Update the documentation to include all the new utilities I created

doc/fvcom_postproc/README.html

@@ -59,6 +59,6 @@ This function is called by:
 0007 <span class="comment">% Revision history</span>
 0008 <span class="comment">%</span>
 0009 <span class="comment">%==============================================================================</span></pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_postproc/index.html

@@ -19,11 +19,13 @@
 
 <h2>Matlab files in this directory:</h2>
 <table>
-<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="README.html">README</a></td><td>README for FVCOM_postproc </td></tr></table>
+<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="README.html">README</a></td><td>README for FVCOM_postproc </td></tr><tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp;<a href="example_surface_plot.html">example_surface_plot</a></td><td>Sample script to extract and generate m_map contours of tracer variables </td></tr></table>
 
 
+<h2>Subsequent directories:</h2>
+<ul style="list-style-image:url(../matlabicon.gif)">
+<li>mat</li><li>plots</li><li>surface_plots</li><li>timeseries</li><li>transect_plots</li></ul>
 
-
-<hr><address>Generated on Wed 02-Nov-2011 21:57:59 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:29 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/README.html

@@ -29,17 +29,19 @@
 <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
 <div class="fragment"><pre class="comment"> README for the FVCOM preprocessing toolbox
 
- This directory contains matlab scripts for preprocessing input files 
- for FVCOM 3.x.   These include files which read a mesh in from SMS, 
+ This directory contains matlab scripts for preprocessing input files
+ for FVCOM 3.x.   These include files which read a mesh in from SMS,
  files that allow you to select open boundary and river nodes and generate
  river, tidal, and wind forcing.  Template files for generating wind forcing
- are also included.  
+ are also included.
 
- Author(s):  
+ Author(s):
     Geoff Cowles (University of Massachusetts Dartmouth)
+    Ricardo Torres (Plymouth Marine Laboratory)
+    Pierre Cazenave (Plymouth Marine Laboratory)
 
  Revision history
-   
+
 ==============================================================================</pre></div>
 
 <!-- crossreference -->
@@ -65,10 +67,12 @@ This function is called by:
 0008 <span class="comment">%</span>
 0009 <span class="comment">% Author(s):</span>
 0010 <span class="comment">%    Geoff Cowles (University of Massachusetts Dartmouth)</span>
-0011 <span class="comment">%</span>
-0012 <span class="comment">% Revision history</span>
+0011 <span class="comment">%    Ricardo Torres (Plymouth Marine Laboratory)</span>
+0012 <span class="comment">%    Pierre Cazenave (Plymouth Marine Laboratory)</span>
 0013 <span class="comment">%</span>
-0014 <span class="comment">%==============================================================================</span></pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+0014 <span class="comment">% Revision history</span>
+0015 <span class="comment">%</span>
+0016 <span class="comment">%==============================================================================</span></pre></div>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/add_coriolis.html

@@ -144,6 +144,6 @@ This function is called by:
 0074 
 0075 
 0076</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/add_obc_nodes_graphic.html

@@ -24,7 +24,7 @@
 <div class="box"><strong>Add a set of obc nodes comprising a single obc boundary to Mesh structure</strong></div>
 
 <h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
-<div class="box"><strong>function [Mobj]  = add_obc_nodes_screen(Mobj,ObcName,ObcType) </strong></div>
+<div class="box"><strong>function [Mobj]  = add_obc_nodes_graphic(Mobj,ObcName,ObcType) </strong></div>
 
 <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
 <div class="fragment"><pre class="comment"> Add a set of obc nodes comprising a single obc boundary to Mesh structure  
@@ -70,7 +70,7 @@ This function is called by:
 
 
 <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
-<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function [Mobj]  = add_obc_nodes_screen(Mobj,ObcName,ObcType)</a>
+<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function [Mobj]  = add_obc_nodes_graphic(Mobj,ObcName,ObcType)</a>
 0002 
 0003 <span class="comment">% Add a set of obc nodes comprising a single obc boundary to Mesh structure</span>
 0004 <span class="comment">% By clicking on points on the screen</span>
@@ -160,6 +160,6 @@ This function is called by:
 0088   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
 0089 <span class="keyword">end</span>;
 0090</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/add_river_nodes_graphic.html

