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https://github.com/matham/nsniff

Records odor sense data.
https://github.com/matham/nsniff

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Records odor sense data.

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README 

          
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



.. image:: https://img.shields.io/pypi/pyversions/nsniff.svg

    :target: https://pypi.python.org/pypi/nsniff/

    :alt: Supported Python versions



.. image:: https://img.shields.io/pypi/v/nsniff.svg

    :target: https://pypi.python.org/pypi/nsniff/

    :alt: Latest Version on PyPI



.. image:: https://coveralls.io/repos/github/matham/nsniff/badge.svg?branch=main

    :target: https://coveralls.io/github/matham/nsniff?branch=main

    :alt: Coverage status



.. image:: https://github.com/matham/nsniff/workflows/Python%20application/badge.svg

    :target: https://github.com/matham/nsniff/actions

    :alt: Github action status



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:



1. Use the recommended RPI Imager and in its settings before writing the image to the SD card provide

   the WiFi etc.

2. 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