Cecilia Martinez Rodriguez - Summer 2023 Research Journal

Week 1

Tuesday, May 30, 2023

Attended a logistics meeting to set up a schedule for the summer and began reading papers.

Wednesday, May 31, 2023

Visited Nevis labs, continued reading, accessed tehanu on my laptop and finished my RCR CITI training.

Thursday, June 1, 2023

Stayed on campus due to logistical issues with moving in. Focused my day on readings.

Friday, June 2, 2023

Attended Veritas group meeting and began introduction to Vegas on tehanu. Read.

Week 2

Monday, June 5, 2023

Read, continued Vegas tutorial (still waiting on response from UCLA in order to run Crab).

Tuesday, June 6, 2023

Edited the necessary Vegas parameters to prepare to run the Crab analysis as soon as I received access, continued reading and preparing some slides for Wednesday meeting.

Wednesday, June 7, 2023

Successfully finished running a Crab analysis through Vegas, read, and presented a small introduction to my project at Veritas weekly meeting.


Thursday, June 8, 2023

Began workiing with my Vegas analysis of B2 1811+31, where I practiced applying my own time cuts and attended the B2 1811+31 bi-weekly meeting.

Friday, June 9, 2023

Ran stages 1-5 of B2 1811+31. In the meantime, read and reviewed some papers. Attended dark matter talk and toured the Xenox lab.

Week 3

Monday, June 12, 2023

Ran stage 6 of B2 1811+31 following the information on Pablo's parameters on the Veritas Wiki (which have since been updated). Reviewed a presentation on Active Galactic Nuclei (M. Errando) to try to unnderstand BL Lacs better.

Tuesday, June 13, 2023

Waiting on response from Pablo about hiis configurationn list. Continued reading, prepared my slides for tomorrow's presentations. Joined GeV -TeV call and attended the REU talk/tour.

Wednesday, June 14, 2023

Finished up today's slides (which had me reading... again) and presented. Checked Pablo's config.ini and asked for his .cfg file.


Thurday, June 15, 2023

Compared Pablo's .cfg file and mine and found several important differences. Updated my file and reran stage 6. Editted the Veritas wiki with Pablo's parameters. Began adding my own summary, included plots, sections form my log file and my .cfg.


Friday, June 16, 2023

Added a few more things to the B2 1811+31 GammaWiki, including my .fits (compressed as .tar), my time cuts, and Pablo's .cfg file. Also started taking a look at the documentation for gammapy to be able to compare Pablo and I's spectra. Attended Neutron Star REU talk.

Week 4

Tuesday, June 20, 2023

Downloaded Gammapy (used pip, which led me to have to delete it and start over. I'm now, as i write this on Thurday, still in the trenches of conda forge... need to work on patience maybe). Started trying to follow gammapy tutorials to create Fit Spectral Models but I started receiving errors and had to install missing modules individually (translation: this may have been a long and conceivably useless detour).

Wednesday, June 21, 2023

Created a new environment, redownoaded gammapy using a modified forge command (that didn't work). Now the error whenever I tried to either download tutorial notebooks.data on my terminal or run anything recquireing import gammapy on Jupyter notebook returned "No module named gammapy," so we are now using a new environment called gammapy-1.1 just as the tutorial does and running conda forge. Made my presentation for Veritas update meetinng 1:30-3 pm. I was able to move mine and Pablo's b2 1811+31 .fits files to the directory I'm gonna use for gammapy once everything is working wiith my download.

Thursday, June 22, 2023

Still waiting on forge since I need access to the gammapy models in order to run the analysis. Logged the last few days on here. Colin helped me download miniconda3 so things went faster --conda-forge can now do things in parallel and this may be the highlight of my week. I ran through the Multi-instrument joint 3D and 1d analysis gammapy tutorial on my notebook and everything seems to be working with this set-up. Plan is to figure out how to just upload my own fits files now. Attended B2 1811+31 meeting, will finish rerunning stage 6 again.

Friday, June 23, 2023

Reran stage 6 of B2 1811+31 flare with 1 TeV E0. Started trying to run my comparison with gammapy following this turoial: https://docs.gammapy.org/1.1/tutorials/analysis-3d/analysis_mwl.html#hawc-1d-dataset-for-flux-point-fitting.

Week 5

Monday, June 26, 2023

The program was having issues interpretting my VEGAS fits files and as a solution, I followed Colin's suggestion to edit my headers to the SED format. I was able to run the overrplot analysis on gammapy to show both Pablo and I's spectra for the b2 1811+31 flare on gammapy, but the upper limits are not being considered.

