Elimination of a potential XSS vulnerability in JAMA documentation
JAMA docs are no longer up-to-date anyway
This commit is contained in:
Mark Baker
parent
ef2de9cc5e
commit
8c688358ba
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<?php
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require_once "includes/header.php";
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require_once "includes/navbar.php";
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require_once "sections/Home.php";
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require_once "includes/footer.php";
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?>
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@ -1,65 +0,0 @@
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<?php
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/**
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* Script to create REGRESS package for download
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*
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* @author Mike Bommarito
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* @author Paul Meagher
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* @version 0.3
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* @modified Apr 2, 2006
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*
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* Note: Script requires the PEAR Archive_Tar package be installed:
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*
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* @see http://pear.php.net/package/Archive_Tar
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*/
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// name and directory of package
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$pkgName = "JAMA";
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// root of PHP/Math build directory
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$buildDir = substr(dirname(__FILE__), 0, -5 - strlen($pkgName));
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// switch to PHP/Math build directory
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chdir($buildDir);
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$tarName = "$pkgName.tar.gz";
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$tarPath = $buildDir.$pkgName."/downloads/".$tarName;
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if($_GET['op'] == "download") {
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require_once('Archive/Tar.php');
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$tar = new Archive_Tar($tarPath);
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// create $pkgName archive under $pkgName folder
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$files = glob("$pkgName/*.php");
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$files = array_merge($files, glob("$pkgName/*.TXT"));
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$files = array_merge($files, glob("$pkgName/docs/*.php"));
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$files = array_merge($files, glob("$pkgName/docs/includes/*.php"));
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$files = array_merge($files, glob("$pkgName/examples/*.php"));
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$files = array_merge($files, glob("$pkgName/tests/*.php"));
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$files = array_merge($files, glob("$pkgName/utils/*.php"));
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$tar->create($files);
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// create the download url
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$webDir = substr($_SERVER['PHP_SELF'], 0, -18);
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$urlPath = "http://".$_SERVER['HTTP_HOST'].$webDir."/downloads";
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// redirect to download url
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header("Location: $urlPath/$tarName");
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}
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include_once "includes/header.php";
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include_once "includes/navbar.php";
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?>
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<p>
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Download current version:
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</p>
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<ul>
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<li><a href='<?php echo $_SERVER['PHP_SELF']."?op=download"; ?>'><?php echo $tarName ?></a></li>
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</ul>
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<?php
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include_once "includes/footer.php";
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?>
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@ -1,166 +0,0 @@
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<?php
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include_once "includes/header.php";
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include_once "includes/navbar.php";
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?>
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<h2>Magic Square Example</h2>
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<p>
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The Jama distribution comes with a magic square example that is used to
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test and benchmark the LU, QR, SVD and symmetric Eig decompositions.
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The example outputs a multi-column table with these column headings:
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</p>
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<table border='1' cellpadding='5' cellspacing='0' align='center'>
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<tr>
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<td><b>n</b></td>
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<td>Order of magic square.</td>
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</tr>
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<tr>
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<td><b>trace</b></td>
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<td>Diagonal sum, should be the magic sum, (n^3 + n)/2.</td>
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</tr>
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<tr>
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<td><b>max_eig</b></td>
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<td>Maximum eigenvalue of (A + A')/2, should equal trace.</td>
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</tr>
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<tr>
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<td><b>rank</b></td>
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<td>Linear algebraic rank, should equal n if n is odd, be less than n if n is even.</td>
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</tr>
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<tr>
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<td><b>cond</b></td>
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<td>L_2 condition number, ratio of singular values.</td>
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</tr>
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<tr>
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<td><b>lu_res</b></td>
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<td>test of LU factorization, norm1(L*U-A(p,:))/(n*eps).</td>
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</tr>
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<tr>
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<td><b>qr_res</b></td>
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<td>test of QR factorization, norm1(Q*R-A)/(n*eps).</td>
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</tr>
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</table>
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<p>
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Running the Java-based version of the matix square example produces these results:
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</p>
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<table border='1' align='center'>
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<tr>
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<th> n </th>
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<th> trace </th>
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<th> max_eig </th>
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<th> rank </th>
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<th> cond </th>
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<th> lu_res </th>
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<th> qr_res </th>
