The code to control the Janelia fly alcohol assay (FlyBar).
Authors: Peter Polidoro polidorop@janelia.hhmi.org
###Experiment Mode (Typical Case)
Open a terminal and run::
faa
Then open a web browser and navigate to http://localhost:5000
Open a terminal and run::
faa -m
Open a terminal and run::
faa -h
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ASUS BP6375-I73770039B No Screen Desktop PC Intel Core i7 3770(3.40GHz) 8GB DDR3 1TB HDD Capacity Intel HD Graphics 4000 newegg item # N82E16883220285
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SIIG 3-Port FireWire PCI Express Card Model NN-E20022-S1. Newegg newegg item # N82E16815150160
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SAMSUNG 840 Series MZ-7TD500KW 2.5" 500GB SATA III Internal Solid State Drive (SSD) newegg item # N82E16820147187 (Quantity 2)
xubuntu-12.04.3-desktop-amd64 md5 hash: 8719cc129fcb766d728a7c101eb6cec4
Open a terminal and run::
sudo apt-get update
sudo apt-get upgrade
Open a terminal and run::
sudo apt-get install git -y
sudo apt-get install gparted -y
sudo gparted
Format second internal harddrive to ext4 with label "data"
Open a terminal and run::
sudo blkid
# check to make sure harddrive device shows up with LABEL="data"
sudo mkdir /media/data
sudo emacs /etc/fstab
Add the following line to fstab::
LABEL=data /media/data ext4 rw,suid,dev,noexec,auto,nouser,sync 0 0
Open a terminal and run::
sudo shutdown -r now
After the computer restarts, open a terminal and run::
sudo chown -R fly:fly /media/data
ln -s /media/data ~/faa_data
On the machine you will use for remote maintenance, open a terminal and run::
sudo apt-get install vinagre
ssh-keygen
ssh-copy-id [remote login name]@[IP address of remote computer]
On the remote computer open a terminal and run::
sudo apt-get install x11vnc
sudo emacs /etc/ssh/sshd_config
Make sure PubkeyAuthentication is set to yes and PasswordAuthentication is set to no.
Open a terminal and run::
sudo apt-get install coriander -y
coriander
# test to make sure camera works properly
Open a terminal and run::
sudo usermod -aG dialout $USER
sudo shutdown -r now
Open a terminal and run::
sudo sh -c 'echo "deb http://packages.ros.org/ros/ubuntu precise main" > /etc/apt/sources.list.d/ros-latest.list'
wget http://packages.ros.org/ros.key -O - | sudo apt-key add -
sudo apt-get update
sudo apt-get dist-upgrade
sudo apt-get install ros-groovy-desktop-full -y
sudo apt-get install ros-groovy-image-pipeline -y
Open a terminal and run::
sudo apt-get install python-rosinstall -y
mkdir ~/ros
rosws init ~/ros/faa_ws /opt/ros/groovy
source ~/ros/faa_ws/setup.bash
rosws set faa --git https://github.com/janelia-idf/fly-alcohol-assay.git
rosws set faa_config --git https://github.com/janelia-idf/fly-alcohol-assay-config.git
rosws update
python ~/ros/faa_ws/faa-config/bash_setup.py
source ~/.bashrc
python ~/ros/faa_ws/faa/install.py
Open a terminal and run::
sudo apt-get install ros-groovy-camera1394 -y
sudo apt-get install ros-groovy-mjpeg-server -y
sudo apt-get install ros-groovy-rosbridge-suite -y
sudo apt-get install ros-groovy-executive-smach-visualization -y
Open a terminal and run::
source $FAA_PYTHON_VIRTUALENV/bin/activate
pip install flask --upgrade
Open a terminal and run::
sudo apt-get install libavcodec-extra-53 vlc
Open a terminal and run::
rosmake faa
The path to the checkerboard pattern is: ~/ros/faa_ws/faa_config/patterns/checkerboard_10mm.svg
Print out at 100% scale using inkscape. Check to make sure each small black square has side length 10mm. Place double-sided tape on back side of printout and then cut out around outer black square borders. Tape onto a 6"x6" flat plate and use roller to press on evenly.
Open a terminal and run::
faa -c
Use 8x6 10mm checkerboard to calibrate the camera. Remove IR filter on camera if necessary and provide enough visible light for camera to see the checkerboard. Wave checkerboard around under camera until 'Calibrate' button activates. Press 'Calibrate' button, then press 'Commit'. Place IR filter back onto camera.
Open a terminal and run::
cd ~/ros/faa_ws/faa
git pull origin master
rosmake faa