Encoding and muxing video using MediaCodec and MediaMuxer

I am developing an App where I decode a video and replace certain frames and re-encode using MediaMuxer and MediaCodec. The App works if I do not replace any frames (except for 1080p videos as I explain below), but when I do, the frames after the replaced ones are pixelated and the video is choppy.

Also, when I try my app with 1920x1080 videos, I get a strange output, where the video is not showing anything, until I scroll to the beginning of the video, then the video starts showing up (but with the same problem mentioned before of pixalation after the edit.

Here is how I configure my encoder:

Video_format.setInteger(MediaFormat.KEY_I_FRAME_INTERVAL, interval);
Video_format.setInteger(MediaFormat.KEY_BIT_RATE, bitRate);
Video_format.setInteger(MediaFormat.KEY_FRAME_RATE, frameRate);
Video_format.setInteger(MediaFormat.KEY_MAX_INPUT_SIZE, 0);
int color_format=MediaCodecInfo.CodecCapabilities.COLOR_FormatYUV420SemiPlanar;
Video_format.setInteger(MediaFormat.KEY_COLOR_FORMAT, color_format);

encoder.configure(Video_format, null, null, MediaCodec.CONFIGURE_FLAG_ENCODE);

So to sum up, I have two problems:

1- Pixelated frames and choppy video after modified frames.

2- Corrupted 1920x1080 videos unless I scroll to the beginning.

Edit

Here is a sample 1080p video unedited, which gives a green screen when I play on VLC and plays incorrectly on the phone unless I scroll to start and now strangely working normally on YouTube, except for a green frame at the start

Here is a sample 720p video edited with also a green frame at the start and clear pixelation and lag after the edit

Here is the code I use to decode an re-encode:

do{
  Bitmap b1;

  if(edited_frames.containsKey(extractor.getSampleTime()))
    b1=BitmapFactory.decodeFile(edited_frames.get(extractor.getSampleTime()));
  else
    b1=decode(extractor.getSampleTime(),Preview_width,Preview_Height);

  if(b1==null) continue;

  Bitmap b_scal=Bitmap.createScaledBitmap(b1, Preview_width, Preview_Height, false);
  if(b_scal==null) continue;
  encode(b_scal, encoder, muxer, videoTrackIndex);
  lastTime=extractor.getSampleTime();
}while(extractor.advance());

The decode method:

private Bitmap decode(final long time,final int width,final int height){
  MediaFormat newFormat = codec.getOutputFormat();
  Bitmap b = null;
  final int TIMEOUT_USEC = 10000;
  ByteBuffer[] decoderInputBuffers = codec.getInputBuffers();
  MediaCodec.BufferInfo info = new MediaCodec.BufferInfo();

  boolean outputDone = false;
  boolean inputDone = false;
  while (!outputDone) {
    if (!inputDone) {
      int inputBufIndex = codec.dequeueInputBuffer(TIMEOUT_USEC);
      if (inputBufIndex >= 0) {
        ByteBuffer inputBuf = decoderInputBuffers[inputBufIndex];

        int chunkSize = extractor.readSampleData(inputBuf, 0);
        if (chunkSize < 0) {
          codec.queueInputBuffer(inputBufIndex, 0, 0, 0L, MediaCodec.BUFFER_FLAG_END_OF_STREAM);
          inputDone = true;
        } else {
          long presentationTimeUs = extractor.getSampleTime();
          codec.queueInputBuffer(inputBufIndex, 0, chunkSize, presentationTimeUs, 0 );
        }
        inputBuf.clear();
        decoderInputBuffers[inputBufIndex].clear();
      } else {
      }
    }
    ByteBuffer[] outputBuffers;
    if (!outputDone) {
      int decoderStatus = codec.dequeueOutputBuffer(info, TIMEOUT_USEC);
      if (decoderStatus == MediaCodec.INFO_TRY_AGAIN_LATER) {
      } else if (decoderStatus == MediaCodec.INFO_OUTPUT_BUFFERS_CHANGED) {
        outputBuffers = codec.getOutputBuffers();
      } else if (decoderStatus == MediaCodec.INFO_OUTPUT_FORMAT_CHANGED) {
        newFormat = codec.getOutputFormat();
      } else if (decoderStatus < 0) {
      } else { 
        if ((info.flags & MediaCodec.BUFFER_FLAG_END_OF_STREAM) != 0) {
          outputDone = true;
        }

        boolean doRender = (info.size != 0);

        codec.releaseOutputBuffer(decoderStatus, false);
        if (doRender) {
          outputBuffers = codec.getOutputBuffers();
          ByteBuffer buffer = outputBuffers[decoderStatus];
          buffer = outputBuffers[decoderStatus];

          outputDone = true;

          byte[] outData = new byte[info.size];
          buffer.get(outData);
          buffer.clear();
          outputBuffers[decoderStatus].clear();
          try {
            int colr_format=-1;
            if(newFormat!=null && newFormat.getInteger(MediaFormat.KEY_COLOR_FORMAT)==21){
              colr_format=ImageFormat.NV21;
            }else if(newFormat!=null && newFormat.getInteger(MediaFormat.KEY_COLOR_FORMAT)!=21){			
              Toast.makeText(getApplicationContext(), "Unknown color format "+format.getInteger(MediaFormat.KEY_COLOR_FORMAT), Toast.LENGTH_LONG).show();
              finish();
              return null;
            }

