Procedure for Installing the Cirpass Data Reduction Pipeline

For personal use only

• Set up the links to the cirpass iraf packages. The most convenient way to do this would be to just move the cirpass/iraf tree directly over to your iraf directory, e.g. with:

          mv -i cirpass/iraf/* iraf/
  

  However, this will overwrite your loginuser.cl file if you already have one. (In this case just add the appropriately modified versions of the lines shown below to your loginuser.cl file). Alternatively you can install to a custom location. You will need to add the following lines to your loginuser.cl file, changing them to reflect the actual location of the cirpass cl code.

         set cirpass= home$Cirpass/
         task $cirpass.pkg = cirpass$cirpass.cl
  

• Define the location of the cirpass executables by setting the environment variable CIRPBIN. Under tcsh this would be:

  setenv CIRPBIN /home/_userid_/cirpass/bin/
  

  (don't forget the trailing forward slash). This needs to be done in any xterm / xgterm from which you start iraf. Ideally just place this line in your login file.
• If you intend to do data pre-processing i.e. you need to make cirpass MEF files from completely unprocessed data (and usually only true if you're sat at the instrument), you will need to edit the iraf variables which specify the location of the cirpass raw and reduced data. These are defined in cirpass.cl and are:

         set cirpraw = /data1/cirpass/
         set cirpred = /data2/datared/
  

  cirpraw is the raw data, produced by the instrument. cirpred is the location for the reduced data. You will need write permission on this directory.

For site-wide access for every user

• Log in as the user iraf. Place the cirpass iraf package in the relevant iraf sub-directory on your system e.g. with:

   mv -i /cirpass_untar_location/cirpass/iraf/* /iraf/extern/ 

  This will move a directory called Cirpass into the site-wide directory. Although see NOTE, 3 points below.
• Edit extern.pkg to define the new package, e.g. from an iraf cl prompt, as user iraf:

  cd hlib$
  vi extern.pkg
  

  (hlib$ usually = /iraf/iraf/unix/hlib or something similar) and add the following two lines before the reset helpdb entry, and changing the cirpass environment variable to reflect the actual installed location, issued in the move command above.

  reset   cirpass		= /iraf/extern/Cirpass/
  task    $cirpass.pkg    = cirpass$cirpass.cl
  

  Note the capital C for the Cirpass directory!!
• The location of the cirpass executables is set in the environment variable CIRPBIN. Every user wishing to use the cirpass package will require this to be set, and so this could be added to the site-wide variables that are set at login. Alternatively, each user could add the following line to e.g. their .mytcshrc:

  setenv CIRPBIN /cirpass_untar_location/cirpass/bin/
  

  (don't forget the trailing forward slash).
• NOTE: The IFUdat and Scripts subdirectories under /cirpass_untar_location/cirpass/ are found relative to the CIRPBIN variable - so if you decide to move the cirpass/bin directory, cirpass/Scripts and cirpass/IFUdat should also be moved to the same place. These are epar able locations in iraf, but things will work with least effort if only cirpass/iraf/* is moved to /iraf/extern/ and all other directories are left with the same structure. Alternatively /cirpass_untar_location/cirpass could be moved to /iraf/extern/ and then the extern.pkg file changed appropriately (reset cirpass = /iraf/extern/cirpass/iraf/Cirpass/, CIRPBIN=/iraf/extern/cirpass/bin/) this would keep all cirpass specific code in the same place, but would result in compiled c code / libraries e.t.c. in your /iraf directory (shouldn't be a problem!).
• If users will be required to do data pre-processing i.e. they have access to cirpass MEF files from completely unprocessed data (and usually only true when sat at the instrument), the iraf variables which specify the location of the cirpass raw and reduced data will need to be edited. These are defined in Cirpass/cirpass.cl and are:

         set cirpraw = /data1/cirpass/
         set cirpred = /data2/datared/
  

  cirpraw is the raw data, produced by the instrument. cirpred is the location for the reduced data. You will need write permission on this directory.

• The cirpass package runs on fits image files. Thus it is necessary to have the iraf image type set to fits (it usually is, from a cl prompt, show imtype should be fits). This can be achieved with:

  reset imtype = fits

  from the cl prompt, or changed permanently by uncommenting and changing the "imh" to "fits" in the:

  #set imtype = "imh"

  line in the ~/iraf/login.cl file.

