[Dart-dev] [5011] DART/trunk/doc/html/Kodiak_release.html: Updated section on New Diagnostics and Documentation as well as
nancy at ucar.edu
nancy at ucar.edu
Tue Jun 14 16:03:21 MDT 2011
Revision: 5011
Author: thoar
Date: 2011-06-14 16:03:21 -0600 (Tue, 14 Jun 2011)
Log Message:
-----------
Updated section on New Diagnostics and Documentation as well as
New Utilities.
Modified Paths:
--------------
DART/trunk/doc/html/Kodiak_release.html
-------------- next part --------------
Modified: DART/trunk/doc/html/Kodiak_release.html
===================================================================
--- DART/trunk/doc/html/Kodiak_release.html 2011-06-14 17:45:41 UTC (rev 5010)
+++ DART/trunk/doc/html/Kodiak_release.html 2011-06-14 22:03:21 UTC (rev 5011)
@@ -31,7 +31,7 @@
<A HREF="#NewModels">New Models</A> /
<A HREF="#ChangedModels">Changed Models</A> /
<A HREF="#NewObs">New Observations</A> /
-<A HREF="#NewDiags">New Diagnostics and Documentation</A> /
+<A HREF="#NewDiagnostics">New Diagnostics and Documentation</A> /
<A HREF="#NewUtilities">New Utilities</A> /
<A HREF="#Legalese">Terms of Use</A>
@@ -632,31 +632,178 @@
<HR>
<H2>New Diagnostics and Documentation</H2>
+<P>
+<strong>Better Web Pages.</strong>
+We've put a lot of effort into expanding
+our documentation, but there's always room for more. For example, please check out the Matlab
+diagnostics section: <a href="http://www.image.ucar.edu/DAReS/DART/DART_Documentation.php#mat_obs">http://www.image.ucar.edu/DAReS/DART/DART_Documentation.php#mat_obs</a> or the pages
+outlining the observation sequence file contents: <a href="http://www.image.ucar.edu/DAReS/DART/DART_Observations.php#obs_seq_overview">http://www.image.ucar.edu/DAReS/DART/DART_Observations.php#obs_seq_overview</a>.
+<br />
+<br />
+<strong>Please let us know where we are lacking.</strong>
+</P>
+
<UL>
+<LI>There is now a
+ <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/index.html">DART/index.html</a>
+ in the DART distribution to quickly guide you to any of the documentation for the
+ routines or modules.
+</LI>
+
<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/DART_LAB/DART_LAB.html">DART_LAB</a><br>
Matlab GUI presentation of fundamental assimilation concepts</LI>
-<LI>linkobs</LI>
-<LI>rank histograms</LI>
-<LI>two (or more) experiment comparisons</LI>
-<LI>native netcdf support in matlab<br>
-Does not depend on CSIRO and netcdf_toolbox; now uses snctools</LI>
-<LI>matlab support for wrf</LI>
+
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/link_obs.m">link_obs.m</a><br />
+ allows one to view multiple observation attributes simultaneously and dynamically
+ select subsets of observations in one view and have those same obs highlighted
+ in the other views. Commonly called 'data brushing'.</LI>
+
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/threed_sphere/obs_diag.html">obs_diag</a>
+ has undergone extensive revision. User-defined levels for all coordinate (height/pressure/etc), arbitrary
+ number of regions, the inclusion of separate copies for all DART QC values, can
+ creates rank histograms from the <em class=file>obs_seq.final</em> files, if possible, and more.</LI>
+
+<LI>Comparing two (or more) experiments<br />
+ <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/two_experiments_profile.m">two_experiments_profile.m</a> and
+ <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/two_experiments_evolution.m">two_experiments_evolution.m</a>
+ compare <strong>multiple</strong> (not just two) <em class=file>obs_diag_output.nc</em>
+ files on the same graphic to allow for easy examination of experiment attributes
+ (rmse, biase, etc.). Some new utilities for subsetting observation sequence files in order to
+ make fair comparisons are described below.</LI>
+
+<LI><a href="http://www.image.ucar.edu/DAReS/DART/DART_Documentation.php#configure_matlab">Simpler netCDF support in Matlab.</a><br />
+ The DART Matlab routines no longer depend on 4 third-party toolboxes, we are down to just
+ <a href="http://mexcdf.sourceforge.net/downloads/">mexnc</a> and
+ <a href="http://mexcdf.sourceforge.net/downloads/">snctools</a>. Soon, we may just use snctools!</LI>
+
+<LI>Matlab support for CAM.<br />
+ CAM is now fully supported for all the Matlab interfaces that are used in the demos -
+ this includes the state-space tools in <em class=file>DART/matlab</em> that allow for
+ determining correlations among state variables, among other things.
+ </LI>
+
+<LI>Matlab support for WRF.<br />
+ WRF is now fully supported for all the Matlab interfaces that are used in the demos -
+ this predominanty includes the state-space tools in <em class=file>DART/matlab</em>
+ like <em class=program>plot_total_err</em>.
