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 hwclock -w 

reboot and then run:

 sudo hwclock -r

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