Remeis-Wiki - User contributions [en]

LXD 75

2021-04-28T11:53:26Z

Kuehnel:

[[Category:Current Members]]

[https://www.meade.com/pub/media/downloads/40/LXD-75C.pdf Instruction manual] of the LXD 75 telescope and tripod

'''MEADE LXD 75 Telescope'''

* to assemble on one of the two east pillars in the garden
* or on its portable tripod for observing elsewhere

'''Tripod'''

* mountable telescopes:
** [[MEADE 10 Inch]]
** [[115mm apochromatic refractor]]
** [[Coronado PST]]
** [http://www.luntsolarsystems-by-apmtelescopes.com/pro_info.php?ebene1=48&id=94473&catchoice1= Solar telescope 60mm H-alpha]
* for information about assembling the tripod see the [[lab course manual]], section telescopes
* don't forget the equipment case

'''Equipment case'''

silver colored case in the main buildings basement (CCD lab room), contains
* Autostar Handbox
* power supply

FAUmail Spam Filter

2020-06-18T09:35:02Z

Kuehnel:

According to the RRZE no filtering on spam emails is performed, but each email is analyzed on spam and ranked accordingly (see [https://www.rrze.fau.de/internet-e-mail/e-mail/anti-spam/spam-analyse/ Spam-Analyse und -Filterung] on the RRZE website). This rank is added to email header as '''X-Spam-Score''' field with values roughly between -19 (most probably no spam) and 7 (very likely to be spam).

In order to reject emails, which are likely to be spam, you have to install an email filter on your own using the X-Spam-Score header field. Luckily, the RRZE email web portal on [https://faumail.uni-erlangen.de faumail.uni-erlangen.de] allows to install email filter, such that you don't have to install filters on all of your devices and mail clients.

== Install filter using the webmail portal ==

=== How to create a new filter ===

<gallery>
File:Email_spam_filter_step1_login.png|'''1)''' Log into [https://faumail.uni-erlangen.de https://faumail.uni-erlangen.de] with your FAU account.
File:Email_spam_filter_step2_settings.png|'''2)''' Choose settings on the right of the top navigation bar.
File:Email_spam_filter_step3.png|'''3a)''' Select "Filters" in the left menu, then "managesieve" below "Filter sets", and then hit the plus button below the "Filters" list.
File:Email_spam_filter_step3b_filterset.png|'''3b)''' You may choose any other filter set than "managesieve". If there is none then create a new list first.
File:Email_spam_filter_step4_new_filter.png|'''4a)''' Create a new filter, which moves emails to the Junk folder if the X-Spam-Score value is greater than a specific value.
File:Email_spam_filter_step4b_xspamscore_field.png|'''4b)''' If the X-Spam-Score field is not listed in the first drop-down menu, then select "..." and enter the field name manually.
File:Email_spam_filter_step5_save.png|'''5)''' Make sure the filter is not disabled and click on "Save" finally.
</gallery>

=== X-Spam-Score Threshold ===

A quick analysis of an inbox resulted in a value of '''4''' as a threshold for the X-Spam-Score field, above which emails are likely to be spam. Please note that this is an example threshold and not an official or recommended value by the RRZE. In particular, some emails distributed via mailing lists may have a high X-Spam-Score value as well. That's why emails should be moved into, e.g., the "Junk" folder and not deleted immediately.

[[Category:Current Members]]

File:Email spam filter step3b filterset.png

2020-06-18T09:34:51Z

Kuehnel:

FAUmail Spam Filter

2020-06-18T09:29:37Z

Kuehnel: /* How to create a new filter */

According to the RRZE no filtering on spam emails is performed, but each email is analyzed on spam and ranked accordingly (see [https://www.rrze.fau.de/internet-e-mail/e-mail/anti-spam/spam-analyse/ Spam-Analyse und -Filterung] on the RRZE website). This rank is added to email header as '''X-Spam-Score''' field with values roughly between -19 (most probably no spam) and 7 (very likely to be spam).

In order to reject emails, which are likely to be spam, you have to install an email filter on your own using the X-Spam-Score header field. Luckily, the RRZE email web portal on [https://faumail.uni-erlangen.de faumail.uni-erlangen.de] allows to install email filter, such that you don't have to install filters on all of your devices and mail clients.

== Install filter using the webmail portal ==

=== How to create a new filter ===

<gallery>
File:Email_spam_filter_step1_login.png|'''1)''' Log into [https://faumail.uni-erlangen.de https://faumail.uni-erlangen.de] with your FAU account.
File:Email_spam_filter_step2_settings.png|'''2)''' Choose settings on the right of the top navigation bar.
File:Email_spam_filter_step3.png|'''3)''' Select "Filters" in the left menu, then "managesieve" below "Filter sets", and then hit the plus button below the "Filters" list.
File:Email_spam_filter_step4_new_filter.png|'''4a)''' Create a new filter, which moves emails to the Junk folder if the X-Spam-Score value is greater than a specific value.
File:Email_spam_filter_step4b_xspamscore_field.png|'''4b)''' If the X-Spam-Score field is not listed in the first drop-down menu, then select "..." and enter the field name manually.
File:Email_spam_filter_step5_save.png|'''5)''' Make sure the filter is not disabled and click on "Save" finally.
</gallery>

=== X-Spam-Score Threshold ===

A quick analysis of an inbox resulted in a value of '''4''' as a threshold for the X-Spam-Score field, above which emails are likely to be spam. Please note that this is an example threshold and not an official or recommended value by the RRZE. In particular, some emails distributed via mailing lists may have a high X-Spam-Score value as well. That's why emails should be moved into, e.g., the "Junk" folder and not deleted immediately.

[[Category:Current Members]]

FAUmail Spam Filter

2020-06-18T09:23:24Z

Kuehnel:

According to the RRZE no filtering on spam emails is performed, but each email is analyzed on spam and ranked accordingly (see [https://www.rrze.fau.de/internet-e-mail/e-mail/anti-spam/spam-analyse/ Spam-Analyse und -Filterung] on the RRZE website). This rank is added to email header as '''X-Spam-Score''' field with values roughly between -19 (most probably no spam) and 7 (very likely to be spam).

In order to reject emails, which are likely to be spam, you have to install an email filter on your own using the X-Spam-Score header field. Luckily, the RRZE email web portal on [https://faumail.uni-erlangen.de faumail.uni-erlangen.de] allows to install email filter, such that you don't have to install filters on all of your devices and mail clients.

== Install filter using the webmail portal ==

=== How to create a new filter ===

<gallery>
File:Email_spam_filter_step1_login.png|'''1)''' Log into [https://faumail.uni-erlangen.de https://faumail.uni-erlangen.de] with your FAU account.
File:Email_spam_filter_step2_settings.png|'''2)''' Choose settings on the right of the top navigation bar.
File:Email_spam_filter_step3.png|'''3)''' Select "Filters" and hit the plus button below the "Filters" list.
File:Email_spam_filter_step4_new_filter.png|'''4a)''' Create a new filter, which moves emails to the Junk folder if the X-Spam-Score value is greater than a specific value.
File:Email_spam_filter_step4b_xspamscore_field.png|'''4b)''' If the X-Spam-Score field is not listed in the first drop-down menu, then select "..." and enter the field name manually.
File:Email_spam_filter_step5_save.png|'''5)''' Make sure the filter is not disabled and click on "Save" finally.
</gallery>

=== X-Spam-Score Threshold ===

A quick analysis of an inbox resulted in a value of '''4''' as a threshold for the X-Spam-Score field, above which emails are likely to be spam. Please note that this is an example threshold and not an official or recommended value by the RRZE. In particular, some emails distributed via mailing lists may have a high X-Spam-Score value as well. That's why emails should be moved into, e.g., the "Junk" folder and not deleted immediately.

[[Category:Current Members]]

File:Email spam filter step4b xspamscore field.png

2020-06-18T09:22:24Z

Kuehnel:

FAUmail Spam Filter

2020-06-18T09:05:37Z

Kuehnel: Created page with "According to the RRZE no filtering on spam emails is performed, but each email is analyzed on spam and ranked accordingly (see [https://www.rrze.fau.de/internet-e-mail/e-mail/..."

According to the RRZE no filtering on spam emails is performed, but each email is analyzed on spam and ranked accordingly (see [https://www.rrze.fau.de/internet-e-mail/e-mail/anti-spam/spam-analyse/ Spam-Analyse und -Filterung] on the RRZE website). This rank is added to email header as '''X-Spam-Score''' field with values roughly between -19 (most probably no spam) and 7 (very likely to be spam).

In order to reject emails, which are likely to be spam, you have to install an email filter on your own using the X-Spam-Score header field. Luckily, the RRZE email web portal on [https://faumail.uni-erlangen.de faumail.uni-erlangen.de] allows to install email filter, such that you don't have to install filters on all of your devices and mail clients.

== Install filter using the webmail portal ==

=== How to create a new filter ===

<gallery>
File:Email_spam_filter_step1_login.png|'''1)''' Log into [https://faumail.uni-erlangen.de https://faumail.uni-erlangen.de] with your FAU account.
File:Email_spam_filter_step2_settings.png|'''2)''' Choose settings on the right of the top navigation bar.
File:Email_spam_filter_step3.png|'''3)''' Select "Filters" and hit the plus button below the "Filters" list.
File:Email_spam_filter_step4_new_filter.png|'''4)''' Create a new filter, which moves emails to the Junk folder if the X-Spam-Score value is greater than a specific value.
File:Email_spam_filter_step5_save.png|'''5)''' Make sure the filter is not disabled and click on "Save" finally.
</gallery>

=== X-Spam-Score Threshold ===

A quick analysis of an inbox resulted in a value of '''4''' as a threshold for the X-Spam-Score field, above which emails are likely to be spam. Please note that this is an example threshold and not an official or recommended value by the RRZE. In particular, some emails distributed via mailing lists may have a high X-Spam-Score value as well. That's why emails should be moved into, e.g., the "Junk" folder and not deleted immediately.

[[Category:Current Members]]

File:Email spam filter step3.png

2020-06-18T09:03:23Z

Kuehnel:

File:Email spam filter step5 save.png

2020-06-18T09:00:20Z

Kuehnel:

File:Email spam filter step4 new filter.png

2020-06-18T09:00:06Z

Kuehnel:

File:Email spam filter step2 settings.png

2020-06-18T08:59:41Z

Kuehnel:

File:Email spam filter step1 login.png

2020-06-18T08:59:24Z

Kuehnel:

Sencha

2020-03-20T09:13:02Z

Kuehnel: Created page with "Category:Admin [https://www.sencha.com/ Sencha] is the company behind the JavaScript Framework [https://www.sencha.com/products/extjs/ ExtJS]. == Software == The Sencha..."

[[Category:Admin]]

[https://www.sencha.com/ Sencha] is the company behind the JavaScript Framework [https://www.sencha.com/products/extjs/ ExtJS].

== Software ==

The Sencha software is installed at
/data/system/software/Sencha
and the main pieces are '''ExtJS''' and Sencha'''CMD''' as available in the corresponding subidrectories.

=== Download/Updating ===

[[File:sencha_software_portal.png|right|500px]]

Up-to-date versions of the Sencha software can be downloaded from the Sencha support at
https://support.sencha.com/
See license below for the login credentials. In most cases you have to open "past versions" in order to download the latest version. On the example screenshot one can see ExtJS 5.0.0 selected for download, but the latest one at this time was 7.1.0.

Please save the downloaded (ZIP) files in
/data/system/software/Sencha/packages
as the '''software''' user.

We regularly update '''ExtJS''', '''Ext Premium Adons''', and '''Sencha CMD'''.

=== Building ===

The Makefile at
/data/system/software/Sencha/Makefile
has targets to build '''ExtJS''', '''Ext Premium Adons''', and '''Sencha CMD'''.
As the '''software''' user open the Makefile for editing and change the version information
on top according to the latest downloaded software in the <code>packages</code> subdirectory.
Then simply call <code>make</code>.

Probably out-dated instructions how to install the software manually are given in
/data/system/software/Sencha/packages/installation_readme.txt

== License and Logins ==

Our license and login information for the support and forum can be found in
/data/system/software/Sencha/license
which is readable by the '''software'' user only.

File:Sencha software portal.png

2020-03-20T08:51:44Z

Kuehnel: After having logged in at https://support.sencha.com/ Sencha software can be downloaded.

After having logged in at https://support.sencha.com/ Sencha software can be downloaded.

PhD hat for Maria

2019-04-25T14:53:24Z

Kuehnel:

====== PhD Hat for Maria ======

==== Private ====

* colored hat: glue rainbow-paper on the hat base (and top) for a colorful hat (*Basti*)
* firefighter (beeper goes of at inconvenient times)
* colored hair
* shoes and socks of different color
* sheep!
*

==== Work ====

* Cyg X-1
* extended work on paper
* line measurements (remeis intern poll)
* timing analysis (power spectra)
* CCD lab instructor
* Web admin: extensive fights with WordPress -> small print for the side of the hat (**Matthias**)

[[Category:Internal]]

LXD 75

2019-02-21T11:01:43Z

Kuehnel:

[[Category:Current Members]]

[https://www.meade.com/media/downloads/40/LXD-75C.pdf Instruction manual] of the LXD 75 telescope and tripod

'''MEADE LXD 75 Telescope'''

* to assemble on one of the two east pillars in the garden
* or on its portable tripod for observing elsewhere

'''Tripod'''

* mountable telescopes:
** [[MEADE 10 Inch]]
** [[115mm apochromatic refractor]]
** [[Coronado PST]]
** [http://www.luntsolarsystems-by-apmtelescopes.com/pro_info.php?ebene1=48&id=94473&catchoice1= Solar telescope 60mm H-alpha]
* for information about assembling the tripod see the [[lab course manual]], section telescopes
* don't forget the equipment case

'''Equipment case'''

silver colored case in the main buildings basement (CCD lab room), contains
* Autostar Handbox
* power supply

Lab course manual

2019-02-21T10:57:38Z

Kuehnel:

== GIT repository ==

git clone phoenix.sternwarte.uni-erlangen.de:/data/git/Praktikumsanleitung.git
cd Praktikumsanleitung
cd anleitung
make

will produce praktikum.pdf
[[Category:Current Members]][[Category:Internal]]

Lab course manual

2019-02-21T10:57:25Z

Kuehnel: Created page with "Category:Current MembersCategory:Internal == GIT repository == git clone phoenix.sternwarte.uni-erlangen.de:/data/git/Praktikumsanleitung.git cd Praktikumsanleit..."

