/**
* file_register_plugins:
* @plugins: Plug-in list to eventually add the plug-in to.
* @file: Plug-in file (full path).
* @buffer: The output from "plugin register".
*
* Parse output from "plugin register" and eventually add it to the
* plugin-list.
*
* Returns: The new plug-in list, with the plug-in eventually prepended.
**/
static GList*
file_register_plugins(GList *plugins,
const gchar *file,
gchar *buffer)
{
FilePluginInfo *info;
gchar *pname = NULL, *file_desc = NULL, *run_modes = NULL, *glob = NULL;
GwyFileOperationType run;
gwy_debug("buffer: <<<%s>>>", buffer);
while (buffer) {
if ((pname = gwy_str_next_line(&buffer))
&& *pname
&& (file_desc = gwy_str_next_line(&buffer))
&& *file_desc
&& (glob = gwy_str_next_line(&buffer))
&& *glob
&& (run_modes = gwy_str_next_line(&buffer))
&& (run = gwy_string_to_flags(run_modes,
file_op_names, -1, NULL))) {
info = g_new0(FilePluginInfo, 1);
info->name = g_strdup(pname);
info->description = g_strdup(file_desc);
if (gwy_file_func_register(info->name, info->description,
&file_plugin_proxy_detect,
(run & GWY_FILE_OPERATION_LOAD)
? file_plugin_proxy_load : NULL,
NULL,
(run & GWY_FILE_OPERATION_EXPORT)
? file_plugin_proxy_export : NULL)) {
info->file = g_strdup(file);
info->run = run;
info->glob = g_strdup(glob);
info->pattern = file_patternize_globs(glob);
info->specificity = file_glob_specificities(glob);
plugins = g_list_prepend(plugins, info);
}
else {
g_free((gpointer)info->name);
g_free((gpointer)info->description);
g_free(info);
}
}
else if (pname && *pname) {
g_warning("failed; "
"pname = %s, file_desc = %s, run_modes = %s, glob = %s",
pname, file_desc, run_modes, glob);
}
while (buffer && *buffer)
gwy_str_next_line(&buffer);
}
return plugins;
}
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 GwyResource*
gwy_gl_material_parse(const gchar *text,
gboolean is_const)
{
GwyGLMaterial *gl_material = NULL;
GwyRGBA ambient, diffuse, specular, emission;
gdouble shininess;
GwyGLMaterialClass *klass;
gchar *str, *p, *line, *end;
g_return_val_if_fail(text, NULL);
klass = g_type_class_peek(GWY_TYPE_GL_MATERIAL);
g_return_val_if_fail(klass, NULL);
p = str = g_strdup(text);
if (!(line = gwy_str_next_line(&p))
|| !gwy_gl_material_parse_component(line, &ambient))
goto fail;
if (!(line = gwy_str_next_line(&p))
|| !gwy_gl_material_parse_component(line, &diffuse))
goto fail;
if (!(line = gwy_str_next_line(&p))
|| !gwy_gl_material_parse_component(line, &specular))
goto fail;
if (!(line = gwy_str_next_line(&p))
|| !gwy_gl_material_parse_component(line, &emission))
goto fail;
if (!(line = gwy_str_next_line(&p)))
goto fail;
shininess = g_ascii_strtod(line, &end);
if (end == line) {
line = NULL;
goto fail;
}
gwy_gl_material_set_rgba(&ambient, &ambient);
gwy_gl_material_set_rgba(&diffuse, &diffuse);
gwy_gl_material_set_rgba(&specular, &specular);
gwy_gl_material_set_rgba(&emission, &emission);
shininess = CLAMP(shininess, 0.0, 1.0);
gl_material = gwy_gl_material_new("",
&ambient, &diffuse, &specular, &emission,
shininess,
is_const);
fail:
if (!line)
g_warning("Cannot parse GL material.");
g_free(str);
return (GwyResource*)gl_material;
}
/**
* proc_register_plugins:
* @plugins: Plug-in list to eventually add the plug-in to.
* @file: Plug-in file (full path).
* @buffer: The output from "plugin register".
*
* Parse output from "plugin register" and eventually add it to the
* plugin-list.
*
* Returns: The new plug-in list, with the plug-in eventually prepended.
