static GwyDataField*
read_text_data(const gchar *buffer,
gint text_data_start,
GHashTable *hash,
GError **error)
{
const gchar *p;
gchar *end;
gint xres, yres, i, power10;
gdouble xreal, yreal, zscale, xoff, yoff, zoff;
GwySIUnit *unitxy, *unitz;
GwyDataField *dfield = NULL;
gdouble *d;
unitxy = gwy_si_unit_new(NULL);
unitz = gwy_si_unit_new(NULL);
if (!get_scales(hash, TRUE,
&xres, &yres, &xreal, &yreal, &xoff, &yoff, unitxy,
&zscale, &zoff, unitz, error))
goto fail;
p = g_hash_table_lookup(hash, "DATA Unit");
gwy_si_unit_set_from_string_parse(unitz, p, &power10);
zscale = pow10(power10);
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
gwy_data_field_set_si_unit_z(dfield, unitz);
d = gwy_data_field_get_data(dfield);
p = (const gchar*)buffer + text_data_start;
for (i = 0; i < xres*yres; i++) {
d[i] = zscale*g_ascii_strtod(p, &end) + zoff;
if (end == p) {
g_set_error(error, GWY_MODULE_FILE_ERROR,
GWY_MODULE_FILE_ERROR_DATA,
_("Cannot parse data values after %d of %d."),
i, xres*yres);
gwy_object_unref(dfield);
goto fail;
}
p = end + (*end == ',');
}
fail:
g_object_unref(unitxy);
g_object_unref(unitz);
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 void
null_offsets(GwyContainer *data,
GwyRunType run)
{
GwyDataField *dfields[3];
GQuark quarks[3];
guint i;
gint id;
g_return_if_fail(run & BASICOPS_RUN_MODES);
gwy_app_data_browser_get_current(GWY_APP_DATA_FIELD, dfields + 0,
GWY_APP_MASK_FIELD, dfields + 1,
GWY_APP_SHOW_FIELD, dfields + 2,
GWY_APP_DATA_FIELD_KEY, quarks + 0,
GWY_APP_MASK_FIELD_KEY, quarks + 1,
GWY_APP_SHOW_FIELD_KEY, quarks + 2,
GWY_APP_DATA_FIELD_ID, &id,
0);
clean_quarks(G_N_ELEMENTS(quarks), quarks, dfields);
for (i = 0; i < G_N_ELEMENTS(dfields); i++) {
if (dfields[i]
&& !gwy_data_field_get_xoffset(dfields[i])
&& !gwy_data_field_get_yoffset(dfields[i])) {
quarks[i] = 0;
dfields[i] = NULL;
}
}
if (!dfields[0] && !dfields[1] && !dfields[2])
return;
gwy_app_undo_qcheckpointv(data, G_N_ELEMENTS(quarks), quarks);
for (i = 0; i < G_N_ELEMENTS(dfields); i++) {
if (dfields[i]) {
gwy_data_field_set_xoffset(dfields[i], 0.0);
gwy_data_field_set_yoffset(dfields[i], 0.0);
gwy_data_field_data_changed(dfields[i]);
}
}
gwy_app_channel_log_add_proc(data, id, id);
}
static GwyContainer*
lif_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
LIFHeader *header = NULL;
LIFMemBlock *memblock = NULL;
LIFFile *file = NULL;
LIFElement *element = NULL;
LIFDimension *dimension = NULL;
LIFChannel *channel = NULL;
gsize size = 0, memblock_size = 0;
gint64 remaining = 0;
gchar *buffer;
const guchar *p;
GError *err = NULL;
GwyDataField *dfield = NULL;
GwyBrick *brick = NULL;
gdouble *data = NULL;
gint i, j, channelno = 0, volumeno = 0;
gchar *strkey, *lutname;
GMarkupParser parser = {
header_start_element,
header_end_element,
header_parse_text, NULL, NULL
};
GMarkupParseContext *context;
XMLParserData *xmldata;
gint x, xres, xstep, y, yres, ystep, z, zres, zstep, offset, res;
gdouble xreal, yreal, zreal, xoffset, yoffset, zoffset;
gdouble zscale = 1.0, wscale = 1.0;
GwySIUnit *siunitxy = NULL, *siunitz = NULL;
GwySIUnit *siunitx = NULL, *siunity = NULL, *siunitw = NULL;
gint power10xy = 1;
gint power10x = 1, power10y = 1, power10z = 1, power10w = 1;
if (!g_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
goto fail;
}
if (size < 13) { /* header too short */
err_TOO_SHORT(error);
goto fail;
}
p = buffer;
remaining = size;
header = g_new0(LIFHeader, 1);
header->magic = gwy_get_gint32_le(&p);
gwy_debug("Magic = %d", header->magic);
