Preprocessing

1. Setting up a new user

1. Download MobaXTerm (MXT) - https://mobaxterm.mobatek.net/download-home-edition.html (Portable Edition)

2. Download RawTherapee within MXT (?can’t remember how to do this)

3. Download Cisco Secure Client

   1. Windows 10 & 11

   2. MacOS 11 and higher

   3. Linux

4. NCSU email & Globus Account

   1. Set up automatically during university onboarding

5. Obtain access to:

• SUNNY/Read, Write Privileges

  • Via @Matthew Kutugata

• NCSU Storage Lockers

  • Via @Mikah Pinegar or @Chris Reberg-Horton

• Azure Storage Explorer

  • Via @Matthew Kutugata or @Mikah Pinegar

• Divided backlog Google Sheets

  • Via @Matthew Kutugata or @Courtney Belcher

2. Establishing VPN:

Open

Connecting Cisco Secure Client

1. Download and Launch Cisco Secure Client.

2. Choose the NCSU VPN - “vpn.ncsu.edu”.

3. Click “Connect”.

4. Enter Username, Password, and “push”, “sms”, or “passcode” to authenticate via Duo.

5. Log into the SUNNY server via MobaXTerm.

3. MobaXTerm (MXT):

Open

Log into MXT

3.1 Log into MXT

1. Open program, choose Light/Dark mode.

2. Click “Start local terminal”.

3. Log into user.

   ssh <user>@SUNNY.ece.ncsu.edu

4. Enter password if prompted.

   1. Password is not displayed while entering. If incorrect, you will be repromoted to enter password.

3.2 Navigate MXT

Choose to go to either the Semifield or Field folder using the respective command:

From here, a user can:

1. Download Field batches

2. Copy Semifield batches

3. Open new screens

4. Launch RawTherapee to create color profiles

5. Send batches into their respective pipelines

6. Check available batches

7. Check/Crosscheck # of images, jpgs, arws, pp3s, etc.

4. Know the differences: Semifield vs Field

It can be easy to get mixed up when working on Semifield and Field batches. Mix-ups will lead to errors and frustrations, so it is important to stay organized, work slowly, and sit down knowing what to focus on in this preprocessing session. This takes time and practice.

4.1 The Semifield

An area of partially controlled plant growth, yielding higher individual plant image count using the BenchBot. Contains white markers with black QR Codes and a black background. Comprised of black pots, potting soil, target species and non-target species.

Semifield batches are usually larger than Field batches.

4.2 The Field

Naturally growing plants found and identified by tech teams. Individuals are documented using a monopod setup. Background includes gray mat setup with images boundaries sometimes consisting of other, non-target plants. Field batches are usually smaller than Semifield batches.

5. Backlog Spreadsheet

Backlog Spreadsheet:

• Filling out each column respectively is important

• Hiding Developed batches' rows helps keep organized

• Color coded format also helps keep organized

  • Downloaded - Field batch has been brought over to local user

  • Downloading - field batch is in the process of being brought to local user

  • Copied - Semifield batch has been brought over to local user

  • Copying - Semifield batch is in the process of being brought to local user

  • Profiled - Batch has been opened within RawTherapee and settings have been toggled appropriately

  • Processing - Batch has been sent into it’s respective pipeline

  • Redo - Must redownload/copy batch again, adjust profile again, then send back into pipeline

  • Revisit - Something seems to have gone wrong in the pipeline. Errors have been given. Must investigate. Image count does not match up, no storage remains, etc.

  • Developed - Batch has been sent through pipeline successfully. Image count matches.