static GwyDataField*
microprof_read_data_field(const MicroProfFile *mfile,
const guchar *buffer)
{
const guint16 *d16 = (const guint16*)buffer;
GwyDataField *dfield;
GwySIUnit *siunit;
gdouble *d;
guint xres, yres, i, j;
xres = mfile->xres;
yres = mfile->yres;
dfield = gwy_data_field_new(xres, yres,
mfile->xrange, mfile->yrange, FALSE);
d = gwy_data_field_get_data(dfield);
for (i = 0; i < yres; i++) {
for (j = 0; j < xres; j++) {
d[(yres-1 - i)*xres + j] = mfile->zscale*GUINT16_FROM_LE(*d16);
d16++;
}
}
siunit = gwy_data_field_get_si_unit_xy(dfield);
gwy_si_unit_set_from_string(siunit, "m");
siunit = gwy_data_field_get_si_unit_z(dfield);
gwy_si_unit_set_from_string(siunit, "m");
return dfield;
}
static void
fill_data_fields(APEFile *apefile,
const guchar *buffer)
{
GwyDataField *dfield;
GwySIUnit *unit;
gdouble *data;
const gchar *zunit;
guint b, n, i, j, k;
gdouble q;
apefile->data = g_new0(GwyDataField*, apefile->ndata);
for (b = apefile->channels, n = 0, k = 0; b; b = b >> 1, k++) {
if (!(b & 1))
continue;
dfield = gwy_data_field_new(apefile->res, apefile->res,
apefile->xreal, apefile->yreal, FALSE);
unit = gwy_data_field_get_si_unit_xy(dfield);
gwy_si_unit_set_from_string(unit, "m");
data = gwy_data_field_get_data(dfield);
buffer += (apefile->res + 1)*sizeof(float);
switch (k) {
case APE_HEIGHT:
case APE_HEIGHT_R:
case APE_AUX2:
case APE_AUX2_R:
q = apefile->z_piezo_factor * 1e-9;
zunit = "m";
break;
case APE_AUX1:
case APE_AUX1_R:
q = 1.0;
zunit = apefile->pg850_image ? "A" : "V";
break;
default:
q = 1.0;
zunit = "V";
break;
}
unit = gwy_data_field_get_si_unit_z(dfield);
gwy_si_unit_set_from_string(unit, zunit);
for (i = 0; i < apefile->res; i++) {
/* There is always one ignored record, do not ask me why... */
buffer += sizeof(float);
for (j = 0; j < apefile->res; j++) {
*(data++) = q*gwy_get_gfloat_le(&buffer);
}
}
apefile->data[n] = dfield;
n++;
}
}
static GwyDataField*
rhk_sm4_page_to_data_field(const RHKPage *page)
{
GwyDataField *dfield;
GwySIUnit *siunit;
const gchar *unit;
const gint32 *pdata;
gint xres, yres, i, j;
gdouble *data;
xres = page->x_size;
yres = page->y_size;
dfield = gwy_data_field_new(xres, yres,
xres*fabs(page->x_scale),
yres*fabs(page->y_scale),
FALSE);
data = gwy_data_field_get_data(dfield);
pdata = (const gint32*)page->data;
for (i = 0; i < yres; i++) {
for (j = 0; j < xres; j++) {
data[i*xres + xres-1 - j] = GINT32_FROM_LE(pdata[i*xres + j])
*page->z_scale + page->z_offset;
}
}
/* XY units */
if (page->strings[RHK_STRING_X_UNITS]
&& page->strings[RHK_STRING_Y_UNITS]) {
if (!gwy_strequal(page->strings[RHK_STRING_X_UNITS],
page->strings[RHK_STRING_Y_UNITS]))
g_warning("X and Y units differ, using X");
unit = page->strings[RHK_STRING_X_UNITS];
}
else if (page->strings[RHK_STRING_X_UNITS])
unit = page->strings[RHK_STRING_X_UNITS];
else if (page->strings[RHK_STRING_Y_UNITS])
unit = page->strings[RHK_STRING_Y_UNITS];
else
unit = NULL;
siunit = gwy_data_field_get_si_unit_xy(dfield);
gwy_si_unit_set_from_string(siunit, unit);
/* Z units */
if (page->strings[RHK_STRING_Z_UNITS])
unit = page->strings[RHK_STRING_Z_UNITS];
else
unit = NULL;
/* Fix some silly units */
if (unit && gwy_strequal(unit, "N/sec"))
unit = "s^-1";
siunit = gwy_data_field_get_si_unit_z(dfield);
gwy_si_unit_set_from_string(siunit, unit);
return dfield;
}
static GwyDataField*
mif_read_data_field(const MIFImageHeader *image_header,
const MIFBlock *block,
const guchar *buffer,
gsize size,
GError **error)
{
gint xres = image_header->setup.xres;
gint yres = image_header->setup.yres;
gdouble xreal = image_header->setup.xreal;
gdouble yreal = image_header->setup.yreal;
gdouble xoff = image_header->setup.xoff;
gdouble yoff = image_header->setup.yoff;
gdouble q = image_header->configuration.scan_int_to_meter;
GwyDataField *dfield;
