主要用到的api

avfilter_register_all()：注册所有AVFilter。
avfilter_graph_alloc()：为FilterGraph分配内存。
avfilter_graph_create_filter()：创建并向FilterGraph中添加一个Filter。
avfilter_graph_parse_ptr()：将一串通过字符串描述的Graph添加到FilterGraph中。
avfilter_graph_config()：检查FilterGraph的配置。
av_buffersrc_add_frame()：向FilterGraph中加入一个AVFrame。
av_buffersink_get_frame()：从FilterGraph中取出一个AVFrame。

源代码：

#include <jni.h>
#include <android/log.h>
#include <android/native_window.h>
#include <android/native_window_jni.h>

extern "C" {
#include "libavcodec/avcodec.h"
#include "libavformat/avformat.h"
#include "libswscale/swscale.h"
#include "libavutil/imgutils.h"

//-----AVfilter-----
#include <libavfilter/avfiltergraph.h>
#include <libavfilter/buffersrc.h>
#include <libavfilter/buffersink.h>
//-----AVfilter-----
};


#define  LOG_TAG    "JNI_TAG"
#define  LOGD(...)  __android_log_print(ANDROID_LOG_ERROR, LOG_TAG, __VA_ARGS__)


const char *filters_descr = "lutyuv='u=128:v=128'";
//const char *filters_descr = "hflip";
//const char *filters_descr = "hue='h=60:s=-3'";
//const char *filters_descr = "crop=2/3*in_w:2/3*in_h";
//const char *filters_descr = "drawbox=x=200:y=200:w=300:h=300:color=pink@0.5";
//const char *filters_descr = "movie=/storage/emulated/0/shuiyin.png[wm];[in][wm]overlay=5:5[out]";
//const char *filters_descr="drawgrid=width=100:height=100:thickness=4:color=pink@0.9";


int getCodecContext(AVCodecParameters *codecpar, AVCodecContext **avCodecContext) {
    AVCodec *dec = avcodec_find_decoder(codecpar->codec_id);
    if (!dec) {
        LOGD("can not find decoder");
        return -1;
    }

    *avCodecContext = avcodec_alloc_context3(dec);
    if (!*avCodecContext) {
        LOGD("can not alloc new decodecctx");
        return -1;
    }

    if (avcodec_parameters_to_context(*avCodecContext, codecpar) < 0) {
        avcodec_free_context(avCodecContext);
        *avCodecContext = NULL;
        LOGD("can not fill decodecctx");
        return -1;
    }

    if (avcodec_open2(*avCodecContext, dec, 0) != 0) {
        LOGD("cant not open audio strames");
        avcodec_free_context(avCodecContext);
        *avCodecContext = NULL;
        return -1;
    }
    return 0;
}


extern "C"
JNIEXPORT void JNICALL
Java_com_zzw_ffmpegdemo_FFmpegHelper_play(JNIEnv *env, jobject instance, jstring url_,
                                          jobject surface) {
    const char *url = env->GetStringUTFChars(url_, 0);

    AVFormatContext *pFormatCtx = NULL;
    AVCodecContext *pCodecCtx = NULL;

    AVFilterContext *buffersink_ctx = NULL;
    AVFilterContext *buffersrc_ctx = NULL;
    AVFilterGraph *filter_graph = NULL;

    //-----------------------------AVCodecContext init start----------------------------
    av_register_all();
    avfilter_register_all();//
    pFormatCtx = avformat_alloc_context();

    // Open video file
    if (avformat_open_input(&pFormatCtx, url, NULL, NULL) != 0) {

        LOGD("Couldn't open url:%s\n", url);
        return; // Couldn't open file
    }

    // Retrieve stream information
    if (avformat_find_stream_info(pFormatCtx, NULL) < 0) {
        LOGD("Couldn't find stream information.");
        return;
    }

