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Commit 17461691 authored by Pierre Cazenave's avatar Pierre Cazenave
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doc/doxysearch.php 0 → 100644
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<?php
/******************************************************************************
*
* $Id:$
*
* Copyright (C) 1997-2003 by Dimitri van Heesch.
*
* Permission to use, copy, modify, and distribute this software and its
* documentation under the terms of the GNU General Public License is hereby
* granted. No representations are made about the suitability of this software
* for any purpose. It is provided "as is" without express or implied warranty.
* See the GNU General Public License for more details.
*
*/
function readInt($file)
{
$b1 = ord(fgetc($file)); $b2 = ord(fgetc($file));
$b3 = ord(fgetc($file)); $b4 = ord(fgetc($file));
return ($b1<<24)|($b2<<16)|($b3<<8)|$b4;
}
function readString($file)
{
$result="";
while (ord($c=fgetc($file))) $result.=$c;
return $result;
}
function readHeader($file)
{
$header =fgetc($file); $header.=fgetc($file);
$header.=fgetc($file); $header.=fgetc($file);
return $header;
}
function computeIndex($word)
{
if (strlen($word)<2) return -1;
// high char of the index
$hi = ord($word{0});
if ($hi==0) return -1;
// low char of the index
$lo = ord($word{1});
if ($lo==0) return -1;
// return index
return $hi*256+$lo;
}
function search($file,$word,&$statsList)
{
$index = computeIndex($word);
if ($index!=-1) // found a valid index
{
fseek($file,$index*4+4); // 4 bytes per entry, skip header
$index = readInt($file);
if ($index) // found words matching first two characters
{
$start=sizeof($statsList);
$count=$start;
fseek($file,$index);
$w = readString($file);
while ($w)
{
$statIdx = readInt($file);
if ($word==substr($w,0,strlen($word)))
{ // found word that matches (as substring)
$statsList[$count++]=array(
"word"=>$word,
"match"=>$w,
"index"=>$statIdx,
"full"=>strlen($w)==strlen($word),
"docs"=>array()
);
}
$w = readString($file);
}
$totalFreq=0;
for ($count=$start;$count<sizeof($statsList);$count++)
{
$statInfo = &$statsList[$count];
fseek($file,$statInfo["index"]);
$numDocs = readInt($file);
$docInfo = array();
// read docs info + occurrence frequency of the word
for ($i=0;$i<$numDocs;$i++)
{
$idx=readInt($file);
$freq=readInt($file);
$docInfo[$i]=array("idx"=>$idx,"freq"=>$freq,"rank"=>0.0);
$totalFreq+=$freq;
if ($statInfo["full"]) $totalfreq+=$freq;
}
// read name an url info for the doc
for ($i=0;$i<$numDocs;$i++)
{
fseek($file,$docInfo[$i]["idx"]);
$docInfo[$i]["name"]=readString($file);
$docInfo[$i]["url"]=readString($file);
}
$statInfo["docs"]=$docInfo;
}
for ($count=$start;$count<sizeof($statsList);$count++)
{
$statInfo = &$statsList[$count];
for ($i=0;$i<sizeof($statInfo["docs"]);$i++)
{
$docInfo = &$statInfo["docs"];
// compute frequency rank of the word in each doc
$statInfo["docs"][$i]["rank"]=
(float)$docInfo[$i]["freq"]/$totalFreq;
}
}
}
}
return $statsList;
}
function combine_results($results,&$docs)
{
foreach ($results as $wordInfo)
{
$docsList = &$wordInfo["docs"];
foreach ($docsList as $di)
{
$key=$di["url"];
$rank=$di["rank"];
if (in_array($key, array_keys($docs)))
{
$docs[$key]["rank"]+=$rank;
$docs[$key]["rank"]*=2; // multiple matches increases rank
}
else
{
$docs[$key] = array("url"=>$key,
"name"=>$di["name"],
"rank"=>$rank
);
}
$docs[$key]["words"][] = array(
"word"=>$wordInfo["word"],
"match"=>$wordInfo["match"],
"freq"=>$di["freq"]
);
}
}
return $docs;
}
function normalize_ranking(&$docs)
{
$maxRank = 0.0000001;
// compute maximal rank
foreach ($docs as $doc)
{
if ($doc["rank"]>$maxRank)
{
$maxRank=$doc["rank"];
}
}
reset($docs);
// normalize rankings
while (list ($key, $val) = each ($docs))
{
$docs[$key]["rank"]*=100/$maxRank;
}
}
function filter_results($docs,&$requiredWords,&$forbiddenWords)
{
$filteredDocs=array();
while (list ($key, $val) = each ($docs))
{
$words = &$docs[$key]["words"];
$copy=1; // copy entry by default
if (sizeof($requiredWords)>0)
{
foreach ($requiredWords as $reqWord)
{
$found=0;
foreach ($words as $wordInfo)
{
$found = $wordInfo["word"]==$reqWord;
if ($found) break;
}
if (!$found)
{
$copy=0; // document contains none of the required words
break;
}
}
}
if (sizeof($forbiddenWords)>0)
{
foreach ($words as $wordInfo)
{
if (in_array($wordInfo["word"],$forbiddenWords))
{
$copy=0; // document contains a forbidden word
break;
}
}
}
if ($copy) $filteredDocs[$key]=$docs[$key];
}
return $filteredDocs;
}
function compare_rank($a,$b)
{
return ($a["rank"]>$b["rank"]) ? -1 : 1;
}
function sort_results($docs,&$sorted)
{
$sorted = $docs;
usort($sorted,"compare_rank");
return $sorted;
}
function report_results(&$docs)
{
echo "<table cellspacing=\"2\">\n";
echo " <tr>\n";
echo " <td colspan=\"2\"><h2>Search Results</h2></td>\n";
echo " </tr>\n";
$numDocs = sizeof($docs);
if ($numDocs==0)
{
echo " <tr>\n";
echo " <td colspan=\"2\">".matches_text(0)."</td>\n";
echo " </tr>\n";
}
else
{
echo " <tr>\n";
