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---+ Research Journal (Summer 2020)

Friday, August 7
   * Last day of summer internship
   * Mostly just getting everything wrapped up and well organized, finishing up any last things

Thursday, August 6
   * Reran point source analysis of Boomerang with the new binning that I used on the extended analysis so they will be easier to compare
   * Worked on cleaning up powerpoint of Boomerang results, added new point source analysis
   * Worked on short write up of summer work for website

Wednesday, August 5
   * Finished final presentation (added lightcurves for 15bn and 17egm)
   * Group meeting/Research talks

Tuesday, August 4
   * Worked on final presentation
   * Extended source analysis of new coordinates of Boomerang finished, converged with TS value of 40.84 (so the source definitely models better as an extended source than as a point source)
   * Added extended source results to the powerpoint I am making of Boomerang analysis

Monday, August 3
   * Point source analysis of new coordinates for Boomerang finished, converged (TS value of 27.4)
   * Started running extended source analysis for the same location (radial disk model with radius of 0.2°)
   * Worked on slides for final presentation
   * Group meeting - confirmed good idea to run the extended source analysis, suggestion to clean up Boomerang slides so we can send them to Kaya
   * Meeting with Reshmi

Friday, July 31
   * Used fermipy "find source" to locate the exact coordinates of the source of the emission that I saw in my initial analysis
   * Started running new analysis centered on that spot
   * Read a number of papers about the area to get a better idea about what is going on with the different sources
   * Started working on slides for final presentation next week

Thursday, July 30
   * Only working part day because it is a Jewish Fast Day
   * Mostly just reading papers - for journal club and about Boomerang and its related sources

Wednesday, July 29
   * Full Boomerang analysis finished running - converged, no detection at the coordinates I used. Did see a fairly bright detection abour half a degree away which is not in the catalogs
   * Met with Deivid - looked at a few papers of higher energy analyses of the area, looks like there are multiple sources in the area (pulsar, PWN, SNR). I had the pulsar as one of the sources in the model (from the 3FHL catalog), and the coordinates I used were almost on top of the pulsar (which seems to be the location of the known radio PWN). The place where I saw the detection seems to be the same location as a TeV source which might be the SNR.
   * Journal club - action items for moving forward
   * Group meeting - got some papers to look at regarding the Boomerang area.

Tuesday, July 28
   * 1year analysis of Boomerang finished running - fit converged, but source was not really detected
   * Ran analysis of Boomerang source for full (almost 12 year) time period
   * Started reading articles for journal clubs
   * 1pm colloqium - "The Beauty of the Hidden Universe: the eROSITA X-ray Sky Survey" (Dr. Christoph Tenzer, University of Tubingen)

Monday, July 27
   * Finished up slides for group meeting
   * Read FGES catalog paper
   * Still haven't been able to find an already made full FGES catalog file, so decided to try creating one myself
   * Combined the xml model files which I found for FGES sources into one xml file to be my FGES catalog file, crosschecking all of the sources with the paper to make sure I have all of the sources in the model which are supposed to be in the FGES catalog
   * My new FGES file seems to be working, started running a 1-year analysis of Boomerang just to make sure both the catalog files (3FHL and FGES) are not having any problems
   * 3pm Group meeting

Friday, July 24
   * Working on few slides - summary of SLSNe call
   * Got the 3FHL catalog working - had a little trouble at first when I tried to use the .fit file, but eventually got it to work with the xml file.
   * Continued to work on trying to find the FGES catalog, I can't find a single file for the FGES catalog. I found a paper about it, and I may have found a set of xml files which each contail the model for one source. I am starting to think I may have to just combine those files myself, there may not be an already combined file.
   * Met with Deivid

Thursday, July 23
   * Read article for journal club
   * Summer colloquium - "Nature's tiniest fundamental matter particles - neutrinos!" (Prof Georgia Karagiorgi)
   * Started to work on summary of SLSNe call
   * Journal club

Wednesday, July 22
   * Downloaded 3FHL catalog into my fermi_analysis directory on tehanu, so should be able to access it from my config file. I'm having more trouble figuring out the FGES catalog (extended sources), I haven't yet found an actual catalog file to use, just a paper about it.
   * Anti-racism journal club readings - "What's the plan for including Tamir Rice in #STEM?" and minutes from physics department town hall
   * Attended Barnard Physics & Astronomy Department meeting
   * Journal club
   * Group meeting - Suggestion to start with Boomerang source instead of HESS J1356-645. Start with shorter analysis first, to make sure the 3FHL and extended catalogs are working, and stay above 10 GeV to avoid pulsed emission. Start by looking to see whether there are any papers with Fermi analysis of any of these sources. Reminder that we are nearing the end of the summer, next week is the last official full week, but we will do final presentations (15 minutes including questions) the next Wednesday (August 5)

