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/*
* $Id: nanosystemz.c 21622 2018-11-13 10:44:18Z yeti-dn $
* Copyright (C) 2018 David Necas (Yeti).
* E-mail: yeti@gwyddion.net.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor,
* Boston, MA 02110-1301, USA.
*/
#include "config.h"
#include <string.h>
#include <libgwyddion/gwymacros.h>
#include <libgwyddion/gwyutils.h>
#include <libgwyddion/gwymath.h>
#include <libprocess/datafield.h>
#include <libgwymodule/gwymodule-file.h>
#include <app/data-browser.h>
#include <app/gwymoduleutils-file.h>
#include "err.h"
#include "get.h"
/* FIXME: This may be actually some version number and not fixed...
* It is equal to 200, which gives a strong version-like vibe.
* Furthermore, the zero second byte may be the length of some seldom seen
* string, not a part of a two-byte item. */
#define MAGIC "\xc8\x00"
#define MAGIC_SIZE (sizeof(MAGIC)-1)
/**
* [FILE-MAGIC-USERGUIDE]
* NanoSystem profilometry
* .spm
* Read
**/
enum {
FIXED_HEADER_SIZE = 38,
};
typedef enum {
XRES_IS_MISSING = 0,
XRES_IS_PRESENT = 13,
} NanosystemzXresFlag;
typedef enum {
MEASUREMENT_PSI = 1,
MEASUREMENT_WSI_WSIE = 4,
} NanosystemzMeasurement;
typedef struct {
guchar magic[2];
gchar *comment;
gchar *datetime;
gchar *setup;
gchar *string1;
NanosystemzMeasurement meas_type;
NanosystemzXresFlag xres_flag;
/* The fixed part -- probably */
guint xres; /* XXX: Not present sometimes??? */
guint yres;
guint another_one; /* Seems equal to 1 */
gdouble dx;
gdouble dy;
guchar zeros[8]; /* Completely zeros -- more strings? */
gdouble scale; /* No idea, but it's another reasonable float */
guchar some_more_zeros[4];
} NanosystemzHeader;
static gboolean module_register (void);
static gint nanosystemz_detect (const GwyFileDetectInfo *fileinfo,
gboolean only_name);
static GwyContainer* nanosystemz_load (const gchar *filename,
GwyRunType mode,
GError **error);
static gsize nanosystemz_read_header (NanosystemzHeader *header,
const guchar *buffer,
gsize size,
GError **error);
static void nanosystemz_header_free (NanosystemzHeader *header);
static gboolean nanosystemz_check_datetime(const NanosystemzHeader *header);
static GwyContainer* create_meta(const NanosystemzHeader *header);
static GwyModuleInfo module_info = {
GWY_MODULE_ABI_VERSION,
&module_register,
N_("Imports NanoSystem profilometry data files."),
"Yeti <yeti@gwyddion.net>",
"0.1",
"David Nečas (Yeti)",
"2018",
};
GWY_MODULE_QUERY2(module_info, nanosystemz)
static gboolean
module_register(void)
{
gwy_file_func_register("nanosystemz",
N_("NanoSystem profilometry files (.spm)"),
(GwyFileDetectFunc)&nanosystemz_detect,
(GwyFileLoadFunc)&nanosystemz_load,
NULL,
NULL);
return TRUE;
}
static gint
nanosystemz_detect(const GwyFileDetectInfo *fileinfo,
gboolean only_name)
{
NanosystemzHeader header;
guint hlen, n;
gint score = 0;
if (only_name)
return 0;
if (fileinfo->buffer_len <= FIXED_HEADER_SIZE + 2 + 5
|| memcmp(fileinfo->head, MAGIC, MAGIC_SIZE) != 0)
return 0;
gwy_clear(&header, 1);
hlen = nanosystemz_read_header(&header,
fileinfo->head, fileinfo->buffer_len, NULL);
if (!hlen)
goto fail;
n = header.xres*header.yres;
if (hlen + n*(sizeof(guint32) + sizeof(guchar)) != fileinfo->file_size)
goto fail;
if (!nanosystemz_check_datetime(&header))
goto fail;
score = 95;
fail:
nanosystemz_header_free(&header);
return score;
}
static GwyContainer*
nanosystemz_load(const gchar *filename,
