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Updated docs for v2

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commit 2c8d4286159dd2a0d728597a535d8c4fd8f19843 1 parent b890d10
@scottransom authored
Showing with 167 additions and 138 deletions.
  1. +21 −17 INSTALL
  2. +0 −121 README
  3. +146 −0 README.md
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38 INSTALL
@@ -11,22 +11,21 @@ Basic steps to install:
your machine, --prefix=/usr/local is the default for FFTW and
is a safe bet).
- If you have a modern version of GCC installed (v3.2 or better)
- and a modern CPU (Intel Pentium IV, or newer; AMD Opteron
- or better, G5), you can get _drastically_ better performance by
- adding the following options:
+ If you are on a modern Intel processor and have a recent version
+ of GCC, you can get much improved performance by adding:
+ --enable-sse2 --enable-avx
- For Intel PIVs or later, EM64Ts, or AMD64s:
- --enable-sse
-
- For Mac G5s:
- --enable-altivec
+ Note that Ubuntu has good FFTW packages now.
2. Install PGPLOT. http://www.astro.caltech.edu/~tjp/pgplot/
You need the X-windows and postscript drivers at a minimum.
+ Note that on 64-bit systems, compiling and linking PGPLOT can
+ be tricky!
+
+ Note that Ubuntu has good PGPLOT packages now.
3. Install TEMPO. Make sure to set the TEMPO environment variable.
- http://pulsar.princeton.edu/tempo/index.html
+ http://tempo.sourceforge.net/
4. Install GLIB (v2.X).
http://library.gnome.org/devel/glib/ On Linux machines this
@@ -35,6 +34,8 @@ Basic steps to install:
glib development package in order to have the required include
files...
+ On Ubuntu, the package you need is: libglib2.0-dev
+
5. Install CFITSIO.
http://heasarc.gsfc.nasa.gov/fitsio/
This is a very easy install and is now needed since PSRFITS
@@ -42,6 +43,8 @@ Basic steps to install:
a pulsar data standard that external tools can actually
view! How about that!)
+ Once again, Ubuntu has CFITSIO packages!
+
6. Define the PRESTO environment variable to the top level
directory of the PRESTO distribution (i.e. this directory).
@@ -55,8 +58,7 @@ Basic steps to install:
only user on the machine when you run this, as it is very
computation intensive and may take a while.
-9. Just for safety's sake (and because SVN sometimes messes up
- file access times), do a "make prep". That will make sure
+9. Just for safety's sake, do a "make prep". That will make sure
that make does not try to run Clig to re-generate all of the
command line interface files.
@@ -77,15 +79,17 @@ Basic steps to install:
13. If you want to use all the python routines (which if you are
doing anything but the most rudimentary analyses you will want
- to), you need Python >= version 2.3, and the _new_ Numpy/SciPy.
- You can get Numpy/Scipy here: http://www.scipy.org/download/
- I recommend using the Subversion versions (and for PRESTO
- as well). In general, the following should work:
+ to), you need Python >= version 2.3, and Numpy/Scipy
+ http://www.numpy.org and http://www.scipy.org
+ In general, the following should work:
"cd $PRESTO/python ; make ; make fftfit"
If it doesnt, you will probably need to edit the Makefile
or setup.py.
14. Go find pulsars!
+Note for Mac users having problems: Paul Ray has been running PRESTO a
+lot and knows the tricks to get it working...
+
Scott Ransom
-Mar 2009
+Jan 2014
View
121 README
@@ -1,121 +0,0 @@
- PRESTO
- ------
-
-http://www.cv.nrao.edu/~sransom/presto/
-
-PRESTO is a large suite of pulsar search and analysis software
-developed by Scott Ransom mostly from scratch. It was primarily
-designed to efficiently search for binary millisecond pulsars from
-long observations of globular clusters (although it has since been
-used in several surveys with short integrations and to process a lot
-of X-ray data as well). It is written primarily in ANSI C, with many
-of the recent routines in Python. According to Steve Eikenberry,
-PRESTO stands for: PulsaR Exploration and Search TOolkit!
