Plotting data and scripts for "The Altitudinal Profile of the Equatorial Ionization Anomaly Response to the intense X9.3 Solar Flare on 6 September 2017"

# Figure Reproduction Package This folder contains the simplified and desensitized plotting package for the 6 September 2017 X9.3 solar flare study, without requiring access to the full original TIEGCM, Swarm, GOES, or intermediate diagnostic files. ## Purpose To make the figure generation procedure clear and accessible to readers, the original complex scripts were separated into two stages: 1. The full physical calculation workflow exports only the core plotting variables into `Fig1_Data.mat` to `Fig7_Data.mat`. 2. The simplified scripts in this folder read those exported `.mat` files and reproduce Figures 1-7 directly. This keeps the physical results unchanged while removing dependence on large raw model files, satellite CDF files, NetCDF products, and local intermediate variables. ## Files | File | Role | | --- | --- | | `Fig1_Data.mat` - `Fig7_Data.mat` | Desensitized exported plotting data for Figures 1-7. | | `figure1.m` - `figure7.m` | Minimal MATLAB plotting scripts. Each script generates one figure. | | `figutil.m` | Shared helper for loading exported data, compatible field lookup, matrix orientation, and the common diverging colormap. | | `run_all_figures.m` | One-command entry point to regenerate all figures. | | `Figure1.png` - `Figure7.png` | Output images generated by the simplified scripts. | ## How To Run Open MATLAB, set the current folder to this directory, and run: ```matlab run_all_figures ``` This regenerates: ```text Figure1.png Figure2.png Figure3.png Figure4.png Figure5.png Figure6.png Figure7.png ``` Each figure can also be generated independently, for example: ```matlab figure5 ``` All scripts save figures using the same format: ```matlab print(fig, 'FigureX', '-dpng', '-r600'); ``` ## Figure Mapping | Figure | Scientific Content | Description | | --- | --- | --- | | Figure 1 | IMF, Dst, GOES soft and hard X-ray fluxes | Clarifies the geomagnetic quiet condition and separates soft/hard X-ray flare signatures. | | Figure 2 | Swarm A/B/C Ne observations versus TIEGCM simulations | Documents model-observation consistency using the exported comparison data. | | Figure 3 | Global altitude-dependent Ne perturbations at 300, 400, and 500 km | Supports the discussion of spatial and vertical EIA response. | | Figure 4 | Altitude-MLat Ne perturbation profile at GLon = 0 deg | Highlights bottomside enhancement and topside depletion. | | Figure 5 | O+ continuity-term diagnostics | Provides mechanism separation for photochemical production, ambipolar diffusion, winds, and E x B transport. | | Figure 6 | Wind-driven vertical drift components | Shows zonal and meridional wind contributions. Panel (a) uses a ±10 m/s scale; panels (b) and (c) use ±40 m/s to reflect the dominant meridional wind forcing. | | Figure 7 | Perturbed vertical E x B drift and horizontal drift vectors | Shows the perturbed vertical E×B drift and horizontal drift vectors, distinguishing downward drift from horizontal arrow directions. | ## Data Desensitization The plotting package is physically desensitized: the scripts do not read the original TIEGCM NetCDF outputs, GOES NetCDF files, Swarm CDF files, magnetic-coordinate files, or diagnostic intermediate structures. Instead, each `.mat` file stores the final arrays needed for plotting. This makes the reproduction step lightweight while preserving the visual appearance and quantitative values of the original figures. The exported data include, for example: - Figure 1: IMF parameters and GOES soft/hard X-ray fluxes. - Figure 2: Swarm/TIEGCM sampled Ne tracks and correlation coefficients. - Figure 3: longitude, latitude, magnetic latitude, SZA or equivalent solar-terminator information, and altitude-layer Ne perturbations. - Figure 4: latitude-altitude slices of absolute and relative Ne perturbations. - Figure 5: four O+ diagnostic-term matrices and the latitude/height axes. - Figure 6: wind-driven vertical drift profiles. - Figure 7: gridded vertical E x B drift and horizontal drift vectors. ## Notes For Readers - The simplified scripts are intended for figure reproduction and inspection, not for rerunning the full TIEGCM simulation. - The full physical workflow remains the source of the exported `.mat` data; this package provides the reader-facing plotting layer for figure reproduction. - The visual settings, including panel positions, font sizes, color limits, contour lines, vector overlays, and 600 dpi PNG export, were kept consistent with the manuscript figures. - Figure 1 uses explicit logarithmic tick labels for the X-ray panels to avoid MATLAB automatic exponent formatting issues. - Key quantitative values reported in the manuscript (peak ΔNe, relative enhancement percentages, wind drift magnitudes, and thermospheric stability statistics) are reproducible directly from the exported .mat files using the diagnostic print statements included in each figure script.