@@ -161,6 +161,6 @@ This function is called by:
 0091   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
 0092 <span class="keyword">end</span>;
 0093</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/add_river_nodes_list.html

@@ -149,6 +149,6 @@ This function is called by:
 0078   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
 0079 <span class="keyword">end</span>;
 0080</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/add_sigma_forDT.html

@@ -91,6 +91,6 @@ This function is called by:
 0045 nc = close(nc);
 0046 
 0047</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/add_sponge_nodes.html

@@ -121,41 +121,42 @@ This function is called by:
 0049 figure
 0050 patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
 0051         <span class="string">'Cdata'</span>,Mobj.h,<span class="string">'edgecolor'</span>,<span class="string">'k'</span>,<span class="string">'facecolor'</span>,<span class="string">'interp'</span>);
-0052 hold on;
-0053 
-0054 <span class="comment">% use ginput2 (which allows zooming and plots points as they are clicked) to let</span>
-0055 <span class="comment">% user select the boundary points</span>
-0056 [xselect] = ginput2(true,<span class="string">'k+'</span>)
-0057 
+0052 axis(<span class="string">'equal'</span>,<span class="string">'tight'</span>)
+0053 hold on;
+0054 
+0055 <span class="comment">% use ginput2 (which allows zooming and plots points as they are clicked) to let</span>
+0056 <span class="comment">% user select the boundary points</span>
+0057 [xselect] = ginput2(true,<span class="string">'k+'</span>)
 0058 
-0059 [npts,jnk] = size(xselect);
-0060 
-0061 <span class="keyword">if</span>(npts == 0)
-0062     fprintf(<span class="string">'you didn''t select any points'</span>)
-0063     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
-0064     <span class="keyword">return</span>
-0065 <span class="keyword">end</span>;
-0066 fprintf(<span class="string">'you selected %d points\n'</span>,npts)
-0067 
-0068 <span class="comment">% snap to the closest vertices</span>
-0069 <span class="keyword">for</span> i=1:npts
-0070     [ipt(i),dist] = <a href="find_nearest_pt.html" class="code" title="function [Point,Distance] = find_nearest_pt(xloc,yloc,Mobj)">find_nearest_pt</a>(xselect(i,1),xselect(i,2),Mobj);
-0071 <span class="keyword">end</span>;
-0072 
-0073 <span class="comment">% replot domain with snapped vertices</span>
-0074 plot(x(ipt),y(ipt),<span class="string">'ro'</span>);
-0075 
-0076 <span class="comment">% add to mesh object</span>
-0077 Mobj.nSponge = Mobj.nSponge + 1;
-0078 Mobj.nSpongeNodes(Mobj.nSponge) = npts;
-0079 Mobj.sponge_nodes(Mobj.nSponge,1:npts) = ipt;
-0080 Mobj.sponge_name{Mobj.nSponge} = SpongeName;
-0081 Mobj.sponge_rad(Mobj.nSponge) = SpongeRadius;
-0082 Mobj.sponge_fac(Mobj.nSponge) = SpongeCoeff;
-0083 
+0059 
+0060 npts = size(xselect,1);
+0061 
+0062 <span class="keyword">if</span>(npts == 0)
+0063     fprintf(<span class="string">'you didn''t select any points'</span>)
+0064     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0065     <span class="keyword">return</span>
+0066 <span class="keyword">end</span>;
+0067 fprintf(<span class="string">'you selected %d points\n'</span>,npts)
+0068 
+0069 <span class="comment">% snap to the closest vertices</span>
+0070 <span class="keyword">for</span> i=1:npts
+0071     [ipt(i),dist] = <a href="find_nearest_pt.html" class="code" title="function [Point,Distance] = find_nearest_pt(xloc,yloc,Mobj)">find_nearest_pt</a>(xselect(i,1),xselect(i,2),Mobj);
+0072 <span class="keyword">end</span>;
+0073 
+0074 <span class="comment">% replot domain with snapped vertices</span>
+0075 plot(x(ipt),y(ipt),<span class="string">'ro'</span>);
+0076 
+0077 <span class="comment">% add to mesh object</span>
+0078 Mobj.nSponge = Mobj.nSponge + 1;
+0079 Mobj.nSpongeNodes(Mobj.nSponge) = npts;
+0080 Mobj.sponge_nodes(Mobj.nSponge,1:npts) = ipt;
+0081 Mobj.sponge_name{Mobj.nSponge} = SpongeName;
+0082 Mobj.sponge_rad(Mobj.nSponge) = SpongeRadius;
+0083 Mobj.sponge_fac(Mobj.nSponge) = SpongeCoeff;
 0084 
-0085 fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
-0086</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+0085 
+0086 fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0087</pre></div>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/add_sponge_nodes_list.html

