deployment tweaks

[djkapner]

These are deployment tweaks required and requested during Pika's dev testing of the app.

1. changing manifest extension from .jsonl to .json

2. linking movie frame rate and trace time axis

webapp movie playback defined by fps passed to imageio_ffmpeg and trace playback defined by pointInterval. These were not connected. Added a playback_factor arg default to 1.0 (real time) that connected these 2 data sources. Demo:

import json                                                               
tpath = "/allen/aibs/informatics/labeling_artifacts/segmentation_run_id_954/trace_1575130.json"                                                     
with open(tpath, "r") as f: 
    print(json.load(f)['pointInterval'])                                                                            
0.25

and

$ ffmpeg -i /allen/aibs/informatics/labeling_artifacts/segmentation_run_id_954/video_1575130.mp4
...
    Stream #0:0(und): Video: h264 (High) ... 4 fps, 4 tbr, 16384 tbn, 8 tbc (default)
...

note that in python:

import imageio_ffmpeg as mpg                                              
vpath = "/allen/aibs/informatics/labeling_artifacts/segmentation_run_id_954/video_1575130.mp4"                                                    
frames, seconds = mpg.count_frames_and_secs(vpath) 
print(frames / seconds)                                                  
4.047058823529412

imageio-ffmpeg has some known issue.

3. Added a video/image normalization strategy.

Thus far the strategy is:

• downsample the video and take average and max projections.
• normalize video and average projection based on quantiles of average projection.
• normalize max projection based on quantiles of max projection. (saturates when treated like video and avg)
• normalization completely at experiment level.
• no per-ROI normalization (in this iteration.)

4. exposing bitrate parameter for potentially helping to control movie sizes.

5. Added timestamp to local transform results folder.

To avoid re-writing some manifest contents. Could get confusing.

[kschelonka]

Ensure traces and videos are on the same time scale. Currently videos are 10FPS and traces are 4 points per second.

[djkapner]

~TODO: add a test for normalize_array~ done