{"id":4510,"date":"2016-04-12T10:56:57","date_gmt":"2016-04-12T20:56:57","guid":{"rendered":"http:\/\/www.eaobservatory.org\/jcmt\/?page_id=4510"},"modified":"2023-10-16T11:08:39","modified_gmt":"2023-10-16T21:08:39","slug":"reductionanalysis-tutorials","status":"publish","type":"page","link":"https:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/","title":{"rendered":"JCMT Data Reduction\/Analysis Tutorials"},"content":{"rendered":"<div id=\"toc_container\" class=\"no_bullets\"><p class=\"toc_title\">Contents<\/p><ul class=\"toc_list\"><li><a href=\"#Tutorials\"><span class=\"toc_number toc_depth_1\">1<\/span> Tutorials<\/a><ul><li><a href=\"#General_Data_Reduction_Tutorials\"><span class=\"toc_number toc_depth_2\">1.1<\/span> General Data Reduction Tutorials<\/a><\/li><li><a href=\"#SCUBA-2_Tutorials\"><span class=\"toc_number toc_depth_2\">1.2<\/span> SCUBA-2 Tutorials<\/a><\/li><li><a href=\"#POL-2_Tutorial\"><span class=\"toc_number toc_depth_2\">1.3<\/span> POL-2 Tutorial<\/a><\/li><li><a href=\"#Heterodyne_Tutorials\"><span class=\"toc_number toc_depth_2\">1.4<\/span> Heterodyne Tutorials<\/a><\/li><li><a href=\"#JCMT_Observing_Tool_Tutorials\"><span class=\"toc_number toc_depth_2\">1.5<\/span> JCMT Observing Tool Tutorials<\/a><\/li><li><a href=\"#Analysis_Tutorials_and_HowTos\"><span class=\"toc_number toc_depth_2\">1.6<\/span> Analysis Tutorials and HowTos<\/a><\/li><li><a href=\"#Python_Starlink_Jupyter_notebooks\"><span class=\"toc_number toc_depth_2\">1.7<\/span> Python &amp; Starlink Jupyter notebooks:<\/a><\/li><li><a href=\"#Datasets_for_Tutorials\"><span class=\"toc_number toc_depth_2\">1.8<\/span> Datasets for Tutorials<\/a><\/li><\/ul><\/li><li><a href=\"#Additional_Training_Materials\"><span class=\"toc_number toc_depth_1\">2<\/span> Additional Training Materials<\/a><\/li><\/ul><\/div>\n\n<h2><span id=\"Tutorials\">Tutorials<\/span><\/h2>\n<p>There are now a number of tutorials offered for new users of the JCMT.<\/p>\n<h3><span id=\"General_Data_Reduction_Tutorials\">General Data Reduction Tutorials<\/span><\/h3>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li style=\"text-align: justify\"><a href=\"https:\/\/www.eaobservatory.org\/JCMT\/user-tutorials\/dr-2023\/\">JCMT data reduction: pipelines, recipes and parameters<\/a> &#8211; Introduction to the Wesley, ORAC-DR and PICARD pipelines, how to select data reduction recipes and customize your reduction via parameter files.<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<h3><span id=\"SCUBA-2_Tutorials\">SCUBA-2 Tutorials<\/span><\/h3>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li style=\"text-align: justify\"><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/reductionanalysis-tutorials\/scuba-2-dr-tutorial-1\/\"><em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorial 1<\/a> &#8211; Simple reduction of a <em>SCUBA-2<\/em> dataset using the <em>ORAC-DR<\/em> pipeline software using different data reduction recipes; an introduction to basic <em>Gaia<\/em> use.<\/li>\n<li style=\"text-align: justify\"><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/reductionanalysis-tutorials\/scuba-2-dr-tutorial-2\/\"><em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorial 2<\/a> &#8211; Modification of the behavior of standard reduction recipes using a <em>recpars<\/em> (Recipe Parameters) file, standard imaging of a <em>SCUBA-2<\/em> dataset using the <em>makemap<\/em> command and manual modification of the process by specifying a different <em>dimmconfig<\/em> file.<\/li>\n<li style=\"text-align: justify\"><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/reductionanalysis-tutorials\/scuba-2-dr-tutorial-3\/\"><em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorial 3<\/a> &#8211; Creation and use of an external mask with a simple <em>SCUBA-2<\/em> dataset. This is usually used to help recover\/improve large scale structure and decrease the negative bowling in large <em>Pong<\/em> maps.<\/li>\n<li style=\"text-align: justify\"><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/reductionanalysis-tutorials\/scuba-2-dr-tutorial-4\/\"><em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorial 4<\/a> &#8211; Use and modification of <em>PICARD<\/em> matched filters for point source detection in an already-reduced map.<\/li>\n<li style=\"text-align: justify\"><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/reductionanalysis-tutorials\/scuba-2-dr-tutorial-5\/\"><em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorial 5<\/a> &#8211; Investigating the contamination in the 850-micron bandpass from CO molecular line emission. This advanced tutorial will reduce and use <em>both<\/em> SCUBA-2 and HARP data.