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资源说明：Post processing of FITS data cubes from Capreole simulations
#+TITLE: =cap-post=
#+AUTHOR: William Henney
#+EMAIL: w.henney@crya.unam.mx
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE: en
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* Postprocess Capreole datasets
All these programs work with datacubes in FITS format. See [[http://github.com/deprecated/ah3-utils][=ah3-utils=]] for how to convert Capreole's native AH3 format to FITS.
** Package layout
+ =doc/cap-post.org= :: Source for documentation in Org-mode format
+ =doc/cap-post.html= :: Compiled HTML file of documentation
+ =src/*.{f90,sh}= :: Programs and convenience scripts
** Compilation
+ First install the [[#dependencies-target][dependencies]]
+ Enter the =src/= directory
+ [OPTIONAL] Copy =local.mk.sample= to =local.mk= and edit it to specify the desired compiler command (=F90C=), compiler options (=F90LAGS=), and libraries to link (=LFITS=).
+ The default values are
#+BEGIN_EXAMPLE
F90C=gfortran
F90FLAGS=-O3
LFITS=/usr/local/lib/libcfitsio.a
#+END_EXAMPLE
+ Compile everything with
#+begin_src bash
make all
#+end_src
+ Most programs are designed to be run in the directory where the data is. For convenience, you may want to set a shell variable to the directory where the programs are, e.g.: =psrc=/path/to/cap-post/src=. So you can then type =sh $psrc/fitsemiss.sh ...=
** Convenience scripts
The general default behavior of these scripts is to process all the save times of a given model in the current directory. Usage is as follows:
#+begin_src bash
sh SCRIPT.sh DATEID RUNID EMTYPE [I1] [I2] [ISTEP]
#+end_src
+ DATEID :: something like =30112005=
+ RUNID :: the one-letter id code, such as =x=
+ EMTYPE :: the code for the emission mechanism, such as =Halpha=
+ I1 :: (optional) the first savetime to process
+ I2 :: (optional) the last savetime to process
+ ISTEP :: (optional) the step in savetimes, such as =100= to process every 100th time
*** fitsemiss.sh
Runs =cubet=, =cubeemiss=, and =makemap= as necessary to generate the emission maps.
** Fortran programs
These programs can be run individually if necessary, although it is generally easier to use the convenience scripts described above.
*** cubestats
Calculate various statistics from the data cubes:
+ Average radius of ionization front, calculated as cube root of volume / (4 pi/3):
+ Volume calculated from mask =x > 0.9=
+ Volume calculated by summing =x= over cells
+ Maximum and minimum i-front radii
+ Mean radius of ionized gas
+ RMS gas velocity dispersion (1D)
+ Mass weighted and volume weighted
+ For ionized and neutral gas
*** cubet
Calculate temperature cube
*** cubevr
Calculate radial velocity cube (from star, assumed at center of grid).
*** cubeemiss
Calculate emissivity cube for a particular emission process (e.g., =Halpha=, =FF06cm=, =N26584=, =neut00=, etc).
*** makemap
Calculate surface brightness maps, for views along the 6 principal axes of the cube: \(\pm x\), \(\pm y\), \(\pm z\).
*** makerotmap
Calculate surface brightness map for view from an arbitrary direction.
*** makevcubes
Calculate Position-Position-Velocity (PPV) cubes from an emissivity cube and cubes of the three valocity components. As with =makemap=, a separate PPV is generated for viewing direction along each of the 6 principal axes.
** Python programs
Note that these programs work best with python version > 2.7 and require various python packages to be installed (=numpy=, =pyfits=, etc).
On our linux servers (as of 2012) it is necessary to use the EPD version of python instead of the system version. For instance, by modifying your path:
#+BEGIN_EXAMPLE
export PATH=/opt/epd/latest/bin:$PATH
#+END_EXAMPLE
*** plotvcube.py
Produces PDF figures of isovelocity or position-velocity cuts through a PPV emission cube.
