static GwyContainer*
aist_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
AistContext context;
guchar *buffer = NULL;
const guchar *p;
gsize remaining, size = 0;
GError *err = NULL;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
p = buffer;
remaining = size;
context.container = gwy_container_new();
context.filename = filename;
context.channel_id = 0;
context.graph_id = 0;
read_aist_tree(&p, &remaining, &context);
gwy_file_abandon_contents(buffer, size, NULL);
if ((context.channel_id == 0) && (context.graph_id == 0)) {
g_object_unref(context.container);
context.container = NULL;
err_NO_DATA(error);
}
return context.container;
}
static GwyContainer*
x3p_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
X3PFile x3pfile;
unzFile zipfile;
zipfile = gwyminizip_unzOpen(filename);
if (!zipfile) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_SPECIFIC,
_("Minizip cannot open the file as a ZIP file."));
return NULL;
}
gwy_clear(&x3pfile, 1);
if (!x3p_parse_main(zipfile, &x3pfile, error))
goto fail;
if (!x3pfile.ndata) {
err_NO_DATA(error);
goto fail;
}
if (!x3pfile.datapos) {
if (!read_binary_data(&x3pfile, zipfile, error))
goto fail;
}
container = gwy_container_new();
if (x3pfile.feature_type == X3P_FEATURE_SUR)
create_images(&x3pfile, container);
else if (x3pfile.feature_type == X3P_FEATURE_PRF)
create_profiles(&x3pfile, container);
else {
g_assert_not_reached();
}
fail:
gwy_debug("calling unzClose()");
unzClose(zipfile);
x3p_file_free(&x3pfile);
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 GwyDataField*
apedax_get_data_field(unzFile uFile,
const gchar *chFileName,
const APEScanSize *scanSize,
gchar *zUnit,
gdouble scale,
GError **error)
{
GwyDataField *dfield = NULL;
GwySIUnit *xyUnit;
GwySIUnit *zSIUnit;
gdouble *data;
guchar *buffer;
gsize size, expectedSize;
unz_file_info uFileInfo;
/*Checking the dimensions*/
if (err_DIMENSION(error, scanSize->XRes)) {
return NULL;
}
if (err_DIMENSION(error, scanSize->YRes)) {
return NULL;
}
/*If XReal it's not greater than 0 or XReal is NaN*/
if (!(fabs(scanSize->XReal) > 0)) {
err_UNSUPPORTED(error, "X scan size");
return NULL;
}
/*Same for YReal*/
if (!(fabs(scanSize->YReal) > 0)) {
err_UNSUPPORTED(error, "Y scan size");
return NULL;
}
expectedSize = scanSize->XRes * scanSize->YRes * sizeof(gdouble);
unzGoToFirstFile(uFile);
if (unzLocateFile(uFile, chFileName, 0) != UNZ_OK) {
gwy_debug("Binary file not found");
err_NO_DATA(error);
return NULL;
}
if (unzGetCurrentFileInfo(uFile,
&uFileInfo,
NULL,
0L,
NULL,
0L,
NULL,
0L) != UNZ_OK) {
err_NO_DATA(error);
return NULL;
}
buffer = apedax_get_file_content(uFile, &uFileInfo, &size, error);
if (buffer == NULL) {
err_NO_DATA(error);
return NULL;
}
if (err_SIZE_MISMATCH(error, expectedSize, size, FALSE)) {
return NULL;
}
dfield = gwy_data_field_new(scanSize->XRes, scanSize->YRes,
scanSize->XReal, scanSize->YReal,
FALSE);
data = gwy_data_field_get_data(dfield);
xyUnit = gwy_data_field_get_si_unit_xy(dfield);
gwy_si_unit_set_from_string(xyUnit, "m");
zSIUnit = gwy_data_field_get_si_unit_z(dfield);
gwy_si_unit_set_from_string(zSIUnit, zUnit);
gwy_debug("Reading RAW data");
gwy_convert_raw_data(buffer,
scanSize->XRes * scanSize->YRes,
1,
GWY_RAW_DATA_DOUBLE,
GWY_BYTE_ORDER_LITTLE_ENDIAN,
data,
scale,
0.0);
return dfield;
}
static GwyContainer*
mif_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
MIFFile mfile;
GwyDataField *dfield;
guint i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (!mif_read_header(buffer, size, &mfile.header, error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
/* TODO: Check file version */
if (!mif_read_image_items(mfile.images, buffer, size, &mfile.header.info,
error)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
/* FIXME: Only v1.7! */
for (i = 0; i < mfile.header.nimages; i++) {
MIFInfoItem *item = mfile.images + i;
MIFImageHeader image_header;
MIFBlock raster, macro_geometry, preview, image, curve, calc;
guint ncalculations;
const guchar *p = buffer + item->image.offset;
GQuark quark;
if (!item->image.size)
continue;
if (item->image.offset > size
|| item->image.size > size
|| item->image.offset + item->image.size > size) {
continue;
}
/* XXX: We cannot use item->image.size because it's bogus, i.e.
* too short. Apparently there is some unaccounted-for space until
* the next block starts, 120 bytes for v1.7 files, after the image
* header which is in fact still occupied by the image header.
