diff --git a/da/doc/Makefile b/da/doc/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..4c501ee2bdb51292924be5024abbe4df4d2f5151 --- /dev/null +++ b/da/doc/Makefile @@ -0,0 +1,130 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build-2.6 +PAPER = +BUILDDIR = build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest + +help: + @echo "Please use \`make <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/CarbonTrackerDataAssimilationShell.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/CarbonTrackerDataAssimilationShell.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/CarbonTrackerDataAssimilationShell" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/CarbonTrackerDataAssimilationShell" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + make -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/da/doc/build/doctrees/contents.doctree b/da/doc/build/doctrees/contents.doctree new file mode 100644 index 0000000000000000000000000000000000000000..1310b394274d5a0c70a28433ae2b941ed8288435 Binary files /dev/null and b/da/doc/build/doctrees/contents.doctree differ diff --git a/da/doc/build/doctrees/documentation.doctree b/da/doc/build/doctrees/documentation.doctree new file mode 100644 index 0000000000000000000000000000000000000000..e8fd7697115d57b44c2204277d2123c38b3aa60b Binary files /dev/null and b/da/doc/build/doctrees/documentation.doctree differ diff --git a/da/doc/build/doctrees/environment.pickle b/da/doc/build/doctrees/environment.pickle new file mode 100644 index 0000000000000000000000000000000000000000..51ffc7389d25d35c03b86adc3df25e5ca3a67118 Binary files /dev/null and b/da/doc/build/doctrees/environment.pickle differ diff --git a/da/doc/build/doctrees/gettingstarted.doctree b/da/doc/build/doctrees/gettingstarted.doctree new file mode 100644 index 0000000000000000000000000000000000000000..6841240e3ca35cf20f43320df21cdeee10c3a27a Binary files /dev/null and b/da/doc/build/doctrees/gettingstarted.doctree differ diff --git a/da/doc/build/doctrees/index.doctree b/da/doc/build/doctrees/index.doctree new file mode 100644 index 0000000000000000000000000000000000000000..fca7dafc706523208c1de0e9b08bda92ec6e87ec Binary files /dev/null and b/da/doc/build/doctrees/index.doctree differ diff --git a/da/doc/build/doctrees/overview.doctree b/da/doc/build/doctrees/overview.doctree new file mode 100644 index 0000000000000000000000000000000000000000..e598a1242b8a91536e63f4ecc5a4b06621835283 Binary files /dev/null and b/da/doc/build/doctrees/overview.doctree differ diff --git a/da/doc/build/doctrees/systemrequirements.doctree b/da/doc/build/doctrees/systemrequirements.doctree new file mode 100644 index 0000000000000000000000000000000000000000..288c2090a5750be0ba5a75b4d0126a557dd3633a Binary files /dev/null and b/da/doc/build/doctrees/systemrequirements.doctree differ diff --git a/da/doc/build/doctrees/tutorial.doctree b/da/doc/build/doctrees/tutorial.doctree new file mode 100644 index 0000000000000000000000000000000000000000..043ada43b367df8cfcade3566b48a388172a636e Binary files /dev/null and b/da/doc/build/doctrees/tutorial.doctree differ diff --git a/da/doc/build/html/.buildinfo b/da/doc/build/html/.buildinfo new file mode 100644 index 0000000000000000000000000000000000000000..7d7a0e71fc4f2801460d289a64ace5a34b7b571c --- /dev/null +++ b/da/doc/build/html/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 29c2fd345d748612ee705cfd9e89ed06 +tags: fbb0d17656682115ca4d033fb2f83ba1 diff --git a/da/doc/build/html/_sources/contents.txt b/da/doc/build/html/_sources/contents.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d8f599a7c2773359f53a2c593a64504bf99ed4d --- /dev/null +++ b/da/doc/build/html/_sources/contents.txt @@ -0,0 +1,13 @@ +.. _contents: + +Contents +======== + +.. toctree:: + :maxdepth: 2 + + System Requirements <systemrequirements> + Installing CTDAS <installing> + CTDAS Overview <overview> + CTDAS Tutorial <tutorial> + CTDAS Documentation <documentation> diff --git a/da/doc/build/html/_sources/documentation.txt b/da/doc/build/html/_sources/documentation.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d69a17624624cb2521b5596b895beeda10a87db --- /dev/null +++ b/da/doc/build/html/_sources/documentation.txt @@ -0,0 +1,5 @@ +.. _documentation: + +Documentation +====================== + diff --git a/da/doc/build/html/_sources/gettingstarted.txt b/da/doc/build/html/_sources/gettingstarted.txt new file mode 100644 index 0000000000000000000000000000000000000000..18d11eac1bf5eb77fd914f086237a89f0e694c33 --- /dev/null +++ b/da/doc/build/html/_sources/gettingstarted.txt @@ -0,0 +1,7 @@ +.. _gettingstarted: + +Getting Started with CTDAS +========================== + +.. automodule:: da.ct.obs + :members: CtObservations diff --git a/da/doc/build/html/_sources/index.txt b/da/doc/build/html/_sources/index.txt new file mode 100644 index 0000000000000000000000000000000000000000..05e8ca132f8f0c7e2f13a57a36741aaf472e33f2 --- /dev/null +++ b/da/doc/build/html/_sources/index.txt @@ -0,0 +1,30 @@ +.. CarbonTracker Data Assimilation Shell documentation master file, created by + sphinx-quickstart on Sun Sep 26 13:39:23 2010. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to the CTDAS documentation! +=================================== + +This is the starting page for the documentation of the CarbonTracker Data Assimilation Shell (CTDAS). + +.. sidebar:: What is CTDAS? + + CTDAS is short for "CarbonTracker Data Assimilation Shell". + This is the implementation of an extendible data assimilation framework for CarbonTracker, + developed by NOAA ESRL & Wageningen University, in close cooperation with many partners around the world. + +The aim of the CTDAS system is to facilitate the use of CarbonTracker, and to +foster its development by its many international partners. At its most basic, the CTDAS is a simple +control system for CarbonTracker that deals with the running, optimization, analysis, and time stepping of the system. +For advanced users, the CTDAS provides an easy way to extend or modify the system by introducing new configurations +for the state vector, for the observations, or even for the transport model or optimization method. + +The CarbonTracker development team welcomes suggestions and feedback on the CTDAS system, and its documentation. + +Follow the link below to start navigating, or use the "next topic" button in the right-hand-side menu. + +.. toctree:: + :maxdepth: 1 + + List of contents <contents> diff --git a/da/doc/build/html/_sources/overview.txt b/da/doc/build/html/_sources/overview.txt new file mode 100644 index 0000000000000000000000000000000000000000..603ef27e2eee976571e4118654d8ac2e86b46c52 --- /dev/null +++ b/da/doc/build/html/_sources/overview.txt @@ -0,0 +1,23 @@ +.. _overview: + +.. index:: overview, philosophy, development centers + +Overview +======== + +This page gives a brief overview of CTDAS, with the intention to