Merge branch 'master' of https://github.com/teuben/nemo

MANIFEST

@@ -7,5 +7,3 @@
   VERSION                    major.minor.patch - see src/scripts/version
   nemo_start.sh.in           Startup  for bourne shell
   nemo_start.csh.in          Startup  for C shell
-
-

docs/man_html/bibcode.html

@@ -12,7 +12,7 @@ <H1>NEMO BIBCODE Manual Reference  </H1>
 is located in NEMO.   For some codes that do not have a manual page,
 the source code file will be mentioned.
 <P>
-Created on: Tue Nov 28 20:50:39 EST 2023 by teuben@DL5420(none)<P>
+Created on: Thu Dec  7 20:25:15 EST 2023 by teuben@DL5420(none)<P>
 <!-- Created by ./make_bibcode.csh - do not edit -->
 <DIR COMPACT>
 <TABLE BORDER>

docs/man_html/ccdfill.1.html

@@ -9,8 +9,10 @@
 HTML automatically generated with <A HREF=http://manpages.ubuntu.com/manpages/bionic/man1/rman.1.html>rman</A><br>
 <a href='#toc'>Table of Contents</a><p>
 
+<p> 
 <h2><a name='sect0' href='#toc0'>Name</a></h2>
 ccdfill - patch up the holes in an image 
+<p> 
 <h2><a name='sect1' href='#toc1'>Synopsis</a></h2>
 <b>ccdfill</b> [parameter=value]
 
@@ -89,16 +91,20 @@ <h2><a name='sect4' href='#toc4'>Caveats</a></h2>
 bi-linear interpolation is needed. See also  <a href='ccdintpol.1.html'><i>ccdintpol(1NEMO)</i></a>
  if your irregulaties
 are regular enough. 
+<p> 
 <h2><a name='sect5' href='#toc5'>See Also</a></h2>
 <a href='image.3.html'>image(3NEMO)</a>
 , <a href='ccdmath.1.html'>ccdmath(1NEMO)</a>
 , <a href='ccdsmooth.1.html'>ccdsmooth(1NEMO)</a>
 ,
 <a href='ccdintpol.1.html'>ccdintpol(1NEMO)</a>
-
+ <br>
+<pre>https://github.com/dokkum/maskfill
+</pre>
 <h2><a name='sect6' href='#toc6'>Author</a></h2>
 Peter Teuben 
-<h2><a name='sect7' href='#toc7'>Update History</a></h2>
+<p> 
+<h2><a name='sect7' href='#toc7'>History</a></h2>
 <br>
 <pre>10-Dec-93<tt> </tt>&nbsp;<tt> </tt>&nbsp;V1.0 Created<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
 22-feb-97<tt> </tt>&nbsp;<tt> </tt>&nbsp;V1.1 added bad=<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
@@ -117,7 +123,7 @@ <h2><a name='sect7' href='#toc7'>Update History</a></h2>
 <li><a name='toc4' href='#sect4'>Caveats</a></li>
 <li><a name='toc5' href='#sect5'>See Also</a></li>
 <li><a name='toc6' href='#sect6'>Author</a></li>
-<li><a name='toc7' href='#sect7'>Update History</a></li>
+<li><a name='toc7' href='#sect7'>History</a></li>
 </ul>
 </body>
 </html>

docs/man_html/hackdens.1.html

@@ -32,7 +32,7 @@ <h2><a name='sect2' href='#toc2'>Description</a></h2>
 <h2><a name='sect3' href='#toc3'>Parameters</a></h2>
  The following parameters are recognized in
 order; they may be given in any order if the keyword is also given. Use
---help to confirm this man page is up to date.  
+<b>--help</b> to confirm this man page is up to date.  
 <dl>
 
 <dt><b>in</b>=<i>in-file</i> </dt>
@@ -46,8 +46,7 @@ <h2><a name='sect3' href='#toc3'>Parameters</a></h2>
 <dt><b>neib</b>=<i>value</i> </dt>
 <dd>Number of neighbors used to determine
 the local density. The default of 6 is the recommended value by Casertano
-&amp; Hut (1985) [default: 6]. 
-<p> </dd>
+&amp; Hut (1985) [default: 6]. </dd>
 
