static gboolean
burleigh_exp_read_header(BurleighExpHeader *header,
gchar *buf,
GError **error)
{
GwySIUnit *yunits = NULL, *dummy = NULL;
gchar *p, *line;
gwy_clear(header, 1);
p = buf;
/* Magic header */
if (!(line = gwy_str_next_line(&p))
|| strncmp(line, MAGIC, MAGIC_SIZE) != 0) {
err_FILE_TYPE(error, "Burleigh export");
return FALSE;
}
/* Skip all other lines starting with a dot */
while ((line = gwy_str_next_line(&p))) {
if (sscanf(line, ".Binary Format, Header Length=%u, Integer %u bits",
&header->length, &header->bpp))
header->binary = TRUE;
if (!line || !p || p[0] != '.')
break;
}
if (!line) {
err_FILE_TYPE(error, "Burleigh export");
return FALSE;
}
if (!parse_scale(&p, "X Scale", &header->xscale, &header->xyunits, error))
return FALSE;
if (!parse_dim(&p, "X Pixel", &header->xres, error))
return FALSE;
if (!parse_scale(&p, "Y Scale", &header->yscale, &yunits, error))
return FALSE;
/* FIXME: Check sanity */
g_object_unref(yunits);
if (!parse_dim(&p, "Y Pixel", &header->yres, error))
return FALSE;
if (!parse_scale(&p, "Z Scale", &header->zscale, &header->zunits, error))
return FALSE;
if (!parse_scale(&p, "Z Res.(value/digital)", &header->zres, &dummy,
error))
return FALSE;
g_object_unref(dummy);
if (!header->binary)
header->length = p - buf;
return TRUE;
}
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 void
header_end_element(G_GNUC_UNUSED GMarkupParseContext *context,
const gchar *element_name,
gpointer user_data,
G_GNUC_UNUSED GError **error)
{
XMLParserData *data;
LIFElement *element;
data = (XMLParserData *)user_data;
// gwy_debug("End name = %s", element_name);
if (gwy_strequal(element_name, "Element")) {
element = (LIFElement *)g_ptr_array_index(data->elements,
data->elements->len - 1);
if (!(element->memid)) {
gwy_debug("Wrong XML: Element has no MemID");
err_FILE_TYPE(error, "Leica LIF");
}
else {
g_array_append_val(data->file->elements, *element);
g_ptr_array_remove_index(data->elements,
data->elements->len - 1);
}
}
user_data = (gpointer)data;
}
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*
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 gboolean
mif_read_header(const guchar *buffer,
gsize size,
MIFHeader *header,
GError **error)
{
const guchar *p = buffer;
if (size <= HEADER_SIZE) {
err_TOO_SHORT(error);
return FALSE;
}
if (memcmp(buffer, MAGIC, MAGIC_SIZE)) {
err_FILE_TYPE(error, "MIF");
return FALSE;
}
gwy_clear(header, 1);
get_CHARARRAY(header->magic, &p);
header->software_version = gwy_get_guint16_be(&p);
header->file_version = gwy_get_guint16_be(&p);
gwy_debug("sw version: %u.%u, file version: %u.%u",
header->software_version/0x100, header->software_version % 0x100,
header->file_version/0x100, header->file_version % 0x100);
/* Version 1.7 is the only actually implemented. Other can be added upon
* request and, namely, provision of the files as each file version is
* different. */
if (header->file_version != 0x107) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Loading of file version %u.%u is not implemented."),
header->file_version/0x100, header->file_version % 0x100);
return FALSE;
}
get_CHARARRAY(header->time, &p);
get_CHARARRAY(header->comment, &p);
header->nimages = gwy_get_guint16_le(&p);
gwy_debug("n images: %u", header->nimages);
header->info.offset = gwy_get_guint32_le(&p);
header->info.size = gwy_get_guint32_le(&p);
gwy_debug("info offset: %zu, info size: %zu", header->info.offset, header->info.size);
get_CHARARRAY(header->unused, &p);
if (header->info.offset < HEADER_SIZE
|| header->info.offset > size
|| header->info.size > size
|| header->info.offset + header->info.size > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File information block is outside the file."));
return FALSE;
}
return TRUE;
}
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*
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 GwyContainer*
stmprg_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
StmprgFile stmprgfile;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield;
char *filename_ta, *ptr;
gboolean ok;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < MAGIC_SIZE || memcmp(buffer, MAGIC_TXT, MAGIC_SIZE) != 0) {
err_FILE_TYPE(error, "Omicron STMPRG");
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
gwy_clear(&stmprgfile, 1);
ok = read_parameters(buffer, size, &stmprgfile, error);
gwy_file_abandon_contents(buffer, size, NULL);
if (!ok)
return NULL;
filename_ta = g_strdup(filename);
ptr = filename_ta + strlen(filename_ta) - 1;
while (g_ascii_isdigit(*ptr) && ptr > filename_ta+1)
ptr--;
if (ptr == filename_ta+1) {
err_DATA_PART(error, filename);
g_free(filename_ta);
return NULL;
}
/* Accept lowercase and uppercase and try the same case for data file */
if (*ptr == 'p' && *(ptr - 1) == 't')
*ptr = 'a';
if (*ptr == 'P' && *(ptr - 1) == 'T')
*ptr = 'A';
if (!gwy_file_get_contents(filename_ta, &buffer, &size, &err)) {
g_free(filename_ta);
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
g_free(filename_ta);
dfield = read_datafield(buffer, size, &stmprgfile, error);
if (dfield) {
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
/* FIXME: with documentation, we could perhaps do better */
gwy_app_channel_title_fall_back(container, 0);
meta = stmprg_get_metadata(&stmprgfile);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
}
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static void
header_start_element(G_GNUC_UNUSED GMarkupParseContext *context,
const gchar *element_name,
