SMART Scripting Guide

1. Return an output pointer array ("ptr_aar") of extracted data.
2. Extract the data and start the IDEA Main Window with the extracted data directly loaded.

To produce an output pointer array of extracted data the IDL syntax is :

IDL> sc_ext_full, bcd_dir = "directoryname/", ptr_aar=ptr_aar

This will extract all FITS BCD data files in directory "directoryname/" (note trailing "/") and write them to the IDL pointer array "ptr_aar".

To extract data and save it to a SMART project do the following :

1. Loading extracted data to a new project :
   1. At the SMART/IDL prompt type the syntax : IDL> sc_ext_full, bcd_dir = "directoryname/", /start_isap
   2. This will extract all FITS BCD data files in directory "directoryname/" (note trailing "/"), invoke the IDEA window and load the extracted data into it.
   3. On quitting the IDEA window it will open the "Project Manager" and "Dataset Manager" windows, load the extracted data and prompt for a new project name.
      The new project can then be saved on exit.
   4. ALTERNATIVE - Before quitting the IDEA window click on the "2Proj" button.
      This will open the "Project Manager" and "Dataset Manager" windows, load the extracted data and prompt for a new project name. The new project can then be saved on exit.

2. Adding extracted data to an existing project :
   1. Open an existing SMART project with the Project Manager? window then open the Dataset Manager? window.
      The "Dataset Manager" window must be open, though it does not need any data in it.
   2. At the SMART/IDL prompt type the syntax : IDL> sc_ext_full, bcd_dir = "directoryname/", /start_isap
   3. This will extract all FITS BCD data files in directory "directoryname/" (note trailing "/"), invoke the IDEA window and load the extracted data into it.
   4. On quitting the IDEA window it will save the extracted data to the currently open dataset in the "Dataset Manager" window.
      On exit the existing open project will be updated and saved with the newly extracted data.
   5. ALTERNATIVE - Before quitting the IDEA window click on the "2Proj" button.
      This will save the extracted data to the currently open dataset in the "Dataset Manager" window.
      On exit the existing open project will be updated with the newly extracted data and can then be saved.

This script can also be run with the "/plotit" option as a quick way to preview the spectra.
For either "ptr_aar" or "/start_isap" type outputs using the "/plotit" keyword will display a plot of flux (Jy) vs wavelength (microns) for each data file as it is extracted.
NOTE : When "/plotit" is used "Enter" must be pressed after each plot is displayed for processing to continue.

The SMART/IDL prompt syntax for the two outputs is :

IDL> sc_ext_full, bcd_dir = "directoryname/", /plotit, ptr_aar=ptr_aar

IDL> sc_ext_full, bcd_dir = "directoryname/", /plotit, /start_isap

This script can be called multiple times without quitting the IDEA Main Window, Dataset Manager?, or Project Manager?.
The header is at : sc_ext_full.pro?

1. Return an output pointer array ("ptr_aar") of extracted data.
2. Extract the data and start the IDEA Main Window with the extracted data directly loaded.

To produce an output pointer array of extracted data the IDL syntax is :

IDL> sc_ext_tapered, bcd_dir = "directoryname/", ptr_aar=ptr_aar

FOR MORE DETAILS ABOUT SCRIPTING, PLEASE CONTACT THE ISC GROUP

THE FOLLOWING IS OBSOLETE

1. A very simple IDL function for extracting a single image from a FITS BCD file : extract1.pro?

   To call it the IDL syntax is : IDL> output = extract1("filename", header=header)

   For bulk extractions this function could be included in another IDL routine that passes the relevant files one by one
   and stores the data produced in an easily accessible form (IDL structure, FITS file, text file, etc.) for later processing.
   However SMART scripting provides other, more powerful and efficient, methods for extracting large datasets. (See below.)

2. An IDL program demonstrating extraction of multiple images in one operation : extract2.pro?

   To call it the IDL syntax is : IDL> extract2, "directoryname/"

   This will extract all FITS BCD data files in directory "directoryname/" (note trailing "/") and write them to ASCII ".txt" files in the calling directory.

3. An IDL program demonstrating extraction of multiple images in one operation with selectable Tapered Column or Gaussian options : extract3.pro?

