Remeis-Wiki - User contributions [en]

Integral

2025-07-30T13:33:44Z

Thalhammer: /* Non-OSA INTEGRAL extraction */

=== INTEGRAL Scripts ===

The Remeis INTEGRAL scripts can be found under

/software/Science/satscripts/intscripts/

on Remeis machines. If you have any questions on how to use them, read the following text and talk to Ingo or Philipp.

=== General remarks on Integral data extraction at Remeis: ===

Initially data is extracted in parallel on a ScWs basis and in a second step combined to the final products. This allows for the usage of [[Slurm|SLURM]] and leads to significantly faster extraction compared to a combined extraction on a single machine. The initial step is launch by the scripts master_sbs. The script can generate spectra and images for ISGRI and spectra for JEMX. No PICsIT, SPI or OMC analysis is run at Remeis. The resulting spectra are then combined using spe_pick while the ISGRI/IBIS images are merged using INT_mosa_ibis. As the spectral extraction requires a catalog containing the sources for which the spectral extraction should be run, it is advised to first generate images & a mosaic to determine, which sources are bright and detected in the field of view.
Generally it is a good idea, if you have not already to have a look at the OSA cookbook, e.g., to check how the paths in the data object locator (DOL) files is supposed to look like or how to prepare a suitable catalog for spectral extraction: https://www.isdc.unige.ch/integral/analysis

Before any OSA analysis can be run the corresponding module has to be load with:
ml integral-osa

Before running any data extraction you need to set up a few soft links:
ln -sf /home/X-ray/INTEGRAL/archive/aux
ln -sf /home/X-ray/INTEGRAL/archive/ic
ln -sf /home/X-ray/INTEGRAL/archive/idx
ln -sf /home/X-ray/INTEGRAL/archive/scw

=== Typical IBIS image/mosaic ===
; 1) Find ScWs that cover your source, e.g., pointing is < 10 degree away from source:
objscw --scwlist "Cyg X-1" --maxdist=10 > scws_all.txt
If you want to use scws_all.txt as input for hte next step remove the header of this file, i.e, the first 6 lines. Importantly you will probalby want to select only a subset of the available observations and therefore perform some selection on the full list of science windows. As a simple example one might image to only use the latest 100 ScWs:
tail -n 100 scws_all.txt > scws_cut.txt
; 2) Start the ScW based analysis:
master_sbs --job=IMA --scwlist=scws_all.txt --energies="30,50,200" --verbose --clobber=yes --path=$PWD
; 3) Generate the required input file for spe_pick
txt2idx element="scws_dols.txt" index="cygx1"
; 4) Run INT_mosa_ibis to generate the a combine mosaic
INT_mosa_ibis --obsgrp=$PWD --dol=scws_dols.txt --destin=$PWD/obs/mosa_cygx1
; 5) Check the images for artifacts and sort out affected ScWs through trial-and-error:
ds9 isgri_mosa_ima.fits[2] -region found.reg -cmap b -scale sqrt -scale limits 0 60 -zoom 2

The resulting image should look something like this:

[[File:mosa_cygx1.png|400px]]

Details about the detected sources, such as there flux and detection significance can be found in the file isgri_mosa_res.fits.

=== Typical IBIS spectral analysis ===
; 1) Again, find ScWs that cover your source and are of interest to you
; 2) Start the ScW based analysis:
master_sbs --job=SPE --scwlist=scws_cut.txt --source="Cyg X-1" --verbose --clobber=yes --path=$PWD --catalog=specat.fits
; 3) Generate the required input file for spe_pick. Check that that all objects in the DOL file exist.
txt2idx element="scws_dols.txt" index="cygx1"
; 4) Run spe_pick to generate the final spectra
spe_pick group="cygx1.fits" source="Cyg X-1" rootname="cygX1_all" instrument="ISGRI"
This will result in background subtracted spectra for the given source. Remember that the source name has exactly the naming in the INTEGRAL reference catalog.

=== Typical IBIS light-curve generation ===
; 1) Quite similar to the spectral extraction. First find ScWs that cover your source, or reuse the previous ScW list:
; 2) Start the ScW based analysis, here for 100s time binning:
master_sbs --job=LC --scwlist=scws_cut.txt --source="Cyg X-1" --verbose --clobber=yes --path=$PWD --catalog=specat.fits --energies=30,120 --deltat=100
This generates a separate light-curve for each ScW at, e.g., obs/250300170010/scw/250300170010.001/250300170010_Cyg_X-1_30-120.lc
; 3) These can then be merged together e.g. using fmerge or ISIS.
ls obs/*/scw/*.001/*_Cyg_X-1_30-120.lc >> lcs.txt
fmerge @lcs.txt Cyg_X1_ibis_lc.fits -

=== Typical IBIS PIF light-curve generation ===
The above light-curves are only reliable down to a time-resolution of 1.0-0.1s. For higher timing resolution the deconvolution becomes unstable and one has to generate light-curves from the event-lists and pixel-illumination fraction (PIF).

; 1) First event lists are generated with the respective Remeis Scripts:
eventlist --path=$PWD --source="Cyg X-1" --scw=$scw --catalog=$cat
This generates a event-list under "obs/266100220010/scw/266100220010.001/events.fits".
For each source in the catalog and the FOV this file includes a column indicating whether a source is illuminated by the respective source.
; 2) Filter the eventfile e.g. with an ftools or an ISIS.
fcopy "events.fits[2][PIF_1==1]" cyg_pif1.fits
; 3) Light-curves can then be generated e.g. with ISIS (lc_from_events)
variable lc = lc_from_events(struct{time=evts.time[n], pi=evts.energy[n]};dt=dt,
gti = fits_read_table(gtiname + "[14]"), minfracexp=.5);

=== Typical JEMX spectral analysis ===
Until revolution 976 (Oct. 10,2010) only one JEM-X unit was operating at any give time. During that time one should therefore run the analysis for both detectors.
; 1) Find ScWs that cover your source. As JEMX has a smaller field of view, its max distance to the source should also be reduced to ~5 degree:
objscw --scwlist "Cyg X-1" --maxdist=5 > scws_jmx.txt
And again, you will probably further select in which ScWs you are interested.
; 2) Generate a RMF with the required binning, e.g., 32 bins:
j_rebin_rmf binlist=STD_032
The RMF does not change between observations and might be reused as long as binning requirements do not change.
(Depending on your fitting software the resulting RMF might give you troubles and needs to be rewritten.)
; 3) Start the ScW based analysis with 32=2^5 logarithmic energy bins:
master_sbs --path=$PWD --scwlist=scws_jemx_cut.txt --job=SPE --source="Cyg X-1" --jemx=1 --clobber=yes --catalog=catalog_jemx.fits --response=jemx_rebinned_rmf.fits --nChanBins=-5
; 4) Generate the required input file for spe_pick
txt2idx element="scws_jmx_dols.txt" index="cygx1"
; 5) Run spe_pick to generate the final spectra.
spe_pick group=cygx1.fits source="Cyg X-1" rootname="cygx1" instrument="JMX1"

=== JEMX images ===
To generate JEMX images there are no dedicated scripts at Remeis, and you have to fall back to the OSA scripts, e.g.:
og_create idxSwg=scw.lst ogid=oph2 baseDir="./" instrument=JMX1
jemx_science_analysis startLevel="IMA2" endLevel="IMA2" jemxNum=1 COR_gainModel=2

=== On catalogs ===
Adapted from the documentation:
While for generally image generation a user generated catalog is not required, if supplied, it needs to keeps the same format of the general reference catalog from which it was built, i.e. it has the extension of the type ”GNRL-REFR-CAT”. This is the correct extension to be used as input for the Imaging step. In Section 7.2 of the OSA manual, you are been shown how to build a catalog for the lightcurve (LCR) and spectral (SPE) step. In that case the catalog, you obtained, specat.fits, was of the type of ”ISGR-SRCLRES” which is the correct format for the LCR and SPE steps. The two formats cannot be switched, meaning that you cannot use a ”GNRL-REFR-CAT” type catalog for SPE and LCR or an ”ISGR-SRCL-RES” one for IMA.

In practice one prepares the catalog used for spectral extraction from the results of the IMA step, taking only into account actually detected sources, e.g. by running the following on the results of INT_mosa_ibis:
fcopy "isgri_srcl_res.fits[1][DETSIG>10]" specat.fits

=== Time selection ===

User generated GTI files can be used to perform time or phase resolved spectral analysis. This is done through the --gtiname & --gtiformat keywords. Consult the master_sbs help for more details. To generate GTI file it is recommended to make use of the OSA script gti_user, e.g., as follows:

gti_user tstart=8170.5 tstop=8171.8 unit=sec begin=0.0 end=50 step=150 repeat=653 gti=user_gti.fits clobber=yes

Or for a to calculate a reverse bary-corrected GTI file. Not that this requires the coordinated and the DOL file of a ScW or Observation Group.

gti_user tstart=8393.16 unit=sec begin=0.0 end=50 step=25 repeat=600 gti=user_gti.fits clobber=yes bary=y group=og_ibis.fits+1

Also note that the light-curves generated by imalc_sbs through master_sbs are already barycenter corrected.

More details can be found in the introduction to INTEGRAL analysis:

https://www.isdc.unige.ch/integral/download/osa/doc/11.2/osa_um_intro.pdf

=== Quick Look Analysis ===

NRT data can also be analysed at Remeis with the usual scripts, require, however, an additional --nrt parameter in most scripts.
Also have a look at http://isdc.unige.ch/heavens/

=== Documentation ===

Useful to know:
http://www.isdc.unige.ch/integral/download/osa/doc/10.0/osa_um_ibis/node27.html
And for the cook-book and general documentation. Reading the IBIS Analysis User Manual is recommend:
https://www.isdc.unige.ch/integral/analysis
Each INTEGTAL script also has a help
master_sbs --help
cat $ISDC_ENV/help/ibis_science_analysis.txt

=== Abbreviations ===
http://www.isdc.unige.ch/integral/support/glossary

* '''DAL''' The Data Access Layer (DAL) is a software library used to manipulate (create, write, read and manage) scientific data.
* '''DOL''' The Data Object Location (DOL) specifies the location of a DAL object, both by the FITS file name and its extension. For instance, /isdc/dev/xxx.fits[2] is a DOL, while xxx.fits is simply the name of a FITS file.

=== Known Issues ===
# In general: check first http://www.isdc.unige.ch/integral/support/faq for the error code you get
# The resulting spectra will not be strictly OGIP compliant, which e.g. ISIS might care about, but can be ignored.

==== Errors mosaicing using custom DOLs ====
If you want to create a mosaic using DOL (Data Object Location) files, sometimes the building interrupts with errors like a Fortran Runtime error (http://www.isdc.unige.ch/integral/support/faq.cgi?SOFT-051) or errors like:

Using and copying first SCW >>/scratch1/beuchert/integral/scw_extr/obs/125400400010/scw/125400400010.001/swg_ibis.fits
<<
Log_0 : 100 elements opened.
Log_0 : 100 elements attached.
Error_1: Can not update the index.

or
Error_1: Can not close the element
or
Error_2: DAL_READ_ERROR : error reading from FITS file
etc.

# Somehow corrupted scws? Collect sets of two scws and create Mosaics based on those. Like that it is easy to enclose corrupted scws.
# An error -2004 (DAL_FILE_NOT_ACCESSIBLE) often results because one of your groups is corrupted. Before restarting the analysis, make a ``dal_clean'', which should be able to do an automatic repair. If it does not work try a ``dal_verify'' to see what is corrupted. Or you can try to open your group (or child group) with fv and look for a file pointed by the group that does not exists. Most of the time removing the line with this wrong file in the group table is fixing your problem.