**/
static GList*
proc_register_plugins(GList *plugins,
const gchar *file,
gchar *buffer)
{
ProcPluginInfo *info;
gchar *pname = NULL, *menu_path = NULL, *run_modes = NULL;
GwyRunType run;
gwy_debug("buffer: <<<%s>>>", buffer);
while (buffer) {
if ((pname = gwy_str_next_line(&buffer))
&& *pname
&& (menu_path = gwy_str_next_line(&buffer))
&& menu_path[0] == '/'
&& (run_modes = gwy_str_next_line(&buffer))
&& (run = gwy_string_to_flags(run_modes,
run_mode_names, -1, NULL))) {
info = g_new(ProcPluginInfo, 1);
info->name = g_strdup(pname);
info->menu_path = g_strconcat(_("/_Plug-Ins"), menu_path, NULL);
info->tooltip = g_strdup_printf(_("Run plug-in %s"), menu_path+1);
info->run = run;
if (gwy_process_func_register(info->name,
proc_plugin_proxy_run,
info->menu_path,
NULL,
info->run,
GWY_MENU_FLAG_DATA,
info->tooltip)) {
info->file = g_strdup(file);
plugins = g_list_prepend(plugins, info);
}
else {
g_free((gpointer)info->name);
g_free((gpointer)info->menu_path);
g_free((gpointer)info->tooltip);
g_free(info);
}
}
else if (pname && *pname) {
g_warning("failed; "
"pname = %s, menu_path = %s, run_modes = %s",
pname, menu_path, run_modes);
}
while (buffer && *buffer)
gwy_str_next_line(&buffer);
}
return plugins;
}
static GwySurface*
read_xyz_points(gchar *p)
{
GwySurface *surface;
GArray *points;
gchar *line, *end;
char comma_fix_char = 0;
points = g_array_new(FALSE, FALSE, sizeof(GwyXYZ));
for (line = gwy_str_next_line(&p); line; line = gwy_str_next_line(&p)) {
GwyXYZ pt;
if (!line[0] || line[0] == '#')
continue;
if (!comma_fix_char) {
comma_fix_char = figure_out_comma_fix_char(line);
if (!comma_fix_char)
continue;
}
for (end = line; *end; end++) {
if (*end == ';')
*end = ' ';
else if (*end == ',')
*end = comma_fix_char;
}
if (!(pt.x = g_ascii_strtod(line, &end)) && end == line)
continue;
line = end;
while (g_ascii_isspace(*line))
line++;
if (!(pt.y = g_ascii_strtod(line, &end)) && end == line)
continue;
line = end;
while (g_ascii_isspace(*line))
line++;
if (!(pt.z = g_ascii_strtod(line, &end)) && end == line)
continue;
g_array_append_val(points, pt);
}
surface = gwy_surface_new_from_data((GwyXYZ*)points->data, points->len);
g_array_free(points, TRUE);
return surface;
}
static gchar*
sdfile_next_line(gchar **buffer,
const gchar *key,
GError **error)
{
guint klen;
gchar *value, *line;
do {
line = gwy_str_next_line(buffer);
} while (line && line[0] == ';');
if (!line) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached when looking for `%s' field."), key);
return NULL;
}
klen = strlen(key);
if (strncmp(line, key, klen) != 0
|| !g_ascii_isspace(line[klen])) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Invalid line found when looking for `%s' field."), key);
return NULL;
}
value = line + klen;
g_strstrip(value);
if (value[0] == '=') {
value++;
g_strstrip(value);
}
return value;
}
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 gboolean
parse_dim(gchar **p,
const gchar *name,
gint *value,
GError **error)
{
gchar *vp, *line;
line = gwy_str_next_line(p);
if (!line) {
err_MISSING_FIELD(error, name);
return FALSE;
}
vp = strchr(line, ':');
if (!vp) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Missing colon in header line."));
return FALSE;
}
*vp = '\0';
vp++;
gwy_debug("<%s> = <%s>", name, vp);
if (!gwy_strequal(line, name)) {
err_MISSING_FIELD(error, name);
return FALSE;
}
*value = strtol(vp, NULL, 10);
if (err_DIMENSION(error, *value))
return FALSE;
return TRUE;
}
static GHashTable*
parse_comment(gchar *text)
{
gchar *line, *value, *p = text;
GHashTable *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 (g_str_has_prefix(line, "Date :")
|| g_str_has_prefix(line, "Time :"))
value = line + 6;
else if (!(value = strchr(line, '=')))
continue;
*value = '\0';
value++;
g_strstrip(line);
g_strstrip(value);
g_hash_table_insert(hash, line, value);
gwy_debug("<%s> = <%s>", line, value);
}
return hash;
}