provide background information for (potential) new users. Afer reading the information below we recommend contacting one of the CTDAS development centers (Wageningen University and NOAA ESRL), or proceed to the :doc:`tutorial`. + +What is CTDAS? +-------------- + +How can you use CTDAS? +---------------------- + +CTDAS Design philosophy +----------------------- + +Extending CTDAS +--------------- + + + diff --git a/da/doc/build/html/_sources/systemrequirements.txt b/da/doc/build/html/_sources/systemrequirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..8abd0d4b0685a7d800c681ceff87b5b92028bc49 --- /dev/null +++ b/da/doc/build/html/_sources/systemrequirements.txt @@ -0,0 +1,53 @@ +.. _systemrequirements: + +System Requirements +====================== + +The CarbonTracker DAS is programmed in python and uses it built-in functionality for many of its tasks. +Users of CTDAS are required to have a python installation on their system, with a small set of +open source add-ons. The minimum requirements are listed below, categorized by functionality. + +Getting the CTDAS code +---------------------- + +* A working ``subversion`` (SVN) installation is needed, to check your system type:: + + $ svn --version + + if the system returns an error, or a version < 1.5.0, please obtain svn from <http://subversion.tigris.org/> + + +Running CTDAS +------------- + +* A ``python2.4`` or later installation. + +.. note:: ``python3`` is not supported, one needs a python2.x version. To check your python version type:: + + $ python --version + +* The python module ``numpy``, not included with a standard installation. You can obtain numpy from <http://numpy.scipy.org> + +* The python module ``Nio`` created by NCAR/UCAR. This package is freely available as a binary download from UCAR's Earth System Grid at <http://www.earthsystemgrid.org> + +.. note:: Registration is required at NCAR/UCAR, their software is free for academic users. + + +Performing inversions +--------------------- + +* An important component of the CTDAS system is the observation operator, usually in the form of an atmospheric + transport model. This model is a stand-alone piece of code that can subsample your state vector, and return a + set of observations. **You therefore require an atmospheric transport model that can run indepently on your + platform.** + +.. note:: If you do not currently have access to such a transport model, or have no resources to run such a model + for long periods of time and for many ensemble configurations, you have probably stumbled onto this page not + understanding exactly what CTDAS is. We refer you to the :ref:`overview` for a more elaborate description. + +* An actual CarbonTracker inversion requires a large collection of input datasets, including + * Observations to be assimilated + * a-priori surface fluxes for your trace components + * a-priori uncertainty distributions for your unknowns + * ... and a few more items + diff --git a/da/doc/build/html/_sources/tutorial.txt b/da/doc/build/html/_sources/tutorial.txt new file mode 100644 index 0000000000000000000000000000000000000000..1528abcfd4c1c982032c3a87febfcc7d32eda9da --- /dev/null +++ b/da/doc/build/html/_sources/tutorial.txt @@ -0,0 +1,5 @@ +.. _tutorial: + +Tutorial +====================== + diff --git a/da/doc/build/html/_static/banner1.png b/da/doc/build/html/_static/banner1.png new file mode 100644 index 0000000000000000000000000000000000000000..d505cf3edc998de70a54fac87cf735639554a004 Binary files /dev/null and b/da/doc/build/html/_static/banner1.png differ diff --git a/da/doc/build/html/_static/basic.css b/da/doc/build/html/_static/basic.css new file mode 100644 index 0000000000000000000000000000000000000000..69f30d4fbe193f515cc3187d91db7216aa3544b9 --- /dev/null +++ b/da/doc/build/html/_static/basic.css @@ -0,0 +1,509 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; 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+jQuery.makeSearchSummary = function(text, keywords, hlwords) { + var textLower = text.toLowerCase(); + var start = 0; + $.each(keywords, function() { + var i = textLower.indexOf(this.toLowerCase()); + if (i > -1) + start = i; + }); + start = Math.max(start - 120, 0); + var excerpt = ((start > 0) ? '...' : '') + + $.trim(text.substr(start, 240)) + + ((start + 240 - text.length) ? '...' : ''); + var rv = $('<div class="context"></div>').text(excerpt); + $.each(hlwords, function() { + rv = rv.highlightText(this, 'highlighted'); + }); + return rv; +} + +/** + * Porter Stemmer + */ +var PorterStemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + +/** + * Search Module + */ +var Search = { + + _index : null, + _queued_query : null, + _pulse_status : -1, + + init : function() { + var params = $.getQueryParameters(); + if (params.q) { + var query = params.q[0]; + $('input[name="q"]')[0].value = query; + this.performSearch(query); + } + }, + + loadIndex : function(url) { + $.ajax({type: "GET", url: url, data: null, success: null, + dataType: "script", cache: true}); + }, + + setIndex : function(index) { + var q; + this._index = index; + if ((q = this._queued_query) !== null) { + this._queued_query = null; + Search.query(q); + } + }, + + hasIndex : function() { + return this._index !== null; + }, + + deferQuery : function(query) { + this._queued_query = query; + }, + + stopPulse : function() { + this._pulse_status = 0; + }, + + startPulse : function() { + if (this._pulse_status >= 0) + return; + function pulse() { + Search._pulse_status = (Search._pulse_status + 1) % 4; + var dotString = ''; + for (var i = 0; i < Search._pulse_status; i++) + dotString += '.'; + Search.dots.text(dotString); + if (Search._pulse_status > -1) + window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something + */ + performSearch : function(query) { + // create the required interface elements + this.out = $('#search-results'); + this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out); + this.dots = $('<span></span>').appendTo(this.title); + this.status = $('<p style="display: none"></p>').appendTo(this.out); + this.output = $('<ul class="search"/>').appendTo(this.out); + + $('#search-progress').text(_('Preparing search...')); + this.startPulse(); + + // index already loaded, the browser was quick! + if (this.hasIndex()) + this.query(query); + else + this.deferQuery(query); + }, + + query : function(query) { + var stopwords = ['and', 'then', 'into', 'it', 'as', 'are', 'in', + 'if', 'for', 'no', 'there', 'their', 'was', 'is', + 'be', 'to', 'that', 'but', 'they', 'not', 'such', + 'with', 'by', 'a', 'on', 'these', 'of', 'will', + 'this', 'near', 'the', 'or', 'at']; + + // stem the searchterms and add them to the correct list + var stemmer = new PorterStemmer(); + var searchterms = []; + var excluded = []; + var hlterms = []; + var tmp = query.split(/\s+/); + var object = (tmp.length == 1) ? tmp[0].toLowerCase() : null; + for (var i = 0; i < tmp.length; i++) { + if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) || + tmp[i] == "") { + // skip this "word" + continue; + } + // stem the word + var word = stemmer.stemWord(tmp[i]).toLowerCase(); + // select the correct list + if (word[0] == '-') { + var toAppend = excluded; + word = word.substr(1); + } + else { + var toAppend = searchterms; + hlterms.push(tmp[i].toLowerCase()); + } + // only add if not already in the list + if (!