The latter:
first create an observation group out of your dol-list of scws.
Creating observation groups is also the canonical way of extracting INTEGRAL/IBIS data.
Before doing that, the soft links as noted above have to be set in the directory.
Then:
cd path/to/dir/with/softlinks/
og_create idxSwg=dol.txt ogid=isgri_gc baseDir="./" instrument=IBIS
ls obs/isgri_gc/
Repair the observation group and included indices/links with
dal_clean inDOL="obs/isgri_gc/og_ibis.fits" chatty="4" checkExt="1"
Now INT_mosa_ibis should work again on the scws in dol.txt

==== How to create mosaics (outdated) ====

First make a list of scws you want to add to a mosaic, i.e., a "dol-file" dol.txt:
/scratch1/beuchert/integral/scw_extr/obs/066200340010/scw/066200340010.001/swg_ibis.fits
/scratch1/beuchert/integral/scw_extr/obs/066200350010/scw/066200350010.001/swg_ibis.fits
/scratch1/beuchert/integral/scw_extr/obs/066200360010/scw/066200360010.001/swg_ibis.fits
Then prepare the directory where the mosaic shall be built in, i.e., set the env. variables to allow INT_mosa_ibis to find indices etc.:
cd /some/path/
ln -s /virgo/b/INTEGRAL/aux/
ln -s /virgo/b/INTEGRAL/idx/
ln -s /virgo/b/INTEGRAL/ic/
ln -s /virgo/b/INTEGRAL/scw/
ln -s /virgo/b/INTEGRAL/cat/
mkdir /some/path/obs/

INT_mosa_ibis --obsgrp=/path/to/all/extracted/scws/ --destin=/path/to/the/prepared/directory/obs/mosa_og/ --dol="dol.txt"

=== Non-OSA INTEGRAL extraction ===

There are a few alternatives by now to using OSA+Remeis scripts:
* To run IBIS and JEMX analysis online there is MMODA at https://www.astro.unige.ch/mmoda/help/mmoda/integral-mission
* If you are interested in SPI data you can do this with the OSA installed here at Remeis, there are however much more reliable and stable pipelines available in form of either SPI-DAI or the SPI-pipeline at MPE organized by Thomas Siegert.

[[Category:Data Extraction]]

Integral

2025-07-30T13:18:16Z

Thalhammer:

Remeis English Checklist

2025-05-15T15:42:20Z

Thalhammer: /* Spelling and Word usage */

====== The Remeis English Checklist ======

(by J. Wilms and K. Pottschmidt)

'''''First of all and most importantly:'''''

* did you read the instructions to authors of the journal? If you are working on a thesis, did you read those of Astronomy and Astrophysics on [https://www.aanda.org/for-authors/language-editing/1-introduction language] and the TeX instructions in file aadoc.pdf, which is part of the Astronomy and Astrophysics package?
* did you read appendix A of the [https://journals.aps.org/files/rmpguide.pdf instructions to authors] of Rev Mod Phys?

==== Punctuation ====

* did you remove all commas before "that"?
* did you end your footnotes and captions with a full stop (".")?
* did you make sure that your use of "data" is correct and uses plural verbs?
* did you make sure that you do not have a ":" anywhere before an equation, but that your equations are seen as part of your sentences?
* did you make sure that you have commas surrounding "i.e." and "e.g."?

==== Spelling and Word usage ====

* do you consistently use either British or American spelling?
* did you run a spell checker over your manuscript? For TeX, use "ispell" or the built in spell checker in emacs.
* did you make sure not to use country prefixes in addresses in the author list?
* did you avoid passive voice as much as possible?
* did you make sure that you are //not// using "The found results are..." and similar German constructs in your text?
* did you make sure that everything in your text that is not your original result is accompanied by proper citations?
* did you make sure that you distinguish between "estimate" and "estimation" by replacing all "estimation" with "estimate"?
* did you replace all uses of "exemplary" by "example"?
* did you replace all uses of "dependency" by "dependence"?
* did you use "short" for length intervals and "brief" for time intervals? (but note that "short of duration" is correct)
* did you replace all uses of "the actual value" by "the real value"? (if you are German, "actual" does not mean "aktuell"!)
* did you remove all uses of "hence" and "thereby"?
* did you make sure that you use "however" as sparingly as possible?
* did you make sure that you did not use "the equation reads..", but rather used "the equation is..." or "the equation is given by..."?
* did you avoid split infinitives? ("to boldly go..." is wrong; yes, in many cases split infinitives are ok in current English, but they tend to be so often used wrongly by non-native speakers that it is best to avoid them)
* did you make sure that you distinguish properly between "this" and "these"?
* did you make use of the "Oxford comma", i.e., do you have a comma before "and" in lists?
* did you use "i.e." and "e.g." correctly, i.e., using "i.e." for a specific clarification or definition and "e.g." where you would otherwise use "for example"?
* did you use the IAU recommended year - month - day sequences (2016 March 15)?
* did you make sure that you did not use contractions such as "didn't" or "you're"?
* did you replace "cf." with "see" everywhere since you know that "cf." means "compare"?
* did you ensure that you use "opportunity" where in German you would be using "Chance" or "Gelegenheit" (and did not use "chance"...)?
* did you make sure that the reader will understand what thing you refer to when using "it" rather than naming it?
* did you make sure that all uses of "this" are followed by the object you are referring to?
* did you use "led" rather than "lead" when using the past tense of the verb "to lead"?
* did you reread the manuscript for internal consistency after you added comments from your coauthors?
* did you make sure that your sentences are short (rule of thumb: if a sentence goes over more than three lines it is probably too long)?
* did you check that you did not combine two sentences that could be separate sentences with "and"?
* did you avoid abbreviations as much as possible and only used them when they are really, really common (HST, AGN, XMM,...)?
* did you check that you defined all abbreviations that you used at their first usage? ("...Active Galactic Nucleus (AGN)..." //not// "...AGN (Active Galactic Nucleus)..." )

==== Citations ====

* did you add the journal to all publications where you list the arXiv-reference and not just blindly copy the erroneous ADS bibtex entry?
* did you make sure that you distinguished between arXiv references where a paper is submitted and references where a paper is already accepted by checking the paper author's comment on the arXiv-page for that article?
* did you remove the page number for all ATEL-references downloaded from ADS and changed the journal name to "Astron. Tel." or "ATEL"? (and similar for IAU telegrams)
* did you add editors and the title of the conference publication to all conference publications?
* did you add the publisher and place information (city only) to all books, conference publications, and other book-like publications that you are citing?
* did you check that your references are correct in that you are using ''\citet{biblabel}'' for references in the text and ''\citep{biblabel}'' for references in parentheses?
* did you make sure that none of your ''\citet{..}'' commands refer to more than one biblabel?
* [added by O. Koenig: did you make sure all SPIE references have an address? (you may want to follow this procedure: go to NASA ADS to get bibtex entry (<code>@inproceedings</code>!), put the entry of "booktitle" into "series", put <code>booktitle = procspie</code> (there should be a <code>@STRING{procspie = "Proc. SPIE."}</code> in <code>mnemonic.bib</code>, go to the SPIE webpage of the paper, get the address, and insert it by hand. A MWE could be <code>@INPROCEEDINGS{Doehring2015a, author = {{D{\"o}hring}, T. and {...}, title = "{The challenge of developing thin mirror shells for future x-ray telescopes}", series = {Optical Systems Design 2015: Optical Fabrication, Testing, and Metrology V}, year = 2015, editor = {{Duparr}, A. and {Geyl}, R.}, booktitle = procspie, volume = {9628}, address = {Jena, Germany}, pages = {962809}}</code>)]

==== Typesetting (mainly in TeX) ====

* did you check for missing spaces between values and units?
* did you make sure that all scientific units are typeset in <code>\mathrm</code>?
* did you make sure not to use constructs such as <code>$\mathrm{m}/\mathrm{s}$</code> by using <code>$\mathrm{m}\,\mathrm{s}^{-1}$</code> instead?
* did you make sure that almost all of your error bars are rounded up to only one significant digit rather than following the DIN-norm (which is not applied in astronomical journals)?
* did you make sure that you are not using any positioning commands for the table or figure environment such as <code>\begin{table}[htpb]</code>?
* did you make sure that your tables have captions above the table, and figures have captions below the figure or next to it (where allowed by the style)?
* did you make sure that you use empty lines to denote the start of a new paragraph rather than the ''\\''-command? (use <code>\parindent{0pt}</code> if you do not want to indent paragraphs)
* did you make sure that there are no paragraph endings above or below <code>\begin{equation}...\end{equation}</code> by ensuring that there is no empty line above or below the ''equation''-environment?
* did you make sure that you are not using <code>$\frac{a}{b}$</code> in normal text, but use <code>$a/b$</code> instead?
* did you make sure that you are not using the <code>displaymath</code>-environment and that all equations are numbered?
* did you make sure that all of your sections, subsections, paragraphs and so on are numbered?
* did you avoid any and all uses of <code>\bf</code>, <code>\it</code>, <code>\sl</code>, or <code>\em</code> and use the proper commands <code>\textbf</code>, <code>\textit</code>, <code>\textsl</code>, and <code>\emph</code> instead?
* did you use the en-dash of TeX for ranges, even if they occur in math, by using <code>--</code> in text mode rather than a minus sign? (that is, did you typeset a range in an equation as <code>$3x$--$5x$</code> or <code>$3x\mbox{--}5x$</code> rather than, erroneously, <code>$3x-5x$</code>?
* did you correctly use the minus-sign and dashes in astronomical source names, where the name contains coordinates and the <q>dash</q> really is a southern declination or Galactic latitude, that is, did you typeset <code>Her X-1</code>, <code>LMC X-3</code>, but <code>GX\,339$-$4</code> or <code>IGR J16318$-$4848</code> (and as a really difficult one: <code>MCG$-$6-30-15</code>)?
** as a side note: When the first part of the source name is a constellation name (e.g., Her X-1) it should be followed by a full space (<code>~</code>), while if the first part of the source name is a catalog (GX, 4U, 2RXS), it should be followed by a half-space (<code>\,</code>).
* did you make sure to typeset hydrogen equivalent columns as <code>$N_\mathrm{H}$</code> rather than $n_H$ or $n_\mathrm{H}$? (note: in astronomy, $n$ denotes a particle density, so it has units of particles per cubic centimeter, while N is a column with units of particles per square centimeter; a certain analysis program uses nH for this parameter, but this does not mean that n should be used in papers).

[[Category:Current Members]]

Guided Tours and Public Outreach

2025-05-12T14:23:21Z

Thalhammer: /* Material and Presentations */

[[Category:internal]]
On this pages you can find all information needed to guide a tour through our observatory for public people.

= General =

Tours are officially '''organized''' by the [http://foerderverein-sternwarte-bamberg.de Foerderverein of the observatory], but '''operated''' by the observatory staff to be insured through the university!

The main platform for the general public is [http://foerderverein-sternwarte-bamberg.de/fuehrungen http://foerderverein-sternwarte-bamberg.de/fuehrungen].

Here, tours can be ordered in two different ways:
* single persons and smaller groups can directly book public and regular guided tours via our webform at https://www.sternwarte.uni-erlangen.de/guided-tours/
* larger groups may directly ask for a tour at a separate date either by email to [mailto:fuehrungen@foerderverein-sternwarte-bamberg.de fuehrungen@foerderverein-sternwarte-bamberg.de] or by phone. All guided tour administrators have access to that email inbox.

The source code of the webform for booking a public tour can be found in the GIT repository at 
[https://www.sternwarte.uni-erlangen.de/gitlab/webmaster/guided-tours https://www.sternwarte.uni-erlangen.de/gitlab/webmaster/guided-tours]. 
All pushes to the master branch are automatically deployed at the official URL above!

== Mailing List / Current "staff" ==

All people interested in giving guided tours are member of the '''internal''' mailing list
[mailto:astro-fuehrungen@lists.fau.de astro-fuehrungen@lists.fau.de], '''please do not share this address with externals.
If you're not on the list but interested in giving tours, just ask Max to add you :-)

New tours are announced via this list. See [[Mailing lists]] for the list administrator.

In charge of organization:
* Nico
* Katrin (Backup and mentor :-)
* Lea (Backup)

Currently, the following people give tours on a regular basis:
* Steven
* Christian
* Aafia
* Amy
* Philipp T.
* Alexey
* Katharina
* Martin
* Nico

= Tip policy =

Starting in 2025, there are fixed "prices" for guided tours called "Unkostenbeitrag" (expense contribution). As a guide you get at least 35 euros and in case of tours on weekends or with observing even more.
The group is informed beforehand their expected expense contribution and asked to transfer the money to the Foerderverein. After the tour, you will get reimbursed by Ingo via bank transfer.