const gchar **attribute_names,
const gchar **attribute_values,
gpointer user_data,
GError **error)
{
const gchar **name_cursor = attribute_names;
const gchar **value_cursor = attribute_values;
gchar *name, *value;
XMLParserData *data;
LIFElement *element;
data = (XMLParserData *)user_data;
// gwy_debug("Name = %s", element_name);
if (gwy_strequal(element_name, "LMSDataContainerHeader")) {
while (*name_cursor) {
if (gwy_strequal(*name_cursor, "Version")) {
data->file->version = atoi(*value_cursor);
}
name_cursor++;
value_cursor++;
}
}
else if (gwy_strequal(element_name, "Element")) {
element = g_new0(LIFElement, 1);
while (*name_cursor) {
if (gwy_strequal(*name_cursor, "Name")) {
element->name = g_strdup(*value_cursor);
}
name_cursor++;
value_cursor++;
}
g_ptr_array_add(data->elements, (gpointer)element);
}
else if (gwy_strequal(element_name, "Memory")) {
if (!(data->elements->len)) {
gwy_debug("Wrong XML Memory block");
err_FILE_TYPE(error, "Leica LIF");
goto fail_xml;
}
element = (LIFElement *)g_ptr_array_index(data->elements,
data->elements->len - 1);
while (*name_cursor) {
if (gwy_strequal(*name_cursor, "Size")) {
element->memsize
= g_ascii_strtoull(*value_cursor, NULL, 10);
}
else if (gwy_strequal(*name_cursor, "MemoryBlockID")) {
element->memid = g_strdup(*value_cursor);
}
name_cursor++;
value_cursor++;
}
if (!(element->memid)) {
gwy_debug("Wrong XML: Element has no MemID");
err_FILE_TYPE(error, "Leica LIF");
}
}
else if (gwy_strequal(element_name, "ChannelDescription")) {
LIFChannel *channel = NULL;
if (!(data->elements->len)) {
gwy_debug("Wrong XML ChannelDescription block");
err_FILE_TYPE(error, "Leica LIF");
goto fail_xml;
}
element = (LIFElement *)g_ptr_array_index(data->elements,
data->elements->len - 1);
channel = g_new0(LIFChannel, 1);
while (*name_cursor) {
if (gwy_strequal(*name_cursor, "Resolution")) {
channel->res = atoi(*value_cursor);
}
else if (gwy_strequal(*name_cursor, "Min")) {
channel->min = g_ascii_strtod(*value_cursor, NULL);
}
else if (gwy_strequal(*name_cursor, "Max")) {
channel->max = g_ascii_strtod(*value_cursor, NULL);
}
else if (gwy_strequal(*name_cursor, "Unit")) {
channel->unit = g_strdup(*value_cursor);
}
else if (gwy_strequal(*name_cursor, "LUTName")) {
channel->lut = g_strdup(*value_cursor);
}
else if (gwy_strequal(*name_cursor, "BytesInc")) {
channel->bytesinc = g_ascii_strtoull(*value_cursor,
NULL, 10);
}
name_cursor++;
value_cursor++;
}
if (!(element->channels)) {
element->channels = g_array_new(FALSE, TRUE,
sizeof(LIFChannel));
}
g_array_append_val(element->channels, *channel);
}
else if (gwy_strequal(element_name, "DimensionDescription")) {
LIFDimension *dimension = NULL;
if (!(data->elements->len)) {
gwy_debug("Wrong XML DimensionDescription block");
err_FILE_TYPE(error, "Leica LIF");
goto fail_xml;
}
element = (LIFElement *)g_ptr_array_index(data->elements,
data->elements->len - 1);
dimension = g_new0(LIFDimension, 1);
while (*name_cursor) {
if (gwy_strequal(*name_cursor, "DimID")) {
dimension->dimid = atoi(*value_cursor);
}
else if (gwy_strequal(*name_cursor, "NumberOfElements")) {
dimension->res = atoi(*value_cursor);
}
else if (gwy_strequal(*name_cursor, "Origin")) {
dimension->origin = g_ascii_strtod(*value_cursor, NULL);
}
else if (gwy_strequal(*name_cursor, "Length")) {
dimension->length = g_ascii_strtod(*value_cursor, NULL);
}
else if (gwy_strequal(*name_cursor, "Unit")) {
dimension->unit = g_strdup(*value_cursor);
}
else if (gwy_strequal(*name_cursor, "BytesInc")) {
dimension->bytesinc = g_ascii_strtoull(*value_cursor,
NULL, 10);
}
name_cursor++;
value_cursor++;
}
if (!(element->dimensions)) {
element->dimensions
= g_array_new(FALSE, TRUE, sizeof(LIFDimension));
}
g_array_append_val(element->dimensions, *dimension);
}
else if (gwy_strequal(element_name,
"ATLConfocalSettingDefinition")) {
if (!(data->elements->len)) {
gwy_debug("Wrong XML ATLConfocalSettingDefinition block");
err_FILE_TYPE(error, "Leica LIF");
goto fail_xml;
}
element = (LIFElement *)g_ptr_array_index(data->elements,
data->elements->len - 1);
if (!(element->metadata)) {
element->metadata = gwy_container_new();
}
while (*name_cursor) {
name = g_strdup(*name_cursor);
value = g_strdup(*value_cursor);
gwy_container_set_string_by_name(element->metadata,
name, value);
g_free(name);
name_cursor++;
value_cursor++;
}
}
fail_xml:
user_data = (gpointer)data;
return;
}
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 gsize
pt3file_read_header(const guchar *buffer,
gsize size,
PicoHarpFile *pt3file,
GError **error)
{
const guchar* (*read_imaging_header)(PicoHarpImagingHeader *header,
const guchar *p);
PicoHarpInstrument instr;
const guchar *p;
guint i, expected_size;
p = buffer;
if (size < HEADER_MIN_SIZE + 2) {
err_TOO_SHORT(error);
return 0;
}
get_CHARARRAY(pt3file->ident, &p);
get_CHARARRAY(pt3file->format_version, &p);
get_CHARARRAY(pt3file->creator_name, &p);
get_CHARARRAY(pt3file->creator_version, &p);
gwy_debug("<%.*s> <%.*s> <%.*s> <%.*s>",
(gint)sizeof(pt3file->ident), pt3file->ident,
(gint)sizeof(pt3file->format_version), pt3file->format_version,
(gint)sizeof(pt3file->creator_name), pt3file->creator_name,
(gint)sizeof(pt3file->creator_version), pt3file->creator_version);
get_CHARARRAY(pt3file->file_time, &p);
get_CHARARRAY(pt3file->crlf, &p);
get_CHARARRAY(pt3file->comment, &p);
if (memcmp(pt3file->ident, MAGIC, MAGIC_SIZE) != 0
|| pt3file->crlf[0] != '\r'
|| pt3file->crlf[1] != '\n') {
err_FILE_TYPE(error, "PicoHarp");
return 0;
}