    // Find the first video stream
    int videoStream = -1, i;
    for (i = 0; i < pFormatCtx->nb_streams; i++) {
        if (pFormatCtx->streams[i]->codecpar->codec_type == AVMEDIA_TYPE_VIDEO
            && videoStream < 0) {
            videoStream = i;
        }
    }
    if (videoStream == -1) {
        LOGD("Didn't find a video stream.");
        return; // Didn't find a video stream
    }

    if (getCodecContext(pFormatCtx->streams[videoStream]->codecpar, &pCodecCtx) != 0) {
        LOGD("Didn't get CodecContext.");
        return;
    }
    //-----------------------------AVCodecContext init end-------------------------------

    //------------------------------filter init start------------------------------------
    char args[512];
    AVFilter *buffersrc = avfilter_get_by_name("buffer");
    AVFilter *buffersink = avfilter_get_by_name("buffersink");//新版的ffmpeg库必须为buffersink
    AVFilterInOut *outputs = avfilter_inout_alloc();
    AVFilterInOut *inputs = avfilter_inout_alloc();

    enum AVPixelFormat pix_fmts[] = {AV_PIX_FMT_YUV420P, AV_PIX_FMT_NONE};

    filter_graph = avfilter_graph_alloc();

    /* buffer video source: the decoded frames from the decoder will be inserted here. */
    snprintf(args, sizeof(args),
             "video_size=%dx%d:pix_fmt=%d:time_base=%d/%d:pixel_aspect=%d/%d",
             pCodecCtx->width, pCodecCtx->height, pCodecCtx->pix_fmt,
             pFormatCtx->streams[videoStream]->time_base.num,
             pFormatCtx->streams[videoStream]->time_base.den,
             pCodecCtx->sample_aspect_ratio.num, pCodecCtx->sample_aspect_ratio.den);

    if (avfilter_graph_create_filter(&buffersrc_ctx, buffersrc, "in",
                                     args, NULL, filter_graph) < 0) {
        LOGD("Cannot create buffer source\n");
        return;
    }
    AVBufferSinkParams *buffersink_params = av_buffersink_params_alloc();
    buffersink_params->pixel_fmts = pix_fmts;
    if (avfilter_graph_create_filter(&buffersink_ctx, buffersink, "out",
                                     NULL, buffersink_params, filter_graph) < 0) {
        LOGD("Cannot create buffer sink\n");
        return;
    }
    av_free(buffersink_params);

    /* Endpoints for the filter graph. */
    outputs->name = av_strdup("in");
    outputs->filter_ctx = buffersrc_ctx;
    outputs->pad_idx = 0;
    outputs->next = NULL;

    inputs->name = av_strdup("out");
    inputs->filter_ctx = buffersink_ctx;
    inputs->pad_idx = 0;
    inputs->next = NULL;

    if ((avfilter_graph_parse_ptr(filter_graph, filters_descr,
                                  &inputs, &outputs, NULL)) < 0) {
        LOGD("Cannot avfilter_graph_parse_ptr\n");
        return;
    }

    if ((avfilter_graph_config(filter_graph, NULL)) < 0) {
        LOGD("Cannot avfilter_graph_config\n");
        return;
    }
    //------------------------------filter init end------------------------------------

    //------------------------------window init start-----------------------------------
    // 获取native window
    ANativeWindow *nativeWindow = ANativeWindow_fromSurface(env, surface);

    // 获取视频宽高
    int videoWidth = pCodecCtx->width;
    int videoHeight = pCodecCtx->height;

    // 设置native window的buffer大小,可自动拉伸
    ANativeWindow_setBuffersGeometry(nativeWindow, videoWidth, videoHeight,
                                     WINDOW_FORMAT_RGBA_8888);
    ANativeWindow_Buffer windowBuffer;
    //------------------------------window init end-----------------------------------


    //------------------------------get data-----------------------------------


    // 用于渲染
    AVFrame *pFrameRGBA = av_frame_alloc();