[[Category:Current Members]][[Category:Internal]]

== GIT repository ==

git clone phoenix.sternwarte.uni-erlangen.de:/data/git/Praktikumsanleitung.git
cd Praktikumsanleitung
cd anleitung
make

will produce praktikum.pdf

Webpages

2019-01-23T13:28:12Z

Kuehnel:

[[Category:Admin]]

We host a number of webpages and domains, which also requires to operate and maintain a few webservers on different machines. Some of theses servers are actually virtual machines. Have a look at [[Virtual Boxes]] in order to look up the host machine.

{| class="wikitable"
! Machine
! Apache version
! PHP version
|-
| cetus
| 2.4.18
| 7.0.32
|-
| hydrus
| 2.2.22
| 5.3.10
|-
| antlia
| 2.4.7
| none
|-
| erosita
| 2.4.18
| 7.0.32
|-
| serpens
| colspan=2|''gitlab implementation''
|}
command to get these information: <code>ssh machine "apache2 -v; php -v"</code>

{| class="wikitable"
! Domain
! Host machine
|-
| [http://www.sternwarte.uni-erlangen.de www.sternwarte.uni-erlangen.de]
| cetus
|-
| [http://www.black-hole.eu www.black-hole.eu]
| hydrus
|-
| [http://erosita.fau.de erosita.fau.de]
| erosita
|-
| [http://serpens.sternwarte.uni-erlangen.de:8181 serpens.sternwarte.uni-erlangen.de:8181]
| serpens
|}

The following table summarized where the files of most web-services or -pages are located.
{| class="wikitable"
! Subdirectory of /data/www/
! URL
! Machine
! Description
|-
| a400.sternwarte.uni-erlangen.de
| [http://www.sternwarte.uni-erlangen.de/older www.sternwarte.uni-erlangen.de/older]
| cetus
| very old webpage
|-
| agendav
| [http://www.sternwarte.uni-erlangen.de/calendar www.sternwarte.uni-erlangen.de/calendar]
| cetus
| calendar frontend agendav
|-
| backups
|
|
| backups of black-hole.eu, created by joomla
|-
| black-hole
| [http://www.black-hole.eu www.black-hole.eu]
| hydrus
| homepage of the Black Hole Universe consortium
|-
| conf2010
| [http://www.sternwarte.uni-erlangen.de/conf2010 www.sternwarte.uni-erlangen.de/conf2010]
| cetus
| conference webpage of "Planetary Systems beyond the Main Sequence"
|-
| dokuwiki
| [http://www.sternwarte.uni-erlangen.de/wiki www.sternwarte.uni-erlangen.de/old/wiki]
| cetus
| our old wiki
|-
| extjs
| www.sternwarte.uni-erlangen.de/extjs
| cetus
| ExtJS Javascript Framework
|-
| google_search_console.html
| [http://www.sternwarte.uni-erlangen.de/google1d587cbddcc53596.html www.sternwarte.uni-erlangen.de/google1d587cbddcc53596.html]
| cetus
| keyfile necessary to access the [https://www.google.com/webmasters/tools/ Google Webmaster Tools]
|-
| git.public
| [http://www.sternwarte.uni-erlangen.de/git www.sternwarte.uni-erlangen.de/git]
| cetus
| GIT repository browser
|-
| guided-tours
| [http://www.sternwarte.uni-erlangen.de/guided-tours www.sternwarte.uni-erlangen.de/guided-tours]
| cetus
| registration form for guided tours (ExtJS based)
|-
| isis
| [http://www.sternwarte.uni-erlangen.de/isis www.sternwarte.uni-erlangen.de/isis]
| cetus
| ISISscripts homepage
|-
| mediawiki
| [http://www.sternwarte.uni-erlangen.de/wiki_new www.sternwarte.uni-erlangen.de/wiki]
| cetus
| our wiki
|-
| new
| [http://www.sternwarte.uni-erlangen.de/old www.sternwarte.uni-erlangen.de/old]
| cetus
| old "new" observatory homepage
|-
| proaccretion
| [http://www.sternwarte.uni-erlangen.de/proaccretion/ www.sternwarte.uni-erlangen.de/proaccretion]
| cetus
| homepage of the ISSI team "Probing the Accretion..."
|-
| pulsar
| [http://pulsar.sternwarte.uni-erlangen.de pulsar.sternwarte.uni-erlangen.de]
| cetus
| pulsar homepage
|-
| registration_forms
| www.sternwarte.uni-erlangen.de/regtool
| cetus
| GIT-clones (from gitlab) and online builds of conference registration forms (ExtJS based)
|-
| SabreDAV
| www.sternwarte.uni-erlangen.de:5232
| cetus
| CalDAV server
|-
| wordpress
| [http://www.sternwarte.uni-erlangen.de www.sternwarte.uni-erlangen.de]
| cetus
| main observatory homepage
|-
| dokuwiki-*
|
|
| backups of the old wiki
|-
! Specific directory
!
!
!
|-
| serpens:/scratch1/gitlab
| [http://serpens.sternwarte.uni-erlangen.de:8181 serpens.sternwarte.uni-erlangen.de:8181]
| serpens
| GitLab
|}

== Webserver ==

This section is still being written. It's supposed to contain detailed information about, e.g., the configuration of each webserver.

=== cetus ===

main webserver

=== hydrus ===

backup webserver with older software for backward compatibility

Converting PS plot from ISIS to PDF

2018-10-24T10:24:23Z

Kuehnel: Created page with "Let's assume you have exported any plot in ISIS into a PostScript (PS) by, e.g., ()=open("myfit.ps/cps"); plot_data(1; res = 1); close_plot(); The resulting PS file will..."

Let's assume you have exported any plot in ISIS into a PostScript (PS) by, e.g.,
()=open("myfit.ps/cps");
plot_data(1; res = 1);
close_plot();
The resulting PS file will be larger than a corresponding PDF version of your plot. Furthermore, if you attache the PS to an email, some people might have problems viewing this format. Fortunately, there are UNIX tools available for converting the PS into a PDF, like
epstopdf myfit.ps
which will create a new file myfit.pdf in this example. However, the rotation of the final PDF might be wrong. To fix this you can use, e.g., [https://www.pdflabs.com/docs/pdftk-man-page/ pdftk] to rotate the final PDF. A one-liner might look like
epstopdf --outfile=- myfit.ps | pdftk - cat 1east output myfit.pdf
Note that we set outfile to - which is equivalent to the standard output pipe (STDOUT), i.e., the PDF will be echoed into your shell. We pipe this output to pdftk, which we need to force reading from the standard input channel (STDIN) by providing - as well. The "1east" option rotates the first page of the PDF by 90° clockwise (to the east).

[[Category:Isis / Slang]]

Talk:Webpages

2018-08-07T11:08:28Z

Kuehnel: Created page with "We should include the /etc/apache2/ configuration soon!"

We should include the /etc/apache2/ configuration soon!

ISISscripts

2018-08-07T08:25:45Z

Kuehnel:

[[Category:Isis / Slang]]
A huge (and extremely useful) collection of useful ISIS functions, written and maintained by the Remeis observatory (and certainly containing thousands of working hours by a variety of people) can be found here:

[http://www.sternwarte.uni-erlangen.de/isis/ http://www.sternwarte.uni-erlangen.de/isis/]

Please cite properly when used!

= How to contribute to the GIT repository =

Log into gitlab, visit [http://www.sternwarte.uni-erlangen.de/gitlab/remeis http://www.sternwarte.uni-erlangen.de/gitlab/remeis] and click on "Request Access".

= How to investigate the source code of available functions =

In order to look up any code of a function as part of the ISISscripts navigate to its GIT-repository. You can see this folder once you require the ISISscripts (which might be done inside your [[ISIS auto start (.isisrc)|.isisrc]]), e.g.,
<pre>loading /home/git/isisscripts.git/share/isisscripts.sl</pre>
Note for Remeis users: the repository is managed by [https://www.sternwarte.uni-erlangen.de/gitlab/remeis/isisscripts GitLab]. A '''local clone''' can be found in /data/git/isisscripts.git

Then change into the source code directory, e.g.,
<pre>cd /home/git/isisscripts.git/src</pre>
Now the tricky part: you need to find that file, where the function which source code you want to investigate is defined. If you're lucky, the file is named according to the function's name (with .sl suffix), so you can try
<pre>find . -iname "mc_sig.sl"</pre>
If this does not work, you can try to grep its function definition
<pre>grep -R "define mc_sig"</pre>

ISIS history file

2018-08-07T08:24:05Z

Kuehnel:

[[Category:Isis / Slang]]
You will make your ISIS-life A TON easier by setting up an ISIS history file that saves any interactive commands you use. They are usually automatically set on the Remeis-cluster, otherwise go to your .bashrc and use:

<code>
ISIS_HISTORY_FILE=/path_where_you_want_your_file_ususally_home/.isis_history
export ISIS_HISTORY_FILE
</code>

Adapt for other shells accordingly.

Install ISIS on Mac

2018-07-31T08:55:52Z

Kuehnel:

This instruction is intended for Mac OS X 10.10 (yosemite) users to "completely" install ISIS including the modules for: gsl, xfig, isisscripts.

Assuming a fresh Mac OS X 10.10 installation (alternatively make sure that /usr/local/ or the prefix path of the installation is empty).

== 1. Install Xcode (latest version) and Xquartz ==
To check whether Xcode is installed execute: \\
<pre>
xcode-select -p
</pre>
on command line

If you see <code>/Applications/Xcode.app/Contents/Developer</code> it should be installed.
Use the App Store to update or install Xcode

Execute <code>xcode-select --install</code>
on command line to install the Xcode command line tools

Xquartz / X11 is no longer included in the latest versions of Mac OS X and need to be installed separately. X11 is also no longer available from Apple directly, but has to be obtained from the [http://xquartz.macosforge.org/landing/ web]. Download X11 and install it. Note: if this link is out of date, search the Web for "OS X Xquartz".
After installation the X11 libraries should now be available in <code>/opt/X11/</code>

== 2. Install Mac Ports ==
Fink could also work, the differences should be some package names and the location of some libraries which should be <code> /opt/local/</code> for Mac Ports or <code>/sw/local/ </code> for Fink.

This instruction assumes that [https://www.macports.org/install.php Mac Ports] will be installed.

== 3. Install packages with Mac Ports ==
There are several packages including their dependencies to be installed. I recommend installing everything with the universal flag set (which includes 32bit and 64bit versions)

<pre>
sudo port install gcc49 +universal
sudo port install gsl +universal
sudo port install transfig +universal
</pre>

These packages install a necessary gfortran compiler as well as necessary libraries to build the slgsl / slxfig module for slang / isis.

== 4. Install HEADAS ==
* Download the latest version of [https://heasarc.gsfc.nasa.gov/lheasoft/download.html HEASOFT (source)]
* Up until HEASOFT 6.15, XSPEC did not work properly on Mac OS X in 64bit mode. As of HEASOFT 6.16 this is no longer the case and the recommendation is to install everything in 64bit. You don't need to set anything to do that, but if you have old compiler flags set to "-m32", remove them!
<pre>
export GCC="/usr/bin/gcc"
export CC="/usr/bin/gcc"
export CXX="/usr/bin/g++"
export FC="/opt/local/bin/gfortran-mp-4.9" # mac ports gfortran compiler
</pre>
* create a directory in your $HOME called Software
* unpack the HEADAS tar file in this directory
* Install HEASOFT from source but use the following configurations
<pre> ./configure --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
make
sudo make install
</pre>
* Add the following to your .profile (change this according to your terminal type and username)
<pre>
export HEADAS="/Users/username/path/to/heasoft/"
alias heainit="source $HEADAS/headas-init.sh
heainit
</pre>
The HEADAS path could/should look something like this:
<pre>
$HEADAS=/Users/chgross/Software/heasoft-6.16/x86-apple-darwin14.1.0/
</pre>
* apply the new settings to your terminal by either closing the current terminal windows and open a new terminal or by writing
<code>source ~/.profile</code> in your command line

== 5. Install slang / slang modules / isis / isisscripts ==

First get the latest versions of slang / jed/ slgsl / slxfig / isis / isisscripts. I recommend using the git repositories. Go to the Software directory in your terminal and clone the repositories:
<pre>
git clone http://space.mit.edu/cxc/isis/isis.git
git clone git://git.jedsoft.org/git/slang.git
git clone git://git.jedsoft.org/git/slxfig.git
git clone git://git.jedsoft.org/git/slgsl.git
git clone git://git.jedsoft.org/git/jed.git
git clone http://www.sternwarte.uni-erlangen.de/git.public/isisscripts
</pre>

Install slang. Go to the slang directory.
<pre>
./configure --with-png=/opt/local/
make
sudo make install
</pre>
Install isis. Go to the isis directory
<pre>
./configure --with-headas=$HEADAS
make
sudo make install
</pre>

Add <tt>'''--with-slang=/path/to/slang'''</tt> to the following configuration set ups in case you installed slang in a different path other than <tt>/usr/local/</tt>

Install jed. Go to the jed directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install slgsl. Go to the slgsl directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib --with-gsl=/opt/local/
make
sudo make install
</pre>

Install slxfig. Go to the slxfig directory
<pre>
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
make
sudo make install
</pre>

Install the isisscripts. Go to the isisscripts directory
<pre>
make
</pre>

Create / modify the [[ISIS auto start (.isisrc)|.isisrc]] file in your <tt>$HOME</tt> directory and add the following line
<pre>
add_to_isis_load_path("/Path/To/isisscripts/share/");
</pre>
This allows the easy access to <tt>require("isisscripts")</tt> in isis.

== 6. Possible problems with other software ==
=== XMM SAS ===
The XMM SAS resets part of your $PATH variable and uses its some of its own libraries. This might break some programs of HEASOFT when the SAS is loaded. As our <tt>xmmscripts</tt> rely on the <tt>ftools</tt>, this behavior is highly inconvenient.
As a workaround install the HEASOFT wrapper by following the instructions [http://heasarc.gsfc.nasa.gov/lheasoft/hwrap.html here].

This will create a new directory with the executables of HEASOFT. Add this directory to your <tt>$PATH</tt> variable (in front of the rest of <tt>$PATH</tt>)!

[[Category:Isis / Slang]]

Isis tutorial walkthrough

2018-07-31T08:55:37Z

Kuehnel:

== A Walk Through ISIS ==

In this first part of the tutorial, in order to get you started we will show you an example for a full X-ray data analysis using a fairly simple spectrum<ref>this section is mainly based on [http://space.mit.edu/home/mnowak/isis_vs_xspec/ Mike Nowak's introduction to isis]</ref>.

