added lots of files relating to data and figures from the paper about…

… AniMAIRE that will be published, so that the data will be storage for future potential usage by others who read the paper. Also modified things so that these files can be used as examples to anyone wanting to do replication of the work.
ssc-maire · Apr 22, 2024 · 4b3d7ee · 4b3d7ee
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diff --git a/.gitattributes b/.gitattributes
diff --git a/README.md b/README.md
@@ -92,6 +92,8 @@ from AniMAIRE import AniMAIRE
 ```
 All of the main useful functions are contained within this `AniMAIRE` module, and all other modules contained in this toolkit are primarily intended to be accessed internally (although don't let that stop you from using or editing them for your own purposes if you wish).
 
+The rest of the README file describes how to run AniMAIRE to produce dose rates for different input parameters. You can also look at and run the examples present in the `AniMAIRE_examples.ipynb` notebook, and the advanced examples in the `notebooks_and_data_and_figures_for_paper/GLE71_plots_for_paper.ipynb` notebook to learn and see in practice how AniMAIRE can be used.
+
 ## Testing that AniMAIRE is working
 
 To test that AniMAIRE works, you can run:

diff --git a/notebooks_and_data_and_figures_for_paper/CommonsavedPAD.pkl b/notebooks_and_data_and_figures_for_paper/CommonsavedPAD.pkl
diff --git a/notebooks_and_data_and_figures_for_paper/CommonsavedSpectrum.pkl b/notebooks_and_data_and_figures_for_paper/CommonsavedSpectrum.pkl
diff --git a/notebooks_and_data_and_figures_for_paper/DLRsavedSpectrum.pkl b/notebooks_and_data_and_figures_for_paper/DLRsavedSpectrum.pkl
diff --git a/notebooks_and_data_and_figures_for_paper/GLE71_plots_for_paper.ipynb b/notebooks_and_data_and_figures_for_paper/GLE71_plots_for_paper.ipynb
diff --git a/notebooks_and_data_and_figures_for_paper/MishevGLE71fittingPaper.html b/notebooks_and_data_and_figures_for_paper/MishevGLE71fittingPaper.html
diff --git a/notebooks_and_data_and_figures_for_paper/README.md b/notebooks_and_data_and_figures_for_paper/README.md
@@ -0,0 +1,13 @@
+## Data for paper, and advanced examples
+
+This directory and the subdirectories contain the notebook and Python scripts that were used to generate all the plots for the scientific paper supporting AniMAIRE.
+
+The full dose rate data across the entirety of GLE71 (the GLE which AniMAIRE was run across in the paper) can be found in `full_event_maps/` as both csv and pkl files (the pkl files are pickle-d Pandas DataFrames). The dose rate map file names referring the just the GLE are the dose rates correspond to anisotropic maps (using parameters determined by [Mishev et al. (2021)](https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020SW002626)), the label `flat` refers to isotropic maps, and the label `total` refers to dose rates added to the cosmic ray-only dose rates.
+
+The images for each figure in the paper and the specific data that were used to generate those figures are placed in the `figure_` subdirectories as both csv and pkl files. 
+
+The `GLE71_plots_for_paper.ipynb` notebook was used to generate all of these data and figures, and if you wish to learn how to generate these figures/data yourself using AniMAIRE you could look through and run this notebook yourself. Note that the Python scripts in this directory contain lots of important functions that get imported by the notebook for various purposes, and some of the directories contained here contain data that is necessary for running these functions. (For instance, `investigationData` contains neutron monitor data from [gle.oulu.fi](https://gle.oulu.fi) that is used in some legacy functions).
+
+Note that if you wish to run the entire notebook from scratch it will likely take several hours to run and reproduce all the plots and data here (AniMAIRE takes about 40 minutes per full world dose rate map on my computer - a Dell XPS 15 laptop with 6 processors). If you want to speed this up, AniMAIRE and the Python scripts I've placed in this directory save all of their results to several cache directories in the directory where it is run. I've left several cache directories I've previously generated in the `cache_directories.zip` file, if you unzip this file and place these cache directories into the same directory as the notebook and Python files here they should speed up calculations by at least a factor of 2. Also on subsequent runs after running the notebook once you should find the notebook will now execute in minutes rather than hours as the notebook will have generated the rest of the cache directories. 
+
+The notebook was also used to generate many additional plots that weren't used in the final paper, these are saved to the `other_images` directory in case they are useful to others (note that many of these have not been tidied up, and may be messy, hard to read and understand).
diff --git a/notebooks_and_data_and_figures_for_paper/WASAVIES_GLE71_digitised_datasets.csv b/notebooks_and_data_and_figures_for_paper/WASAVIES_GLE71_digitised_datasets.csv
@@ -0,0 +1,21 @@
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diff --git a/...d_data_and_figures_for_paper/animations/39kft_heatmap_animation_anisotropic.gif b/...d_data_and_figures_for_paper/animations/39kft_heatmap_animation_anisotropic.gif
diff --git a/...and_data_and_figures_for_paper/animations/39kft_heatmap_animation_isotropic.gif b/...and_data_and_figures_for_paper/animations/39kft_heatmap_animation_isotropic.gif
diff --git a/...igures_for_paper/animations/39kft_heatmap_animation_no_contours_anisotropic.gif b/...igures_for_paper/animations/39kft_heatmap_animation_no_contours_anisotropic.gif
diff --git a/..._figures_for_paper/animations/39kft_heatmap_animation_no_contours_isotropic.gif b/..._figures_for_paper/animations/39kft_heatmap_animation_no_contours_isotropic.gif
diff --git a/...paper/animations/39kft_heatmap_animation_no_contours_total_dose_anisotropic.gif b/...paper/animations/39kft_heatmap_animation_no_contours_total_dose_anisotropic.gif
diff --git a/...r_paper/animations/39kft_heatmap_animation_no_contours_total_dose_isotropic.gif b/...r_paper/animations/39kft_heatmap_animation_no_contours_total_dose_isotropic.gif
diff --git a/...figures_for_paper/animations/39kft_heatmap_animation_total_dose_anisotropic.gif b/...figures_for_paper/animations/39kft_heatmap_animation_total_dose_anisotropic.gif
diff --git a/...d_figures_for_paper/animations/39kft_heatmap_animation_total_dose_isotropic.gif b/...d_figures_for_paper/animations/39kft_heatmap_animation_total_dose_isotropic.gif
diff --git a/notebooks_and_data_and_figures_for_paper/cache_directories.zip b/notebooks_and_data_and_figures_for_paper/cache_directories.zip
diff --git a/notebooks_and_data_and_figures_for_paper/df_with_weighting_factors_full_angles.pkl b/notebooks_and_data_and_figures_for_paper/df_with_weighting_factors_full_angles.pkl
diff --git a/notebooks_and_data_and_figures_for_paper/figure_2/GLE_spectra_comparison.png b/notebooks_and_data_and_figures_for_paper/figure_2/GLE_spectra_comparison.png