header->size = gwy_get_guint32_le(&p);
gwy_debug("Size = %d", header->size);
header->testcode = *(p++);
gwy_debug("Testcode = 0x%x", header->testcode);
if (header->testcode != TESTCODE) {
err_FILE_TYPE(error, "Leica LIF");
goto fail;
}
header->xmllen = gwy_get_guint32_le(&p);
gwy_debug("XML length = %d", header->xmllen);
if (size < 13 + header->xmllen * 2) {
err_TOO_SHORT(error);
goto fail;
}
remaining -= 13;
header->xmlheader = g_convert((const gchar*)p, 2 * header->xmllen,
"UTF-8", "UTF-16", NULL, NULL, NULL);
p += header->xmllen * 2;
remaining -= header->xmllen * 2;
// gwy_debug("%s", header->xmlheader);
/* Parse XML header */
xmldata = g_new0(XMLParserData, 1);
xmldata->file = g_new0(LIFFile, 1);
xmldata->file->elements = g_array_new(FALSE, TRUE,
sizeof(LIFElement));
xmldata->elements = g_ptr_array_new();
context = g_markup_parse_context_new(&parser,
G_MARKUP_TREAT_CDATA_AS_TEXT,
(gpointer)xmldata,
NULL);
if (!g_markup_parse_context_parse(context, header->xmlheader, -1, &err)
|| !g_markup_parse_context_end_parse(context, &err)) {
error = &err;
g_clear_error(&err);
}
g_markup_parse_context_free(context);
file = xmldata->file;
file->header = header;
g_ptr_array_free(xmldata->elements, TRUE);
g_free(xmldata);
/* Reading memblocks */
file->memblocks = g_hash_table_new(g_str_hash, g_str_equal);
while (remaining > 0) {
memblock = lif_read_memblock(p, &memblock_size, file->version);
if (!memblock) {
break;
}
remaining -= memblock_size;
if (remaining >= 0) {
gwy_debug("remaining = %" G_GUINT64_FORMAT "", remaining);
p += memblock_size;
g_hash_table_insert(file->memblocks, memblock->memid,
memblock);
}
}
container = gwy_container_new();
for (i = 0; i < file->elements->len; i++) {
element = &g_array_index(file->elements, LIFElement, i);
if ((element->dimensions == NULL)
|| (element->channels == NULL)) {
gwy_debug("Empty element");
continue;
}
gwy_debug("Dimensions = %d channels=%d",
element->dimensions->len,
element->channels->len);
gwy_debug("memid=%s", element->memid);
/* check if we can load this type of data into
* Gwyddion structures */
res = 0;
if ((element->dimensions->len != 2)
&& (element->dimensions->len != 3)) {
/* check for case ndim == 4 && res == 1 */
for (i = 0; i < element->dimensions->len; i++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, i);
xres = dimension->res;
gwy_debug("dim[%d].res=%d", i, xres);
if (i == 2) {
res = xres;
}
}
if ((element->dimensions->len == 4) && (res == 1)) {
gwy_debug("4D volume");
}
else {
gwy_debug("not loading");
continue;
}
}
memblock = (LIFMemBlock *)g_hash_table_lookup(file->memblocks,
element->memid);
if (!memblock) {
gwy_debug("Failed to locate memblock with key %s",
element->memid);
continue;
}
p = memblock->data;
if (element->dimensions->len == 2) { /* Image */
for (j = 0; j < element->channels->len; j++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, 0);
xres = dimension->res;
xreal = dimension->length;
xoffset = dimension->origin;
xstep = dimension->bytesinc;
siunitxy = gwy_si_unit_new_parse(dimension->unit,
&power10xy);
dimension = &g_array_index(element->dimensions,
LIFDimension, 1);
yres = dimension->res;
yreal = dimension->length;
yoffset = dimension->origin;
ystep = dimension->bytesinc;
if (xreal <= 0.0)
xreal = 1.0;
if (yreal <= 0.0)
yreal = 1.0;
channel = &g_array_index(element->channels,
LIFChannel, j);
offset = channel->bytesinc;
siunitz = gwy_si_unit_new_parse(channel->unit,
&power10z);
zscale = pow10(power10z);
if (offset + (xres - 1) * xstep + (yres - 1)* ystep