=== Inspecting your data set outside of isis ===

In the following tutorial, we will be working on a simple data set from an observation of a black hole, Cygnus X-1, that was obtained with NASA's Rossi X-ray Timing Explorer satellite. The test data set can be downloaded from [http://www.sternwarte.uni-erlangen.de/~wilms/isistut/ here]. It consists of the following parts:
* <code>standard2f_0134off_top.pha</code> -- the spectrum itself. The data are in FITS-format, a standard file format that is used in all of astronomy. You can take a look at what such a file looks like using the <code>fv</code> or <code>fdump</code> programs, which are part of HEASOFT and should already be installed on your machine. ''Outside'' of isis, invoke fv with <pre>fv standard2f_0134off_top.pha</pre> A window pops up that displays the contents of the file. Like all FITS files PHA<ref>"PHA" stands for ''pulse height analyzer'', since X-ray data do usually not contain real energy or wavelength information, since the limited resolution of X-ray detectors does usually not allow directly measuring the photon's energy with high precision</ref> files consist of a so-called primary-header and then multiple extensions, which again contain some human-readable header data that contain information about your data set and the data itself. The header information is given as a keyword name, the value of the keyword, and often a comment that describes the meaning of the keyword. Important keywords are
** <code>OBJECT</code>: The name of the observed object (a string defined by the observer, often - but not always - a meaningful name)
** <code>RA_OBJ</code> and <code>DEC_OBJ</code>: The position of the object (often useful if the <code>OBJECT</code>-keyword is not set or wrong)
** <code>TELESCOP</code> and <code>INSTRUME</code>: The satellite and instrument used
** <code>DATE-OBS</code> and <code>DATE-END</code>: The date and time of the start and the end of the observation
** <code>EXPOSURE</code>: The exposure time, i.e., how long were data accumulated. Note that often <code>EXPOSURE</code> is smaller than the difference between <code>DATE-OBS</code> and <code>DATE-END</code> since the detector could have been switched off for part of the observation, or data were discarded during the data reduction, e.g., because of large background fluxes<ref>The full information about the times during which the data in the spectrum were accumulated is contained in the so-called GTI (good time intervals) extension of the PHA-file</ref>.
** <code>BACKFILE</code>: The name of the PHA-file that defines the background, which is automatically subtracted from the data before fitting.
** <code>RESPFILE</code>: The name of the file containing the detector response matrix (often called "RMF" or "RSP", which describes the mapping from PHA-space to energy space and all detector effects.
** <code>ANCRFILE</code>: The name of the ancilliary response file, often called ARF-file. This file is used by some instruments which separate the detector response into a pure energy redistribution matrix and an effective area. See the X-ray astronomy lectures for details. This keyword has the value <code>NONE</code> if the ARF is already part of the response matrix.
** Further keywords depending on the satellite (often one finds, e.g., <code>TSTART</code> and <code>TSTOP</code> which contain the same information as <code>DATE-OBS</code> and <code>DATE-END</code>, only in a system that is easier to use in calculation than the human-readable information in <code>DATE-OBS</code> and <code>DATE-END</code>).
* <code>standard2f_back_SkyVLE_top_good_0134off.pha</code>: The background spectrum referred to in the <code>BACKFILE</code> keyword of <code>standard2f_0134off_top.pha</code>
* <code>p2_LR1_2010-07-04.rsp</code>: The response matrix referred to in the <code>RESPFILE</code> keyword of <code>standard2f_0134off_top.pha</code>

As mentioned above, you can either take a look at the files with <code>fv</code>, or by dumping the FITS-file on the screen using the <code>fdump</code> command. Here is the output of the latter, showing typical values of the keywords above:
<pre>
wilms@leo:~/isistut> fdump standard2f_0134off_top.pha
Name of optional output file[STDOUT]
Names of columns[]
Lists of rows[-]
SIMPLE = T / file does conform to FITS standard
BITPIX = -32 / number of bits per data pixel
NAXIS = 0 / number of data axes
EXTEND = T / FITS dataset may contain extensions
COMMENT FITS (Flexible Image Transport System) format is defined in 'Astronomy
COMMENT and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H
:
: ... many further lines
:
XTENSION= 'BINTABLE' / binary table extension
BITPIX = 8 / 8-bit bytes
:
:
EXTNAME = 'SPECTRUM' / name of this binary table extension
:
TELESCOP= 'XTE ' / Telescope (mission) name
INSTRUME= 'PCA ' / Instrument name
FILTER = 'NONE ' / Instrument filter in use
EXPOSURE= 2.52800000000001E+03 / Exposure time
:
BACKFILE= 'standard2f_back_SkyVLE_top_good_0134off.pha' / Background FITS file f
CORRFILE= 'standard2f_back_SkyVLE_top_good_0134off.pha' / Correlation FITS file
RESPFILE= 'p2_LR1_2010-07-04.rsp' / Redistribution matrix file (RMF)
ANCRFILE= 'NONE ' / Ancillary response file (ARF)
:
CREATOR = 'SAEXTRCT version 4.2g' / Program name that produced this file
DATE = '2011-06-26T10:08:03' / file creation date (YYYY-MM-DDThh:mm:ss UT)
RA_OBJ = 2.99591705E+02 / RA of First input object
DEC_OBJ = 3.52016983E+01 / DEC of First input object
EQUINOX = 2000.00 / Equinox of the FIRST object
:
DATASUM = '3317156129' / data unit checksum updated 2011-06-26T10:08:03
END

CHANNEL COUNTS STAT_ERR
count count
1 0 2.860600000000000E+04 1.691330836944682E+02
</pre>
The data themselves give, for each PHA-channel, the number of counts measured in the <code>COUNTS</code> column and the uncertainty of the data in the <code>STAT_ERR</code> column. If the data have not been background subtracted before the analysis, which is typical for most instruments except for data from coded mask telescopes, then <code>STAT_ERR</code> will usually have been determined assuming Poisson-statistics, i.e., it is the square-root of the value in <code>COUNTS</code>.

There are many more useful programs to inspect FITS-files. You can get an overview of what is available using
<pre>
wilms@leo:~/isistut> fhelp ftools
</pre>
and if you only want to see the list of general (non satellite-specific) tools
<pre>
wilms@leo:~/isistut> fhelp futils
</pre>
Full information on individual ftools can be obtained with <code>fhelp toolname</code>, e.g.,
<pre>
wilms@leo:~/isistut> fhelp fdump
</pre>
Other useful tools for inspecting FITS-files are, e.g., <code>fstruct</code> and <code>fstatistic</code>.

'''''Exercise 1'''''
# For your example data set, determine the date of the observation, the exposure time, and the name of the background file.
# Use <code>fstruct</code> to determine the structure of the backgrund file and confirm that it is the same as the structure of the PHA file containing the data.

=== Invoking isis ===

Isis is a command-line program and is therefore usually executed from the command line:
<pre>
wilms@leo:~> isis
</pre>
which then prints out some start up messages before you end with the isis prompt:
<pre>
Welcome to ISIS Version 1.6.2-3
Copyright (C) 1998-2012 Massachusetts Institute of Technology

Isis web page: http://space.mit.edu/cxc/isis/
Mailing list archive: http://space.mit.edu/cxc/isis/archive/
Send questions to the mailing list: <isis-users@space.mit.edu>.
For a summary of recent changes, type: "help changes"

isis>
</pre>
As part of its startup, isis executes a file called [[ISIS auto start (.isisrc)|.isisrc]], which is useful for setting up a standard environment.

In the following we will show you an interactive session with isis. It is the typical approach when working with new data to look at these first by hand, in a way similar to that shown here. In later, more advanced analysis you will probably mainly interact with isis through programs, although it should be emphasized that working interactively with data first is always a good idea. This is the only way how you can get a good feeling for your data, even though automated reductions ''are'' important, especially when working on data sets with many different observations.

=== Loading and Inspecting Your Data Set ===

We now load the data we looked at before into isis:
<pre>
pca=load_data("standard2f_0134off_top.pha");
</pre>
The <code>load_data</code> command loads the file given as its argument and returns an unique number that identifies this data set. In the above example, this identifier is stored in the variable called <code>pca</code> (it usually makes sense to use the name of the detector with which the data were taken, although there are exceptions). Note that the command ends with a semicolon. This is standard in slang, the language on which isis is based. Although it is in principle possible to switch off this feature when working interactively with isis<ref>since you are curious: put<pre>Isis_Append_Semicolon=1;</pre> in your <code>~/.isisrc</code></ref>, we recommend you do not use this option -- having to type the semicolon requires you to think before doing something, which is generally a good idea ;-).

If all goes fine, you will be informed that the response matrix includes the ARF. Now check whether isis loaded what you think it should have loaded by looking at some basic information about the background file, the RMF, and the ARF:
<pre>
isis> list_data;
Current Spectrum List:
id instrument part/m src use/nbins A R totcts exp(ksec) target
1 PCA 0 129/ 129 - 1 3.1773e+06 2.528 CYG_X-1
file: standard2f_0134off_top.pha
back: standard2f_back_SkyVLE_top_good_0134off.pha
</pre>
Amongs others, the table columns include
* <code>id</code>: the identifier of this data set,
* <code>nbins</code>: the number of spectral bins,
* <code>totcts</code>: the total counts in the spectrum,
* <code>exp</code>: the exposure time in kiloseconds, and
* <code>target</code>: the nominal source we are working with.
Finally, the output also lists the file name and the associated background file.

Similar information can also be obtained for the response matrix and the ARF using the commands
<pre>
list_rmf;
list_arf;
</pre>
Note that for your data set no information is given back for the ARF, since none was loaded.

Like for all commands in isis, information about the commands can be obtained with
<pre>
isis> help commandname
</pre>
so, for example,
<pre>
isis> help list_arf
</pre>
(If this does not give you help for the command you put in, you can try just
<pre>
isis> commandname;
</pre> without any additional arguments. For some commands that works.)
Some of the help information might appear pure gibberish for you. Ignore this for the moment, with time it will all become clear to you.

A second help function that is very useful is the <code>apropos</code> command. For example, if you want to do something with an ARF, do
<pre>
isis> apropos arf
</pre>
which will return all isis commands that contain "arf" in their name.

'''''Exercise 2'''''
# Load your data set and check that the information given by ISIS using the above commands is identical to the information that you obtained in the previous exercise.

=== Plotting the Data ===

X-ray data analysis of a data set that you do not yet know consists basically of the following steps:
# plot something
# think about what the plot/data set tries to tell you
# try something out (e.g., perform a fit)
# goto 1
and then repeat until you are convinced that everything works as expected. Depending on the data set, the above might take five minutes, but we also had complicated data sets that so far have resulted in 2-3 PhD theses...

Therefore, as the first step, we take a look at our data.

While isis contains some basic plotting routines, it is generally faster to use the very powerful plotting routines developed at MIT and at Remeis/ECAP to look at the data. The reason is that these are more user friendly than the basic isis routines.

In order to do so, we first need to load the Remeis isis scripts. In our standard install, just do a
<pre>
isis> require("isisscripts");
</pre>
The <code>isisscripts</code> are a large set of useful routines developed by many people. If you use them for professional work, please contact J. Wilms first and ask whom to put in the acknowledgments of your paper. They are freely available through a git-repository.

So let's plot the data set:
<pre>
isis> plot_counts(pca);
</pre>
A window pops up, looking something like this

[[File:Walkthrough01.png|center]]

In this standard display, not much can be seen except for the fact that the detector sensitivity is the best at low energies. For this reason, we first switch the plot over to a log-log plot and plot again:
<pre>
isis> xlog;
isis> ylog;
isis> plot_counts(pca);
</pre>
This results in a much nicer plot. With the exception of gratings data, it is usually better to take a look at X-ray data in log-log space, so you should get used to switching over to log-space before doing any plots:

[[File:Walkthrough02.png|center]]

Note that what is shown are counts per PHA bin as a function of energy. Here, the response matrix is used to get an approximate conversion of the channel number to energy. The jump at around 20keV is not a spectral feature, but caused by the detector: at this energy, the standard data mode on RXTE PCA increases the energy width per PHA bin by a factor of two. Since the spectrum changes only slowly at this energy, because of the increase in width twice as many counts are detected in this bin. In addition, the feature at around 30keV is also a detector feature, it mainly reflects the change in sensitivity of this Xe-based proportional counter at the Xe-K-edge, which is at roughly 30keV.

Experience for this detector shows that its calibration is best at energies between 3keV and 22keV, such that for the moment we will ignore what is happening outside of this energy band using isis' <code>notice</code> function:
<pre>
isis> notice_values(pca,3.,22.;unit="keV");
isis> plot_counts(pca);
</pre>
Note that immediately after ignoring, we plot the data again in order to make sure that our command worked as intended. This way you can visually confirm, e.g., that a feature that you want to ignore really was outside of the energy range considered. Furthermore, note that we are explicitly telling isis to work in energy space. This is necessary since for historic reasons many isis commands are by default working in wavelength space.

Other useful isis commands for noticing and ignoring energy and wavelength ranges are
<pre>
ignore(id); % Ignore dataset id
notice(id,a,b); % Notice wavelength range [a,b] in dataset id
notice_en(id,a,b); % Notice energy range [a,b] in dataset id
xnotice(id,a,b); % *Only* notice wavelength range [a,b] in dataset id
xnotice_en(id,a,b); % *Only* notice energy range [a,b] in dataset id
exclude(id); % Don't change the ignored/noticed channels, but
% exclude the whole data set until reinstated with:
include(id); % Reinstate the data with prior excluded channels
</pre>
You can get more information about all of these commands with the <code>.help</code>-command. Note that all of the above commands are "inclusive", in the sense that the energy bins in the spectrum that include the two borders, a and b, are contained in the noticed energy band.

'''''Exercise 3'''''
# Perform the above steps for your data set. In the write up of your homework, include the relevant figures. Prepare these figures as publication-quality (postscript) figures. For this you will have to switch the output to postscript before plotting, and switch back to screen output afterwards:
<pre>isis>plotid = open_print("example.ps/vcps");
isis> keynote_size; nice_width;
isis> plot_counts(pca);
isis> close_print(plotid);
</pre> where <code>example.ps</code> is the file name of the postscript file, and where <code>keynote_size</code> and <code>nice_width</code> set the size of the figure to something that is appropriate for inclusion into a journal article. If you rather work with pdf, convert the ps-file to pdf afterwards, e.g., using Linux <code>epstopdf</code> program.