* MIFBlock says 714 bytes but the true size is 834 = 714 + 120. */
if (!mif_read_image_header(&image_header, &p, size - (p - buffer),
mfile.header.file_version,
error))
continue;
if (p - buffer + 52 > size)
continue;
mif_read_block(&raster, "raster", &p);
mif_read_block(¯o_geometry, "macro_geometry", &p);
mif_read_block(&preview, "preview", &p);
mif_read_block(&image, "image", &p);
mif_read_block(&curve, "curve", &p);
ncalculations = gwy_get_guint32_le(&p);
mif_read_block(&calc, "calc", &p);
gwy_debug("image header true size: %zu",
(gsize)(p - (buffer + item->image.offset)));
dfield = mif_read_data_field(&image_header, &image, buffer, size, NULL);
if (!dfield)
continue;
if (!container)
container = gwy_container_new();
quark = gwy_app_get_data_key_for_id(i);
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
gwy_app_channel_title_fall_back(container, i);
}
if (!container)
err_NO_DATA(error);
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static GwyContainer*
rhkspm32_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GArray *rhkfile;
RHKPage *rhkpage;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
gsize totalpos, pagesize;
GString *key;
guint i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < HEADER_SIZE) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
// niv - rhkfile is an array of rhkpage's, but buffer is where the actual
// raw file data is stored
rhkfile = g_array_new(FALSE, TRUE, sizeof(RHKPage));
totalpos = 0;
while (totalpos < size) {
g_array_set_size(rhkfile, rhkfile->len + 1);
rhkpage = &g_array_index(rhkfile, RHKPage, rhkfile->len - 1);
rhkpage->buffer = buffer + totalpos;
// niv - if the header seems illegal, skip all the next ones as well
// (and cancel the element addition to the g_array)
if (!rhkspm32_read_header(rhkpage, &err)) {
g_warning("failed to read rhk header after %u", rhkfile->len);
g_array_set_size(rhkfile, rhkfile->len - 1);
break;
}
pagesize = rhkpage->data_offset
+ rhkpage->item_size*rhkpage->xres*rhkpage->yres;
if (size < totalpos + pagesize) {
rhkspm32_free(rhkpage);
g_array_set_size(rhkfile, rhkfile->len - 1);
break;
}
totalpos += pagesize;
}
/* Be tolerant and don't fail when we were able to import at least
* something */
if (!rhkfile->len) {
if (err)
g_propagate_error(error, err);
else
err_NO_DATA(error);
gwy_file_abandon_contents(buffer, size, NULL);
g_array_free(rhkfile, TRUE);
return NULL;
}
g_clear_error(&err);
container = gwy_container_new();
key = g_string_new(NULL);
for (i = 0; i < rhkfile->len; i++) {
const gchar *cs;
gchar *s;
gwy_debug("rhk-spm32: processing page %d of %d\n", i+1, rhkfile->len);
rhkpage = &g_array_index(rhkfile, RHKPage, i);
if (rhkpage->type == RHK_TYPE_IMAGE) { // niv - just leaving this alone
dfield = rhkspm32_read_data(rhkpage);
g_string_printf(key, "/%d/data", i);
gwy_container_set_object_by_name(container, key->str, dfield);
g_object_unref(dfield);
g_string_append(key, "/title");
cs = gwy_enum_to_string(rhkpage->scan,
scan_directions,
G_N_ELEMENTS(scan_directions));
if (rhkpage->label) {
if (cs)
s = g_strdup_printf("%s [%s]", rhkpage->label, cs);
else
s = g_strdup(rhkpage->label);
gwy_container_set_string_by_name(container, key->str, s);
}
else
gwy_app_channel_title_fall_back(container, i);
gwy_file_channel_import_log_add(container, i, NULL,
filename);
}
else if (rhkpage->type == RHK_TYPE_LINE) { // niv - after omicron.c
GwySpectra* spectra;
GwyGraphModel *gmodel;
spectra = rhkspm32_read_spectra(rhkpage);
/* converting to graphs, as there is no point in leaving these as
* sps - no xy coordinates, so the spectro tool is kinda clueless */
gwy_debug("processing graph in page %d\n", i);
if ((gmodel = spectra_to_graph(spectra)) != NULL) {
gchar *container_key = NULL;
/* add gmodel to container */
container_key = g_strdup_printf("%s/%d", GRAPH_PREFIX, i);
gwy_container_set_object_by_name(container, container_key,
gmodel);
g_free(container_key);
}
g_object_unref(gmodel);
g_object_unref(spectra);
}
gwy_debug("rhk-spm32: finished parsing page %d \n", i);
meta = rhkspm32_get_metadata(rhkpage);
if (rhkpage->type == RHK_TYPE_IMAGE) {
/* this doesn't really work, but at least the meta data stays
with the graph, even if the metadata viewer won't show it*/
g_string_printf(key, "/%d/meta", i);
}
else if (rhkpage->type == RHK_TYPE_LINE) {
g_string_printf(key, "%s/%d/meta", GRAPH_PREFIX, i);
}
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
}
g_string_free(key, TRUE);
gwy_file_abandon_contents(buffer, size, NULL);
for (i = 0; i < rhkfile->len; i++)
rhkspm32_free(&g_array_index(rhkfile, RHKPage, i));
g_array_free(rhkfile, TRUE);
return container;
}
static GwyContainer*
gxsm_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
static const gchar *dimensions[] = { "time", "value", "dimy", "dimx" };
GwyContainer *data = NULL;
GwyDataField *dfield;
GwySIUnit *siunit;
NetCDF cdffile;
const NetCDFDim *dim;
const NetCDFVar *var;
const NetCDFAttr *attr;
gdouble real;
gint i, power10;
if (!cdffile_load(&cdffile, filename, error))
return NULL;
if (cdffile.nrecs) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("NetCDF records are not supported."));
goto gxsm_load_fail;
}
/* Look for variable "H" or "FloatField". This seems to be how GXSM calls
* data. */
if (!(var = cdffile_get_var(&cdffile, "H"))
&& !(var = cdffile_get_var(&cdffile, "FloatField"))) {
err_NO_DATA(error);
goto gxsm_load_fail;
}
/* Check the dimensions. We only know how to handle time=1 and value=1. */
for (i = 0; i < var->ndims; i++) {
dim = cdffile.dims + var->dimids[i];
if (!gwy_strequal(dim->name, dimensions[i])
|| (i < 2 && dim->length != 1)) {
/* XXX */
err_NO_DATA(error);
goto gxsm_load_fail;
}
}
if (err_DIMENSION(error, cdffile.dims[var->dimids[3]].length)
|| err_DIMENSION(error, cdffile.dims[var->dimids[2]].length))
goto gxsm_load_fail;
dfield = read_data_field((const guchar*)(cdffile.buffer + var->begin),
cdffile.dims[var->dimids[3]].length,
cdffile.dims[var->dimids[2]].length,
var->type);
if ((siunit = read_real_size(&cdffile, "rangex", &real, &power10))) {
/* Use negated positive conditions to catch NaNs */