   To call it for Tapered Column extraction the IDL syntax is : IDL> extract3, "directoryname/", /column, sigma=3.0

   To call it for Gaussian extraction the IDL syntax is : IDL> extract3, "directoryname/", /gaussian, sigma=3.0

   This will perform a gaussian or tapered column extraction of all FITS BCD data files in directory "directoryname/" (note trailing "/") and write them to ASCII ".txt" files in the calling directory.
   For explanation of Tapered Column and Gaussian extraction see : Spectral Extraction Types?
   In both cases the "sigma" keyword is optional and will default to "sigma=4.0" in this script if a value is not supplied.
   NOTE : The value "sigma=3.0" is shown here for example of syntax only. The relevant value of sigma must be chosen for the particular data being extracted.

SMART Scripting - 3 Plane Data

1. A SMART provided PERL script for making 3 plane data.
   

   NOTE :

   To use "sm_make_3plane.pl" you must have PERL installed on your system.
   Once PERL is installed you must add to it the "CFITSIO" file subroutine library, (which allows PERL to handle ".fits" files)
   and the "CFITSIO.pm" interface (which allows PERL to use CFITSIO).
   Information about both CFITSIO and CFITSIO.pm can be found at : CFITSIO - A FITS File Subroutine Library.
   (This is maintained by the NASA Goddard Spaceflight Center.)
   Due to the very large number of possible system configurations, sources for and ways of installing PERL
   the SMART development team cannot advise on how to install PERL, CFITSIO or CFITSIO.pm on any particular system.
   Please see your local system administrator for advice about how best to do this. |

   The syntax at the Unix/Linux prompt is : > ./sm_make_3plane.pl "outfile" "bcd" "data" "unc" "bmask"

   Where :

   outfile	O	Output file (please suffix "3p.fits")
   bcd	I	Input "bcd" file (formerly bcd_fp) for header
   data	I	Input "data" file for data
   unc	I	Input "uncertantity" file
   bmask	I	Input "bmask" file

   The resultant file (3p.fits) contains the header and data from the input files in the order :

   header	from bcd
   data	from data
   header	from unc
   data	from unc
   header	from bmask
   data	from bmask

   SMART handles this format automatically. To read it in your own programs you can use at the SMART/IDL prompt : IDL> data = readfits("filename", header, EXTEN_NO = 0,1,2)

   Where the value of EXTEN_NO designates both the header and data returned.

   Alternatively you can use at the SMART/IDL prompt : IDL> rdfits_struct, "filename", data_structure

   This will return an IDL data structure with 6 tags :

   HDR0	STRING	Array[234]
   IM0	FLOAT	Array[128, 128]
   HDR1	STRING	Array[256]
   IM1	FLOAT	Array[128, 128]
   HDR2	STRING	Array[245]
   IM2	INT	Array[128, 128]

   Please note that for both "readfits" and "rdfits_struct" the first two data planes are floating point type and the last (bmask) is integer.
   (See also File Type and Data Structure Conversion?.)

   The latest version of DS9 also allows reading files of this sort :

   1. Invoke DS9 at the prompt.
   2. Click "File", "Open Other", "Open Multi Ext as Data Cube".
   3. Pick the relevant file from the selection box that then appears.
   4. The chosen file will load automatically display the "Data Cube" window, allowing scrolling through each data plane.

   NOTE : Only the most recent version of DS9 has this facility. If it is missing from your version please upgrade.

2. SMART provided scripts for reading all the FITS files in a given directory and converting them to 3 plane data if necessary :
   1. At the SMART/IDL prompt type : IDL> sc_read_bcd, bcd_dir="directoryname/", ptr_bcd, filetype=filetype, status=status

      where "directoryname/" (note trailing "/") is a directory containg FITS bcd files.
      The header is at : sc_read_fits_bcd.pro?

   2. At the SMART/IDL prompt type : IDL> make_3plane, dirname="/home/me/filesin", pu='1', outdir="/home/me/filesout"

      where :

      dirname	Directory containing initial files.
      pu	If set first 8 files in input directory will be ignored. (PU etc. files.)

      | outdir |Directory to write output files to (must exist).
      If this keyword is not set then output will be written to input directory. |