=== Inspecting ARF and RMF ===

It is always useful in data analysis to have a feeling for the major features introduced by specific properties of the detector used to measure the data. For example, in the spectra above there are drops in detector sensitivity at the K- and L-edges of the detector gas. Usually, the regions around these edges are less well calibrated. Visualizing the ARF and RMF helps in this case (as does reading the user's manual for the satellite you're using...).

It is easy to produce a plot of the RMF:
<pre>
isis> fits_plot_rmf("p2_LR1_2009-05-06.rsp");
</pre>

The resulting plot should be similar to this:

[[File:Rmf.png|center]]

To visualize the sensitivity of the detector we need to plot the effective area of the detector as a function of energy. Depending on the instrument, the detector sensitivity is either saved as a separate ARF (Ancilliary Response File) or it is stored as part of the RMF. In the latter case isis will tell you so with the warning message "RMF includes the effective area" when you load the response. In this case we need to factor the response first:
<pre>
isis> rsp=load_rmf("p2_LR1_2009-05-06.rsp");
RMF includes the effective area
isis> arf=factor_rsp(rsp);
</pre>

We can then get the information about the effective area and plot it:
<pre>
isis> arfdata=get_arf(arf);
isis> xlog;
isis> hplot(_A(arfdata));
</pre>

where the function _A converts the wavelength information contained in the structure arfdata into keV.

[[File:Arf.gif|center]]

=== Performing a First Spectral Fit ===

We are now ready to perform a first spectral fit. We first need to define the spectral model that we want to describe our data with. In general, one first tries to get a rough description of the data, which is for example based on earlier observations of the object, and then refines this spectral model by adding further spectral components if an initial fit was successful. Isis includes a large number of spectral models. Since the models are derived from XSPEC, a good overview is given by the exhaustive list of the models in the [http://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecModels.html XSPEC manual].

What model to use depends on the object one looks at. In most cases, one tries either a power law or a black body first and only later works with more CPU-intensive, physics-based models. Since all X-ray sources are absorbed by the interstellar medium in our Galaxy, one ''always'' includes Galactic absorption.

Here, we know that Cygnus X-1 is a black hole. These often have power-law spectra. We therefore start by trying an absorbed power-law as our fit function:
<pre>
isis>fit_fun("tbabs(1)*powerlaw(1)");
</pre>
Notice the numbers behind the model components. These will be later used to distinguish different fit-functions, e.g., when one works with a source that has a spectrum that can be described as the sum of two power laws of different photon indices.

Next we take a look at our fit parameters:
<pre>
isis> list_par;
tbabs(1)*powerlaw(1)
idx param tie-to freeze value min max
1 tbabs(1).nH 0 0 1 0 100000 10^22
2 powerlaw(1).norm 0 0 1 0 1e+10
3 powerlaw(1).PhoIndex 0 0 1 -2 9
</pre>
Amongst other information, which we will be discussing in a later tutorial, the table contains the following information:
* <code>idx</code>: The index of the parameter (see below)
* <code>param</code>: The name of the parameter. For example, <code>tbabs(1).nH</code> is the absorption column (in units of 10^22 cm-2. The physical meaning of the parameters is explained in the [http://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecModels.html XSPEC manual].
* <code>tie-to</code> and <code>freeze</code>: see later
* <code>value</code>: the current value of the parameter
* <code>min</code> and <code>max</code>: The fit has to remain in the range between these two values.

Before we do our first fit, we take a look at how this model looks like when folded through the detector response matrix. In order to do so we first ask isis to change the model flux such that the predicted count rate is close to the model count rate.
<pre>
isis> renorm_counts;
tbvabs Version 1.0
Cosmic absorption with grains and H2
Wilms, Allen, & McCray 2000
Questions: Adrienne Allen or Joern Wilms
allenu@super.colorado.edu
wilms@astro.uni-tuebingen.de
Parameters[Variable] = 3[1]
Data bins = 45
Chi-square = 898942.6
Reduced chi-square = 20430.51
0
</pre>
Isis has changed the parameter <code>powerlaw(1).norm</code> and has left all other parameters unchanged:
<pre>
isis> list_par;
tbabs(1)*powerlaw(1)
idx param tie-to freeze value min max
1 tbabs(1).nH 0 0 1 0 100000 10^22
2 powerlaw(1).norm 0 0 0.4145608 0 1e+10
3 powerlaw(1).PhoIndex 0 0 1 -2 9
</pre>
Now let us take a look at what the model looks like
<pre>
isis> plot_counts(pca);
</pre>
The resulting plot looks something like this:

[[File:Walkthrough03.png|center]]

Notice that the slope of the spectrum and the data is very different. With a photon index of 1 the spectrum is harder than the data. We therefore change the photon index to something that is more typical for black holes, renorm the spectrum and plot it again:
<pre>
isis> set_par(3,1.7);
isis> renorm_counts;
Parameters[Variable] = 3[1]
Data bins = 45
Chi-square = 339671.5
Reduced chi-square = 7719.808
0
isis> plot_counts(pca);
</pre>
The resulting model looks like this:

[[File:Walkthrough04.png|center]]

Note that the overall slope now looks ok, but there is still some deviation between the data and the model at the soft part of the spectrum, where the model looks too much absorbed. Taking a look at the isis help for <code>set_par</code>, we are being told that instead of changing the parameter by giving <code>set_par</code> its index number, we could also have given the full name of the parameter. So let us remove some absorption to get the curvature at the low energies right, by setting NH to its interstellar value of <latex>N_\mathrm{H}=3\times 10^{21}\,\mathrm{cm}^{-2}</latex>.
<pre>
isis> set_par("tbabs(1).nH",0.3);
isis> renorm_counts;
Parameters[Variable] = 3[1]
Data bins = 45
Chi-square = 314595.1
Reduced chi-square = 7149.888
0
isis> plot_counts(pca);
</pre>
Note that the Chi-square value decreased, meaning that the new description of the model is slightly better than the previous one.

We now have starting values that are good enough to start the proper fitting. Here isis is using a so-called Levenberg-Marquardt-gradient method to minimize chi-square by varying the parameters. This is done step by step, until a (possibly local) minimum is reached. In order to see how the parameters are being varied, we instruct isis to display all intermediate parameter values first, and then perform the fit:
<pre>
isis> Fit_Verbose=1;
isis> fit_counts();
chisqr= 3.1460e+05:
tbabs(1).nH= 3.00000000e-01 powerlaw(1).norm= 2.26407499e+00
powerlaw(1).PhoIndex= 1.70000000e+00
chisqr= 3.1460e+05:
tbabs(1).nH= 3.00030000e-01 powerlaw(1).norm= 2.26407499e+00
powerlaw(1).PhoIndex= 1.70000000e+00
:
: multiple further steps
:
chisqr= 9.6239e+03:
tbabs(1).nH= 0.00000000e+00 powerlaw(1).norm= 1.32707632e+01
powerlaw(1).PhoIndex= 2.61135748e+00
chi-square value converged
Parameters[Variable] = 3[3]
Data bins = 45
Chi-square = 9623.869
Reduced chi-square = 229.1397
0
</pre>
While the reduced chi-square is already much smaller, it is still very much above its ideal value of around unity. Let us take a look what the current best fit looks like by plotting it again:

[[File:Walkthrough05.png|center]]

The model describes the overall shape of the data rather well, but statistically significant residuals remain. We will tackle these in the next section, but first let us save our work so far such that we can start again from the current best fit in case our next steps are not successful:
<pre>
isis> save_par("powerlaw.par");
</pre>
This creates a file called <code>powerlaw.par</code> that can be re-read later using
<pre>
isis> load_par("powerlaw.par");
</pre>
The file is a simple ASCII file that you can either just display on screen (using the unix-command <code>cat powerlaw.par</code> from the shell or any editor of your choice.

'''''Exercise 4'''''
# Perform the procedure described above with "your" data set, documenting all steps.
# If you want to change more than one parameter at a time, instead of using <code>set_par</code> you can also use the <code>edit_par</code> function, which will invoke an editor of your choice with a table like the parameter table above. You can then overwrite all values with your new values, save this temporary file, and exit the editor. Try this with your data set.

=== Improving the Initial Fit ===

Now that we have an initial fit, we can take a closer look at the difference between the data and the model to get a feeling what we can do to improve the model. Since the data values and the model are already rather close together, guessing what is going on by looking at the slight differences between both is not very useful. We therefore plot our data again, but this time not only displaying the data but also the "residuals", that is the difference between the data and the model:
<pre>
isis> plot_data(pca;res=1);
</pre>
This results in the following figure:

[[File:Walkthrough06.png|center]]

Note the following:
* instead of using <code>plot_counts</code> we have used <code>plot_data</code> (which is in reality an alias for the <code>plot_data_counts</code> function. <code>plot_counts</code> displays the counts and the model in terms of counts per keV, while previously we used counts per PHA bin. This is the preferred way to plot X-ray data, since it is slightly closer to showing the proper spectrum than <code>plot_counts</code>.
* Secondly, in addition to plotting the data we are also plotting the residuals, by using the "qualifier" <code>res=1</code>. In Slang/isis, qualifiers are special switches in functions. They all have names (<code>res</code> in the above example), i.e., the order in which they are listed after the initial semicolon does not matter. The most important ways of displaying residuals are
** <code>res=1</code>: Display the residual in terms of chi, i.e., display the value of <latex>(data-model)/\sigma</latex> where <latex>\sigma</latex> is the statistical uncertainty of the bin.
** <code>res=3</code>: Display the ratio between the data and the model, <latex>data/model</latex>.
* other qualifiers that are useful in plotting are:
** <code>mcol=number</code>: the color of the model, number is, well, a number. Avoid <code>mcol=3</code> and <code>mcol=5</code> since these colors do not show up on beamers.
** <code>dcol=number</code>: dito, for the data
** <code>decol=number</code>: dito, for the error bars
** <code>bkg</code>: if <code>bkg=0</code> then plot the data with the background subtracted, if <code>bkg=1</code> also show the background (this will be useful later).
** <code>xrange={min,max}</code>: plot the x-axis from min to max only. Note the curly braces! Set <code>min</code> and/or <code>max</code> to <code>NULL</code> if you want to reset this range to its default value. It is important to remember that <code>xrange</code> just sets the ''plot''-range, you need to use <code>notice</code> to set the energy range that is used for fitting.
** <code>yrange={min,max}</code>: dito, for the y-axis.

As an example, try
<pre>
isis> plot_data(pca;res=1,mcol=2,dcol=1,decol=5);
</pre>

The residuals in the plot tell us two things:
- there is a "bump" around 6.4keV. This is typically an indication that there is an iron Kα line present around 6.4keV.
- there is a "soft excess" at low energies, which might be indicative of an accretion disk.

Looking at the [http://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecModels.html XSPEC] manual tells us that accretion disk spectra are modeled with the <code>diskbb</code> model while emission lines are modeled using the <code>gauss</code> model. However, reading the isis manual tells us that the ''only'' model that has a different name in isis and in XSPEC is <code>gauss</code> where we will have to use <code>egauss</code> instead.

Based with this information we setup the new fit function as follows
<pre>
isis> fit_fun("tbabs(1)*(diskbb(1)+egauss(1)+powerlaw(1))");
</pre>
and identify the new parameters with <code>list_par</code>:
<pre>

isis> list_par;
tbabs(1)*(diskbb(1)+egauss(1)+powerlaw(1))
idx param tie-to freeze value min max
1 tbabs(1).nH 0 0 0 0 100000 10^22
2 diskbb(1).norm 0 0 1 0 1e+10
3 diskbb(1).Tin 0 0 1 0 1000 keV
4 egauss(1).area 0 0 1 0 0 photons/s/cm^2
5 egauss(1).center 0 0 1 0 0 keV
6 egauss(1).sigma 0 0 0.002 1e-06 1 keV
7 powerlaw(1).norm 0 0 13.27076 0 1e+10
8 powerlaw(1).PhoIndex 0 0 2.611357 -2 9
</pre>
We then set the center of the Gaussian to 6.4keV (<code>set_par(5,6.4);</code>) and plot again. Nothing changes. The reason is that we first have to tell isis to recalculate the model. Not doing this automatically after every invocation of <code>set_par</code> makes sense since some models might take up large amounts of CPU time. To recalculate the model, use
<pre>
isis> eval_counts;
</pre>
Plot the model again (using <code>plot_data</code>). You will notice that the Fe line is too strong. Reduce its flux accordingly by changing the <code>area</code> parameter. You will probably need a few attempts to get something that looks ok. Then repeat this procedure with the parameters of the accretion disk until you get something that looks halfway ok. Save this attempt, just to be on the save side, and then perform a fit.

Repeating the above a few times, I managed to coax the following best fit out of the data
<pre>
isis> list_par;
tbabs(1)*(diskbb(1)+egauss(1)+powerlaw(1))
idx param tie-to freeze value min max
1 tbabs(1).nH 0 0 0 0 100000 10^22
2 diskbb(1).norm 0 0 4088.32 0 1e+10
3 diskbb(1).Tin 0 0 0.7163385 0 1000 keV
4 egauss(1).area 0 0 0.07462147 0 0 photons/s/cm^2
5 egauss(1).center 0 0 6.085836 0 0 keV
6 egauss(1).sigma 0 0 1 1e-06 1 keV
7 powerlaw(1).norm 0 0 2.948465 0 1e+10
8 powerlaw(1).PhoIndex 0 0 1.984697 -2 9
</pre>
with
<pre>
Parameters[Variable] = 8[8]
Data bins = 45
Chi-square = 291.7067
Reduced chi-square = 7.883964
</pre>
This fit looks the following:

[[File:Walkthrough07.png|center]]

This is quite ok for such a simple model. Note that there still is some hardening above 10keV and the residuals are not perfect around 8keV either. This is due to the too large width of the simple Gaussian line, limitations in the <code>diskbb</code>-model, and the fact that in this data set the source was in its intermediate state, where the combination of the disk component and the power law is notoriously hard to model.

'''''Exercise 5'''''
# you guessed it: try to find a good fit for your data set.

=== References ===
[[Category:Isis / Slang]]

ISISscripts

2018-07-31T08:54:10Z

Kuehnel:

[[Category:Isis / Slang]]
A huge (and extremely useful) collection of useful ISIS functions, written and maintained by the Remeis observatory (and certainly containing thousands of working hours by a variety of people) can be found here:

[http://www.sternwarte.uni-erlangen.de/isis/ http://www.sternwarte.uni-erlangen.de/isis/]

Please cite properly when used!