For public tours please collect donations at the beginning of the tour. Participants are notified via email of an expected donation of 5 euros.
After giving a public tour please execute the file <code>/home/zalot/publictip.py</code> and follow the instructions :-)

= Offering Tours =

At some point you're perhaps asked to give a tour or if it is possible to have one on a specific date. The latter might occur if Edith is out of her office and her telephone is redirected. In those cases you should know ''and'' check following things:
* '''Who is asking''' for a tour? If you're on the phone ask for a name and write down the phone number where the person can be called!
* The '''number of people should be between 15 and 25'''. Of course, the boundary conditions depend on the person guiding the tour. In a case of doubt, ask the guide or, if none is found yet, you simply can't promise that there will be a tour! In that case you may offer to look for a guide giving the tour anyway (and call the person back), but again don't make any promises! A list of people offering tours can be found below.
* What is the '''average age of the persons attending''' the tour? That's an important point since the content of a tour differs between children and adults, of course. Furthermore some guides have favorite age groups!
* Carefully check the '''date and time of the tour'''!
** It's most likely to find a guide if the weekday of a tour is '''between Monday and Thursday'''. Friday might work if it is before noon, otherwise people might be on the way into the weekend. In all other cases you may offer to look for a guide giving the tour anyway (see the point about the group size above).
** Make sure that there is '''no tour scheduled already'''! For that look into our online calendar (the link can be found below) and on the whiteboard in the copying machine office.
** Related to the last point ensure that there is '''no lab course''' running at the date! The lab course is also marked in our online calendar.
** Usually, a tour will take '''about 1.5 to 2 hours'''.
* See [[Guided Tours and Public Outreach#Tip policy]] for information on the "price" of guided tours.
* '''Observing with our telescopes''' is possible, of course, but only in case of '''night and cloudless weather'''! No kidding, some people are not aware of these facts... ("The day is too bright to see stars.", "I'm sorry, we can't look trough the clouds.", "The weather forecast is too uncertain, we can't promise.") Please check if someone else has already signed in for one of the telescopes on the day/night of the guided tour! '''IMPORTANT:''' Be aware that you are not allowed to operate the telescopes on you own, there ALWAYS has to be at least a second person around. To assure that, you either have to have a second person from the observatory present (at least in the main building) or you have to set up AND disassemble everything while the people from the tour are there. Otherwise no observations are allowed to take place!
* If all the above points are clarified '''mark the tour''' in our [https://www.sternwarte.uni-erlangen.de/calendar/ online calendar] and the whiteboard in the copying machine office. You have to be at a machine at the observatory to have access to the online calendar (to be more precisely: you're machine has to have an internal IP-address). The entry into the online calendar, besides the date and time, should include "for whom is the tour and the group size, contact person and phone number, name of the guide giving the tour". The whiteboard template is as follows: "date, for whom is the tour, time, guide"

= Giving a tour =

Each tour has several stations, where you can show things or talk to the people. Useful information and experiences about that is listed below. It might be helpful as well to read the article about [[intern:Popular_science:start|popular science]] in case you want or have to (if somebody asks) explain scientific aspects.

Note that there is also a separate page about guided tour stations: https://www.sternwarte.uni-erlangen.de/wiki/index.php/Guided_tour_stations

== Preparation ==

'''Before the tour'''
* Shut the doors of all offices in the main building (at least on the ground level) for several reasons: people are not allowed to walk in there and some of us are still working there during tours!
* Remove the northern hemisphere from the model of the inner solar system located in the entrance hall (you may put it into the Knigge room)
* Switch the lights on you need:
** entrance hall
** meteorite showcase (switch is on the right next to it)
** hallway to the meridian building; here are multiple switches
*** main light: right next to the door of the hallway or the backdoor of the main building (labeled "Meridian")
*** info panels: on the opposite wall to the door next to the blue cupboard
*** showcases and Blinkkomparator: in the cutout box up the few stairs on the right wall close to the library, labeled "Linke Steckdosen"
* In case of observations
** make sure that you are '''never''' alone in the domes! There always have to be at least two people present.
** carry the needed oculars into the domes (for observations with the naked eye, the 40cm telescope is strongly recommended)
** do __not__ open the domes (first, it might start raining while nobody is there, and it's more fun for you to let the people do it)
** do __not__ remove the dust covers of the telescopes (wait until the dome has been opened)
** read the [[remeis:start|guide how to operate the telescopes and mountings]]
** after observing: shut down the telescope mounting, put the dust covers back on and close the domes
* In case of showing nice pictures
** make sure enough chairs are available
** switch on the beamer in the library, log into the machine and start your presentation, picture-viewer, ...

'''After the tour'''
* Switch the lights off
* Logout of the used machines and switch the beamer off
* Put on the dust covers of the telescopes in the hallway
* Protect the photo plates on the Blinkkomparator from getting dusty
* '''Move the entry from the whiteboard''' in the copying machine office '''to the list attached to the pin-board''' next to it

== Material and Presentations ==
*Collected information valuable for guided tours: ''/data/media/presentations_for_guided_tours'' and ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/guidedtour.pdf''

*A merger of (picture/video) presentations given at guided tours: ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/guidedtour.odp''

* Presentations & notes on using the CHT during tours: ''/home/thalhammer/userdata/guided_tours/''

*and according videos in ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/videos/''

*Research and activities at Remeis from the radio to the gamma-rays (Tobi Beuchert): ''/data/media/presentations_for_guided_tours/Andrea_tour_material/observations_allwavelength_remeisresearch_beuchert.pdf''

*A presentation showing the astrophotography done at the observatory: ''/data/media/slideshow_astrophotographie/optische_Quellen.pdf''

*A video tour with Joern: ''/data/media/presentations_for_guided_tours/Joerns_example_tour''

*A video tour with Uli (only hallway): ''/data/media/presentations_for_guided_tours/Ulis_example_tour_hall_2019''

*A complete tour by Sebastian Müller: ''/data/media/presentations_for_guided_tours/Sebastians_example_tour''

*Presentations for tours by Andrea Gokus: ''/data/media/presentations_for_guided_tours/Andrea_tour_material'' Contains presentations about the solar system (solar_system.pdf), neutrinos (neutrino_talk.pdf), overview of different objet types (impressions_universe.pdf)

*Andreas tour notes: ''/data/media/presentations_for_guided_tours/Andrea_tour_material/Sternwarten_Fuehrungsnotizen.pdf''

*Amys tour notes: ''/data/media/presentations_for_guided_tours/Guided_Tour_Information_Amy.pdf''

*Tobis tour notes: ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/guidedtour.pdf''

*Information on clocks: ''/data/media/history/2009-01_KlassikUhren_Poehlmann_Max_Ort.pdf''

*Information on history of the observatory and the collection: ''/data/media/history/AstronomischeSammlung.pdf''

*History of the observatory (Litten): ''/data/media/history/Litten-1.pdf'' ''/data/media/history/Litten-2.pdf''

*Last will of Dr. Karl Remeis: ''/data/media/history/Testament_Karl_Remeis.pdf''

*Die Remeis-Sternwarte zu Bamberg 1889-1939, E. Zinner: [https://articles.adsabs.harvard.edu/cgi-bin/nph-iarticle_query?1939VeBam...4....1Z&data_type=PDF_HIGH&whole_paper=YES&type=PRINTER&filetype=.pdf ADS]

== Picture presentation ==

There are different modes for the beamer (e.g. presentation, videos, graphics etc.) which result in a different appearance of the images. Make sure to select a presentation mode in which the pictures appear in an appropriate brightness on the screen. (I think "graphics" was a good one).

== Telescopes in the domes ==
It's nice to show the main mirror to the people so that they can see themselves. To do so, just turn down the telescope in declination. This is only possible for the 40cm as the 50cm-Mount has a mechanical stop.

Sometimes people want to know what we do with the tiny, little telescopes attached on the side of the big ones. Those are guiding-scopes. You can attach a camera to them and let it take pictures of one star. If the star moves (what it shouldn't do) a correction signal is sent to the mount to compensate the movement of the star. Stars can "move" in an image for example due to impreciseness of the mount.

The (dusty) plate in front of the 40cm mirror is called "Schmid-Platte". It is used to improve the imaging of the telescope and to correct several errors of the mirrors like coma and field-curvature. As it is very sensitive to scratching, it won't be cleaned and left dusty. But the dust has hardly any effect on the images as it lays far outside of the focusplane. The optical design is similar to a Ritchey-Chrétien type regarding the capability, but has a spherical main mirror, an aspherical secondary mirror and a lens-corrector (=Schmidt-plate). The price of the telescope and the mount is roughly about 25.000€ altogether.

The 50cm doesn't have a Schmid-Platte but a corrector (lenses) placed in the OAZ. It has an elliptical main mirror and a spherical secondary mirror (Corrected Dall Kirkham). The price of the telescope and the mount is roughly about 65.000€. The secondary mirror is, compared to the size of the main mirror, significantly larger than the 40cm-sec. mirror. This results in a better luminosity an a larger, flat-field which is important for taking images. We can achieve tracking accuracies of about 10min without guiding.

== Tours looking for a guide ==
ATTENTION: tours are not sorted by the date of the tour, but by their request date! 
If you want to give a tour, just email the [mailto:fuehrungen@foerderverein-sternwarte-bamberg.de guide organizers].
{| class="wikitable" style="text-align: center;
! Date & Time
! Language
! Organizer
! Additional information
! Group
! Observing
! Deadline for guides

|-
| Monday, 30.06.2025 at 21:00
| German or English
| Uni Bamberg (AG Theo)
| Tour also possible on July 7
| 25 adults
| Yes
| 09.06.2025

|-
| Thursday, 27.11.2025 at 19:00
| German
| Rotary Club Bamberg (Grupp)
| 2 guides required! Tour also possible on 29.01.2026 or 26.02.2026.
| 30 adults
| Yes
| 30.05.2025

|}

Guided Tours and Public Outreach

2025-05-07T13:03:21Z

Thalhammer: /* Material and Presentations */

[[Category:internal]]
On this pages you can find all information needed to guide a tour through our observatory for public people.

= General =

Tours are officially '''organized''' by the [http://foerderverein-sternwarte-bamberg.de Foerderverein of the observatory], but '''operated''' by the observatory staff to be insured through the university!

The main platform for the general public is [http://foerderverein-sternwarte-bamberg.de/fuehrungen http://foerderverein-sternwarte-bamberg.de/fuehrungen].

Here, tours can be ordered in two different ways:
* single persons and smaller groups can directly book public and regular guided tours via our webform at https://www.sternwarte.uni-erlangen.de/guided-tours/
* larger groups may directly ask for a tour at a separate date either by email to [mailto:fuehrungen@foerderverein-sternwarte-bamberg.de fuehrungen@foerderverein-sternwarte-bamberg.de] or by phone. All guided tour administrators have access to that email inbox.

The source code of the webform for booking a public tour can be found in the GIT repository at 
[https://www.sternwarte.uni-erlangen.de/gitlab/webmaster/guided-tours https://www.sternwarte.uni-erlangen.de/gitlab/webmaster/guided-tours]. 
All pushes to the master branch are automatically deployed at the official URL above!

== Mailing List / Current "staff" ==

All people interested in giving guided tours are member of the '''internal''' mailing list
[mailto:astro-fuehrungen@lists.fau.de astro-fuehrungen@lists.fau.de], '''please do not share this address with externals.
If you're not on the list but interested in giving tours, just ask Max to add you :-)

New tours are announced via this list. See [[Mailing lists]] for the list administrator.

In charge of organization:
* Nico
* Katrin (Backup and mentor :-)
* Lea (Backup)

Currently, the following people give tours on a regular basis:
* Steven
* Christian
* Aafia
* Amy
* Philipp T.
* Alexey
* Katharina
* Martin
* Nico

= Tip policy =

Starting in 2025, there are fixed "prices" for guided tours called "Unkostenbeitrag" (expense contribution). As a guide you get at least 35 euros and in case of tours on weekends or with observing even more.
The group is informed beforehand their expected expense contribution and asked to transfer the money to the Foerderverein. After the tour, you will get reimbursed by Ingo via bank transfer.