> memblock->memsize) {
gwy_debug("Memblock too small");
gwy_debug("%d %" G_GUINT64_FORMAT "",
offset + (xres-1)*xstep + (yres-1)*ystep,
memblock->memsize);
err_SIZE_MISMATCH(error,
memblock->memsize,
offset+(xres-1)*xstep
+(yres-1)*ystep,
FALSE);
goto fail;
}
dfield = gwy_data_field_new(xres, yres,
xreal*pow10(power10xy),
yreal*pow10(power10xy),
TRUE);
gwy_data_field_set_xoffset(dfield,
xoffset*pow10(power10xy));
gwy_data_field_set_yoffset(dfield,
yoffset*pow10(power10xy));
data = gwy_data_field_get_data(dfield);
for (y = 0; y < yres; y++)
for (x = 0; x < xres; x++) {
*(data++) = zscale
* (gdouble)*(p + offset + x*xstep + y*ystep);
}
if (siunitxy) {
gwy_data_field_set_si_unit_xy(dfield, siunitxy);
g_object_unref(siunitxy);
}
if (siunitz) {
gwy_data_field_set_si_unit_z(dfield, siunitz);
g_object_unref(siunitz);
}
strkey = g_strdup_printf("/%d/data", channelno);
gwy_container_set_object_by_name(container,
strkey,
dfield);
g_object_unref(dfield);
g_free(strkey);
if (element->name) {
strkey = g_strdup_printf("/%d/data/title",
channelno);
gwy_container_set_string_by_name(container, strkey,
g_strdup(element->name));
g_free(strkey);
}
if (element->metadata) {
strkey = g_strdup_printf("/%d/meta",
channelno);
gwy_container_set_object_by_name(container,
strkey,
element->metadata);
g_free(strkey);
}
if (channel->lut) {
lutname = NULL;
if (gwy_strequal(channel->lut, "Red"))
lutname = g_strdup_printf("RGB-Red");
else if (gwy_strequal(channel->lut, "Green"))
lutname = g_strdup_printf("RGB-Green");
else if (gwy_strequal(channel->lut, "Blue"))
lutname = g_strdup_printf("RGB-Blue");
else if (gwy_strequal(channel->lut, "Gray"))
lutname = g_strdup_printf("Gray");
if (lutname) {
strkey = g_strdup_printf("/%u/base/palette",
channelno);
gwy_container_set_string_by_name(container,
strkey,
lutname);
g_free(strkey);
}
}
gwy_file_channel_import_log_add(container, channelno,
NULL, filename);
channelno++;
}
}
else if ((element->dimensions->len == 3)
|| ((element->dimensions->len == 4) && (res == 1))) {
/* Volume */
for (j = 0; j < element->channels->len; j++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, 0);
xres = dimension->res;
xreal = dimension->length;
xoffset = dimension->origin;
xstep = dimension->bytesinc;
siunitx = gwy_si_unit_new_parse(dimension->unit,
&power10x);
dimension = &g_array_index(element->dimensions,
LIFDimension, 1);
yres = dimension->res;
yreal = dimension->length;
yoffset = dimension->origin;
ystep = dimension->bytesinc;
siunity = gwy_si_unit_new_parse(dimension->unit,
&power10y);
if (element->dimensions->len == 3) {
dimension = &g_array_index(element->dimensions,
LIFDimension, 2);
}
else {
dimension = &g_array_index(element->dimensions,
LIFDimension, 3);
}
zres = dimension->res;
zreal = dimension->length;
zoffset = dimension->origin;
zstep = dimension->bytesinc;
siunitz = gwy_si_unit_new_parse(dimension->unit,
&power10z);
channel = &g_array_index(element->channels,
LIFChannel, j);
offset = channel->bytesinc;
siunitw = gwy_si_unit_new_parse(channel->unit,
&power10w);
wscale = pow10(power10w);
if (offset
+ (xres-1)*xstep + (yres-1)*ystep + (zres-1)*zstep
> memblock->memsize) {
gwy_debug("Memblock too small");
gwy_debug("%d %" G_GUINT64_FORMAT "",
offset + (xres-1)*xstep
+ (yres-1)*ystep + (zres-1)*zstep,
memblock->memsize);
err_SIZE_MISMATCH(error,
memblock->memsize,
offset + (xres-1)*xstep
+ (yres-1)*ystep + (zres-1)*zstep,
FALSE);
goto fail;
}
brick = gwy_brick_new(xres, yres, zres,
xreal*pow10(power10x),
yreal*pow10(power10y),