static gboolean
parse_scale(gchar **p,
const gchar *name,
double *value,
GwySIUnit **units,
GError **error)
{
gint power10;
gchar *vp, *line;
line = gwy_str_next_line(p);
if (!line) {
err_MISSING_FIELD(error, name);
return FALSE;
}
vp = strchr(line, ':');
if (!vp) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Missing colon in header line."));
return FALSE;
}
*vp = '\0';
vp++;
gwy_debug("<%s> = <%s>", name, vp);
if (!gwy_strequal(line, name)) {
err_MISSING_FIELD(error, name);
return FALSE;
}
*value = g_ascii_strtod(vp, &vp);
*units = gwy_si_unit_new_parse(vp, &power10);
*value *= pow10(power10);
if (!*value) {
g_warning("%s is 0.0, fixing to 1.0", name);
*value = 1.0;
}
return TRUE;
}
static 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 GHashTable*
read_hash(gchar *buffer,
gint *text_data_start,
GError **error)
{
enum {
WHATEVER = 0,
PROCESS_PROFILE,
COMMENT,
} next_is;
GHashTable *hash;
gchar *p, *line, *value;
GString *key;
*text_data_start = 0;
p = buffer;
hash = g_hash_table_new_full(g_str_hash, g_str_equal, g_free, NULL);
line = gwy_str_next_line(&p);
/* Version 4 text data. */
if (gwy_strequal(line, MAGIC_ASCII))
line = gwy_str_next_line(&p);
key = g_string_new(NULL);
g_hash_table_insert(hash, g_strdup("Version"), line + MAGIC_SIZE);
next_is = WHATEVER;
while ((line = gwy_str_next_line(&p))) {
guint len;
gchar *rb;
if (line[0] == '/')
line++;
if (line[0] == '\x1a') {
/* Apparently a binary data marker */
*text_data_start = 0;
break;
}
g_strstrip(line);
/* sections */
if (line[0] == '[' && (rb = strchr(line, ']'))) {
*rb = '\0';
line++;
g_strstrip(line);
gwy_debug("section %s", line);
g_string_assign(key, line);
g_string_append(key, "::");
if (gwy_strequal(line, "PROCESS PROFILE")) {
next_is = PROCESS_PROFILE;
continue;
}
if (gwy_strequal(line, "COMMENT")) {
next_is = COMMENT;
continue;
}
if (g_str_has_prefix(line, "DATA ")) {
line += strlen("DATA");
*text_data_start = p - buffer;
break;
}
next_is = WHATEVER;
/* Other sectioning seems too be uninteresting. */
continue;
}
if (next_is == PROCESS_PROFILE) {
g_hash_table_insert(hash, g_strdup("ProcessProfile"), line);
next_is = WHATEVER;
continue;
}
if (next_is == COMMENT) {
g_hash_table_insert(hash, g_strdup("Comment"), line);
next_is = WHATEVER;
continue;
}
next_is = WHATEVER;
value = strchr(line, ':');
if (!value) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing colon in header line."));
g_hash_table_destroy(hash);
return NULL;
}
*value = '\0';
value++;
g_strstrip(line);
g_strstrip(value);
len = key->len;
g_string_append(key, line);
gwy_debug("%s = %s", key->str, value);
g_hash_table_replace(hash, g_strdup(key->str), value);
g_string_truncate(key, len);
}
if (*text_data_start) {
g_strstrip(line);
if (!g_str_has_prefix(line, "Unit(") || !g_str_has_suffix(line, ")")) {
g_warning("Cannot parse DATA unit: %s", line);
g_hash_table_insert(hash, g_strdup("DATA Unit"), "1");
}
else {
line += strlen("Unit(");
line[strlen(line)-1] = '\0';
g_hash_table_insert(hash, g_strdup("DATA Unit"), line);
}
}
return hash;
}
static GHashTable*
read_hash(gchar **buffer,
GError **error)
{
GHashTable *hash;
NanoscopeValue *value;
gchar *line, *colon;
line = gwy_str_next_line(buffer);
if (line[0] != '\\' || line[1] != '*')
return NULL;
if (gwy_strequal(line, "\\*File list end")) {
gwy_debug("FILE LIST END");
return NULL;
}
hash = g_hash_table_new(g_str_hash, g_str_equal);
g_hash_table_insert(hash, "#self", line + 2); /* self */
gwy_debug("hash table <%s>", line + 2);
while ((*buffer)[0] == '\\' && (*buffer)[1] && (*buffer)[1] != '*') {
line = gwy_str_next_line(buffer) + 1;
if (!line || !line[0] || !line[1] || !line[2]) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Truncated header line."));
goto fail;
}
colon = line;
if (line[0] == '@' && g_ascii_isdigit(line[1]) && line[2] == ':')
colon = line+3;
colon = strchr(colon, ':');
