init

.gitignore

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+/cosleep_RAM
+*.zip

README.md

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+#COsleep 
+Closed- and Open-loop (Slow Ocillations) sleep stimulation (auditory) or recording in _full_-PSG using OpenBCI for sleep.
+
+* Its a **fun project**, but with hard science behind in hardware, software and concept, usable for research.
+* Different modes: e.g. Stimulation, Recording only (just PSG, no stimulation), record on SD card without real-time monitoring/stimulation
+* Setup for OpenBCI sleep recording (125 or 250 Hz sampling rate, 8 or 16 channels, incl. EEG, EOG, EMG and ECG) [here](https://www.spisop.org/openbci/)
+* Build your own sleep lab for under a $1000 and do research-grade recording and reactivation protocols.
+* Its free, its open and its closed-loop too, at least for slow waves/slow oscillations.
+* Targeted & Untargeted Auditory Stimuli Presentation using Configurable Stimuli Playlists (easy to create and mix).
+* Reproduce all the published research in this area, e.g. Targeted Memory Reactivation (TMR, e.g Rudoy et al. 2009) during sleep, or Slow wave enhancement (Ngo et al. 2013)
+* Stimulate during a specific time point of a slow oscillation, and trigger another stimuli after that.
+* Stimulation is activated manually, but disengaged automatically on arousal.
+* See live ERPs from stimulation
+* Latencies considered in stimulation (below 10 ms signal latency, auditory delay down to 24 ms, standard 93 ms)
+* 100% logging what you did, all markers, Lights-off on, checklist for eye movements
+* Lost samples are imputed and logged.
+* works with parallel microSD card recording (250 Hz)
+* Handles all kinds of auditory stimuli, peeps, noises, voices and baaaams! (as long as in wav or mp3 format, or what [_sox_ can handle](http://sox.sourceforge.net/soxformat.html))
+* Detect accurately your **hearing threshold** on any PC with Linux (alsa) down to the deciBel, and stimulate accurately as well with online-adjustments of volume.
+* FUll unfiltered BDF & CSV export (live, and including all markers)
+* Obfuscate your sham/stim condition for blinding your experiment.
+* Realtime-view, scalable channels, with spindle highlighting.
+* Flexible rereferencing
+* ... lots of stuff, see the poster:
+**[A poster with pictures and infographics, lists'n'stuff](https://drive.google.com/open?id=15XmB4hGwDl6L_oVv34uby7bRQaTBXUhu)**
+
+**Tutorial in the making, otherwise ask the author.**
+
+#External Download
+1. [Example Data](https://drive.google.com/open?id=1lG-Q-U_NJ-pon1OYjL4bfOzeRWntyBL9) for testing the simulation (FREDDY is 8 channel, JINGYI is 16 channel data, settings described in [here](https://www.spisop.org/openbci/)
+1. [Example Stimuli (preprocessed)](https://drive.google.com/open?id=1LlGVS8i8-biWbdamWvwoxJH3bp0wo1Ch) for testing the open and closed loop stimulation of voice and tones. Example protocols for those stimuli see in the subfolder [stimulations](http://github.com/Frederik-D-Weber/cosleep/software/installation/source_python/stimulations)
+1. [Binaries, Ubuntu 18.04 LTS x64](https://drive.google.com/open?id=1BkZig25DqL_edzowbonLJYWGkWO9WNGj) compiled using pyinstaller
+1. [Proof of concept learning Chinese in sleep files for ANKI](https://drive.google.com/open?id=1tC-79FaSCWTRyq7YmemzdTrxar4xp6q6) if you like to learn more chinese.
+
+# Requirements
+## EEG
+1. OpenBCI Cyton board (optionally a daisy module)
+1. EEG electrodes
+1. Battery/Power pack
+1. Other stuff to record polysomnography
+1. Motivation to built a little (you can do it!)
+...see tutorial [here](https://www.spisop.org/openbci/)
+
+## PC (minimum recommendation)
+* Dual core 1.2 Ghz
+* 1.5 GB RAM
+* 5 GByte free disk space
+* USB 2.0 port
+* Audio jack (wireless audio due to delay not recommended)
+(e.g. a Rasperry Pi3, Pine64, Rock64, etc. are fine too)
+
+## OS (preferred)
+* Linux, e.g. Ubuntu 12.XX and newer versions it was **tested** under Ubunutu 14.04 LTS and 18.04 LTS) 
+* _low-latency_ kernel preferred (will automatically installed with the _deploy_ scripts)
+
+## Tested PCs, deploy, run and compiled (pyinstaller)
+* Lenovo Thinkpad X220, Intel Core i7-2640M, 16 GByte RAM, fast SSD, Ubuntu 18.04 LTS
+* Lenovo Thinkpad X220, Intel Core i5-2520M, 16 GByte RAM, fast SSD, Ubuntu 14.04 LTS
+* Dell Laptitude, Ubuntu 18.04 LTS

