Installing OS for OSELOTS on New Laptop

First, you need to get the system running scientific linux (done on an Acer laptop, preinstalled with Windows 10):

(Note) - Any Red Hat Enterprise Linux (RHEL) OS appears to do the job.  
(Note) - I try to document all steps taken, but I am not certain that all were necessary (there were some false steps taken in figuring out this process) 

1. Insert USB formatted for Scientific Linux. The one used in this example and that the lab should have looks like this:
   
2. Boot into Windows. 
3. You need to repartition the computer.  Here's how: 
   1. Search 'DISKMGMT.MSC' in the Windows search bar
   2. Right click on the C: partition 
   3. Select amount you'd like to shrink partition by (I recommend giving most of the partition space to Scientific Linux, as we'll be saving lots of data there) 
4. You now need to boot from the USB
   1. Restart Windows while holding the SHIFT key
   2. Select 'Use a Device' 
   3. Select Linux 
   4. This will boot from the USB 
   5. IF YOU CANNOT BOOT FROM USB, you may need to disable Secure Boot (not sure if this is necessary, but I know it was done) 
      1. Enter BIOS by holding F2 on restart 
      2. Move to Boot tab, and set Secure Boot to DISABLED
         1. If you can't, try setting a supervisor password first under the Security tab (see 10 below) 
5. Select 'Test this Media and Install Scientific Linux' option 
6. Select the storage space 
   1. Select the drive that is not the USB stick 
   2. Recommend having partition done automatically (it will claim all of the space that you made available) 
7. BUG NOTE: My mouse clicks would sometime become unresponsive in the Linux boot option.  Restarting the process from Step 4 fixed the issue (annoying, I know) 
8. Once you've selected your storage space, the installation process will start
   1. This took ~120 minutes for me 
9. Once installation is completed, restart machine and enter BIOS
   1. Hold F2 on startup 
10. Do the following (this website was helpful: https://community.acer.com/en/discussion/543729/efi-dual-boot-not-seeing-linux-on-nitro-5-an515-51-78c6): 
    1. ENABLE secure boot (under Boot tab) 
    2. Set a supervisor password (under Security tab) 
    3. Hit ENTER on 'Select an UEFI file as trusted for executing' 
       1. Select HDD0
       2. Select <redhat> (Scientific Linux is based on redhat linux) 
       3. Select grub64.efi
       4. Give the boot a description 
          1. I chose ScientificLinux 
    4. Hit F10 (save and exit) 
    5. Boot into Windows (one more time) 
    6. Restart and enter BIOS (hold F2 on boot up) 
    7. Under Boot tab, move ScientificLinux (or whatever you named the installation) to the top of the boot order list 
11. That should do it! 
    1. If Step 10 (and all sub steps did not work), it's possible you need to do this too, from Windows (I did this, but am not sure it was necessary) 
    2. As admin, open the command prompt
    3. Type what follows the '>' in the command line: > bcdedit /set displaybootmenu yes 

Next, you need to install the PICAM control software:

1. Download the most up to date PICAM software from Princeton Instruments website, or you can download this version: 
   
2. Before running, you'll need to install some basic development tools: 
   1. $ sudo yum groupinstall 'Development Tools' 
   2. $ sudo yum install gtk+-devel gtkz-devel 
3. Change PICam run file permissions and unzip it: 

   1. From the command line: 

   2. $ chmod +x PICam_SDK-v5.10.3.run_.zip 

   3. unzip file.zip 


4. As super user, run the script: 
   1. $ su ./PICam_SDK-v5.10.3.run 

5. This makes a directory in which the PICam software must be made: 
   1. In /opt/PrincetonInstruments/picam/samples/projects/gcc/, do the following as super user: 
   2. $ su
   3. # make -f all.mk 
6. Now move a modified version of the basic configure script into the following directory: 
   1. $ mv sasha_configure /opt/PrincetonInstruments/picam/samples/projects/gcc/objlin/x86_64/debug/ 
   2. sasha_configure can be downloaded here
      
   3. Note it's not human readable.  Just move it to where you're supposed to. 
7. Also move the original .cpp file for that script into this directory (not necessary, but important for reference):
   1. mv sasha_configure.cpp /opt/PrincetonInstruments/picam/samples/source code/platform independent 
   2. sasha_configure.cpp can be downloaded here
      
8. Now we need to change the permissions of the whole Princeton Instruments directory.  
   1. $ cd /opt
   2. $ sudo chmod a=rwx -R PrincetonInstruments 
9. You should now be ready to run the PIXIS control scripts(including some Python libraries): 
   1. Download the doPixisImaging.bash script (below)
      
   2. Download and unzip the tarred directory of Python files:

   3. Put the path where you downloaded untarred the python files in path
      1. Put path ~/.bash_profile file
   4. Move it whichever directory you'd like to run from 
   5. Enter as super user: 

   6. $ su 
   7. Run the following script to take a single bias image 
   8. # bash doPixisImaging.bash -e 0 -n 1 -X Bias -X Bias -d 2021_12_10 -t 2021:12:11:09:00