{"id":4760,"date":"2016-05-04T14:56:52","date_gmt":"2016-05-05T00:56:52","guid":{"rendered":"http:\/\/www.eaobservatory.org\/jcmt\/?page_id=4760"},"modified":"2017-02-23T09:07:08","modified_gmt":"2017-02-23T19:07:08","slug":"scuba-2-dr-tutorial-2","status":"publish","type":"page","link":"https:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/scuba-2-dr-tutorial-2\/","title":{"rendered":"SCUBA-2 Data Reduction \u2013 Tutorial 2"},"content":{"rendered":"

Note:<\/strong> The following tutorial instructions assume that the user has already completed SCUBA-2 DR Tutorial 1<\/a>, and has the associated raw data and basic directory structure already in place.<\/em><\/p>\n

The following instructions assume that the tutorial parent directory is located in the user’s home directory, ~\/ and that the computer to be used already has a functioning installation of the latest version of the Starlink<\/em> software suite (the latest release is available for download here<\/a>). Please also remember to run KAPPA and SMURF first.<\/em><\/p>\n

Recpars<\/em> Files; Manually Running mapmaker<\/em>; dimmconfig<\/em> Files<\/h2>\n

This tutorial demonstrates how to modify the behavior of standard reduction recipes using a Recipe Parameters recpars<\/em> file, how to perform standard imaging of a SCUBA-2<\/em> dataset using the makemap command, and also how to manually modify the process by specifying a different dimmconfig file.<\/p>\n

    \n
  1. \n

    Tutorial 1 demonstrated the possibility of re-running an ORAC-DR<\/em> pipeline reduction with a non-default Recipe. It is, however, also possible to supply a recpars<\/em> (Recipe Parameters) plain text file that specifies the modification of some parameters for a given Recipe reduction without necessarily using a completely different recipe. Common modifications included in SCUBA-2 recpars<\/em> files include changes to (e.g.) the pixel size in the final map or the dimmconfig<\/em> file to be used by the recipe.<\/p>\n

    A number of pre-existing examples of SCUBA-2 recpar<\/em> files can be listed by typing the following:<\/p>\n

    ls $STARLINK_DIR\/bin\/oracdr\/cal\/scuba2\/recpars\/recpars-*.ini<\/code><\/p>\n

    and then using<\/p>\n

    more $STARLINK_DIR\/bin\/oracdr\/cal\/scuba2\/recpars\/recpars-*.ini<\/code><\/p>\n

    to view the contents of a listed recpars<\/em> file for project .<\/p>\n

    In the ~\/tutorial\/reduced<\/em> data directory, experiment with creating a simple recpars<\/em> file and save it with the filename myparams.ini<\/em> .<\/p>\n

    A starting point for your custom recpars<\/em> file might be something like the following:<\/p>\n

    [REDUCE_SCAN]\nMAKEMAP_CONFIG = dimmconfig_bright_extended.lis
    \nMAKEMAP_PIXSIZE=3<\/code><\/p>\n<\/li>\n

  2. \n

    Test the new recpars<\/em> file by re-running the data reduction with:<\/p>\n

    oracdr -loop file -files mylist -recpars myparams.ini<\/code><\/p>\n

    Feel free to experiment with the settings in the recpars<\/em> file and re-run the reduction. As usual, the original reduction can be recovered by simply running the above command without the -recpars myparams.ini<\/em> option.<\/p>\n<\/li>\n

  3. \n

    The next data reduction possibility is to manually run makemap<\/em>, rather than running it via ORAC-DR<\/em>. Switch to the tutorial parent directory, create a second reduced data directory (called reduced2<\/em>) and switch to it:<\/p>\n

    cd ~\/tutorial
    \nmkdir reduced2
    \ncd reduced2<\/code><\/p>\n<\/li>\n

  4. \n

    It is necessary to provide some input parameters in order to run makemap<\/em>. One of these is a list of the input files to be processed. For the purposes of this tutorial, a suitable file was already created during Tutorial 1<\/a>, with the filename mylist<\/em>. Copy this file into the new reduced2<\/em> directory using:<\/p>\n

    cp ..\/reduced\/mylist .\/<\/code><\/p>\n

    If running makemap<\/em> directly, it is also necessary to specify directly which of the underlying dimmconfig<\/em> files (used by the recipes) should be used. These files are also supplied as part of the standard Starlink<\/em> package distribution, and can be listed by typing:<\/p>\n

    ls $STARLINK_DIR\/share\/smurf\/dimmconfig*.lis<\/code><\/p>\n<\/li>\n

  5. \n

    For the purposes of highlighting the impact the correct dimmconfig<\/em> can have on data reduction, the makemap<\/em> command will be run twice for this tutorial, with two contrasting dimmconfig<\/em> files that are provided as part of the standard Starlink<\/em> distribution. Copy two of these to the current working directory:<\/p>\n

    cp $STARLINK_DIR\/share\/smurf\/dimmconfig_bright_extended.lis .\/
    \ncp $STARLINK_DIR\/share\/smurf\/dimmconfig_blank_field.lis .\/<\/code><\/p>\n<\/li>\n

  6. \n

    Run the map-maker with the first dimmconfig file:<\/p>\n

    makemap in=^mylist out=out_be.lis config=^dimmconfig_bright_extended.lis<\/code><\/p>\n

    This should produce an NDF file called out_be.sdf<\/em> .<\/p>\n

  7. \n

    For comparison, re-run the map-maker with the other dimmconfig<\/em> file:<\/p>\n

    makemap in=^mylist out=out_bf.lis config=^dimmconfig_blank_field.lis<\/code><\/p>\n

    This should produce an NDF file called out_bf.sdf<\/em> .<\/p>\n

  8. \n

    Try examining both out_be.sdf<\/em> and out_bf.sdf<\/em> in Gaia<\/em> using the techniques described in Tutorial 1<\/a>. It should be immediately clear which of the two dimmconfig<\/em> files is the more suitable for the type of observations used in these tutorials. As noted in Tutorial 1<\/a>, the default Recipe for the example dataset is REDUCE_SCAN<\/em>, which uses the dimmconfig<\/em> file dimmconfig_jsa_generic.lis<\/em> as its default for science targets.<\/p>\n<\/li>\n

  9. \n

    Feel free to try re-running the process with other standard dimmconfig<\/em> files. For interest, you may also wish to compare and contrast the contents of these files.<\/p>\n<\/li>\n<\/ol>\n

    \n

    Other JCMT data reduction\/analysis tutorials are available here.<\/a><\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

    Note: The following tutorial instructions assume that the user has already completed SCUBA-2 DR Tutorial 1, and has the associated raw data and basic directory structure already in place. The following instructions assume that the tutorial parent directory is located in the user’s home directory, ~\/ and that the computer\u2026 Continue reading<\/a><\/p>\n","protected":false},"author":41,"featured_media":0,"parent":4510,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/4760"}],"collection":[{"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/users\/41"}],"replies":[{"embeddable":true,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/comments?post=4760"}],"version-history":[{"count":35,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/4760\/revisions"}],"predecessor-version":[{"id":6664,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/4760\/revisions\/6664"}],"up":[{"embeddable":true,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/4510"}],"wp:attachment":[{"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/media?parent=4760"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}