pt3file->number_of_curves = gwy_get_guint32_le(&p);
gwy_debug("number_of_curves: %u", pt3file->number_of_curves);
pt3file->bits_per_record = gwy_get_guint32_le(&p);
gwy_debug("bits_per_record: %u", pt3file->bits_per_record);
pt3file->routing_channels = gwy_get_guint32_le(&p);
gwy_debug("routing_channels: %u", pt3file->routing_channels);
pt3file->number_of_boards = gwy_get_guint32_le(&p);
gwy_debug("number_of_boards: %u", pt3file->number_of_boards);
if (pt3file->number_of_boards != 1) {
g_warning("Number of boards is %u instead of 1. Reading one.",
pt3file->number_of_boards);
pt3file->number_of_boards = MAX(pt3file->number_of_boards, 1);
if (size < HEADER_MIN_SIZE + BOARD_SIZE*pt3file->number_of_boards) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("File header is truncated."));
return 0;
}
}
pt3file->active_curve = gwy_get_guint32_le(&p);
pt3file->measurement_mode = gwy_get_guint32_le(&p);
gwy_debug("measurement_mode: %u", pt3file->measurement_mode);
pt3file->sub_mode = gwy_get_guint32_le(&p);
gwy_debug("sub_mode: %u", pt3file->sub_mode);
pt3file->range_no = gwy_get_guint32_le(&p);
pt3file->offset = gwy_get_gint32_le(&p);
pt3file->acquisition_time = gwy_get_guint32_le(&p);
pt3file->stop_at = gwy_get_guint32_le(&p);
pt3file->stop_on_ovfl = gwy_get_guint32_le(&p);
pt3file->restart = gwy_get_guint32_le(&p);
pt3file->display_lin_log = !!gwy_get_guint32_le(&p);
pt3file->display_time_axis_from = gwy_get_guint32_le(&p);
pt3file->display_time_axis_to = gwy_get_guint32_le(&p);
pt3file->display_counts_axis_from = gwy_get_guint32_le(&p);
pt3file->display_counts_axis_to = gwy_get_guint32_le(&p);
for (i = 0; i < G_N_ELEMENTS(pt3file->display_curve); i++) {
pt3file->display_curve[i].map_to = gwy_get_guint32_le(&p);
pt3file->display_curve[i].show = gwy_get_guint32_le(&p);
}
for (i = 0; i < G_N_ELEMENTS(pt3file->auto_param); i++) {
pt3file->auto_param[i].start = gwy_get_gfloat_le(&p);
pt3file->auto_param[i].step = gwy_get_gfloat_le(&p);
pt3file->auto_param[i].end = gwy_get_gfloat_le(&p);
}
pt3file->repeat_mode = gwy_get_guint32_le(&p);
pt3file->repeats_per_curve = gwy_get_guint32_le(&p);
pt3file->repeat_time = gwy_get_guint32_le(&p);
pt3file->repeat_wait_time = gwy_get_guint32_le(&p);
get_CHARARRAY(pt3file->script_name, &p);
p = pt3file_read_board(&pt3file->board, p);
p += BOARD_SIZE*(pt3file->number_of_boards - 1);
pt3file->ext_devices = gwy_get_guint32_le(&p);
pt3file->reserved1 = gwy_get_guint32_le(&p);
pt3file->reserved2 = gwy_get_guint32_le(&p);
pt3file->input0_rate = gwy_get_guint32_le(&p);
pt3file->input1_rate = gwy_get_guint32_le(&p);
pt3file->stop_after = gwy_get_guint32_le(&p);
pt3file->stop_reason = gwy_get_guint32_le(&p);
pt3file->number_of_records = gwy_get_guint32_le(&p);
gwy_debug("number_of_records: %u", pt3file->number_of_records);
pt3file->spec_header_length = 4*gwy_get_guint32_le(&p);
gwy_debug("spec_header_length: %u", pt3file->spec_header_length);
gwy_debug("now at pos 0x%0lx", (gulong)(p - buffer));
if (pt3file->measurement_mode != 2
&& pt3file->measurement_mode != 3) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Measurement mode must be 2 or 3; %u is invalid."),
pt3file->measurement_mode);
return 0;
}
if (pt3file->sub_mode != PICO_HARP_IMAGE) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only area imaging files are supported."));
return 0;
}
if (pt3file->bits_per_record != 32) {
err_BPP(error, pt3file->bits_per_record);
return 0;
}
pt3file->imaging.common.dimensions = gwy_get_guint32_le(&p);
gwy_debug("imaging dimensions: %u", pt3file->imaging.common.dimensions);
if (pt3file->imaging.common.dimensions != 3) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only area imaging files are supported."));
return 0;
}
pt3file->imaging.common.instrument = instr = gwy_get_guint32_le(&p);
gwy_debug("imaging instrument: %u", pt3file->imaging.common.instrument);
if (instr == PICO_HARP_PIE710) {
expected_size = IMAGING_PIE710_SIZE;
read_imaging_header = &read_pie710_imaging_header;
}
else if (instr == PICO_HARP_KDT180) {
expected_size = IMAGING_KDT180_SIZE;
read_imaging_header = &read_kdt180_imaging_header;
}
else if (instr == PICO_HARP_LSM) {
expected_size = IMAGING_LSM_SIZE;
read_imaging_header = &read_lsm_imaging_header;
}
else {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Unknown instrument number %u."),
instr);
return 0;
}
if (pt3file->spec_header_length != expected_size) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Wrong imaging header size: %u instead of %u."),
pt3file->spec_header_length, expected_size);
return 0;
}
if ((p - buffer) + expected_size > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File header is truncated."));
return 0;
}
p = read_imaging_header(&pt3file->imaging, p);
gwy_debug("xres: %u", pt3file->imaging.common.xres);
gwy_debug("yres: %u", pt3file->imaging.common.yres);
if (err_DIMENSION(error, pt3file->imaging.common.xres)
|| err_DIMENSION(error, pt3file->imaging.common.xres))
return 0;
return (gsize)(p - buffer);
}
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 void
apedax_get_channels_data(unzFile uFile,
guchar *scanXmlContent,
gsize contentSize,
const gchar *filename,
GwyContainer *container,
GwyContainer *meta,
const APEScanSize *scanSize,
GError **error)
{
xmlDocPtr doc = NULL;
xmlNodePtr cur = NULL;
xmlXPathContextPtr context;
xmlXPathObjectPtr pathObj;
xmlNodeSetPtr nodeset;
xmlChar *buffer = NULL;
gchar key[256];
gint i;
gint power10 = 0;
gdouble scaleFactor = 1.0;
GwySIUnit *zUnit;
gchar *zUnitString = NULL;