+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+                "http://www.w3.org/TR/REC-html40/loose.dtd">
+<html>
+<head>
+  <title>Description of add_sponge_nodes_list</title>
+  <meta name="keywords" content="add_sponge_nodes_list">
+  <meta name="description" content="Add a set of sponge nodes comprising a single sponge layer to Mesh structure">
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+  <meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
+  <meta name="robots" content="index, follow">
+  <link type="text/css" rel="stylesheet" href="../m2html.css">
+</head>
+<body>
+<a name="_top"></a>
+<div><a href="../index.html">Home</a> &gt;  <a href="index.html">fvcom_prepro</a> &gt; add_sponge_nodes_list.m</div>
+
+<!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png">&nbsp;Master index</a></td>
+<td align="right"><a href="index.html">Index for fvcom_prepro&nbsp;<img alt=">" border="0" src="../right.png"></a></td></tr></table>-->
+
+<h1>add_sponge_nodes_list
+</h1>
+
+<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>Add a set of sponge nodes comprising a single sponge layer to Mesh structure</strong></div>
+
+<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>function [Mobj]  = add_sponge_nodes_list(Mobj,SpongeList,SpongeName,SpongeRadius,SpongeCoeff,plotFig) </strong></div>
+
+<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre class="comment"> Add a set of sponge nodes comprising a single sponge layer to Mesh structure  
+
+ [Mobj] = add_sponge_nodes(Mobj)
+
+ DESCRIPTION:
+    Select using ginput the set of nodes comprising a sponge layer
+
+ INPUT
+    Mobj = Matlab mesh object
+    SpongeList = List of nodes to which to create a Sponge Layer
+    SpongeName = Name of the Sponge Layer
+    SpongeRadius = Radius of influence of the Sponge Layer 
+    SpongeCoeff  = Sponge damping coefficient
+    plotFig = [optional] show a figure of the mesh (1 = yes)
+
+ OUTPUT:
+    Mobj = Matlab mesh object with an additional sponge nodelist
+
+ EXAMPLE USAGE
+    Mobj = add_sponge_nodes(Mobj,'Sponge1',10000,.0001)
+
+ Author(s):  
+    Geoff Cowles (University of Massachusetts Dartmouth)
+    Pierre Cazenave (Plymouth Marine Laboratory)
+
+ Revision history
+    Modifed from add_sponge_nodes to read in nodes from a supplied list.
+    2012-11-26 Add ability to turn off the figures.
+   
+==============================================================================</pre></div>
+
+<!-- crossreference -->
+<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+This function calls:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+This function is called by:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+<!-- crossreference -->
+
+
+
+<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function [Mobj]  = add_sponge_nodes_list(Mobj,SpongeList,SpongeName,SpongeRadius,SpongeCoeff,plotFig)</a>
+0002 
+0003 <span class="comment">% Add a set of sponge nodes comprising a single sponge layer to Mesh structure</span>
+0004 <span class="comment">%</span>
+0005 <span class="comment">% [Mobj] = add_sponge_nodes(Mobj)</span>
+0006 <span class="comment">%</span>
+0007 <span class="comment">% DESCRIPTION:</span>
+0008 <span class="comment">%    Select using ginput the set of nodes comprising a sponge layer</span>
+0009 <span class="comment">%</span>
+0010 <span class="comment">% INPUT</span>
+0011 <span class="comment">%    Mobj = Matlab mesh object</span>
+0012 <span class="comment">%    SpongeList = List of nodes to which to create a Sponge Layer</span>
+0013 <span class="comment">%    SpongeName = Name of the Sponge Layer</span>
+0014 <span class="comment">%    SpongeRadius = Radius of influence of the Sponge Layer</span>
+0015 <span class="comment">%    SpongeCoeff  = Sponge damping coefficient</span>
+0016 <span class="comment">%    plotFig = [optional] show a figure of the mesh (1 = yes)</span>
+0017 <span class="comment">%</span>