echo " <td colspan=\"2\">".matches_text($numDocs);
echo "\n";
echo " </td>\n";
echo " </tr>\n";
$num=1;
foreach ($docs as $doc)
{
echo " <tr>\n";
echo " <td align=\"right\">$num.</td>";
echo "<td><a class=\"el\" href=\"".$doc["url"]."\">".$doc["name"]."</a></td>\n";
echo " <tr>\n";
echo " <td></td><td class=\"tiny\">Matches: ";
foreach ($doc["words"] as $wordInfo)
{
$word = $wordInfo["word"];
$matchRight = substr($wordInfo["match"],strlen($word));
echo "<b>$word</b>$matchRight(".$wordInfo["freq"].") ";
}
echo " </td>\n";
echo " </tr>\n";
$num++;
}
}
echo "</table>\n";
}
function matches_text($num)
{
if ($num==0)
{
return 'Sorry, no documents matching your query.';
}
else if ($num==1)
{
return 'Found 1 document matching your query.';
}
else // $num>1
{
return 'Found '.$num.' documents matching your query. Showing best matches first.';
}
}
function main($idxfile)
{
if(strcmp('4.1.0', phpversion()) > 0)
{
die("Error: PHP version 4.1.0 or above required!");
}
if (!($file=fopen($idxfile,"rb")))
{
die("Error: Search index file could NOT be opened!");
}
if (readHeader($file)!="DOXS")
{
die("Error: Header of index file is invalid!");
}
$query="";
if (array_key_exists("query", $_GET))
{
$query=$_GET["query"];
}
$results = array();
$requiredWords = array();
$forbiddenWords = array();
$foundWords = array();
$word=strtolower(strtok($query," "));
while ($word) // for each word in the search query
{
if (($word{0}=='+')) { $word=substr($word,1); $requiredWords[]=$word; }
if (($word{0}=='-')) { $word=substr($word,1); $forbiddenWords[]=$word; }
if (!in_array($word,$foundWords))
{
$foundWords[]=$word;
search($file,$word,$results);
}
$word=strtolower(strtok(" "));
}
$docs = array();
combine_results($results,$docs);
// filter out documents with forbidden word or that do not contain
// required words
$filteredDocs = filter_results($docs,$requiredWords,$forbiddenWords);
// normalize rankings so they are in the range [0-100]
normalize_ranking($filteredDocs);
// sort the results based on rank
$sorted = array();
sort_results($filteredDocs,$sorted);
// report results to the user
report_results($sorted);
fclose($file);
}
?>
doc/fvcom_postproc/README.html 0 → 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/REC-html40/loose.dtd">
<html>
<head>
<title>Description of README</title>
<meta name="keywords" content="README">
<meta name="description" content="README for FVCOM_postproc">
<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_postproc</a> &gt; README.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_postproc&nbsp;<img alt=">" border="0" src="../right.png"></a></td></tr></table>-->
<h1>README
</h1>
<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="box"><strong>README for FVCOM_postproc</strong></div>
<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="box"><strong>This is a script file. </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"> README for FVCOM_postproc
This directory contains matlab scripts for postrpocessing FVCOM output
Author(s):
Revision history
==============================================================================</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 <span class="comment">% README for FVCOM_postproc</span>
0002 <span class="comment">%</span>
0003 <span class="comment">% This directory contains matlab scripts for postrpocessing FVCOM output</span>
0004 <span class="comment">%</span>
0005 <span class="comment">% Author(s):</span>
0006 <span class="comment">%</span>
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>
</body>
</html>
\ No newline at end of file
doc/fvcom_postproc/index.html 0 → 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/REC-html40/loose.dtd">
<html>
<head>
<title>Index for Directory fvcom_postproc</title>
<meta name="keywords" content="fvcom_postproc">
<meta name="description" content="Index for Directory fvcom_postproc">
<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>
<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_postproc&nbsp;<img alt=">" border="0" src="../right.png"></a></td></tr></table>
<h1>Index for fvcom_postproc</h1>
<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>
<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>
</body>
</html>
\ No newline at end of file
doc/fvcom_prepro/README.html 0 → 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/REC-html40/loose.dtd">
<html>
<head>
<title>Description of README</title>
<meta name="keywords" content="README">
<meta name="description" content="README for the FVCOM preprocessing toolbox">
<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; README.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>README
</h1>
<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="box"><strong>README for the FVCOM preprocessing toolbox</strong></div>
<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="box"><strong>This is a script file. </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"> 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,
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.
