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openslide-util.c
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openslide-util.c
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/*
* OpenSlide, a library for reading whole slide image files
*
* Copyright (c) 2007-2015 Carnegie Mellon University
* Copyright (c) 2015-2022 Benjamin Gilbert
* All rights reserved.
*
* OpenSlide is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation, version 2.1.
*
* OpenSlide 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with OpenSlide. If not, see
* <https://www.gnu.org/licenses/>.
*
*/
#include "openslide-private.h"
#include <stdio.h>
#include <stdarg.h>
#include <string.h>
#include <math.h>
#include <errno.h>
#include <glib.h>
#include <cairo.h>
#include <zlib.h>
#include <zstd.h>
#define KEY_FILE_HARD_MAX_SIZE (100 << 20)
static const char DEBUG_ENV_VAR[] = "OPENSLIDE_DEBUG";
static const struct debug_option {
const char *kw;
enum _openslide_debug_flag flag;
const char *desc;
} debug_options[] = {
{"decoding", OPENSLIDE_DEBUG_DECODING,
"log warnings from format decoding libraries"},
{"detection", OPENSLIDE_DEBUG_DETECTION, "log format detection errors"},
{"jpeg-markers", OPENSLIDE_DEBUG_JPEG_MARKERS,
"verify Hamamatsu restart markers"},
{"performance", OPENSLIDE_DEBUG_PERFORMANCE,
"log conditions causing poor performance"},
{"search", OPENSLIDE_DEBUG_SEARCH,
"log skipped files when searching directory"},
{"sql", OPENSLIDE_DEBUG_SQL,
"log SQL queries"},
{"synthetic", OPENSLIDE_DEBUG_SYNTHETIC,
"openslide_open(\"\") opens a synthetic test slide"},
{"tiles", OPENSLIDE_DEBUG_TILES, "render tile outlines"},
{NULL, 0, NULL}
};
static uint32_t debug_flags;
GKeyFile *_openslide_read_key_file(const char *filename, int32_t max_size,
GKeyFileFlags flags, GError **err) {
/* We load the whole key file into memory and parse it with
* g_key_file_load_from_data instead of using g_key_file_load_from_file
* because the load_from_file function incorrectly parses a value when
* the terminating '\r\n' falls across a 4KB boundary.
* https://bugzilla.redhat.com/show_bug.cgi?id=649936 */
/* this also allows us to skip a UTF-8 BOM which the g_key_file parser
* does not expect to find. */
/* Hamamatsu attempts to load the slide file as a key file. We impose
a maximum file size to avoid loading an entire slide into RAM. */
// hard limit
if (max_size <= 0) {
max_size = KEY_FILE_HARD_MAX_SIZE;
}
max_size = MIN(max_size, KEY_FILE_HARD_MAX_SIZE);
g_autoptr(_openslide_file) f = _openslide_fopen(filename, err);
if (f == NULL) {
return NULL;
}
// get file size and check against maximum
int64_t size = _openslide_fsize(f, err);
if (size == -1) {
return NULL;
}
if (size > max_size) {
g_set_error(err, G_FILE_ERROR, G_FILE_ERROR_NOMEM,
"Key file %s too large", filename);
return NULL;
}
// read
// ensure non-NULL pointer for zero-length file
g_autofree char *buf = g_malloc(size ?: 1);
if (!_openslide_fread_exact(f, buf, size, err)) {
return NULL;
}
/* skip the UTF-8 BOM if it is present. */
int offset = 0;
if (size >= 3 && memcmp(buf, "\xef\xbb\xbf", 3) == 0) {
offset = 3;
}
// parse
g_autoptr(GKeyFile) key_file = g_key_file_new();
if (!g_key_file_load_from_data(key_file,
buf + offset, size - offset,
flags, err)) {
return NULL;
}
return g_steal_pointer(&key_file);
}
static void zlib_error(z_stream *strm, int64_t dst_len, int error_code,
GError **err) {
if (error_code == Z_STREAM_END) {
g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
"Short read while decompressing: %lu/%"PRId64,
strm->total_out, dst_len);