+0018 <span class="comment">% OUTPUT:</span>
+0019 <span class="comment">%    Mobj = Matlab mesh object with an additional sponge nodelist</span>
+0020 <span class="comment">%</span>
+0021 <span class="comment">% EXAMPLE USAGE</span>
+0022 <span class="comment">%    Mobj = add_sponge_nodes(Mobj,'Sponge1',10000,.0001)</span>
+0023 <span class="comment">%</span>
+0024 <span class="comment">% Author(s):</span>
+0025 <span class="comment">%    Geoff Cowles (University of Massachusetts Dartmouth)</span>
+0026 <span class="comment">%    Pierre Cazenave (Plymouth Marine Laboratory)</span>
+0027 <span class="comment">%</span>
+0028 <span class="comment">% Revision history</span>
+0029 <span class="comment">%    Modifed from add_sponge_nodes to read in nodes from a supplied list.</span>
+0030 <span class="comment">%    2012-11-26 Add ability to turn off the figures.</span>
+0031 <span class="comment">%</span>
+0032 <span class="comment">%==============================================================================</span>
+0033 subname = <span class="string">'add_sponge_nodes'</span>;
+0034 
+0035 <span class="keyword">global</span> ftbverbose
+0036 <span class="keyword">if</span>(ftbverbose)
+0037   fprintf(<span class="string">'\n'</span>)
+0038   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
+0039 <span class="keyword">end</span>
+0040 
+0041 <span class="comment">% Do we want a figure showing how we're getting along?</span>
+0042 <span class="keyword">if</span> nargin == 5
+0043     plotFig = 0;
+0044 <span class="keyword">end</span>
+0045 
+0046 <span class="comment">%------------------------------------------------------------------------------</span>
+0047 <span class="comment">% Plot the mesh</span>
+0048 <span class="comment">%------------------------------------------------------------------------------</span>
+0049 <span class="keyword">if</span> plotFig == 1
+0050     <span class="keyword">if</span>(lower(Mobj.nativeCoords(1:3)) == <span class="string">'car'</span>)
+0051         x = Mobj.x;
+0052         y = Mobj.y;
+0053     <span class="keyword">else</span>
+0054         x = Mobj.lon;
+0055         y = Mobj.lat;
+0056     <span class="keyword">end</span>
+0057 
+0058     figure
+0059     patch(<span class="string">'Vertices'</span>,[x,y],<span class="string">'Faces'</span>,Mobj.tri,<span class="keyword">...</span>
+0060             <span class="string">'Cdata'</span>,Mobj.h,<span class="string">'edgecolor'</span>,<span class="string">'k'</span>,<span class="string">'facecolor'</span>,<span class="string">'interp'</span>);
+0061     hold on;
+0062     plot(x(SpongeList),y(SpongeList),<span class="string">'wx'</span>)
+0063     axis(<span class="string">'equal'</span>,<span class="string">'tight'</span>)
+0064 <span class="keyword">end</span>
+0065 
+0066 npts = size(SpongeList,2);
+0067 
+0068 <span class="keyword">if</span>(npts == 0)
+0069     fprintf(<span class="string">'No points in given list'</span>)
+0070     fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0071     <span class="keyword">return</span>
+0072 <span class="keyword">end</span>
+0073 <span class="keyword">if</span>(ftbverbose)
+0074     fprintf(<span class="string">'%d points provided\n'</span>,npts)
+0075 <span class="keyword">end</span>
+0076 
+0077 <span class="comment">% add to mesh object</span>
+0078 Mobj.nSponge = Mobj.nSponge + 1;
+0079 Mobj.nSpongeNodes(Mobj.nSponge) = npts;
+0080 Mobj.sponge_nodes(Mobj.nSponge,1:npts) = SpongeList;
+0081 Mobj.sponge_name{Mobj.nSponge} = SpongeName;
+0082 Mobj.sponge_rad(Mobj.nSponge) = SpongeRadius;
+0083 Mobj.sponge_fac(Mobj.nSponge) = SpongeCoeff;
+0084 
+0085 <span class="keyword">if</span>(ftbverbose)
+0086   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
+0087 <span class="keyword">end</span>
+0088 
+0089</pre></div>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+</body>
+</html>
\ No newline at end of file