• Change to the cirpass installation directory and customise the makefile for your system. The makefile should not require any changes for a redhat linux system. All necessary modifications should be in the top few lines. Check that the compilers are correct (the instpath variable should not need changing) and uncomment any lines appropriate to your operating system. A default install does not include the code linked against pgplot, instructions for compiling this code are below, but should be omitted for now.
• Compile the external cfitsio package used for the fits interface, type:

         make cfitsio
  

  This will take a little while. Now compile the cirpass package
• Type:

         make
  

• Logout and in again if you've edited your login files.
• You should now be ready to go. Start up iraf and type cirpass to load the cirpass package.

If pgplot and cpgplot is already on your system

• Edit the line in the cirpass makefile:

         PGDIR     = $(instpath)/extern/pgplot5.2
  

  to reflect the location of pgplot on your system. Also, modify the lines below this as instructed in the makefile.
• From cirpass/ type:

         make usepgplot
  

• Then set up the environment variable defining the location of pgplot, this is best done in a login file and for tcsh would be:

         setenv PGPLOT_DIR /usr/local/pgplot/location/
  

• You may also want to set the default output device:

         setenv PGPLOT_DEV      /xwindow
  

If pgplot is not already installed

• Run the cirpass2k.bat file, present in the same directory as the pixcel executable on cirpass3 (the detector control computer). This will update the windows registry for the 2K. (To go back to a 1K, run the cirpass1k.bat file)
• Edit the pixcel.ini file on cirpass3 to reflect the larger detector. Change all entries that are 512 (for 1 quadrant of a 1K) to 1024 (for 1 quadrant of a 2K). Also set assemble to false (in the [FITS] section), to stop pixcel attempting to reassemble the four quadrants into 1 file. If you don't do this pixcel will crash when it tries to reassemble the data.
• The pipeline task mosaic reassembles the input files to work around pixcel. This task runs on the raw data and needs to be able to write to the raw data directory. Hence it must be UID and GID data, and must run set-user-id. If you've run setdatapermissions.sh then mosaic will already be correct. Otherwise, change to the cirpass executable directory: /install_location/cirpass/bin/, su to root, and then issue the following commands:

   chown data:data mosaic
   chmod 6755 mosaic
   

  Remember to set assemble back to true if you go back to the 1K, otherwise the pipeline will mosaic the 1k quadrants instead of pixcel, but the differing read out patterns of the two chips means that they require different rotations before mosaicing, so the 1K will come out incorrectly stitched together.
• The original version of the mosaic pipeline task had a memory leak. If mosaic is causing a problem check the source code, /install_location/cirpass/src/mosaic/mosaic.c, and make sure you are using the version modified on 21st August 2003, not the original 10th September 2001 version.
• Hardware: remember to change the SAM in the controller to a 2K SAM, and to use the 2K interface box! The 2K interface box requires the OS / DOS connections to be interchanged, that is, OS connected to DOS and vice-versa.
• The correct 2K sam is HAW2K012 (The sam HAW2K014 used to be required for the following problem, where the correct fix was later discovered to be to set SHUTTER_ENABLE=TRUE in the pixcel.ini file: PixCel in 2K mode can only readout the detector using an NDR sequence. This is due to an error in the pixcel code, whereby it attempts to always operate in RRR mode. This problem is corrected in the SAM - allowing NDR operation, but disabling RRR operation.) The correct 1K sam is HAW452 2 cycle.

Users at the IoA who type "cirpass" from iraf, load the package from /home/cirpass/iraf/Scripts/Cirpass and the C code from /home/cirpass/C/. Modifications to the software should be made (and tested!) in those directories as the user cirpass. The software for public release is maintained in /home/cirpass/Release/. Any files changed as a result of software updates should be copied to the relevant subdirectory below Release and then the distribution tar ball recreated with:

cd /home/cirpass/Release
gtar -zcvf cirp_code_20030428.tar.gz cirpass
su optics
cd /home/optics/public_html/cirpass/Software/
cp /home/cirpass/Release/cirp_code_20030428.tar.gz .
rm cirp_soft.tar.gz
ln -s cirp_code_20030428.tar.gz cirp_soft.tar.gz
exit