Tuesday, July 21
   * 9am SLSNe call - will work on summary slides of this call to present at the group meeting next Monday
   * Worked on finishing up PWN sources background slides
   * 1pm colloquium - "Radio Galaxies and their Powerful Jets" (Jodi Christiansen)
   * Did some more research on using alternative catalogs in fermipy
   * 7pm PWN Fermi call

Monday, July 20
   * continued to work on background research/slides for PWN sources
   * Met with Reshmi - she helped me find some information for some of the sources which I was having more trouble finding information for, and we discussed what to do going forward with analysis (generally following the procedure from the paper)
   * Tried to run a 1-year analysis of one of the sources (HESS J1747-281) using only the 4FGL model, it did not converge
   * Group meeting - asked about how to use a different catalog in the analysis. Suggestion that it might be already in fermipy, in which case I just need to find it and see what the proper name is for calling it in the config file. Otherwise I should be able to download the catalog from the Fermi website and use it like that
   * Got another paper suggestion to read

Friday, July 17
   * PWN analysis meeting scheduled for next Tuesday, 7pm
   * Reading papers - trying to find information about a few of the specific sources which I'm having trouble finding details for, and looking for details on how to run the Fermi analysis for a PWN specifically
   * The VERITAS/Fermi paper talks about including other catalogs in the analysis - it looks like there is no updated version of the FHL or FGES catalogs, so most up to date is 3FHL and FGES
   * Not sure how to use a different catalog with our fermipy pipeline?

Thursday, July 16
   * Had medical appointment in the morning
   * Worked on background research on the 7 PWN sources, started working on making slides with information
   * Started reading the paper "VERITAS and Fermi-LAT observations of TeV gamma-ray sources discovered by HAWC in the 2HWC catalog"

Wednesday, July 15
   * VERITAS collaboration meeting
   * Getting started with PWN analysis - doing some background research on sources and procedure
   * Met with Reshmi - Discussed how to procede with the PWN project. There is a call being planning with Kaya Mori's group, probably for next week sometime. Got some papers/websites to look for information about the sources.
   * Plan to do background research on the sources, prepare a slide of information for each of them, and get started on a 2-year analysis of one source to get started with (only use energy above 5 GeV)

Tuesday, July 14
   * VERITAS collaboration meeting
   * Summer colloquium - pSCT talk by Massimo
   * Started looking for papers about doing Fermi analysis for PWNe to get a better idea of how things work - found a few papers which will hopefully be helpful to look at
   * I have a few questions about how to go forward with the PWNe analyses - How long a time period should I be using? I'm also confused about the list of sources I got. Some of the PWNe have multiple 3FGL or 4FGL sources listed next to them, so does that mean I should run an analysis for each of those sources? Also most of the fermi catalog sources are listed as being offset from the PWN sources, which I would think means that they aren't actually the same source, so I'm just not quite sure what I'm supposed to be doing.
   * 1. eHWC J2019+368 ... 3FGL J2021.1+3651 (offset: 16.50')<br />2. eHWC J1850+001 ... 3FGL J1850.5&minus;0024 (offset: 32.8')<br />3. VER J2228+609 ... 3FGL J2229+6114 (offset: 23.1'), 3FGL J2225.8+6045 (offset: 36.20')<br />4. HESS J1356&minus;645 ... 4FGL J1355.1&minus;6420e, 3FGL 1356.6&minus;6428 (offset: 4.41')<br />5. HESS J1420&minus;607 ... 4FGL J1420.3&minus;6046e, 3FGL 1420.0&minus;6048 (offset: 3.89')<br />6. HESS J1418&minus;609 ... 4FGL J1417.7&minus;6057, 4FGL J1418.7&minus;6057, 3FGL 1418.6&minus;6058 (offset: 4.81')<br />7. HESS J1747&minus;281 ... 3FGL J1747.0&minus;2828 (offset: 19.96') 3FGL J1748.3&minus;2815c (offset: 19.25')