doc/fvcom_prepro/add_stations_list.html

+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+                "http://www.w3.org/TR/REC-html40/loose.dtd">
+<html>
+<head>
+  <title>Description of add_stations_list</title>
+  <meta name="keywords" content="add_stations_list">
+  <meta name="description" content="Add a set of stations at which FVCOM will output time series.">
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+  <meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
+  <meta name="robots" content="index, follow">
+  <link type="text/css" rel="stylesheet" href="../m2html.css">
+</head>
+<body>
+<a name="_top"></a>
+<div><a href="../index.html">Home</a> &gt;  <a href="index.html">fvcom_prepro</a> &gt; add_stations_list.m</div>
+
+<!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png">&nbsp;Master index</a></td>
+<td align="right"><a href="index.html">Index for fvcom_prepro&nbsp;<img alt=">" border="0" src="../right.png"></a></td></tr></table>-->
+
+<h1>add_stations_list
+</h1>
+
+<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>Add a set of stations at which FVCOM will output time series.</strong></div>
+
+<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="box"><strong>function [Mobj]  = add_stations_list(Mobj,Positions,Names,Dist) </strong></div>
+
+<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre class="comment"> Add a set of stations at which FVCOM will output time series.
+
+ [Mobj] = add_stations_list(Mobj,Positions,Names,Dist)
+
+ DESCRIPTION:
+    Supply a list of positions (in the same coordinate system as the
+    native coordinates of the grid) and a cell array of names. Nearest
+    grid node to those supplied will be used in the output file.
+
+ INPUT
+    Mobj = Matlab mesh object
+    Positions = 2xn array of the XY positions of the stations
+    Names = Cell array of the names of the stations defined in Positions
+    Dist = Maximum distance from a station for a node to be included
+
+    Optionally supply positions as a 4xn array with spherical x and y and
+    cartesian x and y in columns 1, 2, 3 and 4, respectively. The
+    values in Mobj.nativecoords will be used for the distance check, so
+    ensure Dist is in those units.
+
+ OUTPUT:
+    Mobj = Matlab mesh object with an additional cell array containing id,
+    x, y, nodelist, depth and station name.
+
+ EXAMPLE USAGE
+    Mobj = add_stations_list(Mobj, [-5.54, 50.103; -3.0865, 58.441], ...
+    {'Newlyn', 'Wick'}, 0.25)
+
+ Author(s):
+    Pierre Cazenave (Plymouth Marine Laboratory)
+
+
+ Revision history
+    2012-11-30 First version.
+
+==========================================================================</pre></div>
+
+<!-- crossreference -->
+<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+This function calls:
+<ul style="list-style-image:url(../matlabicon.gif)">
+<li><a href="find_nearest_pt.html" class="code" title="function [Point,Distance] = find_nearest_pt(xloc,yloc,Mobj)">find_nearest_pt</a>	Find nearest point in Mesh structure to (x,y)</li></ul>
+This function is called by:
+<ul style="list-style-image:url(../matlabicon.gif)">
+</ul>
+<!-- crossreference -->
+
+
+
+<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function [Mobj]  = add_stations_list(Mobj,Positions,Names,Dist)</a>
+0002 
+0003 <span class="comment">% Add a set of stations at which FVCOM will output time series.</span>
+0004 <span class="comment">%</span>
+0005 <span class="comment">% [Mobj] = add_stations_list(Mobj,Positions,Names,Dist)</span>
+0006 <span class="comment">%</span>