$.contains(toAppend, word)) + toAppend.push(word); + }; + var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" ")); + + // console.debug('SEARCH: searching for:'); + // console.info('required: ', searchterms); + // console.info('excluded: ', excluded); + + // prepare search + var filenames = this._index.filenames; + var titles = this._index.titles; + var terms = this._index.terms; + var objects = this._index.objects; + var objtypes = this._index.objtypes; + var objnames = this._index.objnames; + var fileMap = {}; + var files = null; + // different result priorities + var importantResults = []; + var objectResults = []; + var regularResults = []; + var unimportantResults = []; + $('#search-progress').empty(); + + // lookup as object + if (object != null) { + for (var prefix in objects) { + for (var name in objects[prefix]) { + var fullname = (prefix ? prefix + '.' : '') + name; + if (fullname.toLowerCase().indexOf(object) > -1) { + match = objects[prefix][name]; + descr = objnames[match[1]] + _(', in ') + titles[match[0]]; + // XXX the generated anchors are not generally correct + // XXX there may be custom prefixes + result = [filenames[match[0]], fullname, '#'+fullname, descr]; + switch (match[2]) { + case 1: objectResults.push(result); break; + case 0: importantResults.push(result); break; + case 2: unimportantResults.push(result); break; + } + } + } + } + } + + // sort results descending + objectResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); + }); + + importantResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); + }); + + unimportantResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); + }); + + + // perform the search on the required terms + for (var i = 0; i < searchterms.length; i++) { + var word = searchterms[i]; + // no match but word was a required one + if ((files = terms[word]) == null) + break; + if (files.length == undefined) { + files = [files]; + } + // create the mapping + for (var j = 0; j < files.length; j++) { + var file = files[j]; + if (file in fileMap) + fileMap[file].push(word); + else + fileMap[file] = [word]; + } + } + + // now check if the files don't contain excluded terms + for (var file in fileMap) { + var valid = true; + + // check if all requirements are matched + if (fileMap[file].length != searchterms.length) + continue; + + // ensure that none of the excluded terms is in the + // search result. + for (var i = 0; i < excluded.length; i++) { + if (terms[excluded[i]] == file || + $.contains(terms[excluded[i]] || [], file)) { + valid = false; + break; + } + } + + // if we have still a valid result we can add it + // to the result list + if (valid) + regularResults.push([filenames[file], titles[file], '', null]); + } + + // delete unused variables in order to not waste + // memory until list is retrieved completely + delete filenames, titles, terms; + + // now sort the regular results descending by title + regularResults.sort(function(a, b) { + var left = a[1].toLowerCase(); + var right = b[1].toLowerCase(); + return (left > right) ? -1 : ((left < right) ? 1 : 0); + }); + + // combine all results + var results = unimportantResults.concat(regularResults) + .concat(objectResults).concat(importantResults); + + // print the results + var resultCount = results.length; + function displayNextItem() { + // results left, load the summary and display it + if (results.length) { + var item = results.pop(); + var listItem = $('<li style="display:none"></li>'); + if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') { + // dirhtml builder + var dirname = item[0] + '/'; + if (dirname.match(/\/index\/$/)) { + dirname = dirname.substring(0, dirname.length-6); + } else if (dirname == 'index/') { + dirname = ''; + } + listItem.append($('<a/>').attr('href', + DOCUMENTATION_OPTIONS.URL_ROOT + dirname + + highlightstring + item[2]).html(item[1])); + } else { + // normal html builders + listItem.append($('<a/>').attr('href', + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX + + highlightstring + item[2]).html(item[1])); + } + if (item[3]) { + listItem.append($('<span> (' + item[3] + ')</span>')); + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { + $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + + item[0] + '.txt', function(data) { + if (data != '') { + listItem.append($.makeSearchSummary(data, searchterms, hlterms)); + Search.output.append(listItem); + } + listItem.slideDown(5, function() { + displayNextItem(); + }); + }); + } else { + // no source available, just display title + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } + } + // search finished, update title and status message + else { + Search.stopPulse(); + Search.title.text(_('Search Results')); + if (!resultCount) + Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.')); + else + Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount)); + Search.status.fadeIn(500); + } + } + displayNextItem(); + } +} + +$(document).ready(function() { + Search.init(); +}); diff --git a/da/doc/build/html/_static/sphinxdoc.css b/da/doc/build/html/_static/sphinxdoc.css new file mode 100644 index 0000000000000000000000000000000000000000..c7e6e335a29dbe36ddfc0666dc2603e637040cb0 --- /dev/null +++ b/da/doc/build/html/_static/sphinxdoc.css @@ -0,0 +1,339 @@ +/* + * sphinxdoc.css_t + * ~~~~~~~~~~~~~~~ + * + * Sphinx stylesheet -- sphinxdoc theme. Originally created by + * Armin Ronacher for Werkzeug. + * + * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +@import url("basic.css"); + +/* -- page layout ----------------------------------------------------------- */ + +body { + font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva', + 'Verdana', sans-serif; + font-size: 14px; + letter-spacing: -0.01em; + line-height: 150%; + text-align: center; + background-color: #BFD1D4; + color: black; + padding: 0; + border: 1px solid #aaa; + + margin: 0px 80px 0px 80px; + min-width: 740px; +} + +div.document { + background-color: white; + text-align: left; + background-image: url(contents.png); + background-repeat: repeat-x; +} + +div.bodywrapper { + margin: 0 240px 0 0; + border-right: 1px solid #ccc; +} + +div.body { + margin: 0; + padding: 0.5em 20px 20px 20px; +} + +div.related { + font-size: 1em; +} + +div.related ul { + background-image: url(navigation.png); + height: 2em; + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; +} + +div.related ul li { + margin: 0; + padding: 0; + height: 2em; + float: left; +} + +div.related ul li.right { + float: right; + margin-right: 5px; +} + +div.related ul li a { + margin: 0; + padding: 0 5px 0 5px; + line-height: 1.75em; + color: #EE9816; +} + +div.related ul li a:hover { + color: #3CA8E7; +} + +div.sphinxsidebarwrapper { + padding: 0; +} + +div.sphinxsidebar { + margin: 0; + padding: 0.5em 15px 15px 0; + width: 210px; + float: right; + font-size: 1em; + text-align: left; +} + +div.sphinxsidebar h3, div.sphinxsidebar h4 { + margin: 1em 0 0.5em 0; + font-size: 1em; + padding: 0.1em 0 0.1em 0.5em; + color: white; + border: 1px solid #86989B; + background-color: #AFC1C4; +} + +div.sphinxsidebar h3 a { + color: white; +} + +div.sphinxsidebar ul { + padding-left: 1.5em; + margin-top: 7px; + padding: 0; + line-height: 130%; +} + +div.sphinxsidebar ul ul { + margin-left: 20px; +} + +div.footer { + background-color: #E3EFF1; + color: #86989B; + padding: 3px 8px 3px 0; + clear: both; + font-size: 0.8em; + text-align: right; +} + +div.footer a { + color: #86989B; + text-decoration: underline; +} + +/* -- body styles ----------------------------------------------------------- */ + +p { + margin: 0.8em 0 0.5em 0; +} + +a { + color: #CA7900; + text-decoration: none; +} + +a:hover { + color: #2491CF; +} + +div.body a { + text-decoration: underline; +} + +h1 { + margin: 0; + padding: 0.7em 0 0.3em 0; + font-size: 1.5em; + color: #11557C; +} + +h2 { + margin: 1.3em 0 0.2em 0; + font-size: 1.35em; + padding: 0; +} + +h3 { + margin: 1em 0 -0.3em 0; + font-size: 1.2em; +} + +div.body h1 a, div.body h2 a, div.body h3 a, div.body h4 a, div.body h5 a, div.body h6 a { + color: black!important; +} + +h1 a.anchor, h2 a.anchor, h3 a.anchor, h4 a.anchor, h5 a.anchor, h6 a.anchor { + display: none; + margin: 0 0 0 0.3em; + padding: 0 0.2em 0 0.2em; + color: #aaa!important; +} + +h1:hover a.anchor, h2:hover a.anchor, h3:hover a.anchor, h4:hover a.anchor, +h5:hover a.anchor, h6:hover a.anchor { + display: inline; +} + +h1 a.anchor:hover, h2 a.anchor:hover, h3 a.anchor:hover, h4 a.anchor:hover, +h5 a.anchor:hover, h6 a.anchor:hover { + color: #777; + background-color: #eee; +} + +a.headerlink { + color: #c60f0f!important; + font-size: 1em; + margin-left: 6px; + padding: 0 4px 0 4px; + text-decoration: none!important; +} + +a.headerlink:hover { + background-color: #ccc; + color: white!important; +} + +cite, code, tt { + font-family: 'Consolas', 'Deja Vu Sans Mono', + 'Bitstream Vera Sans Mono', monospace; + font-size: 0.95em; + letter-spacing: 0.01em; +} + +tt { + background-color: #f2f2f2; + border-bottom: 1px solid #ddd; + color: #333; +} + +tt.descname, tt.descclassname, tt.xref { + border: 0; +} + +hr { + border: 1px solid #abc; + margin: 2em; +} + +a tt { + border: 0; + color: #CA7900; +} + +a tt:hover { + color: #2491CF; +} + +pre { + font-family: 'Consolas', 'Deja Vu Sans Mono', + 'Bitstream Vera Sans Mono', monospace; + font-size: 0.95em; + letter-spacing: 0.015em; + line-height: 120%; + padding: 0.5em; + border: 1px solid #ccc; + background-color: #f8f8f8; +} + +pre a { + color: inherit; + text-decoration: underline; +} + +td.linenos pre { + padding: 0.5em 0; +} + +div.quotebar { + background-color: #f8f8f8; + max-width: 250px; + float: right; + padding: 2px 7px; + border: 1px solid #ccc; +} + +div.topic { + background-color: #f8f8f8; +} + +table { + border-collapse: collapse; + margin: 0 -0.5em 0 -0.5em; +} + +table td, table th { + padding: 0.2em 0.5em 0.2em 0.5em; +} + +div.admonition, div.warning { + font-size: 0.9em; + margin: 1em 0 1em 0; + border: 1px solid #86989B; + background-color: #f7f7f7; + padding: 0; +} + +div.admonition p, div.warning p { + margin: 0.5em 1em 0.5em 1em; + padding: 0; +} + +div.admonition pre, div.warning pre { + margin: 0.4em 1em 0.4em 1em; +} + +div.admonition p.admonition-title, +div.warning p.admonition-title { + margin: 0; + padding: 0.1em 0 0.1em 0.5em; + color: white; + border-bottom: 1px solid #86989B; + font-weight: bold; + background-color: #AFC1C4; +} + +div.warning { + border: 1px solid #940000; +} + +div.warning p.admonition-title { + background-color: #CF0000; + border-bottom-color: #940000; +} + +div.admonition ul, div.admonition ol, +div.warning ul, div.warning ol { + margin: 0.1em 0.5em 0.5em 3em; + padding: 0; +} + +div.versioninfo { + margin: 1em 0 0 0; + border: 1px solid #ccc; + background-color: #DDEAF0; + padding: 8px; + line-height: 1.3em; + font-size: 0.9em; +} + +.viewcode-back { + font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva', + 'Verdana', sans-serif; +} + +div.viewcode-block:target { + background-color: #f4debf; + border-top: 1px solid #ac9; + border-bottom: 1px solid #ac9; +} diff --git a/da/doc/build/html/_static/underscore.js b/da/doc/build/html/_static/underscore.js new file mode 100644 index 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/> + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '', + VERSION: '0.1', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <link rel="top" title="CarbonTracker DAS" href="index.html" /> + </head> + <body> +<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px"> +<a href="#"><img src="_static/banner1.png" border="0" alt="CarbonTracker"/></a> +</div> + + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="#" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="index.html">CarbonTracker DAS</a> »</li> + </ul> + </div> + 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href="#W"><strong>W</strong></a> + </div> +<h2 id="A">A</h2> +<table width="100%" class="indextable genindextable"><tr> + <td width="33%" valign="top"><dl> + <dt><a href="gettingstarted.html#da.ct.obs.CtObservations.AddModelDataMismatch">AddModelDataMismatch() (da.ct.obs.CtObservations method)</a></dt> + <dt><a href="gettingstarted.html#da.ct.obs.CtObservations.AddObs">AddObs() (da.ct.obs.CtObservations method)</a></dt> +</dl></td> + <td width="33%" valign="top"><dl> + <dt><a href="gettingstarted.html#da.ct.obs.CtObservations.AddSimulations">AddSimulations() (da.ct.obs.CtObservations method)</a></dt> +</dl></td> +</tr></table> + +<h2 id="C">C</h2> +<table width="100%" class="indextable genindextable"><tr> + <td width="33%" valign="top"><dl> + <dt><a href="gettingstarted.html#da.ct.obs.CtObservations">CtObservations (class in da.ct.obs)</a></dt> +</dl></td> +</tr></table> + +<h2 id="D">D</h2> +<table width="100%" class="indextable genindextable"><tr> + <td width="33%" valign="top"><dl> + <dt><a href="gettingstarted.html#module-da.ct.obs">da.ct.obs (module)</a></dt> +</dl></td> + <td width="33%" valign="top"><dl> + <dt><a href="overview.html#index-0">development centers</a></dt> +</dl></td> +</tr></table> + +<h2 id="O">O</h2> +<table width="100%" class="indextable genindextable"><tr> + <td width="33%" valign="top"><dl> + <dt><a href="overview.html#index-0">overview</a></dt> +</dl></td> +</tr></table> + +<h2 id="P">P</h2> +<table width="100%" class="indextable