gdouble *data;
const gint16 *d16;
gint i, j;
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
return NULL;
if (!block->size || block->offset > size || block->size > size
|| block->offset + block->size > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Image data are outside the file."));
return NULL;
}
if (err_SIZE_MISMATCH(error, xres*yres*sizeof(gint16), block->size, FALSE))
return NULL;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
data = gwy_data_field_get_data(dfield);
d16 = (const gint16*)(buffer + block->offset);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), "m");
// FIXME: Don't know why this factor. It seems to match what MIF spmview
// profile reader shows though.
q *= 1.0e4;
for (i = 0; i < yres; i++) {
for (j = 0; j < yres; j++) {
data[(yres-1 - i)*xres + j] = q*GINT16_FROM_LE(d16[i*xres + j]);
}
}
return dfield;
}
static GwyDataField*
jeol_read_data_field(const guchar *buffer,
const JEOLImageHeader *header)
{
GwyDataField *dfield;
const gchar *unitstr;
gdouble q, z0;
switch (header->spm_misc_param.measurement_signal) {
case JEOL_MEASUREMENT_SIGNAL_TOPOGRAPHY:
z0 = Nanometer*header->z0;
q = (header->z255 - header->z0)/65535.0*Nanometer;
unitstr = "m";
break;
case JEOL_MEASUREMENT_SIGNAL_LINEAR_CURRENT:
z0 = Nanoampere*header->z0;
q = (header->z255 - header->z0)/65535.0*Nanoampere;
unitstr = "A";
break;
/* We just guess it's always voltage. At least sometimes it is. */
case JEOL_MEASUREMENT_SIGNAL_AUX1:
case JEOL_MEASUREMENT_SIGNAL_AUX2:
z0 = header->z0;
q = (header->z255 - header->z0)/65535.0;
unitstr = "V";
break;
default:
return NULL;
break;
}
dfield = gwy_data_field_new(header->xres, header->yres,
Nanometer*header->xreal,
Nanometer*header->yreal,
FALSE);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), unitstr);
gwy_convert_raw_data(buffer, header->xres*header->yres, 1,
GWY_RAW_DATA_UINT16, GWY_BYTE_ORDER_LITTLE_ENDIAN,
gwy_data_field_get_data(dfield), q, z0);
return dfield;
}
static void
create_images(const X3PFile *x3pfile, GwyContainer *container)
{
gint id;
for (id = 0; id < x3pfile->zres; id++) {
GwyContainer *meta;
guint n = x3pfile->xres*x3pfile->yres, k;
GwyDataField *dfield, *mask;
const gboolean *valid = x3pfile->valid + id*n;
GQuark quark;
gchar buf[40];
dfield = gwy_data_field_new(x3pfile->xres,
x3pfile->yres,
x3pfile->xres*x3pfile->dx,
x3pfile->yres*x3pfile->dy,
FALSE);
memcpy(dfield->data, x3pfile->values + id*n, n*sizeof(gdouble));
for (k = 0; k < n; k++) {
if (!valid[k])
dfield->data[k] = NAN;
}
quark = gwy_app_get_data_key_for_id(id);
gwy_container_set_object(container, quark, dfield);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), "m");
gwy_app_channel_title_fall_back(container, id);
gwy_app_channel_check_nonsquare(container, id);
if ((mask = gwy_app_channel_mask_of_nans(dfield, TRUE))) {
quark = gwy_app_get_mask_key_for_id(id);
gwy_container_set_object(container, quark, mask);
g_object_unref(mask);
}
g_object_unref(dfield);
if ((meta = get_meta(x3pfile))) {
g_snprintf(buf, sizeof(buf), "/%u/meta", id);
gwy_container_set_object_by_name(container, buf, meta);
g_object_unref(meta);
}
}
}
static void
create_merged_field(GwyContainer *data, gint id1,
GwyDataField *dfield1, GwyDataField *dfield2,
gint px1, gint py1, gint px2, gint py2,
GwyMergeBoundaryType boundary, GwyMergeDirectionType dir,
gboolean create_mask, gboolean crop_to_rectangle)
{
GwyDataField *result, *outsidemask = NULL;
gint newxres, newyres, newid;
gwy_debug("field1 %dx%d", dfield1->xres, dfield1->yres);
gwy_debug("field2 %dx%d", dfield2->xres, dfield2->yres);
gwy_debug("px1: %d, py1: %d, px2: %d, py2: %d", px1, py1, px2, py2);
result = gwy_data_field_new_alike(dfield1, FALSE);
newxres = MAX(dfield1->xres + px1, dfield2->xres + px2);
newyres = MAX(dfield1->yres + py1, dfield2->yres + py2);