+ The <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/models/wrf/matlab/map_wrf.m">map_wrf.m</a> function can finally plot WRF fields now that the required metadata is part of the
+ <em class=file>Posterior_Diag.nc</em>,
+ <em class=file>Prior_Diag.nc</em>, and (not required)
+ <em class=file>True_State.nc</em> files. It's a small step to augment this routine to make
+ publication-quality figures of WRF fields.
+ </LI>
+
<LI>regression tests for wrf</LI>
-<LI>other new model support</LI>
-<LI>better web pages</LI>
-<LI>plot wind vectors from netcdf obs files</LI>
-<LI>plot correlations</LI>
-<LI>top level index page in distribution</LI>
-<LI>optional detailed execution trace messages from filter</LI>
-<LI>input.nml contents written out to diag netCDF files</LI>
-<LI>better error checking in obs_sequence creation to avoid out-of-time-order
- observations being inserted by incorrect programs</LI>
-<LI>better error checking in the open_file() routine</LI>
-<LI>individual html pages have links back to the index page, have the
-namelists moved up to be the first thing in the page after the
-Overview, and other minor formatting improvements</LI>
+
+<LI>other new model support<br />
+ The <em class=file>simple_advection</em> and <em class=file>MITgcm_ocean</em> are fully
+ supported in the Matlab diagnostics.
+</LI>
+
+<LI>Optional detailed execution trace messages from
+ <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/filter/filter.html">filter</a> by setting
+ the namelist variable <em class=code>trace_execution</em>.</LI>
+
+<LI><em class=file>input.nml</em> contents preserved in <em class=file>True_State.nc</em>,
+ <em class=file>Prior_Diag.nc</em>, and <em class=file>Posterior_Diag.nc</em> as
+ variable <em class=code>inputnml</em>.</LI>
+
+<LI>Better error checking in obs_sequence creation to avoid out-of-time-order
+ observations being inserted by incorrect programs.</LI>
+
+<LI>Better error checking in the <em class=program>utilities_mod</em>
+ <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/utilities/utilities_mod.html#open_file">open_file</a>() routine.</LI>
+
+<LI>In the DART code tree, individual html pages have links back to the index page,
+ the namelists are moved up to be more prominent, and have other minor
+ formatting improvements.</LI>
+
+<LI>The following Matlab observation-space diagnostic routines have been <strong>removed</strong>:
+ <table width = 100% cellpadding=2>
+ <tr><td valign=top>fit_ens_mean_time.m </td>
+ <td>plotted the temporal evolution of the ensemble mean of some quantity.</td></tr>
+ <tr><td valign=top>fit_ens_spread_time.m </td>
+ <td>plotted the temporal evolution of the ensemble spread of some quantity.</td></tr>
+ <tr><td valign=top>fit_mean_spread_time.m </td>
+ <td>plotted the temporal evolution of the mean and spread of some quantity.</td></tr>
+ <tr><td valign=top>obs_num_time.m </td>
+ <td>plotted the temporal evolution of the observation density. </td></tr>
+ <tr><td valign=top>fit_ens_mean_vertical.m</td>
+ <td>plotted the vertical profile of the ensemble mean of some quantity.</td></tr>
+ <tr><td valign=top>fit_ens_bias_vertical.m</td>
+ <td>plotted the vertical profile of the bias of the ensemble mean of some quantity.</td></tr>
+ <tr><td valign=top>obs_num_vertical.m </td>
+ <td>plotted the vertical profile of the observation density.</td></tr>
+ </table>
+</LI>
+
+<LI>The following Matlab observation-space diagnostic routines have been <strong>added</strong>:
+ <table width = 100% cellpadding=2>
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_profile.m">plot_profile.m</a></td>
+ <td>plots the vertical profile of any quantity for any copy with an overlay of
+ the observation density and number of observations assimilated.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_rmse_xxx_profile.m">plot_rmse_xxx_profile.m</a></td>
+ <td>plots the vertical profile of the rmse and any quantity for any copy with an
+ overlay of the observation density and number of observations assimilated.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_bias_xxx_profile.m">plot_bias_xxx_profile.m</a></td>
+ <td>plots the vertical profile of the bias and any quantity for any copy with an
+ overlay of the observation density and number of observations assimilated.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/two_experiments_profile.m">two_experiments_profile.m</a></td>
+ <td>plots the vertical profile of any quantity for any copy for multiple experiments
+ with an overlay of the observation density and number of observations assimilated
+ in each experiment.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_evolution.m">plot_evolution.m</a></td>
+ <td>plots the temporal evolution of any quantity for any copy with an overlay of
+ the observation density and number of observations assimilated.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_rmse_xxx_evolution.m">plot_rmse_xxx_evolution.m</a></td>
+ <td>plots the temporal evolution of the rmse and any quantity for any copy with an
+ overlay of the observation density and number of observations assimilated.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/two_experiments_evolution.m">two_experiments_evolution.m</a></td>
+ <td>plots the temporal evolution for any quantity for any copy for multiple
+ experiements with an overlay of the observation density and number of
+ observations assimilated in each experiment.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/read_obs_netcdf.m">read_obs_netcdf.m</a></td>
+ <td>reads a netCDF format observation sequence file. Simply need a single copy
+ and a single qc - no actual observation required. </td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_obs_netcdf.m">plot_obs_netcdf.m</a></td>
+ <td>reads and plots the locations and values of any copy of the observations in
+ a DART netCDF format observation sequence file.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_obs_netcdf_diffs.m">plot_obs_netcdf_diffs.m</a></td>
+ <td>reads and plots the locations and the difference of any two copies of the
+ observations in a DART netCDF format observation sequence file.</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_wind_vectors.m">plot_wind_vectors.m</a></td>
+ <td>reads and plots the wind vectors of the observations in a DART netCDF format
+ observation sequence file (created by
+ <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_seq_to_netcdf.html">obs_seq_to_netcdf.f90</a>)</td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/link_obs.m">link_obs.m</a></td>
+ <td>data brushing tool. Explores many facets of the observations simultaneously. </td></tr>
+
+ <tr><td valign=top><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_rank_histogram.m">plot_rank_histogram.m</a></td>
+ <td>If the ensemble members were preserved in the <em class=file>obs_seq.final</em>
+ file, <em class=program>obs_diag</em> will create rank histogram information
+ and store it in the <em class=file>obs_diag_output.nc</em> file.