 <dt><b>rneib</b>=<i>value</i> </dt>
 <dd>Initial radius to search the neighbors.
@@ -128,60 +127,65 @@ <h2><a name='sect4' href='#toc4'>Notes</a></h2>
 <h2><a name='sect5' href='#toc5'>Examples</a></h2>
 The following example takes
 an N-body snapshot, sort the particles in the order of the distance from
-the C.M., and calculate local density. <br>
-<pre>   snapcenter nbody.dat nbody.centered
-   snapsort nbody.centered nbody.sorted 
-   hackdens nbody.sorted nbody.density
-</pre>One can also weight the particles by its potential to some power. For this
-we create a Plummer sphere, without centering, and compute the center in
-two ways: <br>
-<pre>   mkplummer - 100 zerocm=f | snapsort - - rank=r &gt; p.dat
-   snapcenter p.dat . report=t
-   hackdens p.dat - | snapcenter  - . weight=dens report=t
-   hackforce p.dat - | snapcenter - . weight="-phi*phi*phi" report=t
-   hackforce p.dat - | snapcenter - . weight="phi*phi*phi*phi" report=t
-
-</pre>Note that in this case the Plummer sphere should have the correct mathematical
+the C.M., and calculate local density.  
+<p>    snapcenter nbody.dat nbody.centered<br>
+    snapsort nbody.centered nbody.sorted <br>
+    hackdens nbody.sorted nbody.density<br>
+
+<p>  One can also weight the particles by its potential to some power. For
+this we create a Plummer sphere, without centering, and compute the center
+in two ways:  
+<p>    mkplummer - 100 zerocm=f | snapsort - - rank=r &gt; p.dat<br>
+    snapcenter p.dat . report=t<br>
+    hackdens p.dat - | snapcenter  - . weight=dens report=t<br>
+    hackforce p.dat - | snapcenter - . weight="-phi*phi*phi" report=t<br>
+    hackforce p.dat - | snapcenter - . weight="phi*phi*phi*phi" report=t<br>
+    <br>
+  Note that in this case the Plummer sphere should have the correct mathematical
 center, and not <i>centered</i>. This snippet of code is expanded in a script $NEMO/scripts/csh/centering.sh,
 in which these different methods can also be applied to different models,
-as expanded in the following table. <br>
-<pre>    nbody=100 models:     Plummer   King1   King3   King5  DeVauc
-    -------------------------------------------------------------
-    snapcenter  on m:       0.102   0.029*  0.030*  0.033   0.299
-    snapcenter  on dens:    0.060   0.039   0.036   0.030   0.030*
-    snapcenter  on phi:     0.053
-    snapcenter  on phi^2:   0.050*
-    snapcenter  on phi^3:   0.052   0.032   0.030   0.026*  0.035
-    snapcenter  on phi^4:   0.054   0.034   0.032   0.027   0.031
-    snapcenterp:            0.080
-    snapmnmx on min phi:    0.122
-    snapmnmx on m 50% phi:  0.058
-    snapmnmx on m 33% phi:  0.063                           0.053
-    snapmnmx on m 25% phi:  0.067
-    rockstart on m:         0.082:
-A (*) denotes the best method for that model.
-</pre>Although for a Plummer sphere the best method is more than twice as good
-than the worst method, this does not apply to other models. <p>
+as expanded in the following table.  
+<p>     nbody=100 models:     Plummer
+  King1   King3   King5  DeVauc<br>
+     -------------------------------------------------------------<br>
+     snapcenter  on m:       0.102   0.029*  0.030*  0.033   0.299<br>
+     snapcenter  on dens:    0.060   0.039   0.036   0.030   0.030*<br>
+     snapcenter  on phi:     0.053<br>
+     snapcenter  on phi^2:   0.050*<br>
+     snapcenter  on phi^3:   0.052   0.032   0.030   0.026*  0.035<br>
