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	tindex.php - cosmo - front and backend for Markov-Chain Monte Carlo inversion o…
	git clone git://src.adamsgaard.dk/cosmo
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	tindex.php (15417B)
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	1 <?php
	2
	3 // reCAPTCHA setup
	4 require_once('recaptchalib.php');
	5
	6 // your secret key
	7 $secret = "6LeMrRATAAAAAOdcvVGi6PfR__XGOVoUP7lCqHp1";
	8
	9 // empty response
	10 $response = null;
	11
	12 // check secret key
	13 $reCaptcha = new ReCaptcha($secret);
	14
	15 // if submitted check response
	16 if ($_POST["g-recaptcha-response"]) {
	17 $response = $reCaptcha->verifyResponse(
	18 $_SERVER["REMOTE_ADDR"],
	19 $_POST["g-recaptcha-response"]
	20 );
	21 }
	22
	23 // include top of html template
	24 include('head.html');
	25
	26 ?>
	27 <script src="//ajax.googleapis.com/ajax/libs/jquery/2.0.0/jquery…
	28 <script type="text/javascript" src="js/history-form-prefiller.js…
	29 <?php
	30
	31 if (isset($_GET['wait_id']) && !empty($_GET['wait_id'])) {
	32
	33 // read status file contents
	34 if (!$statusfile = fopen("/home/adc/cosmo/input/status_" . $_GET['wa…
	35 echo("Error! Sample data not found.");
	36 }
	37
	38 $status = fgets($statusfile);
	39 fclose($statusfile);
	40
	41 $show_percentage = false;
	42 if (strpos($status, '<!--') !== false) {
	43 $percentage = preg_replace('/.*<!--/', '', $status);
	44 $percentage = preg_replace('/-->/', '', $percentage);
	45 $percentage = preg_replace('/ /', '', $percentage);
	46 $show_percentage = true;
	47 }
	48
	49 // redirect to results page if computations are complete
	50 if (strcmp($status, "Computations complete") == 0) {
	51 header("Location: /index.php?results_id=" . $_GET['wait_id']);
	52 }
	53
	54 // refresh the page every 5 seconds while computations are running
	55 ?>
	56 <meta http-equiv="refresh" content="5" >
	57 <?php
	58 }
	59
	60 include('navigation.html');
	61 ?>
	62 <main>
	63 <?php
	64 if (isset($_GET['wait_id']) && !empty($_GET['wait_id'])) {
	65 ?>
	66
	67 <div class="container">
	68
	69 <br><br><br><br>
	70 <div class="row center">
	71 <h2 class="header col s12 orange-text">Please wait</h2>
	72 </div>
	73
	74 <div class="row center">
	75 <h4 class="header col s12">
	76 <?php
	77 echo $status;
	78 ?>
	79 </h4>
	80 </div>
	81
	82 <div class="row progress center-align s12">
	83 <?php
	84 if ($show_percentage) { ?>
	85 <div class="determinate"
	86 style="width: <?php echo($percentage); ?>%"></div>
	87 <?php
	88 } else { ?>
	89 <div class="indeterminate"></div>
	90 <?php } ?>
	91 </div>
	92
	93 <div class="row center valign-wrapper">
	94
	95 <p class="flow-text">
	96 Please wait while the inversion computations are taking place.
	97 These may make take several minutes to complete. For long waits …
	98 bookmark this page and revisit it later. Please do not resubmit …
	99 sample.</p>
	100 </div>
	101
	102 <div class="row center-align">
	103 <p class="center-align"> If the computations are queued for more…
	104 hours, please contact <a href="mailto:[email protected]…
	105 Damsgaard</a>.</p>
	106 </div>
	107 <br><br><br><br><br><br>
	108
	109 </div>
	110
	111 <?php
	112 } elseif (isset($_GET['results_id']) && !empty($_GET['results_id'])) {
	113 // show plots
	114 ?>
	115
	116 <div class="section no-pad-bot" id="index-banner">
	117 <div class="container">
	118 <br><br>
	119 <!-- page header -->
	120 <h2 class="header center orange-text">MCMC inversion results…
	121
	122 <div class="row">
	123 <div class="col s12">
	124 <div class="card">
	125 <div class="card-image">
	126 <?php
	127 include('output/' . $_GET['results_id'] . '_Walks.ht…
	128 ?>
	129 </div>
	130 <div class="card-content">
	131 <h5 class="blue-text">
	132 Results</h5>
	133 <p>The table shows the general statistical results…
	134 interglacial erosion rate (ε<sub>int</sub>…
	135 glacial erosion rate (ε<sub>gla</sub>), cl…
	136 record threshold value
	137 (δ<sup>18</sup>O<sub>threshold</sub>), and t…
