Tracking_features

Various codes that are implementation of feature tracking; Data used comes from COBOL5D and MURAM simulations

Note

Content will be added and/or updated on weakly (to daily) basis 😀

29. 1. 2024.

Added the MURAM_exp.ipynb Jupyter notebook in initial stage of development.

30. 1. 2024.

Added the Tracking_h5.ipynb Jupyter notebook with purpose of checking the validity of data.

Updating MURAM_exp.ipynb with additional testing of polarisation and vertical component of magnetic field. Correlation checked.

Updated Tau.ipynb - added code regarding convolution of velocities and a gaussian; correlation between filtered velocities checked.

01. 2. 2024.

In Tau_ipynb added the visual representation of correlation between filtered velocities.

11. 2. 2024.

Tau_ipynb - fixed the convolution by using gaussian_filter function instead of convolve.

20. 2. 2024.

COBOL_TIME.ipynb added. Basic check up done. FLCT doesn't produce expected results...

COBOL_TIME.ipynb, eventhough crude needs to be run on SUPERAST.

Important

Pearson's coefficient is very low at the moment. Advised to check alternative methods.

Added extract.py and Extract_series.py as an expansion of functionality - a light python script that will be used in conjunction with COBOL_TIME.ipynb.

23. 2. 2024.

Updated Extracted_series.py with loop through all the files and determining correlation between FLCT velocities and velocities given in simulation.

25. 2. 2024.

Extracted_series.py updated: added the gaussian_filter convolution before checking the value of Pearson's coefficient.
COBOL_TIME.ipynb updated: using the data stored in fits file (look Extracted_series.py) determined that the correlation between the velocities from simulation and velocities that FLCT calculated is low. The depth is constant and the moments in time series which were used for comparison were arbitrarily chosen.
Depth or layer at which we are "looking at" can be changed in script and we will need to find the one with best results.

27. 2. 2024.

Added Extracted_basic.py, a python script that writes T, B_z, V_x, V_y V_z to a fits file and then compares these V_x and V_y averaged between every two adjacent timestamps in our timeseries and V_x and V_y derived using FLCT on T (temperature) and B_z (z-component of magnetic field). The result are two scatter plots that compare said velocities in order to visualise the correlation or lack thereof.

07. 3. 2024.

Added Histogram.py, a python script that makes use of fits file and plots histograms of x component velocity of average velocity from simulation and velocities derived from the said simulation using FLCT on temperature and z component of magnetic field. Will be updated to do the same using y components, as well as to study statistics more closely.

15. 3. 2024.

Added Velocity_diff.py, a python script that makes uses fits file to import V_x, V_y, T and B_z values for the specific layer of Sun's photosphere in order to compare those simulation values with the FLCT-derived values for horizontal velocities and calculates the correlation between them. Also does the same type of comparison after filtering velocities using gaussian filter.

21. 3. 2024.

Added Write_to_fits.py, which writes T, V_x, V_y, V_z, B_z and bolometric magnitude into a fits file,
FLCT_calc.py which uses FLCT algorithm in conjuction with T, B_z and bolometric magnitude to calculate velocities and
Corr_calculation.py, which compares aforementioned velocities with the ones from simulation.

9. 4. 2024.

Added Muram_to_goodform.py, a script that gives two fits files as result. One contains the MuRAM data reshaped into suitable shape for synth function defined in minimal_synth_muram.py, while the other reduces the size of test atmosphere another project (due to large CPU usage) and
minimal_synth_muram.py, which is supposed to synthesise the spectrum using given z, T, V_z and P_gas contained in fits file, thus giving intensity of spectral line that should be compared to known value in order to determine how valid our code is.

17. 4. 2024.

Added Muram_1D.py as a fix for previously uploaded Muram_to_goodform.py (might be removed) which didn't account for all values of temperature and pressure correctly, thus neglecting several parts of Sun's atmosphere in physical sense.

29. 4. 2024.

Added several python scripts and a jupyter notebook in which parts of their codes are shown.

1. ISSI_2D_tracking_write_data.py This code checks how many slices are in user's directorium and takes the data in form of numpy arrays for needed physical paramters that are then written to new fits file.
2. ISSI_2D_FALC_calc.py In here the application of FLCT based on temperature can be found. The calculated velocities are then written to separate fits files for easier later usage.
3. ISSI_2D_corr_calc.py Calculating correlation between V_x, V_y from simulation and V_x, V_y that FLCT gives back.
4. Low_number_check.ipynb Jupyter notebook which contains example of how these codes are used.