if (!((real = fabs(real)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
real = 1.0;
}
gwy_data_field_set_xreal(dfield, real*pow10(power10));
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
}
if ((siunit = read_real_size(&cdffile, "rangey", &real, &power10))) {
/* Use negated positive conditions to catch NaNs */
if (!((real = fabs(real)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
real = 1.0;
}
gwy_data_field_set_yreal(dfield, real*pow10(power10));
/* must be the same gwy_data_field_set_si_unit_xy(dfield, siunit); */
g_object_unref(siunit);
}
if ((siunit = read_real_size(&cdffile, "rangez", &real, &power10))) {
/* rangez seems to be some bogus value, take only units */
gwy_data_field_set_si_unit_z(dfield, siunit);
gwy_data_field_multiply(dfield, pow10(power10));
g_object_unref(siunit);
}
if ((siunit = read_real_size(&cdffile, "dz", &real, &power10))) {
/* on the other hand the units seem to be bogus here, take the range */
gwy_data_field_multiply(dfield, real);
g_object_unref(siunit);
}
data = gwy_container_new();
gwy_container_set_object_by_name(data, "/0/data", dfield);
g_object_unref(dfield);
if ((attr = cdffile_get_attr(var->attrs, var->nattrs, "long_name"))
&& attr->type == NC_CHAR
&& attr->nelems) {
gwy_container_set_string_by_name(data, "/0/data/title",
g_strndup(attr->values, attr->nelems));
}
gxsm_load_fail:
gwy_file_abandon_contents(cdffile.buffer, cdffile.size, NULL);
cdffile_free(&cdffile);
return data;
}
static GwyContainer*
rhk_sm4_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
RHKFile rhkfile;
RHKObject *obj, o;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
const guchar *p;
GString *key = NULL;
guint i, imageid = 0, graphid = 0;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
gwy_clear(&rhkfile, 1);
if (size < HEADER_SIZE) {
err_TOO_SHORT(error);
goto fail;
}
/* File header */
p = buffer + MAGIC_OFFSET + MAGIC_TOTAL_SIZE;
rhkfile.page_count = gwy_get_guint32_le(&p);
rhkfile.object_count = gwy_get_guint32_le(&p);
rhkfile.object_field_size = gwy_get_guint32_le(&p);
gwy_debug("page_count: %u, object_count: %u, object_field_size: %u",
rhkfile.page_count, rhkfile.object_count,
rhkfile.object_field_size);
if (rhkfile.object_field_size != OBJECT_SIZE)
g_warning("Object field size %u differs from %u",
rhkfile.object_field_size, OBJECT_SIZE);
rhkfile.reserved1 = gwy_get_guint32_le(&p);
rhkfile.reserved2 = gwy_get_guint32_le(&p);
/* Header objects */
if (!(rhkfile.objects = rhk_sm4_read_objects(buffer, p, size,
rhkfile.object_count,
RHK_OBJECT_FILE_HEADER,
error)))
goto fail;
/* Find page index header */
if (!(obj = rhk_sm4_find_object(rhkfile.objects, rhkfile.object_count,
RHK_OBJECT_PAGE_INDEX_HEADER,
RHK_OBJECT_FILE_HEADER, error))
|| !rhk_sm4_read_page_index_header(&rhkfile.page_index_header,
obj, buffer, size, error))
goto fail;
/* There, find the page index array. That's a single object in the object
* list but it contains a page_count-long sequence of page indices. */
rhkfile.page_indices = g_new0(RHKPageIndex,
rhkfile.page_index_header.page_count);
if (!(obj = rhk_sm4_find_object(rhkfile.page_index_header.objects,
rhkfile.page_index_header.object_count,
RHK_OBJECT_PAGE_INDEX_ARRAY,
RHK_OBJECT_PAGE_INDEX_HEADER, error)))
goto fail;
o = *obj;
for (i = 0; i < rhkfile.page_index_header.page_count; i++) {
if (!rhk_sm4_read_page_index(rhkfile.page_indices + i, &o,
buffer, size, error))
goto fail;
/* Carefully move to the next page index */
o.offset += o.size + OBJECT_SIZE*rhkfile.page_indices[i].object_count;
}
container = gwy_container_new();
key = g_string_new(NULL);
/* Read pages */
for (i = 0; i < rhkfile.page_index_header.page_count; i++) {
RHKPageIndex *pi = rhkfile.page_indices + i;
RHKPage *page = &pi->page;
/* Page must contain header */
if (!(obj = rhk_sm4_find_object(pi->objects, pi->object_count,
RHK_OBJECT_PAGE_HEADER,
RHK_OBJECT_PAGE_INDEX, error))
|| !rhk_sm4_read_page_header(page, obj, buffer, size, error))
goto fail;
/* Page must contain data */
if (!(obj = rhk_sm4_find_object(pi->objects, pi->object_count,
RHK_OBJECT_PAGE_DATA,
RHK_OBJECT_PAGE_INDEX, error))
|| !rhk_sm4_read_page_data(page, obj, buffer, error))
goto fail;
/* Page may contain strings */
if (!(obj = rhk_sm4_find_object(page->objects, page->object_count,
RHK_OBJECT_STRING_DATA,
RHK_OBJECT_PAGE_HEADER, NULL))
|| !rhk_sm4_read_string_data(page, obj, pi->page.string_count,
buffer)) {
g_warning("Failed to read string data in page %u", i);
}
/* Read the data */
if (pi->data_type == RHK_DATA_IMAGE) {
GwyDataField *dfield = rhk_sm4_page_to_data_field(page);
GQuark quark = gwy_app_get_data_key_for_id(imageid);
const gchar *scandir, *name;
gchar *title;
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
if ((name = page->strings[RHK_STRING_LABEL])) {
scandir = gwy_enum_to_string(page->scan_dir, scan_directions,
G_N_ELEMENTS(scan_directions));
g_string_assign(key, g_quark_to_string(quark));
g_string_append(key, "/title");
if (scandir && *scandir)
title = g_strdup_printf("%s [%s]", name, scandir);
else
title = g_strdup(name);
gwy_container_set_string_by_name(container, key->str, title);
}
meta = rhk_sm4_get_metadata(pi, page);
g_string_printf(key, "/%u/meta", imageid);
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
imageid++;
}
else if (pi->data_type == RHK_DATA_LINE) {
GwyGraphModel *gmodel;
RHKSpecDriftHeader drift_header;
RHKSpecInfo spec_info;
G_GNUC_UNUSED gboolean have_header = FALSE, have_info = FALSE;
gwy_debug("page_type %u", page->page_type);
gwy_debug("line_type %u", page->line_type);
gwy_debug("page_sizes %u %u", page->x_size, page->y_size);
/* Page may contain drift header */
if ((obj = rhk_sm4_find_object(page->objects, page->object_count,
RHK_OBJECT_SPEC_DRIFT_HEADER,
RHK_OBJECT_PAGE_HEADER, NULL))
&& rhk_sm4_read_drift_header(&drift_header, obj, buffer)) {
gwy_debug("drift_header OK");
have_header = TRUE;
}
if ((obj = rhk_sm4_find_object(page->objects, page->object_count,
RHK_OBJECT_SPEC_DRIFT_DATA,
RHK_OBJECT_PAGE_HEADER, NULL))
&& rhk_sm4_read_spec_info(&spec_info, obj, buffer)) {
gwy_debug("spec_info OK");
have_info = TRUE;
}