For public tours please collect donations at the beginning of the tour. Participants are notified via email of an expected donation of 5 euros.
After giving a public tour please execute the file <code>/home/zalot/publictip.py</code> and follow the instructions :-)

= Offering Tours =

At some point you're perhaps asked to give a tour or if it is possible to have one on a specific date. The latter might occur if Edith is out of her office and her telephone is redirected. In those cases you should know ''and'' check following things:
* '''Who is asking''' for a tour? If you're on the phone ask for a name and write down the phone number where the person can be called!
* The '''number of people should be between 15 and 25'''. Of course, the boundary conditions depend on the person guiding the tour. In a case of doubt, ask the guide or, if none is found yet, you simply can't promise that there will be a tour! In that case you may offer to look for a guide giving the tour anyway (and call the person back), but again don't make any promises! A list of people offering tours can be found below.
* What is the '''average age of the persons attending''' the tour? That's an important point since the content of a tour differs between children and adults, of course. Furthermore some guides have favorite age groups!
* Carefully check the '''date and time of the tour'''!
** It's most likely to find a guide if the weekday of a tour is '''between Monday and Thursday'''. Friday might work if it is before noon, otherwise people might be on the way into the weekend. In all other cases you may offer to look for a guide giving the tour anyway (see the point about the group size above).
** Make sure that there is '''no tour scheduled already'''! For that look into our online calendar (the link can be found below) and on the whiteboard in the copying machine office.
** Related to the last point ensure that there is '''no lab course''' running at the date! The lab course is also marked in our online calendar.
** Usually, a tour will take '''about 1.5 to 2 hours'''.
* See [[Guided Tours and Public Outreach#Tip policy]] for information on the "price" of guided tours.
* '''Observing with our telescopes''' is possible, of course, but only in case of '''night and cloudless weather'''! No kidding, some people are not aware of these facts... ("The day is too bright to see stars.", "I'm sorry, we can't look trough the clouds.", "The weather forecast is too uncertain, we can't promise.") Please check if someone else has already signed in for one of the telescopes on the day/night of the guided tour! '''IMPORTANT:''' Be aware that you are not allowed to operate the telescopes on you own, there ALWAYS has to be at least a second person around. To assure that, you either have to have a second person from the observatory present (at least in the main building) or you have to set up AND disassemble everything while the people from the tour are there. Otherwise no observations are allowed to take place!
* If all the above points are clarified '''mark the tour''' in our [https://www.sternwarte.uni-erlangen.de/calendar/ online calendar] and the whiteboard in the copying machine office. You have to be at a machine at the observatory to have access to the online calendar (to be more precisely: you're machine has to have an internal IP-address). The entry into the online calendar, besides the date and time, should include "for whom is the tour and the group size, contact person and phone number, name of the guide giving the tour". The whiteboard template is as follows: "date, for whom is the tour, time, guide"

= Giving a tour =

Each tour has several stations, where you can show things or talk to the people. Useful information and experiences about that is listed below. It might be helpful as well to read the article about [[intern:Popular_science:start|popular science]] in case you want or have to (if somebody asks) explain scientific aspects.

Note that there is also a separate page about guided tour stations: https://www.sternwarte.uni-erlangen.de/wiki/index.php/Guided_tour_stations

== Preparation ==

'''Before the tour'''
* Shut the doors of all offices in the main building (at least on the ground level) for several reasons: people are not allowed to walk in there and some of us are still working there during tours!
* Remove the northern hemisphere from the model of the inner solar system located in the entrance hall (you may put it into the Knigge room)
* Switch the lights on you need:
** entrance hall
** meteorite showcase (switch is on the right next to it)
** hallway to the meridian building; here are multiple switches
*** main light: right next to the door of the hallway or the backdoor of the main building (labeled "Meridian")
*** info panels: on the opposite wall to the door next to the blue cupboard
*** showcases and Blinkkomparator: in the cutout box up the few stairs on the right wall close to the library, labeled "Linke Steckdosen"
* In case of observations
** make sure that you are '''never''' alone in the domes! There always have to be at least two people present.
** carry the needed oculars into the domes (for observations with the naked eye, the 40cm telescope is strongly recommended)
** do __not__ open the domes (first, it might start raining while nobody is there, and it's more fun for you to let the people do it)
** do __not__ remove the dust covers of the telescopes (wait until the dome has been opened)
** read the [[remeis:start|guide how to operate the telescopes and mountings]]
** after observing: shut down the telescope mounting, put the dust covers back on and close the domes
* In case of showing nice pictures
** make sure enough chairs are available
** switch on the beamer in the library, log into the machine and start your presentation, picture-viewer, ...

'''After the tour'''
* Switch the lights off
* Logout of the used machines and switch the beamer off
* Put on the dust covers of the telescopes in the hallway
* Protect the photo plates on the Blinkkomparator from getting dusty
* '''Move the entry from the whiteboard''' in the copying machine office '''to the list attached to the pin-board''' next to it

== Material and Presentations ==
*Collected information valuable for guided tours: ''/data/media/presentations_for_guided_tours'' and ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/guidedtour.pdf''

*A merger of (picture/video) presentations given at guided tours: ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/guidedtour.odp''

*Short collection of notes on using the CHT during tours: ''/home/thalhammer/userdata/guided_tours/how_to_cht/main.pdf''

*and according videos in ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/videos/''

*Research and activities at Remeis from the radio to the gamma-rays (Tobi Beuchert): ''/data/media/presentations_for_guided_tours/Andrea_tour_material/observations_allwavelength_remeisresearch_beuchert.pdf''

*A presentation showing the astrophotography done at the observatory: ''/data/media/slideshow_astrophotographie/optische_Quellen.pdf''

*A video tour with Joern: ''/data/media/presentations_for_guided_tours/Joerns_example_tour''

*A video tour with Uli (only hallway): ''/data/media/presentations_for_guided_tours/Ulis_example_tour_hall_2019''

*A complete tour by Sebastian Müller: ''/data/media/presentations_for_guided_tours/Sebastians_example_tour''

*Presentations for tours by Andrea Gokus: ''/data/media/presentations_for_guided_tours/Andrea_tour_material'' Contains presentations about the solar system (solar_system.pdf), neutrinos (neutrino_talk.pdf), overview of different objet types (impressions_universe.pdf)

*Andreas tour notes: ''/data/media/presentations_for_guided_tours/Andrea_tour_material/Sternwarten_Fuehrungsnotizen.pdf''

*Amys tour notes: ''/data/media/presentations_for_guided_tours/Guided_Tour_Information_Amy.pdf''

*Tobis tour notes: ''/userdata/data/beuchert/work/teaching/guidedtour/presentation/guidedtour.pdf''

*Information on clocks: ''/data/media/history/2009-01_KlassikUhren_Poehlmann_Max_Ort.pdf''

*Information on history of the observatory and the collection: ''/data/media/history/AstronomischeSammlung.pdf''

*History of the observatory (Litten): ''/data/media/history/Litten-1.pdf'' ''/data/media/history/Litten-2.pdf''

*Last will of Dr. Karl Remeis: ''/data/media/history/Testament_Karl_Remeis.pdf''

*Die Remeis-Sternwarte zu Bamberg 1889-1939, E. Zinner: [https://articles.adsabs.harvard.edu/cgi-bin/nph-iarticle_query?1939VeBam...4....1Z&data_type=PDF_HIGH&whole_paper=YES&type=PRINTER&filetype=.pdf ADS]

== Picture presentation ==

There are different modes for the beamer (e.g. presentation, videos, graphics etc.) which result in a different appearance of the images. Make sure to select a presentation mode in which the pictures appear in an appropriate brightness on the screen. (I think "graphics" was a good one).

== Telescopes in the domes ==
It's nice to show the main mirror to the people so that they can see themselves. To do so, just turn down the telescope in declination. This is only possible for the 40cm as the 50cm-Mount has a mechanical stop.

Sometimes people want to know what we do with the tiny, little telescopes attached on the side of the big ones. Those are guiding-scopes. You can attach a camera to them and let it take pictures of one star. If the star moves (what it shouldn't do) a correction signal is sent to the mount to compensate the movement of the star. Stars can "move" in an image for example due to impreciseness of the mount.

The (dusty) plate in front of the 40cm mirror is called "Schmid-Platte". It is used to improve the imaging of the telescope and to correct several errors of the mirrors like coma and field-curvature. As it is very sensitive to scratching, it won't be cleaned and left dusty. But the dust has hardly any effect on the images as it lays far outside of the focusplane. The optical design is similar to a Ritchey-Chrétien type regarding the capability, but has a spherical main mirror, an aspherical secondary mirror and a lens-corrector (=Schmidt-plate). The price of the telescope and the mount is roughly about 25.000€ altogether.

The 50cm doesn't have a Schmid-Platte but a corrector (lenses) placed in the OAZ. It has an elliptical main mirror and a spherical secondary mirror (Corrected Dall Kirkham). The price of the telescope and the mount is roughly about 65.000€. The secondary mirror is, compared to the size of the main mirror, significantly larger than the 40cm-sec. mirror. This results in a better luminosity an a larger, flat-field which is important for taking images. We can achieve tracking accuracies of about 10min without guiding.

== Tours looking for a guide ==
ATTENTION: tours are not sorted by the date of the tour, but by their request date! 
If you want to give a tour, just email the [mailto:fuehrungen@foerderverein-sternwarte-bamberg.de guide organizers].
{| class="wikitable" style="text-align: center;
! Date & Time
! Language
! Organizer
! Additional information
! Group
! Observing
! Deadline for guides

|-
| Monday, 30.06.2025 at 21:00
| German or English
| Uni Bamberg (AG Theo)
| Tour also possible on July 7
| 25 adults
| Yes
| 09.06.2025

|-
| Thursday, 27.11.2025 at 19:00
| German
| Rotary Club Bamberg (Grupp)
| 2 guides required! Tour also possible on 29.01.2026 or 26.02.2026.
| 30 adults
| Yes
| 30.05.2025
|}

Nicer

2025-04-10T13:31:29Z

Thalhammer: Update on RMF/ARF selection

== NICER data extraction ==

NICER is a soft X-ray observatory on board the ISS. Biggest difference to many
other modern X-ray satellites are its silicon drift detectors and X-ray
concentrators (instead of focusing mirrors), which together do not permit
imaging capabilities. While this simplifies the data extraction, it is also required
to simulate a background for each observation. Previously downloaded
NICER observations can be found under /data/X-ray/nicer/.

=== Preparation:===

To apply the the latest calibration and filtering, first run
'xtiprepare'. The script will produce cleaned event
files inside the subdirectory 'reprocessed' inside 'prepdir'.

<pre>
#!/bin/csh

set datadir = /data/X-ray/nicer/data/2200570101
set prepdir = '/userdata/data/$user/where/ever/you/want'

xtiprepare --datadir=$datadir --prepdir=$prepdir
</pre>

If you notice an increased background in the resulting spectra, you
can apply additional filter criteria during the preparation. See
'xtiprepare --help' for more information.

=== Spectrum and Light-curve Extraction:===

To produce light-curves, spectra and apply barycenter correction
'xtiextract' can be used as follows.

<pre>
#!/bin/csh

set prepdir = '/userdata/data/$user/where/ever/you/want'
set dirname = 'extraction_123'

xtiextract --name=$dirname --prepdir=$prepdir

</pre>

The produced spectrum and light-curve can then be found in the
subdirecory 'dirname' in $prepdir. Observation-specific
response files are generated and header keywords are set accordingly. It is still advisable to double-check that they are correctly loaded into e.g. ISIS.

=== Background generation: ===

As we cannot produce a background spectrum from an off-source region on the
detector, a background spectrum has to be modeled. Currently there are three
different tools available for that purpose (sw', '3c50' and 'scorpeon').
One based on external parameters during the observation (i.e., space weather,
solar angle and cutoff-rigidity of earths B-field), one based on the internal
distribution of measured events and one using both and giving the user the
option to adjust/fit the different background components.

You can switch between them using the bkgmod_ parameter of extraction.
Only the sw-model is currently able to also provide background light-curves.
For more information see : 
https://heasarc.gsfc.nasa.gov/docs/nicer/tools/nicer_bkg_est_tools.html

=== Issues to keep in mind: ===

Feel free to expand this list whenever you came across any new issues.

''' Optical loading: '''

When optical light is reflected onto the detectors, this can
significantly increase the low-energy background below 3keV. This is
most significant for solar angles below ~70 degrees. However, due to
its position on the ISS this can also happen at any solar angle when
light is reflected by other part of the ISS.

''' Polar Horns: '''

Unlike other observatories in LEO the ISS is on an orbit with a quite
high inclination of 51.6 degrees. This means the ISS passes through
the so called polar horn regions, where the outer Van Allen belt reach
LEO. These regions can feature an increased population of energetic
electrons, which can induce a strong background signal in NICER,
particular at higher energies. 
See this "science nugget" for more information: 
https://heasarc.gsfc.nasa.gov/docs/nicer/science_nuggets/20180809.html

''' Overly aggressive filtering: '''

It can happen, that e.g. optical loading leads to a filter parameter
exceeding the standard filter criteria for most of certain
observations.
If that happens you should check the .mkf-file and see whether any of the parameters
exceeds the default filter criteria specified in the fhelp of nimaketime.
This can be done e.g. using fplot:
fplot *.mkf TIME "FPM_UNDERONLY_COUNT SUN_ANGLE FPM_OVERONLY_COUNT SUNSHINE "

Such an observation might still be of interest, however.
In that case one might want to increase the allowed range e.g. for
"underonly_range" in "xtiprepare".