zreal*pow10(power10z),
TRUE);
gwy_brick_set_xoffset(brick, xoffset*pow10(power10x));
gwy_brick_set_yoffset(brick, yoffset*pow10(power10y));
gwy_brick_set_zoffset(brick, zoffset*pow10(power10z));
data = gwy_brick_get_data(brick);
for (z = 0; z < zres; z++)
for (y = 0; y < yres; y++)
for (x = 0; x < xres; x++) {
*(data++) = wscale * (gdouble)*(p + offset
+ x*xstep + y*ystep + z*zstep);
}
if (siunitx) {
gwy_brick_set_si_unit_x(brick, siunitx);
g_object_unref(siunitx);
}
if (siunity) {
gwy_brick_set_si_unit_y(brick, siunity);
g_object_unref(siunity);
}
if (siunitz) {
gwy_brick_set_si_unit_z(brick, siunitz);
g_object_unref(siunitz);
}
if (siunitw) {
gwy_brick_set_si_unit_w(brick, siunitw);
g_object_unref(siunitw);
}
strkey = g_strdup_printf("/brick/%d", volumeno);
gwy_container_set_object_by_name(container,
strkey,
brick);
g_free(strkey);
if (element->name) {
strkey = g_strdup_printf("/brick/%d/title",
volumeno);
gwy_container_set_string_by_name(container, strkey,
g_strdup(element->name));
g_free(strkey);
}
if (element->metadata) {
strkey = g_strdup_printf("/brick/%d/meta",
volumeno);
gwy_container_set_object_by_name(container,
strkey,
element->metadata);
g_free(strkey);
}
if (channel->lut) {
lutname = NULL;
if (gwy_strequal(channel->lut, "Red"))
lutname = g_strdup_printf("RGB-Red");
else if (gwy_strequal(channel->lut, "Green"))
lutname = g_strdup_printf("RGB-Green");
else if (gwy_strequal(channel->lut, "Blue"))
lutname = g_strdup_printf("RGB-Blue");
else if (gwy_strequal(channel->lut, "Gray"))
lutname = g_strdup_printf("Gray");
if (lutname) {
strkey = g_strdup_printf("/brick/%d/preview/palette",
volumeno);
gwy_container_set_string_by_name(container,
strkey,
lutname);
g_free(strkey);
}
}
dfield = gwy_data_field_new(xres, yres,
xreal, yreal, FALSE);
gwy_brick_mean_plane(brick, dfield,
0, 0, 0,
xres, yres, -1, FALSE);
strkey = g_strdup_printf("/brick/%d/preview",
volumeno);
gwy_container_set_object_by_name(container,
strkey,
dfield);
g_free(strkey);
g_object_unref(brick);
g_object_unref(dfield);
gwy_file_volume_import_log_add(container, volumeno,
NULL, filename);
volumeno++;
} /* for (channels) */
} /* if (volume) */
}
fail:
/* freeing all stuff */
if (file) {
if (file->memblocks) {
g_hash_table_foreach_remove(file->memblocks,
lif_remove_memblock,
NULL);
g_hash_table_unref(file->memblocks);
}
if (file->elements) {
for (i = 0; i < file->elements->len; i++) {
element = &g_array_index(file->elements, LIFElement, i);
if (element->dimensions) {
for (j = 0; j < element->dimensions->len; j++) {
dimension = &g_array_index(element->dimensions,
LIFDimension, j);
if (dimension->unit)
g_free(dimension->unit);
}
g_array_free(element->dimensions, TRUE);
}
if (element->channels) {
for (j = 0; j < element->channels->len; j++) {
channel = &g_array_index(element->channels,
LIFChannel, j);
if (channel->unit)
g_free(channel->unit);
if (channel->lut)
g_free(channel->lut);
}
g_array_free(element->channels, TRUE);
}
if (element->name)
g_free(element->name);
if (element->memid)
g_free(element->memid);
if (element->metadata)
g_object_unref(element->metadata);
}
g_array_free(file->elements, TRUE);
}
g_free(file);
}
if (header->xmlheader)
g_free(header->xmlheader);
if (header) {
g_free(header);
}
return container;
}
static GwyDataField*
read_binary_data(const gchar *buffer,
gsize size,
GHashTable *hash,
GError **error)
{
ShimadzuDataType data_type;
gint xres, yres, i;
guint expected;
gdouble xreal, yreal, zscale, xoff, yoff, zoff;
GwySIUnit *unitxy, *unitz;