gchar *binFileName = NULL;
GwyDataField *dfield;
GwyContainer *tmp;
if (scanXmlContent == NULL || contentSize == 0)
return;
gwy_clear(key, sizeof(key));
doc = xmlReadMemory(scanXmlContent,
contentSize,
"scan.xml",
NULL,
0);
if (doc == NULL)
goto fail;
context = xmlXPathNewContext(doc);
if (context == NULL)
goto fail;
pathObj = xmlXPathEvalExpression("/Scan/Channels/Channel", context);
if (pathObj == NULL) {
xmlXPathFreeContext(context);
goto fail;
}
/*There must be at least one channel*/
if (xmlXPathNodeSetIsEmpty(pathObj->nodesetval)) {
xmlXPathFreeObject(pathObj);
xmlXPathFreeContext(context);
err_NO_DATA(error);
return;
}
nodeset = pathObj->nodesetval;
if (nodeset->nodeNr <= 0)
goto fail;
for (i = 0; i < nodeset->nodeNr; i++) {
cur = nodeset->nodeTab[i]->xmlChildrenNode;
while (cur) {
/*Label*/
if (gwy_strequal((gchar*)cur->name, "Label")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
g_snprintf(key, sizeof(key), "/%d/data/title", i);
gwy_container_set_string_by_name(container, key, g_strdup(buffer));
xmlFree(buffer);
}
/*Factor*/
if (gwy_strequal((gchar*)cur->name, "ConversionFactor")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
scaleFactor = g_ascii_strtod((gchar*)buffer, NULL);
xmlFree(buffer);
}
/*Unit*/
if (gwy_strequal((gchar*)cur->name, "DataUnit")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
zUnitString = g_strdup((gchar*)buffer);
zUnit = gwy_si_unit_new_parse(zUnitString, &power10);
xmlFree(buffer);
g_object_unref(zUnit);
}
/*Binary file name*/
if (gwy_strequal((gchar*)cur->name, "BINFile")) {
buffer = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
binFileName = g_strdup((gchar*)buffer);
xmlFree(buffer);
}
cur = cur->next;
}
scaleFactor *= pow(10.0, power10);
dfield = apedax_get_data_field(uFile,
binFileName,
scanSize,
zUnitString,
scaleFactor,
error);
if (dfield) {
g_snprintf(key, sizeof(key), "/%d/data", i);
gwy_container_set_object_by_name(container, key, dfield);
g_object_unref(dfield);
gwy_file_channel_import_log_add(container, i, NULL,
filename);
tmp = gwy_container_duplicate(meta);
g_snprintf(key, sizeof(key), "/%d/meta", i);
gwy_container_set_object_by_name(container, key, tmp);
g_object_unref(tmp);
}
}
xmlXPathFreeObject(pathObj);
xmlXPathFreeContext(context);
xmlFreeDoc(doc);
return;
fail:
err_FILE_TYPE(error, FILE_TYPE);
if (doc)
xmlFreeDoc(doc);
return;
}
static 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 GwyContainer*
oldmda_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
OldMDAFile mdafile;
gchar *head, *buffer = NULL;
gchar *buffer2 = NULL;
gchar *dataname = NULL, *dname;
GMarkupParser parser = { start_element, end_element, parse_text, NULL, NULL };
GMarkupParseContext *context;
gsize size, size2;
MDAXMLParams params;
GError *err = NULL;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
gwy_clear(&mdafile, 1);
head = g_strndup(buffer, 1024);
if (!check_magic(head)) {
err_FILE_TYPE(error, "NTMDT old MDA");
g_free(head);
goto fail;
}
g_free(head);
params.xdata = g_array_new(FALSE, TRUE, sizeof(gdouble));
params.numaxes = 0;
params.axes = g_array_new(FALSE, FALSE, sizeof(MDAAxis));
params.flag = MDA_XML_NONE;
context = g_markup_parse_context_new(&parser, G_MARKUP_TREAT_CDATA_AS_TEXT,
¶ms, NULL);
if (!g_markup_parse_context_parse(context, buffer, size, &err)
|| !g_markup_parse_context_end_parse(context, &err)) {
g_clear_error(&err);
g_markup_parse_context_free(context);
}
else {
g_markup_parse_context_free(context);
}
if (params.axes->len != 4) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Incorrect number of axes in parameter file."));
goto fail;
}
oldmda_read_params(¶ms, &mdafile);
dname = g_strdelimit(params.dataname, "\\/", G_DIR_SEPARATOR);
if (!(dataname = oldmda_find_data_name(filename, dname))) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("No corresponding data file was found for header file."));
goto fail;
}
if (!g_file_get_contents(dataname, &buffer2, &size2, &err)) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_IO,
_("Cannot load data file: %s"), err->message);
g_clear_error(&err);
goto fail;
}
if ((size2 != params.arraysize * params.datacellmemsize)
|| (params.arraysize != mdafile.xres * mdafile.yres * mdafile.zres)) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_IO,
_("Data file is too short."));
g_clear_error(&err);
goto fail2;
}
container = gwy_container_new();
mdafile.data = container;
mdafile.filename = dataname;
oldmda_read_data(&mdafile, buffer2);
fail2:
g_free(buffer2);
fail:
oldmda_free(¶ms);
g_free(buffer);
return container;
}
static GwyContainer*
csmfile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
GHashTable *hash = NULL;
guchar *d24, *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
guint xres, yres, bmpsize, header_size, maxval, i, j;
gdouble real, zmin, zmax, q, z0;
GwyTextHeaderParser parser;
GwySIUnit *unit = NULL;
gchar *value, *end, *header = NULL;
gdouble *data;
gint power10;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < BMP_HEADER_SIZE) {
err_TOO_SHORT(error);
goto fail;
}
if (!read_bmp_header(buffer, &xres, &yres, &bmpsize)
|| size <= bmpsize) {
err_FILE_TYPE(error, "CSM");
goto fail;
}
header_size = size - bmpsize;
header = g_new(gchar, header_size + 1);
memcpy(header, buffer + bmpsize, header_size);
header[header_size] = '\0';
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
hash = gwy_text_header_parse(header, &parser, NULL, NULL);
/* Do NOT use the fields Image width, Image height from the added footer.