            int[] arrrr=new int[format.getInteger(MediaFormat.KEY_WIDTH)* format.getInteger(MediaFormat.KEY_HEIGHT)];
            YUV_NV21_TO_RGB(arrrr, outData, format.getInteger(MediaFormat.KEY_WIDTH), format.getInteger(MediaFormat.KEY_HEIGHT));

            lastPresentationTimeUs = info.presentationTimeUs;

            b = Bitmap.createBitmap(arrrr, format.getInteger(MediaFormat.KEY_WIDTH), format.getInteger(MediaFormat.KEY_HEIGHT), Bitmap.Config.ARGB_8888);
          } catch (Exception e) {
            e.printStackTrace();
          }
        }
      }
    }
  }
  return b;
}

And here is the encode method:

private void encode(Bitmap b, MediaCodec encoder, MediaMuxer muxer, int track_indx){
  MediaCodec.BufferInfo enc_info = new MediaCodec.BufferInfo();
  boolean enc_outputDone = false;
  boolean enc_inputDone = false;

  final int TIMEOUT_USEC = 10000;

  ByteBuffer[] encoderInputBuffers = encoder.getInputBuffers();
  ByteBuffer[] enc_outputBuffers = encoder.getOutputBuffers();

  while (!enc_outputDone) {
    if (!enc_inputDone) {
      int inputBufIndex = encoder.dequeueInputBuffer(TIMEOUT_USEC);
      if (inputBufIndex >= 0) {
        ByteBuffer inputBuf = encoderInputBuffers[inputBufIndex];
        int chunkSize = 0;

        if(b==null){
        }else{
          int mWidth = b.getWidth();
          int mHeight = b.getHeight();

          byte [] yuv = new byte[mWidth*mHeight*3/2];
          int [] argb = new int[mWidth * mHeight];

          b.getPixels(argb, 0, mWidth, 0, 0, mWidth, mHeight);
          encodeYUV420SP(yuv, argb, mWidth, mHeight);

          b.recycle();
          b=null;
          inputBuf.put(yuv);
          chunkSize = yuv.length;
        }

        if (chunkSize < 0) {
          encoder.queueInputBuffer(inputBufIndex, 0, 0, 0L,
							MediaCodec.BUFFER_FLAG_END_OF_STREAM);
        } else {
          long presentationTimeUs = extractor.getSampleTime();
          Log.i("Encode","Encode Time: "+presentationTimeUs);
          encoder.queueInputBuffer(inputBufIndex, 0, chunkSize, presentationTimeUs, 0);
          inputBuf.clear();

          encoderInputBuffers[inputBufIndex].clear();
          enc_inputDone=true;
        }
      }
    }
    if (!enc_outputDone) {
      int enc_decoderStatus = encoder.dequeueOutputBuffer(enc_info, TIMEOUT_USEC);
      if (enc_decoderStatus == MediaCodec.INFO_TRY_AGAIN_LATER) {
      } else if (enc_decoderStatus == MediaCodec.INFO_OUTPUT_BUFFERS_CHANGED) {
        enc_outputBuffers = encoder.getOutputBuffers();
      } else if (enc_decoderStatus == MediaCodec.INFO_OUTPUT_FORMAT_CHANGED) {
        MediaFormat newFormat = encoder.getOutputFormat();
      } else if (enc_decoderStatus < 0) {
      } else { 
        if ((enc_info.flags & MediaCodec.BUFFER_FLAG_END_OF_STREAM) != 0) {
          enc_outputDone = true;
      }

      boolean enc_doRender = (enc_info.size != 0);
      encoder.releaseOutputBuffer(enc_decoderStatus, false);
      if (enc_doRender) {
        enc_outputDone = true;
        ByteBuffer enc_buffer = enc_outputBuffers[enc_decoderStatus];

        try {
          muxer.writeSampleData(track_indx, enc_buffer, enc_info);
        } catch (Exception e) {
          e.printStackTrace();
        }
        enc_buffer.clear();
        enc_outputBuffers[enc_decoderStatus].clear();
      }
    }
  }
}

The pixelation is most likely due to wrong frame timestamps, so make sure your frames' timestamps increase monotonically and are the same when you pass them to MediaCodec and MediaMuxer. In this specific case, you only need to replace the data for the frame you're going to replace, leaving its timestamp as it was in the original stream.

Make sure you're converting the bitmap to the YUV color space and you're using a correct pixel format. Android stores bitmaps in RGBA with 4 bytes per pixel, you need to convert this to YUV with Y value for each pixel and U and V values for a block of 2x2, then lay them out in separate planes in the byte array that goes into the codec.

Also, some time ago I made an example app that resizes videos using MediaCodec, it may help you as well: https://github.com/grishka/android-video-transcoder