gwy_data_field_resample(result, newxres, newyres, GWY_INTERPOLATION_NONE);
if (create_mask && !crop_to_rectangle) {
outsidemask = gwy_data_field_new_alike(result, FALSE);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(outsidemask),
NULL);
}
put_fields(dfield1, dfield2, result, outsidemask,
boundary, px1, py1, px2, py2);
if (crop_to_rectangle) {
GwyOrientation orientation = GWY_ORIENTATION_HORIZONTAL;
if (dir == GWY_MERGE_DIRECTION_UP || dir == GWY_MERGE_DIRECTION_DOWN)
orientation = GWY_ORIENTATION_VERTICAL;
crop_result(result, dfield1, dfield2, orientation, px1, py1, px2, py2);
}
gwy_app_data_browser_get_current(GWY_APP_CONTAINER, &data, 0);
newid = gwy_app_data_browser_add_data_field(result, data, TRUE);
gwy_app_set_data_field_title(data, newid, _("Merged images"));
gwy_app_sync_data_items(data, data, id1, newid,
FALSE,
GWY_DATA_ITEM_PALETTE,
GWY_DATA_ITEM_MASK_COLOR,
GWY_DATA_ITEM_RANGE,
0);
if (outsidemask) {
if (gwy_data_field_get_max(outsidemask) > 0.0) {
GQuark quark = gwy_app_get_mask_key_for_id(newid);
gwy_container_set_object(data, quark, outsidemask);
}
g_object_unref(outsidemask);
}
gwy_app_channel_log_add_proc(data, -1, newid);
g_object_unref(result);
}
static GwyContainer*
amb_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
guchar *buffer = NULL;
const guchar *p;
gdouble *data;
guint i, j;
gsize size = 0;
GError *err = NULL;
guint xres, yres;
GwyDataField *dfield;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size <= HEADER_SIZE) {
err_TOO_SHORT(error);
goto fail;
}
/* The two bytes before are usually zeroes */
p = buffer + XRES_OFFSET;
xres = gwy_get_guint32_le(&p);
p = buffer + YRES_OFFSET;
yres = gwy_get_guint32_le(&p);
gwy_debug("xres: %u yres: %u", xres, yres);
/* The four bytes after might be a float, then there are four more bytes. */
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
goto fail;
if (err_SIZE_MISMATCH(error, 4*xres*yres + HEADER_SIZE, size, TRUE))
goto fail;
dfield = gwy_data_field_new(xres, yres, 1.0, 1.0*yres/xres,
FALSE);
data = gwy_data_field_get_data(dfield);
p = buffer + HEADER_SIZE;
for (i = 0; i < yres; i++) {
for (j = 0; j < xres; j++)
data[i*xres + j] = gwy_get_gfloat_le(&p);
}
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), "m");
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup("Topography"));
g_object_unref(dfield);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static GwyDataField*
pt3file_extract_counts(const PicoHarpFile *pt3file,
const LineTrigger *linetriggers,
const guchar *p)
{
GwyDataField *dfield;
guint xres, yres, i, lineno, pixno, n;
guint64 globaltime, globalbase, start, stop;
gdouble pix_resol;
gdouble *d;
xres = pt3file->imaging.common.xres;
yres = pt3file->imaging.common.yres;
n = pt3file->number_of_records;
if (pt3file->imaging.common.instrument == PICO_HARP_PIE710)
pix_resol = pt3file->imaging.pie710.pix_resol;
else if (pt3file->imaging.common.instrument == PICO_HARP_KDT180)
pix_resol = pt3file->imaging.kdt180.pix_resol;
else {
g_return_val_if_reached(NULL);
}
if (!(pix_resol = fabs(pix_resol))) {
g_warning("Pixel size is 0.0, fixing to 1.0");
pix_resol = 1.0;
}
pix_resol *= 1e-6;
dfield = gwy_data_field_new(xres, yres, pix_resol*xres, pix_resol*yres,
TRUE);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
d = gwy_data_field_get_data(dfield);
lineno = 0;
start = linetriggers[lineno].start;
stop = linetriggers[lineno].stop;
globaltime = globalbase = 0;
for (i = 0; i < n; i++) {
PicoHarpT3Record rec;
p = read_t3_record(&rec, p);
if (rec.channel == 15) {
if (rec.nsync == 0 && rec.time == 0)
globalbase += 0x10000;
continue;
}
globaltime = globalbase | rec.nsync;
while (lineno < yres && globaltime >= linetriggers[lineno].stop) {
lineno++;
if (lineno == yres)
break;
start = linetriggers[lineno].start;
stop = linetriggers[lineno].stop;