Author(s):
Geoff Cowles (University of Massachusetts Dartmouth)
Revision history
==============================================================================</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 <span class="comment">% README for the FVCOM preprocessing toolbox</span>
0002 <span class="comment">%</span>
0003 <span class="comment">% This directory contains matlab scripts for preprocessing input files</span>
0004 <span class="comment">% for FVCOM 3.x. These include files which read a mesh in from SMS,</span>
0005 <span class="comment">% files that allow you to select open boundary and river nodes and generate</span>
0006 <span class="comment">% river, tidal, and wind forcing. Template files for generating wind forcing</span>
0007 <span class="comment">% are also included.</span>
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>
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>
</body>
</html>
\ No newline at end of file
doc/fvcom_prepro/add_coriolis.html 0 → 100644
View file @ 17461691
<!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_coriolis</title>
<meta name="keywords" content="add_coriolis">
<meta name="description" content="Generate latitude used for FVCOM Coriolis file">
<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_coriolis.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_coriolis
</h1>
<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="box"><strong>Generate latitude used for FVCOM Coriolis file</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_coriolis(Mobj,cortype,fval) </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"> Generate latitude used for FVCOM Coriolis file
[Mobj] = function add_coriolis(Mobj,varargin)
DESCRIPTION:
add Coriolis parameter to Matlab mesh object
INPUT
Mobj = matlab mesh object
[optional] cortype = coriolis type
'uselatitude' (default): use Mobj.lat
'constant'
[optional] fval = constant latitude for constant Coriolis
OUTPUT:
Mobj = matlab structure containing Mesh data + fvcom Coriolis
EXAMPLE USAGE
Mobj = add_coriolis(Mobj,'constant',41.0)
Mobj = add_coriolis(Mobj)
Author(s):
Geoff Cowles (University of Massachusetts Dartmouth)
Revision history
==============================================================================</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)">
<li><a href="example.html" class="code" title="">example</a> example demonstrating reading in a 2DM file and constructing a model</li></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_coriolis(Mobj,cortype,fval) </a>
0002
0003 <span class="comment">% Generate latitude used for FVCOM Coriolis file</span>
0004 <span class="comment">%</span>
0005 <span class="comment">% [Mobj] = function add_coriolis(Mobj,varargin)</span>
0006 <span class="comment">%</span>
0007 <span class="comment">% DESCRIPTION:</span>
0008 <span class="comment">% add Coriolis parameter to Matlab mesh object</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">% [optional] cortype = coriolis type</span>
0013 <span class="comment">% 'uselatitude' (default): use Mobj.lat</span>
0014 <span class="comment">% 'constant'</span>
0015 <span class="comment">% [optional] fval = constant latitude for constant Coriolis</span>
0016 <span class="comment">%</span>
0017 <span class="comment">% OUTPUT:</span>
0018 <span class="comment">% Mobj = matlab structure containing Mesh data + fvcom Coriolis</span>
0019 <span class="comment">%</span>
0020 <span class="comment">% EXAMPLE USAGE</span>
0021 <span class="comment">% Mobj = add_coriolis(Mobj,'constant',41.0)</span>
0022 <span class="comment">% Mobj = add_coriolis(Mobj)</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">%</span>
0027 <span class="comment">% Revision history</span>