* Even though it is specifically added by Benyuan it can disagree with the
* BMP diemsions and when they disagree the BMP diemsions are apparently
* right. */
if (err_DIMENSION(error, xres))
goto fail;
if (err_DIMENSION(error, yres))
goto fail;
if (!(value = g_hash_table_lookup(hash, "ScanSize"))) {
err_MISSING_FIELD(error, "ScanSize");
goto fail;
}
real = g_ascii_strtod(value, NULL);
/* Use negated positive conditions to catch NaNs */
if (!((real = fabs(real)) > 0)) {
g_warning("Real size is 0.0, fixing to 1.0");
real = 1.0;
}
if (!(value = g_hash_table_lookup(hash, "HeightScale"))) {
err_MISSING_FIELD(error, "HeightScale");
goto fail;
}
zmax = g_ascii_strtod(value, &end);
unit = gwy_si_unit_new_parse(end, &power10);
/* Optional stuff for which we try to fall back. */
if (!(value = g_hash_table_lookup(hash, "StartHeightScale")))
zmin = 0.0;
else
zmin = g_ascii_strtod(value, NULL);
if (!(value = g_hash_table_lookup(hash, "MaxValue")))
maxval = 0xffff;
else
maxval = MAX(atoi(value), 1);
dfield = gwy_data_field_new(xres, yres, real*Nanometre, real*Nanometre,
FALSE);
data = gwy_data_field_get_data(dfield);
d24 = buffer + BMP_HEADER_SIZE;
q = pow10(power10)*(zmax - zmin)/maxval;
z0 = pow10(power10)*zmin;
for (i = 0; i < yres; i++) {
gdouble *row = data + (yres-1 - i)*xres;
for (j = 0; j < xres; j++, row++, d24 += 3)
*row = (d24[0] + 256.0*d24[1])*q + z0;
}
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_data_field_set_si_unit_z(dfield, unit);
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
meta = gwy_container_new();
g_hash_table_foreach(hash, store_meta, meta);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
if ((value = g_hash_table_lookup(hash, "sTitle"))
&& g_utf8_validate(value, -1, NULL)) {
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(value));
}
else
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
GWY_OBJECT_UNREF(unit);
if (header)
g_free(header);
if (hash)
g_hash_table_destroy(hash);
return container;
}
static GwyContainer*
jeol_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
JEOLImageHeader image_header;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize expected_size, size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
const gchar *title;
gchar *s;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < JEOL_DATA_START) {
err_TOO_SHORT(error);
goto fail;
}
if (memcmp(buffer, MAGIC, MAGIC_SIZE) != 0) {
err_FILE_TYPE(error, "JEOL");
goto fail;
}
jeol_read_image_header(buffer, &image_header);
/* Elementrary sanity */
if (image_header.bpp != 16) {
err_BPP(error, image_header.bpp);
goto fail;
}
if (err_DIMENSION(error, image_header.xres)
|| err_DIMENSION(error, image_header.yres))
goto fail;
expected_size = image_header.bpp/8 * image_header.xres*image_header.yres;
if (err_SIZE_MISMATCH(error, JEOL_DATA_START + expected_size, size, FALSE))
goto fail;
if (image_header.image_type != JEOL_IMAGE || image_header.compressed) {
err_NO_DATA(error);
goto fail;
}
/* Use negated positive conditions to catch NaNs */
if (!((image_header.xreal = fabs(image_header.xreal)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
image_header.xreal = 1.0;
}
if (!((image_header.yreal = fabs(image_header.yreal)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
image_header.yreal = 1.0;
}
dfield = jeol_read_data_field(buffer + JEOL_DATA_START, &image_header);
if (!dfield) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("The type of data is unknown. "
"Please report it to the developers."));
goto fail;
}
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
/* Title */
s = g_convert(image_header.internal_filename, -1,
"iso-8859-1", "utf-8", NULL, NULL, NULL);
if (s)
g_strstrip(s);
if (s && *s)
gwy_container_set_string_by_name(container, "/0/data/title", s);
else {
title = gwy_flat_enum_to_string(image_header.data_source,
G_N_ELEMENTS(data_sources),
data_sources, data_sources_name);
if (title)
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(title));
}
/* Meta */
meta = jeol_get_metadata(&image_header);
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:
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static GwyContainer*
apedax_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
GwyContainer *meta = NULL;
unzFile uFile;
unz_file_info uFileInfo;
guchar *buffer;
gsize size = 0;
gboolean apdt_flag = FALSE;
gchar *lowercaseFilename;
APEScanSize scanSize;
scanSize.XRes = 0;
scanSize.YRes = 0;
scanSize.XReal = 0.0;
scanSize.YReal = 0.0;
lowercaseFilename = g_ascii_strdown(filename, -1);
if (g_str_has_suffix(filename, APDT_EXTENSION)) {
apdt_flag = TRUE;
}
g_free(lowercaseFilename);
gwy_debug("Opening the file with MiniZIP");
uFile = gwyminizip_unzOpen(filename);
if (uFile == NULL) {
if (apdt_flag) {
err_FILE_TYPE(error, APDT_FILE_TYPE);
}
else {
err_FILE_TYPE(error, FILE_TYPE);
}
unzClose(uFile);
return NULL;
}
gwy_debug("Locating the XML file");
if (unzLocateFile(uFile, "scan.xml", 0) != UNZ_OK) {
if (apdt_flag) {
err_FILE_TYPE(error, APDT_FILE_TYPE);
}
else {
err_FILE_TYPE(error, FILE_TYPE);
}
unzClose(uFile);
return NULL;
}
gwy_debug("Getting the XML file info");
if (unzGetCurrentFileInfo(uFile,
&uFileInfo,
NULL,
0L,
NULL,
0L,
NULL,
0L) != UNZ_OK) {
err_OPEN_READ(error);
unzClose(uFile);
return NULL;