''' Large event files: '''

The downloaded eventfiles are generally compressed and are extracted to memory
before the data processing. This fails for large eventfiles of several GB.
In this case one has to unzip the file event_cl/niXXXXXXXXXX_0mpu7_ufa.evt.gz
before running xtiprepare.

''' Active FPMs: '''

NICER has 56 focal-plane modules (FPMs) of which 52 are usually active. For
different reasons, e.g. annealing, sometimes some FPMs are switched off. And
sometimes you have excluded certain FPMs because of their increased background
(especially FPM 14 & 34). In both cases you have to be careful to scale the ARF
or generate a new one. So one should check the event files how many detectors where
active during the observation. 
More info here: https://heasarc.gsfc.nasa.gov/docs/nicer/analysis_threads/arf-rmf/

''' Damage to the optical bench '''

On May 22, 2023, between 13:00 and 14:00 UTC, NICER appears to have developed a
visible-light leak in the X-ray Timing Instrument (XTI) optical bench. This leads to
and increase in the undershoot rate, background at soft energies and can lead to
detectors switching off, telemetry saturation, and spurious timing features.
This only affects observations performed during orbital days. Night time observations
are unaffected.

[[Category:Data Extraction]]

Chandra

2025-03-06T17:03:04Z

Thalhammer: /* Chandra */

====== Chandra ======

Generally, if you run into errors, try and unload HEASoft.

===== HETG =====

As of Aug 2014, the old Chandra HETG extraction scripts by Manfred are deprecated. They were good for Ciao Versions up to 4.2. Ciao 4.3 already has a bug that does not cause error messages with this script but whose bug fix is not implemented. On top of that a lot has changed. We have newer extraction scripts working with Ciao-4.6 that should be much easier to maintain with future changes to data preparation with Ciao, as the data preparation is now based on ''chandra_repro''.

Data preparation and data extraction are two separate steps, i.e., the data only needs to be prepared / reprocessed once (making sure the newest and most appropriate CALDB information is used for each observation), but then can be used for extration of spectra, lightcurves, and images multiple times, e.g., with different GTIs. The scripts can be found at:
<code>
/data/system/software/scripts/chandrascripts/
</code>
and are called ''chandraprepare'' and ''gratingsextract''. Calling the scripts with no option or with ''--help'' will print a description of available options / arguments to STDOUT.

==== Caveats ====
<code>
The scripts currently have issues with data in CC mode.
</code>

<code>
If there are multiple event1 files in the archive directory, the script will exit with a warning.
</code>
Correct use of multi-event1 file observation is pending implementation. Talk to the Remeis Chandra-point of contact.

==== chandraprepare ====
Example bash script to call chandraprepare (update the Ciao version if applicable):
<pre>
#!/bin/bash

. /data/system/software/chandra/ciao-4.6/ciao-4.6/bin/ciao.bash

export CHANDRATOOLS=/data/system/software/scripts/chandrascripts

chandraprepare=${CHANDRATOOLS}/chandraprepare

cdata=/eu/X-ray/Chandra/archive/${obsid}/
obsid=1600
datadir=${cdata}/${obsid}

${chandraprepare} --datadir=${datadir} --prepdir=test${obsid}
</pre>

==== gratingsextract ====
Example bash script to call gratingsextract (update the Ciao version if applicable):
<pre>
#!/bin/bash

. /data/system/software/chandra/ciao-4.6/ciao-4.6/bin/ciao.bash

export CHANDRATOOLS=/data/system/software/scripts/chandrascripts

extract=${CHANDRATOOLS}/gratingsextract

obsid=1600
name=full

${extract} --prepdir=${obsid} --name=${name} --heg --meg --order=-1,1 --dt=25.5 --energyband=500,1500,3000,10000
</pre>

==== Loading data in ISIS ====
The above scripts create individual files for each arm/order, even for lightcurves. While the old Manfred-scripts wrote loadscripts to ease loading the data in ISIS, the new script do not provide ''loaddata.sl'' scripts anymore. The naming scheme for the extracted data changed slightly and is now generic enough to allow for common load functions for HETG data. Talk to Natalie for functions that easily load spectral data (preserving the order established by the old extraction scripts to allow for compatibility with old isis ''par'' files), individual lightcurves and the sum over lightcurves.

Eventually, these function will make it into the ''isisscripts''.

----

===== LETG =====

Theoretically, the new scripts described above can handle LETG observations. However, this is largely untested.

----

===== ACIS-I =====
Global scripts are yet missing.

[[Category:Data Extraction]]

Chandra

2025-03-06T17:02:40Z

Thalhammer: /* Chandra */

====== Chandra ======

If you run into errors, try and unload HEASoft.

===== HETG =====

As of Aug 2014, the old Chandra HETG extraction scripts by Manfred are deprecated. They were good for Ciao Versions up to 4.2. Ciao 4.3 already has a bug that does not cause error messages with this script but whose bug fix is not implemented. On top of that a lot has changed. We have newer extraction scripts working with Ciao-4.6 that should be much easier to maintain with future changes to data preparation with Ciao, as the data preparation is now based on ''chandra_repro''.

Data preparation and data extraction are two separate steps, i.e., the data only needs to be prepared / reprocessed once (making sure the newest and most appropriate CALDB information is used for each observation), but then can be used for extration of spectra, lightcurves, and images multiple times, e.g., with different GTIs. The scripts can be found at:
<code>
/data/system/software/scripts/chandrascripts/
</code>
and are called ''chandraprepare'' and ''gratingsextract''. Calling the scripts with no option or with ''--help'' will print a description of available options / arguments to STDOUT.

==== Caveats ====
<code>
The scripts currently have issues with data in CC mode.
</code>

<code>
If there are multiple event1 files in the archive directory, the script will exit with a warning.
</code>
Correct use of multi-event1 file observation is pending implementation. Talk to the Remeis Chandra-point of contact.

==== chandraprepare ====
Example bash script to call chandraprepare (update the Ciao version if applicable):
<pre>
#!/bin/bash

. /data/system/software/chandra/ciao-4.6/ciao-4.6/bin/ciao.bash

export CHANDRATOOLS=/data/system/software/scripts/chandrascripts

chandraprepare=${CHANDRATOOLS}/chandraprepare

cdata=/eu/X-ray/Chandra/archive/${obsid}/
obsid=1600
datadir=${cdata}/${obsid}

${chandraprepare} --datadir=${datadir} --prepdir=test${obsid}
</pre>

==== gratingsextract ====
Example bash script to call gratingsextract (update the Ciao version if applicable):
<pre>
#!/bin/bash

. /data/system/software/chandra/ciao-4.6/ciao-4.6/bin/ciao.bash

export CHANDRATOOLS=/data/system/software/scripts/chandrascripts

extract=${CHANDRATOOLS}/gratingsextract

obsid=1600
name=full

${extract} --prepdir=${obsid} --name=${name} --heg --meg --order=-1,1 --dt=25.5 --energyband=500,1500,3000,10000
</pre>

==== Loading data in ISIS ====
The above scripts create individual files for each arm/order, even for lightcurves. While the old Manfred-scripts wrote loadscripts to ease loading the data in ISIS, the new script do not provide ''loaddata.sl'' scripts anymore. The naming scheme for the extracted data changed slightly and is now generic enough to allow for common load functions for HETG data. Talk to Natalie for functions that easily load spectral data (preserving the order established by the old extraction scripts to allow for compatibility with old isis ''par'' files), individual lightcurves and the sum over lightcurves.

Eventually, these function will make it into the ''isisscripts''.

----

===== LETG =====

Theoretically, the new scripts described above can handle LETG observations. However, this is largely untested.

----

===== ACIS-I =====
Global scripts are yet missing.

[[Category:Data Extraction]]

Guided tour stations

2024-12-12T14:14:31Z

Thalhammer: /* Coelostat */

This is a collection of the stations that can be visited during a tour through the observatory. This page is meant to give some information on those stations, what they show, where they came from, and what they have been used for (if applicable).

== Hallway ==

''The information here is mostly taken from the tour given by Joern and recorded by Matthias.''

=== Dr. Karl Remeis' telescope ===

[[File:remeis-table-telescope.jpg|center|150px|Dr. Karl Remeis' table telscope]]
This telescope was owned privately by Dr. Karl Remeis. It was manufactured in the workshop of Utzschneider and Frauenhofer between 1815 and 1845. It has a very small field of view, more similar to Newtons' telescope.

=== First glass cabinet ===

<gallery mode="packed" widths=150px>
File:first-glass-cabinet-left.jpg|Glass cabinet left side
File:first-glass-cabinet-right.jpg|Glass cabinet right side
</gallery>
The cabinet contains a collection of instruments used to measure positions and to calibrate instruments. On the bottom left are levels to determined the plane of the horizon. A level calibrator allows to check the accuracy of the instrument. A screw allows to adjust where the air bubble inside the level is. If the level is oriented parallel to the horizontal plane the air bubble is in the center of the scale.

The bottom right wooden construction is used as an artificial horizon. In some cases, where it is difficult to determine the horizon plane, a reflecting liquid (like mercury) is poured on the surface. Due to the law of reflection the incoming and reflected light has the same angle at the reflection surface. From this the horizontal plane can be determined. The containers in the back were used to store the reflecting liquids. The wooden housing on the right is used to shield against motion of the air.

The two instruments on the wall are an Oktant and Sextant. Both are used to measure angles from the horizon. The difference between those are that an Oktant covers 1/8th of a circle, the Sextant 1/6th.

=== First tall glass cabinet ===

<gallery mode="packed" widths=150px>
File:first-tall-cabinet-bottom.jpg|First tall glass cabinet bottom
File:first-tall-cabinet-top.jpg|First tall glass cabinet top
</gallery>
The cabinet contains two "universal instruments", tools that allow to measure angles between two objects. The instruments were bought by Dr. Karl Remeis.

=== Small wooden telescope ===

[[File:small-refractor.jpg|center|150px|Wooden telescope]]

=== Coelostat ===

[[File:coelostat.jpg|center|150px|Coelostat]]

Ein Coelostat der Münchner Firma Linhoff: Er war Teil der Venustransit-Expedition 1874 zu den Aucklandinseln, und wurde 1899 von der Sternwarte erworben. Diese setzte ihn bis 1950 für einen 100-mm-Heliographen ein, mit dem 1350 Sonnenaufnahmen zur Untersuchung der Flecken entstanden. Jedoch ist einer der beiden Spiegel in der aktuellen Konfiguration fehlerhaft montiert und wäre daher nicht funktionsfähig.

=== Right ascension and declination disks ===

[[File:telescope-mount-disks.jpg|center|150px|Right ascension and declination disks]]
These disks get attached to the mount of the telescope and allow to adjust the orientation to precise coordinates.

=== Hanging cabinet ===

[[File:hanging-cabinet.jpg|center|150px|Hanging cabinet with oculars for the Schroeder refractor]]

=== Schröder refractor ===

[[File:schroeder-refractor.jpg|center|150px|Schroeder refractor]]

=== Stone carved sky charts ===

<gallery mode="packed" widths=150px>
File:sky-chart-stone-1.jpg|Print stone for the sky surveys (1)
File:sky-chart-stone-2.jpg|Print stone for the sky surveys (2)
</gallery>

=== Telescope auto tracking ===

[[File:auto-guider.jpg|center|150px|Mechanical auto guider with flywheels]]

=== Second tall glass cabinet ===

<gallery mode="packed" widths=150px>
File:second-tall-cabinet-bottom.jpg|Bottom
File:second-tall-cabinet-middle.jpg|middle
File:second-tall-cabinet-top.jpg|Top
</gallery>
At the bottom are two apertures that allow to reduce the light of the star under investigation for a telescope. A second, reference, star is used to match the visual brightness with this aperture. With this one can determine the relative brightness between the two stars in amounts of blocked light by the aperture.

In the middle, prism circle (?). Similar to a Sextant, allows to measure angles but uses a full circle and prisms instead of mirrors.

Top shows a small telescope. Origin unknown.