-
-Written with portability, ease-of-use, and memory efficiency in mind,
-it can currently handle raw data from the following pulsar machines or
-formats:
-
- * PSRFITS search-format data (as from GUPPI at the GBT, the
- Mock Spectrometers at Arecibo, and much new and archived data
- from Parkes)
- * 1-, 2-, 4-, and 8-bit filterbank format from SIGPROC
- * Wideband Arecibo Pulsar Processor (WAPP) at Arecibo
- * The Parkes and Jodrell Bank 1-bit filterbank formats
- * SPIGOT at the GBT (may it RIP...)
- * Berkeley-Caltech Pulsar Machine (BCPM) at the GBT (may it RIP...)
- * A time series composed of single precision (i.e. 4-byte)
- floating point data
- * Photon arrival times (or events) in ASCII or double-precision
- binary formats
-
-The software is composed of numerous routines designed to handle three
-main areas of pulsar analysis:
-
- 1. Data Preparation: Interference detection (rfifind) and removal
- (zapbirds) , de-dispersion (prepdata, prepsubband, and
- mpiprepsubband), barycentering (via TEMPO).
-
- 2. Searching: Fourier-domain acceleration (accelsearch),
- single-pulse (single_pulse_search.py), and phase-modulation or
- sideband searches (search_bin).
-
- 3. Folding: Candidate optimization (prepfold) and Time-of-Arrival
- (TOA) generation (get_TOAs.py).
-
- 4. Misc: Data exploration (readfile, exploredat, explorefft),
- de-dispersion planning (DDplan.py), date conversion (mjd2cal,
- cal2mjd), tons of python pulsar/astro libraries, average pulse
- creation, flux density estimation, and more...
-
-Many additional utilities are provided for various tasks that are
-often required when working with pulsar data such as time conversions,
-Fourier transforms, time series and FFT exploration, byte-swapping,
-etc.
-
-The Fourier-Domain acceleration search technique that PRESTO uses in
-the routine accelsearch is described in Ransom, Eikenberry, and
-Middleditch (2002), and the phase-modulation search technique used by
-search_bin is described in Ransom, Cordes, and Eikenberry (2003).
-Some other basic information about PRESTO can be found in my thesis.
-I will eventually get around to finishing the documentation for
-PRESTO, but until then you should know that each routine returns its
-basic usage when you call it with no arguments. I am also willing to
-provide limited support via email or telephone (434-296-0320).
-
-Tutorial(!): Note that in the "docs" directory there is a now a
-tutorial which walks you through all the main steps of finding pulsars
-using PRESTO.
-
-To date, PRESTO has discovered nearly two hundred pulsars, including
-more than 100 recycled pulsars, most of which are in binaries!
-
-Getting it: The PRESTO source code is released under the GPL and can
-be browsed or gotten from here in many different ways (including
-zipped or tar'd or via git). If you are too lazy to read how to get
-it but have git on your system do:
-
-> git clone git://github.com/scottransom/presto.git
-
-To update it on a regular basis do
-
-> cd $PRESTO
-> git pull
-
-and then re-make things in $PRESTO/src.
-
-If you don't want to mess with git (which means that you will need to
-re-install a tarball whenever there are updates) you can get it from
-the "Download Source" link on the github page.
-
-If you plan to tweak the code, I highly suggest that you use git and
-clone the directory (or fork it using an account on github). Read the
-following "living document" on how to develop and collaborate in a
-relatively sane way using git:
- http://matthew-brett.github.com/pydagogue/gitwash_build.html
-If you plan on doing any significant development, please let me know
-and I'll either add you as a developer, or we can push/pull changes
-via git/github (see the "gitwash" document above). Code contributions
-and/or patches to fix bugs are most welcome!
-
-NOTE: for barycentering data, PRESTO uses TEMPO. You should get the
-newest version from Sourceforge. You will also need FFTW, CFITSIO,
-and PGPLOT.
