nsniff: A Python repository from matham

NSniff

Ceed is an in vitro experiment that stimulates brain slices and records their activity.

For more information: https://matham.github.io/nsniff/index.html

To install https://matham.github.io/nsniff/installation.html

Protocol file

You can use a CSV file to import a sequence of hardware states and their duration the program can run through.

The format of the CSV file is something like duration,valve_banana,valve_apple,valve_kiwi,valve_orange,mfc_1,mfc_2,key,label.

There must be a header row that adheres to the labels as follows:

duration is the first row and the duration of this row. That is the state of the hardware will be set to the values of the row and then it'll wait for duration.
value_xxx is the next n columns, which is equal to the number of valves (relays) in the system. They are counted from left to right in the GUI which correspond to these n columns. The column label must be prefixed with value_ and can have any suffix. The suffix can be used to name the odor value etc.
value_m is the next m columns, which is equal to the number of MFCs in the system. They are counted from left to right in the GUI which correspond to these m columns. The column label must be prefixed with mfc_ and can have any suffix. The suffix can be used to name the MFC.
key is a single character that can be used within the GUI to trigger to run through the sequence of all the rows that contain this character. Or no character, in which case if no character is entered in the GUI, those empty rows will be run through.
label is any string (not containing commas) that is logged

Software installation

Install the dependencies with

``` sudo apt install python3 python3-dev python3-pip python3 -m pip install --upgrade pip virtualenv cd Desktop python3 -m virtualenv venv cd venv/ source bin/activate

git clone https://github.com/matham/pymoa-remote.git pip install -e pymoa-remote/[network] pip install https://github.com/matham/kivy-trio/archive/master.zip git clone https://github.com/matham/pymoa.git pip install -e pymoa/ ```

Finally start the server with KIVY_NO_ARGS=1 pymoa_quart_app --port port --host "ip".

auto start

sudo nano /lib/systemd/system/pymoa_remote.service

paste::

[Unit] Description=MyMoa-remote server After=multi-user.target network-online.target systemd-networkd-wait-online.service Wants=network-online.target systemd-networkd-wait-online.service Requires=systemd-networkd-wait-online.service

StartLimitIntervalSec=1000 StartLimitBurst=10

[Service] Restart=on-failure RestartSec=10s Environment="PYMOA_REMOTE_PORT=5378" Environment="PYMOA_REMOTE_HOST=rasppi03wifi.cplab.cornell.edu" Environment="KIVY_NO_ARGS=1" Environment="PYMOA_REMOTE_SERVE=/home/pi/Desktop/venv/bin/pymoa_quart_app" ExecStart=/bin/bash -c '$${PYMOA_REMOTE_SERVE} --port $${PYMOA_REMOTE_PORT} --host $${PYMOA_REMOTE_HOST}'

[Install] WantedBy=multi-user.target

sudo chmod 644 /lib/systemd/system/pymoa_remote.service sudo systemctl daemon-reload sudo systemctl enable pymoa_remote.service sudo systemctl start pymoa_remote

systemctl status pymoa_remote

sudo journalctl -u pymoa_remote https://serverfault.com/a/413408

Hardware setup

The following describes how to set up a Raspberry Pi to control the Stratuscent sensors, valves, and MFCs as a remote server that we can connect to and control from another computer on the network.

RPi

The RPi may come with a noobs SD card or a blank card. Either way we need to install the latest RPi OS directly so we can use it headless and connect it to the wifi/ethernet.

Install the recommended OS (currently Raspberry Pi OS 32-bits) following this guide using a USB sd card reader.

To configure the RPi so you can connect over ssh and provide it the WiFi credentials you can either:

Use the recommended RPI Imager and in its settings before writing the image to the SD card provide the WiFi etc.
Or we'll provide a file with configuration details after writing to the SD card. Once the OS is installed to the card, open the SD card again on a PC and follow this guide. Essentially, in the SD root directory of the boot partition, create a empty file called ssh this will enable ssh. Then create a file called wpa_supplicant.conf as well with contents:
```
country=US
ctrl_interface=DIR=/var/run/wpa_supplicant GROUP=netdev
update_config=1

network={
    ssid="network-name"
    psk="password"
}
```
replacing the ssid and psk with the WiFi details.

Then, insert the SD card and power ON the RPi, wait a little bit for it to set up and connect to your router. Then, log into your router to get the IP of the RPi. Log into the RPi using ssh pi@ip with default password raspberry (unless you changed it).

Update the OS using with:

sudo apt update
sudo apt dist-upgrade

If you would like to connect directly to RPi using ethernet as it is directly connected to your PC, try following this guide.

Stratuscent sensors

https://community.silabs.com/s/article/cp210x-legacy-programming-utilities?language=en_US https://inegm.medium.com/persistent-names-for-usb-serial-devices-in-linux-dev-ttyusbx-dev-custom-name-fd49b5db9af1 ls /dev/ sudo nano /etc/udev/rules.d/99-usb-serial.rules sudo udevadm control --reload-rules && sudo udevadm trigger SUBSYSTEM=="tty", ATTRS{idVendor}=="10c4", ATTRS{serial}=="10023B", SYMLINK+="SScent10023B"

Connecting MOD-IO:

UART:

sudo raspi-config - Expand filesystem and enable serial on advanced page, exit and reboot. sudo nano /boot/config.txt - add dtoverlay=pi3-disable-bt sudo nano /boot/cmdline.txt - remove "console=serial0,115200" or (ttyAMA0) reboot

I2C: desolder R15 and R17

https://www.abelectronics.co.uk/kb/article/1/i2c-part-2---enabling-i-c-on-the-raspberry-pi

Enable I2C using sudo raspi-config, option 5 and enable it. Then do `sh sudo apt install i2c-tools // list all devices sudo i2cdetect -y 1 pip install smbus2 `

It communicates over I2C and boards can be connected sequentially, but they need to be powered independently. Barrel connector power should be 8V-30V DC. Blue twin is opto-isolated digital input (same range as power). Blue triplet is opto-isolated analog output relay (5A/250VAC). Green is 4 analog inputs (0 - 3.3V). UEXT is connected to I2C pins of RPi: connect ground, scl to scl and sda to sda. Connect them in series, they each need power. Update the address from default 0x58 to e.g. 0x22 using i2cset -y -f 2 0x58 0xF0 0x22.

ADC

Enable SPI using sudo raspi-config, option 5 and enable it.

Install

sudo apt install python3-pigpio pigpio pip install pigpio for venv sudo pigpiod to start daemon

``` git clone https://github.com/ul-gh/PiPyADC.git

```

MFC

Keep 120R leave default switches, full-auto

# In /boot/config.txt: sudo nano /boot/config.txt # Add the following, int_pin is set according to the actual welding mode(BCM coding): dtoverlay=sc16is752-spi1,int_pin=24

After reboot, the driver of SC16IS752 will be loaded into the system kernel. At this time, you can run ls /dev to see that there will be more devices as follows: ttySC0 ttySC1

matham/nsniff