+0007 <span class="comment">% DESCRIPTION:</span>
+0008 <span class="comment">%    Supply a list of positions (in the same coordinate system as the</span>
+0009 <span class="comment">%    native coordinates of the grid) and a cell array of names. Nearest</span>
+0010 <span class="comment">%    grid node to those supplied will be used in the output file.</span>
+0011 <span class="comment">%</span>
+0012 <span class="comment">% INPUT</span>
+0013 <span class="comment">%    Mobj = Matlab mesh object</span>
+0014 <span class="comment">%    Positions = 2xn array of the XY positions of the stations</span>
+0015 <span class="comment">%    Names = Cell array of the names of the stations defined in Positions</span>
+0016 <span class="comment">%    Dist = Maximum distance from a station for a node to be included</span>
+0017 <span class="comment">%</span>
+0018 <span class="comment">%    Optionally supply positions as a 4xn array with spherical x and y and</span>
+0019 <span class="comment">%    cartesian x and y in columns 1, 2, 3 and 4, respectively. The</span>
+0020 <span class="comment">%    values in Mobj.nativecoords will be used for the distance check, so</span>
+0021 <span class="comment">%    ensure Dist is in those units.</span>
+0022 <span class="comment">%</span>
+0023 <span class="comment">% OUTPUT:</span>
+0024 <span class="comment">%    Mobj = Matlab mesh object with an additional cell array containing id,</span>
+0025 <span class="comment">%    x, y, nodelist, depth and station name.</span>
+0026 <span class="comment">%</span>
+0027 <span class="comment">% EXAMPLE USAGE</span>
+0028 <span class="comment">%    Mobj = add_stations_list(Mobj, [-5.54, 50.103; -3.0865, 58.441], ...</span>
+0029 <span class="comment">%    {'Newlyn', 'Wick'}, 0.25)</span>
+0030 <span class="comment">%</span>
+0031 <span class="comment">% Author(s):</span>
+0032 <span class="comment">%    Pierre Cazenave (Plymouth Marine Laboratory)</span>
+0033 <span class="comment">%</span>
+0034 <span class="comment">%</span>
+0035 <span class="comment">% Revision history</span>
+0036 <span class="comment">%    2012-11-30 First version.</span>
+0037 <span class="comment">%</span>
+0038 <span class="comment">%==========================================================================</span>
+0039 subname = <span class="string">'add_stations_list'</span>;
+0040 <span class="keyword">global</span> ftbverbose
+0041 <span class="keyword">if</span>(ftbverbose)
+0042   fprintf(<span class="string">'\n'</span>)
+0043   fprintf([<span class="string">'begin : '</span> subname <span class="string">'\n'</span>])
+0044 <span class="keyword">end</span>;
+0045 
+0046 <span class="comment">%--------------------------------------------------------------------------</span>
+0047 <span class="comment">% Check the inputs</span>
+0048 <span class="comment">%--------------------------------------------------------------------------</span>
+0049 nPos = size(Positions, 1);
+0050 nNames = size(Names, 1);
+0051 <span class="keyword">if</span> nPos ~= nNames
+0052     error(<span class="string">'The number of the supplied station positions and names do not match (%i and %i respectively)'</span>, nPos, nNames)
+0053 <span class="keyword">end</span>
+0054 
+0055 <span class="comment">%--------------------------------------------------------------------------</span>
+0056 <span class="comment">% For each site in the supplied positions, find the nearest node ID</span>
