Sun_GAN

See my honours thesis for a full description of the system.

Environments

Data processing

A conda environment used for all data processing tasks. A similar conda
environment can be constructed from requirements.txt or using the command:
conda activate ./Data_env/
conda create --prefix ./Data_env
conda config --add channels conda-forge
conda install sunpy=3.0.1 astropy=4.3.post1 numpy=1.21.1 drms=0.6.2 opencv=4.5.2 matplotlib=3.4.2 requests=2.26.0 scikit-image=0.18.2 imageio=2.9.0 pandas=1.3.1 pillow=8.3.1

Training/Testing

Training and testing of each GAN was done in a
Monarch environment created using the
following commands:

module load anaconda/5.1.0-Python3.6-gcc5
module load cudnn/7.6.5-cuda10.1
module load tensorflow/2.3.0
These can similarly be unloaded by using the commands:
module unload anaconda/5.1.0-Python3.6-gcc5
module unload cudnn/7.6.5-cuda10.1
module unload tensorflow/2.3.0

Pipeline: Data Preparation

The pipeline for downloading and preparing the data used throughout this project.

Data collection

Download fits data (SDO AIA/HMI, STEREO EUVI and phase maps):
./Scripts/Data_collection.sh or
sbatch ./Scripts/Data_collection.sh (Monarch).
The STEREO data is downloaded such that it is synchronised with the phase maps.

Data processing

The processing pipleine consists of

1. Converting SDO and STEREO fits data into local numpy arrays (.npy), and get
   percentiles of the data
2. Reproject the seismic maps (phase maps) from a Carrington Heliographic
   projection to a Helioprojective-cartesian projection, convert to numpy arrays
   and get percentiles.
3. Remove outliers in each dataset
4. change saturation for EUV and magnetogram data
5. normalise data (put data between -1 and 1 for magnetograms, and between 0 and
   1 for the other datasets)
6. Remove trends in EUV data caused by instrument degredation
7. Create a database (image.db) that maps the connections between the
   different data types

The data processing pipeline can be run as follows:
./Scripts/data_processing.sh or
sbatch ./Scripts/data_processing.sh (Monarch).

Pipeline: UV-GAN

The pipeline for generating synthetic magnetograms from EUV 304 Angstrom
full-disk solar images. Trains by comparing SDO EUV images with SDO
magnetograms. It is a good idea to initially run the GAN for a small number of
itterations (e.g. 20) to ensure everything is working as it should before
running a full scale model.

1. Train model on SDO AIA EUV images and SDO HMI magnetograms:
   ./Scripts/train_UV_GAN.sh or
   sbatch ./Scripts/train_UV_GAN.sh (Monarch). See train_UV_GAN.sh for
   additional settings such as # itterations, model name etc.
2. A plot of loss vs iteration can be generated by running
   Scripts/plot_flux_UV_GAN.sh for a specified model. The resultant plot can
   be seen in Plots/loss.png
3. Evaluate model by testing model on AIA and EUVI data
   ./Scripts/test_UV_GAN.sh or
   sbatch ./Scripts/test_UV_GAN.sh (Monarch). See test_UV_GAN.sh for
   additional settings such as # itterations, model name etc. This additionally
   applies a mask to selected outputs to aid in training the seismic GAN

Pipeline: Seismic-GAN

The pipeline for generating synthetic magnetograms from farside seismic maps.
Trains by comparing farside seismic maps to synthetic magnetograms generated
from STEREO EUV data. It is a good idea to initially run the GAN for a small
number of itterations (e.g. 20) to ensure everything is working as it should
before running a full scale model.

1. Train model on seismic maps and synthetic STEREO magnetograms:
   ./Scripts/train_seismic_GAN.sh or
   sbatch ./Scripts/train_seismic_GAN.sh (Monarch). See train_seismic_GAN.sh
   for additional settings such as # itterations, model name etc.
2. A plot of loss vs iteration can be generated by running
   Scripts/plot_flux_Seismic_GAN.sh for a specified model. The resultant plot
   can be seen in Plots/loss.png
3. Evaluate model by testing model on seismic maps
   ./Scripts/test_seismic_GAN.sh or
   sbatch ./Scripts/test_seismic_GAN.sh (Monarch). See test_seismic_GAN.sh for
   additional settings such as # itterations, model name, testing set etc.

Evaluation:

Getting the unsigned magnetic flux vs time

• The python script: Data_processing/get_unsigned_flux.py gets the unsigned
  flux for a given dataset of normalised magnetograms, and saves it as a numpy
  file in the directory Data/unsigned_flux.
• the script Scripts/get_flux_UV_GAN.sh can be used to run this file on the
  HMI dataset, and the output of the UV GAN, with options to specify the model,
  iterations etc.
• the script Scripts/get_flux_Seismic_GAN.sh can be used to run this file on
• The file Plotting/plot_flux.py plots given fluxes vs time, and can be run
  the output of the Seismic GAN, again with options to specify the model,
  iterations etc. using Scripts/plot_flux_UV_GAN.sh or
  Scripts/plot_flux_Seismic_GAN.sh to make plots corresponding to the UV GAN
  or Seismic GAN respectively. These pltos can be found in Plots/flux.

Comparing GAN outputs with true magnetograms

• You can make plots comparing the synthetic magnetograms with the true
  magnetograms, by running Scripts/compare_magnetograms.sh, and specifying the
  model, and iterations. The output will be in the folder:
  Data/[model]_on_[testing set]/ITER[iteration]_comparison

Miscellaneous Plotting:

• Plot percentiles of the different data types:
  python Plotting/plot_percentiles.py
  The plot will be created in the Plots/ directory
• View a numpy array from file (enter in path to file when prompted):
  python Plotting/view_specific_npy.py
  The plot will be created in the Plots/ directory
• Plot a magnetogram from numpy file (enter in path to file when prompted):
  python Plotting/plot_specific_magnetogram.py The plot will be created in
  the Plots/ directory
• Plot a dataset of magnetograms:
  Plotting/plot_magnetograms.py
  The plots will show up in the directory specified in the python file.