if (!colon || !g_ascii_isspace(colon[1])) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing colon in header line."));
goto fail;
}
*colon = '\0';
do {
colon++;
} while (g_ascii_isspace(*colon));
value = parse_value(line, colon);
if (value)
g_hash_table_insert(hash, line, value);
}
/* Fix random stuff in Nanoscope E files */
if ((value = g_hash_table_lookup(hash, "Samps/line"))
&& !g_hash_table_lookup(hash, "Number of lines")
&& value->hard_value_units
&& g_ascii_isdigit(value->hard_value_units[0])) {
NanoscopeValue *val;
val = g_new0(NanoscopeValue, 1);
val->hard_value = g_ascii_strtod(value->hard_value_units, NULL);
val->hard_value_str = value->hard_value_units;
g_hash_table_insert(hash, "Number of lines", val);
}
return hash;
fail:
g_hash_table_destroy(hash);
return NULL;
}
static GwyContainer*
text_dump_import(gchar *buffer,
gsize size,
const gchar *filename,
GError **error)
{
gchar *val, *key, *pos, *line, *title;
GwyContainer *data;
GwyDataField *dfield;
gdouble xreal, yreal;
gint xres, yres, id;
GwySIUnit *uxy, *uz;
const guchar *s;
gdouble *d;
gsize n;
data = gwy_container_new();
pos = buffer;
while ((line = gwy_str_next_line(&pos)) && *line) {
val = strchr(line, '=');
if (!val || *line != '/') {
g_warning("Garbage key: %s", line);
continue;
}
if ((gsize)(val - buffer) + 1 > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached when value was expected."));
goto fail;
}
*val = '\0';
val++;
if (!gwy_strequal(val, "[") || !pos || *pos != '[') {
gwy_debug("<%s>=<%s>", line, val);
if (*val)
gwy_container_set_string_by_name(data, line, g_strdup(val));
else
gwy_container_remove_by_name(data, line);
continue;
}
g_assert(pos && *pos == '[');
pos++;
dfield = NULL;
gwy_container_gis_object_by_name(data, line, &dfield);
id = 0;
sscanf(line, "/%d", &id);
/* get datafield parameters from already read values, failing back
* to values of original data field */
key = g_strconcat(line, "/xres", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
xres = atoi(s);
else if (dfield)
xres = gwy_data_field_get_xres(dfield);
else {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing data field width."));
goto fail;
}
g_free(key);
key = g_strconcat(line, "/yres", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
yres = atoi(s);
else if (dfield)
yres = gwy_data_field_get_yres(dfield);
else {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing data field height."));
goto fail;
}
g_free(key);
key = g_strconcat(line, "/xreal", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
xreal = g_ascii_strtod(s, NULL);
else if (dfield)
xreal = gwy_data_field_get_xreal(dfield);
else {
g_warning("Missing real data field width.");
xreal = 1.0; /* 0 could cause troubles */
}
g_free(key);
key = g_strconcat(line, "/yreal", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
yreal = g_ascii_strtod(s, NULL);
else if (dfield)
yreal = gwy_data_field_get_yreal(dfield);
else {
g_warning("Missing real data field height.");
yreal = 1.0; /* 0 could cause troubles */
}
g_free(key);
if (!(xres > 0 && yres > 0 && xreal > 0 && yreal > 0)) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Data field dimensions are not positive numbers."));
goto fail;
}
key = g_strconcat(line, "/unit-xy", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
uxy = gwy_si_unit_new((const gchar*)s);
else if (dfield) {
uxy = gwy_data_field_get_si_unit_xy(dfield);
uxy = gwy_si_unit_duplicate(uxy);
}
else {
g_warning("Missing lateral units.");
uxy = gwy_si_unit_new("m");
}
g_free(key);
key = g_strconcat(line, "/unit-z", NULL);
if (gwy_container_gis_string_by_name(data, key, &s))
uz = gwy_si_unit_new((const gchar*)s);
else if (dfield) {
uz = gwy_data_field_get_si_unit_z(dfield);
uz = gwy_si_unit_duplicate(uz);
}
else {
g_warning("Missing value units.");
uz = gwy_si_unit_new("m");
}
g_free(key);
key = g_strconcat(line, "/title", NULL);
title = NULL;
gwy_container_gis_string_by_name(data, key, (const guchar**)&title);