G_GNUC_UNUSED GwyRunType mode,
GError **error)
{
GwyContainer *container = NULL, *meta;
guchar *buffer = NULL;
gsize imagesize, masksize, n, hlen, size = 0;
GError *err = NULL;
NanosystemzHeader header;
GwyDataField *dfield, *mask;
if (!gwy_file_get_contents(filename, &buffer, &size, &err)) {
err_GET_FILE_CONTENTS(error, &err);
return NULL;
}
gwy_clear(&header, 1);
if (!(hlen = nanosystemz_read_header(&header, buffer, size, error)))
goto fail;
if (memcmp(header.magic, MAGIC, MAGIC_SIZE) != 0) {
err_FILE_TYPE(error, "Nanosystemz");
goto fail;
}
/* Use negated positive conditions to catch NaNs */
if (!((header.dx = fabs(header.dx)) > 0)) {
g_warning("Real x pixel size is 0.0, fixing to 1.0");
header.dx = 1.0;
}
header.dx *= 1e-3;
if (!((header.dy = fabs(header.dy)) > 0)) {
g_warning("Real y pixel size is 0.0, fixing to 1.0");
header.dy = 1.0;
}
header.dy *= 1e-3;
n = header.xres*header.yres;
imagesize = n*sizeof(guint32);
masksize = n;
if (err_SIZE_MISMATCH(error, hlen + imagesize + masksize, size, TRUE))
goto fail;
container = gwy_container_new();
dfield = gwy_data_field_new(header.xres, header.yres,
header.xres*header.dx, header.yres*header.dy,
FALSE);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_xy(dfield), "m");
mask = gwy_data_field_new_alike(dfield, FALSE);
gwy_convert_raw_data(buffer + hlen, n, 1,
GWY_RAW_DATA_FLOAT, G_LITTLE_ENDIAN,
gwy_data_field_get_data(dfield), 1e-6, 0.0);
gwy_data_field_invert(dfield, TRUE, FALSE, FALSE);
gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), "m");
gwy_container_set_object(container,
gwy_app_get_data_key_for_id(0), dfield);
g_object_unref(dfield);
/* FIXME: I see values
* - 1 for good data
* - 2 for some kind of bad data (WSIE)
* - 8 for some kind of bad data (PSI and WSIE)
* Or something like
* that. The probably correspond to some bits set -- masking anything
* that is not equal to 1 (presumably good data) seems reasonable. */
gwy_convert_raw_data(buffer + hlen + imagesize, n, 1,
GWY_RAW_DATA_UINT8, G_LITTLE_ENDIAN,
gwy_data_field_get_data(mask), 1.0, -1.0);
gwy_data_field_invert(mask, TRUE, FALSE, FALSE);
gwy_container_set_object(container,
gwy_app_get_mask_key_for_id(0), mask);
g_object_unref(mask);
meta = create_meta(&header);
gwy_container_set_object(container,
gwy_app_get_data_meta_key_for_id(0), meta);
g_object_unref(meta);
gwy_app_channel_title_fall_back(container, 0);
gwy_file_channel_import_log_add(container, 0, NULL, filename);
fail:
nanosystemz_header_free(&header);
gwy_file_abandon_contents(buffer, size, NULL);
return container;
}
static gboolean
read_pascal_string(const guchar *buffer, const guchar **p, gsize size,
gchar **s,
GError **error)
{
guint len;
if (size - (*p - buffer) < 1) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File is truncated."));
return FALSE;
}
len = *((*p)++);
/* Represent empty strings as NULL; they are common. */
if (!len) {
gwy_debug("NULL string");
*s = NULL;
return TRUE;
}
if (size - (*p - buffer) < len) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File is truncated."));
return FALSE;
}
*s = g_new(gchar, len+1);
gwy_assign(*s, *p, len);
(*s)[len] = '\0';
*p += len;
gwy_debug("string of length %u <%s>", len, *s);
return TRUE;
}
static gsize
nanosystemz_read_header(NanosystemzHeader *header,
const guchar *buffer, gsize size,
GError **error)
{
const guchar *p = buffer;
get_CHARARRAY(header->magic, &p);
