size, &mfile.header.info,
error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
/* FIXME: Only v1.7! */
for (i = 0; i < mfile.header.nimages; i++) {
MIFInfoItem *item = mfile.images + i;
MIFImageHeader image_header;
MIFBlock raster, macro_geometry, preview, image, curve, calc;
guint ncalculations;
const guchar *p = buffer + item->image.offset;
GQuark quark;
if (!item->image.size)
continue;
if (item->image.offset > size
|| item->image.size > size
|| item->image.offset + item->image.size > size) {
continue;
}
/* XXX: We cannot use item->image.size because it's bogus, i.e.
* too short. Apparently there is some unaccounted-for space until
* the next block starts, 120 bytes for v1.7 files, after the image
* header which is in fact still occupied by the image header.
* MIFBlock says 714 bytes but the true size is 834 = 714 + 120. */
if (!mif_read_image_header(&image_header, &p, size - (p - buffer),
mfile.header.file_version,
error))
continue;
if (p - buffer + 52 > size)
continue;
mif_read_block(&raster, "raster", &p);
mif_read_block(¯o_geometry, "macro_geometry", &p);
mif_read_block(&preview, "preview", &p);
mif_read_block(&image, "image", &p);
mif_read_block(&curve, "curve", &p);
ncalculations = gwy_get_guint32_le(&p);
mif_read_block(&calc, "calc", &p);
gwy_debug("image header true size: %zu",
(gsize)(p - (buffer + item->image.offset)));
dfield = mif_read_data_field(&image_header, &image, buffer, size, NULL);
if (!dfield)
continue;
if (!container)
container = gwy_container_new();
quark = gwy_app_get_data_key_for_id(i);
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
gwy_app_channel_title_fall_back(container, i);
}
if (!container)
err_NO_DATA(error);
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
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 GwyContainer*
sly_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta = NULL;
gchar *buffer = NULL;
GError *err = NULL;
GHashTable *hash = NULL;
gchar *p, *line, *value;
guint expecting_data = 0;
SensolyticsChannel *channels = NULL;
Dimensions dimensions;
gint ndata = 0, i;
if (!g_file_get_contents(filename, &buffer, NULL, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
p = buffer;
line = gwy_str_next_line(&p);
g_strstrip(line);
if (!gwy_strequal(line, MAGIC)) {
err_FILE_TYPE(error, "Sensolytics");
goto fail;
}
hash = g_hash_table_new(g_str_hash, g_str_equal);
for (line = gwy_str_next_line(&p); line; line = gwy_str_next_line(&p)) {
if (!line[0])
continue;
if (expecting_data) {
expecting_data--;
/* The columns are comma-separated and numbers use decimal points.
* Do not tempt the number parsing functions more than necessary
* and fix commas to tab characters. */
g_strdelimit(line, ",", '\t');
/* Ignore X, Y and Z, each is two values */
for (i = 0; i < 6; i++)
g_ascii_strtod(line, &line);
for (i = 0; i < ndata; i++)
channels[i].data[expecting_data]
= channels[i].q * g_ascii_strtod(line, &line);
}
else {
g_strstrip(line);
if (line[0] != '#') {
g_warning("Comment line does not start with #.");
continue;
}
do {
line++;
} while (g_ascii_isspace(*line));
if (g_str_has_prefix(line, "X [")) {
if (channels) {
g_warning("Multiple data headers!?");
continue;
}
if (!read_dimensions(hash, &ndata, &dimensions, error)
|| !(channels = create_fields(hash, line,
ndata, &dimensions)))
goto fail;
expecting_data = dimensions.xres * dimensions.yres;
continue;
}
value = strchr(line, ':');
if (!value) {
if (!gwy_strequal(line, "ArrayScan"))
g_warning("Non-parameter-like line %s", line);
continue;
}
*value = '\0';
g_strchomp(line);
do {
value++;
} while (g_ascii_isspace(*value));
if (gwy_strequal(line, "Warning"))
continue;
gwy_debug("<%s>=<%s>", line, value);
g_hash_table_insert(hash, line, value);
}
}
if (!channels) {
err_NO_DATA(error);
goto fail;
}
container = gwy_container_new();
for (i = 0; i < ndata; i++) {
GQuark key = gwy_app_get_data_key_for_id(i);