=== Cameras ===

<gallery mode="packed" widths=150px>
File:photo-plate-cam-1.jpg|Camera 1
File:photo-plate-cam-2.jpg|Camera 2
File:photo-plate-cam-3.jpg|Camera 3
</gallery>
The lenses in front of the gray boxes, cylinders allow to mount photo plates on their back. This way one can take pictures of the night sky. Remember, this is pre CCD times.

=== Schmidt camera ===

<gallery mode="packed" widths=150px>
File:schmidt-cam-1.jpg|Camera 1
File:schmidt-cam-2.jpg|Camera 2 (show inside!)
</gallery>
The design of the Schmidt camera allowed to reduce the manufacturing costs drastically. This gave hobby astronomers access to affordable instruments. It was achieved by replacing the costly parabolic mirror with a much cheaper spherical mirror plus a correction lens to reduce the errors from the spherical shape.

=== Sky survey cabinet ===

[[File:sky-survey-cabinet.jpg|center|150px|Survey cabinet]]

=== Cassegrain telescope from Boyden observatory ===

<gallery mode="packed" widths=150px>
File:boyde-cassegrain.jpg|Survey cabinet
File:survey-cam-array.jpg|Survey cabinet
</gallery>

=== Blinkkomparator ===

[[File:blinkkomparator.jpg|center|150px|The Blinkkomparater]]

=== Wavelength posters ===

=== Eclipse posters ===

=== Sun projector ===

[[File:sun-projector.jpg|center|150px|Sun projector]]

[[Category:Internal]]
[[Category:Guided-tours]]

Pulse Profiles: A quickstart guide

2024-06-07T15:00:34Z

Thalhammer: /* Pulse profiles from event files */

=== Pulse Profiles in ISIS ===

This is a very short introduction on how to generate X-ray pulse profile in ISIS. To begin, you need either the arrival times of all the events in your observation or a light-curve of this observation. While it is less important when using a local pulse period and a short observation, it would be advisable to use barycentered times and depending on your source apply also orbital correction (usually less important).

In the following we will use a NICER observation of EXO 2030+375 as an example.

=== Pulse profiles from event files ===

First we want to describe the generation of pulse profiles directly from the (cleaned) event file. For this we load the event file into ISIS. Then we might want to select the events by their energy, which is usually quantified in the PI or PHA parameter in the eventfile. For NICER the relationship is simply
EN / 1keV = PI * 0.01 .
For NuSTAR the relation would be
EN / 1keV = PI * 0.04 + 1.6 .

<pre>
variable filename = "/userdata/data/thalhammer/3C50_EXO230_highres/4201960150/ni4201960150_0mpu7_cl.evt";

variable evts = fits_read_table(filename);

variable n = where (50 < evts.pi < 1000 );
variable tms = evts.time [n] ;
</pre>

To find the local pulse period we use the function "epfold" (make sure to consult 'help epfold') to fold the event times onto a range of trial pulse periods and calculate according to some statistic where the resulting profile shows the most deviation from flat noise.
It is crucial for both speed and accuracy of this step to provide a reasonable range of periods.
Further you want to provide the GTIs where events were actually detectable.

<pre>
variable gti = fits_read_table( filename + "[GTI]");

variable ep = epfold(tms,41.15,41.25;gti=gti);
</pre>

To find the local period we will first have a look at the resulting statistic and determine its maximum. You know that your results are reliable if the plot below "looks like its giving you the finger" and has a clear maximum:

<pre>
xlabel("ep.p"); ylabel("ep.stat");
plot(ep.p , ep.stat);

variable p = ep.p [wherefirstmax (ep.stat)];
</pre>

[[file:Epfold.png|560px]]

Finding the peak of this function can also be made more precise, e.g. by fitting a Gaussian, but we will keep it simple in this example. Now that we know the local period, we can simply fold on this period to get profile. Consult "help pfold" if you want e.g. a higher number of phase bins:

<pre>
variable pf = pfold(tms, p ;gti=gti);
hplot_with_err (pf);
</pre>

[[file:Pprofile.png|560px]]

=== Pulse profiles from light-curves ===

The whole thing can also be done using light-curves. The advantage is that this includes for some observatories, e.g. NuSTAR, additional corrections such as vignetting. Further this allows for background to be subtracted. However, each energy selection requires a new run of e.g nuextract. The script would then look like this:

<pre>
variable filename = "ni4201960150_0.01s_0500eV-10000eV.lc";
variable dt = 0.01;
variable lc = fits_read_table(filename);
variable gti = fits_read_table(filename+"[GTI]");

variable ep = epfold(lc.time,lc.rate,41.0,41.4;gti=gti ,dt=dt*lc.fracexp);
variable p = ep.p [wherefirstmax (ep.stat)];

variable pf = pfold(lc.time,lc.rate, p;dt=dt,gti=gti,fracexp=lc.fracexp);

</pre>

=== Further resources: ===
* It might be interesting to read up on some of the higher level functions implemented by Matthias: find_peak, pulseperiod_search, pulseperiod_magic, pulseperiod_epfold
* There is also a pulse profile review in work. A draft of which can be obtained e.g. by asking Joern.

[[Category:Isis / Slang]]

Pulse Profiles: A quickstart guide

2024-06-07T12:44:13Z

Thalhammer:

=== Pulse Profiles in ISIS ===

This is a very short introduction on how to generate X-ray pulse profile in ISIS. To begin, you need either the arrival times of all the events in your observation or a light-curve of this observation. While it is less important when using a local pulse period and a short observation, it would be advisable to use barycentered times and depending on your source apply also orbital correction (usually less important).

In the following we will use a NICER observation of EXO 2030+375 as an example.

=== Pulse profiles from event files ===

First we want to describe the generation of pulse profiles directly from the (cleaned) event file. For this we load the event file into ISIS. Then we might want to select the events by their energy, which is usually quantified in the PI or PHA parameter in the eventfile. For NICER the relationship is simply
EN / 1keV = PI * 0.01 .
For NuSTAR the relation would be
EN / 1keV = E = PI * 0.04 + 1.6 .

<pre>
variable filename = "/userdata/data/thalhammer/3C50_EXO230_highres/4201960150/ni4201960150_0mpu7_cl.evt";

variable evts = fits_read_table(filename);

variable n = where (50 < evts.pi < 1000 );
variable tms = evts.time [n] ;
</pre>

To find the local pulse period we use the function "epfold" (make sure to consult 'help epfold') to fold the event times onto a range of trial pulse periods and calculate according to some statistic where the resulting profile shows the most deviation from flat noise.
It is crucial for both speed and accuracy of this step to provide a reasonable range of periods.
Further you want to provide the GTIs where events were actually detectable.

<pre>
variable gti = fits_read_table( filename + "[GTI]");

variable ep = epfold(tms,41.15,41.25;gti=gti);
</pre>

To find the local period we will first have a look at the resulting statistic and determine its maximum. You know that your results are reliable if the plot below "looks like its giving you the finger" and has a clear maximum:

<pre>
xlabel("ep.p"); ylabel("ep.stat");
plot(ep.p , ep.stat);

variable p = ep.p [wherefirstmax (ep.stat)];
</pre>

[[file:Epfold.png|560px]]

Finding the peak of this function can also be made more precise, e.g. by fitting a Gaussian, but we will keep it simple in this example. Now that we know the local period, we can simply fold on this period to get profile. Consult "help pfold" if you want e.g. a higher number of phase bins:

<pre>
variable pf = pfold(tms, p ;gti=gti);
hplot_with_err (pf);
</pre>

[[file:Pprofile.png|560px]]

=== Pulse profiles from light-curves ===

The whole thing can also be done using light-curves. The advantage is that this includes for some observatories, e.g. NuSTAR, additional corrections such as vignetting. Further this allows for background to be subtracted. However, each energy selection requires a new run of e.g nuextract. The script would then look like this:

<pre>
variable filename = "ni4201960150_0.01s_0500eV-10000eV.lc";
variable dt = 0.01;
variable lc = fits_read_table(filename);
variable gti = fits_read_table(filename+"[GTI]");

variable ep = epfold(lc.time,lc.rate,41.0,41.4;gti=gti ,dt=dt*lc.fracexp);
variable p = ep.p [wherefirstmax (ep.stat)];

variable pf = pfold(lc.time,lc.rate, p;dt=dt,gti=gti,fracexp=lc.fracexp);

</pre>

=== Further resources: ===
* It might be interesting to read up on some of the higher level functions implemented by Matthias: find_peak, pulseperiod_search, pulseperiod_magic, pulseperiod_epfold
* There is also a pulse profile review in work. A draft of which can be obtained e.g. by asking Joern.

[[Category:Isis / Slang]]

Pulse Profiles: A quickstart guide

2024-06-07T12:42:42Z

Thalhammer:

=== Pulse Profiles in ISIS ===

This is a very short introduction on how to generate X-ray pulse profile in ISIS. To begin, you need either the arrival times of all the events in your observation or a light-curve of this observation. While it is less important when using a local pulse period and a short observation, it would be advisable to use barycentered times and depending on your source apply also orbital correction (usually less important).

In the following we will use a NICER observation of EXO 2030+375 as an example.

=== Pulse profiles from event files ===

First we want to describe the generation of pulse profiles directly from the (cleaned) event file. For this we load the event file into ISIS. Then we might want to select the events by their energy, which is usually quantified in the PI or PHA parameter in the eventfile. For NICER the relationship is simply
EN / 1keV = PI * 0.01 .
For NuSTAR the relation would be
EN / 1keV = E = PI * 0.04 + 1.6 .

<pre>
variable filename = "/userdata/data/thalhammer/3C50_EXO230_highres/4201960150/ni4201960150_0mpu7_cl.evt";

variable evts = fits_read_table(filename);

variable n = where (50 < evts.pi < 1000 );
variable tms = evts.time [n] ;
</pre>

To find the local pulse period we use the function "epfold" (make sure to consult 'help epfold') to fold the event times onto a range of trial pulse periods and calculate according to some statistic where the resulting profile shows the most deviation from flat noise.
It is crucial for both speed and accuracy of this step to provide a reasonable range of periods.
Further you want to provide the GTIs where events were actually detectable.

<pre>
variable gti = fits_read_table( filename + "[GTI]");

variable ep = epfold(tms,41.15,41.25;gti=gti);
</pre>

To find the local period we will first have a look at the resulting statistic and determine its maximum. You know that your results are reliable if the plot below "looks like its giving you the finger" and has a clear maximum:

<pre>
xlabel("ep.p"); ylabel("ep.stat");
plot(ep.p , ep.stat);

variable p = ep.p [wherefirstmax (ep.stat)];
</pre>

[[file:Epfold.png]]

Finding the peak of this function can also be made more precise, e.g. by fitting a Gaussian, but we will keep it simple in this example. Now that we know the local period, we can simply fold on this period to get profile. Consult "help pfold" if you want e.g. a higher number of phase bins:

<pre>
variable pf = pfold(tms, p ;gti=gti);
hplot_with_err (pf);
</pre>

[[file:Pprofile.png]]

=== Pulse profiles from light-curves ===

The whole thing can also be done using light-curves. The advantage is that this includes for some observatories, e.g. NuSTAR, additional corrections such as vignetting. Further this allows for background to be subtracted. However, each energy selection requires a new run of e.g nuextract. The script would then look like this:

<pre>
variable filename = "ni4201960150_0.01s_0500eV-10000eV.lc";
variable dt = 0.01;
variable lc = fits_read_table(filename);
variable gti = fits_read_table(filename+"[GTI]");

variable ep = epfold(lc.time,lc.rate,41.0,41.4;gti=gti ,dt=dt*lc.fracexp);
variable p = ep.p [wherefirstmax (ep.stat)];

variable pf = pfold(lc.time,lc.rate, p;dt=dt,gti=gti,fracexp=lc.fracexp);

</pre>

=== Further resources: ===
* It might be interesting to read up on some of the higher level functions implemented by Matthias: find_peak, pulseperiod_search, pulseperiod_magic, pulseperiod_epfold
* There is also a pulse profile review in work. A draft of which can be obtained e.g. by asking Joern.

[[Category:Isis / Slang]]

Pulse Profiles: A quickstart guide

2024-06-07T12:37:14Z

Thalhammer:

=== Pulse Profiles in ISIS ===

This is a very short introduction on how to generate X-ray pulse profile in ISIS. To begin, you need either the arrival times of all the events in your observation or a light-curve of this observation. While it is less important when using a local pulse period and a short observation, it would be advisable to use barycentered times and depending on your source apply also orbital correction (usually less important).

