Page Comparison

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1. Adding steps about the tools and installing those tools ( rawtherapee, mobaxterm)

2. Steps in rawtherapee

3. Command line instructions

4. Pics or screenshots will be very helpful

   1. Provide video overview

5. Requirements

   1. How to get requirements

6. Additional requirements and instructions

   1. Azure

   2. SUNNY

   3. NFS Locker Access

Backlog Spreadsheet:

1. Download Batch

When downloading a Semifield batch, we need to copy it over to the local user from the NFS Lockers.

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We must know the number of images in the original batch. This can be checked using this command line:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-upload/<batch>/*.ARW | wc -l

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To exit the screen, use CTRL+A D

3.1 Checking the success of the pipeline

If there is an indication the pipeline is finished running, we want to crosscheck the number of images within the original batch with the number of jpgs and pp3s created.

We can use both of these lines respectively:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-developed-images/<batch>/images/*.jpg | wc -l

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-developed-images/<batch>/images/*.pp3 | wc -l

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If the number of jps and pp3s are not equivalent to the original number of images, try running the pipeline again within the screen. Double check the name of the batch that was typed in, this is where errors are likely to happen. Also, be sure to be navigated to the Semifield folder. If we are within the Field folder, the pipeline will not be successful.

Backlog Spreadsheet:

Common & Useful Commands

Available batches:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-upload/ -lh

# of images in batch:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-upload/<batch>/*.ARW | wc -l

# of jpgs processed:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-developed-images/<batch>/images/*.jpg | wc -l

# of pp3 files created:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-developed-images/<batch>/images/*.pp3 | wc -l

Blob Analyzer

4. Blob Analyzer

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4.1 Installing conda (miniconda) 

Use these commands below from the command line in the SUNNY server:

mkdir -p ~/miniconda3

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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh

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bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

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rm  ~/miniconda3/miniconda.sh

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~/miniconda3/bin/conda init bash

Close the remote connection, then

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SSH back in

4.2 Setting up a conda environment

Still in the command line inside of SUNNY:

conda create -n <your env name> python=3.10

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conda activate <your env name>

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cd /home/psa_images/analyze_blobs

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pip install -r requirements.txt

4.3 Running the code 

Your conda environment must be activated to run the code.

Run these in the command line.:

conda activate <your env name>

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cd /home/psa_images/analyze_blobs

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python ANALYZE_BLOB.py

1. Creates 2 time stamped files in the “results” folder in the main project directory. 

   1. A text files that provides a general summary of missing batches

   2. A csv file that can be viewed in excel or google docs

5. Common & Useful Commands

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Available batches:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-upload/ -lh

# of images in batch:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-upload/<batch>/*.ARW | wc -l

# of jpgs processed:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-developed-images/<batch>/images/*.jpg | wc -l

# of pp3 files created:

ls /mnt/research-projects/s/screberg/longterm_images2/semifield-developed-images/<batch>/images/*.pp3 | wc -l