<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<h3><span id=\"POL-2_Tutorial\">POL-2 Tutorial<\/span><\/h3>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li style=\"text-align: justify\"><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/pol-2-dr-tutorial-1\/\"><em>POL-2<\/em> Data Reduction\/Analysis Tutorial 1<\/a> &#8211; Simple reduction of a <em>SCUBA-2<\/em> dataset using the <em>SMURF pol2map<\/em> command; an introduction to basic <em>Gaia<\/em> polarimetry toolbox use.<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<h3><span id=\"Heterodyne_Tutorials\">Heterodyne Tutorials<\/span><\/h3>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li style=\"text-align: justify\"><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/reductionanalysis-tutorials\/heterodyne-dr-tutorial-1\/\">Heterodyne Instrument Data Reduction\/Analysis Tutorial 1<\/a> &#8211; Simple reduction and analysis of heterodyne datasets using the <em>ORAC-DR<\/em> pipeline software.<\/li>\n<li style=\"text-align: justify\"><a href=\"https:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/heterodyne-instrument-data-reduction-tutorial-2\/\">Heterodyne Instrument Data Reduction\/Analysis Tutorial 2<\/a> &#8211; building on the basic\/simple Data Reduction and Analysis tutorial.\u00a0Modification of the behavior of standard reduction recipes using a <em>recpars.<\/em><\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<h3><span id=\"JCMT_Observing_Tool_Tutorials\">JCMT Observing Tool Tutorials<\/span><\/h3>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li><a href=\"https:\/\/www.eaobservatory.org\/JCMT\/user-tutorials\/ot-2023\/\">General JCMT Observing Tool tutorial<\/a> (2023 version) \u2014 Introduction to the OT, how to organize programs and use the built-in validator.<\/li>\n<li><a href=\"http:\/\/www.eaobservatory.org\/JCMT\/observing-tool-tutorials\/jcmt_ot_basics.html\">JCMT Observing Tool basics tutorial<\/a> (2020 version) \u2014 Installation of the OT, creation of a simple program and visualization with the position editor.<\/li>\n<li><a href=\"http:\/\/www.eaobservatory.org\/JCMT\/observing-tool-tutorials\/jcmt_ot_tricks.html\">JCMT Observing tool tricks tutorial<\/a> (2020 version) \u2014 Inheritance, folders, survey containers and understanding of validation results.<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<h3 class=\"entry-title\"><span id=\"Analysis_Tutorials_and_HowTos\">Analysis Tutorials and HowTos<\/span><\/h3>\n<p><a href=\"http:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/starlink-analysis\/\">Analysis with Starlink tutorial<\/a> &#8211; looking at some of the many analysis tools within Starlink<\/p>\n<p>Analysis How-Tos: these are short tutorials also available as jupyter notebooks from <a href=\"https:\/\/github.com\/eaobservatory\/Tutorials\">here<\/a>,\u00a0 and data available from <a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/AnalysisHowTosData-2019-10.tar.gz\">here<\/a><\/p>\n<ol>\n<li><a href=\"https:\/\/www.eaobservatory.org\/JCMT\/user-tutorials\/analysis\/1-masking-based-on-peaksnr.html\">Masking Cubes based on peak SNR\u00a0<\/a><\/li>\n<li><a href=\"https:\/\/www.eaobservatory.org\/JCMT\/user-tutorials\/analysis\/2-calculating-fluxes.html\">Calculating SCUBA-2 fluxes<\/a><\/li>\n<li><a href=\"https:\/\/www.eaobservatory.org\/JCMT\/user-tutorials\/analysis\/3-excitation-temperature-12CO.html\">Estimating Excitation Temperatures from 12CO<\/a><\/li>\n<li><a href=\"https:\/\/www.eaobservatory.org\/JCMT\/user-tutorials\/analysis\/4-clumpfinding.html\">Clumpfinding<\/a><\/li>\n<\/ol>\n<h3><\/h3>\n<h3><span id=\"Python_Starlink_Jupyter_notebooks\">Python &amp; Starlink Jupyter notebooks:<\/span><\/h3>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li><a href=\"https:\/\/github.com\/eaobservatory\/Tutorials\/blob\/master\/starlink-pywrapper%20Example.ipynb\">starlink-pywrapper introduction and overview notebook<\/a><\/li>\n<li><a href=\"https:\/\/github.com\/eaobservatory\/Tutorials\/blob\/master\/Starlink%20Analysis%20%28Python%29.ipynb\"> Python version of the Starlink Analysis tutorial<\/a><\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<h3><span id=\"Datasets_for_Tutorials\">Datasets for Tutorials<\/span><\/h3>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li><a href=\"https:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/2023-London\/tutorial_prp.tar.gz\"> Dataset for JCMT data reduction: pipelines, recipes and parameters<\/a> (Filesize: ~260 