Tuesday, June 27, 2023

Began editting the two fits files, adding a TS and "is_UL" column (T/F) to emulate the Hawc fits format and see if that fixes the bug where Upper Limits are plugged in as regular points. The Boolean defined Upper Limits, with TS < 4, as True. After rerunniing the analysis, this still did not fix the issue, so I went in and editted the dnde, flux_err, and flux_ul column contents to be in acccordance with the HAWC format, where ULs are Null is dnde and flux_err and regular points are Null in flux_ul.

Wednesday, June 28, 2023

Running the editted fits files, now with null values, produced a plot of only real points, which is not what we wanted. Changing the headers from flux_err and flux_ul to dnde_err and dnde_ul fixed this, which produced an overplot of mine and Pablo's spectra in agreement and with upper limits accounted for. Attended and presentd a small update at Veritas weekly meeting.

Thursday, June 29, 2023

Went through DQM plots and decided the time cuts for the quiescent B2_1811+31 data that I will be working on now. Am currently working on running the first stages of Vegas, but I need to edit LT/EA to 22.

Friday, June 30, 2023

I tried running stages 1-5 of VEGAS for the low data of the source but I ran into issues with the storage space on tehanu. While that is geting resolved, I made a tutorial version of my notebook detailing how to edit a vegas .fits file into a .fiits file that gammapy can read in order to produce a. joint analysis plot. Running_a_Gammapy_Joint_Analysis.ipynb

Week 6

Monday, July 3, 2023

I checked on the storage issue and noticed that it looked better so I tried downloading stages 1-5 of Vegas once more and it worked! I now have a .json file. Everything with the .json file seems right, so I submitted and am now waiting for it to run.

Wednesday, July 5, 2023

I ran stage 6 for the quiescent data and plotted the spectral comparison using gammapy. There was some issues with the binning and dubious upper limits but overall the results look promising, showing that the low data tended to be below the "real" bins from the flare.

Thursday-Sunday, July 6-9, 2023

Worked remotely and intermittently, but was able to rerun stage 6 using the adjusted binning so that the gammapy analysis would be more starightforward. I also have a scatterplot of dnde_err vs Energy. As Eileen asked during the B2_1811+31 meeting, I checked the excess plot of stage 6 (during one of the reruns) and it all looked like background noise.

Week 7 - reconstructed from my slack messages to colin, excellent recordkeeping I say

Monday, July 10, 2023

I plotted log scaled dnde_err v Energy for the Quiescent and Flare data as well as he Excess v Energy plot that Ruo and Colin suggested I create to see what was going on with the ULs in the Flare v Quiescent spectrum plot. In the Excess plot, I weighed the Non-AlphaNoff by the time exposure of each data set to make sure the analysis was comparable. It looked reasonable, with the Flare having noticeablly higher excess counts.

Tuesday, July 11, 2023

I used gammapy to fit the fllare data to a spetral model, in this case an absorbed power law. Once I optimized the index and amplitude parameter the e2dnde plot looked very good, so I moved onto the quiescent data. Due to the upper limits, the fit optimization failed when running with the vegas st6 fits file, so the plotted model was not fitting against the data.

Wednesday, July 12, 2023

I first tried running the data as if all points were real with all is_UL=False, which didn't produce anything uselful, so I checked what would happen if I set the TS<3 for is_UL=True, and the analysis was still not producing anything useful. Colin suggested I run the "stage 6" analysis through gammapy instead of just the fitting to avoid the issues with upper limits so I started taking a llook at Deivid's github.

Thursday, July 13, 2023

Once Colin sent me the vts_dl3_b21811_quiescent.tar file, I was able to untar that and use it to follow Deivid's example on running the gammapy analysis. The plot produced through that tutorial, which compared vegas sage 6 to gammapy was a bit convoluted, but it worked and I was able to get optimized parameters for the model.

Friday, July 14, 2023

I took the index and amplitude parameters that fitting the new file gave me and plotted the e2dnde spectrum with the absorbed pwl model separately and, once I added the error band, it looked reasonable. A small issue with this analysis has been that one of the runs, 105626, has too much noise to produce the dl3 file for it so it's missing from that file.

... We realized there was an issue with my time cuts in the vegas analysis of the quiescent data, so I had to go back and revise my config file so I could rerun stage 5.

Week 8

Monday, July 17, 2023


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Topic revision: r15 - 2023-07-17 - CeciliaMartinezRodriguez
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