+ <em class=program>plot_rank_histogram.m</em> will plot it.
+ There are instructions on how to view the results with <em class=program>ncview</em>
+ or <a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/diagnostics/matlab/plot_rank_histogram.m">plot_rank_histogram.m</a>
+ on the
+ <a href="http://www.image.ucar.edu/DAReS/DART/DART_Documentation.php#obs_diagnostics">DART Observation-space Diagnostics</a>
+ page.</td></tr>
+ </table>
+</LI>
</UL>
+
<!--==================================================================-->
<A NAME="NewUtilities"></A>
@@ -664,23 +811,42 @@
<H2>New Utilities</H2>
<UL>
-<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_seq_to_netcdf.html">convert obs_seq files to netCDF</a><br>
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_seq_to_netcdf.html"
+ >obs_seq_to_netcdf</a><br />
+ Almost any DART observation sequences may be converted to a netCDF format file. I still haven't figured out how to succinctly store
+ some of the radar observation metadata, but the observation values, locations, QC values etc. will be converted. This allows for variety
+ of new diagnostics.
</LI>
-<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_seq_coverage.html">observation coverage</a><br>
+
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_seq_coverage.html"
+ >obs_seq_coverage</a><br />
+ is a step towards determining what locations and quantities are repeatedly observed during a specific time interval. This
+ may be used to determine a network of observations that will be used to verify forecasts.
</LI>
-<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_selection.html">observation selection</a><br>
+
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_selection.html"
+ >obs_selection</a><br />
+ is an optional companion routine to <em class=program>obs_seq_coverage</em>. This thins the observation sequence files to contain
+ just the desired set of observations to use in the forecast step. There's no point evaluating all the observations that
+ will not be used in the verification ...
</LI>
-<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_seq_verify.html">observation verification</a><br>
+
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_seq_verify.html"
+ >obs_seq_verify</a><br />
+ is a companion routine to <em class=program>obs_seq_coverage</em>. This creates a netCDF file with variables that should
+ make the calculation of skill scores, etc. <em>easy</em>. Variables like:
+ <tt>METAR_U_10_METER_WIND(analysisT, stations, levels, copy, nmembers, forecast_lead)</tt>
</LI>
-<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_common_subset.html">
-select common observation subsets</a><br>
+
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/obs_sequence/obs_common_subset.html"
+ >select common observation subsets</a><br>
A tool that operates on two (will be extended to more) <em class=file>obs_seq.final</em>
files which were output from two different runs of filter. Assumes the same
<em class=file>obs_seq.out</em> input file was used in both cases. Outputs two new
<em class=file>obs_seq.final.new</em> files containing only the observations which were
-assimilated in both experiments. It makes a comparision with the diagnostic tools easier
-to interpret.
+assimilated in both experiments. It allows for a fair comparision with the diagnostic tools.
</LI>
+
<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/utilities/restart_file_tool.html">restart file tool</a><br>
Generic tool that works on any DART restart file. It is compiled with
the corresponding model_mod which tells it how large the state vector is.
@@ -718,7 +884,8 @@
first job step can start from a restart file as all subsequent job steps do and
allows the use of a single <em class=file>input.nml</em> file.
</LI>
-<LI>replace WRF fields tool<br>
+<LI><a href="https://proxy.subversion.ucar.edu/DAReS/DART/trunk/models/wrf/WRF_DART_utilities/replace_wrf_fields.html"
+>replace WRF fields tool</a><br>
WRF-specific tool that moves netCDF variables from one
file to another. Field names to be moved can be specified
directly in the namelist or can be listed in a separate file.</LI>
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