= How to investigate the source code of available functions =

In order to look up any code of a function as part of the ISISscripts navigate to its GIT-repository. You can see this folder once you require the ISISscripts (which might be done inside your [[ISIS auto start (.isisrc)|.isisrc]]), e.g.,
<pre>loading /home/git/isisscripts.git/share/isisscripts.sl</pre>
Note for Remeis users: the repository is managed by [https://www.sternwarte.uni-erlangen.de/gitlab/remeis/isisscripts GitLab]. A '''local clone''' can be found in /data/git/isisscripts.git

Then change into the source code directory, e.g.,
<pre>cd /home/git/isisscripts.git/src</pre>
Now the tricky part: you need to find that file, where the function which source code you want to investigate is defined. If you're lucky, the file is named according to the function's name (with .sl suffix), so you can try
<pre>find . -iname "mc_sig.sl"</pre>
If this does not work, you can try to grep its function definition
<pre>grep -R "define mc_sig"</pre>

Help for ISIS/S-Lang

2018-07-31T08:53:51Z

Kuehnel:

The help/description of S-Lang or ISIS functions -- which can be obtained, e.g., with <code>isis> help function_name</code> --
is defined in plain text files.
(In order to take effect, these must be introduced to S-Lang's help system via [http://www.jedsoft.org/slang/doc/html/slangfun-9.html#ss9.1 add_doc_file]
-- which is usually performed by S-Lang or ISIS itself, or by an external module.
[http://www.jedsoft.org/slang/doc/html/slangfun-9.html#ss9.5 get_doc_files] can be used to query at runtime which files are available.)

Although these help files could, in principle, be edited directly,
most programs from the S-Lang ecosystem generate them from text macro files,
which are rendered by the [http://www.jedsoft.org/jed/madewithjed.html|tmexpand script (using jed)].

Advantages of defining ''logically structured'' tm-files (using macros like <tt>\usage</tt>, <tt>\description</tt>, ...)
--
rather than ''physically formatted'' help files -- are:
* The structural elements (like <tt>USAGE</tt>, <tt>DESCRIPTION</tt>, ...) will always be rendered consistently.
* The same text macro file can be rendered in different formats -- for example also produce PDF documentation (see, e.g., the [http://www.jedsoft.org/slang/docs.html S-Lang] and [http://space.mit.edu/cxc/isis/manual.html ISIS] manuals) besides S-Lang help files.
(<tt>tmexpand</tt> can simply use different macro definitions. Note the similarity to LaTeX!)

For convenience (and more correct documentation... ;-)), text macros can be directly defined within the source code.
<tt>tmexpand</tt> comes with a <tt>tm-strip</tt> script that extracts text macros from comments enclosed by <tt>%!%+</tt> and <tt>%!%-</tt> (in S-Lang files).

A help definition within the ISISscripts,
which [http://www.sternwarte.uni-erlangen.de/git.public/?p=isisscripts;a=blob;f=doc/Makefile automatically] run the <tt>tm-strip</tt> -- <tt>tmexpand</tt> pipeline,
might look like that:
<pre>
%!%+
%\function{function_name}
%\synopsis{short description}
%\usage{type return_value = function_name( arguments );}
%\altusage{alternative usage, if applicable}
%\qualifiers{
%\qualifier{qualifier1}{: description}
%\qualifier...
%}
%\description
% Describe the function and tell what it does.
%\example
% Give an example of the usage here.
%\seealso{function_name2, function_name3}
%!%-
</pre>

For example, the help of the <tt>CCF_1D</tt> function:
<pre>
%%%%%%%%%%%%%
define CCF_1d()
%%%%%%%%%%%%%
%!%+
%\function{CCF_1d}
%\synopsis{calculates the cross correlation function of two (1d) arrays}
%\usage{Double_Type CCF = CCF_1d(a1, a2, Integer_Type dx);
%\altusage{Array_Type CCF[] = CCF_1d(a1, a2);}
%}
%\qualifiers{
%\qualifier{notperiodic}{: no periodic boundary conditions at the edges.}
%}
%\description
% The arrays \code{a1} and \code{a2} from which the CCF is to be computed can
% either be passed directly or by a reference to the arrays (see example).
% This function computes the correlation of a1[x] and a2[x-dx],
% where the index x takes all values such that x and x-dx are contained:
% \code{CCF = sum_x { (a1[x]-<a1>)/|a1| * (a2[x]-dx)-<a2>)/|a2| }}
% The norm \code{|a| = sqrt{ sum_x a[x]^2 }} ensures that \code{CCF_1d(a, +-a, 0) = +-1}.
% for any array \code{a}.\n
% \n
% If just a1 and a2 are give, the function returns an array which
% contains all possible correlations between them. Its first entry
% responds to dx=0, the second to dx=1, ... .\n
% \n
% By default, periodic boundary conditions are taken at the edges
% of the array.
%
%\example
% variable a1 = Double_Type[N]; % some data
% variable a2 = Double_Type[N]; % some other data
% variable DX = [-N/2;N/2];
% variable CCF = array_map(Double_Type, &CCF_1d, &a1, &a2, DX);
% % If used with array_map, explicit references to a1 and a2 are required,
% % as each function call to CCF_1d has to get the full array.
% variable dx_opt = DX[where( abs(CCF) == max(abs(CCF)) )];\n
% \n
% or\n
% \n
% variable a1 = Double_Type[N];
% variable a2 = Double_Type[N];
% variable CCF[] = CFF_1d(a1,a2);
%\seealso{CCF_2d}
%!%-
</pre>

gives the following output when called by <code>help CFF_1d</code>:
<pre>
SYNOPSIS
calculates the cross correlation function of two (1d) arrays

USAGE
Double_Type CCF = CCF_1d(a1, a2, Integer_Type dx);
% or
Array_Type CCF[] = CCF_1d(a1, a2);

QUALIFIERS
; notperiodic: no periodic boundary conditions at the edges.

DESCRIPTION
The arrays a1 and a2 from which the CCF is to be computed can
either be passed directly or by a reference to the arrays (see example).
This function computes the correlation of a1[x] and a2[x-dx],
where the index x takes all values such that x and x-dx are contained:
CCF = sum_x { (a1[x]-<a1>)/|a1| * (a2[x]-dx)-<a2>)/|a2| }
The norm |a| = sqrt{ sum_x a[x]^2 } ensures that CCF_1d(a, +-a, 0) = +-1.
for any array a.

If just a1 and a2 are give, the function returns an array which
contains all possible correlations between them. Its first entry
responds to dx=0, the second to dx=1, ... .

By default, periodic boundary conditions are taken at the edges
of the array.

EXAMPLE
variable a1 = Double_Type[N]; % some data
variable a2 = Double_Type[N]; % some other data
variable DX = [-N/2;N/2];
variable CCF = array_map(Double_Type, &CCF_1d, &a1, &a2, DX);
% If used with array_map, explicit references to a1 and a2 are required,
% as each function call to CCF_1d has to get the full array.
variable dx_opt = DX[where( abs(CCF) == max(abs(CCF)) )];

or

variable a1 = Double_Type[N];
variable a2 = Double_Type[N];
variable CCF[] = CFF_1d(a1,a2);

SEE ALSO
CCF_2d
</pre>

The macros <tt>\n</tt> and <tt>\code</tt> are not relevant for plain text help files,
but may become important to structure {{:isis:ccf_1d.pdf|PDF output}}.

=== Create your own help files ===

Here is what you can do to use tm-strip and tmexpand to generate help files for your private function collections:
* install the [http://www.jedsoft.org/snapshots/ tmexpand package]
* copy the *.tm files from <tt>isisscripts/doc/share/</tt> to where you can easily access them locally on you machine
* write the help to your own functions as explained above
* run <tt>tm-strip</tt> and <tt>tmexpand</tt> as
<pre>
tm-strip yourfuns.sl >> yourfuns.tm
tmexpand -Ipath/to/isisscripts/doc/share -Mslhlp_isisscripts yourfuns.tm yourfuns.txt
</pre>
* discard <tt>yourfuns.tm</tt>
* <tt>add_doc_file("yourfuns.txt");</tt> for ISIS to find your new help file. If you'd like to have the help files available at all times without loading them by hand, you can add this command to your [[ISIS auto start (.isisrc)|.isssrc]]. As an alternative, you can add the help directly through <tt>yourfuns.sl</tt> in the manner of the isisscripts:
<pre>
$1 = __FILE__[[:-4]]+".txt";
ifnot(path_is_absolute($1)) $1 = path_concat(getcwd(), $1);
if(stat_file($1)!=NULL) set_doc_files([$1, get_doc_files()]);
</pre>
However, this particular set of command only works if your help files are in the same folder as
your scripts and you are not accessing your script through a softlink. It works correctly, if you
required your function collection through a location that is added to your ISIS load path.

[[Category:Isis / Slang]]

Help for ISIS/S-Lang

2018-07-31T08:53:24Z

Kuehnel:

The help/description of S-Lang or ISIS functions -- which can be obtained, e.g., with <code>isis> help function_name</code> --
is defined in plain text files.
(In order to take effect, these must be introduced to S-Lang's help system via [http://www.jedsoft.org/slang/doc/html/slangfun-9.html#ss9.1 add_doc_file]
-- which is usually performed by S-Lang or ISIS itself, or by an external module.
[http://www.jedsoft.org/slang/doc/html/slangfun-9.html#ss9.5 get_doc_files] can be used to query at runtime which files are available.)

Although these help files could, in principle, be edited directly,
most programs from the S-Lang ecosystem generate them from text macro files,
which are rendered by the [http://www.jedsoft.org/jed/madewithjed.html|tmexpand script (using jed)].

Advantages of defining ''logically structured'' tm-files (using macros like <tt>\usage</tt>, <tt>\description</tt>, ...)
--
rather than ''physically formatted'' help files -- are:
* The structural elements (like <tt>USAGE</tt>, <tt>DESCRIPTION</tt>, ...) will always be rendered consistently.
* The same text macro file can be rendered in different formats -- for example also produce PDF documentation (see, e.g., the [http://www.jedsoft.org/slang/docs.html S-Lang] and [http://space.mit.edu/cxc/isis/manual.html ISIS] manuals) besides S-Lang help files.
(<tt>tmexpand</tt> can simply use different macro definitions. Note the similarity to LaTeX!)

For convenience (and more correct documentation... ;-)), text macros can be directly defined within the source code.
<tt>tmexpand</tt> comes with a <tt>tm-strip</tt> script that extracts text macros from comments enclosed by <tt>%!%+</tt> and <tt>%!%-</tt> (in S-Lang files).

A help definition within the ISISscripts,
which [http://www.sternwarte.uni-erlangen.de/git.public/?p=isisscripts;a=blob;f=doc/Makefile automatically] run the <tt>tm-strip</tt> -- <tt>tmexpand</tt> pipeline,
might look like that:
<pre>
%!%+
%\function{function_name}
%\synopsis{short description}
%\usage{type return_value = function_name( arguments );}
%\altusage{alternative usage, if applicable}
%\qualifiers{
%\qualifier{qualifier1}{: description}
%\qualifier...
%}
%\description
% Describe the function and tell what it does.
%\example
% Give an example of the usage here.
%\seealso{function_name2, function_name3}
%!%-
</pre>

For example, the help of the <tt>CCF_1D</tt> function:
<pre>
%%%%%%%%%%%%%
define CCF_1d()
%%%%%%%%%%%%%
%!%+
%\function{CCF_1d}
%\synopsis{calculates the cross correlation function of two (1d) arrays}
%\usage{Double_Type CCF = CCF_1d(a1, a2, Integer_Type dx);
%\altusage{Array_Type CCF[] = CCF_1d(a1, a2);}
%}
%\qualifiers{
%\qualifier{notperiodic}{: no periodic boundary conditions at the edges.}
%}
%\description
% The arrays \code{a1} and \code{a2} from which the CCF is to be computed can
% either be passed directly or by a reference to the arrays (see example).
% This function computes the correlation of a1[x] and a2[x-dx],
% where the index x takes all values such that x and x-dx are contained:
% \code{CCF = sum_x { (a1[x]-<a1>)/|a1| * (a2[x]-dx)-<a2>)/|a2| }}
% The norm \code{|a| = sqrt{ sum_x a[x]^2 }} ensures that \code{CCF_1d(a, +-a, 0) = +-1}.
% for any array \code{a}.\n
% \n
% If just a1 and a2 are give, the function returns an array which
% contains all possible correlations between them. Its first entry
% responds to dx=0, the second to dx=1, ... .\n
% \n
% By default, periodic boundary conditions are taken at the edges
% of the array.
%
%\example
% variable a1 = Double_Type[N]; % some data
% variable a2 = Double_Type[N]; % some other data
% variable DX = [-N/2;N/2];
% variable CCF = array_map(Double_Type, &CCF_1d, &a1, &a2, DX);
% % If used with array_map, explicit references to a1 and a2 are required,
% % as each function call to CCF_1d has to get the full array.
% variable dx_opt = DX[where( abs(CCF) == max(abs(CCF)) )];\n
% \n
% or\n
% \n
% variable a1 = Double_Type[N];
% variable a2 = Double_Type[N];
% variable CCF[] = CFF_1d(a1,a2);
%\seealso{CCF_2d}
%!%-
</pre>

gives the following output when called by <code>help CFF_1d</code>:
<pre>
SYNOPSIS
calculates the cross correlation function of two (1d) arrays

USAGE
Double_Type CCF = CCF_1d(a1, a2, Integer_Type dx);
% or
Array_Type CCF[] = CCF_1d(a1, a2);

QUALIFIERS
; notperiodic: no periodic boundary conditions at the edges.

DESCRIPTION
The arrays a1 and a2 from which the CCF is to be computed can
either be passed directly or by a reference to the arrays (see example).
This function computes the correlation of a1[x] and a2[x-dx],
where the index x takes all values such that x and x-dx are contained:
CCF = sum_x { (a1[x]-<a1>)/|a1| * (a2[x]-dx)-<a2>)/|a2| }
The norm |a| = sqrt{ sum_x a[x]^2 } ensures that CCF_1d(a, +-a, 0) = +-1.
for any array a.

If just a1 and a2 are give, the function returns an array which
contains all possible correlations between them. Its first entry
responds to dx=0, the second to dx=1, ... .

By default, periodic boundary conditions are taken at the edges
of the array.