}
if (globaltime >= start && globaltime < stop) {
pixno = (xres*(globaltime - start)/(stop - start));
pixno = MIN(pixno, xres-1);
if (pt3file->imaging.common.bidirectional && lineno % 2)
d[xres*lineno + (xres-1 - pixno)] += 1.0;
else
d[xres*lineno + pixno] += 1.0;
}
}
return dfield;
}
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 void
run_noninteractive(NoiseSynthArgs *args,
const GwyDimensionArgs *dimsargs,
GwyContainer *data,
GwyDataField *dfield,
gint oldid,
GQuark quark)
{
GwySIUnit *siunit;
gboolean replace = dimsargs->replace && dfield;
gboolean add = dimsargs->add && dfield;
gint newid;
if (args->randomize)
args->seed = g_random_int() & 0x7fffffff;
if (replace) {
/* Always take a reference so that we can always unref. */
g_object_ref(dfield);
gwy_app_undo_qcheckpointv(data, 1, &quark);
if (!add)
gwy_data_field_clear(dfield);
gwy_app_channel_log_add_proc(data, oldid, oldid);
}
else {
if (add)
dfield = gwy_data_field_duplicate(dfield);
else {
gdouble mag = pow10(dimsargs->xypow10) * dimsargs->measure;
dfield = gwy_data_field_new(dimsargs->xres, dimsargs->yres,
mag*dimsargs->xres, mag*dimsargs->yres,
TRUE);
siunit = gwy_data_field_get_si_unit_xy(dfield);
gwy_si_unit_set_from_string(siunit, dimsargs->xyunits);
siunit = gwy_data_field_get_si_unit_z(dfield);
gwy_si_unit_set_from_string(siunit, dimsargs->zunits);
}
}
noise_synth_do(args, dimsargs, dfield);
if (replace)
gwy_data_field_data_changed(dfield);
else {
if (data) {
newid = gwy_app_data_browser_add_data_field(dfield, data, TRUE);
if (oldid != -1)
gwy_app_sync_data_items(data, data, oldid, newid, FALSE,
GWY_DATA_ITEM_GRADIENT,
0);
}
else {
newid = 0;
data = gwy_container_new();
gwy_container_set_object(data, gwy_app_get_data_key_for_id(newid),
dfield);
gwy_app_data_browser_add(data);
gwy_app_data_browser_reset_visibility(data,
GWY_VISIBILITY_RESET_SHOW_ALL);
g_object_unref(data);
}
gwy_app_set_data_field_title(data, newid, _("Generated"));
gwy_app_channel_log_add_proc(data, add ? oldid : -1, newid);
}
g_object_unref(dfield);
}
static GwyContainer*
int_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta;
GwyDataField *dfield = NULL, *mfield = NULL;
CodeVGridDataType type;
gchar *line, *p, *comment, *end, *buffer = NULL;
const gchar *unit, *title;
gchar **fields = NULL;
gsize size;
GError *err = NULL;
gdouble xreal, yreal;
gint i, xres, yres, no_data_value = 32767;
guint fi;
gdouble scale_size, wavelength, q = 1.0, x_scale = 1.0;
gboolean nearest_neighbour = FALSE;
gdouble *data, *mdata;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
/* Skip comments. */
p = buffer;
for (line = gwy_str_next_line(&p);
line && line[0] == '!';
line = gwy_str_next_line(&p)) {
gwy_debug("comment <%s>", line);
}
if (!line) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
/* The title. */
comment = line;
if (!(line = gwy_str_next_line(&p))) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
gwy_debug("comment <%s>", comment);
fields = split_line_in_place(line);
if (!fields
|| g_strv_length(fields) < 8
|| !gwy_strequal(fields[0], "GRD")
|| !(xres = atoi(fields[1]))
|| !(yres = atoi(fields[2]))
|| !(type = gwy_stramong(fields[3],
"SUR", "WFR", "FIL", "THV", "BIR", "CAO",
NULL))
|| !gwy_strequal(fields[4], "WVL")
|| (!(wavelength = g_ascii_strtod(fields[5], &end))
&& end == fields[5])) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
gwy_debug("type %u (%s)", type, fields[3]);
gwy_debug("xres %d, yres %d", xres, yres);
gwy_debug("wavelength %g", wavelength);
fi = 6;
if (gwy_strequal(fields[fi], "NNB")) {
nearest_neighbour = TRUE;
fi++;
}
gwy_debug("nearest_neighbour %d", nearest_neighbour);
if (!fields[fi] || !gwy_strequal(fields[fi], "SSZ")) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
fi++;