gwy_data_field_invert(channels[i].dfield, FALSE, TRUE, FALSE);
gwy_container_set_object(container, key, channels[i].dfield);
gwy_app_channel_check_nonsquare(container, i);
if (channels[i].name) {
gchar *s = g_strconcat(g_quark_to_string(key), "/title", NULL);
gwy_container_set_string_by_name(container, s,
g_strdup(channels[i].name));
g_free(s);
}
else
gwy_app_channel_title_fall_back(container, i);
gwy_file_channel_import_log_add(container, i, NULL, filename);
}
meta = get_meta(hash);
clone_meta(container, meta, ndata);
g_object_unref(meta);
fail:
g_free(buffer);
if (hash)
g_hash_table_destroy(hash);
if (channels) {
for (i = 0; i < ndata; i++)
g_object_unref(channels[i].dfield);
g_free(channels);
}
return container;
}
static GwyContainer*
spmlab_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
gchar *title = NULL;
gint dir;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
/* 2048 is wrong. moreover it differs for r5 and r4, kasigra uses 5752 for
* r5 */
if (size < 2048) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
if (buffer[0] != '#' || buffer[1] != 'R') {
err_FILE_TYPE(error, "Thermicroscopes SpmLab");
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
switch (buffer[2]) {
case '3':
case '4':
case '5':
case '6':
case '7':
dfield = read_data_field(buffer, size, buffer[2], &title, &dir, error);
break;
default:
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Unknown format version %c."), buffer[2]);
break;
}
gwy_file_abandon_contents(buffer, size, NULL);
if (!dfield)
return NULL;
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
if (title)
gwy_container_set_string_by_name(container, "/0/data/title", title);
else
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
/* TODO: Store direction to metadata, if known */
return container;
}
static GwyContainer*
shimadzu_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
GwyDataField *dfield = NULL;
GError *err = NULL;
gchar *buffer = NULL;
GHashTable *hash;
gchar *head;
gsize size = 0;
gboolean ok;
gint text_data_start;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < HEADER_SIZE + 2) {
err_TOO_SHORT(error);
return NULL;
}
if (memcmp(buffer, MAGIC, MAGIC_SIZE) != 0
&& !(memcmp(buffer, MAGIC_ASCII, MAGIC_ASCII_SIZE) == 0
&& (memcmp(buffer + MAGIC_ASCII_SIZE+1,
MAGIC, MAGIC_SIZE) == 0
|| memcmp(buffer + MAGIC_ASCII_SIZE+2,
MAGIC, MAGIC_SIZE) == 0))) {
err_FILE_TYPE(error, "Shimadzu");
g_free(buffer);
return NULL;
}
head = g_memdup(buffer, HEADER_SIZE+1);
head[HEADER_SIZE] = '\0';
/* text_data_start is set to nonzero if data are text */
hash = read_hash(head, &text_data_start, error);
ok = !!hash;
if (ok) {
if (text_data_start)
dfield = read_text_data(buffer, text_data_start, hash, error);
else
dfield = read_binary_data(buffer, size, hash, error);
ok = !!dfield;
}
if (ok) {
GQuark quark;
const gchar *title;
container = gwy_container_new();
quark = gwy_app_get_data_key_for_id(0);
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
meta = shimadzu_get_metadata(hash);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
title = g_hash_table_lookup(hash, "Channel");
if (title && *title)
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(title));
else
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
}
g_free(head);
g_free(buffer);
g_hash_table_destroy(hash);
return container;
}
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 GwyContainer*
ezdfile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
EZDSection *section = NULL;
GwyDataField *dfield = NULL;
GPtrArray *ezdfile;
guint header_size, n;
gint i;
gchar *p;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (strncmp(buffer, MAGIC, MAGIC_SIZE)
|| !(header_size = find_data_start(buffer, size))) {
err_FILE_TYPE(error, "EZD/NID");
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
ezdfile = g_ptr_array_new();