genindextable"><tr> + <td width="33%" valign="top"><dl> + <dt><a href="overview.html#index-0">philosophy</a></dt> +</dl></td> +</tr></table> + +<h2 id="W">W</h2> +<table width="100%" class="indextable genindextable"><tr> + <td width="33%" valign="top"><dl> + <dt><a href="gettingstarted.html#da.ct.obs.CtObservations.WriteSampleInfo">WriteSampleInfo() (da.ct.obs.CtObservations method)</a></dt> +</dl></td> +</tr></table> + + + + </div> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="#" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="index.html">CarbonTracker DAS</a> »</li> + </ul> + </div> + <div class="footer"> + © Copyright 2010, Wouter Peters. + Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0.3. + </div> + </body> +</html> \ No newline at end of file diff --git a/da/doc/build/html/gettingstarted.html b/da/doc/build/html/gettingstarted.html new file mode 100644 index 0000000000000000000000000000000000000000..600496a2f3926c051e4adbdeebcdc662334c7bd9 --- /dev/null +++ b/da/doc/build/html/gettingstarted.html @@ -0,0 +1,141 @@ + + +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Getting Started with CTDAS — CarbonTracker DAS</title> + <link rel="stylesheet" href="_static/sphinxdoc.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '', + VERSION: '0.1', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <link rel="top" title="CarbonTracker DAS" href="index.html" /> + </head> + <body> +<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px"> +<a href="#"><img src="_static/banner1.png" border="0" alt="CarbonTracker"/></a> +</div> + + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="index.html">CarbonTracker DAS</a> »</li> + </ul> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/gettingstarted.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" size="18" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-da.ct.obs"> +<span id="getting-started-with-ctdas"></span><span id="gettingstarted"></span><h1>Getting Started with CTDAS<a class="headerlink" href="#module-da.ct.obs" title="Permalink to this headline">¶</a></h1> +<p>Author : peters</p> +<p>Revision History: +File created on 28 Jul 2010.</p> +<dl class="class"> +<dt id="da.ct.obs.CtObservations"> +<em class="property">class </em><tt class="descclassname">da.ct.obs.</tt><tt class="descname">CtObservations</tt><a class="headerlink" href="#da.ct.obs.CtObservations" title="Permalink to this definition">¶</a></dt> +<dd><p>an object that holds data + methods and attributes needed to manipulate mixing ratio values</p> +<dl class="method"> +<dt id="da.ct.obs.CtObservations.AddModelDataMismatch"> +<tt class="descname">AddModelDataMismatch</tt><big>(</big><em>DaCycle</em><big>)</big><a class="headerlink" href="#da.ct.obs.CtObservations.AddModelDataMismatch" title="Permalink to this definition">¶</a></dt> +<dd><p>Get the model-data mismatch values for this cycle.</p> +</dd></dl> + +<dl class="method"> +<dt id="da.ct.obs.CtObservations.AddObs"> +<tt class="descname">AddObs</tt><big>(</big><big>)</big><a class="headerlink" href="#da.ct.obs.CtObservations.AddObs" title="Permalink to this definition">¶</a></dt> +<dd><p>Returns a MixingRatioList holding individual MixingRatioSample objects for all obs in a file</p> +<p>The CarbonTracker mixing ratio files are provided as one long list of obs for all possible dates. So we can +either:</p> +<ol class="arabic simple"> +<li>read all, and the subselect the data we will use in the rest of this cycle</li> +<li>Use nco to make a subset of the data</li> +</ol> +<p>For now, we will stick with option (1)</p> +</dd></dl> + +<dl class="method"> +<dt id="da.ct.obs.CtObservations.AddSimulations"> +<tt class="descname">AddSimulations</tt><big>(</big><em>filename</em>, <em>silent=True</em><big>)</big><a class="headerlink" href="#da.ct.obs.CtObservations.AddSimulations" title="Permalink to this definition">¶</a></dt> +<dd><p>Adds model simulated values to the mixing ratio objects</p> +</dd></dl> + +<dl class="method"> +<dt id="da.ct.obs.CtObservations.WriteSampleInfo"> +<tt class="descname">WriteSampleInfo</tt><big>(</big><em>DaCycle</em><big>)</big><a class="headerlink" href="#da.ct.obs.CtObservations.WriteSampleInfo" title="Permalink to this definition">¶</a></dt> +<dd><p>Write the information needed by the observation operator to a file. Return the filename that was written for later use</p> +<p>For CarbonTracker, the input files are already in a format suitable for TM5 to read. All we need to do return the name of the file +that served as input for the Observation object.</p> +</dd></dl> + +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="index.html">CarbonTracker DAS</a> »</li> + </ul> + </div> + <div class="footer"> + © Copyright 2010, Wouter Peters. + Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0.3. + </div> + </body> +</html> \ No newline at end of file diff --git a/da/doc/build/html/index.html b/da/doc/build/html/index.html new file mode 100644 index 0000000000000000000000000000000000000000..658ef6415de8f5c48b61ea8cc5019ee847f5c0bf --- /dev/null +++ b/da/doc/build/html/index.html @@ -0,0 +1,128 @@ + + +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Welcome to the CTDAS documentation! — CarbonTracker DAS</title> + <link rel="stylesheet" href="_static/sphinxdoc.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '', + VERSION: '0.1', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <link rel="top" title="CarbonTracker DAS" href="#" /> + <link rel="next" title="Contents" href="contents.html" /> + </head> + <body> +<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px"> +<a href="#"><img src="_static/banner1.png" border="0" alt="CarbonTracker"/></a> +</div> + + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="contents.html" title="Contents" + accesskey="N">next</a> |</li> + <li><a href="#">CarbonTracker DAS</a> »</li> + </ul> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Next topic</h4> + <p class="topless"><a href="contents.html" + title="next chapter">Contents</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/index.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" size="18" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="welcome-to-the-ctdas-documentation"> +<h1>Welcome to the CTDAS documentation!<a class="headerlink" href="#welcome-to-the-ctdas-documentation" title="Permalink to this headline">¶</a></h1> +<p>This is the starting page for the documentation of the CarbonTracker Data Assimilation Shell (CTDAS).</p> +<div class="sidebar"> +<p class="first sidebar-title">What is CTDAS?</p> +<p class="last">CTDAS is short for “CarbonTracker Data Assimilation Shell”. +This is the implementation of an extendible data assimilation framework for CarbonTracker, +developed by NOAA ESRL & Wageningen University, in close cooperation with many partners around the world.