if (!read_pascal_string(buffer, &p, size, &header->comment, error)
|| !read_pascal_string(buffer, &p, size, &header->datetime, error)
|| !read_pascal_string(buffer, &p, size, &header->setup, error)
|| !read_pascal_string(buffer, &p, size, &header->string1, error))
return 0;
if (size - (p - buffer) < FIXED_HEADER_SIZE) {
g_set_error(error, GWY_MODULE_FILE_ERROR, GWY_MODULE_FILE_ERROR_DATA,
_("File is truncated."));
return 0;
}
header->meas_type = *(p++);
gwy_debug("meas_type %u", header->meas_type);
header->xres_flag = *(p++);
gwy_debug("xres_flag %u", header->xres_flag);
if (header->xres_flag == XRES_IS_MISSING) {
header->yres = gwy_get_guint32_le(&p);
header->xres = 640; /* FIXME FIXME FIXME */
}
else {
header->xres = gwy_get_guint32_le(&p);
header->yres = gwy_get_guint32_le(&p);
}
gwy_debug("res %dx%d", header->xres, header->yres);
header->another_one = gwy_get_guint32_le(&p);
gwy_debug("another_one %u", header->another_one);
header->dx = gwy_get_gfloat_le(&p);
header->dy = gwy_get_gfloat_le(&p);
gwy_debug("real pixel %gx%g", header->dx, header->dy);
get_CHARARRAY(header->zeros, &p);
gwy_debug("zeros %02x %02x %02x %02x %02x %02x %02x %02x",
header->zeros[0], header->zeros[1],
header->zeros[2], header->zeros[3],
header->zeros[4], header->zeros[5],
header->zeros[6], header->zeros[7]);
header->scale = gwy_get_gfloat_le(&p);
gwy_debug("scale %g", header->scale);
get_CHARARRAY(header->some_more_zeros, &p);
gwy_debug("some_more_zeros %02x %02x %02x %02x",
header->some_more_zeros[0], header->some_more_zeros[1],
header->some_more_zeros[2], header->some_more_zeros[3]);
return (gsize)(p - buffer);
}
static void
nanosystemz_header_free(NanosystemzHeader *header)
{
g_free(header->comment);
g_free(header->datetime);
g_free(header->setup);
g_free(header->string1);
}
static gboolean
nanosystemz_check_datetime(const NanosystemzHeader *header)
{
const gchar *dt = header->datetime;
if (!dt || strlen(dt) != 19)
return FALSE;
if (!g_ascii_isdigit(dt[0]) || !g_ascii_isdigit(dt[1])
|| !g_ascii_isdigit(dt[2]) || !g_ascii_isdigit(dt[3])
|| dt[4] != '-'
|| !g_ascii_isdigit(dt[5]) || !g_ascii_isdigit(dt[6])
|| dt[7] != '-'
|| !g_ascii_isdigit(dt[8]) || !g_ascii_isdigit(dt[9])
|| dt[10] != ' '
|| !g_ascii_isdigit(dt[11]) || !g_ascii_isdigit(dt[12])
|| dt[13] != ':'
|| !g_ascii_isdigit(dt[14]) || !g_ascii_isdigit(dt[15])
|| dt[16] != ':'
|| !g_ascii_isdigit(dt[17]) || !g_ascii_isdigit(dt[18]))
return FALSE;
return TRUE;
}
static GwyContainer*
create_meta(const NanosystemzHeader *header)
{
GwyContainer *meta = gwy_container_new();
const gchar *s;
gchar *v;
if ((s = header->comment))
gwy_container_set_const_string_by_name(meta, "Comment", s);
if ((s = header->datetime))
gwy_container_set_const_string_by_name(meta, "Date and Time", s);
if ((s = header->setup))
gwy_container_set_const_string_by_name(meta, "Setup", s);
if ((s = header->string1))
gwy_container_set_const_string_by_name(meta, "String1", s);
v = g_strdup_printf("%g", header->scale);
gwy_container_set_string_by_name(meta, "Value1", v);
v = g_strdup_printf("%.1f nm", header->dx/1e-9);
gwy_container_set_string_by_name(meta, "Pixel size X", v);
v = g_strdup_printf("%.1f nm", header->dy/1e-9);
gwy_container_set_string_by_name(meta, "Pixel size Y", v);
return meta;
}
/* vim: set cin et ts=4 sw=4 cino=>1s,e0,n0,f0,{0,}0,^0,\:1s,=0,g1s,h0,t0,+1s,c3,(0,u0 : */
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