if (!(scale_size = g_ascii_strtod(fields[fi], &end)) && end == fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
gwy_debug("scale_size %g", scale_size);
if (!scale_size) {
g_warning("Zero SSZ, fixing to 1.0");
scale_size = 1.0;
}
fi++;
if (fields[fi] && gwy_strequal(fields[fi], "NDA")) {
fi++;
if (!fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
no_data_value = atoi(fields[fi]);
fi++;
}
gwy_debug("no_data_value %d", no_data_value);
if (fields[fi] && gwy_strequal(fields[fi], "XSC")) {
fi++;
if (!fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
if (!(x_scale = g_ascii_strtod(fields[fi], &end))
&& end == fields[fi]) {
err_FILE_TYPE(error, "Code V INT");
goto fail;
}
fi++;
}
gwy_debug("x_scale %g", x_scale);
if (!x_scale) {
g_warning("Zero XSC, fixing to 1.0");
x_scale = 1.0;
}
/* There may be more stuff but we do not know anything about it. */
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
goto fail;
yreal = 1.0;
xreal = x_scale*yreal;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, TRUE);
if (type == CODEV_INT_SURFACE_DEFORMATION) {
q = 1e-6*wavelength/scale_size;
unit = "m";
title = "Surface";
}
else if (type == CODEV_INT_WAVEFRONT_DEFORMATION) {
q = 1e-6*wavelength/scale_size;
unit = "m";
title = "Wavefront";
}
else {
g_warning("Don't know how to convert this grid data type to physical "
"units.");
title = fields[3];
}
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), unit);
mfield = gwy_data_field_new_alike(dfield, TRUE);
data = gwy_data_field_get_data(dfield);
mdata = gwy_data_field_get_data(mfield);
for (i = 0; i < xres*yres; i++, p = end) {
gint value = strtol(p, &end, 10);
if (value != no_data_value && (type != CODEV_INT_INTENSITY_FILTER
|| value >= 0)) {
mdata[i] = 1.0;
data[i] = q*value;
}
}
if (!gwy_app_channel_remove_bad_data(dfield, mfield))
gwy_object_unref(mfield);
container = gwy_container_new();
/*
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
from F. Riguet : apparently no flip is needed (the raw data import module
gives the correct orientation without further flipping)
*/
gwy_container_set_object(container, gwy_app_get_data_key_for_id(0), dfield);
g_object_unref(dfield);
gwy_app_channel_check_nonsquare(container, 0);
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(title));
if (mfield) {
/*
gwy_data_field_invert(mfield, FALSE, TRUE, FALSE);
*/
gwy_container_set_object(container, gwy_app_get_mask_key_for_id(0),
mfield);
g_object_unref(mfield);
}
meta = gwy_container_new();
gwy_container_set_string_by_name(meta, "Comment", g_strdup(comment));
gwy_container_set_string_by_name(meta, "Interpolation",
g_strdup(nearest_neighbour
? "NNB" : "Linear"));
gwy_container_set_string_by_name(meta, "Wavelength",
g_strdup_printf("%g μm", wavelength));
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
g_free(fields);
g_free(buffer);
return container;
}
static GwyContainer*
csmfile_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *meta, *container = NULL;
GHashTable *hash = NULL;
guchar *d24, *buffer = NULL;
gsize size = 0;
GError *err = NULL;
GwyDataField *dfield = NULL;
guint xres, yres, bmpsize, header_size, maxval, i, j;
gdouble real, zmin, zmax, q, z0;
GwyTextHeaderParser parser;
GwySIUnit *unit = NULL;
gchar *value, *end, *header = NULL;
gdouble *data;
gint power10;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < BMP_HEADER_SIZE) {
err_TOO_SHORT(error);
goto fail;
}
if (!read_bmp_header(buffer, &xres, &yres, &bmpsize)
|| size <= bmpsize) {
err_FILE_TYPE(error, "CSM");
goto fail;
}
header_size = size - bmpsize;
header = g_new(gchar, header_size + 1);
memcpy(header, buffer + bmpsize, header_size);
header[header_size] = '\0';
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
hash = gwy_text_header_parse(header, &parser, NULL, NULL);
/* Do NOT use the fields Image width, Image height from the added footer.