GwyDataField *dfield = NULL;
gdouble *d;
const gchar *s;
if (!(s = g_hash_table_lookup(hash, "DataType"))) {
err_MISSING_FIELD(error, "DataType");
return NULL;
}
if (g_ascii_strcasecmp(s, "short") == 0)
data_type = SHIMADZU_SHORT;
else if (g_ascii_strcasecmp(s, "float") == 0)
data_type = SHIMADZU_FLOAT;
else {
err_UNSUPPORTED(error, "DataType");
return NULL;
}
unitxy = gwy_si_unit_new(NULL);
unitz = gwy_si_unit_new(NULL);
if (!get_scales(hash, FALSE,
&xres, &yres, &xreal, &yreal, &xoff, &yoff, unitxy,
&zscale, &zoff, unitz, error))
goto fail;
expected = data_type*xres*yres + HEADER_SIZE;
if (err_SIZE_MISMATCH(error, expected, size, FALSE))
goto fail;
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
gwy_data_field_set_si_unit_xy(dfield, unitxy);
gwy_data_field_set_si_unit_z(dfield, unitz);
d = gwy_data_field_get_data(dfield);
if (data_type == SHIMADZU_SHORT) {
const gint16 *d16 = (const gint16*)(buffer + HEADER_SIZE);
for (i = 0; i < xres*yres; i++)
d[i] = zscale*GUINT16_FROM_LE(d16[i]) + zoff;
}
else if (data_type == SHIMADZU_FLOAT) {
const guchar *p = buffer + HEADER_SIZE;
for (i = 0; i < xres*yres; i++)
d[i] = zscale*gwy_get_gfloat_le(&p) + zoff;
}
else {
g_assert_not_reached();
}
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
fail:
g_object_unref(unitxy);
g_object_unref(unitz);
return dfield;
}
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);
}
static GwyContainer*
gsf_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta = NULL;
GwyDataField *dfield = NULL;
GwyTextHeaderParser parser;
GwySIUnit *unit;
guchar *p, *value, *buffer = NULL, *header = NULL;
const guchar *datap;
GHashTable *hash = NULL;
gsize size, expected_size;
GError *err = NULL;
gdouble xreal, yreal, xoff, yoff;
guint i, xres, yres;
gdouble *d;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
if (size < MAGIC_SIZE || memcmp(buffer, MAGIC, MAGIC_SIZE) != 0) {
err_FILE_TYPE(error, "Gwyddion Simple Field");
goto fail;
}
p = buffer + MAGIC_SIZE;
datap = memchr(p, '\0', size - (p - buffer));
if (!datap) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File header is truncated."));
goto fail;
}
header = g_strdup(p);
datap += 4 - ((datap - buffer) % 4);
gwy_clear(&parser, 1);
parser.key_value_separator = "=";
if (!(hash = gwy_text_header_parse(header, &parser, NULL, NULL))) {
g_propagate_error(error, err);
goto fail;
}
xres = read_pixel_size(hash, "XRes", error);
yres = read_pixel_size(hash, "YRes", error);
if (!xres || !yres)
goto fail;
expected_size = (datap - buffer) + sizeof(gfloat)*xres*yres;
if (err_SIZE_MISMATCH(error, expected_size, size, TRUE))
goto fail;
xreal = read_real_size(hash, "XReal");
yreal = read_real_size(hash, "YReal");
dfield = gwy_data_field_new(xres, yres, xreal, yreal, FALSE);
xoff = read_real_offset(hash, "XOffset");
yoff = read_real_offset(hash, "YOffset");
gwy_data_field_set_xoffset(dfield, xoff);
gwy_data_field_set_yoffset(dfield, yoff);
value = g_hash_table_lookup(hash, "XYUnits");
unit = gwy_si_unit_new(value);
gwy_data_field_set_si_unit_xy(dfield, unit);
g_object_unref(unit);
value = g_hash_table_lookup(hash, "ZUnits");
unit = gwy_si_unit_new(value);
gwy_data_field_set_si_unit_z(dfield, unit);
g_object_unref(unit);
d = gwy_data_field_get_data(dfield);
for (i = xres*yres; i; i--)
*(d++) = gwy_get_gfloat_le(&datap);
container = gwy_container_new();
gwy_container_set_object(container, gwy_app_get_data_key_for_id(0), dfield);
g_object_unref(dfield);
if ((value = g_hash_table_lookup(hash, "Title"))) {
/* FIXME: Ensure valid UTF-8 */