/* We got the contained string but that would disappear. */
title = g_strdup(title);
g_free(key);
n = xres*yres*sizeof(gdouble);
if ((gsize)(pos - buffer) + n + 3 > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached inside a data field."));
goto fail;
}
dfield = GWY_DATA_FIELD(gwy_data_field_new(xres, yres, xreal, yreal,
FALSE));
gwy_data_field_set_si_unit_xy(dfield, GWY_SI_UNIT(uxy));
gwy_object_unref(uxy);
gwy_data_field_set_si_unit_z(dfield, GWY_SI_UNIT(uz));
gwy_object_unref(uz);
d = gwy_data_field_get_data(dfield);
#if (G_BYTE_ORDER == G_LITTLE_ENDIAN)
memcpy(d, pos, n);
#else
gwy_memcpy_byte_swap(pos, (guint8*)d,
sizeof(gdouble), xres*yres, sizeof(gdouble)-1);
#endif
pos += n;
val = gwy_str_next_line(&pos);
if (!gwy_strequal(val, "]]")) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing end of data field marker."));
gwy_object_unref(dfield);
goto fail;
}
gwy_container_remove_by_prefix(data, line);
gwy_container_set_object_by_name(data, line, dfield);
g_object_unref(dfield);
if (title) {
key = g_strconcat(line, "/title", NULL);
gwy_container_set_string_by_name(data, key, title);
g_free(key);
}
gwy_file_channel_import_log_add(data, id, NULL, filename);
}
return data;
fail:
gwy_container_remove_by_prefix(data, NULL);
g_object_unref(data);
return NULL;
}
static GwyDataField*
sdfile_read_data_text(SDFile *sdfile,
GError **error)
{
gint i, n;
GwyDataField *dfield;
gdouble *data;
gchar *p, *end, *line;
dfield = gwy_data_field_new(sdfile->xres, sdfile->yres,
sdfile->xres * sdfile->xscale,
sdfile->yres * sdfile->yscale,
FALSE);
data = gwy_data_field_get_data(dfield);
n = sdfile->xres * sdfile->yres;
switch (sdfile->data_type) {
case SDF_UINT8:
case SDF_SINT8:
case SDF_UINT16:
case SDF_SINT16:
case SDF_UINT32:
case SDF_SINT32:
p = sdfile->data;
for (i = 0; i < n; i++) {
data[i] = strtol(p, (gchar**)&end, 10);
if (p == end) {
g_object_unref(dfield);
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached when reading sample #%d "
"of %d"), i, n);
return NULL;
}
p = end;
}
break;
case SDF_FLOAT:
case SDF_DOUBLE:
p = sdfile->data;
for (i = 0; i < n; i++) {
data[i] = g_ascii_strtod(p, (gchar**)&end);
if (p == end) {
g_object_unref(dfield);
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("End of file reached when reading sample #%d "
"of %d"), i, n);
return NULL;
}
p = end;
}
break;
default:
g_return_val_if_reached(NULL);
break;
}
/* Find out if there is anything beyond the end-of-data-marker */
while (*end && *end != '*')
end++;
if (!*end) {
gwy_debug("Missing end-of-data marker `*' was ignored");
return dfield;
}
do {
end++;
} while (g_ascii_isspace(*end));
if (!*end)
return dfield;
/* Read the extra stuff */
end--;
sdfile->extras = g_hash_table_new(g_str_hash, g_str_equal);
while ((line = gwy_str_next_line(&end))) {
g_strstrip(line);
if (!*line || *line == ';')
continue;
for (p = line; g_ascii_isalnum(*p); p++)
;
if (!*p || (*p != '=' && !g_ascii_isspace(*p)))
continue;
*p = '\0';
p++;
while (*p == '=' || g_ascii_isspace(*p))
p++;
if (!*p)
continue;
g_strstrip(p);
gwy_debug("extra: <%s> = <%s>", line, p);
g_hash_table_insert(sdfile->extras, line, p);
}
return dfield;
}
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 gboolean
unisoku_read_header(gchar *buffer,
UnisokuFile *ufile,
GError **error)
{
gchar *line;
gint type1, type2;
line = gwy_str_next_line(&buffer);
if (!line)
return FALSE;
NEXT(buffer, line, error);
/* garbage */
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "i", &ufile->format_version) != 1) {
err_UNSUPPORTED(error, _("format version"));
return FALSE;
}
NEXT(buffer, line, error);
ufile->date = g_strdup(line);
NEXT(buffer, line, error);
ufile->time = g_strdup(line);
NEXT(buffer, line, error);
ufile->sample_name = g_strdup(line);
NEXT(buffer, line, error);
ufile->remark = g_strdup(line);
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "ii", &ufile->ascii_flag, &type1) != 2) {