EXAMPLE
variable a1 = Double_Type[N]; % some data
variable a2 = Double_Type[N]; % some other data
variable DX = [-N/2;N/2];
variable CCF = array_map(Double_Type, &CCF_1d, &a1, &a2, DX);
% If used with array_map, explicit references to a1 and a2 are required,
% as each function call to CCF_1d has to get the full array.
variable dx_opt = DX[where( abs(CCF) == max(abs(CCF)) )];

or

variable a1 = Double_Type[N];
variable a2 = Double_Type[N];
variable CCF[] = CFF_1d(a1,a2);

SEE ALSO
CCF_2d
</pre>

The macros <tt>\n</tt> and <tt>\code</tt> are not relevant for plain text help files,
but may become important to structure {{:isis:ccf_1d.pdf|PDF output}}.

=== Create your own help files ===

Here is what you can do to use tm-strip and tmexpand to generate help files for your private function collections:
* install the [http://www.jedsoft.org/snapshots/ tmexpand package]
* copy the *.tm files from <tt>isisscripts/doc/share/</tt> to where you can easily access them locally on you machine
* write the help to your own functions as explained above
* run <tt>tm-strip</tt> and <tt>tmexpand</tt> as
<pre>
tm-strip yourfuns.sl >> yourfuns.tm
tmexpand -Ipath/to/isisscripts/doc/share -Mslhlp_isisscripts yourfuns.tm yourfuns.txt
</pre>
* discard <tt>yourfuns.tm</tt>
* <tt>add_doc_file("yourfuns.txt");</tt> for ISIS to find your new help file. If you'd like to have the help files available at all times without loading them by hand, you can add this command to your [[ISIS auto start (.isisrc)|.isissrc]]. As an alternative, you can add the help directly through <tt>yourfuns.sl</tt> in the manner of the isisscripts:
<pre>
$1 = __FILE__[[:-4]]+".txt";
ifnot(path_is_absolute($1)) $1 = path_concat(getcwd(), $1);
if(stat_file($1)!=NULL) set_doc_files([$1, get_doc_files()]);
</pre>
However, this particular set of command only works if your help files are in the same folder as
your scripts and you are not accessing your script through a softlink. It works correctly, if you
required your function collection through a location that is added to your ISIS load path.

[[Category:Isis / Slang]]

ISISscripts

2018-07-31T08:53:03Z

Kuehnel:

[[Category:Isis / Slang]]
A huge (and extremely useful) collection of useful ISIS functions, written and maintained by the Remeis observatory (and certainly containing thousands of working hours by a variety of people) can be found here:

[http://www.sternwarte.uni-erlangen.de/isis/ http://www.sternwarte.uni-erlangen.de/isis/]

Please cite properly when used!

= How to investigate the source code of available functions =

In order to look up any code of a function as part of the ISISscripts navigate to its GIT-repository. You can see this folder once you require the ISISscripts (which might be done inside your [[ISIS auto start (.isisrc)|.isissrc]]), e.g.,
<pre>loading /home/git/isisscripts.git/share/isisscripts.sl</pre>
Note for Remeis users: the repository is managed by [https://www.sternwarte.uni-erlangen.de/gitlab/remeis/isisscripts GitLab]. A '''local clone''' can be found in /data/git/isisscripts.git

Then change into the source code directory, e.g.,
<pre>cd /home/git/isisscripts.git/src</pre>
Now the tricky part: you need to find that file, where the function which source code you want to investigate is defined. If you're lucky, the file is named according to the function's name (with .sl suffix), so you can try
<pre>find . -iname "mc_sig.sl"</pre>
If this does not work, you can try to grep its function definition
<pre>grep -R "define mc_sig"</pre>

ISIS auto start (.isisrc)

2018-07-31T08:50:43Z

Kuehnel: Created page with "As part of its startup, ISIS executes a file called <code>~/.isisrc</code> (i.e., the file named <code>.isisrc</code> which is located in your $HOME directory). This file is u..."

As part of its startup, ISIS executes a file called <code>~/.isisrc</code> (i.e., the file named <code>.isisrc</code> which is located in your $HOME directory). This file is useful for setting up a standard environment. We recommend this file to be short and to include only the most important commands.

Example .isisrc:
<pre>
% allow the easy access to require("isisscripts")
add_to_isis_load_path("/Path/To/isisscripts/share/");

% you might even require the ISISscripts on startup
require("isisscripts");

% set the solar abundance vector and X-ray cross-sections,
% which is important to calculate the X-ray absorption correctly
()=xspec_abund("wilm");
()=xspec_xsect("vern");

% set your desired editor used by, e.g., edit_par
putenv("EDITOR=emacs -nw");
</pre>

ISISscripts

2018-07-31T08:40:46Z

Kuehnel:

[[Category:Isis / Slang]]
A huge (and extremely useful) collection of useful ISIS functions, written and maintained by the Remeis observatory (and certainly containing thousands of working hours by a variety of people) can be found here:

[http://www.sternwarte.uni-erlangen.de/isis/ http://www.sternwarte.uni-erlangen.de/isis/]

Please cite properly when used!

= How to investigate the source code of available functions =

In order to look up any code of a function as part of the ISISscripts navigate to its GIT-repository. You can see this folder once you start ISIS, e.g.,
<pre>loading /home/git/isisscripts.git/share/isisscripts.sl</pre>
Note for Remeis users: the repository is managed by [https://www.sternwarte.uni-erlangen.de/gitlab/remeis/isisscripts GitLab]. A '''local clone''' can be found in /data/git/isisscripts.git

Then change into the source code directory, e.g.,
<pre>cd /home/git/isisscripts.git/src</pre>
Now the tricky part: you need to find that file, where the function which source code you want to investigate is defined. If you're lucky, the file is named according to the function's name (with .sl suffix), so you can try
<pre>find . -iname "mc_sig.sl"</pre>
If this does not work, you can try to grep its function definition
<pre>grep -R "define mc_sig"</pre>

Category:Isis / Slang

2018-07-31T08:32:41Z

Kuehnel:

'''This page is being [https://www.sternwarte.uni-erlangen.de/wiki/index.php/Category_talk:Isis_/_Slang discussed].'''

The [http://space.mit.edu/cxc/isis/|Interactive Spectral Interpretation System (ISIS)] was developed at MIT for the analysis of X-ray spectra.

Note that this page was just copy-pasted from the old wiki. This is only a short list of instructions that will be available. I do not think that a full list of all instructions should go here for the new wiki, I'm trying to find another solution for that (Matthias: ''What about looking at the content of the category below?'') In the end, I think only the instructions to get isis running and first steps should be here (Matthias: ''I disagree because category pages (like this) are not considered during searches! That's why I have created pages with the "ISIS history file" and "ISISscripts" separately''). I will move all the advanced stuff like defining models, timing tools, etc. somewhere else.
* [[ISIS_introduction_for_the_new_bachelor_students|Introduction for the bachelor students]]
* [[Isis_tutorial|ISIS Tutorial (X-ray astronomy lecture 2012)]]
* [[Plotting_with_the_S-Lang_Xfig_module|Plotting with the S-Lang Xfig module, instructions and examples]]
* [[How_to_define_your_own_models_in_ISIS|Define your own models in ISIS]]
* [[Questions_and_Answers| Questions and Answers]]
* [http://www.sternwarte.uni-erlangen.de/git.public/?p=isisscripts;a=history;f=README| README file] for using/.../changing the [http://www.sternwarte.uni-erlangen.de/isis/ ISISscripts]
* [[Timing_tools|Use timing tools with ISIS]]
* [[Parallel_Error_Calculation_using_MPI_and_SLmpi|Parallel Error Calculation using MPI and SLmpi]]
* [[Fake_an_Observation_with_ISIS|fake an observation with isis]]
* [[Fit2dcurve|fit a curve to a 2D data set via parameterized polynomials]]
* [[Simfit|Simultaneous Fits of a large number of observations]]
* [[Fitting_Equivalent_Widths|fitting equivalent widths directly]]
* [[ Emcee|emcee - the Markov-Chain-Monte-Carlo hammer]]
* [[Install_ISIS_on_Mac|install on a MAC OS X (10.10 yosemite) - fresh]]
* [[Making_tables_with_sltable|Quickly generate a LaTeX table of spectral parameters with uncertainties]]

== S-Lang tips & tricks ==
* [[Modules | S-Lang modules (function packages)]]
* writing helps for functions
* [[Functions_within_structures|functions within structures]]
* [[Function_nesting|function nesting]]
* [[Self-value_management|self-value-management]]
* [[Changing_qualifiers_before_passing_them_on|changing qualifiers before passing them on]]
* speed up code
** [[Iterating_over_an_array_-_three_different_for-loops|iterating over an array - three different for-loops]]
** [[Ternary_operator_%3F|ternary operator ?: ]]
** [[Profiling|profile - Run-time profiler: Analyses (nested) function run-times]]
* [[Pass_information_to_a_fit_function_via_metadata|passing information to a fit function via metadata]]
* [[References_to_variables|References to variables]]
* [[Name_of_the_calling_function_(ISIS/Slang)| Name of the calling function]]

[[Category:Software]]

Category:Isis / Slang

2018-07-31T08:32:25Z

Kuehnel:

'''This page is being [https://www.sternwarte.uni-erlangen.de/wiki/index.php?title=Category:Isis_/_Slang discussed].'''

The [http://space.mit.edu/cxc/isis/|Interactive Spectral Interpretation System (ISIS)] was developed at MIT for the analysis of X-ray spectra.

Note that this page was just copy-pasted from the old wiki. This is only a short list of instructions that will be available. I do not think that a full list of all instructions should go here for the new wiki, I'm trying to find another solution for that (Matthias: ''What about looking at the content of the category below?'') In the end, I think only the instructions to get isis running and first steps should be here (Matthias: ''I disagree because category pages (like this) are not considered during searches! That's why I have created pages with the "ISIS history file" and "ISISscripts" separately''). I will move all the advanced stuff like defining models, timing tools, etc. somewhere else.
* [[ISIS_introduction_for_the_new_bachelor_students|Introduction for the bachelor students]]
* [[Isis_tutorial|ISIS Tutorial (X-ray astronomy lecture 2012)]]
* [[Plotting_with_the_S-Lang_Xfig_module|Plotting with the S-Lang Xfig module, instructions and examples]]
* [[How_to_define_your_own_models_in_ISIS|Define your own models in ISIS]]
* [[Questions_and_Answers| Questions and Answers]]
* [http://www.sternwarte.uni-erlangen.de/git.public/?p=isisscripts;a=history;f=README| README file] for using/.../changing the [http://www.sternwarte.uni-erlangen.de/isis/ ISISscripts]
* [[Timing_tools|Use timing tools with ISIS]]
* [[Parallel_Error_Calculation_using_MPI_and_SLmpi|Parallel Error Calculation using MPI and SLmpi]]
* [[Fake_an_Observation_with_ISIS|fake an observation with isis]]
* [[Fit2dcurve|fit a curve to a 2D data set via parameterized polynomials]]
* [[Simfit|Simultaneous Fits of a large number of observations]]
* [[Fitting_Equivalent_Widths|fitting equivalent widths directly]]
* [[ Emcee|emcee - the Markov-Chain-Monte-Carlo hammer]]
* [[Install_ISIS_on_Mac|install on a MAC OS X (10.10 yosemite) - fresh]]
* [[Making_tables_with_sltable|Quickly generate a LaTeX table of spectral parameters with uncertainties]]

== S-Lang tips & tricks ==
* [[Modules | S-Lang modules (function packages)]]
* writing helps for functions
* [[Functions_within_structures|functions within structures]]
* [[Function_nesting|function nesting]]
* [[Self-value_management|self-value-management]]
* [[Changing_qualifiers_before_passing_them_on|changing qualifiers before passing them on]]
* speed up code
** [[Iterating_over_an_array_-_three_different_for-loops|iterating over an array - three different for-loops]]
** [[Ternary_operator_%3F|ternary operator ?: ]]
** [[Profiling|profile - Run-time profiler: Analyses (nested) function run-times]]
* [[Pass_information_to_a_fit_function_via_metadata|passing information to a fit function via metadata]]
* [[References_to_variables|References to variables]]
* [[Name_of_the_calling_function_(ISIS/Slang)| Name of the calling function]]

[[Category:Software]]

Category:Internal

2018-07-31T08:32:15Z

Kuehnel:

'''This page is being [https://www.sternwarte.uni-erlangen.de/wiki/index.php/Category_talk:Internal discussed].'''

This page (and all other pages in the namespace 'intern') can only be viewed when logged-in.

=== Administrative stuff ===

* '''[[Ocotber 24th: Open House]]'''

* [[Common Practices at Remeis]]

==== Travels ====

* [[How to combine business and private travel]]

=== Lab course ===

[[How the lab manuals are structured and how you can edit them]]

[[Planning page for the 40cm imaging experiment]]

[[Planning page for the CCD lab ]]

[[Tables to fill in dates and comments for every group]]

[[Location of the lab equipment]]

[[What to mention in the computer introduction]]

=== Lit Club ===
[[List of Literature Club Talks]]

=== Hardware ===

[[List of servers in the Remeis Cluster]]

=== Mac Minis ===

Here are some short information about the Mac Minis in Erlangen:
* Link to the ecap wiki (works only in erlangen or in bamberg) - https://doku.ecap.physik.uni-erlangen.de/
* When you login in the keyboard layout will always be english
* The size of your $HOME directory is limited to 20 GB - only store files here, which cannot be reproduced e.g. scripts, etc..
* Store all the other stuff in /local/scratch
* Following programs will be installed on our Mac Minis:
**ISIS
**IDL
**HEADAS(FTOOLS)
**DS9
=== eROSITA ===

* [[EROSITA|eROSITA - Bamberg]]
* [[ERosita Coding standards|Coding standards]]
* [[Needed functions and libraries]]
* [[Q&A]]
* [[ERosita Preprocessing|Preprocessing]]
* [[TODO]]
* [[Fpipe|fpipe-Treffen Tübingen 28.10.2010]]
* [[Datatypes|length of datatypes in C]]

=== TANAMI ===

* '''[[TANAMI| TANAMI - Start]]'''
* '''[[TANAMI - public]]'''

=== Proposals ===

When submitting a proposal for satellite observations usually a list of earlier successful proposals is added. To make it easier to find those relevant for the individual observatory and the scientific aim of the current proposal, [[Proposals| here]] is a list of proposals our group was involved in. Please include title, PI/CoIs, cycle and publications based on the observation.