+     snapcenter  on phi^4:   0.054   0.034   0.032   0.027   0.031<br>
+     snapcenterp:            0.080<br>
+     snapmnmx on min phi:    0.122<br>
+     snapmnmx on m 50% phi:  0.058<br>
+     snapmnmx on m 33% phi:  0.063                           0.053<br>
+     snapmnmx on m 25% phi:  0.067<br>
+     rockstart on m:         0.082:<br>
+
+<p> A (*) denotes the best method for that model. 
+<p>  
+<p> </pre>Although for a Plummer
+sphere the best method is more than twice as good than the worst method,
+this does not apply to other models. <p>
 <a href='density.1falcON.html'><i>density(1falcON)</i></a>
-
-is considerable faster, about twice with their K=32 default.  <br>
-<pre>mkplummer - 100000 |is considerable faster, about twice with their K=32 default.
-
- snapscale - - mscale=10 |about twice with their K=32 default. 
- snapsort - - |about twice with their K=32 default. 
- density - - give=mxvr |about twice with their K=32 default. 
- snapshell - &rsquo;10**[-4:4:0.1]&rsquo; dens  |about twice with their K=32 default. 
- tabmath - - &rsquo;log(%1),log(%4)&rsquo; all |
- tabplot - 1 2 -4 4 -14 2  line=1,1 point=2,0.1
-vs.
-mkplummer - 100000 |line=1,1 point=2,0.1
- snapscale - - mscale=10 |
- snapsort - - |
- hackdens - - |
- snapshell - &rsquo;10**[-4:4:0.1]&rsquo; dens  |
- tabmath - - &rsquo;log(%1),log(%4)&rsquo; all |
- tabplot - 1 2 -4 4 -14 2  line=1,1 point=2,0.1
-</pre>
+ is considerable faster,
+about twice with their K=32 default.   
+<p> mkplummer - 100000 |\  snapscale - -
+mscale=10 |\<br>
+  snapsort - - |\<br>
+  density - - give=mxvr |\<br>
+  snapshell - &rsquo;10**[-4:4:0.1]&rsquo; dens  |\<br>
+  tabmath - - &rsquo;log(%1),log(%4)&rsquo; all |\<br>
+  tabplot - 1 2 -4 4 -14 2  line=1,1 point=2,0.1<br>
+
+<p> vs. 
+<p> mkplummer - 100000 |\  snapscale - - mscale=10 |\<br>
+  snapsort - - |\<br>
+  hackdens - - |\<br>
+  snapshell - &rsquo;10**[-4:4:0.1]&rsquo; dens  |\<br>
+  tabmath - - &rsquo;log(%1),log(%4)&rsquo; all |\<br>
+  tabplot - 1 2 -4 4 -14 2  line=1,1 point=2,0.1<br>
+
+<p>  
 <p> 
 <h2><a name='sect6' href='#toc6'>Bugs</a></h2>
 The local density is calculated using (neib-1)th neighbor. Calculation
@@ -233,11 +237,11 @@ <h2><a name='sect11' href='#toc11'>History</a></h2>
 6-jul-89<tt> </tt>&nbsp;<tt> </tt>&nbsp;doc updated?<tt> </tt>&nbsp;<tt> </tt>&nbsp;Jun
 23-oct-90<tt> </tt>&nbsp;<tt> </tt>&nbsp;doc updated<tt> </tt>&nbsp;<tt> </tt>&nbsp;Peter
 18-jul-92<tt> </tt>&nbsp;<tt> </tt>&nbsp;printf -&gt; dprintf to make it pipable<tt> </tt>&nbsp;<tt> </tt>&nbsp;Peter
-24-may-02<tt> </tt>&nbsp;<tt> </tt>&nbsp;fixed running out of bits for large-N systems<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
+24-may-02<tt> </tt>&nbsp;<tt> </tt>&nbsp;fixed running out of bits for large-N <tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
 11-aug-2022<tt> </tt>&nbsp;<tt> </tt>&nbsp;added example hackforce vs. hackdens<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
 21-sep-2023<tt> </tt>&nbsp;<tt> </tt>&nbsp;added direct=<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
 11-oct-2023<tt> </tt>&nbsp;<tt> </tt>&nbsp;V3.0 added norm=1 as a new default<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
-12-oct-2023<tt> </tt>&nbsp;<tt> </tt>&nbsp;V3.0 - proper mass scaling as well as nbody scaling<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
+12-oct-2023<tt> </tt>&nbsp;<tt> </tt>&nbsp;V3.0 proper mass/nbody scaling <tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
 </pre><p>
 