err_INVALID(error, _("format flags"));
return FALSE;
}
ufile->data_type = type1;
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "ii", &ufile->xres, &ufile->yres) != 2) {
err_INVALID(error, _("resolution"));
return FALSE;
}
if (err_DIMENSION(error, ufile->xres) || err_DIMENSION(error, ufile->yres))
return FALSE;
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "ii", &type1, &type2) != 2) {
/* FIXME */
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Missing or invalid some integers heaven knows what "
"they mean but that should be here."));
return FALSE;
}
ufile->dim_x = type1;
ufile->dim_y = type2;
NEXT(buffer, line, error);
ufile->unit_x = g_strdup(line);
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "ddi",
&ufile->start_x, &ufile->end_x,
&ufile->log_flag_x) != 3) {
err_INVALID(error, _("x scale parameters"));
return FALSE;
}
NEXT(buffer, line, error);
ufile->unit_y = g_strdup(line);
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "ddii",
&ufile->start_y, &ufile->end_y,
&ufile->ineq_flag, &ufile->log_flag_y) != 4) {
err_INVALID(error, _("y scale parameters"));
return FALSE;
}
/* Use negated positive conditions to catch NaNs */
if (!(ufile->end_x - ufile->start_x > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
ufile->start_x = 0.0;
ufile->end_x = 1.0;
}
if (!(ufile->end_y - ufile->start_y > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
ufile->start_y = 0.0;
ufile->end_y = 1.0;
}
NEXT(buffer, line, error);
ufile->unit_z = g_strdup(line);
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "ddddi",
&ufile->max_raw_z, &ufile->min_raw_z,
&ufile->max_z, &ufile->min_z,
&ufile->log_flag_z) != 5) {
err_INVALID(error, _("z scale parameters"));
return FALSE;
}
NEXT(buffer, line, error);
if (unisoku_sscanf(line, "dddi",
&ufile->stm_voltage, &ufile->stm_current,
&ufile->scan_time, &ufile->accum) != 4) {
err_INVALID(error, _("data type parameters"));
return FALSE;
}
NEXT(buffer, line, error);
/* reserved */
NEXT(buffer, line, error);
ufile->stm_voltage_unit = g_strdup(line);
NEXT(buffer, line, error);
ufile->stm_current_unit = g_strdup(line);
NEXT(buffer, line, error);
ufile->ad_name = g_strdup(line);
/* There is more stuff after that, but heaven knows what it means... */
return TRUE;
}
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 gboolean
omicron_read_header(gchar *buffer,
OmicronFile *ofile,
GError **error)
{
gchar *line, *val, *comment;
ofile->meta = g_hash_table_new(g_str_hash, g_str_equal);
while ((line = gwy_str_next_line(&buffer))) {
/* FIXME: This strips 2nd and following lines from possibly multiline
* fields like Comment. */
if (!line[0] || line[0] == ';' || g_ascii_isspace(line[0]))
continue;
val = strchr(line, ':');
if (!val) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Missing colon in header line."));
return FALSE;
}
if (val == line) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Header line starts with a colon."));
return FALSE;
}
*val = '\0';
val++;
g_strstrip(line);
comment = strchr(val, ';');
if (comment) {
/* If the coment has the form ;[units], move the [units] part after
* the number. */
if (comment[1] == '[' && (g_ascii_isalpha(comment[2])
|| comment[2] == '%')) {
gchar *c, *s = comment-1;
while (g_ascii_isspace(*s))
s--;
s++;
c = comment + 1;
*c = ' ';
while (*c && *c != ']')
*(s++) = *(c++);
*s = '\0';
}
else
*comment = '\0';
comment++;
g_strstrip(comment);
}
g_strstrip(val);
if (gwy_strequal(line, "Topographic Channel")) {
OmicronTopoChannel *channel;
gwy_debug("Topographic Channel found (type %c)", val[0]);
channel = g_new0(OmicronTopoChannel, 1);
channel->type = val[0];
if (!omicron_read_topo_header(&buffer, channel, error)) {
g_free(channel);
return FALSE;
}
if (!ofile->topo_channels)
ofile->topo_channels = g_ptr_array_new();
g_ptr_array_add(ofile->topo_channels, channel);
}