-
-Final Thoughts: Please let me know if you decide to use PRESTO for any
-"real" searches. And if you find anything with it, it would be great
-if you would cite either my thesis or whichever of the two papers
-listed above is appropriate. Thanks!
-
-Acknowledgements: Big thanks go to Steve Eikenberry for his help
-developing the algorithms, Dunc Lorimer for the basic code which is
-used to process BCPM and WAPP data, David Kaplan for lots of help with
-the GBT SPIGOT code, Jason Hessels for many contributions to the
-Python routines (and along with Maggie Livingstone for the rednoise
-reduction routine), Anne Archibald (for significant help with the
-recent accelsearch improvements), and Paul Demorest, Paul Ray, Ingrid
-Stairs, Fernando Camilo, Cees Bassa, Patrick Lazarus, Mike Keith,
-Slavko Bogdanov, and Paulo Freire for many comments and suggestions
-(and even some patches!).
-
-Scott Ransom <sransom@nrao.edu>
View
146 README.md
@@ -0,0 +1,146 @@
+# PRESTO v2
+
+http://www.cv.nrao.edu/~sransom/presto/
+
+PRESTO is a large suite of pulsar search and analysis software
+developed by Scott Ransom mostly from scratch. It was primarily
+designed to efficiently search for binary millisecond pulsars from
+long observations of globular clusters (although it has since been
+used in several surveys with short integrations and to process a lot
+of X-ray data as well). It is written primarily in ANSI C, with many
+of the recent routines in Python. According to Steve Eikenberry,
+PRESTO stands for: PulsaR Exploration and Search TOolkit!
+
+## New in this release:
+ * WAPP, BCPM, Spigot, and 1-bit analog filterbank data are deprecated!
+ (see below)
+ * Dramatically improved internal handling (giving better dynamic
+ range and RFI removal) of PSRFITS and SIGPROC filterbank data
+ * Massive speed-ups (factors of 2 or more) of `accelsearch` when
+ all of the F-Fdot plane can fit into core memory (that can be set
+ by changing values in `include/meminfo.h`)
+ * Many bug fixes and several new scripts (including new orbit fitters)
+
+PRESTO is written with portability, ease-of-use, and memory efficiency
+in mind, it can currently handle raw data from the following pulsar
+machines or formats:
+
+ * PSRFITS search-format data (as from GUPPI at the GBT, PUPPI and
+ the Mock Spectrometers at Arecibo, and much new and archived data
+ from Parkes
+ * 1-, 2-, 4-, 8-, and 32-bit (float) filterbank format from SIGPROC
+ * A time series composed of single precision (i.e. 4-byte)
+ floating point data
+ * Photon arrival times (or events) in ASCII or double-precision
+ binary formats
+
+Notice that the following formats which *used* to be supported are not:
+
+ * Wideband Arecibo Pulsar Processor (WAPP) at Arecibo
+ * The Parkes and Jodrell Bank 1-bit filterbank formats
+ * SPIGOT at the GBT (may it RIP...)
+ * Berkeley-Caltech Pulsar Machine (BCPM) at the GBT (may it RIP...)
+
+If you need to process them, you can either checkout the "classic"
+branch of PRESTO, which is not being actively developed. Or you can
+use `DSPSR` to convert those formats into SIGPROG filterbank format
+(and/or maybe someday soon, PSRFITS search format). You can grab
+DSPSR [here](http://dspsr.sourceforge.net). If you *really* need to
+get one of these machines working in PRESTO v2, let me know and we can
+probably make it happen. It will take a day or two of porting for
+each backend.
+
+The software is composed of numerous routines designed to handle three
+main areas of pulsar analysis:
+
+1. Data Preparation: Interference detection (`rfifind`) and removal
+ (`zapbirds`) , de-dispersion (`prepdata`, `prepsubband`, and
+ `mpiprepsubband`), barycentering (via TEMPO).