 <hr><p>

docs/man_html/qtrun.l.html

@@ -0,0 +1,105 @@
+<!-- manual page source format generated by PolyglotMan v3.2, -->
+<!-- available at http://polyglotman.sourceforge.net/ -->
+
+<html>
+<head>
+<title>QTRUN(1) manual page</title>
+</head>
+<body bgcolor='white'>
+HTML automatically generated with <A HREF=http://manpages.ubuntu.com/manpages/bionic/man1/rman.1.html>rman</A><br>
+<a href='#toc'>Table of Contents</a><p>
+
+<p> 
+<h2><a name='sect0' href='#toc0'>Name</a></h2>
+qtrun - automatic GUI builder and frontend to run shell scripts or
+
+<p>programs 
+<p> 
+<h2><a name='sect1' href='#toc1'>Synopsis</a></h2>
+<b>qtrun</b> [-option value...] <i>script</i> 
+<p> 
+<h2><a name='sect2' href='#toc2'>Description</a></h2>
+<i>qtrun</i> presents
+an interactive graphical user interface to a shell <i>script</i> or program that
+conforms to a &lsquo;&lsquo;key=val&rsquo;&rsquo; interface. <p>
+It is based off <a href='tkrun.l.html'><i>tkrun(lNEMO)</i></a>
+, and supposed
+to be mostly compatible with it. A few format enhancements were proposed
+for qtrun. See "TKRUN V2" below. 
+<p> 
+<h2><a name='sect3' href='#toc3'>Options</a></h2>
+The following options parameters
+are currently recognized.  
+<dl>
+
+<dt><b>-h, --help</b> </dt>
+<dd>help </dd>
+
+<dt><b>-d, --debug</b> </dt>
+<dd>debug </dd>
+
+<dt><b>-v, --version</b> </dt>
+<dd>show version
+
+<p> </dd>
+</dl>
+
+<h2><a name='sect4' href='#toc4'>Tkrun V2</a></h2>
+In version 2 of this format we have implemented this via this
+new python based qtrun Here the format can be run via bash, csh and python
+in the <br>
+<pre>    key=val  # help    #&gt; GUI
+</pre>specification, but the client software (bash/csh/python/....) is responsible
+to properly parse the <i>key=val</i> command line arguments.  Here are the proposed
+
+<p>GUI tags with generic key=val/help sections 
+<p>  
+<p>    in=foo        # input
+file      #&gt; IFILE<br>
+    out=bar       # output file     #&gt; OFILE<br>
+    text=hello    # some text       #&gt; ENTRY<br>
+    mode=gauss    # the mode        #&gt; RADIO gauss,newton,leibniz<br>
+    stats=mean    # what to show    #&gt; CHECK sum,mean,sigma,skewness,kurtosis<br>
+    n=3.141592    # the n value     #&gt; SCALE 0:10:0.01<br>
+    k=3.141592    # k, use n        #&gt; LINK  n<br>
+
+<p>  
+<p> 
+<h2><a name='sect5' href='#toc5'>See Also</a></h2>
+<a href='wish.1.html'>wish(1)</a>
+, <a href='zenity.1.html'>zenity(1)</a>
+, <a href='qtun.1.html'>qtun(1NEMO)</a>
+ <br>
+<pre>https://github.com/teuben/agui - development version 
+</pre>
+<p> 
+<h2><a name='sect6' href='#toc6'>Author</a></h2>
+Kylie Gong, Peter Teuben 
+<p> 
+<h2><a name='sect7' href='#toc7'>Files</a></h2>
+<br>
+<pre>~/.tkrunrc<tt> </tt>&nbsp;<tt> </tt>&nbsp;(optional) global configuration file
+$run.key<tt> </tt>&nbsp;<tt> </tt>&nbsp;keyword file in which key=val pairs are maintained
+$NEMO/scripts/templates <tt> </tt>&nbsp;<tt> </tt>&nbsp;example templates of key=val parsing
+</pre>
+<p> 
+<h2><a name='sect8' href='#toc8'>History</a></h2>
+<br>
+<pre>aug-2023<tt> </tt>&nbsp;<tt> </tt>&nbsp;experimental version released<tt> </tt>&nbsp;<tt> </tt>&nbsp;KG/PJT
+</pre><p>
+
+<hr><p>
+<a name='toc'><b>Table of Contents</b></a><p>
+<ul>
+<li><a name='toc0' href='#sect0'>Name</a></li>
+<li><a name='toc1' href='#sect1'>Synopsis</a></li>
+<li><a name='toc2' href='#sect2'>Description</a></li>
+<li><a name='toc3' href='#sect3'>Options</a></li>
+<li><a name='toc4' href='#sect4'>Tkrun V2</a></li>
+<li><a name='toc5' href='#sect5'>See Also</a></li>
+<li><a name='toc6' href='#sect6'>Author</a></li>
+<li><a name='toc7' href='#sect7'>Files</a></li>
+<li><a name='toc8' href='#sect8'>History</a></li>
+</ul>
+</body>
+</html>