=== Public Outreach ===

* In general, [mailto:Katharina.Leiter@physik.uni-wuerzburg.de Katha Leiter] is the responsible person for outreach in the group of M. Kadler in Wuerzburg. You may want to talk to her.
* Guided Tours and Public Outreach at Remeis
** [[Guided Tours and Public Outreach | general informations and knowledge base]] for guides
** [http://www.sternwarte.uni-erlangen.de/intern/Kalender/index.php online calender] - where the tours have to be listed in addition to the whiteboad in the copymachine office
** [[available presentation and videos]]
* [[popular science]] - how to explain "what we do" and physical phenomena to the public

=== Miscellaneous ===

[[cinema | Movie schedule for the Remeis Movie Club]]

[[phd_hat_list | List of future PhD's for hat matters]]

[[RCL]]

[[Remeis Gardening]]

[[Category:Internal]]

Category talk:Internal

2018-07-31T08:31:43Z

Kuehnel: Created page with "Matthias: Category pages are not considered during searches! Thus, relevant information '''has to be written''' in a separate page! I suggest to move any information on catego..."

Matthias:
Category pages are not considered during searches! Thus, relevant information '''has to be written''' in a separate page! I suggest to move any information on category pages into corresponding pages. In addition, providing a content as we did in the old wiki is not necessary here, because the category pages already list all associated pages at the end!

Category:Isis / Slang

2018-07-31T08:30:37Z

Kuehnel:

'''This page is being [https://www.sternwarte.uni-erlangen.de/wiki/index.php?title=Category:Isis_/_Slang&action=submit discussed].'''

The [http://space.mit.edu/cxc/isis/|Interactive Spectral Interpretation System (ISIS)] was developed at MIT for the analysis of X-ray spectra.

Note that this page was just copy-pasted from the old wiki. This is only a short list of instructions that will be available. I do not think that a full list of all instructions should go here for the new wiki, I'm trying to find another solution for that (Matthias: ''What about looking at the content of the category below?'') In the end, I think only the instructions to get isis running and first steps should be here (Matthias: ''I disagree because category pages (like this) are not considered during searches! That's why I have created pages with the "ISIS history file" and "ISISscripts" separately''). I will move all the advanced stuff like defining models, timing tools, etc. somewhere else.
* [[ISIS_introduction_for_the_new_bachelor_students|Introduction for the bachelor students]]
* [[Isis_tutorial|ISIS Tutorial (X-ray astronomy lecture 2012)]]
* [[Plotting_with_the_S-Lang_Xfig_module|Plotting with the S-Lang Xfig module, instructions and examples]]
* [[How_to_define_your_own_models_in_ISIS|Define your own models in ISIS]]
* [[Questions_and_Answers| Questions and Answers]]
* [http://www.sternwarte.uni-erlangen.de/git.public/?p=isisscripts;a=history;f=README| README file] for using/.../changing the [http://www.sternwarte.uni-erlangen.de/isis/ ISISscripts]
* [[Timing_tools|Use timing tools with ISIS]]
* [[Parallel_Error_Calculation_using_MPI_and_SLmpi|Parallel Error Calculation using MPI and SLmpi]]
* [[Fake_an_Observation_with_ISIS|fake an observation with isis]]
* [[Fit2dcurve|fit a curve to a 2D data set via parameterized polynomials]]
* [[Simfit|Simultaneous Fits of a large number of observations]]
* [[Fitting_Equivalent_Widths|fitting equivalent widths directly]]
* [[ Emcee|emcee - the Markov-Chain-Monte-Carlo hammer]]
* [[Install_ISIS_on_Mac|install on a MAC OS X (10.10 yosemite) - fresh]]
* [[Making_tables_with_sltable|Quickly generate a LaTeX table of spectral parameters with uncertainties]]

== S-Lang tips & tricks ==
* [[Modules | S-Lang modules (function packages)]]
* writing helps for functions
* [[Functions_within_structures|functions within structures]]
* [[Function_nesting|function nesting]]
* [[Self-value_management|self-value-management]]
* [[Changing_qualifiers_before_passing_them_on|changing qualifiers before passing them on]]
* speed up code
** [[Iterating_over_an_array_-_three_different_for-loops|iterating over an array - three different for-loops]]
** [[Ternary_operator_%3F|ternary operator ?: ]]
** [[Profiling|profile - Run-time profiler: Analyses (nested) function run-times]]
* [[Pass_information_to_a_fit_function_via_metadata|passing information to a fit function via metadata]]
* [[References_to_variables|References to variables]]
* [[Name_of_the_calling_function_(ISIS/Slang)| Name of the calling function]]

[[Category:Software]]

Category talk:Isis / Slang

2018-07-31T08:27:11Z

Kuehnel: Created page with "Matthias: As I've written within the page already, category pages are not considered during searches! Thus, relevant information '''has to be written''' in a separate pa..."

Matthias: 
As I've written within the page already, category pages are not considered during searches! Thus, relevant information '''has to be written''' in a separate page! I suggest to move any information on category pages into corresponding pages. In addition, providing a content as we did in the old wiki is not necessary here, because the category pages already list all associated pages at the end!

Category:Isis / Slang

2018-07-31T08:20:53Z

Kuehnel:

The [http://space.mit.edu/cxc/isis/|Interactive Spectral Interpretation System (ISIS)] was developed at MIT for the analysis of X-ray spectra.

Note that this page was just copy-pasted from the old wiki. This is only a short list of instructions that will be available. I do not think that a full list of all instructions should go here for the new wiki, I'm trying to find another solution for that (Matthias: ''What about looking at the content of the category below?'') In the end, I think only the instructions to get isis running and first steps should be here (Matthias: ''I disagree because category pages (like this) are not considered during searches! That's why I have created pages with the "ISIS history file" and "ISISscripts" separately''). I will move all the advanced stuff like defining models, timing tools, etc. somewhere else.
* [[ISIS_introduction_for_the_new_bachelor_students|Introduction for the bachelor students]]
* [[Isis_tutorial|ISIS Tutorial (X-ray astronomy lecture 2012)]]
* [[Plotting_with_the_S-Lang_Xfig_module|Plotting with the S-Lang Xfig module, instructions and examples]]
* [[How_to_define_your_own_models_in_ISIS|Define your own models in ISIS]]
* [[Questions_and_Answers| Questions and Answers]]
* [http://www.sternwarte.uni-erlangen.de/git.public/?p=isisscripts;a=history;f=README| README file] for using/.../changing the [http://www.sternwarte.uni-erlangen.de/isis/ ISISscripts]
* [[Timing_tools|Use timing tools with ISIS]]
* [[Parallel_Error_Calculation_using_MPI_and_SLmpi|Parallel Error Calculation using MPI and SLmpi]]
* [[Fake_an_Observation_with_ISIS|fake an observation with isis]]
* [[Fit2dcurve|fit a curve to a 2D data set via parameterized polynomials]]
* [[Simfit|Simultaneous Fits of a large number of observations]]
* [[Fitting_Equivalent_Widths|fitting equivalent widths directly]]
* [[ Emcee|emcee - the Markov-Chain-Monte-Carlo hammer]]
* [[Install_ISIS_on_Mac|install on a MAC OS X (10.10 yosemite) - fresh]]
* [[Making_tables_with_sltable|Quickly generate a LaTeX table of spectral parameters with uncertainties]]

== S-Lang tips & tricks ==
* [[Modules | S-Lang modules (function packages)]]
* writing helps for functions
* [[Functions_within_structures|functions within structures]]
* [[Function_nesting|function nesting]]
* [[Self-value_management|self-value-management]]
* [[Changing_qualifiers_before_passing_them_on|changing qualifiers before passing them on]]
* speed up code
** [[Iterating_over_an_array_-_three_different_for-loops|iterating over an array - three different for-loops]]
** [[Ternary_operator_%3F|ternary operator ?: ]]
** [[Profiling|profile - Run-time profiler: Analyses (nested) function run-times]]
* [[Pass_information_to_a_fit_function_via_metadata|passing information to a fit function via metadata]]
* [[References_to_variables|References to variables]]
* [[Name_of_the_calling_function_(ISIS/Slang)| Name of the calling function]]

[[Category:Software]]

ISIS history file

2018-07-31T08:17:25Z

Kuehnel: Created page with "You will make your ISIS-life A TON easier by setting up an ISIS history file that saves any interactive commands you use. They are usually automatically set on the Remeis-clus..."

You will make your ISIS-life A TON easier by setting up an ISIS history file that saves any interactive commands you use. They are usually automatically set on the Remeis-cluster, otherwise go to your .bashrc and use:

<code>
ISIS_HISTORY_FILE=/path_where_you_want_your_file_ususally_home/.isis_history
export ISIS_HISTORY_FILE
</code>

Adapt for other shells accordingly.

ISISscripts

2018-07-31T08:15:59Z

Kuehnel: Created page with "Category:Isis / Slang A huge (and extremely useful) collection of useful ISIS functions, written and maintained by the Remeis observatory (and certainly containing thousan..."

Mailing lists

2018-07-24T14:16:07Z

Kuehnel: Kuehnel moved page Mailing lists to List of mailing lists

#REDIRECT [[List of mailing lists]]

List of mailing lists

2018-07-24T14:16:07Z

Kuehnel: Kuehnel moved page Mailing lists to List of mailing lists

A list of mailing lists is provided in the following. If you want to be added to or removed from a list talk to the list administrator. Some lists are closed and, thus, on invitation only.

{|class="wikitable"
!List
!Admin
!Note
|-
|all@sternwarte.uni-erlangen.de
|Max
|
|-
|xray@sternwarte.uni-erlangen.de
|Max
|closed
|-
|stellar@sternwarte.uni-erlangen.de
|Max
|closed
|-
|multi@sternwarte.uni-erlangen.de
|Max
|closed
|-
|astro-fuehrungen@sternwarte.uni-erlangen.de
|Max
|
|-
|astro-xmag@sternwarte.uni-erlangen.de
|Ingo
|closed
|}

[[Category:Internal]]

Guided Tours and Public Outreach

2018-07-24T14:15:22Z

Kuehnel:

On this pages you can find all informations needed to guide a tour through our observatory for public people.

At least, that's the aim of this page, so please add information if you think its missing!

= Platform =

'''The following is important:''' 
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. The email address is a forwarding to a certain person of the mailing list (see below).

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 mailing list 
[mailto:astro-fuehrungen@lists.fau.de astro-fuehrungen@lists.fau.de] 
Please '''do not share''' this address with anybody outside of the observatory!

New tours without a guide yet are usually announced via this list. See [[Mailing lists]] for the list administrator.

Currently, the following people are on this list (probably outdated!). A * markes the person who receives email to fuehrungen@foerderverein...:
* Simon (*)
* David
* Katha (from Wuerzburg)
* Andreas
* Manami
* Matthias

If you're not on the list but interested in giving tours, just ask Max to add you :-)

= 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 (usually to one phone in the Knigge room). 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 ohter 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 copymachine 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'''.
* Clarify the '''costs for a tour''' beforehand!! Unfortunately, we are '''not allowed to ask for money''' for giving a tour! The only way for getting money is to tell the people that they are welcomed to '''donate money to the [http://foerderverein-sternwarte-bamberg.de/| Foerderverein der Sternwarte]'''. In nearly every case the people or the one asking for a tour will pay something. A rule of thumb is that '''every person donates 3 EUR''' (for children 2 EUR are alright as well). __For your ears only__: 1 EUR per attended person of the donated money will be transfered to the Förderverein (the current treasurer is Ingo, leave the money on his desk with a short note stating the number of people and what kind of a tour this was), the rest is for the guide! There will be a contact phone-number available, best would be to call the contacts-person before the tour to tell them these infos...
* '''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!
* If all the above points are clarified '''mark the tour''' in our [https://www.sternwarte.uni-erlangen.de/calendar/ online calender] and the whiteboard in the copymachine 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 calender, 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.

== 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
** 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]]
* 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
* Shut down the telescope mounting, put the dust covers back on and close the domes
* 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 copymachine office '''to the list attached to the pin-board''' next to it

== Welcome speech ==

== Solar system model ==

== Meteorite showcase ==

== Hallway - instrument exhibition ==

== Outreach Material, Presentations ==
Collected information valuable for guided tours:
''/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''

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

The promotion video by M. Langejahn (Wuerzburg, AG Kadler):
''/home/langejahn/Public/LNdW.mp4''

Research and activities at Remeis from the radio to the gamma-rays:
''/userdata/data/beuchert/work/teaching/guidedtour/presentation/research_at_remeis.pdf''

== Picture presentation ==

There are different modes for the beamer (e.g. presentation, videos, graphics etc.) which result in a different appereance of the images. Make sure to select a presentation mode in which the pictures appear in an appropriate brightnes 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 als 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€ alltogether.

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.

== Observing ==

[[Category:Internal]]

List of mailing lists

2018-07-24T14:14:33Z

Kuehnel: Created page with "A list of mailing lists is provided in the following. If you want to be added to or removed from a list talk to the list administrator. Some lists are closed and, thus, on inv..."