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</tr>
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<tr>
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<td>3</td><td>15</td><td>15.000</td><td>3</td><td>4.330</td><td>0.000</td><td>11.333</td>
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</tr>
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<tr>
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<td>4</td><td>34</td><td>34.000</td><td>3</td><td> Inf</td><td>0.000</td><td>13.500</td>
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<tr>
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<td>5</td><td>65</td><td>65.000</td><td>5</td><td>5.462</td><td>0.000</td><td>14.400</td>
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</tr>
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<tr>
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<td>6</td><td>111</td><td>111.000</td><td>5</td><td> Inf</td><td>5.333</td><td>16.000</td>
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</tr>
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<tr>
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<td>7</td><td>175</td><td>175.000</td><td>7</td><td>7.111</td><td>2.286</td><td>37.714</td>
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</tr>
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<tr>
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<td>8</td><td>260</td><td>260.000</td><td>3</td><td> Inf</td><td>0.000</td><td>59.000</td>
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</tr>
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<tr>
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<td>9</td><td>369</td><td>369.000</td><td>9</td><td>9.102</td><td>7.111</td><td>53.333</td>
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</tr>
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<tr>
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<td>10</td><td>505</td><td>505.000</td><td>7</td><td> Inf</td><td>3.200</td><td>159.200</td>
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</tr>
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<tr>
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<td>11</td><td>671</td><td>671.000</td><td>11</td><td>11.102</td><td>2.909</td><td>215.273</td>
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</tr>
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<tr>
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<td>12</td><td>870</td><td>870.000</td><td>3</td><td> Inf</td><td>0.000</td><td>185.333</td>
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</tr>
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<tr>
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<td>13</td><td>1105</td><td>1105.000</td><td>13</td><td>13.060</td><td>4.923</td><td>313.846</td>
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</tr>
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<tr>
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<td>14</td><td>1379</td><td>1379.000</td><td>9</td><td> Inf</td><td>4.571</td><td>540.571</td>
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</tr>
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<tr>
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<td>15</td><td>1695</td><td>1695.000</td><td>15</td><td>15.062</td><td>4.267</td><td>242.133</td>
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</tr>
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<tr>
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<td>16</td><td>2056</td><td>2056.000</td><td>3</td><td> Inf</td><td>0.000</td><td>488.500</td>
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</tr>
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<tr>
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<td>17</td><td>2465</td><td>2465.000</td><td>17</td><td>17.042</td><td>7.529</td><td>267.294</td>
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</tr>
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<tr>
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<td>18</td><td>2925</td><td>2925.000</td><td>11</td><td> Inf</td><td>7.111</td><td>520.889</td>
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</tr>
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<tr>
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<td>19</td><td>3439</td><td>3439.000</td><td>19</td><td>19.048</td><td>16.842</td><td>387.368</td>
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</tr>
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<tr>
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<td>20</td><td>4010</td><td>4010.000</td><td>3</td><td> Inf</td><td>14.400</td><td>584.800</td>
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</tr>
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<tr>
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<td>21</td><td>4641</td><td>4641.000</td><td>21</td><td>21.035</td><td>6.095</td><td>1158.095</td>
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</tr>
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<tr>
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<td>22</td><td>5335</td><td>5335.000</td><td>13</td><td> Inf</td><td>6.545</td><td>1132.364</td>
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</tr>
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<tr>
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<td>23</td><td>6095</td><td>6095.000</td><td>23</td><td>23.037</td><td>11.130</td><td>1268.870</td>
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</tr>
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<tr>
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<td>24</td><td>6924</td><td>6924.000</td><td>3</td><td> Inf</td><td>10.667</td><td>827.500</td>
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</tr>
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<tr>
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<td>25</td><td>7825</td><td>7825.000</td><td>25</td><td>25.029</td><td>35.840</td><td>1190.400</td>
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</tr>
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<tr>
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<td>26</td><td>8801</td><td>8801.000</td><td>15</td><td> Inf</td><td>4.923</td><td>1859.077</td>
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</tr>
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<tr>
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<td>27</td><td>9855</td><td>9855.000</td><td>27</td><td>27.032</td><td>37.926</td><td>1365.333</td>
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</tr>
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<tr>
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<td>28</td><td>10990</td><td>10990.000</td><td>3</td><td> Inf</td><td>34.286</td><td>1365.714</td>
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</tr>
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<tr>
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<td>29</td><td>12209</td><td>12209.000</td><td>29</td><td>29.025</td><td>30.897</td><td>1647.448</td>
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</tr>
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<tr>
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<td>30</td><td>13515</td><td>13515.000</td><td>17</td><td> Inf</td><td>8.533</td><td>2571.733</td>
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</tr>
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<tr>
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<td>31</td><td>14911</td><td>14911.000</td><td>31</td><td>31.027</td><td>33.032</td><td>1426.581</td>
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</tr>
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<tr>
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<td>32</td><td>16400</td><td>16400.000</td><td>3</td><td> Inf</td><td>0.000</td><td>1600.125</td>
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</tr>
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</table>
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<center>Elapsed Time = 0.710 seconds</center>
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<p>
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The magic square example does not fare well when <a href='../examples/MagicSquareExample.php'>run as a PHP script</a>. For a 32x32 matrix array
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it takes around a second to complete just the last row of computations in the above table.
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Hopefully this result will spur PHP developers to find optimizations and better attuned algorithms
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to speed things up. Matrix algebra is a great testing ground for ideas about time and memory
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performance optimation. Keep in perspective that PHP JAMA scripts are still plenty fast for use as
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a tool for learning about matrix algebra and quickly extending your knowledge with new scripts
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to apply knowledge.