* Even though it is specifically added by Benyuan it can disagree with the
* BMP diemsions and when they disagree the BMP diemsions are apparently
* right. */
if (err_DIMENSION(error, xres))
goto fail;
if (err_DIMENSION(error, yres))
goto fail;
if (!(value = g_hash_table_lookup(hash, "ScanSize"))) {
err_MISSING_FIELD(error, "ScanSize");
goto fail;
}
real = g_ascii_strtod(value, NULL);
/* Use negated positive conditions to catch NaNs */
if (!((real = fabs(real)) > 0)) {
g_warning("Real size is 0.0, fixing to 1.0");
real = 1.0;
}
if (!(value = g_hash_table_lookup(hash, "HeightScale"))) {
err_MISSING_FIELD(error, "HeightScale");
goto fail;
}
zmax = g_ascii_strtod(value, &end);
unit = gwy_si_unit_new_parse(end, &power10);
/* Optional stuff for which we try to fall back. */
if (!(value = g_hash_table_lookup(hash, "StartHeightScale")))
zmin = 0.0;
else
zmin = g_ascii_strtod(value, NULL);
if (!(value = g_hash_table_lookup(hash, "MaxValue")))
maxval = 0xffff;
else
maxval = MAX(atoi(value), 1);
dfield = gwy_data_field_new(xres, yres, real*Nanometre, real*Nanometre,
FALSE);
data = gwy_data_field_get_data(dfield);
d24 = buffer + BMP_HEADER_SIZE;
q = pow10(power10)*(zmax - zmin)/maxval;
z0 = pow10(power10)*zmin;
for (i = 0; i < yres; i++) {
gdouble *row = data + (yres-1 - i)*xres;
for (j = 0; j < xres; j++, row++, d24 += 3)
*row = (d24[0] + 256.0*d24[1])*q + z0;
}
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_data_field_set_si_unit_z(dfield, unit);
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", dfield);
g_object_unref(dfield);
meta = gwy_container_new();
g_hash_table_foreach(hash, store_meta, meta);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
if ((value = g_hash_table_lookup(hash, "sTitle"))
&& g_utf8_validate(value, -1, NULL)) {
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(value));
}
else
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
GWY_OBJECT_UNREF(unit);
if (header)
g_free(header);
if (hash)
g_hash_table_destroy(hash);
return container;
}
static GwyContainer*
hitachi_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta;
GdkPixbuf *pixbuf = NULL;
GwyDataField *dfield = NULL;
gchar *value, *imagename = NULL, *header = NULL;
guchar *pixels;
GHashTable *hash = NULL;
GError *err = NULL;
gdouble dx;
gint pxres, pyres, hxres, hyres, rowstride, nchannels, i, j;
gdouble *data;
if (!(hash = hitachi_load_header(filename, &header, error)))
return NULL;
if (!require_keys(hash, error,
"ImageName", "DataSize", "PixelSize",
NULL))
goto fail;
value = g_hash_table_lookup(hash, "ImageName");
if (!(imagename = hitachi_find_data_name(filename, value))) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("No corresponding data file was found for header file."));
goto fail;
}
if (!(pixbuf = gdk_pixbuf_new_from_file(imagename, &err))) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_IO,
_("Cannot load image: %s"), err->message);
g_clear_error(&err);
goto fail;
}
/* We know the image dimensions so check them. */
pxres = gdk_pixbuf_get_width(pixbuf);
pyres = gdk_pixbuf_get_height(pixbuf);
value = g_hash_table_lookup(hash, "DataSize");
if (sscanf(value, "%ux%u", &hxres, &hyres) != 2) {
err_INVALID(error, "DataSize");
goto fail;
}