+
+2. Searching: Fourier-domain acceleration (`accelsearch`), single-pulse
+ (`single_pulse_search.py`), and phase-modulation or sideband searches
+ (`search_bin`).
+
+3. Folding: Candidate optimization (`prepfold`) and Time-of-Arrival
+ (TOA) generation (`get_TOAs.py`).
+
+4. Misc: Data exploration (`readfile`, `exploredat`, `explorefft`),
+ de-dispersion planning (`DDplan.py`), date conversion (`mjd2cal`,
+ `cal2mjd`), tons of python pulsar/astro libraries, average pulse
+ creation, flux density estimation, and more...
+
+Many additional utilities are provided for various tasks that are
+often required when working with pulsar data such as time conversions,
+Fourier transforms, time series and FFT exploration, byte-swapping,
+etc.
+
+The Fourier-Domain acceleration search technique that PRESTO uses in
+the routine accelsearch is described in [Ransom, Eikenberry, and
+Middleditch
+(2002)](http://adsabs.harvard.edu/abs/2002AJ....124.1788R), and the
+phase-modulation search technique used by search_bin is described in
+[Ransom, Cordes, and Eikenberry
+(2003)](http://adsabs.harvard.edu/abs/2003ApJ...589..911R). Some
+other basic information about PRESTO can be found in my
+[thesis](http://www.cv.nrao.edu/~sransom/ransom_thesis_2001.pdf). I
+will eventually get around to finishing the documentation for PRESTO,
+but until then you should know that each routine returns its basic
+usage when you call it with no arguments. I am also willing to
+provide limited support via email or telephone (434-296-0320).
+
+Tutorial(!): Note that in the "docs" directory there is a now a
+tutorial which walks you through all the main steps of finding pulsars
+using PRESTO.
+
+To date, PRESTO has discovered well over two hundred pulsars,
+including more than 120 recycled pulsars, most of which are in
+binaries!
+
+## Getting it:
+The PRESTO source code is released under the GPL and
+can be browsed or gotten from here in many different ways
+(including zipped or tar'd or via git). If you are too lazy to
+read how to get it but have git on your system do:
+
+> git clone git://github.com/scottransom/presto.git
+
+To update it on a regular basis do
+
+> cd $PRESTO
+> git pull
+
+and then re-make things in $PRESTO/src.
+
+For more detailed installation instructions, see INSTALL.
+
+If you don't want to mess with git (which means that you will need to
+re-install a tarball whenever there are updates) you can get it from
+the "Download Source" link on the github page.
+
+If you plan to tweak the code, I highly suggest that you use git and
+clone the directory (or fork it using an account on github). Read the
+following "living document" on how to develop and collaborate in a
+relatively sane way using git:
+ http://docs.scipy.org/doc/numpy/dev/gitwash/index.html
+If you plan on doing any significant development, please let me know
+and I'll either add you as a developer, or we can push/pull changes
+via git/github (see the "gitwash" document above). Code contributions
+and/or patches to fix bugs are most welcome!
+
+Final Thoughts: Please let me know if you decide to use PRESTO for any
+"real" searches. And if you find anything with it, it would be great
+if you would cite either my thesis or whichever of the two papers
+listed above is appropriate. Thanks!
+
+Acknowledgements: Big thanks go to Steve Eikenberry for his help
+developing the algorithms, Dunc Lorimer for the basic code which is
+used to process BCPM and WAPP data, David Kaplan for lots of help with
+the GBT SPIGOT code, Jason Hessels for many contributions to the
+Python routines (and along with Maggie Livingstone for the rednoise
+reduction routine), Anne Archibald (for significant help with the
+recent accelsearch improvements), and Paul Demorest, Paul Ray, Ingrid
+Stairs, Fernando Camilo, Cees Bassa, Patrick Lazarus, Mike Keith,
+Slavko Bogdanov, and Paulo Freire for many comments and suggestions
+(and even some patches!).
+
+Scott Ransom <sransom@nrao.edu>
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