}
buffer = apedax_get_file_content(uFile, &uFileInfo, &size, error);
container = gwy_container_new();
meta = apedax_get_meta(buffer, size, &scanSize, apdt_flag);
if (meta == NULL) {
gwy_debug("Metadata Container is NULL");
g_object_unref(container);
g_free(buffer);
err_FILE_TYPE(error, FILE_TYPE);
unzClose(uFile);
return NULL;
}
apedax_get_channels_data(uFile,
buffer,
size,
filename,
container,
meta,
&scanSize,
error);
g_free(buffer);
g_object_unref(meta);
unzClose(uFile);
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 GwyContainer*
zeiss_load_tiff(const GwyTIFF *tiff, GError **error)
{
GwyContainer *container = NULL, *meta = NULL;
GwyDataField *dfield;
GwySIUnit *siunit;
GwyTIFFImageReader *reader = NULL;
GHashTable *hash = NULL;
gint i, power10;
gchar *value, *end, *comment = NULL;
gdouble *data;
gboolean new_file;
double factor, dx;
/* Comment with parameters is common for all data fields */
if (!gwy_tiff_get_string0(tiff, ZEISS_HEADER_TAG, &comment)) {
err_FILE_TYPE(error, "Carl Zeiss SEM");
goto fail;
}
if (strstr(comment, MAGIC_COMMENT))
new_file = TRUE;
else if (g_str_has_prefix(comment, SOMEWHAT_LESS_MAGIC_COMMENT))
new_file = FALSE;
else {
err_FILE_TYPE(error, "Carl Zeiss SEM");
goto fail;
}
/* Read the comment header. */
if (new_file) {
hash = parse_comment(comment);
if ((value = g_hash_table_lookup(hash, "Image Pixel Size"))) {
gwy_debug("Using dx from Image Pixel Size: %s", value);
}
else if ((value = g_hash_table_lookup(hash, "Pixel Size"))) {
gwy_debug("Using dx from Pixel Size: %s", value);
}
else {
err_MISSING_FIELD(error, "Pixel Size");
goto fail;
}
}
else {
/* The first thing is the pixel size, apparently. */
value = comment + strlen(SOMEWHAT_LESS_MAGIC_COMMENT);
gwy_debug("Using dx from old-style comment: %s", value);
}
dx = g_ascii_strtod(value, &end);
/* Use negated positive conditions to catch NaNs */
if (!((dx = fabs(dx)) > 0)) {
g_warning("Real pixel size is 0.0, fixing to 1.0");
dx = 1.0;
}
if (!new_file)
end = "m";
/* Request a reader, this ensures dimensions and stuff are defined.
* NB: Newer versions store the image as RGB. Not useful here; just
* average the channels. */
if (!(reader = gwy_tiff_get_image_reader(tiff, 0, 3, error)))
goto fail;
siunit = gwy_si_unit_new_parse(end, &power10);
factor = pow10(power10);
dfield = gwy_data_field_new(reader->width, reader->height,
reader->width * factor * dx,
reader->height * factor * dx,
FALSE);
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
data = gwy_data_field_get_data(dfield);
if (reader->samples_per_pixel > 1) {
gdouble *datarow = g_new(gdouble, reader->width);
gint ch, j, spp = reader->samples_per_pixel;
gwy_data_field_clear(dfield);
for (i = 0; i < reader->height; i++) {
for (ch = 0; ch < spp; ch++) {
gwy_tiff_read_image_row(tiff, reader, 0, i, 1.0, 0.0, datarow);
for (j = 0; j < reader->width; j++)
data[i*reader->width + j] += datarow[j];
}
}
g_free(datarow);
gwy_data_field_multiply(dfield, 1.0/spp);
gwy_data_field_invalidate(dfield);
}
else {
for (i = 0; i < reader->height; i++)
gwy_tiff_read_image_row(tiff, reader, 0, i, 1.0, 0.0,
data + i*reader->width);
}
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup("Secondary electron count"));
if (new_file) {
meta = gwy_container_new();
g_hash_table_foreach(hash, add_meta, meta);
if (gwy_container_get_n_items(meta))
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
}
fail:
if (hash)
g_hash_table_destroy(hash);
g_free(comment);
return container;
}
static GwyContainer*
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*
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*
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 gboolean
mprofile_read_header(const guchar *buffer,
gsize size,
MProFile *mprofile,
GError **error)
{
const guchar *p;
guint i;
p = buffer;
if (size < HEADER_SIZE + 2) {
err_TOO_SHORT(error);
return FALSE;
}
get_CHARARRAY(mprofile->magic, &p);
if (memcmp(mprofile->magic, MAGIC, MAGIC_SIZE) != 0) {
err_FILE_TYPE(error, "MetroPro");
return FALSE;
}
mprofile->header_format = gwy_get_guint16_be(&p);
if (mprofile->header_format != 1) {
err_UNSUPPORTED(error, "FormatVersion");
return FALSE;
}
mprofile->header_size = gwy_get_guint32_be(&p);
gwy_debug("header_format: %d, header_size: %d",
mprofile->header_format, mprofile->header_size);
if (mprofile->header_size < 570) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File header is too short."));
return FALSE;
}
if (mprofile->header_size > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File header is larger than file."));
return FALSE;
}
mprofile->software_type = gwy_get_guint16_be(&p);
get_CHARARRAY0(mprofile->software_date, &p);
gwy_debug("software_type: %d, software_date: %s",
mprofile->software_type, mprofile->software_date);
mprofile->version_major = gwy_get_guint16_be(&p);
mprofile->version_minor = gwy_get_guint16_be(&p);
mprofile->version_micro = gwy_get_guint16_be(&p);
gwy_debug("version: %d.%d.%d",
mprofile->version_major,
mprofile->version_minor,
mprofile->version_micro);
mprofile->intens_xoff = gwy_get_guint16_be(&p);
mprofile->intens_yoff = gwy_get_guint16_be(&p);
mprofile->intens_xres = gwy_get_guint16_be(&p);
mprofile->intens_yres = gwy_get_guint16_be(&p);
gwy_debug("INTENS xres: %d, yres: %d, xoff: %d, yoff: %d",