</p> +</div> +<p>The aim of the CTDAS system is to facilitate the use of CarbonTracker, and to +foster its development by its many international partners. At its most basic, the CTDAS is a simple +control system for CarbonTracker that deals with the running, optimization, analysis, and time stepping of the system. +For advanced users, the CTDAS provides an easy way to extend or modify the system by introducing new configurations +for the state vector, for the observations, or even for the transport model or optimization method.</p> +<p>The CarbonTracker development team welcomes suggestions and feedback on the CTDAS system, and its documentation.</p> +<p>Follow the link below to start navigating, or use the “next topic” button in the right-hand-side menu.</p> +<div class="toctree-wrapper compound"> +<ul> +<li class="toctree-l1"><a class="reference internal" href="contents.html">List of contents</a></li> +</ul> +</div> +</div> + + + </div> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="contents.html" title="Contents" + >next</a> |</li> + <li><a href="#">CarbonTracker DAS</a> »</li> + </ul> + </div> + <div class="footer"> + © Copyright 2010, Wouter Peters. + Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0.3. + </div> + </body> +</html> \ No newline at end of file diff --git a/da/doc/build/html/objects.inv b/da/doc/build/html/objects.inv new file mode 100644 index 0000000000000000000000000000000000000000..8739c2600244456b02a8d454a478e15cc889bb6d --- /dev/null +++ b/da/doc/build/html/objects.inv @@ -0,0 +1,6 @@ +# Sphinx inventory version 2 +# Project: CarbonTracker Data Assimilation Shell +# Version: 0.1 +# The remainder of this file is compressed using zlib. +xڥR;k�0��+�jѮق %CH��e�j�H�s���ڑD�$��l���ӝZ@T� (<���R�4-^h;�X�F?-�kD)O�o�-�Պ���~�c"�z<����Xd"�7N��I��7`Q�rv�P���$�o��-b����h�`��+�����t'����^yK��:7|��'��]P�qo32��e�)X���a���ā=��^$�-�&V��NS +l%�6EvNҹ�0�1�-B����{���9hX��P#�c��(6*�ÂM�����ҿg]�g^���G� \ No newline at end of file diff --git a/da/doc/build/html/overview.html b/da/doc/build/html/overview.html new file mode 100644 index 0000000000000000000000000000000000000000..4eca782c72941240799a4f13d0843d3ae559a076 --- /dev/null +++ b/da/doc/build/html/overview.html @@ -0,0 +1,146 @@ + + +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Overview — CarbonTracker DAS</title> + <link rel="stylesheet" href="_static/sphinxdoc.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '', + VERSION: '0.1', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <link rel="top" title="CarbonTracker DAS" href="index.html" /> + <link rel="up" title="Contents" href="contents.html" /> + <link rel="next" title="Tutorial" href="tutorial.html" /> + <link rel="prev" title="System Requirements" href="systemrequirements.html" /> + </head> + <body> +<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px"> +<a href="#"><img src="_static/banner1.png" border="0" alt="CarbonTracker"/></a> +</div> + + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="tutorial.html" title="Tutorial" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="systemrequirements.html" title="System Requirements" + accesskey="P">previous</a> |</li> + <li><a href="index.html">CarbonTracker DAS</a> »</li> + <li><a href="contents.html" accesskey="U">Contents</a> »</li> + </ul> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h3><a href="index.html">Table Of Contents</a></h3> + <ul> +<li><a class="reference internal" href="#">Overview</a><ul> +<li><a class="reference internal" href="#what-is-ctdas">What is CTDAS?</a></li> +<li><a class="reference internal" href="#how-can-you-use-ctdas">How can you use CTDAS?</a></li> +<li><a class="reference internal" href="#ctdas-design-philosophy">CTDAS Design philosophy</a></li> +<li><a class="reference internal" href="#extending-ctdas">Extending CTDAS</a></li> +</ul> +</li> +</ul> + + <h4>Previous topic</h4> + <p class="topless"><a href="systemrequirements.html" + title="previous chapter">System Requirements</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="tutorial.html" + title="next chapter">Tutorial</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/overview.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" size="18" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <span class="target" id="overview"></span><div class="section" id="index-0"> +<span id="id1"></span><h1>Overview<a class="headerlink" href="#index-0" title="Permalink to this headline">¶</a></h1> +<p>This page gives a brief overview of CTDAS, with the intention to provide background information for (potential) new users. Afer reading the information below we recommend contacting one of the CTDAS development centers (Wageningen University and NOAA ESRL), or proceed to the <a class="reference internal" href="tutorial.html"><em>Tutorial</em></a>.</p> +<div class="section" id="what-is-ctdas"> +<h2>What is CTDAS?<a class="headerlink" href="#what-is-ctdas" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="how-can-you-use-ctdas"> +<h2>How can you use CTDAS?<a class="headerlink" href="#how-can-you-use-ctdas" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="ctdas-design-philosophy"> +<h2>CTDAS Design philosophy<a class="headerlink" href="#ctdas-design-philosophy" title="Permalink to this headline">¶</a></h2> +</div> +<div class="section" id="extending-ctdas"> +<h2>Extending CTDAS<a class="headerlink" href="#extending-ctdas" title="Permalink to this headline">¶</a></h2> +</div> +</div> + + + </div> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="tutorial.html" title="Tutorial" + >next</a> |</li> + <li class="right" > + <a href="systemrequirements.html" title="System Requirements" + >previous</a> |</li> + <li><a href="index.html">CarbonTracker DAS</a> »</li> + <li><a href="contents.html" >Contents</a> »</li> + </ul> + </div> + <div class="footer"> + © Copyright 2010, Wouter Peters. + Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0.3. + </div> + </body> +</html> \ No newline at end of file diff --git a/da/doc/build/html/py-modindex.html b/da/doc/build/html/py-modindex.html new file mode 100644 index 0000000000000000000000000000000000000000..dc9b3d29c10fcbb14fe41ef692a2df2bcf63b5fc --- /dev/null +++ b/da/doc/build/html/py-modindex.html @@ -0,0 +1,117 @@ + + +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; 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The minimum requirements are listed below, categorized by functionality.</p> +<div class="section" id="getting-the-ctdas-code"> +<h2>Getting the CTDAS code<a class="headerlink" href="#getting-the-ctdas-code" title="Permalink to this headline">¶</a></h2> +<ul> +<li><p class="first">A working <tt class="docutils literal"><span class="pre">subversion</span></tt> (SVN) installation is needed, to check your system type:</p> +<div class="highlight-python"><pre>$ svn --version</pre> +</div> +<p>if the system returns an error, or a version < 1.5.0, please obtain svn from <<a class="reference external" href="http://subversion.tigris.org/">http://subversion.tigris.org/</a>></p> +</li> +</ul> +</div> +<div class="section" id="running-ctdas"> +<h2>Running CTDAS<a class="headerlink" href="#running-ctdas" title="Permalink to this headline">¶</a></h2> +<ul class="simple"> +<li>A <tt class="docutils literal"><span class="pre">python2.4</span></tt> or later installation.