else if (gwy_strequal(line, "Spectroscopy Channel")) {
OmicronSpectroChannel *channel;
gwy_debug("Spectroscopic Channel found (chan %s)", val);
channel = g_new0(OmicronSpectroChannel, 1);
channel->chan = val;
if (!omicron_read_spectro_header(&buffer, channel, error)) {
g_free(channel);
return FALSE;
}
if (!ofile->spectro_channels)
ofile->spectro_channels = g_ptr_array_new();
g_ptr_array_add(ofile->spectro_channels, channel);
}
else {
gwy_debug("<%s> = <%s>", line, val);
g_hash_table_insert(ofile->meta, line, val);
}
}
GET_FIELD(ofile->meta, val, "Image Size in X", error);
ofile->xres = abs(atoi(val));
GET_FIELD(ofile->meta, val, "Image Size in Y", error);
ofile->yres = abs(atoi(val));
if (err_DIMENSION(error, ofile->xres)
|| err_DIMENSION(error, ofile->yres))
return FALSE;
GET_FIELD(ofile->meta, val, "Field X Size in nm", error);
ofile->xreal = g_ascii_strtod(val, NULL);
GET_FIELD(ofile->meta, val, "Field Y Size in nm", error);
ofile->yreal = g_ascii_strtod(val, NULL);
/* Use negated positive conditions to catch NaNs */
if (!((ofile->xreal = fabs(ofile->xreal)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
ofile->xreal = 1.0;
}
if (!((ofile->yreal = fabs(ofile->yreal)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
ofile->yreal = 1.0;
}
ofile->xreal *= Nanometer;
ofile->yreal *= Nanometer;
return TRUE;
}
static void
gfilter_load_args(GwyContainer *container,
GFilterArgs *args)
{
GwyInventory *inventory;
gchar *filename, *buffer;
gsize size;
guint i;
inventory = gwy_grain_values();
*args = gfilter_defaults;
gwy_container_gis_boolean_by_name(container, update_key, &args->update);
gwy_container_gis_int32_by_name(container, expanded_key, &args->expanded);
gwy_container_gis_enum_by_name(container, logical_key, &args->logical);
for (i = 0; i < NQUANTITIES; i++) {
RangeRecord *rr = args->ranges + i;
gchar buf[sizeof(quantity_key) + 10];
g_snprintf(buf, sizeof(buf), "%s%u", quantity_key, i+1);
gwy_container_gis_string_by_name(container, buf,
(const guchar**)&rr->quantity);
}
args->ranges_history = g_hash_table_new_full(g_str_hash, g_str_equal,
NULL, range_record_free);
filename = g_build_filename(gwy_get_user_dir(), "grain_filter", "ranges",
NULL);
if (g_file_get_contents(filename, &buffer, &size, NULL)) {
gchar *p = buffer, *line;
for (line = gwy_str_next_line(&p); line; line = gwy_str_next_line(&p)) {
g_strstrip(line);
if (*line) {
GwyGrainValue *gvalue;
RangeRecord *rr;
gchar *s = line, *end;
gdouble lower, upper;
lower = g_ascii_strtod(s, &end);
s = end;
upper = g_ascii_strtod(s, &end);
if (end == s) {
g_warning("Invalid grain_filter range record: %s.", line);
continue;
}
s = end;
g_strstrip(s);
if (!(gvalue = gwy_inventory_get_item(inventory, s))) {
g_warning("Invalid grain_filter range record: %s.", line);
continue;
}
rr = g_slice_new(RangeRecord);
rr->lower = lower;
rr->upper = upper;
rr->quantity = gwy_resource_get_name(GWY_RESOURCE(gvalue));
g_hash_table_insert(args->ranges_history,
(gpointer)rr->quantity, rr);
}
}
g_free(buffer);
}
g_free(filename);
gfilter_sanitize_args(args);
}
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 gboolean
file_read_header(GPtrArray *ezdfile,
gchar *buffer,
GError **error)
{
EZDSection *section = NULL;
gchar *p, *line;
guint len;
while ((line = gwy_str_next_line(&buffer))) {
line = g_strstrip(line);
if (!(len = strlen(line)))
continue;
if (line[0] == '[' && line[len-1] == ']') {
section = g_new0(EZDSection, 1);
g_ptr_array_add(ezdfile, section);
line[len-1] = '\0';
section->name = g_strdup(line + 1);
section->meta = g_hash_table_new_full(g_str_hash, g_str_equal,
g_free, g_free);
gwy_debug("Section <%s>", section->name);
continue;
}
if (!section) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Garbage before first header section."));
return FALSE;
}
/* Skip comments */
if (g_str_has_prefix(line, "--"))
continue;
p = strchr(line, '=');