/* FIXME: RHK_STRING_PLL_PRO_STATUS may contain interesting
* metadata. But we have not place where to put it. */
if ((gmodel = rhk_sm4_page_to_graph_model(page))) {
graphid++;
gwy_container_set_object(container,
gwy_app_get_graph_key_for_id(graphid),
gmodel);
g_object_unref(gmodel);
}
}
}
if (!imageid && !graphid)
err_NO_DATA(error);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
rhk_sm4_free(&rhkfile);
if (!imageid && !graphid) {
gwy_object_unref(container);
}
if (key)
g_string_free(key, TRUE);
return container;
}
static GwyContainer*
mprofile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
MProFile mprofile;
GwyContainer *meta, *container = NULL;
GwyDataField *dfield = NULL, *vpmask = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
gsize expected;
GString *key;
const gchar *title;
guint n, i;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (!mprofile_read_header(buffer, size, &mprofile, error))
return NULL;
expected = mprofile.header_size
+ 2*mprofile.nbuckets*mprofile.intens_xres*mprofile.intens_yres
+ 4*mprofile.phase_xres*mprofile.phase_yres;
if (err_SIZE_MISMATCH(error, expected, size, TRUE)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
n = fill_data_fields(&mprofile, buffer);
gwy_file_abandon_contents(buffer, size, NULL);
if (!n) {
err_NO_DATA(error);
return NULL;
}
key = g_string_new(NULL);
container = gwy_container_new();
for (i = 0; i < n; i++) {
if (i > 0) {
dfield = mprofile.intensity_data[i-1];
vpmask = mprofile.intensity_mask[i-1];
title = "Intensity";
}
else {
dfield = mprofile.phase_data;
vpmask = mprofile.phase_mask;
title = "Phase";
}
g_string_printf(key, "/%d/data", i);
gwy_container_set_object_by_name(container, key->str, dfield);
g_string_printf(key, "/%d/data/title", i);
gwy_container_set_string_by_name(container, key->str, g_strdup(title));
if (vpmask) {
g_string_printf(key, "/%d/mask", i);
gwy_container_set_object_by_name(container, key->str, vpmask);
}
meta = mprofile_get_metadata(&mprofile);
g_string_printf(key, "/%d/meta", i);
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
}
g_string_free(key, TRUE);
for (n = 0; n < mprofile.nbuckets; n++) {
gwy_object_unref(mprofile.intensity_data[n]);
gwy_object_unref(mprofile.intensity_mask[n]);
}
gwy_object_unref(mprofile.phase_data);
gwy_object_unref(mprofile.phase_mask);
return container;
}
static GwyContainer*
rawxyz_load(const gchar *filename,
GwyRunType mode,
GError **error)
{
GwyContainer *settings, *container = NULL;
GwySurface *surface = NULL;
RawXYZArgs args;
GwySIUnit *unit;
gint power10;
gdouble q;
gchar *buffer = NULL;
gsize size;
GError *err = NULL;
gboolean ok;
guint k;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
surface = read_xyz_points(buffer);
g_free(buffer);
if (!surface->n) {
err_NO_DATA(error);
goto fail;
}
settings = gwy_app_settings_get();
rawxyz_load_args(settings, &args);
if (mode == GWY_RUN_INTERACTIVE) {
ok = rawxyz_dialog(&args, surface);
rawxyz_save_args(settings, &args);
if (!ok) {
err_CANCELLED(error);
goto fail;
}
}
unit = gwy_si_unit_new_parse(args.xy_units, &power10);
if (power10) {
q = pow10(power10);
for (k = 0; k < surface->n; k++) {
surface->data[k].x *= q;
surface->data[k].y *= q;
}
gwy_surface_invalidate(surface);
}
gwy_serializable_clone(G_OBJECT(unit),
G_OBJECT(gwy_surface_get_si_unit_xy(surface)));
unit = gwy_si_unit_new_parse(args.z_units, &power10);
if (power10) {
q = pow10(power10);
for (k = 0; k < surface->n; k++)
surface->data[k].z *= q;
gwy_surface_invalidate(surface);
}
gwy_serializable_clone(G_OBJECT(unit),
G_OBJECT(gwy_surface_get_si_unit_z(surface)));
container = gwy_container_new();
gwy_container_set_object(container, gwy_app_get_surface_key_for_id(0),
surface);
gwy_app_xyz_title_fall_back(container, 0);
gwy_file_xyz_import_log_add(container, 0, NULL, filename);
fail:
g_free(args.xy_units);
g_free(args.z_units);
GWY_OBJECT_UNREF(surface);
return container;
}
static GwyContainer*
omicron_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
OmicronFile ofile;
GwyContainer *container = NULL, *meta;
gchar *text = NULL;
GError *err = NULL;
GwyDataField *dfield = NULL;
GwySpectra *spectra = NULL;
gchar key[32];
guint i;
/* @text must not be destroyed while @ofile is still in used because
* all strings are only references there */
if (!g_file_get_contents(filename, &text, NULL, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
gwy_clear(&ofile, 1);
ofile.filename = filename;
if (!omicron_read_header(text, &ofile, error))
goto fail;
if (!ofile.topo_channels || !ofile.topo_channels->len) {
err_NO_DATA(error);
goto fail;
}
container = gwy_container_new();
/* First Load the Topographic Data */
for (i = 0; i < ofile.topo_channels->len; i++) {
OmicronTopoChannel *channel;
channel = g_ptr_array_index(ofile.topo_channels, i);
dfield = omicron_read_data(&ofile, channel, error);
if (!dfield) {
gwy_object_unref(container);
goto fail;
}
g_snprintf(key, sizeof(key), "/%u/data", i);
gwy_container_set_object_by_name(container, key, dfield);
g_object_unref(dfield);
if (channel->name) {
gchar *s;
g_snprintf(key, sizeof(key), "/%u/data/title", i);
if (channel->scandir == SCAN_FORWARD)
s = g_strdup_printf("%s (Forward)", channel->name);
else if (channel->scandir == SCAN_BACKWARD)
s = g_strdup_printf("%s (Backward)", channel->name);
else
s = g_strdup(channel->name);
gwy_container_set_string_by_name(container, key, s);
}
if ((meta = omicron_make_meta(&ofile))) {
g_snprintf(key, sizeof(key), "/%u/meta", i);
gwy_container_set_object_by_name(container, key, meta);
g_object_unref(meta);
}
}
/* Then load the spectroscopy data. */
/*
* There are two types of spectroscopy file:
*
* a) Single Point Spectroscopy Files
* Single point which is stored by SCALA as an ascii file. Any number of
* single point spectrums may be aquired, but the number is normally
* quite small. These files are identified by their filename *.cs[0..3]
*
* b) Binary Spectroscopy Files
* When large numbers of spectra are aquired on a regular grid they are
* stored in BE binary. These data are aquired during the scan, and so
* can be aquired during the forward scan or the backward scan.
