File: openslideload.c

package info (click to toggle)
vips 8.4.5-1%2Bdeb9u1
  • links: PTS
  • area: main
  • in suites: stretch
  • size: 25,724 kB
  • sloc: ansic: 102,605; cpp: 57,527; sh: 4,957; xml: 3,317; python: 3,105; makefile: 1,089; perl: 40
file content (268 lines) | stat: -rw-r--r-- 7,176 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
/* load openslide from a file
 *
 * 5/12/11
 * 	- from openslideload.c
 * 28/2/12
 * 	- convert "layer" to "level" where externally visible
 * 11/4/12
 * 	- convert remaining uses of "layer" to "level"
 * 20/9/12
 * 	- add Leica filename suffix
 *	- drop glib log handler (unneeded with >= 3.3.0)
 */

/*

    This file is part of VIPS.
    
    VIPS 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; 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 Lesser General Public License for more details.

    You should have received a copy of the GNU Lesser 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

 */

/*

    These files are distributed with VIPS - http://www.vips.ecs.soton.ac.uk

 */

/*
#define DEBUG
 */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif /*HAVE_CONFIG_H*/
#include <vips/intl.h>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include <vips/vips.h>
#include <vips/buf.h>
#include <vips/internal.h>

#ifdef HAVE_OPENSLIDE

#include "openslide2vips.h"

typedef struct _VipsForeignLoadOpenslide {
	VipsForeignLoad parent_object;

	/* Filename for load.
	 */
	char *filename; 

	/* Load this level.
	 */
	int level;

	/* Crop to image bounds.
	 */
	gboolean autocrop;

	/* Load this associated image. 
	 */
	char *associated;

} VipsForeignLoadOpenslide;

typedef VipsForeignLoadClass VipsForeignLoadOpenslideClass;

G_DEFINE_TYPE( VipsForeignLoadOpenslide, vips_foreign_load_openslide, 
	VIPS_TYPE_FOREIGN_LOAD );

static VipsForeignFlags
vips_foreign_load_openslide_get_flags_filename( const char *filename )
{
	/* We can't tell from just the filename, we need to know what part of
	 * the file the user wants. But it'll usually be partial.
	 */
	return( VIPS_FOREIGN_PARTIAL );
}

static VipsForeignFlags
vips_foreign_load_openslide_get_flags( VipsForeignLoad *load )
{
	VipsForeignLoadOpenslide *openslide = (VipsForeignLoadOpenslide *) load;
	VipsForeignFlags flags;

	flags = 0;
	if( !openslide->associated )
		flags |= VIPS_FOREIGN_PARTIAL;

	return( flags );
}

static int
vips_foreign_load_openslide_header( VipsForeignLoad *load )
{
	VipsForeignLoadOpenslide *openslide = (VipsForeignLoadOpenslide *) load;

	if( vips__openslide_read_header( openslide->filename, load->out, 
		openslide->level, openslide->autocrop, 
		openslide->associated ) )
		return( -1 );

	VIPS_SETSTR( load->out->filename, openslide->filename );

	return( 0 );
}

static int
vips_foreign_load_openslide_load( VipsForeignLoad *load )
{
	VipsForeignLoadOpenslide *openslide = (VipsForeignLoadOpenslide *) load;

	if( !openslide->associated ) {
		if( vips__openslide_read( openslide->filename, load->real, 
			openslide->level, openslide->autocrop ) )
			return( -1 );
	}
	else {
		if( vips__openslide_read_associated( 
			openslide->filename, load->real, 
			openslide->associated ) )
			return( -1 );
	}

	return( 0 );
}

static const char *vips_foreign_openslide_suffs[] = {
	".svs", 	/* Aperio */
	".vms", ".vmu", ".ndpi",  /* Hamamatsu */
	".scn",		/* Leica */
	".mrxs", 	/* MIRAX */
	".svslide",	/* Sakura */
	".tif", 	/* Trestle */
	".bif", 	/* Ventana */
	NULL
};

static void
vips_foreign_load_openslide_class_init( VipsForeignLoadOpenslideClass *class )
{
	GObjectClass *gobject_class = G_OBJECT_CLASS( class );
	VipsObjectClass *object_class = (VipsObjectClass *) class;
	VipsForeignClass *foreign_class = (VipsForeignClass *) class;
	VipsForeignLoadClass *load_class = (VipsForeignLoadClass *) class;

	gobject_class->set_property = vips_object_set_property;
	gobject_class->get_property = vips_object_get_property;

	object_class->nickname = "openslideload";
	object_class->description = _( "load file with OpenSlide" );