mprofile->intens_xres, mprofile->intens_yres,
mprofile->intens_xoff, mprofile->intens_yoff);
mprofile->nbuckets = gwy_get_guint16_be(&p);
mprofile->intens_range = gwy_get_guint16_be(&p);
mprofile->intens_nbytes = gwy_get_guint32_be(&p);
gwy_debug("intens_nbytes: %d, expecting: %d",
mprofile->intens_nbytes,
2*mprofile->intens_xres*mprofile->intens_yres*mprofile->nbuckets);
mprofile->phase_xoff = gwy_get_guint16_be(&p);
mprofile->phase_yoff = gwy_get_guint16_be(&p);
mprofile->phase_xres = gwy_get_guint16_be(&p);
mprofile->phase_yres = gwy_get_guint16_be(&p);
gwy_debug("PHASE xres: %d, yres: %d, xoff: %d, yoff: %d",
mprofile->phase_xres, mprofile->phase_yres,
mprofile->phase_xoff, mprofile->phase_yoff);
mprofile->phase_nbytes = gwy_get_guint32_be(&p);
gwy_debug("phase_nbytes: %d, expecting: %d",
mprofile->phase_nbytes,
4*mprofile->phase_xres*mprofile->phase_yres);
mprofile->timestamp = gwy_get_guint32_be(&p);
get_CHARARRAY0(mprofile->comment, &p);
gwy_debug("comment: %s", mprofile->comment);
mprofile->source = gwy_get_guint16_be(&p);
mprofile->scale_factor = gwy_get_gfloat_be(&p);
mprofile->wavelength_in = gwy_get_gfloat_be(&p);
mprofile->numeric_aperture = gwy_get_gfloat_be(&p);
mprofile->obliquity_factor = gwy_get_gfloat_be(&p);
mprofile->magnification = gwy_get_gfloat_be(&p);
mprofile->camera_res = gwy_get_gfloat_be(&p);
mprofile->acquire_mode = gwy_get_guint16_be(&p);
gwy_debug("acquire_mode: %d", mprofile->acquire_mode);
mprofile->intens_avgs = gwy_get_guint16_be(&p);
if (!mprofile->intens_avgs)
mprofile->intens_avgs = 1;
mprofile->pzt_cal = gwy_get_guint16_be(&p);
mprofile->pzt_gain_tolerance = gwy_get_guint16_be(&p);
mprofile->pzt_gain = gwy_get_guint16_be(&p);
mprofile->part_thickness = gwy_get_gfloat_be(&p);
mprofile->agc = gwy_get_guint16_be(&p);
mprofile->target_range = gwy_get_gfloat_be(&p);
p += 2;
mprofile->min_mod = gwy_get_guint32_be(&p);
mprofile->min_mod_pts = gwy_get_guint32_be(&p);
mprofile->phase_res = gwy_get_guint16_be(&p);
mprofile->min_area_size = gwy_get_guint32_be(&p);
mprofile->discont_action = gwy_get_guint16_be(&p);
mprofile->discont_filter = gwy_get_gfloat_be(&p);
mprofile->connection_order = gwy_get_guint16_be(&p);
mprofile->data_inverted = gwy_get_guint16_be(&p);
mprofile->camera_width = gwy_get_guint16_be(&p);
mprofile->camera_height = gwy_get_guint16_be(&p);
mprofile->system_type = gwy_get_guint16_be(&p);
mprofile->system_board = gwy_get_guint16_be(&p);
mprofile->system_serial = gwy_get_guint16_be(&p);
mprofile->instrument_id = gwy_get_guint16_be(&p);
get_CHARARRAY0(mprofile->objective_name, &p);
get_CHARARRAY0(mprofile->part_num, &p);
gwy_debug("part_num: %s", mprofile->part_num);
mprofile->code_vtype = gwy_get_guint16_be(&p);
mprofile->phase_avgs = gwy_get_guint16_be(&p);
mprofile->subtract_sys_err = gwy_get_guint16_be(&p);
p += 16;
get_CHARARRAY0(mprofile->part_ser_num, &p);
mprofile->refactive_index = gwy_get_gfloat_be(&p);
mprofile->remove_tilt_bias = gwy_get_guint16_be(&p);
mprofile->remove_fringes = gwy_get_guint16_be(&p);
mprofile->max_area_size = gwy_get_guint32_be(&p);
mprofile->setup_type = gwy_get_guint16_be(&p);
p += 2;
mprofile->pre_connect_filter = gwy_get_gfloat_be(&p);
mprofile->wavelength2 = gwy_get_gfloat_be(&p);
mprofile->wavelength_fold = gwy_get_guint16_be(&p);
mprofile->wavelength1 = gwy_get_gfloat_be(&p);
mprofile->wavelength3 = gwy_get_gfloat_be(&p);
mprofile->wavelength4 = gwy_get_gfloat_be(&p);
get_CHARARRAY0(mprofile->wavelength_select, &p);
mprofile->fda_res = gwy_get_guint16_be(&p);
get_CHARARRAY0(mprofile->scan_description, &p);
gwy_debug("scan_description: %s", mprofile->scan_description);
mprofile->nfiducials = gwy_get_guint16_be(&p);
for (i = 0; i < G_N_ELEMENTS(mprofile->fiducials); i++)
mprofile->fiducials[i] = gwy_get_gfloat_be(&p);
mprofile->pixel_width = gwy_get_gfloat_be(&p);
mprofile->pixel_height = gwy_get_gfloat_be(&p);
mprofile->exit_pupil_diam = gwy_get_gfloat_be(&p);
mprofile->light_level_pct = gwy_get_gfloat_be(&p);
mprofile->coords_state = gwy_get_guint32_be(&p);
mprofile->xpos = gwy_get_gfloat_be(&p);
mprofile->ypos = gwy_get_gfloat_be(&p);
mprofile->zpos = gwy_get_gfloat_be(&p);
mprofile->xrot = gwy_get_gfloat_be(&p);
mprofile->yrot = gwy_get_gfloat_be(&p);
mprofile->zrot = gwy_get_gfloat_be(&p);
mprofile->coherence_mode = gwy_get_guint16_be(&p);
mprofile->surface_filter = gwy_get_guint16_be(&p);
get_CHARARRAY0(mprofile->sys_err_file, &p);
get_CHARARRAY0(mprofile->zoom_desc, &p);
return TRUE;
}
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*
gsf_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta = NULL;
GwyDataField *dfield = NULL;
GwyTextHeaderParser parser;
GwySIUnit *unit;
guchar *p, *value, *buffer = NULL, *header = NULL;
const guchar *datap;
GHashTable *hash = NULL;
gsize size, expected_size;
GError *err = NULL;
gdouble xreal, yreal, xoff, yoff;
guint i, xres, yres;
gdouble *d;
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) != 0) {
err_FILE_TYPE(error, "Gwyddion Simple Field");
goto fail;
}
p = buffer + MAGIC_SIZE;
datap = memchr(p, '\0', size - (p - buffer));
if (!datap) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File header is truncated."));
goto fail;
}
header = g_strdup(p);
datap += 4 - ((datap - buffer) % 4);
