Android使用Opencv环境配置可以查看：http://www.jianshu.com/p/d3cf603a8b71
Mat与Bitmap互转 主要在native-lib中代码实现

#include <opencv2/opencv.hpp>
#include <android/bitmap.h>
#define LOGE(...) ((void)__android_log_print(ANDROID_LOG_ERROR, "error", __VA_ARGS__))
#define LOGD(...) ((void)__android_log_print(ANDROID_LOG_DEBUG, "debug", __VA_ARGS__))

void BitmapToMat2(JNIEnv *env, jobject& bitmap, Mat& mat, jboolean needUnPremultiplyAlpha) {
    AndroidBitmapInfo info;
    void *pixels = 0;
    Mat &dst = mat;

    try {
        LOGD("nBitmapToMat");
        CV_Assert(AndroidBitmap_getInfo(env, bitmap, &info) >= 0);
        CV_Assert(info.format == ANDROID_BITMAP_FORMAT_RGBA_8888 ||
                  info.format == ANDROID_BITMAP_FORMAT_RGB_565);
        CV_Assert(AndroidBitmap_lockPixels(env, bitmap, &pixels) >= 0);
        CV_Assert(pixels);
        dst.create(info.height, info.width, CV_8UC4);
        if (info.format == ANDROID_BITMAP_FORMAT_RGBA_8888) {
            LOGD("nBitmapToMat: RGBA_8888 -> CV_8UC4");
            Mat tmp(info.height, info.width, CV_8UC4, pixels);
            if (needUnPremultiplyAlpha) cvtColor(tmp, dst, COLOR_mRGBA2RGBA);
            else tmp.copyTo(dst);
        } else {
            // info.format == ANDROID_BITMAP_FORMAT_RGB_565
            LOGD("nBitmapToMat: RGB_565 -> CV_8UC4");
            Mat tmp(info.height, info.width, CV_8UC2, pixels);
            cvtColor(tmp, dst, COLOR_BGR5652RGBA);
        }
        AndroidBitmap_unlockPixels(env, bitmap);
        return;
    } catch (const cv::Exception &e) {
        AndroidBitmap_unlockPixels(env, bitmap);
        LOGE("nBitmapToMat catched cv::Exception: %s", e.what());
        jclass je = env->FindClass("org/opencv/core/CvException");
        if (!je) je = env->FindClass("java/lang/Exception");
        env->ThrowNew(je, e.what());
        return;
    } catch (...) {
        AndroidBitmap_unlockPixels(env, bitmap);
        LOGE("nBitmapToMat catched unknown exception (...)");
        jclass je = env->FindClass("java/lang/Exception");
        env->ThrowNew(je, "Unknown exception in JNI code {nBitmapToMat}");
        return;
    }
}

void BitmapToMat(JNIEnv *env, jobject& bitmap, Mat& mat) {
    BitmapToMat2(env, bitmap, mat, false);
}

void MatToBitmap2
        (JNIEnv *env, Mat& mat, jobject& bitmap, jboolean needPremultiplyAlpha) {
    AndroidBitmapInfo info;
    void *pixels = 0;
    Mat &src = mat;

    try {
        LOGD("nMatToBitmap");
        CV_Assert(AndroidBitmap_getInfo(env, bitmap, &info) >= 0);
        CV_Assert(info.format == ANDROID_BITMAP_FORMAT_RGBA_8888 ||
                  info.format == ANDROID_BITMAP_FORMAT_RGB_565);
        CV_Assert(src.dims == 2 && info.height == (uint32_t) src.rows &&
                  info.width == (uint32_t) src.cols);
        CV_Assert(src.type() == CV_8UC1 || src.type() == CV_8UC3 || src.type() == CV_8UC4);
        CV_Assert(AndroidBitmap_lockPixels(env, bitmap, &pixels) >= 0);
        CV_Assert(pixels);
        if (info.format == ANDROID_BITMAP_FORMAT_RGBA_8888) {
            Mat tmp(info.height, info.width, CV_8UC4, pixels);
            if (src.type() == CV_8UC1) {
                LOGD("nMatToBitmap: CV_8UC1 -> RGBA_8888");
                cvtColor(src, tmp, COLOR_GRAY2RGBA);
            } else if (src.type() == CV_8UC3) {
                LOGD("nMatToBitmap: CV_8UC3 -> RGBA_8888");
                cvtColor(src, tmp, COLOR_RGB2RGBA);
            } else if (src.type() == CV_8UC4) {
                LOGD("nMatToBitmap: CV_8UC4 -> RGBA_8888");
                if (needPremultiplyAlpha)
                    cvtColor(src, tmp, COLOR_RGBA2mRGBA);
                else
                    src.copyTo(tmp);
            }
        } else {
            // info.format == ANDROID_BITMAP_FORMAT_RGB_565
            Mat tmp(info.height, info.width, CV_8UC2, pixels);
            if (src.type() == CV_8UC1) {
                LOGD("nMatToBitmap: CV_8UC1 -> RGB_565");
                cvtColor(src, tmp, COLOR_GRAY2BGR565);
            } else if (src.type() == CV_8UC3) {
                LOGD("nMatToBitmap: CV_8UC3 -> RGB_565");
                cvtColor(src, tmp, COLOR_RGB2BGR565);
            } else if (src.type() == CV_8UC4) {
                LOGD("nMatToBitmap: CV_8UC4 -> RGB_565");
                cvtColor(src, tmp, COLOR_RGBA2BGR565);
            }
        }
        AndroidBitmap_unlockPixels(env, bitmap);
        return;
    } catch (const cv::Exception &e) {
        AndroidBitmap_unlockPixels(env, bitmap);
        LOGE("nMatToBitmap catched cv::Exception: %s", e.what());
        jclass je = env->FindClass("org/opencv/core/CvException");
        if (!je) je = env->FindClass("java/lang/Exception");
        env->ThrowNew(je, e.what());
        return;
    } catch (...) {
        AndroidBitmap_unlockPixels(env, bitmap);
        LOGE("nMatToBitmap catched unknown exception (...)");
        jclass je = env->FindClass("java/lang/Exception");
        env->ThrowNew(je, "Unknown exception in JNI code {nMatToBitmap}");
        return;
    }
}

void MatToBitmap(JNIEnv *env, Mat& mat, jobject& bitmap) {
    MatToBitmap2(env, mat, bitmap, false);
}

jni调用列子

JNIEXPORT void JNICALL Java_com_hzzj_opencv_demo_CppMosaicUtils_opencvImageblur(
        JNIEnv *env, jobject jobj, jobject jsrcBitmap){

    Mat mat_image_src ;
    BitmapToMat(env,jsrcBitmap,mat_image_src);//图片转化成mat
    Mat mat_image_dst;
    blur(mat_image_src, mat_image_dst, Size2i(10,10));
    //第四步：转成java数组->更新
    MatToBitmap(env,mat_image_dst,jsrcBitmap);//mat转成化图片
}