p = g_strndup(buffer, header_size - DATA_MAGIC_SIZE);
if (!file_read_header(ezdfile, p, error)) {
gwy_file_abandon_contents(buffer, size, NULL);
g_free(p);
return NULL;
}
g_free(p);
n = find_data_offsets(buffer + header_size, size - header_size, ezdfile,
error);
if (!n) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
container = gwy_container_new();
i = 0;
for (n = 0; n < ezdfile->len; n++) {
gchar key[24];
section = (EZDSection*)g_ptr_array_index(ezdfile, n);
if (!section->data)
continue;
dfield = gwy_data_field_new(section->xres, section->yres,
1.0, 1.0, FALSE);
read_data_field(dfield, section);
g_snprintf(key, sizeof(key), "/%d/data", i);
gwy_container_set_object_by_name(container, key, dfield);
g_object_unref(dfield);
fix_scales(section, i, container);
meta = ezdfile_get_metadata(ezdfile, n);
if (meta) {
g_snprintf(key, sizeof(key), "/%d/meta", i);
gwy_container_set_object_by_name(container, key, meta);
g_object_unref(meta);
}
i++;
}
gwy_file_abandon_contents(buffer, size, NULL);
ezdfile_free(ezdfile);
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 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*
mprofile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
MProFile mprofile;
GwyContainer *meta, *container = NULL;
GwyDataField *dfield = NULL, *vpmask = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
gsize expected;
GString *key;
const gchar *title;
guint n, i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (!mprofile_read_header(buffer, size, &mprofile, error))
return NULL;
expected = mprofile.header_size
+ 2*mprofile.nbuckets*mprofile.intens_xres*mprofile.intens_yres
+ 4*mprofile.phase_xres*mprofile.phase_yres;
if (err_SIZE_MISMATCH(error, expected, size, TRUE)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
n = fill_data_fields(&mprofile, buffer);
gwy_file_abandon_contents(buffer, size, NULL);
if (!n) {
err_NO_DATA(error);
return NULL;
}
key = g_string_new(NULL);
container = gwy_container_new();
for (i = 0; i < n; i++) {
if (i > 0) {
dfield = mprofile.intensity_data[i-1];
vpmask = mprofile.intensity_mask[i-1];
title = "Intensity";
}
else {
dfield = mprofile.phase_data;
vpmask = mprofile.phase_mask;
title = "Phase";
}
g_string_printf(key, "/%d/data", i);
gwy_container_set_object_by_name(container, key->str, dfield);
g_string_printf(key, "/%d/data/title", i);
gwy_container_set_string_by_name(container, key->str, g_strdup(title));
if (vpmask) {
g_string_printf(key, "/%d/mask", i);
gwy_container_set_object_by_name(container, key->str, vpmask);
}
meta = mprofile_get_metadata(&mprofile);
g_string_printf(key, "/%d/meta", i);
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
}
g_string_free(key, TRUE);
for (n = 0; n < mprofile.nbuckets; n++) {
gwy_object_unref(mprofile.intensity_data[n]);
gwy_object_unref(mprofile.intensity_mask[n]);
}
gwy_object_unref(mprofile.phase_data);
gwy_object_unref(mprofile.phase_mask);
return container;
}
static GwyContainer*
amb_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gdouble *data;
guint i, j;
gsize size = 0;
GError *err = NULL;
guint xres, yres;
GwyDataField *dfield;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size <= HEADER_SIZE) {
err_TOO_SHORT(error);
goto fail;
}
/* The two bytes before are usually zeroes */
p = buffer + XRES_OFFSET;
xres = gwy_get_guint32_le(&p);
p = buffer + YRES_OFFSET;
yres = gwy_get_guint32_le(&p);
gwy_debug("xres: %u yres: %u", xres, yres);
/* The four bytes after might be a float, then there are four more bytes. */
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
goto fail;
if (err_SIZE_MISMATCH(error, 4*xres*yres + HEADER_SIZE, size, TRUE))
goto fail;
dfield = gwy_data_field_new(xres, yres, 1.0, 1.0*yres/xres,
FALSE);
data = gwy_data_field_get_data(dfield);
p = buffer + HEADER_SIZE;
for (i = 0; i < yres; i++) {
for (j = 0; j < xres; j++)
data[i*xres + j] = gwy_get_gfloat_le(&p);
}