*
* Forwards scan files can be indentified from their filename *.sf[0..3]
* Backward scan files can be indentified from their filename *.sb[0..3]
*/
if (ofile.spectro_channels) {
for (i = 0; i < ofile.spectro_channels->len; i++) {
OmicronSpectroChannel *channel;
channel = g_ptr_array_index(ofile.spectro_channels, i);
if (omicron_has_extension(channel->filename, "cs")) {
gchar *t;
GQuark quark;
spectra = omicron_read_cs_data(&ofile, channel, error);
if (!spectra) {
gwy_object_unref(container);
goto fail;
}
if (!gwy_spectra_get_n_spectra(spectra)) {
gwy_debug("Spectra %u is empty, ignoring", i);
g_object_unref(spectra);
continue;
}
/* FIXME */
t = g_strconcat(channel->chan, "-", channel->param, NULL);
gwy_spectra_set_title(spectra, t);
g_free(t);
quark = gwy_app_get_spectra_key_for_id(i);
gwy_container_set_object(container, quark, spectra);
g_object_unref(spectra);
}
else if (omicron_has_extension(channel->filename, "sf")
|| omicron_has_extension(channel->filename, "sb")) {
/* FIXME */
}
else {
g_warning("Cannot determine spectra type of %s",
channel->filename);
}
}
}
fail:
omicron_file_free(&ofile);
g_free(text);
return container;
}
static GwyGraphModel*
sensofar_read_profile(SensofarDataDesc *data_desc,
const guchar **p,
gsize size,
GError **error)
{
GwyGraphModel *gmodel;
GwyGraphCurveModel *gcmodel;
guint xres, yres, j, n;
GwySIUnit *units = NULL;
gdouble *xdata, *ydata;
gdouble dx;
yres = gwy_get_guint32_le(p);
if (yres != 1)
g_warning("ysize is not 1 for profile");
xres = gwy_get_guint32_le(p);
gwy_debug("Data size: %dx%d", xres, yres);
if (err_SIZE_MISMATCH(error, xres*yres*sizeof(gfloat),
size - 2*sizeof(guint32), FALSE))
return NULL;
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
return NULL;
if (!((data_desc->axes_config.mppx
= fabs(data_desc->axes_config.mppx)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
data_desc->axes_config.mppx = 1.0;
}
xdata = g_new(gdouble, xres);
ydata = g_new(gdouble, xres);
dx = data_desc->axes_config.mppx * Micrometer;
for (j = n = 0; j < xres; j++) {
gdouble v = gwy_get_gfloat_le(p);
if (v != 1000001.0) {
xdata[n] = dx*j;
ydata[n] = v*Micrometer;
n++;
}
}
if (!n) {
g_free(xdata);
g_free(ydata);
err_NO_DATA(error);
return NULL;
}
gmodel = gwy_graph_model_new();
g_object_set(gmodel, "title", _("Profile"), NULL);
units = gwy_si_unit_new("m"); // values are in um only
g_object_set(gmodel, "si-unit-x", units, NULL);
g_object_unref(units);
units = gwy_si_unit_new("m"); // values are in um only
g_object_set(gmodel, "si-unit-y", units, NULL);
g_object_unref(units);
gcmodel = gwy_graph_curve_model_new();
gwy_graph_curve_model_set_data(gcmodel, xdata, ydata, n);
g_object_set(gcmodel,
"mode", GWY_GRAPH_CURVE_LINE,
"description", _("Profile"),
NULL);
gwy_graph_model_add_curve(gmodel, gcmodel);
g_object_unref(gcmodel);
return gmodel;
}
static GwyContainer*
apefile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
APEFile apefile;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
guint b, i, n;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
p = buffer;
apefile.version = *(p++);
if (size < 1294) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
apefile.spm_mode = *(p++);
p += 2; /* Skip VisualBasic VARIANT type type */
apefile.scan_date = gwy_get_gdouble_le(&p);
apefile.maxr_x = gwy_get_gfloat_le(&p);
apefile.maxr_y = gwy_get_gfloat_le(&p);
apefile.x_offset = gwy_get_guint32_le(&p);
apefile.y_offset = gwy_get_guint32_le(&p);
apefile.size_flag = gwy_get_guint16_le(&p);
apefile.res = 16 << apefile.size_flag;
if (err_DIMENSION(error, apefile.res)) {
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
apefile.acquire_delay = gwy_get_gfloat_le(&p);
apefile.raster_delay = gwy_get_gfloat_le(&p);
apefile.tip_dist = gwy_get_gfloat_le(&p);
apefile.v_ref = gwy_get_gfloat_le(&p);
if (apefile.version == 1) {
apefile.vpmt1 = gwy_get_guint16_le(&p);
apefile.vpmt2 = gwy_get_guint16_le(&p);
}
else {
apefile.vpmt1 = gwy_get_gfloat_le(&p);
apefile.vpmt2 = gwy_get_gfloat_le(&p);
}
apefile.remark = g_strndup(p, 120);
p += 120;
apefile.x_piezo_factor = gwy_get_guint32_le(&p);
apefile.y_piezo_factor = gwy_get_guint32_le(&p);
apefile.z_piezo_factor = gwy_get_guint32_le(&p);
apefile.hv_gain = gwy_get_gfloat_le(&p);
apefile.freq_osc_tip = gwy_get_gdouble_le(&p);
apefile.rotate = gwy_get_gfloat_le(&p);
apefile.slope_x = gwy_get_gfloat_le(&p);
apefile.slope_y = gwy_get_gfloat_le(&p);
apefile.topo_means = gwy_get_guint16_le(&p);
apefile.optical_means = gwy_get_guint16_le(&p);
apefile.error_means = gwy_get_guint16_le(&p);
/*
g_printerr("%04x %04x %04x\n",
apefile.topo_means, apefile.optical_means, apefile.error_means);
*/
apefile.channels = gwy_get_guint32_le(&p);
apefile.ndata = 0;
for (b = apefile.channels; b; b = b >> 1)
apefile.ndata += (b & 1);
apefile.range_x = gwy_get_gfloat_le(&p);
apefile.range_y = gwy_get_gfloat_le(&p);
apefile.subversion = gwy_get_guint16_le(&p);
/* Read everything since the header is long enough, check the version
* later when we decide whether to use these values or not. */
/* Since 2.1 */
apefile.hv_gain_z = gwy_get_gfloat_le(&p);
/* Since 2.2 */
apefile.fast2_0 = gwy_get_gdouble_le(&p);
apefile.fast2_1 = gwy_get_gdouble_le(&p);
apefile.fast2_2 = gwy_get_gdouble_le(&p);
apefile.fast2_3 = gwy_get_gdouble_le(&p);
/* Since 2.3 */
apefile.pg850_image = !!gwy_get_guint16_le(&p);
/* Since 2.4 */
apefile.xy_hv_status = gwy_get_gint16_le(&p);
apefile.z_hv_status = gwy_get_gint16_le(&p);
/* reserved */
p += 2;
apefile.xreal = apefile.maxr_x * apefile.x_piezo_factor * apefile.range_x
* apefile.hv_gain/65535.0 * 1e-9;
apefile.yreal = apefile.maxr_y * apefile.y_piezo_factor * apefile.range_y
* apefile.hv_gain/65535.0 * 1e-9;