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
if (!(hash = gwy_text_header_parse(header, &parser, NULL, NULL))) {
g_propagate_error(error, err);
goto fail;
}
xres = read_pixel_size(hash, "XRes", error);
yres = read_pixel_size(hash, "YRes", error);
if (!xres || !yres)
goto fail;
expected_size = (datap - buffer) + sizeof(gfloat)*xres*yres;
if (err_SIZE_MISMATCH(error, expected_size, size, TRUE))
goto fail;
xreal = read_real_size(hash, "XReal");
yreal = read_real_size(hash, "YReal");
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
xoff = read_real_offset(hash, "XOffset");
yoff = read_real_offset(hash, "YOffset");
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
value = g_hash_table_lookup(hash, "XYUnits");
unit = gwy_si_unit_new(value);
gwy_data_field_set_si_unit_xy(dfield, unit);
g_object_unref(unit);
value = g_hash_table_lookup(hash, "ZUnits");
unit = gwy_si_unit_new(value);
gwy_data_field_set_si_unit_z(dfield, unit);
g_object_unref(unit);
d = gwy_data_field_get_data(dfield);
for (i = xres*yres; i; i--)
*(d++) = gwy_get_gfloat_le(&datap);
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, "Title"))) {
/* FIXME: Ensure valid UTF-8 */
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(value));
}
else
gwy_app_channel_title_fall_back(container, 0);
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);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
if (header)
g_free(header);
if (hash)
g_hash_table_destroy(hash);
return container;
}
static GwyContainer*
jpkscan_load_tiff(const gchar *filename, GError **error)
{
GwyContainer *container = NULL;
GwyContainer *meta = NULL;
TIFF *tiff;
gint ilen;
gint jlen;
gint idx = 0;
gushort bps;
gushort photo;
gushort planar;
gdouble ulen, vlen;
tiff = TIFFOpen(filename, "r");
if (!tiff) {
/* This can be I/O too, but it's hard to tell the difference. */
err_FILE_TYPE(error, _("JPK scan"));
return NULL;
}
/* sanity check, grid dimensions must be present! */
if (!(tiff_get_custom_double(tiff, JPK_TIFFTAG_Grid_uLength, &ulen)
&& tiff_get_custom_double(tiff, JPK_TIFFTAG_Grid_vLength, &vlen))) {
TIFFClose(tiff);
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File does not contain grid dimensions."));
return NULL;
}
container = gwy_container_new();
meta = gwy_container_new();
/* FIXME: I'm unable to meaningfully sort out the metadata to channels,
* so each one receives an identical copy of the global metadata now. */
tiff_load_meta(tiff, meta);
gwy_debug("ulen: %g vlen: %g", ulen, vlen);
do {
if (!TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &ilen)) {
g_warning("Could not get image width, skipping");
continue;
}
if (!TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &jlen)) {
g_warning("Could not get image length, skipping");
continue;
}
TIFFGetFieldDefaulted(tiff, TIFFTAG_BITSPERSAMPLE, &bps);
if (!TIFFGetField(tiff, TIFFTAG_PHOTOMETRIC, &photo)) {
g_warning("Could not get photometric tag, skipping");
continue;
}
/* we are only interested in 16bit grayscale */
switch (photo) {
case PHOTOMETRIC_MINISBLACK:
case PHOTOMETRIC_MINISWHITE:
if (bps == 16)
break;
default:
continue;
}
if (TIFFGetField(tiff, TIFFTAG_PLANARCONFIG, &planar)
&& planar != PLANARCONFIG_CONTIG) {
g_warning("Can only handle planar data, skipping");
continue;
}
tiff_load_channel(tiff, container, meta, idx++, ilen, jlen, ulen, vlen);
}
while (TIFFReadDirectory(tiff));
TIFFClose(tiff);
g_object_unref(meta);
return container;
}
static gboolean
cdffile_load(NetCDF *cdffile,
const gchar *filename,
GError **error)
{
GError *err = NULL;
const guchar *p;
gwy_clear(cdffile, 1);
if (!gwy_file_get_contents(filename, &cdffile->buffer, &cdffile->size,
&err)) {
err_GET_FILE_CONTENTS(error, &err);
return FALSE;
}
if (cdffile->size < 32) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(cdffile->buffer, cdffile->size, NULL);
return FALSE;
}
p = cdffile->buffer;
/* Header */
if (memcmp(p, MAGIC1, MAGIC_SIZE) == 0)
cdffile->version = 1;
else if (memcmp(p, MAGIC2, MAGIC_SIZE) == 0)
cdffile->version = 2;
else {
err_FILE_TYPE(error, "NetCDF");
gwy_file_abandon_contents(cdffile->buffer, cdffile->size, NULL);
return FALSE;
}
gwy_debug("Header: CDF v%d", (gint)cdffile->version);
p += MAGIC_SIZE;
/* N Records */
cdffile->nrecs = gwy_get_guint32_be(&p);
gwy_debug("nrecs %d", cdffile->nrecs);
/* Dimensions */
if (!cdffile_read_dim_array(&cdffile->dims, &cdffile->ndims,
cdffile->buffer, cdffile->size, &p, error)) {
cdffile_free(cdffile);
gwy_file_abandon_contents(cdffile->buffer, cdffile->size, NULL);
return FALSE;
}
/* Global attributes */
if (!cdffile_read_attr_array(&cdffile->attrs, &cdffile->nattrs,
cdffile->buffer, cdffile->size, &p, error)) {
cdffile_free(cdffile);
gwy_file_abandon_contents(cdffile->buffer, cdffile->size, NULL);
return FALSE;
}
/* Variables */
if (!cdffile_read_var_array(&cdffile->vars, &cdffile->nvars,
cdffile->version,
cdffile->buffer, cdffile->size, &p, error)) {
cdffile_free(cdffile);
gwy_file_abandon_contents(cdffile->buffer, cdffile->size, NULL);
return FALSE;
}
cdffile->data_start = (gsize)(p - cdffile->buffer);
/* Sanity check */
if (!cdffile_validate_vars(cdffile, error)) {
cdffile_free(cdffile);
gwy_file_abandon_contents(cdffile->buffer, cdffile->size, NULL);
return FALSE;
}
return TRUE;
}
