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Evaluate a phyllotaxis measurement (case1) Use sm-dtw with simulated dataLink

How to use the 'sm-dtw' assessment tool with simulated synthetic phyllotaxis data

  • Download and view the full tutorial video. See also below how to navigate rapidely into the content of this video.

  • related readme procedure: you can also help by reading the readme of the project.

ObjectiveLink

  • generate synthetic data to use the sm-dtw program
  • use sm-dtw
  • evaluate the prediction made by sm-dtw

PrerequisiteLink

you only need to install docker. No other third-party software (R, python, jupyter, conda) is required, as all the programs are run from inside the docker container

Step-by-step tutorialLink

1. Download the docker imageLink

It should be downloaded automatically when trying to run the docker for the first time

docker run -p 8888:8888 -it roboticsmicrofarms/sm-dtw_demo:latest bash

2. Using jupyter notebook inside a docker:Link

Running the Jupyter notebook:Link

  1. In your local machine, create a working directory to store the results generated by the notebook. It will be mounted inside the container, where its name will be "docker_sandbox". The name in you local machine can be identical or different, but keep the name inside the docker to avoid further changes in the notebooks. Sop open a terminal and type: 
mkdir docker_sandbox # this folder can be created anywhere in your local machine
cd docker_sandbox # Move into this working directory
  1. Start the container:

docker run -v $(pwd):/myapp/docker_sandbox -p 8888:8888 -it roboticsmicrofarms/sm-dtw_demo:latest bash
Note: you can start this command from anywhere in your local machine by correctly mapping the mounted volume in the string before the semi-column (-v path/in/your/machine:/myapp/docker_sandbox)

  1. Inside the container, serve the notebooks by entering the following command after the running container's prompt (which should be something like: (dtw) root@aa7632c1fc29:/myapp#):
jupyter notebook Phyllotaxis-sim-eval/notebooks/docker_run --ip 0.0.0.0 --no-browser --allow-root
  1. Outside the docker, start your browser
  2. enter the url with token:"http://127.0.0.1:8888/?token=....." or directly Ctrl+click on it
  3. select the correct kernel (R, dtw or bash, as indicated in the first cell of the notebook)
  4. run the notebook !

Outline of the tutorial videoLink

Here is the main content of the video and indicative time to help you directly jump into the chapters you are interested in !

Chapter Time start Content description
Introduction 00min 00s Romi Project, object of this video
Content Outline 00min 30s details the content of the video
What is sm-dtw ? 1min 05s general description of sm-dtw program
Why/when do I need 'sm-dtw' 2min 40s Presents the precise example of our use for phyllotaxis measurement in Romi and propose other possible user cases
Where to find online written documentation 8min15 provides a link to the 'readme' page of the github repo of the project
Docker & Jupyter notebooks 8min 47 Download and start docker + start Jupyter Notebooks Prepare a working folder to store your data on your local machine
Step1 (1st Jupyter notebook) 12min 12s Explains how to simulate synthetic data made of a sequence of reference phyllotaxis data (angles and internodes) a test sequence containing errors
Step2 (2nd Jupyter notebook) 28min 15s Explains how to realignthe two phyllotaxis sequences generated in step1 using sm-dtw
Step3 (3rd Jupyter notebook) 39min 11s Explains how to check that the alignment prediction made by sm-dtw correspond to the errors generated in step1
Quit and close Jupyter notebooks and docker container 51min 20s proper procedure to close and quit jupyter notebooks and the docker container.