Getting Started

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Setting up BIDS

Linux

Debian, Ubuntu, Mint

  • TODO

Arch

  • TODO

Windows

Do all of the following in cmd (that is what is meant by terminal)

Install Reach-Examples

  • download the JDK for Java 8 (or choose the latest Java version) from the java website
  • install the JDK with default options
  • set JAVA_OPTS
 > set JAVA_OPTS=-server -Xms3g -Xmx6g
  • download SBT from the scala website
  • run the installer with default options
  • close and reopen any terminals you have open
  • In a terminal run SBT (ensure your network remains connected, as things will be downloaded from maven repos.)
 > sbt
  • download git from the git website
  • install git with default options
  • close and reopen any terminals you have open
  • In a terminal make a directory to store the BIDS project. We will create a directory 'Src' (intended to store all source code we work on, including BIDS) with a directory 'BIDS' inside
 > mkdir Src
 > cd Src
 > mkdir BIDS
 > cd BIDS
  • clone the reach-examples repository
 > git clone https://github.com/dsidi/reach-examples
  • change to the reach-examples directory
 > cd reach-examples
  • edit your PATH variable. (NOTE: this may be replaced with setx at the command line in the future. I need to look into it. -David)
    • In a terminal, do (you may need to replace jdk1.8.0_91 with something similar but different)
        > cd c:\Program Files\Java\jdk1.8.0_91\bin
    • now highlight the path to the left of the ">" (not including the ">") and do <ctrl><c> to copy it
    • right click the cmd icon on the task bar, and click "run as administrator"
      • set the path
          > setx path "%path%;<ctrl><v> /M"
        where <ctrl><v> is you pressing those keys to paste in the path you just copied.
  • In a new terminal, change to the reach-examples directory. For my case, this is
 > cd Src\BIDS\reach-examples
  • run reach-examples with sbt (again sbt will download several things, so ensure your connection to the internet is up)
 > sbt run
  • when prompted, type the number of the selection for com.yourorg.GroundStringsEntryPoint
  • If no errors are shown, move to the next section

Install BIDS

Install Scikit-learn

  • install numpy from pre-built binaries here (choose the filename with both '27' in it [for Python 2.7.x] and either 'amd64' (if you're 64 bit architecture) or 'win32' (otherwise)
  • install scipy from pre-built binaries here (choose the filename with both '27' in it [for Python 2.7.x] and either 'amd64' (if you're 64 bit architecture) or 'win32' (otherwise)
  • install scikit-learn from pre-built binaries here (choose the filename with both '27' in it [for Python 2.7.x] and either 'amd64' (if you're 64 bit architecture) or 'win32' (otherwise)
  • close all terminals (including the one with SBT running in it, if you left it open)

Get the BIDS code

  • in a new terminal change to the directory containing reach-examples, then clone the BIDS repository (so that the BIDS directory and the reach-examples directory are siblings:
 > cd Src\BIDS
 > git clone https://github.com/ua-sista/bigmech.git

Install BIDS dependencies

  • in a new terminal, install virtual env from pip:
 > pip install virtualenvwrapper-win
  • make a bids environment. If you do not use Python 2.7.x as your python interpreter (calling
    python --version
    on the command line will tell you), you'll need to do
 > mkvirtualenv --python=C:\Python27\python.exe bids

possibly substituting a different path to the python.exe for Python2.7.x if it's not in the default location. If you do use python 2.7.x, you can just do

 > mkvirtualenv bids
    • you should now see (bids) in your command prompt
  • install the Visual C++ compiler for Python 2.7 (try not to cry)
  • install the requirements for the BIDS project using pip and the modified requirements.txt file
 > pip install -r requirements.txt
  • now change to the BIDS directory. In my case
 > cd Src\BIDS\bigmech

Add BIDS paths to PYTHONPATH

  • we need to add the path to bioCausalRelationLearner to your path (similar to what we did before to add javac to the path)
    • first get the path to the bioCausalRelationLearner
      • in a new terminal, go to the directory containing the file bioCausalRelationLearner.py. This file is in the directory for BIDS that you cloned earlier. For me it is in
          > cd Src\BIDS\bigmech\bioIncrementalDistantSupervision
      • highlight the path to the left of the ">" (not including the ">"), and copy with <ctrl><c>
      • close the terminal
    • Click Start, then Settings. Type "environment" into the search box in the corner of the settings window
    • Click "edit the system environment variables"
    • Click the "Environment Variables..." button
    • Try to find "PYTHONPATH" in the "System variables" box. If it is there, click "Edit..." and add a semicolon, then paste from the clipboard. If it is not, click New... and name the variable PYTHONPATH, and paste from the clipboard into the Variable value field.
    • Click OK to save the settings, then OK again in the next window

Run the unit tests

  • now we'll run the unit test for training the classifier. First we run the reach server.
  • In a new terminal, go to the reach-examples directory and do
 > run sbt 

selecting the entry point exactly as above

  • In a second new terminal, go to the BIDS source directory and run the python unittest test_train:
 > cd Src\BIDS\bigmech
 > python -m unittest test.test_IncrementalDistantSupervision.IncrementalDistantSupervisionTests.test_train
  • If you see "Training classifier..." followed by an error about a .pkl file missing, you are good (this will be fixed very shortly)

Mac