Mouse Cage Imaging

This is a mouse imaging system designed to take timelapse photos every 10 minutes, even overnight in complete darkness. It uses 3D parts to mount a Raspberry Pi, and an Infrared Camera to a mouse cage.

Parts:

• Element14 Raspberry Pi 3 B+ Motherboard
• 16 GB Noons Micro SD Card
• Smraza Camera Module for Raspberry Pi 3 with 5MP 1080p OV5647 Video Webcam Supports Night Vision Compatible with Raspberry Pi 3b 2 Model B B+
• DS3231 Real Time Clock Module 3.3V/5V with battery For Raspberry Pi and Arduino
• Adafruit Case Lid
• Adafruit Base Case
• Adafruit 5V 2.5A PS

Real Time Clock Setup

 echo "dtoverlay=i2c-rtc,ds3231" >>/boot/config.txt

edit the /lib/udev/hwclock-set file (sudo nano /lib/udev/hwclock-set) and "comment out" the following lines"

 if [ -e /run/systemd/system ] ; then
 exit 0
 fi

so they become:

 #if [ -e /run/systemd/system ] ; then
 # exit 0
 #fi

Update the HW Clock from system time, assuming the Raspberry PI had is network connected.

 sudo ntpdate time.umassmed.edu
 sudo hwclock -w 

reboot and then run:

 sudo hwclock -r

Not sure if anything below is needed

 sudo apt-get purge fake-hwclock
 sudo systemctl start hwclock
 sudo systemctl enable hwclock
 sudo vi /lib/udev/hwclock-set
 sudo update-rc.d hwclock.sh enable

Infrared Camera Setup

Enable Camera

 sudo raspi-config

Timelapse Scripts

 cd; mkdir timelapse;mkdir bin
 
 sudo apt-get install pmount

Create a /home/pi/bin/camera.sh and add the following text

 DATE=$(date +"%Y-%m-%d_%H%M")
 
 raspistill --annotate 12 -w 1296 -h 972 -hf -vf -o /home/pi/timelapse/$DATE.jpg
 /bin/bash /home/pi/bin/sync_files.bash

Create a /home/pi/bin/sync_file.bash and add the following text

 #!/bin/bash
 
 if [ -d /home/pi/timelapse ]
 then
       if [ ! -d /media/mouse ]
       then
               pmount /dev/sda1 /media/mouse
       fi
 
       if [ ! -d /media/mouse ]
       then
               pmount /dev/sdb1 /media/mouse
       fi
 
       if [ ! -d /media/mouse ]
       then
               pmount /dev/sdc1 /media/mouse
       fi
 
       if [ ! -d /media/mouse ]
       then
               pmount /dev/sdd1 /media/mouse
       fi
 
       if [ -d /media/mouse ]
       then
               if [ ! -d /media/mouse/timelapse ]
               then
                       mkdir /media/mouse/timelapse
               fi
 
               if [ -d /media/mouse/timelapse ]
               then
                       rsync -aq /home/pi/timelapse/*.jpg /media/mouse/timelapse/
               fi
       fi
 
       if [ -d /media/mouse ]
       then
               pumount /media/mouse
       fi
 fi

Edit a crontab for user PI and add the following text:

 # m h  dom mon dow   command
 0,10,20,30,40,50 * * * * sh /home/pi/bin/camera.sh 2>&1
 0 17 * * 5 rm -rf /home/pi/timelapse/*.jpg 2>&1

Edit usbstick.rules

 sudo vi /etc/udev/rules.d/usbstick.rules

Add the following line:

 ACTION=="add", KERNEL=="sd[a-z][0-9]", TAG+="systemd", ENV{SYSTEMD_WANTS}="usbstick-handler@%k"

Edit usbstick-handler@.service

 sudo vi /lib/systemd/system/usbstick-handler@.service

Add the following lines:

 [Unit]
 Description=Mount USB sticks
 BindsTo=dev-%i.device
 After=dev-%i.device
 
 [Service]
 Type=oneshot
 RemainAfterExit=yes
 ExecStart=/usr/local/bin/cpmount /dev/%I
 ExecStop=/usr/bin/pumount /dev/%I

Edit /usr/local/bin/cpmount and the following lines:

 #!/bin/bash
 /usr/bin/pmount --umask 000 --noatime -w --sync $1 mouse

 if mountpoint -q /media/mouse  
 then

if [ ! -d /media/mouse/timelapse ] then

			mkdir /media/mouse/timelapse

fi

fi