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), "m");
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup("Topography"));
g_object_unref(dfield);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static GwyContainer*
rhkspm32_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GArray *rhkfile;
RHKPage *rhkpage;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
gsize totalpos, pagesize;
GString *key;
guint i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < HEADER_SIZE) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
// niv - rhkfile is an array of rhkpage's, but buffer is where the actual
// raw file data is stored
rhkfile = g_array_new(FALSE, TRUE, sizeof(RHKPage));
totalpos = 0;
while (totalpos < size) {
g_array_set_size(rhkfile, rhkfile->len + 1);
rhkpage = &g_array_index(rhkfile, RHKPage, rhkfile->len - 1);
rhkpage->buffer = buffer + totalpos;
// niv - if the header seems illegal, skip all the next ones as well
// (and cancel the element addition to the g_array)
if (!rhkspm32_read_header(rhkpage, &err)) {
g_warning("failed to read rhk header after %u", rhkfile->len);
g_array_set_size(rhkfile, rhkfile->len - 1);
break;
}
pagesize = rhkpage->data_offset
+ rhkpage->item_size*rhkpage->xres*rhkpage->yres;
if (size < totalpos + pagesize) {
rhkspm32_free(rhkpage);
g_array_set_size(rhkfile, rhkfile->len - 1);
break;
}
totalpos += pagesize;
}
/* Be tolerant and don't fail when we were able to import at least
* something */
if (!rhkfile->len) {
if (err)
g_propagate_error(error, err);
else
err_NO_DATA(error);
gwy_file_abandon_contents(buffer, size, NULL);
g_array_free(rhkfile, TRUE);
return NULL;
}
g_clear_error(&err);
container = gwy_container_new();
key = g_string_new(NULL);
for (i = 0; i < rhkfile->len; i++) {
const gchar *cs;
gchar *s;
gwy_debug("rhk-spm32: processing page %d of %d\n", i+1, rhkfile->len);
rhkpage = &g_array_index(rhkfile, RHKPage, i);
if (rhkpage->type == RHK_TYPE_IMAGE) { // niv - just leaving this alone
dfield = rhkspm32_read_data(rhkpage);
g_string_printf(key, "/%d/data", i);
gwy_container_set_object_by_name(container, key->str, dfield);
g_object_unref(dfield);
g_string_append(key, "/title");
cs = gwy_enum_to_string(rhkpage->scan,
scan_directions,
G_N_ELEMENTS(scan_directions));
if (rhkpage->label) {
if (cs)
s = g_strdup_printf("%s [%s]", rhkpage->label, cs);
else
s = g_strdup(rhkpage->label);
gwy_container_set_string_by_name(container, key->str, s);
}
else
gwy_app_channel_title_fall_back(container, i);
gwy_file_channel_import_log_add(container, i, NULL,
filename);
}
else if (rhkpage->type == RHK_TYPE_LINE) { // niv - after omicron.c
GwySpectra* spectra;
GwyGraphModel *gmodel;
spectra = rhkspm32_read_spectra(rhkpage);
/* converting to graphs, as there is no point in leaving these as
* sps - no xy coordinates, so the spectro tool is kinda clueless */
gwy_debug("processing graph in page %d\n", i);
if ((gmodel = spectra_to_graph(spectra)) != NULL) {
gchar *container_key = NULL;
/* add gmodel to container */
container_key = g_strdup_printf("%s/%d", GRAPH_PREFIX, i);
gwy_container_set_object_by_name(container, container_key,
gmodel);
g_free(container_key);
}
g_object_unref(gmodel);
g_object_unref(spectra);
}
gwy_debug("rhk-spm32: finished parsing page %d \n", i);
meta = rhkspm32_get_metadata(rhkpage);
if (rhkpage->type == RHK_TYPE_IMAGE) {
/* this doesn't really work, but at least the meta data stays
with the graph, even if the metadata viewer won't show it*/
g_string_printf(key, "/%d/meta", i);
}
else if (rhkpage->type == RHK_TYPE_LINE) {
g_string_printf(key, "%s/%d/meta", GRAPH_PREFIX, i);
}
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
}
g_string_free(key, TRUE);
gwy_file_abandon_contents(buffer, size, NULL);
for (i = 0; i < rhkfile->len; i++)
rhkspm32_free(&g_array_index(rhkfile, RHKPage, i));
g_array_free(rhkfile, TRUE);
return container;
}