14. 5. 2024.

The previously added scripts and notebook have been updated to include continuum intensity at 500nm as a new "windowing parameter".

15. 5. 2024.

Added Example.ipynb jupyter notebook that uses pyFLCT with I_continuum as windowing parameter using cadence of 30 s, and FWHM = 1200, 2400 km.

16. 5. 2024.

Added Degraded_data_QS.ipynb jupyter notebook that uses pyFLCT with degraded (Convolved with Airy disk of 1m telescope at 500 nm) I_continuum as windowing parameter for different combinations of cadences and FWHMs.
Added Degraded_data_QS_testing.ipynb jupyter notebook that is reserved for further testing of this, with Brian's input and advices. So far, it is safe to say that FWHM = 200 km doesn't really track the flows from the simulaton.

27. 5. 2024.

Added Two_frames_check.ipynb jupyter notebook that will be used to represent the influence of values assinged to cadence and FWHM on the tracking algorithm of FLCT.
Minor changes to 2D_tracking_FLCT_calc_mpi.py.

29. 5. 2024.

Added Miniexample.ipynb, jupyter notebook used to debbug discrepancy between two method of loading data - numpy.fromfile and read_slice from muram script. Both are used to open binary files, but the latter one is well-documented, while the first one is user-dependent, as in user has to manually test each array to determine which parameter is in question.

4. 6. 2024.

Updated Miniexample.ipynb to show (visualise) flow fields as derived using (py)FLCT on the whole timeseries of slices at optical delpth $\tau=0.1$, where continuum intensity at 500 nm was used as windowing parameter. Furthermore, flow field of V_x derived from FLCT is compared to flow field averaged V_x that is loaded from simulation. The results so far show that some parts are correctly tracked while others aren't correlated.

6. 6. 2024.

Added MEAN_VEL.py python script that writes V_x and V_y into fits file, as well as computes mean values and writes them in separate fits file.
Miniexample.ipynb - added function for temporal averaging of series; added comparison between FLCT V_x, V_y and filtered simulation V_x, V_y (gaussian_filter).
CONCLUSION - V_xflct has high correlation with transposed V_ysimfiltered and vice versa.

13. 6. 2024.

Minor updates to Miniexample.ipynb.

19. 6. 2024.

Added Np_fromfile_vs_read.ipynb notebook in which we deduce how to compare V_x and V_y from simulation with ones derived by FCLT. It shows what and how to transpose before comparison takes place, as well as how can variables be introduced so that x can be compared with x, y compared with y.

26. 6. 2024.

Added Meeting_pres.ipynb, notebook focused on establishing differences between velocities FLCT calculated for cadence of 30s and FWHM = {100, 300, 600, 1200}km. The said velocities have been averaged, and filter was applied to the ones that come directly from simulation in order to see if there is good correlation between pyFLCT and simulation; i.e if tracking works correctly. Furthermore, we have tried to see how size of apodizing window affects tracking while also searching for best $\sigma$ to use for gaussian_filter in order to get the maximum possible correlation.

27. 6. 2024.

Minor changes to plots in Meeting_pres.ipynb.

12. 7. 2024.

Added Synth_data_test.ipynb. It is a notebook in which we test how FLCT behaves on synthetised spectra, i.e. on different wavelenghts and how it correlates with the ones from simulation.

14. 7. 2024.

Added Synth_TAU(0.1, 1).ipynb . This is a notebook in which we tested the correlation between FLCT velocities and synthetised spectra at different $\lambda$, specifically at those close to the line centre. The goal is to find at what $\tau$ can we recover flow using spectral lines.

16. 7. 2024.

Synth_TAU(0.1, 1).ipynb - Added comparison of FLCT velocities derived from synthetised spectra and FLCT velocities derived from simulation using intensity (cont) as windowing parameter.

27. 7. 2024.

Synth_TAU(0.1, 1).ipynb - Further comparisons done. Looking into correlation between intensities used for tracking.

14. 8. 2024.

Synth_TAU(0.1, 1).ipynb - RMS contrast for synthetised spectra and convolved synthetised spectra compared. Comparison yields valid results.

21. 8. 2024.