Monday, July 13
   * Made slides for group meeting - SN2020jhm results
   * VERITAS collaboration meeting
   * Group meeting - showed my 20jhm results, briefly discussed plans going forward -- start working on fermi analysis of PWNe

Friday, July 10
   * Continued working on SN2020jhm.
   * Ran analysis for 2 months of data from the discovery date, and for 1 month of data from approximately peak date
   * Both analyses converged - unsurprisingly there does not seem to be any detected emission from the source, though we did get upper limits

Thursday, July 9
   * Wasn't feeling very well, so wasn't able to get very much work done
   * Got names of PWNe for NuSTAR, but plan to finish the short analysis of SN2020jhm before moving on to the new sources
   * Started working on SN2020jhm

Wednesday, July 8
   * Finishing up SLSNe presentation
   * Read article for anti-racist journal club
   * Met with Deivid - went over presentation, clarified a few points, Deivid showed me the results he's getting for the "mystery source" from bin4 of SN2017egm (now called PS J1030.9+4510)
   * Journal club
   * Group meeting - presented SLSNe, discussed next steps: work on short analysis of new SN2020jhm, then do some Fermi work with PWNe for NuSTAR project (will get more details soon)

Tuesday, July 7
   * Continued background reading
   * Worked on SLSNe background presentation for tomorrow's group meeting
   * 1pm colloquium - Dr. Elisabetta Bissaldi (gamma ray bursts)

Monday, July 6
   * Uploaded SN2017egm new results comparison powerpoint to this journal page
   * Planning to focus the next couple days on catching up on background reading for SLSNe project, with the goal of making a background presentation at this week's Wednesday group meeting
   * 3pm group meeting

Friday, July 3
   * Off for 4th of July holiday

Thursday, July 2
   * Working on non-converged bins of 17egm
   * Finished working on SN2017egm - all the bins converged, but bin4 seems a little odd. It has a TS value of 0, compared to all the other bins which at least register something, and has an eflux value of order 10^-10 (compared to values of the order of 10^-6 for the other time bins). Deivid and I also noticed that this bin has what appears to be an unknown source, so we should probably do some more investigation into that.
   * Read article for physics journal club
   * 1pm colloquium - Prof Dan Kabat on black holes
   * 4pm journal club

Wednesday, July 1
   * Read article for anti-racism journal club
   * Continued working on rerun of 17egm using fermipy
   * 1pm journal club
   * 2pm Group meeting
   * Finished initial run of 17egm, most of the bins converged. Started working on the bins which didn't converge, will continue tomorrow.

Tuesday, June 30
   * Made a table of eflux values for 15bn to compare to Deivid, we both have lower eflux value in bin5 than in the other bins
   * Met with Deivid, discussing long term plan: I will redo the 17egm analysis using fermipy, work on my background presentation for next week, then work on a one month analysis of new source SN2020jhm. Deivid will work on the sensitivity calculations. Once I finish these we can discuss with Reshmi maybe working on a fermi analysis for NuS TAR.
   * Attended Prof John Parsons summer colloquium
   * Started rerunning 17egm

Monday, June 29
   * Finished up 15bn (had to rerun a couple bins today, but now all should be done)
   * Put the results in a comparison powerpoint with Deivid's results (attached on this page)
   * A few of Deivid's bins had upper limits which were much lower than the other bins. I have not had a chance to look whether mine are similar or not (will check on that tomorrow)
   * Group meeting - updated that I am pretty much finished with 17egm and 15bn, discussed next steps: I will make a background presentation for next week, and will run a quick analysis for 2020jhm, even though we're still very close to peak and therefore wouldn't expect there to be any gamma rays yet (but it is good to check anyway, just in case there could be something weird going on, especially since with fermipy it is fast and easy to get the analysis going)
   * Discussed possibility of working on sensitivity predictions for CTA with Deivid, will discuss more at a later point

Friday, June 26
   * Continued to work on the bins of 15bn that had not converged
   * All of the bins have converged, as well as the full 3-year time period
   * Started to work on putting the results into a powerpoint for comparison to Deivid's results

Thursday, June 25
   * Continued working on 15bn analysis, working on the first time bin (which hadn't converged yet) using jupyter notebook
   * Met with Prof Mukherjee to discuss longer term plan - after finishing 15bn analysis, could move on to analysis of the new SLSNe source. After that we will need to decide whether to move on to fermi analyses of different type of sources (like PWN) or whether to stay with the SLSNe project in a different way
   * Read journal club article
   * Attended journal club