gwy_container_set_string_by_name(container, "/0/data/title",
g_strdup(value));
}
else
gwy_app_channel_title_fall_back(container, 0);
meta = gwy_container_new();
g_hash_table_foreach(hash, add_meta, meta);
if (gwy_container_get_n_items(meta))
gwy_container_set_object_by_name(container, "/0/meta", meta);
g_object_unref(meta);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
gwy_file_abandon_contents(buffer, size, NULL);
if (header)
g_free(header);
if (hash)
g_hash_table_destroy(hash);
return container;
}
static GwyContainer*
fits_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL;
fitsfile *fptr = NULL;
GwyDataField *field = NULL, *mask;
gint status = 0; /* Must be initialised to zero! */
gint hdutype, naxis, anynull, nkeys, k;
glong res[3]; /* First index is the fast looping one. */
char strvalue[FLEN_VALUE];
gchar *invalid = NULL;
gdouble real, off;
if (fits_open_image(&fptr, filename, READONLY, &status)) {
err_FITS(error, status);
return NULL;
}
if (fits_get_hdu_type(fptr, &hdutype, &status)) {
err_FITS(error, status);
goto fail;
}
gwy_debug("hdutype %d", hdutype);
if (hdutype != IMAGE_HDU) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only two-dimensional images are supported."));
goto fail;
}
if (fits_get_img_dim(fptr, &naxis, &status)) {
err_FITS(error, status);
goto fail;
}
gwy_debug("naxis %d", naxis);
if (naxis != 2 && naxis != 3) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only two-dimensional images are supported."));
goto fail;
}
if (fits_get_img_size(fptr, naxis, res, &status)) {
err_FITS(error, status);
goto fail;
}
if (naxis == 3 && res[2] != 1) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("Only two-dimensional images are supported."));
goto fail;
}
gwy_debug("xres %ld, yres %ld", res[0], res[1]);
if (err_DIMENSION(error, res[0]) || err_DIMENSION(error, res[1]))
goto fail;
field = gwy_data_field_new(res[0], res[1], res[0], res[1], FALSE);
invalid = g_new(gchar, res[0]*res[1]);
if (fits_read_imgnull(fptr, TDOUBLE, 1, res[0]*res[1],
field->data, invalid, &anynull, &status)) {
err_FITS(error, status);
goto fail;
}
container = gwy_container_new();
gwy_container_set_object_by_name(container, "/0/data", field);
/* Failures here are non-fatal. We already have an image. */
if (fits_get_hdrspace(fptr, &nkeys, NULL, &status)) {
g_warning("Cannot get the first hdrspace.");
goto fail;
}
if (!fits_read_key(fptr, TSTRING, "BUINT ", strvalue, NULL, &status)) {
gint power10;
gwy_debug("BUINT = <%s>", strvalue);
gwy_si_unit_set_from_string_parse(gwy_data_field_get_si_unit_z(field),
strvalue, &power10);
if (power10)
gwy_data_field_multiply(field, pow10(power10));
}
status = 0;
if (get_real_and_offset(fptr, 1, res[0], &real, &off)) {
if (real < 0.0) {
off += real;
real = -real;
gwy_data_field_invert(field, FALSE, TRUE, FALSE);
}
gwy_data_field_set_xreal(field, real);
gwy_data_field_set_xoffset(field, off);
}
if (get_real_and_offset(fptr, 2, res[1], &real, &off)) {
if (real < 0.0) {
off += real;
real = -real;
gwy_data_field_invert(field, TRUE, FALSE, FALSE);
}
gwy_data_field_set_yreal(field, real);
gwy_data_field_set_yoffset(field, off);
}
/* Create a mask of invalid data. */
for (k = 0; k < field->xres*field->yres; k++) {
if (invalid[k])
field->data[k] = NAN;
}
if ((mask = gwy_app_channel_mask_of_nans(field, TRUE))) {
gwy_container_set_object_by_name(container, "/0/mask", mask);
g_object_unref(mask);
}
fail:
fits_close_file(fptr, &status);
gwy_object_unref(field);
g_free(invalid);
return container;
}