} else if (strm->msg) {
g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
"Decompression failure: %s (%s)",
zError(error_code), strm->msg);
} else {
g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
"Decompression failure: %s", zError(error_code));
}
}
void *_openslide_inflate_buffer(const void *src, int64_t src_len,
int64_t dst_len,
GError **err) {
g_autofree void *dst = g_malloc(dst_len);
z_stream strm = {
.avail_in = src_len,
.avail_out = dst_len,
.next_in = (Bytef *) src,
.next_out = (Bytef *) dst
};
int64_t error_code = inflateInit(&strm);
if (error_code != Z_OK) {
zlib_error(&strm, dst_len, error_code, err);
return NULL;
}
error_code = inflate(&strm, Z_FINISH);
if (error_code != Z_STREAM_END || (int64_t) strm.total_out != dst_len) {
inflateEnd(&strm);
zlib_error(&strm, dst_len, error_code, err);
return NULL;
}
error_code = inflateEnd(&strm);
if (error_code != Z_OK) {
zlib_error(&strm, dst_len, error_code, err);
return NULL;
}
return g_steal_pointer(&dst);
}
void *_openslide_zstd_decompress_buffer(const void *src, int64_t src_len,
int64_t dst_len, GError **err) {
g_autofree void *dst = g_try_malloc(dst_len);
if (!dst) {
g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
"Couldn't allocate %"PRId64" bytes for zstd decompression",
dst_len);
return NULL;
}
size_t rc = ZSTD_decompress(dst, dst_len, src, src_len);
if (ZSTD_isError(rc)) {
g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
"zstd decompression error: %s", ZSTD_getErrorName(rc));
return NULL;
}
if ((int64_t) rc != dst_len) {
g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
"Short read while decompressing: %"PRIu64"/%"PRId64,
(uint64_t) rc, dst_len);
return NULL;
}
return g_steal_pointer(&dst);
}
int64_t _openslide_compute_seek(int64_t initial, int64_t length,
int64_t offset, int whence) {
int64_t result = initial;
switch (whence) {
case SEEK_SET:
result = offset;
break;
case SEEK_CUR:
result += offset;
break;
case SEEK_END:
result = length + offset;
break;
default:
g_assert_not_reached();
}
return result;
}
bool _openslide_parse_int64(const char *value, int64_t *result) {
char *endptr;
errno = 0;
*result = g_ascii_strtoll(value, &endptr, 10); // ci-allow
// fail on overflow/underflow
if (value[0] == 0 || endptr[0] != 0 || errno == ERANGE) {
*result = 0;
return false;
}
return true;
}
bool _openslide_parse_uint64(const char *value, uint64_t *result,
unsigned base) {
char *endptr;
errno = 0;
*result = g_ascii_strtoull(value, &endptr, base); // ci-allow
// fail on overflow
if (value[0] == 0 || endptr[0] != 0 || errno == ERANGE) {
*result = 0;
return false;
}
return true;
}
double _openslide_parse_double(const char *value) {
// Canonicalize comma to decimal point, since the locale of the
// originating system sometimes leaks into slide files.
// This will break if the value includes grouping characters.
g_autofree char *canonical = g_strdup(value);
g_strdelimit(canonical, ",", '.');
char *endptr;
errno = 0;
double result = g_ascii_strtod(canonical, &endptr); // ci-allow
// fail on overflow/underflow
if (canonical[0] == 0 || endptr[0] != 0 || errno == ERANGE) {
return NAN;
}
return result;
}
char *_openslide_format_double(double d) {
char buf[G_ASCII_DTOSTR_BUF_SIZE];
g_ascii_dtostr(buf, sizeof buf, d);
return g_strdup(buf);
}
// if the src prop is an int, canonicalize it and copy it to dest
void _openslide_duplicate_int_prop(openslide_t *osr, const char *src,
const char *dest) {
g_return_if_fail(g_hash_table_lookup(osr->properties, dest) == NULL);
char *value = g_hash_table_lookup(osr->properties, src);
int64_t result;
