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  1. <?php
  2. 	$page_title = 'Run temp analysis';
  3. 	require('../directoryinfo.php');
  4. 	include('../connect.php');
  5. 	include('functions.php');
  6. 	require_once('../header.html');
  7. ?>
  8.  
  9. <!-- Form For Executing Code -->
  10. <form action="map_figure.php" method="post" name="file_select">
  11. 	<fieldset>
  12.  
  13. 	<table align="left" cellspacing=15>
  14. 		<tr><td colspan="2"><input type="checkbox" checked name="go" value="yes"><STRONG>draw map</STRONG></td></tr>
  15. 		<tr><td colspan=2><input type="submit" name="submit" value="Submit"></td></tr>
  16. 	</table>
  17. 	</fieldset>
  18. </form>
  19.  
  20. <?php
  21. 	error_reporting(E_ALL);	
  22. 	if(isset($_POST['go'])) {
  23. 		$t0 = microtime(true);
  24.  
  25. 		$q_time_scale = "SELECT interval_name, age_bottom, age_top, intervals.id FROM intervals 
  26. 		WHERE interval_name IN ('Whiterock', 'Chazyan', 'Blackriverian', 'Shermanian', 'Richmondian', 'Hirnantian', 'Rhuddanian', 'Aeronian', 'Telychian', 'Wenlock')
  27. 		ORDER BY age_bottom";
  28. 		$time_scale = mysqli_query($connect_macrostrat, $q_time_scale);         
  29. 		$n_bin = mysqli_num_rows($time_scale);
  30.  
  31. 		while($row = mysqli_fetch_assoc($time_scale)) {			
  32. 			if($row['interval_name'] == 'Blackriverian') {
  33. 				$int_name[] = 'Blackriveran-Kirkfield';
  34. 				$int_bottom[] = $row['age_bottom'];
  35. 				$int_top[] = 457.0000;
  36. 			} else if($row['interval_name'] == 'Shermanian') {
  37. 				$int_name[] = 'Shermanian-Maysvillian';
  38. 				$int_bottom[] = $row['age_bottom'];
  39. 				$int_top[] = 450.0000;
  40. 			} else {
  41. 				$int_name[] = $row['interval_name'];
  42. 				$int_bottom[] = $row['age_bottom'];
  43. 				$int_top[] = $row['age_top'];
  44. 			}
  45. 			$int_id[] = $row['id'];
  46. 		}
  47. 		mysqli_free_result($time_scale);
  48. 		$n_int = count($int_name);
  49.  
  50. 		$base_ordovician = 488.3;
  51. 		$study_max = max($int_bottom);
  52. 		$study_min = min($int_top);
  53.  
  54.  
  55. 		//////////////
  56. 		//
  57. 		// Column data saved as columns.csv
  58. 		//
  59. 		//////////////
  60. 		$q = "SELECT cols.id FROM cols 
  61. 		INNER JOIN col_groups ON col_groups.id=col_group_id 
  62. 		INNER JOIN projects ON projects.id=project_id
  63. 		WHERE project LIKE 'North America' AND col_group NOT LIKE 'Mexico' AND cols.id NOT IN (34, 111, 139, 218, 586, 587) AND status_code='active'";
  64. 		$columns = mysqli_query($connect_macrostrat, $q);       		
  65. 		while($row = mysqli_fetch_assoc($columns)) $my_cols[] = $row['id'];
  66. 		mysqli_free_result($columns);
  67.  
  68.  
  69. 		//////////////
  70. 		//
  71. 		// get packages	
  72. 		//
  73. 		//////////////		
  74. 		$temp_pkg = split_packages('marine');	
  75. 		for($i=0; $i<count($temp_pkg); ++$i) {
  76. 			$q = "SELECT col_id, max(b.age_bottom) bottom, min(t.age_top) top, count(distinct units.id) n_unit FROM units
  77. 			INNER JOIN intervals b ON b.id=FO
  78. 			INNER JOIN intervals t ON t.id=LO
  79. 			WHERE units.id IN ($temp_pkg[$i])";
  80. 			$result=mysqli_query($connect_macrostrat, $q);
  81. 			$row=mysqli_fetch_assoc($result);
  82. 			if(in_array($row['col_id'], $my_cols)===TRUE && $row['bottom']>$study_min && $row['top']<$study_max) $my_pkg[] = $temp_pkg[$i];	
  83. 			mysqli_free_result($result);
  84. 		}
  85. 		$all_units = implode(",",$my_pkg);
  86.  
  87.  