</li> +</ul> +<div class="admonition note"> +<p class="first admonition-title">Note</p> +<p><tt class="docutils literal"><span class="pre">python3</span></tt> is not supported, one needs a python2.x version. To check your python version type:</p> +<div class="last highlight-python"><pre>$ python --version</pre> +</div> +</div> +<ul class="simple"> +<li>The python module <tt class="docutils literal"><span class="pre">numpy</span></tt>, not included with a standard installation. You can obtain numpy from <<a class="reference external" href="http://numpy.scipy.org">http://numpy.scipy.org</a>></li> +<li>The python module <tt class="docutils literal"><span class="pre">Nio</span></tt> created by NCAR/UCAR. This package is freely available as a binary download from UCAR’s Earth System Grid at <<a class="reference external" href="http://www.earthsystemgrid.org">http://www.earthsystemgrid.org</a>></li> +</ul> +<div class="admonition note"> +<p class="first admonition-title">Note</p> +<p class="last">Registration is required at NCAR/UCAR, their software is free for academic users.</p> +</div> +</div> +<div class="section" id="performing-inversions"> +<h2>Performing inversions<a class="headerlink" href="#performing-inversions" title="Permalink to this headline">¶</a></h2> +<ul class="simple"> +<li>An important component of the CTDAS system is the observation operator, usually in the form of an atmospheric +transport model. This model is a stand-alone piece of code that can subsample your state vector, and return a +set of observations. <strong>You therefore require an atmospheric transport model that can run indepently on your +platform.</strong></li> +</ul> +<div class="admonition note"> +<p class="first admonition-title">Note</p> +<p class="last">If you do not currently have access to such a transport model, or have no resources to run such a model +for long periods of time and for many ensemble configurations, you have probably stumbled onto this page not +understanding exactly what CTDAS is. We refer you to the <em class="xref std std-ref">overview</em> for a more elaborate description.</p> +</div> +<ul> +<li><dl class="first docutils"> +<dt>An actual CarbonTracker inversion requires a large collection of input datasets, including</dt> +<dd><ul class="first last simple"> +<li>Observations to be assimilated</li> +<li>a-priori surface fluxes for your trace components</li> +<li>a-priori uncertainty distributions for your unknowns</li> +<li>... and a few more items</li> +</ul> +</dd> +</dl> +</li> +</ul> +</div> +</div> + + + </div> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="overview.html" title="Overview" + >next</a> |</li> + <li class="right" > + <a href="contents.html" title="Contents" + >previous</a> |</li> + <li><a href="index.html">CarbonTracker DAS</a> »</li> + <li><a href="contents.html" >Contents</a> »</li> + </ul> + </div> + <div class="footer"> + © Copyright 2010, Wouter Peters. + Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0.3. + </div> + </body> +</html> \ No newline at end of file diff --git a/da/doc/build/html/tutorial.html b/da/doc/build/html/tutorial.html new file mode 100644 index 0000000000000000000000000000000000000000..874da6d5e9e5332b34457c6d3a2f5e23be8370eb --- /dev/null +++ b/da/doc/build/html/tutorial.html @@ -0,0 +1,122 @@ + + +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; 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text-align: left; padding: 10px 10px 15px 15px"> +<a href="#"><img src="_static/banner1.png" border="0" alt="CarbonTracker"/></a> +</div> +{% endblock %} diff --git a/da/doc/source/conf.py b/da/doc/source/conf.py new file mode 100644 index 0000000000000000000000000000000000000000..097333b4526d77dc09898f55fc7f7626bfbf6490 --- /dev/null +++ b/da/doc/source/conf.py @@ -0,0 +1,217 @@ +# -*- coding: utf-8 -*- +# +# CarbonTracker Data Assimilation Shell documentation build configuration file, created by +# sphinx-quickstart on Sun Sep 26 13:39:23 2010. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(),'../../../'))) +print sys.path + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'CarbonTracker Data Assimilation Shell' +copyright = u'2010, Wouter Peters' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '0.1' +# The full version, including alpha/beta/rc tags. +release = '0.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = [] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'sphinxdoc' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +html_title = 'CarbonTracker DAS' + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = './images/carbontracker.png' + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'CarbonTrackerDataAssimilationShelldoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +# The paper size ('letter' or 'a4'). +#latex_paper_size = 'letter' + +# The font size ('10pt', '11pt' or '12pt'). +#latex_font_size = '10pt' + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'CarbonTrackerDataAssimilationShell.tex', u'CarbonTracker Data Assimilation Shell Documentation', + u'Wouter Peters', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Additional stuff for the LaTeX preamble. +#latex_preamble = '' + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'carbontrackerdataassimilationshell', u'CarbonTracker Data Assimilation Shell Documentation', + [u'Wouter Peters'], 1) +] diff --git a/da/doc/source/contents.rst b/da/doc/source/contents.rst new file mode 100644 index 0000000000000000000000000000000000000000..1d8f599a7c2773359f53a2c593a64504bf99ed4d --- /dev/null +++ b/da/doc/source/contents.rst @@ -0,0 +1,13 @@ +.. _contents: + +Contents +======== + +.. toctree:: + :maxdepth: 2 + + System Requirements <systemrequirements> + Installing CTDAS <installing> + CTDAS Overview <overview> + CTDAS Tutorial <tutorial> + CTDAS Documentation <documentation> diff --git a/da/doc/source/docdesign.rtf b/da/doc/source/docdesign.rtf new file mode 100644 index 0000000000000000000000000000000000000000..d83f512dcda592e05d4bc302e91e55ad31df27a5 --- /dev/null +++ b/da/doc/source/docdesign.rtf @@ -0,0 +1,47 @@ +{\rtf1\ansi\ansicpg1252\cocoartf1038\cocoasubrtf320 +{\fonttbl\f0\fswiss\fcharset0 Helvetica;} +{\colortbl;\red255\green255\blue255;} +\paperw11900\paperh16840\margl1440\margr1440\vieww9000\viewh8400\viewkind0 +\pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\ql\qnatural\pardirnatural + +\f0\fs24 \cf0 Design of CT Documentation\ +\ +\ +Welcome\ +System Requirements\ +Installation\ +\ +Contents\ +\ +Overview