docs/source/examples.rst

@@ -40,7 +40,7 @@ on your CPU and test your patience and integrator.
 These models are produced in so-called RMS-units in which the
 gravitational constant :math:`G=1`, the total mass :math:`M=1`, and binding energy
 :math:`E=-1/2`.
-In case you would like virial units
+In case you would like virial units (also known as N-body units)
 (see also:
 Heggie & Mathieu, :math:`E=-1/4`,
 in: *The use of supercomputers in stellar
@@ -443,15 +443,15 @@ then passed on for a quick and dirty plot (shown below).
 Handling large datasets
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-One of NEMOs weaknesses is also it's strong point: programs must
+One of NEMOs weaknesses is arguably also its strong point: programs must
 generally be able to fit all their data in (virtual) memory.
 Although programs usually free memory associated with data
 that is not needed anymore, there is a very clear maximum
 to the number of particles it can handle in a snapshot. By 
 default\footnote{one can recompile NEMO in single precision and define
 {\tt body.h} with less wastefull members}
 a particle takes up about 100 bytes, which limits the size of a 
-snapshots on workstations.
+snapshots.
 
 It may happen that your data was generated on a machine which had
 a lot more memory

docs/source/filestr.rst

@@ -358,3 +358,5 @@ Rotation Curves Fitting Functions, except they are peculiar to the
 result of a projected circular streaming model. The program
 *rotcurshape(1NEMO)* is the only program that uses these functions, the
 manual page has a lot more details.
+
+.. include:: fits.rst

docs/source/fits.rst

@@ -3,8 +3,11 @@ FITS
 
 
 FITS is one of the earliest data formats used in (observational) astronomy, and
-NEMO handles some of the conversions from and to FITS. 
+NEMO handles some of the conversions from and to FITS, as well as some
+FITS utilities.
 
+.. 20 ccdfits*    504 fitsccd*   588 fitsglue*    4 fitsmerge*  576 fitstab*   596 snapfits*
+.. 576 fits8to16*    4 fitsedit*  580 fitshead*  580 fitssplit*  584 scanfits*  504 tabfits*
 
 
 For the SDFITS extension there is limited support in `sdinfo` and `scanfits`.

docs/source/glossary.rst

@@ -18,7 +18,8 @@ Glossary
   ccd
       Synonymous for image; most programs in NEMO which handle
       images start or end with ``ccd``, e.g.
-      ``ccdfits``, ``fitsccd``, ``ccdmath``.
+      ``ccdfits``, ``fitsccd``, ``ccdmath``. Most programs handle
+      1D, 2D and 3D "ccd" images.
 
   ECSV
       (Enhanced Character Separated Values) a popular
@@ -27,6 +28,7 @@ Glossary
 
   falcon
       A subpackage in NEMO that hosts the gyrfalcON code.
+      See ``$NEMO/usr/dehnen/falcON``.
 
   fie
       Most expressions that you give to
@@ -47,7 +49,8 @@ Glossary
 
   GIPSY
       The Groningen Image Processing System. A number of concepts in NEMO, and
-      a few routines, have been taken liberally from :term:`GIPSY`.
+      a few routines, have been taken liberally from :term:`GIPSY`. See also
+      https://www.astro.rug.nl/~gipsy/
 
 
   history
@@ -129,7 +132,7 @@ Glossary
       four data types commonly used in NEMO.
 
   voxel
-      See pixel
+      A three dimensional pixel. See also pixel
 
   yapp
       "Yet Another Plotting Package", the library