/* Use negated positive conditions to catch NaNs */
if (!((apefile.xreal = fabs(apefile.xreal)) > 0)) {
g_warning("Real x size is 0.0, fixing to 1.0");
apefile.xreal = 1.0;
}
if (!((apefile.yreal = fabs(apefile.yreal)) > 0)) {
g_warning("Real y size is 0.0, fixing to 1.0");
apefile.yreal = 1.0;
}
gwy_debug("version = %u.%u, spm_mode = %u",
apefile.version, apefile.subversion, apefile.spm_mode);
gwy_debug("scan_date = %f", apefile.scan_date);
gwy_debug("maxr_x = %g, maxr_y = %g", apefile.maxr_x, apefile.maxr_y);
gwy_debug("x_offset = %u, y_offset = %u",
apefile.x_offset, apefile.y_offset);
gwy_debug("size_flag = %u", apefile.size_flag);
gwy_debug("acquire_delay = %g, raster_delay = %g, tip_dist = %g",
apefile.acquire_delay, apefile.raster_delay, apefile.tip_dist);
gwy_debug("v_ref = %g, vpmt1 = %g, vpmt2 = %g",
apefile.v_ref, apefile.vpmt1, apefile.vpmt2);
gwy_debug("x_piezo_factor = %u, y_piezo_factor = %u, z_piezo_factor = %u",
apefile.x_piezo_factor, apefile.y_piezo_factor,
apefile.z_piezo_factor);
gwy_debug("hv_gain = %g, freq_osc_tip = %g, rotate = %g",
apefile.hv_gain, apefile.freq_osc_tip, apefile.rotate);
gwy_debug("slope_x = %g, slope_y = %g",
apefile.slope_x, apefile.slope_y);
gwy_debug("topo_means = %u, optical_means = %u, error_means = %u",
apefile.topo_means, apefile.optical_means, apefile.error_means);
gwy_debug("channel bitmask = %03x, ndata = %u",
apefile.channels, apefile.ndata);
gwy_debug("range_x = %g, range_y = %g",
apefile.range_x, apefile.range_y);
n = (apefile.res + 1)*(apefile.res + 1)*sizeof(float);
if (size - (p - buffer) != n*apefile.ndata) {
g_warning("Expected data size %u, but it's %u.",
n*apefile.ndata, (guint)(size - (p - buffer)));
apefile.ndata = MIN(apefile.ndata, (size - (p - buffer))/n);
}
if (!apefile.ndata) {
err_NO_DATA(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
fill_data_fields(&apefile, p);
gwy_file_abandon_contents(buffer, size, NULL);
container = gwy_container_new();
/* All metadata seems to be per-file (global) */
meta = apefile_get_metadata(&apefile);
for (b = apefile.channels, n = 0, i = 0; b; b = b >> 1, i++) {
GwyContainer *tmp;
gchar *title;
gchar key[32];
if (!(b & 1))
continue;
g_snprintf(key, sizeof(key), "/%d/data", n);
dfield = apefile.data[n];
gwy_container_set_object_by_name(container, key, dfield);
g_object_unref(apefile.data[n]);
g_snprintf(key, sizeof(key), "/%d/data/title", n);
/*
* Channel labelling based on SPM Mode
*/
switch (apefile.spm_mode) {
case SPM_MODE_SNOM:
title = gwy_enuml_to_string(i,
"Height", APE_HEIGHT,
"Height-R", APE_HEIGHT_R,
"NSOM", APE_NSOM,
"NSOM-R", APE_NSOM_R,
"Error", APE_ERROR,
"Error-R", APE_ERROR_R,
"NSOM2", APE_NSOM2,
"NSOM2-R", APE_NSOM2_R,
"Lateral", APE_AUX1,
"Z-Z0", APE_AUX2,
"Lateral-R", APE_AUX1_R,
"Z-Z0-R", APE_AUX2_R,
NULL);
break;
case SPM_MODE_AFM_NONCONTACT:
case SPM_MODE_AFM_CONTACT:
case SPM_MODE_PHASE_DETECT_AFM:
title = gwy_enuml_to_string(i,
"Height", APE_HEIGHT,
"Height-R", APE_HEIGHT_R,
"IN1", APE_NSOM,
"IN1-R", APE_NSOM_R,
"Error", APE_ERROR,
"Error-R", APE_ERROR_R,
"IN2", APE_NSOM2,
"IN2-R", APE_NSOM2_R,
"Lateral", APE_AUX1,
"Z-Z0", APE_AUX2,
"Lateral-R", APE_AUX1_R,
"Z-Z0-R", APE_AUX2_R,
NULL);
break;
default:
title = gwy_enuml_to_string(i,
"Height", APE_HEIGHT,
"Height-R", APE_HEIGHT_R,
"IN1", APE_NSOM,
"IN1-R", APE_NSOM_R,
"Error", APE_ERROR,
"Error-R", APE_ERROR_R,
"IN2", APE_NSOM2,
"IN2-R", APE_NSOM2_R,
"Aux1", APE_AUX1,
"Z-Z0", APE_AUX2,
"Aux1-R", APE_AUX1_R,
"Z-Z0-R", APE_AUX2_R,
NULL);
break;
}
if (title && *title)
gwy_container_set_string_by_name(container, key, g_strdup(title));
tmp = gwy_container_duplicate(meta);
g_snprintf(key, sizeof(key), "/%d/meta", n);
gwy_container_set_object_by_name(container, key, tmp);
g_object_unref(tmp);
gwy_file_channel_import_log_add(container, n, NULL, filename);
n++;
}
g_object_unref(meta);
g_free(apefile.remark);
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*
nanoscope_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
GError *err = NULL;
gchar *buffer = NULL;
gchar *p;
const gchar *self;
gsize size = 0;
NanoscopeFileType file_type;
NanoscopeData *ndata;
NanoscopeValue *val;
GHashTable *hash, *scannerlist = NULL, *scanlist = NULL;
GList *l, *list = NULL;
gint i, xres = 0, yres = 0;
gboolean ok, has_version = FALSE;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
file_type = NANOSCOPE_FILE_TYPE_NONE;
if (size > MAGIC_SIZE) {
if (!memcmp(buffer, MAGIC_TXT, MAGIC_SIZE))
file_type = NANOSCOPE_FILE_TYPE_TXT;
else if (!memcmp(buffer, MAGIC_BIN, MAGIC_SIZE))
file_type = NANOSCOPE_FILE_TYPE_BIN;
}
if (!file_type) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File is not a Nanoscope file, "
"or it is a unknown subtype."));
g_free(buffer);
return NULL;
}
gwy_debug("File type: %d", file_type);
/* as already know file_type, fix the first char for hash reading */
*buffer = '\\';
p = buffer;
while ((hash = read_hash(&p, &err))) {
ndata = g_new0(NanoscopeData, 1);
ndata->hash = hash;
list = g_list_append(list, ndata);
}
if (err) {
g_propagate_error(error, err);
ok = FALSE;
}
else
ok = TRUE;
for (l = list; ok && l; l = g_list_next(l)) {
ndata = (NanoscopeData*)l->data;
hash = ndata->hash;
self = g_hash_table_lookup(hash, "#self");
/* The alternate names were found in files written by some beast
* called Nanoscope E software */
if (gwy_strequal(self, "Scanner list")
|| gwy_strequal(self, "Microscope list")) {
scannerlist = hash;
continue;
}
if (gwy_strequal(self, "File list")) {
has_version = !!g_hash_table_lookup(hash, "Version");
gwy_debug("has Version: %d", has_version);
continue;
}
if (gwy_strequal(self, "Ciao scan list")
|| gwy_strequal(self, "Afm list")
|| gwy_strequal(self, "NC Afm list")) {