	138 erosion over the last 1 Myr (E), produced the Mark…
	139 Monte-Carlo inversion. Results are displayed per w…
	140 and on average. The 50th percentiles (also called …
	141 quartile) denote the median parameter value. The 2…
	142 percentiles (first quartile) marks the value that …
	143 the lowest 25% percent of data from the highest 75…
	144 The 75th percentiles mark the limit to the upper 2…
	145 data. If the 25th, 50th, and 75th percentile value…
	146 parameter are close, the parameter is well constra…
	147 If a single walker produces values with significant
	148 deviation from the others, remove it from the data
	149 set. NaN results in total erosion rate mean that t…
	150 exceeds values which are possible to constrain.</p>
	151 </div>
	152 <div class="card-action">
	153 <a href="output/<?php
	154 echo($_GET['results_id']); ?>_Walks.csv"
	155 target="_blank">Link to CSV</a>
	156 (right click to save, can be imported to Excel, Matlab…
	157 </div>
	158 </div>
	159 </div>
	160
	161 <div class="row">
	162 <!--<div class="col s12 m8 offset-m2">-->
	163 <div class="col s12">
	164 <div class="card">
	165 <div class="card-image">
	166 <img src="output/<?php
	167 echo($_GET['results_id']); ?>_Walks-6.png">
	168 <!--<span class="card-title blue-text text-darke…
	169 Generalized model parameter values</span>-->
	170 </div>
	171 <div class="card-content">
	172 <h5 class="blue-text">
	173 Generalized model parameter values</h5>
	174 <p>The histograms show the distribution of (a)
	175 interglacial erosion rate, (b) glacial erosion rat…
	176 timing of last deglaciation, and (d)
	177 d<sup>18</sup>O<sub>threshold</sub> levels that pr…
	178 the best fit to the supplied TCN concentrations.
	179 The vertical axis indicates the number of
	180 simulations included in each bin out of the 10,000
	181 simulations that followed the MCMC burn-in phase f…
	182 MCMC walker. The solid magenta lines denote the m…
	183 values (second quartile), while the dashed magenta…
	184 denote the lower and upper quartiles (25th and 75th
	185 percentiles, respectively). A parameter is well
	186 constrained if the histogram has a single, distinc…
	187 and relatively close median, lower and upper quart…
	188 values. Flat histograms denote that the parameters…
	189 well constrained.</p>
	190 </div>
	191 <div class="card-action">
	192 <a href="output/<?php
	193 echo($_GET['results_id']); ?>_Walks-6.png"
	194 target="_blank">Link to PNG</a>
	195 <a href="output/<?php
	196 echo($_GET['results_id']); ?>_Walks-6.pdf"
	197 target="_blank">Link to PDF</a>
	198 <a href="output/<?php
	199 echo($_GET['results_id']); ?>_Walks-6.fig"
	200 target="_blank">Link to FIG</a>
	201 <br>
	202 <a href="output/<?php
	203 echo($_GET['results_id']); ?>_Walks-eps_int.txt"
	204 target="_blank">ε<sub>int</sub> data</a>
	205 <a href="output/<?php
	206 echo($_GET['results_id']); ?>_Walks-eps_gla.txt"
	207 target="_blank">ε<sub>gla</sub> data</a>
	208 <a href="output/<?php
	209 echo($_GET['results_id']); ?>_Walks-t_degla.txt"
	210 target="_blank"><i>t</i><sub>degla</sub> data</a>
	211 <a href="output/<?php
	212 echo($_GET['results_id']); ?>_Walks-d18O_thresho…
	213 target="_blank">δ<sup>18</sup>O<sub>threshold…
	214 </div>
	215 </div>
	216 </div>
	217 </div>
	218
	219
	220 <div class="row">
	221 <!--<div class="col s12 m8 offset-m2">-->
	222 <div class="col s12">
	223 <div class="card">
	224 <div class="card-image">
	225 <img src="output/<?php
	226 echo($_GET['results_id']); ?>_Walks-5.png">
	227 <!--
	228 <span class="card-title blue-text text-darken-2">
	229 Model parameter values per inversion walker</spa…
	230 -->
	231 </div>
	232 <div class="card-content">
	233 <h5 class="blue-text">
	234 Model parameter values per inversion walker</h…
	235 <p>The histograms show the distribution of (a)
	236 interglacial erosion rate, (b) glacial erosion rat…
	237 timing of last deglaciation, and (d)
	238 d<sup>18</sup>O<sub>threshold</sub> levels that pr…
	239 the best fit to the supplied TCN concentrations. T…