+0057 <span class="comment">%--------------------------------------------------------------------------</span>
+0058 
+0059 <span class="comment">% Check for whether the input has both spherical and cartesian.</span>
+0060 <span class="keyword">if</span> size(Positions, 2) &gt; 2
+0061     <span class="comment">% Now check for which is the native coordinate system, and output the</span>
+0062     <span class="comment">% station positions in that coordinate system.</span>
+0063     <span class="keyword">if</span> strcmpi(Mobj.nativeCoords, <span class="string">'cartesian'</span>)
+0064         cols = [3, 4];
+0065     <span class="keyword">elseif</span> strcmpi(Mobj.nativeCoords, <span class="string">'spherical'</span>)
+0066         cols = [1, 2];
+0067     <span class="keyword">else</span>
+0068         error(<span class="string">'Unknown native coordinate system string: %s'</span>, Mobj.nativeCoords)
+0069     <span class="keyword">end</span>
+0070 <span class="keyword">else</span>
+0071     <span class="comment">% We have to assume the positions are in the grid's native coordinate</span>
+0072     <span class="comment">% system.</span>
+0073     cols = [1, 2];
+0074 <span class="keyword">end</span>
+0075 
+0076 inc = 1;
+0077 <span class="comment">% out = cell(nPos, 1);</span>
+0078 
+0079 <span class="keyword">for</span> s=1:nPos
+0080     [node, dist] = <a href="find_nearest_pt.html" class="code" title="function [Point,Distance] = find_nearest_pt(xloc,yloc,Mobj)">find_nearest_pt</a>(Positions(s, cols(1)), Positions(s, cols(2)), Mobj);
+0081 
+0082     <span class="keyword">if</span> dist &gt;= Dist
+0083         <span class="comment">% Skip out for this station</span>
+0084         <span class="keyword">if</span>(ftbverbose)
+0085             fprintf(<span class="string">'Skipping station %s (%g, %g). Nodal distance from station position = %f\n'</span>, Names{s}, Positions(s, 1), Positions(s, 2), dist)
+0086         <span class="keyword">end</span>
+0087         <span class="keyword">continue</span>
+0088     <span class="keyword">end</span>
+0089     out{inc} = {inc, Positions(s, cols(1)), Positions(s, cols(2)), node, Mobj.h(node), Names{s}};
+0090     inc = inc + 1;
+0091 <span class="keyword">end</span>
+0092 
+0093 Mobj.stations = out;</pre></div>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+</body>
+</html>
\ No newline at end of file

doc/fvcom_prepro/add_var_FVCOM_river.html

@@ -172,6 +172,6 @@ This function is called by:
 0098   fprintf([<span class="string">'end   : '</span> subname <span class="string">'\n'</span>])
 0099 <span class="keyword">end</span>;
 0100</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/elems2nodes.html

@@ -123,6 +123,6 @@ This function is called by:
 0057 
 0058 <span class="comment">%fprintf(['end   : ' subname '\n'])</span>
 0059</pre></div>
-<hr><address>Generated on Wed 02-Nov-2011 21:58:00 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
+<hr><address>Generated on Tue 18-Dec-2012 12:37:31 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
 </body>
 </html>
\ No newline at end of file

doc/fvcom_prepro/estimate_ts.html

@@ -24,15 +24,15 @@
 <div class="box"><strong>Estimate time step at each node</strong></div>
 
 <h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
-<div class="box"><strong>function [Mobj] = estimate_ts(Mobj) </strong></div>
+<div class="box"><strong>function [Mobj] = estimate_ts(Mobj,u,zeta) </strong></div>
 
 <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
-<div class="fragment"><pre class="comment"> Estimate time step at each node