	/* We need to be ahead of the tiff sniffer since many OpenSlide
	 * formats are tiff derivatives. If we see a tiff which would be
	 * better handled by the vips tiff loader we are careful to say no.
	 *
	 * We need to be ahead of JPEG, since MRXS images are also
	 * JPEGs.
	 */
	foreign_class->priority = 100;
	foreign_class->suffs = vips_foreign_openslide_suffs;

	load_class->is_a = vips__openslide_isslide;
	load_class->get_flags_filename = 
		vips_foreign_load_openslide_get_flags_filename;
	load_class->get_flags = vips_foreign_load_openslide_get_flags;
	load_class->header = vips_foreign_load_openslide_header;
	load_class->load = vips_foreign_load_openslide_load;

	VIPS_ARG_STRING( class, "filename", 1, 
		_( "Filename" ),
		_( "Filename to load from" ),
		VIPS_ARGUMENT_REQUIRED_INPUT, 
		G_STRUCT_OFFSET( VipsForeignLoadOpenslide, filename ),
		NULL );

	VIPS_ARG_INT( class, "level", 10,
		_( "Level" ),
		_( "Load this level from the file" ),
		VIPS_ARGUMENT_OPTIONAL_INPUT,
		G_STRUCT_OFFSET( VipsForeignLoadOpenslide, level ),
		0, 100000, 0 );

	VIPS_ARG_BOOL( class, "autocrop", 11,
		_( "Autocrop" ),
		_( "Crop to image bounds" ),
		VIPS_ARGUMENT_OPTIONAL_INPUT,
		G_STRUCT_OFFSET( VipsForeignLoadOpenslide, autocrop ),
		FALSE ); 

	VIPS_ARG_STRING( class, "associated", 12, 
		_( "Associated" ),
		_( "Load this associated image" ),
		VIPS_ARGUMENT_OPTIONAL_INPUT, 
		G_STRUCT_OFFSET( VipsForeignLoadOpenslide, associated ),
		NULL );
}

static void
vips_foreign_load_openslide_init( VipsForeignLoadOpenslide *openslide )
{
}

#endif /*HAVE_OPENSLIDE*/

/**
 * vips_openslideload:
 * @filename: file to load
 * @out: decompressed image
 * @...: %NULL-terminated list of optional named arguments
 *
 * Optional arguments:
 *
 * * @level: load this level
 * * @associated: load this associated image
 * * @autocrop: crop to image bounds
 *
 * Read a virtual slide supported by the OpenSlide library into a VIPS image.
 * OpenSlide supports images in Aperio, Hamamatsu, MIRAX, Sakura, Trestle,
 * and Ventana formats.
 *
 * To facilitate zooming, virtual slide formats include multiple scaled-down
 * versions of the high-resolution image.  These are typically called
 * "levels".  By default, vips_openslideload() reads the highest-resolution
 * level (level 0).  Set @level to the level number you want.
 *
 * In addition to the slide image itself, virtual slide formats sometimes
 * include additional images, such as a scan of the slide's barcode.
 * OpenSlide calls these "associated images".  To read an associated image,
 * set @associated to the image's name.
 * A slide's associated images are listed in the
 * "slide-associated-images" metadata item.
 *
 * The output of this operator is always RGBA.
 *
 * See also: vips_image_new_from_file().
 *
 * Returns: 0 on success, -1 on error.
 */
int
vips_openslideload( const char *filename, VipsImage **out, ... )
{
	va_list ap;
	int result;

	va_start( ap, out );
	result = vips_call_split( "openslideload", ap, filename, out );
	va_end( ap );

	return( result );
}