if (hxres != pxres || hyres != pyres) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Field DataSize %ux%u does not match image dimensions "
"%ux%u."),
hxres, hyres, pxres, pyres);
goto fail;
}
if (err_DIMENSION(error, hxres) || err_DIMENSION(error, hyres))
goto fail;
dx = g_ascii_strtod(g_hash_table_lookup(hash, "PixelSize"), NULL);
/* Use negated positive conditions to catch NaNs */
if (!((dx = fabs(dx)) > 0)) {
g_warning("Pixel size is 0.0, fixing to 1.0");
dx = 1.0;
}
dx *= Nanometre;
dfield = gwy_data_field_new(hxres, hyres, hxres*dx, hyres*dx, FALSE);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
data = gwy_data_field_get_data(dfield);
pixels = gdk_pixbuf_get_pixels(pixbuf);
rowstride = gdk_pixbuf_get_rowstride(pixbuf);
nchannels = gdk_pixbuf_get_n_channels(pixbuf);
for (i = 0; i < hyres; i++) {
gdouble *drow = data + i*hxres;
guchar *p = pixels + i*rowstride;
for (j = 0; j < hxres; j++, p += nchannels)
drow[j] = (p[0] + p[1] + p[2])/765.0;
}
container = gwy_container_new();
gwy_container_set_object(container, gwy_app_get_data_key_for_id(0), dfield);
g_object_unref(dfield);
if ((value = g_hash_table_lookup(hash, "SampleName"))
&& *value)
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(value));
else
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup("SEM"));
meta = gwy_container_new();
g_hash_table_foreach(hash, store_meta, meta);
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_object_unref(pixbuf);
g_free(imagename);
g_free(header);
g_hash_table_destroy(hash);
return container;
}
static GwyDataField*
mif_read_data_field(const MIFImageHeader *image_header,
const MIFBlock *block,
const guchar *buffer,
gsize size,
GError **error)
{
const MIFScanSetup *setup = &image_header->setup;
const MIFImageConfiguration *configuration = &image_header->configuration;
gint xres = setup->xres;
gint yres = setup->yres;
gdouble xreal = setup->xreal * image_header->configuration.xcal;
gdouble yreal = setup->yreal * image_header->configuration.ycal;
gdouble xoff = setup->xoff;
gdouble yoff = setup->yoff;
gdouble q = configuration->zcal/65536.0;
GwyDataField *dfield;
gdouble *data, *linecorrdata = NULL;
gsize datasize;
const gint16 *d16;
gint i, j;
if (err_DIMENSION(error, xres) || err_DIMENSION(error, yres))
return NULL;
if (!block->size || block->offset > size || block->size > size
|| block->offset + block->size > size) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Image data are outside the file."));
return NULL;
}
datasize = xres*yres*sizeof(gint16);
if (err_SIZE_MISMATCH(error, datasize, block->size, FALSE))
return NULL;
if (datasize + yres*sizeof(gint16) <= block->size) {
gwy_debug("There may be %u correction data after the image.", yres);
linecorrdata = g_new(gdouble, yres);
d16 = (const gint16*)(buffer + block->offset + datasize);
for (i = 0; i < yres; i++) {
linecorrdata[i] = pow(2.0, d16[i] - 13);
gwy_debug("corr[%u] %g", i, linecorrdata[i]);
}
}
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
data = gwy_data_field_get_data(dfield);
d16 = (const gint16*)(buffer + block->offset);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), "m");
// XXX: Don't know why this range. A user got it from DME. Have no idea
// why scan_int_to_meter does not appear here.