Added Convolved.ipynb and Spektralna_linija.ipynb. First one shows various tests applied to convovled synthetised spectra, while the latter is focused on correlation between FLCT velocities derived from synthetised spectra and simulation velocities at different values of $\log{\tau}$.

13. 10. 2024.

Added Paper.ipynb notebook in which we compare how continuum intensity (I_cont), temperature (T) and T⁴ differ in behaviour when taken to be windowing parameter. After that, we compute correlation between velocities derived using said parameter and simulation velocities.

18. 10. 2024.

Added Wvls.ipynb, a notebook that will be used to compare velocities FLCT derived using continuum intensity at 500 nm and velocities FLCT derived from spectra Lightweaver synthetised using different wavelenghts (and spectral line).

18. 10. 2024.

Wvls.ipynb updated, intensity at more wavelenghts analysed and compared to continuum intensity at 500 nm from simulation.

23. 10. 2024.

Added Wvls600.ipynb, a notebook that will be used to compare velocities FLCT derived using continuum intensity at 500 nm and velocities FLCT derived from spectra Lightweaver synthetised using different wavelenghts, but using FWHM of 600 km (+ some plotting).

25. 10. 2024.

Wvls600.ipynb updated, intensity at more wavelenghts analysed and compared to continuum intensity at 500 nm from simulation. Plotted I_LW and I_cont500, both used for tracking. Preliminary results show that intensity at most of $\lambda$-s can be used equally as the one from simulation.

5. 11. 2024.

Added TimeAvg.ipynb, where we shall store plots, calculation of correlation coefficients and test how time averaging impacts the correlation.

13. 11. 2024.

Added 100_fits_test.ipynb. It features comparison of FLCT velocities that result from tracking on Lightweaver synthetised intensity at 500 nm, on MURaM simulated continuum intensity and on MURaM simulated continuum intensity when timestep between two adjacent snapshots is increased. At the moment, it seems an error has occured during tracking on synthetised spectrum.

03. 12. 2024.

Added Checkup_timeavg.ipynb. Analysis of how choice of cadence and later choice of FWHM for Gaussian with which we convolve temporaly averaged velocities impacts the correlation between velocities with cadence 10 s, and velocities with cadence {20, 30, 40, 50, 60}s for 3 cases - FWHM = {300, 600, 1200} km.

12. 12. 2024.

Added Separate.ipynb. Tracked first pair and fourth pair of LW series at 500 nm and compared them to first and fourth element of all velocities that result from tracking MURaM intensity using FWHM = 600 km and cadence = 30 s.

20. 12. 2024.

Added Lightweaver_31steps.ipynb. Comparison of MURaM simulation velocities, FLCT velocities that result from tracking Lightweaver intensity at 500nm and FLCT velocities that result from tracking MURaM intensity at 500 nm. Tracking Lightweaver intensity proves to be difficult.

28. 12. 2024.

Updated 31 steps notebook. Analysed the velocities tracked at 3 different wavelengths that correspond to Section 3.2. Added I_min_map.py and I_minimum_tracking.py. These scripts are meant to locate wavelength at which intensity reaches minimal value, take those intensity maps and write them to new files on which tracking will be possible.

05. 01. 2025.

Added FixedWavelenth.ipynb that makes use of results from previosly added python scripts for fixed wavelength tracking. Right now, only FWHM = 600 km have been obtained. FWHM = 300 km is work in progress.

11. 01. 2025.

Added Temp_and_Bz_vs_SIM.ipynb that deals with comparison of FLCT FWHM = 600 km, cadence = 10 s results from B_z and MURaM simulation velocities at $\log\tau = \{-1, -2, -3\}$. The files that result from applying FLCT on Temperature at these $\tau$ values will be added later.

12. 01. 2025.

Temp_and_Bz_vs_SIM.ipynb updated.
Comparison of FLCT FWHM = 600 km, cadence = 10 s results from Temperature and MURaM simulation velocities at $\log\tau = \{-1, -2, -3\}$ added.

14. 01. 2025.

Temp_and_Bz_vs_SIM.ipynb updated.
Comparison of FLCT FWHM = 600 km, cadence = 10 s results from Temperature and MURaM simulation velocities at $\log\tau = 0$ added, as well as comparison of FLCT B_z and MURaM simulation velocities at $\log\tau = -4$.

15. 01. 2025.