if (!p) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Malformed header line (missing =)."));
return FALSE;
}
*p = '\0';
p++;
if (gwy_strequal(line, "SaveMode")) {
if (strcmp(p, "Binary"))
g_warning("SaveMode is not Binary, this is not supported");
}
else if (gwy_strequal(line, "SaveBits"))
section->bitdepth = atol(p);
else if (gwy_strequal(line, "SaveSign")) {
section->sign = gwy_strequal(p, "Signed");
if (!section->sign)
g_warning("SaveSign is not Signed, this is not supported");
}
else if (gwy_strequal(line, "SaveOrder")) {
if (gwy_strequal(p, "Intel"))
section->byteorder = G_LITTLE_ENDIAN;
else
g_warning("SaveOrder is not Intel, this is not supported");
}
else if (gwy_strequal(line, "Frame")) {
if (gwy_strequal(p, "Scan forward"))
section->direction = SCAN_FORWARD;
else if (gwy_strequal(p, "Scan backward"))
section->direction = SCAN_BACKWARD;
}
else if (gwy_strequal(line, "Points"))
section->xres = atol(p);
else if (gwy_strequal(line, "Lines"))
section->yres = atol(p);
/* FIXME: this is ugly, and incorrect for non-2D data */
else if (gwy_strequal(line, "Dim0Name"))
section->xrange.name = g_strdup(p);
else if (gwy_strequal(line, "Dim1Name"))
section->yrange.name = g_strdup(p);
else if (gwy_strequal(line, "Dim2Name"))
section->zrange.name = g_strdup(p);
else if (gwy_strequal(line, "Dim0Unit"))
section->xrange.unit = g_strdup(p);
else if (gwy_strequal(line, "Dim1Unit"))
section->yrange.unit = g_strdup(p);
else if (gwy_strequal(line, "Dim2Unit"))
section->zrange.unit = g_strdup(p);
else if (gwy_strequal(line, "Dim0Min"))
section->xrange.min = g_ascii_strtod(p, NULL);
else if (gwy_strequal(line, "Dim1Min"))
section->yrange.min = g_ascii_strtod(p, NULL);
else if (gwy_strequal(line, "Dim2Min"))
section->zrange.min = g_ascii_strtod(p, NULL);
else if (gwy_strequal(line, "Dim0Range"))
section->xrange.range = g_ascii_strtod(p, NULL);
else if (gwy_strequal(line, "Dim1Range"))
section->yrange.range = g_ascii_strtod(p, NULL);
else if (gwy_strequal(line, "Dim2Range"))
section->zrange.range = g_ascii_strtod(p, NULL);
else
g_hash_table_replace(section->meta, g_strdup(line), g_strdup(p));
}
return TRUE;
}
/* NB: Buffer must be writable and nul-terminated, its initial part is
* overwritten */
static gboolean
sdfile_read_header_text(gchar **buffer,
gsize *len,
SDFile *sdfile,
GError **error)
{
gchar *val, *p;
/* We do not need exact lenght of the minimum file */
if (*len < SDF_MIN_TEXT_SIZE) {
err_TOO_SHORT(error);
return FALSE;
}
gwy_clear(sdfile, 1);
p = *buffer;
val = g_strstrip(gwy_str_next_line(&p));
strncpy(sdfile->version, val, sizeof(sdfile->version));
READ_STRING(p, "ManufacID", val, sdfile->manufacturer, error)
READ_STRING(p, "CreateDate", val, sdfile->creation, error)
READ_STRING(p, "ModDate", val, sdfile->modification, error)
READ_INT(p, "NumPoints", val, sdfile->xres, TRUE, error)
READ_INT(p, "NumProfiles", val, sdfile->yres, TRUE, error)
READ_FLOAT(p, "Xscale", val, sdfile->xscale, TRUE, error)
READ_FLOAT(p, "Yscale", val, sdfile->yscale, TRUE, error)
READ_FLOAT(p, "Zscale", val, sdfile->zscale, TRUE, error)
READ_FLOAT(p, "Zresolution", val, sdfile->zres, FALSE, error)
READ_INT(p, "Compression", val, sdfile->compression, FALSE, error)
READ_INT(p, "DataType", val, sdfile->data_type, FALSE, error)
READ_INT(p, "CheckType", val, sdfile->check_type, FALSE, error)
/* at least */
if (sdfile->data_type < SDF_NTYPES)
sdfile->expected_size = 2*sdfile->xres * sdfile->yres;
else
sdfile->expected_size = -1;
/* Skip possible extra header lines */
do {
val = gwy_str_next_line(&p);
if (!val)
break;
val = g_strstrip(val);
if (g_ascii_isalpha(val[0])) {
gwy_debug("Extra header line: <%s>\n", val);
}
} while (val[0] == ';' || g_ascii_isalpha(val[0]));
if (!val || *val != '*') {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Missing data start marker (*)."));
return FALSE;
}
*buffer = p;
*len -= p - *buffer;
sdfile->data = (gchar*)*buffer;
return TRUE;
}