/Note that this program only works with Sac and Jane's PPV cubes (usually with names =*vc-*=). It currently doesn't work with the cubes generated by =makevcubes.f90= (with names =*vcube-*=)./
**** Command line options for plotvcube.py
#+BEGIN_EXAMPLE
$ python ../cap-post/src/plotvcube.py -h
usage: plotvcube.py [-h] [--slice-mode {x-slit,y-slit,isovel}]
[--display {contour,grayscale,both}]
[--iwindow IWINDOW IWINDOW] [--vlimits VLIMITS VLIMITS]
cubename
Plot isovel and PV images from PPV emission cubes
positional arguments:
cubename Name of FITS file containing PPV emission cube
optional arguments:
-h, --help show this help message and exit
--slice-mode {x-slit,y-slit,isovel}
Mode of operation - which way to slice (default:
isovel)
--display {contour,grayscale,both}
How to display the image (default: both)
--iwindow IWINDOW IWINDOW
Range of positions or velocities to sum over (in pixel
units) (default: None)
--vlimits VLIMITS VLIMITS
Minimum and maximum velocities in cube (default:
[-78.107, 73.896])
#+END_EXAMPLE
**** Examples of using plotvcube.py
Show PV image of narrow y-slit, summing from x=30 to x=35.
#+BEGIN_SRC sh
python ../cap-post/src/plotvcube.py 10042012_y_0030vc-Halpha --slice-mode y-slit --iwindow 30 35
#+END_SRC
Show isovelocity image of broad velocity channel summing from v=1 to v=50.
#+BEGIN_SRC sh
python ../cap-post/src/plotvcube.py 10042012_y_0030vc-Halpha --slice-mode isovel --iwindow 1 50
#+END_SRC
*** makemovie.py
Make movies of evolution at a fixed viewing angle or rotation at a fixed evolutionary time.
**** Examples of using makemovie.py
These are the command that were used to generate the movies included in Will's talk at the Warsaw conference, July 2012.
#+BEGIN_SRC sh
# Evolution movies
for ANGLE in 0 215 135; do
python ../cap-post/src/makemovie.py 04052012_4 \
--time 3 --mode evo --frames 28 --brightscale 1e8 --orient $ANGLE $ANGLE
python ../cap-post/src/makemovie.py 04052012_4 \
--time 3 --mode evo --emtypes neut00 PAH000 FF06cm \
--emshort CPF --brightscale 1.0 --bandscales 3e6 0.15 0.25 \
--orient $ANGLE $ANGLE --frames 28
done
# Tumble movies
python ../cap-post/src/makemovie.py 04052012_4 --time 30
python ../cap-post/src/makemovie.py 04052012_4 --time 20 --brightscale 2e7
python ../cap-post/src/makemovie.py 04052012_4 --time 10
for TIME in 10 20 30; do
python ../cap-post/src/makemovie.py 04052012_4 \
--time $TIME --emtypes neut00 PAH000 FF06cm --emshort CPF --brightscale 1.0 \
--bandscales 3e6 0.15 0.25
done
#+END_SRC
** Library modules
*** wfitsutils
Read and write FITS files.
*** emissmod
General mechanism for emissivity calculations.
*** em2levmod
Specific functions for particular types of emission line.
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** External dependencies
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Many of the Fortran progams use my =wfitsutils= module, which depends on the CFITSIO library. This may be installed as follows:
*** Fedora
#+BEGIN_SRC bash
sudo yum install cfitsio
#+END_SRC
*** Mac OS X via Homebrew
#+BEGIN_SRC bash
brew install cfitsio
#+END_SRC
*** Other
Install from [[http://freshmeat.net/projects/cfitsio][source]], e.g., like this:
#+BEGIN_EXAMPLE
wget ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3250.tar.gz
tar xzf cfitsio3250.tar.gz
cd cfitsio
./configure --prefix=/usr/local
make
sudo make install
#+END_EXAMPLE
Of course, you will want to change =3250= to te latest version. If you don't have =wget= you can use =curl= instead (=curl URL -o FILENAME=).
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