https://github.com/douglase/reduce50coron

https://github.com/douglase/reduce50coron

Last synced: 2 months ago
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• Host: GitHub
• URL: https://github.com/douglase/reduce50coron
• Owner: douglase
• Created: 2022-05-21T19:36:21.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-06-19T17:07:19.000Z (7 months ago)
• Last Synced: 2024-10-13T09:48:53.447Z (3 months ago)
• Language: Jupyter Notebook
• Size: 16.3 MB
• Stars: 0
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# STIS EPS ERI REDUCTION PIPELINE

## Instructions for Docker (recommended for running on personal computer):

This will work on Linux and MacOS natively, and on Windows with WSL (https://learn.microsoft.com/en-us/windows/wsl/install) 

Prerequisites:

1. Docker 

2. Git

3. 

For a list of all STIS coronagraphic images: https://www.stsci.edu/~STIS/monitors/tdf/stis_tdf_coronagraphic.html

To run:

1. Download into local directory using git: 

`git clone https://github.com/saikrishanthpm/reduce50coron.git`

2. Navigate into downloaded directory: 

`cd reduce50coron`

3. Build dockerfile into image:

`docker build -t pipeline .`

4. Run docker container from image:

`docker run -p 8888:8888 -v /path/to/reduce50coron/:/home/jovyan pipeline`

5. You should have a link that is generated after the previous command. Copy and paste it into a web brwoser. 

6. Once Jupyter Lab is open, open a terminal window inside the container

7. In the terminal, type:

`bash data_download_scripts/del_eri_ref.sh` followed by

`bash data_download_scripts/eps_eri_trg.sh`

8. The directories `del_eri_ref` and `eps_eri_trg` contain all 50CORON files for Delta Eridani and Epsilon Eridani. This is a good starting point to test that the pipeline is working and producing reasonable results. 

9. After this you can run the Jupyter Notebook called Pipeline.ipynb

## Instructions for Singularity (recommended for running on HPC):

1. Start an interactive desktop session on your HPC and start a terminal window. This is to ensure that the Jupyter Notebook runs properly. 

2. Download into local directory using git: 

`git clone https://github.com/saikrishanthpm/reduce50coron.git`

3. Navigate into downloaded directory: 

`cd reduce50coron`

4. Edit the last line of the def file to reflect the path to reduce50coron. 

5. Build Singularity image from definition file:

`singularity build stispipeline.sif stispipeline.def`

6. Run singularity container as shell from image:

`singularity shell stispipeline.sif`

7. Execute `bash data_download_scripts/eps_eri_trg.sh` and `bash data_download_scripts/wedgea1_0.sh`. This will download all of WEDGE A1.0 and Epsilon Eridani files. Alternately, instead of downloading WEDGE A1.0, one can also only download Delta Eridani reference files for troubleshooting using `bash data_download_scripts/del_eri_ref.sh`.

8. To reproduce the figure in the paper, change the reference directory to `wedgea1_0` in the pipeline jupyter notebbok, use 90 components, and set maxiters to 1E4. For troubleshooting, if Delta Eridani files have been downloaded, continue with the default values set.