Wednesday, June 24
   * Send Deivid the 17egm comparison powerpoint (also attached that presentation on this page), we will spend some time soon going through all of the results in detail
   * Finished the initial run through of 15bn with tehanu fermipy (all bins) -- not all of the bins converged, so will need to work on playing with those models more to make them converge, but they ran successfully and gave results, which is great
   * Met with Deivid, discussed the 17egm comparisons (how/what exactly to compare considering that my index was fixed and his was free), and talked about the next steps for 15bn (specifically discussed using jupyter notebook to allow a more interactive way of changing the model in real time by fixing/freeing/deleting sources
   * Group meeting - discussion of whether to rerun 17egm with free index (decision to hold off for the moment, maybe return to it after I finish up with 15bn), and more discussion of which output products are best to compare in this situation
   * APS webinar - Making Physics Inclusive and Equitable

Tuesday, June 23
   * Solved the Invalid DISPLAY variable error -- switched to using the -Y flag for ssh instead of the -X flag
   * Successfully got the 15bn analysis running
   * Finished organizing 2017egm files, put the results in a powerpoint with Deivid's results for easy comparison -- as I was looking at the results, I noticed that the model that I used was a very constrained one (had all index parameters fixed, even for 17egm itself). The fits did converge, but it was not the same model that Deivid used, and probably did not get as accurate results.
   * Attended Summer Colloquium -- Dr. Zsuzsanna Marka

Monday, June 22
   * Finished getting fermipy set up, made config files, made time cuts to remove time periods where the sun is in the area before starting the analysis
   * Tried to run analysis for one time bin of 15bn on fermipy, ran into a new error (RuntimeError: Invalid DISPLAY variable), but did successfully get past the point where fermitools was failing before
   * Group meeting
   * Working on getting 2017egm files organized

Thursday, June 18
   * Finished reading journal club article
   * Started getting fermipy set up, following Ari's slides as well as looking at general fermipy information online
   * Attended Daniel Savin's colloquium
   * Attended journal club - in addition to discussing the article, made up rotation plan for the summer (I will be leading journal club on July 9)

Wednesday, June 17
   * Tried running analysis step by step rather than using my script (on tehanu), in case the script was somehow the issue, but it still didn't work
   * Discovered that when I transfered my 2017egm files between computers they got somewhat mixed up and out of order, so I will need to spend some time getting them sorted out before I can compare results directly to Deivid's (didn't have time today)
   * Met with Deivid
   * Started reading the article for Thursday's journal club
   * Group meeting - general consensus that I should switch over to using fermipy because it doesn't look like we will be able to get fermitools working again soon

Tuesday, June 16
   * Tried to run PG1553 on tehanu without using files from my computer (accessing data and creating files completely through tehanu) - ran into a floating point error at gtsrcmaps step
   * So, currently have two issues: the out of range error at likelihood step on all machines regardless of data/model, and this new floating point error at gtsrcmaps on tehanu (it works fine on my computer)
   * Spent some time looking around online trying to see if anyone has had these issues - I did find someone wrote in on the fermi github about a likelihood out of bounds error, but the issue was closed without there being any comments, so I'm not sure what to make of that
   * 1pm - Attended Prof Mukherjee's colloquium
   * 4pm - Attended Prof Mike Nowak's Washington University talk on high energy astrophysics analysis softwares
Monday, June 15
   * Started working on getting my SN2017egm results from last summer organized so I can start comparing the results with Deivid's results
   * Tried running PG1553 analysis on tehanu, had to deal with a few minor issues to start running
   * a couple of minor issues - had to figure out all the right paths for the files and scripts. bdlikeSED uses pyfits, which doesn't seem to exist anymore, so had to change it to using astropy.io.fits.
   * Attended group meeting
   * The run failed at the same place and with the same error as it did when running on my machine. Will look into this more tomorrow.