if (value && _openslide_parse_int64(value, &result)) {
g_hash_table_insert(osr->properties,
g_strdup(dest),
g_strdup_printf("%"PRId64, result));
}
}
// if the src prop is a double, canonicalize it and copy it to dest
void _openslide_duplicate_double_prop(openslide_t *osr, const char *src,
const char *dest) {
g_return_if_fail(g_hash_table_lookup(osr->properties, dest) == NULL);
char *value = g_hash_table_lookup(osr->properties, src);
if (value) {
double result = _openslide_parse_double(value);
if (!isnan(result)) {
g_hash_table_insert(osr->properties, g_strdup(dest),
_openslide_format_double(result));
}
}
}
void _openslide_set_background_color_prop(openslide_t *osr,
uint8_t r, uint8_t g, uint8_t b) {
g_return_if_fail(g_hash_table_lookup(osr->properties,
OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR) == NULL);
g_hash_table_insert(osr->properties,
g_strdup(OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR),
g_strdup_printf("%.02X%.02X%.02X", r, g, b));
}
void _openslide_set_bounds_props_from_grid(openslide_t *osr,
struct _openslide_grid *grid) {
g_return_if_fail(g_hash_table_lookup(osr->properties,
OPENSLIDE_PROPERTY_NAME_BOUNDS_X) == NULL);
double x, y, w, h;
_openslide_grid_get_bounds(grid, &x, &y, &w, &h);
g_hash_table_insert(osr->properties,
g_strdup(OPENSLIDE_PROPERTY_NAME_BOUNDS_X),
g_strdup_printf("%"PRId64,
(int64_t) floor(x)));
g_hash_table_insert(osr->properties,
g_strdup(OPENSLIDE_PROPERTY_NAME_BOUNDS_Y),
g_strdup_printf("%"PRId64,
(int64_t) floor(y)));
g_hash_table_insert(osr->properties,
g_strdup(OPENSLIDE_PROPERTY_NAME_BOUNDS_WIDTH),
g_strdup_printf("%"PRId64,
(int64_t) (ceil(x + w) - floor(x))));
g_hash_table_insert(osr->properties,
g_strdup(OPENSLIDE_PROPERTY_NAME_BOUNDS_HEIGHT),
g_strdup_printf("%"PRId64,
(int64_t) (ceil(y + h) - floor(y))));
}
bool _openslide_clip_tile(uint32_t *tiledata,
int64_t tile_w, int64_t tile_h,
int64_t clip_w, int64_t clip_h,
GError **err) {
if (clip_w >= tile_w && clip_h >= tile_h) {
return true;
}
g_autoptr(cairo_surface_t) surface =
cairo_image_surface_create_for_data((unsigned char *) tiledata,
CAIRO_FORMAT_ARGB32,
tile_w, tile_h,
tile_w * 4);
g_autoptr(cairo_t) cr = cairo_create(surface);
cairo_set_operator(cr, CAIRO_OPERATOR_CLEAR);
cairo_rectangle(cr, clip_w, 0, tile_w - clip_w, tile_h);
cairo_fill(cr);
cairo_rectangle(cr, 0, clip_h, tile_w, tile_h - clip_h);
cairo_fill(cr);
return _openslide_check_cairo_status(cr, err);
}
// note: g_getenv() is not reentrant
void _openslide_debug_init(void) {
const char *debug_str = g_getenv(DEBUG_ENV_VAR);
if (!debug_str) {
return;
}
g_auto(GStrv) keywords = g_strsplit(debug_str, ",", 0);
bool printed_help = false;
for (char **kw = keywords; *kw; kw++) {
g_strstrip(*kw);
bool found = false;
for (const struct debug_option *opt = debug_options; opt->kw; opt++) {
if (!g_ascii_strcasecmp(*kw, opt->kw)) {
debug_flags |= 1 << opt->flag;
found = true;
break;
}
}
if (!found && !printed_help) {
printed_help = true;
g_message("%s options (comma-delimited):", DEBUG_ENV_VAR);
for (const struct debug_option *opt = debug_options; opt->kw; opt++) {
g_message(" %-15s - %s", opt->kw, opt->desc);
}
}
}
}
bool _openslide_debug(enum _openslide_debug_flag flag) {
return !!(debug_flags & (1 << flag));
}
void _openslide_performance_warn_once(gint *warned_flag,
const char *str, ...) {
if (_openslide_debug(OPENSLIDE_DEBUG_PERFORMANCE)) {
if (warned_flag == NULL ||
g_atomic_int_compare_and_exchange(warned_flag, 0, 1)) {
va_list ap;
va_start(ap, str);
g_logv(G_LOG_DOMAIN, G_LOG_LEVEL_MESSAGE, str, ap);
va_end(ap);
}
}
}