In the following we will use a NICER observation of EXO 2030-375 as an example.

=== Pulse profiles from event files ===

First we want to describe the generation of pulse profiles directly from the (cleaned) event file. For this we load the event file into ISIS. Then we might want to select the events by their energy, which is usually quantified in the PI or PHA parameter in the eventfile. For NICER the relationship is simply
EN / 1keV = PI * 0.01 .
For NuSTAR the relation would be
EN / 1keV = E = PI * 0.04 + 1.6 .

<pre>
variable filename = "/userdata/data/thalhammer/3C50_EXO230_highres/4201960150/ni4201960150_0mpu7_cl.evt";

variable evts = fits_read_table(filename);

variable n = where (50 < evts.pi < 1000 );
variable tms = evts.time [n] ;
</pre>

To find the local pulse period we use the function "epfold" (make sure to consult "help epfold") to fold the event times onto a range of trial pulse periods and calculate according to some statistic where the resulting profile shows the most deviation from flat noise.
It is crucial for both speed and accuracy of this step to provide a reasonable range of periods.
Further you want to provide the GTIs where events were actually detectable.

<pre>
variable gti = fits_read_table( filename + "[GTI]");

variable ep = epfold(tms,41.15,41.25;gti=gti);
</pre>

To find the local period we will first have a look at the resulting statistic and determine its maximum. You know that your results are reliable if the plot below "looks like its giving you the finger" and has a clear maximum:

<pre>
xlabel("ep.p"); ylabel("ep.stat");
plot(ep.p , ep.stat);

variable p = ep.p [wherefirstmax (ep.stat)];
</pre>

[[file:Epfold.png]]

Finding the peak of this function can also be made more precise, e.g. by fitting a Gaussian, but will keep it simple in this example. Now that we know the local period, we can simply fold on this period to get profile. Consult "help pfold" if you want e.g. a higher number of phase bins:

<pre>
variable pf = pfold(tms, p ;gti=gti);
hplot_with_err (pf);
</pre>

[[file:Pprofile.png]]

=== Pulse profiles from light-curves ===

The whole thing can also be done using light-curves. The advantage is that this includes for some observatories, e.g. NuSTAR, addition corrections such as vignetting and a background can be subtracted. However, each energy selection requires a new run of e.g nuextract. The script would then look like this

<pre>
variable filename = "ni4201960150_0.01s_0500eV-10000eV.lc";
variable dt = 0.01;
variable lc = fits_read_table(filename);
variable gti = fits_read_table(filename+"[GTI]");

variable ep = epfold(lc.time,lc.rate,41.0,41.4;gti=gti ,dt=dt*lc.fracexp);
variable p = ep.p [wherefirstmax (ep.stat)];

variable pf = pfold(lc.time,lc.rate, p;dt=dt,gti=gti,fracexp=lc.fracexp);

</pre>

=== Further resources: ===
* It might be interesting to read up on the help for some of the higher level functions implemented by Matthias: find_peak, pulseperiod_search, pulseperiod_magic, pulseperiod_epfold
* There is also a pulse profile review in work. A draft of which can be captained from some people at the observatory

[[Category:Isis / Slang]]

Pulse Profiles: A quickstart guide

2024-06-07T12:34:29Z

Thalhammer: Typos

=== Pulse Profiles in ISIS ===

This is a very short introduction on how to generate X-ray pulse profile in ISIS. To begin, you need either the arrival times of all the events in your observation or a light-curve of this observation. While it is less important when using a local pulse period and a short observation, it would be advisable to use barycentered times and depending on your source apply also orbital correction (usually less important).

In the following we will use a NICER observation of EXO 2030-375 as an example.

=== Pulse profiles from event files ===

First we want to describe the generation of pulse profiles directly from the (cleaned) event file. For this we load the event file into isis. Then we might want to select the event by their energy, which is usually quantified in the PI or PHA parameter. For NICER the relationship is simply
EN / 1keV = PI * 0.01
For NuSTAR the relation would be
EN / 1keV = E = PI * 0.04 + 1.6

<pre>
variable filename = "/userdata/data/thalhammer/3C50_EXO230_highres/4201960150/ni4201960150_0mpu7_cl.evt";

variable evts = fits_read_table(filename);

variable n = where (50 < evts.pi < 1000 );
variable tms = evts.time [n] ;
</pre>

To find the local pulse period we use the function "epfold" (make sure to consult "help epfold") to fold the event times onto a range of trial pulse profiles and calculate according to some statistic where the resulting profile shows the most deviation from flat noise.
It is crucial for both speed and accuracy of this step to provide a reasonable range of periods to sample.
Further you want to provide the GTIs where events where actually detectable.

<pre>
variable gti = fits_read_table( filename + "[GTI]");

variable ep = epfold(tms,41.15,41.25;gti=gti);
</pre>

To find the local period we will first have a look at the resulting statistic and determine its maximum. You know that your results are reliable if the plot below "looks like its giving you the finger" and has a clear maximum:

<pre>
xlabel("ep.p"); ylabel("ep.stat");
plot(ep.p , ep.stat);

variable p = ep.p [wherefirstmax (ep.stat)];
</pre>

[[file:Epfold.png]]

Finding the peak of this function can also be made more precise, e.g. by fitting a Gaussian, but will keep it simple in this example. Now that we know the local period, we can simply fold on this period to get profile. Consult "help pfold" if you want e.g. a higher number of phase bins:

<pre>
variable pf = pfold(tms, p ;gti=gti);
hplot_with_err (pf);
</pre>

[[file:Pprofile.png]]

=== Pulse profiles from light-curves ===

The whole thing can also be done using light-curves. The advantage is that this includes for some observatories, e.g. NuSTAR, addition corrections such as vignetting and a background can be subtracted. However, each energy selection requires a new run of e.g nuextract. The script would then look like this

<pre>
variable filename = "ni4201960150_0.01s_0500eV-10000eV.lc";
variable dt = 0.01;
variable lc = fits_read_table(filename);
variable gti = fits_read_table(filename+"[GTI]");

variable ep = epfold(lc.time,lc.rate,41.0,41.4;gti=gti ,dt=dt*lc.fracexp);
variable p = ep.p [wherefirstmax (ep.stat)];

variable pf = pfold(lc.time,lc.rate, p;dt=dt,gti=gti,fracexp=lc.fracexp);

</pre>

=== Further resources: ===
* It might be interesting to read up on the help for some of the higher level functions implemented by Matthias: find_peak, pulseperiod_search, pulseperiod_magic, pulseperiod_epfold
* There is also a pulse profile review in work. A draft of which can be captained from some people at the observatory

[[Category:Isis / Slang]]

Pulse Profiles: A quickstart guide

2024-06-07T12:13:24Z

Thalhammer: Quick-start guide on pulse profiles in ISIS

=== Pules Profiles in ISIS ===

This is supposed to be a very short introduction on how to generate X-ray pulse profile in ISIS. To begin with you need on either the arrival times of all the events in your observation or a light-curve of this observation. While it is less important when using a local pulse period and a short observation, it would be advisable to use barycentered times and depending on your source apply also orbital correction (usually less important).

In the following we will use a NICER observation of EXO 2030-375 as an example.

=== Pulse profiles from event files ===

First we want to describe the generation of pulse profiles directly from the (cleaned) event file. For this we load the event file into isis. Then we might want to select the event by their energy, which is usually quantified in the PI or PHA parameter. For NICER the relationship is simply
EN / 1keV = PI * 0.01
For NuSTAR the relation would be
EN / 1keV = E = PI * 0.04 + 1.6

<pre>
variable filename = "/userdata/data/thalhammer/3C50_EXO230_highres/4201960150/ni4201960150_0mpu7_cl.evt";

variable evts = fits_read_table(filename);

variable n = where (50 < evts.pi < 1000 );
variable tms = evts.time [n] ;
</pre>

To find the local pulse period we use the function "epfold" (make sure to consult "help epfold") to fold the event times onto a range of trial pulse profiles and calculate according to some statistic where the resulting profile shows the most deviation from flat noise.
It is crucial for both speed and accuracy of this step to provide a reasonable range of periods to sample.
Further you want to provide the GTIs where events where actually detectable.

<pre>
variable gti = fits_read_table( filename + "[GTI]");

variable ep = epfold(tms,41.15,41.25;gti=gti);
</pre>

To find the local period we will first have a look at the resulting statistic and determine its maximum. You know that your results are reliable if the plot below "looks like its giving you the finger" and has a clear maximum:

<pre>
xlabel("ep.p"); ylabel("ep.stat");
plot(ep.p , ep.stat);

variable p = ep.p [wherefirstmax (ep.stat)];
</pre>

[[file:Epfold.png]]

Finding the peak of this function can also be made more precise, e.g. by fitting a Gaussian, but will keep it simple in this example. Now that we know the local period, we can simply fold on this period to get profile. Consult "help pfold" if you want e.g. a higher number of phase bins:

<pre>
variable pf = pfold(tms, p ;gti=gti);
hplot_with_err (pf);
</pre>

[[file:Pprofile.png]]

=== Pulse profiles from light-curves ===

The whole thing can also be done using light-curves. The advantage is that this includes for some observatories, e.g. NuSTAR, addition corrections such as vignetting and a background can be subtracted. However, each energy selection requires a new run of e.g nuextract. The script would then look like this

<pre>
variable filename = "ni4201960150_0.01s_0500eV-10000eV.lc";
variable dt = 0.01;
variable lc = fits_read_table(filename);
variable gti = fits_read_table(filename+"[GTI]");

variable ep = epfold(lc.time,lc.rate,41.0,41.4;gti=gti ,dt=dt*lc.fracexp);
variable p = ep.p [wherefirstmax (ep.stat)];

variable pf = pfold(lc.time,lc.rate, p;dt=dt,gti=gti,fracexp=lc.fracexp);

</pre>

=== Further resources: ===
* It might be interesting to read up on the help for some of the higher level functions implemented by Matthias: find_peak, pulseperiod_search, pulseperiod_magic, pulseperiod_epfold
* There is also a pulse profile review in work. A draft of which can be captained from some people at the observatory

[[Category:Isis / Slang]]

File:Pprofile.png

2024-06-07T12:08:17Z

Thalhammer: A random pulse profile of EXO2030+375 to illustrate a typical pfold result

== Summary ==
A random pulse profile of EXO2030+375 to illustrate a typical pfold result

File:Epfold.png

2024-06-07T12:07:16Z

Thalhammer: Period vs Statistic of a typical epfold run

== Summary ==
Period vs Statistic of a typical epfold run

2023-06-07T10:34:07Z

Thalhammer: /* Background generation: */

== NICER data extraction ==

NICER is a soft X-ray observatory on board the ISS. Biggest difference to many
other modern X-ray satellites are its silicon drift detectors and X-ray
concentrators (instead of focusing mirrors), which together do not permit
imaging capabilities. While this simplifies the data extraction, it is also required
to simulate a background for each observation. Previously downloaded
NICER observations can be found under /satdata/X-ray/nicer/.

=== Preparation:===

To apply the the latest calibration and filtering, first run
'xtiprepare'. The script will produce cleaned event
files inside the subdirectory 'reprocessed' inside 'prepdir'.

<pre>
#!/bin/csh

set datadir = /data/X-ray/nicer/data/2200570101
set prepdir = '/userdata/data/$user/where/ever/you/want'

xtiprepare --datadir=$datadir --prepdir=$prepdir
</pre>

If you notice an increased background in the resulting spectra, you
can apply additional filter criteria during the preparation. See
'xtiprepare --help' for more information.

=== Spectrum and Light-curve Extraction:===

To produce light-curves, spectra and apply barycenter correction
'xtiextract' can be used as follows.

<pre>
#!/bin/csh

set prepdir = '/userdata/data/$user/where/ever/you/want'
set dirname = 'extraction_123'

xtiextract --name=$dirname --prepdir=$prepdir

</pre>

The produced spectrum and light-curve can then be found in the
subdirecory 'dirname' in $prepdir. Currently no observation-specific
response files are generated, but instead soft links to the current ARF
& RMF files included in the CALDB are generated.

=== Background generation: ===

As we cannot produce a background spectrum from an off-source region on the
detector, a background spectrum has to be modeled. Currently there are three
different tools available for that purpose (sw', '3c50' and 'scorpeon').
One based on external parameters during the observation (i.e., space weather,
solar angle and cutoff-rigidity of earths B-field), one based on the internal
distribution of measured events and one using both and giving the user the
option to adjust/fit the different background components.