Friday, June 12
   * Checked the fits files involved in the analysis, there doesn't seem to be any issue of corrupted files
   * Worked on getting set up with tehanu and Ari's fermipy setup
   * First thing I want to try is moving the PG1553 files onto tehanu and running their analysis there (because I am more confident with that model than with the one for SN2015bn, so I will test it first before moving on to 15bn)
   * Ended up having to move the bdlikeSED and make4FGLxml scripts over from my computer, I don't know how to access them within the tehanu setup (since they aren't part of the standard fermitools)

Thursday, June 11
   * Met with Deivid - discussed current status of fermitools troubleshooting (still haven't fixed it), as well as ideas for moving forward on that and other things
   * Goal to compare my fermi results for 2017egm from last summer with Deivid's results on the VERITAS wiki - first step will be to look through my own results to make sure they are all in order and complete
   * Last idea for troubleshooting fermitools - look at the fits files using astropy to make sure they are not corrupted
   * However, since it seems unlikely that we will solve the fermitools issue soon, making plans to switch to using either Qi or Ari's setup on tehanu
   * Had an issue with getting onto tehanu, but Bill Seligman helped me get it fixed, so it should be working now

Wednesday, June 10
   * Particles for Justice strike

Tuesday, June 9
   * Continued fermitools troubleshooting - tried running without 15bn in the model, double checked that I'm using most up to date diffuse models, tried using different optimizers
   * None of these things solved the issue, and I am currently out of ideas for what to try next
   * Finished reading the X-ray paper

Monday, June 8
   * Continued troubleshooting: tried reinstalling fermitools and anaconda, didn't help with the error. Trying to look online to see if anyone has had similar issues with fermitools, so far no luck.
   * Colin sent out a doodle poll for times for journal club
   * Group meeting - discussion of Wednesday's strike for social justice and the summer colloquium series (sign up on link)
   * Some fermi suggestions from group meeting: try running analysis with SN2015bn out of the model, make sure using the most up to date diffuse models, try using different optimizers.
   * Qi made a setup of fermitools on tehanu last year, if it is still up and I can't get my setup working maybe I can try using my files in that setup
   * Next Wednesday undergrads will give a short presentation on background material after reading papers
Thursday, June 4 - Friday, June 5
   * Continued working on troubleshooting fermi analysis, spoke more about it with Deivid via slack
   * I've determined that the issue is not specific to the particular model file I was using, or to 2015bn as a source (I tried different models, and did a test analysis with a different source, which also failed)
   * The next step will be trying to completely reinstall fermitools and see if that helps
<p dir="ltr">Wednesday, June 3</p>
   * <p dir="ltr">Continued to work on troubleshooting fermi analysis</p>
   * <p dir="ltr">Met with Deivid to discuss background theory of SLSNe and the magnetar model, as well as to work on troubleshooting the error</p>
   * <p dir="ltr">We came up with some ideas to work on, including looking through the xml file to make sure there are no obvious issues, trying to run the analysis for other time bins, and changing the model. Also discussed strategies for how to choose to fix/free sources in the model in general.</p>
   * <p dir="ltr">Group meeting</p>
<p dir="ltr">Tuesday, June 2</p>
   * <p dir="ltr">Tried to work on fermi analysis of SN2015bn, ran into error at the actual likelihood step "Attempt to set the value outside of existing bounds. Value nan is not between 1e-05 and 1000"</p>
   * <p dir="ltr">(was successful at preparing the preliminary files with all of the time cuts to remove contamination from the sun)</p>
   * <p dir="ltr">spent the rest of the day troubleshooting</p>
      * <p dir="ltr">I determined that I had updated Fermitools recently, so I tried undoing the update, but it didn’t make a difference.</p>
      * <p dir="ltr">Tried using different model files, including one which had worked in an earlier analysis, but continued to get the same error</p>
<p dir="ltr">Monday, June 1</p>
   * <p dir="ltr">Various orientation meetings, discussed plans for the summer. Primary goal is to finish the SLSNe analyses and get more familiar with the theory.</p>
   * <p dir="ltr">Attended Ari's fermipy tutorial</p>
   * <p dir="ltr">started reading the X-ray SN2015bn paper</p>

-- <span style="background-color: transparent;">%USERSIG{PazitRabinowitz - 2020-06-03}%</span>

---++ Comments

<br /><span style="background-color: transparent;">%COMMENT%</span>
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
pptx	2017egm_compareNewResults.pptx	r1	manage	41716.4 K	2020-07-06 - 18:13	PazitRabinowitz	Comparison of my new fermipy results with Deivid's fermipy results for SN2017egm
pptx	2017egm_compareOldResults.pptx	r1	manage	10543.0 K	2020-07-06 - 18:11	PazitRabinowitz	Comparison of my fermitools results with Deivid's fermipy results for SN2017egm
pptx	2015bn_compareResults.pptx	r2 r1	manage	43378.0 K	2020-06-29 - 18:26	PazitRabinowitz
Topic revision: r45 - 2020-08-07 - PazitRabinowitz
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