get_scan_list_res(hash, &xres, &yres);
scanlist = hash;
}
if (!gwy_strequal(self, "Ciao image list")
&& !gwy_strequal(self, "AFM image list")
&& !gwy_strequal(self, "NCAFM image list"))
continue;
ndata->data_field = hash_to_data_field(hash, scannerlist, scanlist,
file_type, has_version,
size, buffer,
xres, yres,
&p, error);
ok = ok && ndata->data_field;
}
if (ok) {
gchar key[40];
i = 0;
container = gwy_container_new();
for (l = list; l; l = g_list_next(l)) {
ndata = (NanoscopeData*)l->data;
if (ndata->data_field) {
g_snprintf(key, sizeof(key), "/%d/data", i);
gwy_container_set_object_by_name(container, key,
ndata->data_field);
if ((val = g_hash_table_lookup(ndata->hash, "@2:Image Data"))
&& val->soft_scale) {
g_snprintf(key, sizeof(key), "/%d/data/title", i);
gwy_container_set_string_by_name(container, key,
g_strdup(val->soft_scale));
}
meta = nanoscope_get_metadata(ndata->hash, list);
g_snprintf(key, sizeof(key), "/%d/meta", i);
gwy_container_set_object_by_name(container, key, meta);
g_object_unref(meta);
gwy_app_channel_check_nonsquare(container, i);
i++;
}
}
if (!i)
gwy_object_unref(container);
}
for (l = list; l; l = g_list_next(l)) {
ndata = (NanoscopeData*)l->data;
gwy_object_unref(ndata->data_field);
if (ndata->hash)
g_hash_table_destroy(ndata->hash);
g_free(ndata);
}
g_free(buffer);
g_list_free(list);
if (!container && ok)
err_NO_DATA(error);
return container;
}
static GwyContainer*
rhk_sm3_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GPtrArray *rhkfile;
RHKPage *rhkpage;
GwyContainer *meta, *container = NULL;
guchar *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
const guchar *p;
GString *key;
guint i, count;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < HEADER_SIZE) {
err_TOO_SHORT(error);
gwy_file_abandon_contents(buffer, size, NULL);
return NULL;
}
rhkfile = g_ptr_array_new();
p = buffer;
count = 0;
gwy_debug("position %04x", p - buffer);
while ((rhkpage = rhk_sm3_read_page(&p, &size, &err))) {
gwy_debug("Page #%u read OK", count);
count++;
rhkpage->pageno = count;
gwy_debug("position %04x", p - buffer);
if (rhkpage->type != RHK_TYPE_IMAGE) {
gwy_debug("Page is not IMAGE, skipping");
rhk_sm3_page_free(rhkpage);
continue;
}
g_ptr_array_add(rhkfile, rhkpage);
}
/* Be tolerant and don't fail when we were able to import at least
* something */
if (!rhkfile->len) {
if (err)
g_propagate_error(error, err);
else
err_NO_DATA(error);
gwy_file_abandon_contents(buffer, size, NULL);
g_ptr_array_free(rhkfile, TRUE);
return NULL;
}
g_clear_error(&err);
container = gwy_container_new();
key = g_string_new("");
for (i = 0; i < rhkfile->len; i++) {
const gchar *cs;
gchar *s;
rhkpage = g_ptr_array_index(rhkfile, i);
dfield = rhk_sm3_page_to_data_field(rhkpage);
g_string_printf(key, "/%d/data", i);
gwy_container_set_object_by_name(container, key->str, dfield);
g_object_unref(dfield);
p = rhkpage->strings[RHK_STRING_LABEL];
cs = gwy_enum_to_string(rhkpage->scan_dir,
scan_directions, G_N_ELEMENTS(scan_directions));
if (p && *p) {
g_string_append(key, "/title");
if (cs)
s = g_strdup_printf("%s [%s]", p, cs);
else
s = g_strdup(p);
gwy_container_set_string_by_name(container, key->str, s);
}
meta = rhk_sm3_get_metadata(rhkpage);
g_string_printf(key, "/%d/meta", i);
gwy_container_set_object_by_name(container, key->str, meta);
g_object_unref(meta);
gwy_app_channel_check_nonsquare(container, i);
}
g_string_free(key, TRUE);
gwy_file_abandon_contents(buffer, size, NULL);
for (i = 0; i < rhkfile->len; i++)
rhk_sm3_page_free(g_ptr_array_index(rhkfile, i));
g_ptr_array_free(rhkfile, TRUE);
return container;
}
static GwyContainer*
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
read_binary_data(X3PFile *x3pfile, unzFile *zipfile, GError **error)
{
GwyRawDataType rawtype;
gsize size;
guchar *bindata;
gchar *s;
guint i;
s = g_hash_table_lookup(x3pfile->hash, DATA_LINK_PREFIX "/PointDataLink");
if (!s) {
err_NO_DATA(error);
return FALSE;
}
gwy_debug("binary data file %s", s);
if (unzLocateFile(zipfile, s, 1) != UNZ_OK) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_IO,
_("File %s is missing in the zip file."), s);
return FALSE;
}
s = g_hash_table_lookup(x3pfile->hash, AXES_PREFIX "/CZ/DataType");
if (!s) {
err_MISSING_FIELD(error, AXES_PREFIX "CZ/DataType");
return FALSE;
}
if (!x3p_file_get_data_type(s, &rawtype, error))
return FALSE;
if (!(bindata = x3p_get_file_content(zipfile, &size, error)))
return FALSE;
if (err_SIZE_MISMATCH(error, x3pfile->ndata * gwy_raw_data_size(rawtype),
size, TRUE)) {
g_free(bindata);
return FALSE;
}
gwy_convert_raw_data(bindata, x3pfile->ndata, 1,
rawtype, GWY_BYTE_ORDER_LITTLE_ENDIAN,
x3pfile->values, x3pfile->dz, x3pfile->zoff);
g_free(bindata);
for (i = 0; i < x3pfile->ndata; i++)
x3pfile->valid[i] = TRUE;
s = g_hash_table_lookup(x3pfile->hash, DATA_LINK_PREFIX "/ValidPointsLink");
if (!s)
return TRUE;
if (unzLocateFile(zipfile, s, 1) != UNZ_OK) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_IO,
_("File %s is missing in the zip file."), s);
return FALSE;
}
if (!(bindata = x3p_get_file_content(zipfile, &size, error)))
return FALSE;
if (err_SIZE_MISMATCH(error, (x3pfile->ndata + 7)/8, size, TRUE)) {
g_free(bindata);
return FALSE;
}
for (i = 0; i < x3pfile->ndata; i++)
x3pfile->valid[i] = bindata[i/8] & (1 << (i % 8));
g_free(bindata);
return TRUE;
}
static guint
find_data_offsets(const gchar *buffer,
gsize size,
GPtrArray *ezdfile,
GError **error)
{
EZDSection *dataset, *section;
GString *grkey;
guint required_size = 0;
gint ngroups, nchannels, i, j, k;
guint ndata = 0;
gchar *p;
/* Sanity check */
if (!ezdfile->len) {
err_NO_DATA(error);
return 0;
}
dataset = (EZDSection*)g_ptr_array_index(ezdfile, 0);