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</p>
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<p>
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To learn more about the subject of magic squares you can visit the <a href='http://mathforum.org/alejandre/magic.square.html'>Drexel Math Forum on Magic Squares</a>.
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You can also learn more by carefully examining the <code>MagicSquareExample.php</code> source code below.
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</p>
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<?php
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highlight_file("../examples/MagicSquareExample.php");
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include_once "includes/footer.php";
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?>
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<div id="credits">
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<p>
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Brought to you by:
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</p>
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<ul>
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<li><a href="http://math.nist.gov/">National Institute of Standards and Technology</a></li>
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<li><a href="http://math.nist.gov/">MathWorks</a></li>
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<li><a href="http://math.nist.gov/javanumerics/jama/">JAMA : A Java Matrix Package</a></li>
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<li>Paul Meagher</li>
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<li>Michael Bommarito</li>
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<li>Lukasz Karapuda</li>
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<li>Bartek Matosiuk</li>
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</ul>
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</div>
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</body>
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</html>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<title>JAMA v1.0.1</title>
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<meta name="description" content="JAMA v1.0.1 - Port of the proposed standard Java Matrix Library to PHP" />
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<meta name="robots" content="index, follow" />
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<meta name="keywords" content="php, matrix, matrix library, cholesky decomposition, eigenvalue decomposition, eigenvector, lu decomposition, qr decomposition, singular value decomposition" />
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<link rel="stylesheet" type="text/css" href="style.css" />
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</head>
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<body>
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<center>
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<hr />
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[ <a href="index.php">index.php</a> ] [ <a href="docs.php">docs.php</a> ] [ <a href="package.php">package.php</a> ] [ <a href="test.php">test.php</a> ] [ <a href="example.php">example.php</a> ] [ <a href="download.php">download.php</a> ]
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<hr />
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</center>
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<?php
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include_once "includes/header.php";
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include_once "includes/navbar.php";
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?>
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<p>
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JAMA is a proposed standard matrix class for Java. The JAMA introduction
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describes "JAMA : A Java Matrix Package" in this way:
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</p>
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<blockquote>
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JAMA is a basic linear algebra package for Java. It provides user-level classes for
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constructing and manipulating real, dense matrices. It is meant to provide sufficient
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functionality for routine problems, packaged in a way that is natural and understandable
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to non-experts. It is intended to serve as the standard matrix class for Java, and
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will be proposed as such to the Java Grande Forum and then to Sun. A straightforward
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public-domain reference implementation has been developed by the MathWorks and NIST as
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a strawman for such a class. We are releasing this version in order to obtain public
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comment. There is no guarantee that future versions of JAMA will be compatible with this one.
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</blockquote>
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<p>
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The development team below has successfully ported the JAMA API to PHP. You can explore
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this site to learn more about this project and it's current development status.
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</p>
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<?php
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include_once "includes/credits.php";
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include_once "includes/footer.php";
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?>
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<?php
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include_once "includes/header.php";
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include_once "includes/navbar.php";
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?>
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<p>
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Source Listing:
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</p>
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<ul>
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<?php
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chdir("../");
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$files = glob("*.php");
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$files = array_merge($files, glob("util/*.php"));
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foreach ($files as $fileName) {
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?>
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<li><a href="package.php?view=<?php echo sha1($fileName);?>"><?php echo $fileName;?></a> - <?php echo date ("F d Y - g:i a", filemtime($fileName));?></li>
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<?php
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}
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?>
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</ul>
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<?php
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if( isset($_REQUEST['view']) ) {
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$hash = $_REQUEST['view'];
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$n = array_search($hash, array_map(sha1, $files));
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$fileName = $files[$n];
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?>
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<hr />
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Viewing: <?php echo $fileName;?>
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<hr />
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<?php
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highlight_file($fileName);
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?>
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<hr />
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<?php
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}
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include_once "includes/footer.php";
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?>
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<?php
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include_once "includes/header.php";
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include_once "includes/navbar.php";
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?>
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<p>
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The first script your should run when you install Jama is the TestMatrix.php script.
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</p>
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<p>
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This will run the unit tests for methods in the <code>Matrix.php</code> class. Because
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the Matrix.php class can be used to invoke all the decomposition methods the <code>TestMatrix.php</code>
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script is a test suite for the whole Jama package.
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</p>
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<p>
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The original <code>TestMatrix.java</code> code uses try/catch error handling. We will
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eventually create a build of JAMA that will take advantage of PHP5's new try/catch error
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handling capabilities. This will improve our ability to replicate all the unit tests that
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appeared in the original (except for some print methods that may not be worth porting).
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</p>
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<p>
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You can <a href='../test/TestMatrix.php'>run the TestMatrix.php script</a> to see what
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unit tests are currently implemented. The source of the <code>TestMatrix.php</code> script
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is provided below. It is worth studying carefully for an example of how to do matrix algebra
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programming with Jama.
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</p>
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<?php
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highlight_file("../test/TestMatrix.php");
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include_once "includes/footer.php";
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?>
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