if (!configuration->z_linearized)
q *= 15e-6;
else
q *= 20e-6;
for (i = 0; i < yres; i++) {
gdouble qi = linecorrdata ? q*linecorrdata[i] : q;
for (j = 0; j < yres; j++) {
data[(yres-1 - i)*xres + j] = qi*GINT16_FROM_LE(d16[i*xres + j]);
}
}
g_free(linecorrdata);
return dfield;
}
static void
psdflp_do(const PSDFLPArgs *args, GwyDataField *dfield, GwyDataField *lpsdf)
{
enum { N = 4 };
GwyDataField *reout, *imout;
gint pxres, pyres, fxres, fyres;
gint i, j, fi, pi;
gdouble *ldata, *redata, *imdata;
gdouble *cosphi, *sinphi;
gdouble xreal, yreal, f0, f_max, b, p;
reout = gwy_data_field_new_alike(dfield, FALSE);
imout = gwy_data_field_new_alike(dfield, FALSE);
gwy_data_field_2dfft(dfield, NULL, reout, imout,
args->window, GWY_TRANSFORM_DIRECTION_FORWARD,
GWY_INTERPOLATION_ROUND, /* Ignored */
TRUE, 1);
pxres = reout->xres;
pyres = reout->yres;
redata = gwy_data_field_get_data(reout);
imdata = gwy_data_field_get_data(imout);
for (i = 0; i < pxres*pyres; i++)
redata[i] = redata[i]*redata[i] + imdata[i]*imdata[i];
gwy_data_field_2dfft_humanize(reout);
gwy_data_field_filter_gaussian(reout, args->sigma);
for (i = 0; i < pxres*pyres; i++)
redata[i] = sqrt(redata[i]);
fxres = pxres/2;
fyres = pyres/2;
gwy_data_field_resample(lpsdf, fxres, fyres, GWY_INTERPOLATION_NONE);
ldata = gwy_data_field_get_data(lpsdf);
xreal = dfield->xreal;
yreal = dfield->yreal;
f0 = 2.0/MIN(xreal, yreal);
f_max = 0.5*MIN(pxres/xreal, pyres/yreal);
if (f_max <= f0) {
g_warning("Minimum frequency is not smaller than maximum frequency.");
}
b = log(f_max/f0)/fyres;
/* Incorporate some prefactors to sinphi[] and cosphi[], knowing that
* cosine is only ever used for x and sine for y frequencies. */
cosphi = g_new(gdouble, (N+1)*fxres);
sinphi = g_new(gdouble, (N+1)*fxres);
for (j = 0; j < fxres; j++) {
gdouble phi_from = 2.0*G_PI*j/fxres;
gdouble phi_to = 2.0*G_PI*(j + 1.0)/fxres;
for (pi = 0; pi <= N; pi++) {
gdouble phi = ((pi + 0.5)*phi_from + (N - 0.5 - pi)*phi_to)/N;
cosphi[j*(N+1) + pi] = cos(phi)*xreal;
sinphi[j*(N+1) + pi] = sin(phi)*yreal;
}
}
for (i = 0; i < fyres; i++) {
gdouble f_from = f0*exp(b*i);
gdouble f_to = f0*exp(b*(i + 1.0));
for (j = 0; j < fxres; j++) {
const gdouble *cosphi_j = cosphi + j*(N+1);
const gdouble *sinphi_j = sinphi + j*(N+1);
guint n = 0;
gdouble s = 0.0;
for (fi = 0; fi <= N; fi++) {
gdouble f = ((fi + 0.5)*f_from + (N - 0.5 - fi)*f_to)/N;
for (pi = 0; pi <= N; pi++) {
gdouble x = f*cosphi_j[pi] + pxres/2.0,
y = f*sinphi_j[pi] + pyres/2.0;
if (G_UNLIKELY(x < 0.5
|| y < 0.5
|| x > pxres - 1.5
|| y > pyres - 1.5))
continue;
p = gwy_data_field_get_dval(reout, x, y,
GWY_INTERPOLATION_SCHAUM);
s += p;
n++;
}
}
if (!n)
n = 1;
ldata[i*fxres + j] = 2.0*G_PI/fxres * s/n*(f_to - f_from);
}
}
g_object_unref(imout);
g_object_unref(reout);
gwy_data_field_set_xreal(lpsdf, 2.0*G_PI);
gwy_data_field_set_xoffset(lpsdf, 0.0);
gwy_data_field_set_yreal(lpsdf, log(f_max/f0));
gwy_data_field_set_yoffset(lpsdf, log(f0));
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(lpsdf), "");
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(lpsdf), "");
gwy_data_field_normalize(lpsdf);
}