You can switch between them using the bkgmod_ parameter of extraction.
Only the sw-model is curreltly able to also provide background light-curves.
For more information see : 
https://heasarc.gsfc.nasa.gov/docs/nicer/tools/nicer_bkg_est_tools.html

=== Issues to keep in mind: ===

Feel free to expand this list whenever you came across any new issues.

''' Optical loading: '''

When optical light is reflected onto the detectors, this can
significantly increase the low-energy background below 3keV. This is
most significant for solar angles below ~70 degrees. However, due to
its position on the ISS this can also happen at any solar angle when
light is reflected by other part of the ISS.

''' Polar Horns: '''

Unlike other observatories in LEO the ISS is on an orbit with a quite
high inclination of 51.6 degrees. This means the ISS passes through
the so called polar horn regions, where the outer Van Allen belt reach
LEO. These regions can feature an increased population of energetic
electrons, which can induce a strong background signal in NICER,
particular at higher energies. 
See this "science nugget" for more information: 
https://heasarc.gsfc.nasa.gov/docs/nicer/science_nuggets/20180809.html

''' Overly aggressive filtering: '''

It can happen, that e.g. optical loading leads to a filter parameter
exceeding the standard filter criteria for most of certain
observations.
If that happens you should check the .mkf-file and see whether any of the parameters
exceeds the default filter criteria specified in the fhelp of nimaketime.
This can be done e.g. using fplot:
fplot *.mkf TIME "FPM_UNDERONLY_COUNT SUN_ANGLE FPM_OVERONLY_COUNT SUNSHINE "

Such an observation might still be of interest, however.
In that case one might want to increase the allowed range e.g. for
"underonly_range" in "xtiprepare".

''' Large event files: '''

The downloaded eventfiles are generally compressed and are extracted to memory
before the data processing. This fails for large eventfiles of several GB.
In this case one has to unzip the file event_cl/niXXXXXXXXXX_0mpu7_ufa.evt.gz
before running xtiprepare.

''' Active FPMs: '''

NICER has 56 focal-plane modules (FPMs) of which 52 are usually active. For
different reasons, e.g. annealing, sometimes some FPMs are switched off. And
sometimes you have excluded certain FPMs because of their increased background
(especially FPM 14 & 34). In both cases you have to be careful to scale the ARF
or generate a new one. So one should check the event files how many detectors where
active during the observation. 
More info here: https://heasarc.gsfc.nasa.gov/docs/nicer/analysis_threads/arf-rmf/

''' Damage to the optical bench '''

On May 22, 2023, between 13:00 and 14:00 UTC, NICER appears to have developed a
visible-light leak in the X-ray Timing Instrument (XTI) optical bench. This leads to
and increase in the undershoot rate, background at soft energies and can lead to
detectors switching off, telemetry saturation, and spurious timing features.
This only affects observations performed during orbital days. Night time observations
are unaffected.

[[Category:Data Extraction]]

Nicer

2023-06-07T10:09:14Z

Thalhammer:

== NICER data extraction ==

NICER is a soft X-ray observatory on board the ISS. Biggest difference to many
other modern X-ray satellites are its silicon drift detectors and X-ray
concentrators (instead of focusing mirrors), which together do not permit
imaging capabilities. While this simplifies the data extraction, it is also required
to simulate a background for each observation. Previously downloaded
NICER observations can be found under /satdata/X-ray/nicer/.

=== Preparation:===

To apply the the latest calibration and filtering, first run
'xtiprepare'. The script will produce cleaned event
files inside the subdirectory 'reprocessed' inside 'prepdir'.

<pre>
#!/bin/csh

set datadir = /data/X-ray/nicer/data/2200570101
set prepdir = '/userdata/data/$user/where/ever/you/want'

xtiprepare --datadir=$datadir --prepdir=$prepdir
</pre>

If you notice an increased background in the resulting spectra, you
can apply additional filter criteria during the preparation. See
'xtiprepare --help' for more information.

=== Spectrum and Light-curve Extraction:===

To produce light-curves, spectra and apply barycenter correction
'xtiextract' can be used as follows.

<pre>
#!/bin/csh

set prepdir = '/userdata/data/$user/where/ever/you/want'
set dirname = 'extraction_123'

xtiextract --name=$dirname --prepdir=$prepdir

</pre>

The produced spectrum and light-curve can then be found in the
subdirecory 'dirname' in $prepdir. Currently no observation-specific
response files are generated, but instead soft links to the current ARF
& RMF files included in the CALDB are generated.

=== Background generation: ===

As we cannot produce a background spectrum from an off-source region on the
detector, a background spectrum has to be modeled. Currently there are two
different tools available for that purpose. One based on external parameters
during the observation (i.e., space weather, solar angle and cutoff-rigidity of
earths B-field) amd one based on the internal distribution of measured events.
Both are still in active development and might not be able to produce realistic
spectra for all observations. In that case a simple reference observation of one
of the RXTE background fields might be used instead. 
Both tools are further described on the instruments webpage: 
https://heasarc.gsfc.nasa.gov/docs/nicer/tools/nicer_bkg_est_tools.html

=== Issues to keep in mind: ===

Feel free to expand this list whenever you came across any new issues.

''' Optical loading: '''

When optical light is reflected onto the detectors, this can
significantly increase the low-energy background below 3keV. This is
most significant for solar angles below ~70 degrees. However, due to
its position on the ISS this can also happen at any solar angle when
light is reflected by other part of the ISS.

''' Polar Horns: '''

Unlike other observatories in LEO the ISS is on an orbit with a quite
high inclination of 51.6 degrees. This means the ISS passes through
the so called polar horn regions, where the outer Van Allen belt reach
LEO. These regions can feature an increased population of energetic
electrons, which can induce a strong background signal in NICER,
particular at higher energies. 
See this "science nugget" for more information: 
https://heasarc.gsfc.nasa.gov/docs/nicer/science_nuggets/20180809.html

''' Overly aggressive filtering: '''

It can happen, that e.g. optical loading leads to a filter parameter
exceeding the standard filter criteria for most of certain
observations.
If that happens you should check the .mkf-file and see whether any of the parameters
exceeds the default filter criteria specified in the fhelp of nimaketime.
This can be done e.g. using fplot:
fplot *.mkf TIME "FPM_UNDERONLY_COUNT SUN_ANGLE FPM_OVERONLY_COUNT SUNSHINE "

Such an observation might still be of interest, however.
In that case one might want to increase the allowed range e.g. for
"underonly_range" in "xtiprepare".

''' Large event files: '''

The downloaded eventfiles are generally compressed and are extracted to memory
before the data processing. This fails for large eventfiles of several GB.
In this case one has to unzip the file event_cl/niXXXXXXXXXX_0mpu7_ufa.evt.gz
before running xtiprepare.

''' Active FPMs: '''

NICER has 56 focal-plane modules (FPMs) of which 52 are usually active. For
different reasons, e.g. annealing, sometimes some FPMs are switched off. And
sometimes you have excluded certain FPMs because of their increased background
(especially FPM 14 & 34). In both cases you have to be careful to scale the ARF
or generate a new one. So one should check the event files how many detectors where
active during the observation. 
More info here: https://heasarc.gsfc.nasa.gov/docs/nicer/analysis_threads/arf-rmf/

''' Damage to the optical bench '''

On May 22, 2023, between 13:00 and 14:00 UTC, NICER appears to have developed a
visible-light leak in the X-ray Timing Instrument (XTI) optical bench. This leads to
and increase in the undershoot rate, background at soft energies and can lead to
detectors switching off, telemetry saturation, and spurious timing features.
This only affects observations performed during orbital days. Night time observations
are unaffected.

[[Category:Data Extraction]]

Nicer

2023-06-07T10:06:36Z

Thalhammer:

== NICER data extraction ==

NICER is a soft X-ray observatory on board the ISS. Biggest difference to many
other modern X-ray satellites are its silicon drift detectors and X-ray
concentrators (instead of focusing mirrors), which together do not permit
imaging capabilities. While this simplifies the data extraction, it is also required
to simulate a background for each observation. Previously downloaded
NICER observations can be found under /satdata/X-ray/nicer/.

=== Preparation:===

To apply the the latest calibration and filtering, first run
'xtiprepare'. The script will produce cleaned event
files inside the subdirectory 'reprocessed' inside 'prepdir'.

<pre>
#!/bin/csh

set datadir = /data/X-ray/nicer/data/2200570101
set prepdir = '/userdata/data/$user/where/ever/you/want'

xtiprepare --datadir=$datadir --prepdir=$prepdir
</pre>

If you notice an increased background in the resulting spectra, you
can apply additional filter criteria during the preparation. See
'xtiprepare --help' for more information.

=== Spectrum and Light-curve Extraction:===

To produce light-curves, spectra and apply barycenter correction
'xtiextract' can be used as follows.

<pre>
#!/bin/csh

set prepdir = '/userdata/data/$user/where/ever/you/want'
set dirname = 'extraction_123'

xtiextract --name=$dirname --prepdir=$prepdir

</pre>

The produced spectrum and light-curve can then be found in the
subdirecory 'dirname' in $prepdir. Currently no observation-specific
response files are generated, but instead soft links to the current ARF
& RMF files included in the CALDB are generated.

=== Background generation: ===

As we cannot produce a background spectrum from an off-source region on the
detector, a background spectrum has to be modeled. Currently there are two
different tools available for that purpose. One based on external parameters
during the observation (i.e., space weather, solar angle and cutoff-rigidity of
earths B-field) amd one based on the internal distribution of measured events.
Both are still in active development and might not be able to produce realistic
spectra for all observations. In that case a simple reference observation of one
of the RXTE background fields might be used instead. 
Both tools are further described on the instruments webpage: 
https://heasarc.gsfc.nasa.gov/docs/nicer/tools/nicer_bkg_est_tools.html

=== Issues to keep in mind: ===

Feel free to expand this list whenever you came across any new issues.

''' Optical loading: '''

When optical light is reflected onto the detectors, this can
significantly increase the low-energy background below 3keV. This is
most significant for solar angles below ~70 degrees. However, due to
its position on the ISS this can also happen at any solar angle when
light is reflected by other part of the ISS.

''' Polar Horns: '''

Unlike other observatories in LEO the ISS is on an orbit with a quite
high inclination of 51.6 degrees. This means the ISS passes through
the so called polar horn regions, where the outer Van Allen belt reach
LEO. These regions can feature an increased population of energetic
electrons, which can induce a strong background signal in NICER,
particular at higher energies. 
See this "science nugget" for more information: 
https://heasarc.gsfc.nasa.gov/docs/nicer/science_nuggets/20180809.html

''' Overly aggressive filtering: '''

It can happen, that e.g. optical loading leads to a filter parameter
exceeding the standard filter criteria for most of certain
observations.
If that happens you should check the .mkf-file and see whether any of the parameters
exceeds the default filter criteria specified in the fhelp of nimaketime.
This can be done e.g. using fplot:
fplot *.mkf TIME "FPM_UNDERONLY_COUNT SUN_ANGLE FPM_OVERONLY_COUNT SUNSHINE "

Such an observation might still be of interest, however.
In that case one might want to increase the allowed range e.g. for
"underonly_range" in "xtiprepare".

''' Large event files: '''

The downloaded eventfiles are generally compressed and are extracted to memory
before the data processing. This fails for large eventfiles of several GB.
In this case one has to unzip the file event_cl/niXXXXXXXXXX_0mpu7_ufa.evt.gz
before running xtiprepare.

''' Active FPMs: '''

NICER has 56 focal-plane modules (FPMs) of which 52 are usually active. For
different reasons, e.g. annealing, sometimes some FPMs are switched off. And
sometimes you have excluded certain FPMs because of their increased background
(especially FPM 14 & 34). In both cases you have to be careful to scale the ARF
or generate a new one. So one should check the event files how many detectors where
active during the observation. 
More info here: https://heasarc.gsfc.nasa.gov/docs/nicer/analysis_threads/arf-rmf/

''' Damage to the optical bench '''
On May 22, 2023, between 13:00 and 14:00 UTC, NICER appears to have developed a
visible-light leak in the X-ray Timing Instrument (XTI) optical bench. This leads to
and increase in the undershoot rate, background at soft energies and can lead to
detectors switching off, telemetry saturation, and spurious timing features.
This only affects observations performed during orbital days. Night time observations
are unaffected.

[[Category:Data Extraction]]