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Author: jweisber

bash script to loop over unix linux command

Published by jweisber on 2019-09-12

taken roughly from https://www.cyberciti.biz/faq/bash-for-loop/

either chmod this file to make it executable and run it by typing /.filename; or else

type bash ./filename

#!/bin/bash

for i in {1..9}

do

ls -als puppi_blah$i.fits

done

on the other hand, infinite loop (straight from above link)

for (( ; ; ))
do
   echo "infinite loops [ hit CTRL+C to stop]"
done

Loop with break on error (straight from above link)

for I in 1 2 3 4 5
do
  statements1      #Executed for all values of ''I'', up to a disaster-condition if any.
  statements2
  if (disaster-condition)
  then
	break       	   #Abandon the loop.
  fi
  statements3          #While good and, no disaster-condition.
done

idl status / hosts 2018 Jun

Published by jweisber on 2018-06-28

idl 8.3 is on deneb and canopus.  I have no maintenance contract on them any more, so they are frozen at that version.  They reside on local disks on each machine at /usr/local/exelis. . .

i dropped maint on mirzam for about 10 months in 2016(?). When I picked it up again, we loaded idl 8.6 into /usr/local/harris/ . . .

–Joel

fits psrfits file read/write routines

Published by jweisber on 2018-06-15

We (Bruce mainly) installed psrfits file read/write routines.  they required regular fits file read/write routines (cfitsio).

 

cfitsio is in /usr/share/astro/cfitsio/

psrfits routines are in /usr/share/astro/psrfits_utils-master/

inside it are two executables:

psrfits_singlepulse and  psrfits_subband

 

psrfits_singlepulse -h : Usage: psrfits_singlepulse [options] input_filename_base or filenames

psrfits_subband: Partially de-disperse and subband PSRFITS search-mode data.

Note: also check http://www.atnf.csiro.au/research/pulsar/index.html?n=Main.Psrfits  for psrfits definition.

calculate weighted (mean and SDM) in IDL

Published by jweisber on 2018-03-11

At least for now, function wmeanandsig.pro is in /data/psrdata/rmgalprojs

If you create an array of RM and an equal-sized array of sig_RM (with no ∞ sig_RM’s), then:

wmean_and_sdm=wmeanandsig(RM,sig_RM)

will put the weighted mean and weighted sdm into a two-element array  called wmean_and_sdm

(and the way functions work, you can replace the variable that above i call “wmean_and_sdm”, with

a variable of any name you wish)

Right now there is a “driver” program in the same directory, called, “wmeanandsigDRIVER.pro”  .  It

is a module that tests wmeanandsig.pro  .  I used it extensively to do so, to the point where I can now

call wmeanandsig.pro “ready to go”   .  (Luckily the NIST web pages give sample input/output for weighted

mean and for weighted SDM, which I endeavored to match.)

Caution: In 2018 April, I changed the calculation of the weighted SDM.  Previously, we had used the NIST definition, which changed the data weights so as to achieve reduced χ^2 to 1.  (The NIST webpage gave a formula for wgtd SD but did not note that it included this readjustment. )  In 2018 April, I changed the calculation to be

σ^2_wgtdmean = 1 / [ Σ 1/σ^2_j]. Note that this calculation depends entirely on the σ_j’s of the data points, and nothing else (such as deviation from mean).

–Joel

idl save set query contents

Published by jweisber on 2018-03-02

Here’s how to figure out the contents of a save set.

1. This is the classic way:
restore,’filename.sav’,/verbose  will list the variable names in the saveset.

help, variable_name will then give details on any such variable.

2. This  is the modern (object-oriented) way. Note that it does not require a restore:

[After http://northstar-www.dartmouth.edu/doc/idl/html_6.2/IDL_Savefile.html#wp1034474 ] :

Use the IDL_Savefile object to query the contents of a SAVE file containing data and selectively restore variables.

So first, create a savefile object out of of the .sav file:   sObj = obj_new(‘IDL_Savefile’, ‘p2206.B1913+16.wapp4.53958.0004_shifted.sav’)

Typically, IDL_Savefile::Contents is the first method called on a savefile object; the information retrieved indicates the number of different types of items contained in the file (variables, routines, etc.).

sContents = sObj->Contents()

one type of query of sContents is:  print, sContents.N_var
20

Next, a call to IDL_Savefile::Names is used to obtain the names of items of a specific type.

sNames = sObj ->Names()
print,snames
ACTUAL_NRECS BINSHIFT BW DELFREQ IDLFILE LSRK NBIN NCHAN OBSJULDATE OBSTIME PROFILE_VERSION ROUNDBINSHIFT SCANNO SHIFTONOFFA SHIFTONOFFB
SHIFTTOTA SHIFTTOTB SRC VEL WAPPHOST

Then,  IDL_Savefile::Size can be used to determine the size of a given (named) variable in the file:

size_of_shiftonoffa = sObj->Size(‘shiftonoffA’)
print, size_of_shiftonoffA
1    512   4    512,  which means:

If no keywords are set, SIZE returns a vector of integer type. The first element is equal to the number of dimensions of Expression. This value is zero if Expression is scalar or undefined. The next elements contain the size of each dimension, one element per dimension (none if Expression is scalar or undefined). After the dimension sizes, the last two elements contain the type code (zero if undefined) and the number of elements in Expression, respectively. The type codes are listed at https://www.harrisgeospatial.com/docs/size.html.  (the four here means floating point).

 

–Joel

ATNF PSR catalog from the command line

Published by jweisber on 2018-01-23

It is possible to access the ATNF catalog from the command line. Then various unix commands may be used on the output to create tailored data. The catalog software is now in /data/psrdata/psrcat. There is a README there that gives directions on how to use it.

Note that it accesses a database file on disk which may or may not be the latest version!

Also note that you need not supply the db_file parameter if you desire that it default to the location given in the environment variable PSRCAT_FILE    (you may find the value of that variable by typing

printenv PSRCAT_FILE

if you got your .cshrc from me (Joel) relatively recently, you will probably get
/usr/share/astro/psrhome/psrcat/psrcat.db

I have linked that locataion to the psrcat.db file that is “actually” in /data/psrdata/psrcat

so when i type psrcat -v from that directory, I indeed get the current catalogue version, v1.57:

“Software version: 1.49
“Catalogue version number = 1.57”

I may or may not update the catalog in the future.

Note also that the psrchive suite now accesses the same catalog through a link.  That is, the only file in

/usr/share/astro/psrhome/psrcat is a link to the above /data/psrdata/psrcat/psrcat.db

(OK I also did the same with glitch.db)