	240 one histogram per model parameter for each MCMC wa…
	241 The <!--fraction indicates the number of simulatio…
	242 included in--> vertical axis indicates the number …
	243 simulations included in each bin out of the 10,000
	244 simulations that followed the MCMC burn-in phase.<…
	245 </div>
	246 <div class="card-action">
	247 <a href="output/<?php
	248 echo($_GET['results_id']); ?>_Walks-5.png"
	249 target="_blank">Link to PNG</a>
	250 <a href="output/<?php
	251 echo($_GET['results_id']); ?>_Walks-5.pdf"
	252 target="_blank">Link to PDF</a>
	253 <a href="output/<?php
	254 echo($_GET['results_id']); ?>_Walks-5.fig"
	255 target="_blank">Link to FIG</a>
	256 <br>
	257 <?php include('output/' . $_GET['results_id'] . '_Walk…
	258 </div>
	259 </div>
	260 </div>
	261 </div>
	262
	263 <div class="row">
	264 <!--<div class="col s12 m8 offset-m2">-->
	265 <div class="col s12">
	266 <div class="card">
	267 <div class="card-image">
	268 <img src="output/<?php
	269 echo($_GET['results_id']); ?>_Walks-7.png">
	270 <!--
	271 <span class="card-title blue-text text-darken-2">
	272 Erosion history</span>-->
	273 </div>
	274 <div class="card-content">
	275 <h5 class="blue-text">
	276 Median-based model of sample history</h5>
	277 <p>
	278 (a) Two-stage glacial-interglacial model based on …
	279 selected climate record and the median
	280 δ<sup>18</sup>O<sub>threshold</sub> value fr…
	281 first figure above. Timing and duration of glacia…
	282 interglacial periods are defined by the threshold …
	283 that is applied to the climate record.
	284
	285 (b) Binary exposure history between glaciations
	286 characterized by total exposure and interglacials …
	287 any exposure.
	288
	289 (c) Erosion rate through time which alternates bet…
	290 interglacial and glacial erosion rate magnitude, b…
	291 median values presented above.
	292
	293 In all three figures the vertical dashed lines den…
	294 median age of the last deglaciation.
	295
	296 </p>
	297 </div>
	298 <div class="card-action">
	299 <a href="output/<?php
	300 echo($_GET['results_id']); ?>_Walks-7.png"
	301 target="_blank">Link to PNG</a>
	302 <a href="output/<?php
	303 echo($_GET['results_id']); ?>_Walks-7.pdf"
	304 target="_blank">Link to PDF</a>
	305 <a href="output/<?php
	306 echo($_GET['results_id']); ?>_Walks-7.fig"
	307 target="_blank">Link to FIG</a>
	308 </div>
	309 </div>
	310 </div>
	311 </div>
	312
	313 <div class="row">
	314 <!--<div class="col s12 m8 offset-m2">-->
	315 <div class="col s12">
	316 <div class="card">
	317 <div class="card-image">
	318 <img src="output/<?php
	319 echo($_GET['results_id']); ?>_Walks-8.png">
	320 <!--
	321 <span class="card-title blue-text text-darken-2">
	322 Erosion history</span>-->
	323 </div>
	324 <div class="card-content">
	325 <h5 class="blue-text">
	326 Exhumation history</h5>
	327 <p>
	328 Mean (black) and 25 and 75 percentiles (red) of sa…
	329 exhumation history. There is one subplot per MCMC …
	330 </p>
	331 </div>
	332 <div class="card-action">
	333 <a href="output/<?php
	334 echo($_GET['results_id']); ?>_Walks-8.png"
	335 target="_blank">Link to PNG</a>
	336 <a href="output/<?php
	337 echo($_GET['results_id']); ?>_Walks-8.pdf"
	338 target="_blank">Link to PDF</a>
	339 <a href="output/<?php
	340 echo($_GET['results_id']); ?>_Walks-8.fig"
	341 target="_blank">Link to FIG</a>
	342 </div>
	343 </div>
	344 </div>
	345 </div>
	346
	347 <div class="row">
	348 <div class="col s12">
	349 <div class="card">
	350 <div class="card-image">
	351 <?php
	352 include('output/' . $_GET['results_id'] . '_Walks-in…
	353 ?>
	354 </div>
	355 <div class="card-content">
	356 <h5 class="blue-text">
	357 Input parameters</h5>
	358 <p>This table summarizes the supplied input parame…
	359 values.</p>
	360
	361 </div>
	362 </div>
	363 </div>
	364 </div>
	365
	366
	367 <?php
	368 } else {
	369 ?>
	370 <div ng-view>
	371 <!-- content is injected here -->
	372 </div>
	373 <?php } ?>
	374
	375 </main>
	376
	377 <?php include('foot.html'); ?>
	378
	379