MB)<\/li>\n<li><a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/JCMT_SCUBA-2_tutorial1_2016.tar.gz\"> Dataset for <em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorials 1 &#8211; 3 &amp; 5<\/a> (Filesize: ~650 MB)<\/li>\n<li><a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/JCMTTutorial-MatchFilter.tar.gz\"> Dataset for <em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorial 4<\/a> (Filesize: ~31 MB)<\/li>\n<li><a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/JCMT_POL-2_tutorial1_2017_raw_only.tar.gz\"> Dataset for <em>POL-2<\/em> Data Reduction\/Analysis Tutorial 1 (raw data only)<\/a> (Filesize: ~2.9 GB) and <a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/JCMT_POL-2_tutorial1_2019_reduced_only.tar.gz\">dataset for <em>POL-2<\/em> Data Reduction\/Analysis Tutorial 1 (reduced data only)<\/a> (Filesize: ~276 MB)<\/li>\n<li><a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/JCMT_HETERODYNE_tutorial_2016.tar.gz\"> Dataset for <em>Heterodyne<\/em> Data Reduction\/Analysis Tutorial 1 <em>also<\/em> required for <em>SCUBA-2<\/em> Data Reduction\/Analysis Tutorial 5<\/a> (Filesize: ~77 MB)<\/li>\n<li><a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/JCMT_HETERODYNE_analysis_tutorial_2016.tar.gz\"> Dataset for Example <em>Heterodyne<\/em> Data Cube Analysis Script (see below)<\/a> (Filesize: ~125 MB)<\/li>\n<li><a href=\"https:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/2023-London\/tutorial_ot.tar.gz\">Example files for General JCMT Observing Tool tutorial<\/a> (Filesize: ~21 MB)<\/li>\n<li><a href=\"http:\/\/www.eaobservatory.org\/JCMT\/observing-tool-tutorials\/ot_basics_tutorial_files.tar.gz\">Example files for JCMT Observing Tool basics tutorial<\/a><\/li>\n<li><a href=\"http:\/\/www.eaobservatory.org\/JCMT\/observing-tool-tutorials\/ot_tricks_tutorial_files.tar.gz\">Example files for JCMT Observing Tool tricks tutorial<\/a><\/li>\n<li><a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/JCMT_tutorial_2018_Starlink_Analysis.tar.gz\">Starlink Analysis tutorials (Python and non python)<\/a><\/li>\n<li><a href=\"http:\/\/ftp.eao.hawaii.edu\/jcmt\/usersmeetings\/AnalysisHowTosData-2019-10.tar.gz\">Analysis How Tos<\/a><\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<h2><span id=\"Additional_Training_Materials\">Additional Training Materials<\/span><\/h2>\n<ul>\n<li style=\"list-style-type: none\">\n<ol>\n<li style=\"text-align: justify\">Getting started with Starlink: <a href=\"http:\/\/www.eaobservatory.org\/jcmt\/wp-content\/uploads\/sites\/2\/2016\/04\/StarlinkBeginner.pdf\" rel=\"\">A two-page cheat-sheet is available here.<\/a><\/li>\n<li style=\"text-align: justify\">Example commands used for analysing heterodyne cubes: <a href=\"http:\/\/www.eao.hawaii.edu\/~sgraves\/analysing_molecular_data.sh\">A shell script using the example data given above is available here.<\/a>\n<p style=\"text-align: justify\"><strong>Note:<\/strong> The intention of this script is that the user will read the comments in that file and try the commands in a directory where the example data have been unzipped. This is not exactly a tutorial, but rather a source of additional hints.<\/p>\n<\/li>\n<li style=\"text-align: justify\">For users new to computing we recommend reading the &#8220;<a href=\"https:\/\/arxiv.org\/abs\/1609.00037\">Good Enough Practices in Scientific Computing&#8221;\u00a0 Wilson et al. 2016<\/a>.<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Tutorials There are now a number of tutorials offered for new users of the JCMT. General Data Reduction Tutorials JCMT data reduction: pipelines, recipes and parameters &#8211; Introduction to the Wesley, ORAC-DR and PICARD pipelines, how to select data reduction recipes and customize your reduction via parameter files. SCUBA-2 Tutorials\u2026 <a class=\"continue-reading-link\" href=\"https:\/\/www.eaobservatory.org\/jcmt\/science\/reductionanalysis-tutorials\/\">Continue reading<\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"parent":69,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/4510"}],"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\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/comments?post=4510"}],"version-history":[{"count":176,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/4510\/revisions"}],"predecessor-version":[{"id":12969,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/4510\/revisions\/12969"}],"up":[{"embeddable":true,"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/pages\/69"}],"wp:attachment":[{"href":"https:\/\/www.eaobservatory.org\/jcmt\/wp-json\/wp\/v2\/media?parent=4510"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}