    // Determine required buffer size and allocate buffer
    // buffer中数据就是用于渲染的,且格式为RGBA
    int numBytes = av_image_get_buffer_size(AV_PIX_FMT_RGBA, pCodecCtx->width, pCodecCtx->height,
                                            1);
    uint8_t *buffer = (uint8_t *) av_malloc(numBytes * sizeof(uint8_t));
    av_image_fill_arrays(pFrameRGBA->data, pFrameRGBA->linesize, buffer, AV_PIX_FMT_RGBA,
                         pCodecCtx->width, pCodecCtx->height, 1);

    // 由于解码出来的帧格式不是RGBA的,在渲染之前需要进行格式转换
    SwsContext *sws_ctx = sws_getContext(pCodecCtx->width,
                                         pCodecCtx->height,
                                         pCodecCtx->pix_fmt,
                                         pCodecCtx->width,
                                         pCodecCtx->height,
                                         AV_PIX_FMT_RGBA,
                                         SWS_BILINEAR,
                                         NULL,
                                         NULL,
                                         NULL);

    AVPacket *packet = av_packet_alloc();
    int count = 0;
    while (av_read_frame(pFormatCtx, packet) == 0) {
        // Is this a packet from the video stream?
        if (packet->stream_index == videoStream) {
            // Decode video frame
            if (avcodec_send_packet(pCodecCtx, packet) != 0) {
                break;
            }

            AVFrame *pFrame = av_frame_alloc();

            while (avcodec_receive_frame(pCodecCtx, pFrame) == 0) {
                // lock native window buffer
                ANativeWindow_lock(nativeWindow, &windowBuffer, 0);

                //for AVfilter start
                pFrame->pts = av_frame_get_best_effort_timestamp(pFrame);
                //* push the decoded frame into the filtergraph
                if (av_buffersrc_add_frame(buffersrc_ctx, pFrame) == 0) {
                    av_buffersink_get_frame(buffersink_ctx, pFrame);
                } else{
                    LOGD("Could not av_buffersrc_add_frame");
                }
                // 格式转换
                sws_scale(sws_ctx, (uint8_t const *const *) pFrame->data,
                          pFrame->linesize, 0, pCodecCtx->height,
                          pFrameRGBA->data, pFrameRGBA->linesize);

                // 获取stride
                uint8_t *dst = (uint8_t *) windowBuffer.bits;
                int dstStride = windowBuffer.stride * 4;
                uint8_t *src = (pFrameRGBA->data[0]);
                int srcStride = pFrameRGBA->linesize[0];

                // 由于window的stride和帧的stride不同,因此需要逐行复制
                int h;
                for (h = 0; h < videoHeight; h++) {
                    memcpy(dst + h * dstStride, src + h * srcStride, srcStride);
                }
                ANativeWindow_unlockAndPost(nativeWindow);

                count++;
                LOGD("解码渲染%d帧", count);
            }
            av_frame_free(&pFrame);
            av_free(pFrame);
        }
    }

    ANativeWindow_release(nativeWindow);
    av_packet_free(&packet);
    sws_freeContext(sws_ctx);

    avfilter_inout_free(&outputs);
    av_free(outputs);
    avfilter_inout_free(&inputs);
    av_free(inputs);

    av_free(buffer);
    av_frame_free(&pFrameRGBA);
    av_free(pFrameRGBA);

    avfilter_graph_free(&filter_graph); //for avfilter
    // Close the codecs
    avcodec_close(pCodecCtx);
    avcodec_free_context(&pCodecCtx);
    pCodecCtx = NULL;

    // Close the video file
    avformat_close_input(&pFormatCtx);
    avformat_free_context(pFormatCtx);
    pFormatCtx = NULL;

    env->ReleaseStringUTFChars(url_, url);
}

更多的特效使用： http://www.ffmpeg.org/ffmpeg-filters.html