forked from openslide/openslide-java
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathopenslide-jni.c
219 lines (171 loc) · 6.64 KB
/
openslide-jni.c
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
/*
* OpenSlide, a library for reading whole slide image files
*
* Copyright (c) 2007-2010 Carnegie Mellon University
* 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
* <http://www.gnu.org/licenses/>.
*
*/
#include <jni.h>
#include <openslide.h>
static jboolean osj_can_open(JNIEnv *env, jobject obj, jstring *filename) {
const char *filename2 = (*env)->GetStringUTFChars(env, filename, NULL);
if (filename2 == NULL) {
return JNI_FALSE;
}
jboolean result = openslide_can_open(filename2);
(*env)->ReleaseStringUTFChars(env, filename, filename2);
return result;
}
static jlong osj_open(JNIEnv *env, jobject obj, jstring *filename) {
const char *filename2 = (*env)->GetStringUTFChars(env, filename, NULL);
if (filename2 == NULL) {
return 0;
}
openslide_t *osr = openslide_open(filename2);
(*env)->ReleaseStringUTFChars(env, filename, filename2);
return (jlong) osr;
}
static jint osj_get_layer_count(JNIEnv *env, jobject obj, jlong osr) {
return openslide_get_layer_count((openslide_t *) osr);
}
static void osj_get_layer_dimensions(JNIEnv *env, jobject obj, jlong osr, jint layer,
jlongArray dim) {
int64_t dims[2];
openslide_get_layer_dimensions((openslide_t *) osr, layer, dims, dims + 1);
(*env)->SetLongArrayRegion(env, dim, 0, 2, dims);
}
static jdouble osj_get_layer_downsample(JNIEnv *env, jobject obj, jlong osr, jint layer) {
return openslide_get_layer_downsample((openslide_t *) osr, layer);
}
static void osj_close(JNIEnv *env, jobject obj, jlong osr) {
openslide_close((openslide_t *) osr);
}
static jobjectArray string_array_to_jobjectArray(JNIEnv *env, const char * const *strs) {
jclass strclazz = (*env)->FindClass(env, "java/lang/String");
if (strclazz == NULL) {
return NULL;
}
// count length
int len = 0;
const char * const *tmp = strs;
while (*tmp++ != NULL) {
len++;
}
// new array
jobjectArray arr = (*env)->NewObjectArray(env, len, strclazz, NULL);
if (arr == NULL) {
return NULL;
}
// set
int i;
for (i = 0; i < len; i++) {
jstring str = (*env)->NewStringUTF(env, strs[i]);
if (str == NULL) {
return NULL;
}
(*env)->SetObjectArrayElement(env, arr, i, str);
(*env)->DeleteLocalRef(env, str);
}
return arr;
}
static jobjectArray osj_get_property_names(JNIEnv *env, jobject obj, jlong osr) {
return string_array_to_jobjectArray(env, openslide_get_property_names((openslide_t *) osr));
}
static jstring osj_get_property_value(JNIEnv *env, jobject obj, jlong osr, jstring name) {
const char *name2 = (*env)->GetStringUTFChars(env, name, NULL);
if (name2 == NULL) {
return NULL;
}
const char *val = openslide_get_property_value((openslide_t *) osr, name2);
(*env)->ReleaseStringUTFChars(env, name, name2);
if (val == NULL) {
return NULL;
}
return (*env)->NewStringUTF(env, val);
}
static jobjectArray osj_get_associated_image_names(JNIEnv *env, jobject obj, jlong osr) {
return string_array_to_jobjectArray(env, openslide_get_associated_image_names((openslide_t *) osr));
}
static void osj_read_region(JNIEnv *env, jobject obj, jlong osr, jintArray dest,
jlong x, jlong y, jint layer, jlong w, jlong h) {
uint32_t *dest2 = (*env)->GetPrimitiveArrayCritical(env, dest, NULL);
if (dest2 == NULL) {
return;
}
openslide_read_region((openslide_t *) osr, dest2, x, y, layer, w, h);
(*env)->ReleasePrimitiveArrayCritical(env, dest, dest2, 0);
}
static void osj_get_associated_image_dimensions(JNIEnv *env, jobject obj, jlong osr,
jstring name, jlongArray dim) {
int64_t dims[2];
const char *name2 = (*env)->GetStringUTFChars(env, name, NULL);
if (name2 == NULL) {
return;
}
openslide_get_associated_image_dimensions((openslide_t *) osr, name2, dims, dims + 1);
(*env)->SetLongArrayRegion(env, dim, 0, 2, dims);
(*env)->ReleaseStringUTFChars(env, name, name2);
}
static void osj_read_associated_image(JNIEnv *env, jobject obj, jlong osr,
jstring name, jintArray dest) {
const char *name2 = (*env)->GetStringUTFChars(env, name, NULL);
if (name2 == NULL) {
return;
}
uint32_t *dest2 = (*env)->GetPrimitiveArrayCritical(env, dest, NULL);
if (dest2 == NULL) {
return;
}
openslide_read_associated_image((openslide_t *) osr, name2, dest2);
(*env)->ReleasePrimitiveArrayCritical(env, dest, dest2, 0);
(*env)->ReleaseStringUTFChars(env, name, name2);
}
static jstring osj_get_error(JNIEnv *env, jobject obj, jlong osr) {
const char *val = openslide_get_error((openslide_t *) osr);
if (val == NULL) {
return NULL;
}
return (*env)->NewStringUTF(env, val);
}
static JNINativeMethod methods[] = {
{ "openslide_can_open", "(Ljava/lang/String;)Z", (void *) osj_can_open },
{ "openslide_open", "(Ljava/lang/String;)J", (void *) osj_open },
{ "openslide_get_layer_count", "(J)I", (void *) osj_get_layer_count },
{ "openslide_get_layer_dimensions", "(JI[J)V", (void *) osj_get_layer_dimensions },
{ "openslide_get_layer_downsample", "(JI)D", (void *) osj_get_layer_downsample },
{ "openslide_close", "(J)V", (void *) osj_close },
{ "openslide_get_property_names", "(J)[Ljava/lang/String;", (void *) osj_get_property_names },
{ "openslide_get_property_value", "(JLjava/lang/String;)Ljava/lang/String;", (void *) osj_get_property_value },
{ "openslide_get_associated_image_names", "(J)[Ljava/lang/String;", (void *) osj_get_associated_image_names },
{ "openslide_read_region", "(J[IJJIJJ)V", (void *) osj_read_region },
{ "openslide_get_associated_image_dimensions", "(JLjava/lang/String;[J)V", (void *) osj_get_associated_image_dimensions },
{ "openslide_read_associated_image", "(JLjava/lang/String;[I)V", (void *) osj_read_associated_image },
{ "openslide_get_error", "(J)Ljava/lang/String;", (void *) osj_get_error },
};
JNIEXPORT jint JNICALL JNI_OnLoad(JavaVM *vm, void *reserved) {
JNIEnv* env;
if ((*vm)->GetEnv(vm, (void**) &env, JNI_VERSION_1_4) != JNI_OK) {
return -1;
}
jclass clazz = (*env)->FindClass(env, "edu/cmu/cs/openslide/OpenSlideJNI");
if (clazz == NULL) {
return -1;
}
if ((*env)->RegisterNatives(env, clazz, methods, 13) != JNI_OK) {
return -1;
}
return JNI_VERSION_1_4;
}