Temp_and_Bz_vs_SIM.ipynb updated.
Comparison of FLCT FWHM = 600 km, cadence = 10 s results from Temperature and Intensity at 500 nm, and MURaM velocities at $\log\tau = 0$ done. Conclusion is that intensity is better choice as tracking parameter due to artefacts that can be seen in temperature.

24. 01. 2025.

TimeAvg.ipynb notebook updated with results for tracking B_z at $\log\tau = 0$ for dt = 10 s.

31. 01. 2025.

Added Planck_vs_Bz.ipynb that deals with comparison of FLCT FWHM = 600 km, cadence = 30 s results from B_z and MURaM simulation velocities at $\log\tau = \{-1, -2, -3\}$. Comparison of FLCT FWHM = 600 km, cadence = 30 s results from Planck's function and MURaM simulation velocities at $\log\tau = \{-1, -2, -3\}$ used instead of ones that result from tracking Temperature because B_$\lambda$ more closely resembles "Radiation Intensity" - what we would get by tracking intensity.

18. 02. 2025.

Comparison of FLCT FWHM = {300, 600}km, cadence = 30 s results from B_z and Temperature vs. MURaM simulation velocities at $\log\tau = \{-1, -2, -3. -4\}$. We conclude that B_z is much better choice than temperature, because B_z largely changes due to an advection process, while $T$ experinces strong contributions due to radiative transport.

27. 02. 2025.

Uploaded Synth_snapi.ipynb in which testing and visualization of synthesized data (spectral lines) will be done.

28. 02. 2025.

Synth_snapi updated with comparison of ME inversion B_z-s for Fe I 525.0 nm and Mg I b2 517.2 nm with B_z-s at $\log\tau = \{0, -1, -2, -3\}$.

06. 03. 2025.

Uploaded FLCT_Thresh.ipynb. Here we test the effect threshold has on resulting horizontal velocities in FLCT when B_z is tracking parameter. Two chosen values are 50 Gauss and 100 Gauss and correlation with MURaM V_x and V_y is given for both. Analysis suggests that inculding threshold (excluding pixels below threshold values in FLCT calculation) actually descreases correlation with original velocities.

11. 03. 2025.

Uploaded ME_Bz_track.py. This is a short script for tracking Bz inferred using ME inversion of Fe I and Mg I b2 spectral lines.

12. 03. 2025.

Uploaded MilneEddington_Bz_tracking.ipynb. Notebook in which we visualize tracking results (from Bz inferred using ME inversion of Fe I and Mg I b2 spectral lines).

19. 03. 2025.

Uploaded WFA_MgIb2.ipynb. Notebook in which we visualize tracking results from Bz inferred in weak-field approximation applied to Mg I b2 spectral line.

27. 03. 2025.

Various updates with goal of improving visual representation of results. Trying new statistic tests.

02. 04. 2025.

Uploaded Final_plot_table.ipynb. Notebook in which we visualize tracking results from Bz inferred in weak-field approximation applied to Mg I b2 spectral line and Bz inferred using ME inversion of Fe I, all at one place.

06. 04. 2025.

A few updates regarding curl calculation in python. Also added .png-s.

11. 04. 2025.

A lot of minor visual changes to plots, labels and their sizes in some notebooks for clarity.

16. 04. 2025.

Uploaded Appendix.ipynb, where all work related to LOS velocity will be stored.

26. 05. 2025.

Final_plot_table notebook updated:

• Added functions that determine divergence and vorticity of flows
• Calculated divergence and vorticity from tracked velocities and compared to simulations
• Plotted those fields
• Determined the power of vorticity and power of divergence - their difference is negative; what this implies remains to be determined

19. 06. 2025.

Uploaded Power_curl.ipynb, where sum(|div($v$)|²)/area and sum(|curl($v$)|²)/area are calculated. Correlation between div. of ground-truth flows (MURaM velocities) and div. of FLCT-inferred is significantly better if FLCT velocity field is smoothed before computing its divergence.

30. 06. 2025.

Uploaded Video.ipynb, where we use time-series of MURaM velocities and ME (or WFA) inversion $B_z$ from which FLCT infers velocities to create a short video (time-lapse).

01. 07. 2025. - 18. 10. 2025.

Various calculations and plotting. Subscript 500 added for all instances of $\tau$. Suggestions for clarity implemented. Divergence and curl of FLCT velocities need to be additionally smoothed before direct comparison.