of CTDAS\ + Design philosophy\ + Extensions\ +\ +Tutorial\ + Getting Started\ + Creating rc-files\ + Creating a run script\ + Setting up your platform\ + Running an inversion\ + Starting a new job\ + Restart from a crash\ + Extend an existing simulation\ + Modifying the system\ + Defining your own classes\ + Creating a new pipeline\ +\ +Reference/Documentation\ + Cycle Control\ + Platforms\ + DA System\ + Observations\ + State Vectors\ + Optimization\ + Observation Operator\ + Pipeline\ + Baseclasses\ + I/O\ +\ +Modules, Classes, Functions\ +\ + } \ No newline at end of file diff --git a/da/doc/source/documentation.rst b/da/doc/source/documentation.rst new file mode 100644 index 0000000000000000000000000000000000000000..7d69a17624624cb2521b5596b895beeda10a87db --- /dev/null +++ b/da/doc/source/documentation.rst @@ -0,0 +1,5 @@ +.. _documentation: + +Documentation +====================== + diff --git a/da/doc/source/gettingstarted.rst b/da/doc/source/gettingstarted.rst new file mode 100644 index 0000000000000000000000000000000000000000..18d11eac1bf5eb77fd914f086237a89f0e694c33 --- /dev/null +++ b/da/doc/source/gettingstarted.rst @@ -0,0 +1,7 @@ +.. _gettingstarted: + +Getting Started with CTDAS +========================== + +.. automodule:: da.ct.obs + :members: CtObservations diff --git a/da/doc/source/images/carbontracker.png b/da/doc/source/images/carbontracker.png new file mode 100644 index 0000000000000000000000000000000000000000..e6da1e1af8e9f84166f8c5518014f351e66efd31 Binary files /dev/null and b/da/doc/source/images/carbontracker.png differ diff --git a/da/doc/source/index.rst b/da/doc/source/index.rst new file mode 100644 index 0000000000000000000000000000000000000000..05e8ca132f8f0c7e2f13a57a36741aaf472e33f2 --- /dev/null +++ b/da/doc/source/index.rst @@ -0,0 +1,30 @@ +.. CarbonTracker Data Assimilation Shell documentation master file, created by + sphinx-quickstart on Sun Sep 26 13:39:23 2010. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to the CTDAS documentation! +=================================== + +This is the starting page for the documentation of the CarbonTracker Data Assimilation Shell (CTDAS). + +.. sidebar:: What is CTDAS? + + CTDAS is short for "CarbonTracker Data Assimilation Shell". + This is the implementation of an extendible data assimilation framework for CarbonTracker, + developed by NOAA ESRL & Wageningen University, in close cooperation with many partners around the world. + +The aim of the CTDAS system is to facilitate the use of CarbonTracker, and to +foster its development by its many international partners. At its most basic, the CTDAS is a simple +control system for CarbonTracker that deals with the running, optimization, analysis, and time stepping of the system. +For advanced users, the CTDAS provides an easy way to extend or modify the system by introducing new configurations +for the state vector, for the observations, or even for the transport model or optimization method. + +The CarbonTracker development team welcomes suggestions and feedback on the CTDAS system, and its documentation. + +Follow the link below to start navigating, or use the "next topic" button in the right-hand-side menu. + +.. toctree:: + :maxdepth: 1 + + List of contents <contents> diff --git a/da/doc/source/overview.rst b/da/doc/source/overview.rst new file mode 100644 index 0000000000000000000000000000000000000000..603ef27e2eee976571e4118654d8ac2e86b46c52 --- /dev/null +++ b/da/doc/source/overview.rst @@ -0,0 +1,23 @@ +.. _overview: + +.. index:: overview, philosophy, development centers + +Overview +======== + +This page gives a brief overview of CTDAS, with the intention to provide background information for (potential) new users. Afer reading the information below we recommend contacting one of the CTDAS development centers (Wageningen University and NOAA ESRL), or proceed to the :doc:`tutorial`. + +What is CTDAS? +-------------- + +How can you use CTDAS? +---------------------- + +CTDAS Design philosophy +----------------------- + +Extending CTDAS +--------------- + + + diff --git a/da/doc/source/systemrequirements.rst b/da/doc/source/systemrequirements.rst new file mode 100644 index 0000000000000000000000000000000000000000..8abd0d4b0685a7d800c681ceff87b5b92028bc49 --- /dev/null +++ b/da/doc/source/systemrequirements.rst @@ -0,0 +1,53 @@ +.. _systemrequirements: + +System Requirements +====================== + +The CarbonTracker DAS is programmed in python and uses it built-in functionality for many of its tasks. +Users of CTDAS are required to have a python installation on their system, with a small set of +open source add-ons. The minimum requirements are listed below, categorized by functionality. + +Getting the CTDAS code +---------------------- + +* A working ``subversion`` (SVN) installation is needed, to check your system type:: + + $ svn --version + + if the system returns an error, or a version < 1.5.0, please obtain svn from <http://subversion.tigris.org/> + + +Running CTDAS +------------- + +* A ``python2.4`` or later installation. + +.. note:: ``python3`` is not supported, one needs a python2.x version. To check your python version type:: + + $ python --version + +* The python module ``numpy``, not included with a standard installation. You can obtain numpy from <http://numpy.scipy.org> + +* The python module ``Nio`` created by NCAR/UCAR. This package is freely available as a binary download from UCAR's Earth System Grid at <http://www.earthsystemgrid.org> + +.. note:: Registration is required at NCAR/UCAR, their software is free for academic users. + + +Performing inversions +--------------------- + +* An important component of the CTDAS system is the observation operator, usually in the form of an atmospheric + transport model. This model is a stand-alone piece of code that can subsample your state vector, and return a + set of observations. **You therefore require an atmospheric transport model that can run indepently on your + platform.** + +.. note:: If you do not currently have access to such a transport model, or have no resources to run such a model + for long periods of time and for many ensemble configurations, you have probably stumbled onto this page not + understanding exactly what CTDAS is. We refer you to the :ref:`overview` for a more elaborate description. + +* An actual CarbonTracker inversion requires a large collection of input datasets, including + * Observations to be assimilated + * a-priori surface fluxes for your trace components + * a-priori uncertainty distributions for your unknowns + * ... and a few more items + diff --git a/da/doc/source/tutorial.rst b/da/doc/source/tutorial.rst new file mode 100644 index 0000000000000000000000000000000000000000..1528abcfd4c1c982032c3a87febfcc7d32eda9da --- /dev/null +++ b/da/doc/source/tutorial.rst @@ -0,0 +1,5 @@ +.. _tutorial: + +Tutorial +====================== +