2018-06-20T09:43:45Z

Kuehnel:

{{chart/start|align=center|summary=Contents of the Remeis wiki}}
{{chart| | | | | | | | Wiki | | | | | | Wiki=[[Main Page | '''Remeis Wiki''']]}}
{{chart| | , |-|-|-|-|-|-| + |-|-|-|-|-|-|v|~|~|~|~|~|~|7 | }}
{{chart| Info | | | | | Software | | | | | Physics | | | | | Internal | |
Info=[[:Category:General Information|'''General Information''']]|Software=[[:Category:Software|'''Software''']]|
Physics=[[:Category:Science|'''Science''']]|Internal=[[:Category:Internal|Internal]]}}
{{chart| !| | | | | | |!| | | | | | |!| | | | | | | |:| }}
{{chart| )| curr | | | |)|cfits| | | |)|Accr | | | | admin | |
curr=[[:Category:Current_Members|For Current Members]]|cfits=[[:Category:CFITSIO_/_FPIPE|CFITSIO/FPIPE]]|
Accr=[[:Category:Accreting_X-ray_Pulsars|Accreting X-ray Pulsars]]|admin=[[:Category:Admin|Admin]]}}
{{chart| !| | | | | | |!| | | | | | |!| }}
{{chart| )| Obs | | | |)| data | | | |)|Atom| | | |
Obs=[[:Category:Observatory|On the Observatory]]|data=[[:Category:Data_Extraction|Data Extraction]]|Atom=[[:Category:Atomic_Physics|Atomic Physics]]}}
{{chart| !| | | | | | |!| | | | | | |! | }}
{{chart| `| visit | | | |)| git| | | |`|ero| | | |
visit=[[:Category:Visitors|For Visitors]]|git=[[:Category:GIT|GIT]]|ero=[[:Category:{{lcfirst:eROSITA}}|eROSITA]]}}
{{chart| | | | | | | |!| | | | | | | | }}
{{chart| | | | | | | |)|isis| | | | | | | | |isis=[[:Category:Isis_/_Slang|ISIS/Slang]]}}
{{chart| | | | | | | |!| |!| | | | | | }}
{{chart| | | | | | | |!| |`|xfig| | | | | | |xfig=[[:Category:SLxfig|SLxfig]]}}
{{chart| | | | | | | |!| | | | | | | | }}{{chart| | | | | | | |)|KDE| | | | | | | | |KDE=[[:Category:KDE|KDE]]}}
{{chart| | | | | | | |!| | | | | | | | }}
{{chart| | | | | | | |)|LaTeX| | | | | | | | |LaTeX=[[:Category:LaTeX|LaTeX]]}}
{{chart| | | | | | | |!| | | | | | | | }}
{{chart| | | | | | | |)|RCL| | | | | | | | |RCL=[[:Category:RCL|Remeis C Library]]}}
{{chart| | | | | | | |!| | | | | | | | }}
{{chart| | | | | | | |)|slurm| | | | | | | |slurm=[[:Category:Slurm|Slurm]]}}
{{chart| | | | | | | |!| | | | | | | | }}
{{chart| | | | | | | |)|tools| | | | | | | |tools=[[:Category:Tools|Tools]]}}
{{chart| | | | | | | |!| | | | | | | | }}
{{chart| | | | | | | |)|troub| | | | | | | |troub=[[:Category:Trouble_Shooting|Trouble Shooting]]}}
{{chart| | | | | | | |!| | | | | | | | }}
{{chart| | | | | | | |`|remot| | | | | | | |remot=[[:Category:Working_Remotely|Working Remotely]]}}
{{chart/end}}

Main Page

2018-06-20T09:10:34Z

Kuehnel:

== Welcome to the Wiki of the Dr. Karl Remeis Observatory ==

This is our new wiki. Please use the '''Search Remeis-Wiki box''' on the upper right corner to search for the page or information you are looking for. You may '''browse the content''' of the wiki using the [[Contents| Contents]] link in the menu on the left.

In order to edit or create new pages you have to '''log in''' using the same username and password than for the Remeis machines. In case you are a former or external member please choose the corresponding domain additionally. Please visit the [[Help:How_to| How to]] page before you start editing the wiki! For trial reasons, use the [[sandbox|sandbox]].

If you have questions or suggestions, please feel free to talk to Maria.

Note: You can find the old wiki at [http://www.sternwarte.uni-erlangen.de/old/wiki http://www.sternwarte.uni-erlangen.de/old/wiki], but editing has been disabled.

Needed functions and libraries

2018-06-19T13:21:49Z

Kuehnel:

* '''time and date functions (will be done by Christoph):'''
* ero_date_of_MJD
* ero_date_of_eroday
* ero_date_of_today
* ero_MJD_of_date
* ero_MJD_of_today
* ero_MJD_of_eroday
* ero_eroday_of_date
* ero_eroday_of_MJD
* ero_eroday_of_today

* '''I/O functions (done, testing required):'''
* ero_create_file
* ero_create_fits_tbl
* ero_create_fits_img_2D <- more dimensions required?
* ero_open_file
* ero_open_fits_tbl
* ero_open_fits_img
* ero_close_file
* ero_close_fits
* ero_copy_file
* ero_remove_file
* ero_get_dir
* ero_create_dir
* ero_remove_dir
* ero_file_exists
* ero_check_access

* '''checksum functions (done, testing required)'''
* ero_create_checksum
* ero_update_checksum
* ero_verify_checksum
* <del>ero_remove_checksum</del> (most probably not necessary)

* '''admin notification function(s)'''

* '''warning function(s)'''

* '''logging function(s)'''

[[Category:Internal]][[Category:EROSITA]]

Fpipe Meeting 1

2018-06-19T13:18:29Z

Kuehnel:

[[Category:Internal]][[Category:EROSITA]]

==== pipeline definition ====

extra: fuer multipipe -> sequentielle Abarbeitung von pipelines
<code xml>
<pipelinedefinition multi = "TRUE"> test
<pipedef> test
<Substruktur> Nur fuer Strukturierungszwecke
<Tool> test
<fpipeserverstart> FeederTool infile="##INFILE[0]##" outfile="##OUTFILE[0]##" semid="##SEMID##" wlocks="##WLOCKS,/##" or="##O_R,/##" + additional parameters modul spezifisch
<infile sema = "true/false" (true heisst Infile wird mit Semaphoren geschuetzt) source = "true/false" (datei existiert bereits zu beginn der pipeline)>
<outfile sema = "true/false" source = "true/false" temporary = "true/false" (loescht die datei nach Beendigung der pipeline/multipipe>
</code>

Add a test directory with default outputs of specific files in there in order to test if major changes in libraries changed the input/output. isdc_cmp is the function to use but we can ask INGO :)

TODO: Christoph will add uname == Darwin and uname == Linux to the configure script to change some things like ''*.so'' and ''*.dylib''.

NOTE: mgtime will perform on an ASCII File

==== EventFeeder ====
Having explained our wishes to Stefan and Henry we came to the conclusion that it would make sense to write our own EventFeeder which does all the file and directory watching stuff and - if needed - other small tasks which have to be done prior to invoking the actual pipe.
In this context we should use the kernel-function //inotify// (//kqueue// on Mac) which allows the user to add a watch on file system elements. If these elements change (read, write, delete...) the kernel will notify the program which called the function.

Common Practices at Remeis

2018-06-18T14:53:33Z

Kuehnel:

== Common Practices at Remeis ==

'''From an e-mail by J. Wilms on 2016 June 14 to the X-ray gang'''

''We try to be as flexible as possible, and I trust that you are adults and do not exploit the system. A minimum time for coordination in the group and knowing what everybody is doing is necessary. This time is the group meeting, and for this reason you have to be there and you should be prepared to discuss what you're doing there. If you do something else on the side, this is also fine, but it should not negatively impact on your research. It is on you to be able to manage your different tasks, and the expectation is that research has to come first.''

=== Working Times ===

'''Added by a request of J. Wilms on 2016 June 15'''

Is is expected that you are in the office in Bamberg for at least ~3 days per week. Although we have flexible working times, arriving at 10 a.m. latest is a good practice to ensure significant overlap with your colleagues.

'''From an e-mail by J. Wilms on 2016 June 14 to the X-ray gang'''

''working from home or Erlangen is ok (except for [...] [the group meetings]), but [...] [your supervisor] and the people you're working with directly need to know where you are. This means that you need to be reachable by email or phone, and you need to be working. As a rule of thumb: BSc-, MSc-, and PhD-thesis work is the equivalent to a full time job, irrespective of what your contracts say. Full time means 40+ hours per week. If you're working on the side this is fine - you know that we try to be supportive here - but this does not mean that you should subtract off the time you're making money from the time you're spending on your research, which - I repeat myself - should keep you busy equivalent to a full time job. If you find that you cannot manage this schedule when working from home, then I strongly suggest that you go to the office.''

''Due to the international nature of our work, it is to be expected that you have to be able to attend telecons after 18:00.''

=== Illness & Vacation ===

'''From an e-mail by J. Wilms on 2016 June 14 to the X-ray gang'''

''if you are ill, always(!) notify Edith, [...] [your supervisor], *and* the people you're working with (i.e., all BSc/MSc students also have a PhD student as point of contact and (s)he should also know).''

''if you plan to go on vacation, talk to [...] [your supervisor] first. [...] [We] will usually say yes, but there are some times you should avoid not being here, especially times before project deadlines, proposal deadlines, and the lab courses. This applies to everybody in the group.''

''once your vacation has been approved or if you're going to a conference, put down the dates of your absence on the white board next to the xerox machine.''

=== X-ray Group Meeting ===

'''From an E-mail by J. Wilms on 2016 June 14 to the X-ray gang'''

''group meeting starts Tuesdays, 10:00. The presence of everybody in the group (hiwis, BSc, MSc, PhD, postdocs) is *mandatory*. The only reason not to show up is if you're ill or if you have a lecture. In this case, please let me know. Do not assume I remember because you told me two weeks ago...''

=== Journal Club ===

Incomplete [[intern:litclub|list of past Literature Clubs]]

'''From an e-mail by M. Oertel on 2016 June 14 to the X-ray gang'''

''[...] assume that *everybody currently working in the xray-group is participating*.''

''Litclub is always (except during lab) on Tuesdays at 11:30 after the [X-ray] group-meeting. On every Monday I randomly choose someone for the next Litclub. There's a list of astronomy-papers which I will then send to you and you choose one (ideally not strongly correlated to your current work) and prepare a ~10 minute summary-talk. The talk will be in English. You don't have to understand everything they did in the paper, you just have to explain the central idea. One of the main aspects is to practice fast-paper-reading-and-understanding, therefore it has to be on a short notice (meaning Monday morning). This is also to prevent you from spending a few days on preparing. If you come across any interesting paper you think could fit (even if you haven't read it) please send a link to me so that I can add it to the list. You can decline when I ask you on Mondays but please only do so if you have a deadline (proposal or thesis...)/are sick...''

''It really is a good opportunity to practice giving talks, summarizing content and also it is a nice get-together for discussing interesting astro-stuff''

'''From an e-mail by J. Wilms on 2016 June 14 to the X-ray gang'''

''Your attendance and active participation is very strongly suggested. It is good for you.''

=== PhD-Hat and -Celebration tradition ===

[[intern:phd_hat_list|List of future PhDs]]

'''From an e-mail by M. Kuehnel in 2016 June 14 to almost everybody'''

''[...] this tradition is not alive in every institute. From my personal experience I know places where PhDs just defend and vanish without getting a hat, party, or anything personal from the colleagues. This is not how your 3+ years should end.''

''We have the tradition at our institute that every PhD candidate gets a self-made hat after having defended her or his thesis. Also, a big party is organized for her or his after the defence. It is a common agreement that the hat and the party is *mainly build and organized by all other PhD students*. Of course, also contributions from bachelor or master students are very well welcomed, too. Thus, it is very much appreciate (if not expected) that /everybody/ contributes and not only a few. It is not expected, however, to spent hours, even ~20 minutes are enough (for, e.g., searching and printing a picture, which is supposed to be put on the hat).''

''The main organization of the hat building process and the party is traditionally done by the PhD student, which is supposed to finish her or his PhD next. [...] This person is''
* ''the initiator of the hat building process and the organization of the party by, e.g., writing emails to everybody (expect to the PhD candidate, of course) in the first place. Creating a wiki-page for the hat might be useful here as well.''
* ''not expected to do all the work, but rather delegate the different tasks and keep the overview, i.e., is the main contact in case of questions. Here, the contribution of everybody is needed to complete all tasks! Here, quasi-regular meetings scheduled by the responsible person have been helpful.''
* ''trying to keep everybody updated and informed about, e.g., the hat status or the defence date. As you see, nobody needs to be afraid of this job.''

''Furthermore (and here we are really privileged), our PhD supervisor sponsors the party and hat with a certain amount. The usual case in other institutes is that the PhD candidate her- or himself pays for the party! Note that often the sponsoring is not sufficient for all expenses. In the past, this was solved in an uncomplicated way by either "basst scho" ("it's fine") from the people who had small expenses (like for the hat) or by the main organizer [...].''

=== Dishwasher Etiquette ===

'''From an e-mail by S. Falkner in 2016 August 29 to everybody'''

[''Please follow the following guideline to avoid a messy kitchen, frustrated Coworkers and unnecessary excessive use of the dishwasher:] ''

In case the dishwasher is full, check if it is clean

(YES): Has it just finished and still hot?
* (YES): Open it completely for cooling and every one too see.
* (NO): Empty it COMPLETELY and put your dirty dishes in and check if there is other dirty stuff to put in!
(NO): Can you make some room for your stuff?
* (YES): Perfect, now you can start it if there is really no more room.
* (NO): Start it and EITHER clean your dishes in the sink (and do not just throw it in their) OR wait till the dishwasher is done and put it in then!.

In case the dishwasher is not full, please do a quick check if the dishes look clean:

(YES): Empty it COMPLETELY and put your dirty dishes in and check if there is other dirty stuff to put in! Especially on Monday mornings it may happen that the dishwasher is only half full but clean as someone was nice and turned it on Friday afternoon, such that the dishwasher doesn't grow to life over the weekend.

(NO): Put your stuff in and ask yourself if it is Friday afternoon and no one else around any more?
* (YES): Start the dishwasher
* (NO): You may wait until you leave

In general it would be nice if all could care more about the kitchen. If
everyone would do care it would not be necessary for some of us to clean
up quite a mess, but only a little bit for all of us.

[[Category:Current Members]][[Category:internal]]

ERosita Coding standards

2018-06-18T14:52:16Z

Kuehnel:

[[Category:EROSITA]][[Category:Internal]]

===== NRTA library coding standards =====

* **variables**: written in lowercase <code c>
int name_of_variable;</code>
* **constants**: marked with 'c' at the beginning <code c>
const int cname_of_variable;</code>
* **statics**: marked with 's' at the beginning <code c>
static int sname_of_variable;</code>
* **globals**: marked with 'g' at the beginning <code c>
int gname_of_variable;</code>
* **pointers (and arrays)**: marked with '*p' at the beginning <code c>
int *pname_of_pointer;
long pnaxes[2] = {xsize, ysize};</code>
* **loop variables**: use double letters, starting with 'ii' and 'jj' <code c>
int ii, jj;
for(ii = 0; ii < 50; ii++) {
for(jj = 0; jj < 10; jj++) {
printf("do something...\n");
}
}</code>
* **functions**: all functions start with 'ero_' and have '_' between separate words <code c>
void ero_name_of_function(void);</code>
* **structures**: start with capital letter <code c>
struct Structure {
int blah;
char some_string[80];
(void)(*pero_some_function)(int, char*);
};</code>
* **enums**: to be favored over preprocessor directives (#define ...); name of enum prefixes each entry <code c>
enum List {
LIST_ENTRY_A = 1,
LIST_ENTRY_B = 2,
LIST_ENTRY_C = 3
};</code>
* **typedefs**: objects to end with '_t' <code c>
typedef unsigned int size_t;</code>