_deploy.sh

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+#!/bin/bash
+sudo bash deploy/configure_ubuntu.sh
+sudo bash deploy/install_additional_software.sh
+#sudo bash deploy/create_RAMdisk_example.sh

_recompile.sh

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+#!/bin/bash
+cd ${PWD}/software/installation/source_python/
+bash deploy.sh
+bash compile.sh

deploy/configure_ubuntu.sh

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+#!/bin/bash
+# tested in Ubuntu 18.04 LTS
+# required setup for cosleep to work
+sudo apt-get -y install linux-lowlatency
+sudo apt-get -y install sox
+sudo apt-get -yes install libsox-fmt-mp3
+## workaround for permission of recorder_simulation to the ttyUSB*
+sudo chmod 666 /dev/ttyUSB*
+sudo usermod -a -G dialout $USER
+
+# recommended setup
+sudo add-apt-repository ppa:danielrichter2007/grub-customizer
+sudo apt-get update
+sudo apt-get -y install grub-customizer
+
+gsettings set org.gnome.desktop.interface clock-show-seconds true
+gsettings set org.gnome.nautilus.preferences executable-text-activation ask
+
+# optional software and setup
+## for python to run and compile the packages
+sudo apt-get -y install cmake
+sudo apt-get -y install python # probably already up to date
+sudo apt-get -y install python-pip
+sudo apt-get -y install python-qt4
+sudo apt-get -y install python-alsaaudio
+
+# to run from Files by double clicking
+sudo apt-get -y install nautilus-actions # might not work
+
+# to configure and check sound card properties
+sudo apt-get -y install jackd2
+
+## to track the CPU usage in a GUI
+sudo add-apt-repository ppa:cpug-devs/ppa
+sudo apt-get update
+sudo apt-get -y install cpu-g # might not work
+
+

deploy/create_RAMdisk_example.sh

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+#!/bin/bash
+cd ../
+mkdir cosleep_RAM
+sudo mount -t tmpfs -o size=4000M none cosleep_RAM
+rsync -av --progress ./ cosleep_RAM/
+# see https://wiki.ubuntuusers.de/RAM-Disk_erstellen/
+# sudo umount ${PWD}/../cosleep_RAM
+

deploy/install_QjackCtl.sh

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+#!/bin/bash
+sudo apt-get -y install qtbase5-dev-tools qtbase5-dev qt5-default qttools5-dev-tools
+cd ${BASEDIR}/../software/installation/qjackctl-0.5.2
+sudo apt-get -y install libjack-dev
+./configure
+make
+sudo make install
+
+

deploy/install_additional_software.sh

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+#!/bin/bash
+bash install_edf_browser.sh
+bash install_QjackCtl.sh

deploy/install_anki.sh

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+#!/bin/bash
+sudo apt-get -y install mplayer
+sudo apt-get -y install mpv
+sudo apt-get -y install anki

deploy/install_edf_browser.sh

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+#!/bin/bash
+sudo apt-get -y install g++ make git-core 
+#sudo apt-get -y install qtbase5-dev-tools qtbase5-dev qt5-default
+sudo apt-get -y install qt4-qmake libqt4-dev
+cd ${BASEDIR}/../software/installation/edfbrowser_164_source
+sudo qmake-qt4
+sudo make
+sudo make install

software/anki.sh

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+#!/bin/bash
+anki

software/edfbrowser.sh

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+#!/bin/bash
+cd ${PWD}/data
+edfbrowser