if (strcmp(dataset->name, "DataSet")) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("First section isn't DataSet"));
return 0;
}
if (!(p = g_hash_table_lookup(dataset->meta, "GroupCount"))
|| (ngroups = atol(p)) <= 0) {
err_INVALID(error, _("GroupCount in [DataSet]"));
return 0;
}
/* Scan groups */
grkey = g_string_new("");
for (i = 0; i < ngroups; i++) {
g_string_printf(grkey, "Gr%d-Count", i);
if (!(p = g_hash_table_lookup(dataset->meta, grkey->str))) {
g_warning("No count for group %u", i);
continue;
}
if ((nchannels = atol(p)) <= 0)
continue;
/* Scan channels inside a group, note it's OK there's less channels
* than specified */
for (j = 0; j < nchannels; j++) {
g_string_printf(grkey, "Gr%d-Ch%d", i, j);
if (!(p = g_hash_table_lookup(dataset->meta, grkey->str)))
continue;
section = NULL;
for (k = 1; k < ezdfile->len; k++) {
section = (EZDSection*)g_ptr_array_index(ezdfile, k);
if (gwy_strequal(section->name, p))
break;
}
if (!section) {
g_warning("Cannot find section for %s", p);
continue;
}
/* Compute data position */
gwy_debug("Data %s at offset %u from data start",
grkey->str, required_size);
gwy_debug("xres = %d, yres = %d, bpp = %d, z-name = %s",
section->xres, section->yres, section->bitdepth,
section->zrange.name);
if (section->yres < 2) {
gwy_debug("Skipping 1D data Gr%d-Ch%d. FIXME.", i, j);
continue;
}
ndata++;
section->data = buffer + required_size;
required_size += section->xres * section->yres
* (section->bitdepth/8);
if (required_size > size) {
g_warning("Truncated file, %s doesn't fit", grkey->str);
g_string_free(grkey, TRUE);
section->data = NULL;
return 0;
}
section->group = i;
section->channel = j;
}
}
g_string_free(grkey, TRUE);
if (!ndata)
err_NO_DATA(error);
return ndata;
}
static GwyContainer*
ols_load_tiff(const GwyTIFF *tiff, const gchar *filename, GError **error)
{
const gchar *colour_channels[] = { "Red", "Green", "Blue" };
const gchar *colour_channel_gradients[] = {
"RGB-Red", "RGB-Green", "RGB-Blue"
};
GwyContainer *container = NULL;
GwyDataField *dfield;
GwySIUnit *siunit;
GwyTIFFImageReader *reader = NULL;
GwyTextHeaderParser parser;
GHashTable *hash;
gint i, power10;
gchar *comment = NULL;
const gchar *s1;
GError *err = NULL;
guint spp, ch, id = 0, dir_num = 0;
gdouble *data;
gdouble z_axis = 1.0, xy_axis, factor;
GQuark quark;
GString *key;
/* Comment with parameters is common for all data fields */
if (!gwy_tiff_get_string0(tiff, GWY_TIFFTAG_IMAGE_DESCRIPTION, &comment)
|| !strstr(comment, MAGIC_COMMENT)) {
g_free(comment);
err_FILE_TYPE(error, "OLS");
return NULL;
}
/* Read the comment header. */
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
parser.section_template = "[\x1a]";
parser.endsection_template = "[\x1a End]";
parser.section_accessor = "::";
hash = gwy_text_header_parse(comment, &parser, NULL, NULL);
key = g_string_new(NULL);
for (dir_num = 0; dir_num < gwy_tiff_get_n_dirs(tiff); dir_num++) {
reader = gwy_tiff_image_reader_free(reader);
/* Request a reader, this ensures dimensions and stuff are defined. */
reader = gwy_tiff_get_image_reader(tiff, dir_num, 3, &err);
if (!reader) {
g_warning("Ignoring directory %u: %s", dir_num, err->message);
g_clear_error(&err);
continue;
}
spp = reader->samples_per_pixel;
g_string_printf(key, "Data %u Info::XY Convert Value", dir_num+1);
if (!(s1 = g_hash_table_lookup(hash, key->str))) {
g_warning("Cannot find 'XY Convert Value' for data %u.", dir_num+1);
continue;
}
xy_axis = g_ascii_strtod(s1, NULL);
if (!((xy_axis = fabs(xy_axis)) > 0)) {
g_warning("Real size step is 0.0, fixing to 1.0");
xy_axis = 1.0;
}
g_string_printf(key, "Data %u Info::Z Convert Value", dir_num+1);
if (!(s1 = g_hash_table_lookup(hash, key->str))) {
g_warning("Cannot find 'Z Convert Value' for data %u.", dir_num+1);
continue;
}
z_axis = g_ascii_strtod(s1, NULL);
for (ch = 0; ch < spp; ch++) {
siunit = gwy_si_unit_new_parse("nm", &power10);
factor = pow10(power10);
dfield = gwy_data_field_new(reader->width, reader->height,
reader->width * xy_axis * factor,
reader->height * xy_axis * factor,
FALSE);
// units
gwy_data_field_set_si_unit_xy(dfield, siunit);
g_object_unref(siunit);
if (spp == 1) {
if (dir_num == 1)
siunit = gwy_si_unit_new_parse("nm", &power10);
else
siunit = gwy_si_unit_new_parse("1e-6", &power10);
}
else {
siunit = gwy_si_unit_new(NULL);
power10 = 0;
}
gwy_data_field_set_si_unit_z(dfield, siunit);
g_object_unref(siunit);
factor = z_axis * pow10(power10);
data = gwy_data_field_get_data(dfield);
for (i = 0; i < reader->height; i++)
gwy_tiff_read_image_row(tiff, reader, ch, i, factor, 0.0,
data + i*reader->width);
/* add read datafield to container */
if (!container)
container = gwy_container_new();
quark = gwy_app_get_data_key_for_id(id);
gwy_container_set_object(container, quark, dfield);
g_object_unref(dfield);
g_string_printf(key, "%s/title", g_quark_to_string(quark));
if (spp == 1) {
/* Channel 0 is texture */
if (dir_num == 0) {
gwy_container_set_string_by_name(container, key->str,
g_strdup("Texture"));
}
/* Channel 1 is topography */
else if (dir_num == 1) {
g_string_printf(key, "%s/title", g_quark_to_string(quark));
gwy_container_set_string_by_name(container, key->str,
g_strdup("Height"));
}
}
else {
gwy_container_set_string_by_name(container, key->str,
g_strdup(colour_channels[ch]));
g_string_printf(key, "/%d/base/palette", id);
gwy_container_set_string_by_name
(container, key->str,
g_strdup(colour_channel_gradients[ch]));
}
gwy_file_channel_import_log_add(container, id, NULL, filename);
id++;
}
}
g_hash_table_destroy(hash);
g_string_free(key, TRUE);
g_free(comment);
if (reader) {
gwy_tiff_image_reader_free(reader);
reader = NULL;
}
if (!container)
err_NO_DATA(error);
return container;
}