  88. 		//////////////
  89. 		//
  90. 		// units saved as O_S_units.csv
  91. 		//
  92. 		//////////////
  93. 		$units_file = "O_S_units.csv";
  94. 		$fh = fopen($units_file, 'w') or die("can't open file");
  95. 		chmod($units_file, 0777);
  96. 		$file_row = "unit_id, col_id, age_bottom, age_top, color\n";
  97. 		fwrite($fh, $file_row);
  98. 		$q = "SELECT units.id, col_id, b.age_bottom, t.age_top, color FROM units
  99. 		INNER JOIN intervals b ON b.id=FO
  100. 		INNER JOIN intervals t ON t.id=LO
  101. 		WHERE units.id IN (".$all_units.") and b.age_bottom>$study_min AND t.age_top<$study_max"; //echo $q."<br>";
  102. 		$result=mysqli_query($connect_macrostrat, $q);
  103. 		while($row=mysqli_fetch_assoc($result)) {
  104. 			$file_row = $row['id'].",".$row['col_id'].",".$row['age_bottom'].",".$row['age_top'].",".$row['color']."\n";
  105. 			fwrite($fh, $file_row);
  106. 		}
  107. 		fclose($fh);
  108. 		mysqli_free_result($result);
  109. 		echo 'File <a href="'.$units_file.'">'.$units_file.'</a> saved<BR>';
  110.  
  111.  
  112. 		//////////////
  113. 		//
  114. 		// pbdb_collections saved as O_S_collections.csv
  115. 		//
  116. 		//////////////
  117. 		$fh = fopen("collections.csv", "r");
  118. 		$my_collections = fgetcsv($fh, 100000, ",")
  119. 		echo "There are ".count($data)." collections<br>";
  120. 		fclose($fh); 
  121.  
  122. 		$pbdb_file = "O_S_collections.csv";
  123. 		$fh = fopen($pbdb_file, 'w') or die("can't open file");
  124. 		chmod($pbdb_file, 0777);
  125. 		$file_row = "collection_no, unit_id, lat, lng\n";
  126. 		fwrite($fh, $file_row);
  127. 		$q = "SELECT collection_no, unit_id, lat, lng FROM pbdb_matches
  128. 		WHERE collection_no IN (".implode(",",$my_collections).")";
  129. 		$result=mysqli_query($connect_macrostrat, $q);
  130. 		while($row=mysqli_fetch_assoc($result)) {
  131. 			$file_row = $row['collection_no'].",".$row['unit_id'].",".$row['lat'].",".$row['lng']."\n";
  132. 			fwrite($fh, $file_row);
  133. 		}
  134. 		fclose($fh);
  135. 		mysqli_free_result($result);
  136. 		echo 'File <a href="'.$pbdb_file.'">'.$pbdb_file.'</a> saved<BR>';
  137.  
  138.  
  139. 		//////////////
  140. 		//
  141. 		// draw map in R
  142. 		//
  143. 		//////////////
  144.  
  145. 		$r_file = "temp.r";
  146. 		$fh = fopen($r_file, 'w') or die("can't open file");
  147. 		chmod($r_file, 0777);
  148.  
  149. 		$r_script = "
  150. 			source('myFunctions.r')
  151. 			library(maps)
  152. 			library(mapproj)
  153.  
  154. 			time.scale <- read.csv(file='time_scale.csv', header=TRUE); n.bins <- nrow(time.scale)
  155. 			units <- read.csv(file='O_S_units.csv', header=TRUE)
  156. 			polygons <- read.csv(file='column_polygons.csv', header=TRUE)
  157. 			pbdb <- read.csv(file='O_S_collections.csv', header=TRUE)
  158.  
  159. 			## make maps
  160. 			lon.limit <- c(-172,-50)
  161. 			lat.limit <- c(25,83)
  162.  
  163. 			map.orient <- c(54,-103,0)
  164.  
  165. 			map.data <- map('world', c('USA', 'Canada'), xlim=lon.limit, ylim=lat.limit, proj='azequalarea',orient=map.orient, plot=FALSE, interior=FALSE)
  166.  
  167. 			map.color <- 'gray25'  # solid dark gray
  168. 			pbdb.color <- rgb(1,0,0,0.3)  # transparent red
  169.  
  170. 			rock.colors <- matrix(NA, nrow=15, ncol=3)
  171. 			rock.colors[,1] <- c('blue','gray light','tan','orange','yellow','blue green','pink','brown dark','green dark','brown','green light','brown light','blue dark','gray','green')
  172. 			rock.colors[,2] <- c('#6BA1FF','#7C7C7C','#9A9469','#FF8400','#FFFF00','#00FFFF','#FF80A8','#55432F','#008800','#55432F','#008800','#55432F','#3838FF','#7C7C7C','#008800')
  173. 			rock.colors[,3] <- c('carbonate','fine clastics','mixed clastics','coarse clastics','sands','chert','evaporite','metamorphic','plutonic','metamorphic','volcanic','metamorphic','mixed carb/clast','fine clastics','volcanics')
  174. 			rock.colors <- rock.colors[order(rock.colors[,1]),]
  175.  
  176. 			top.units <- vector(mode='numeric', length=nrow(units)); counter <- 1
  177. 			pdf(file='map_figure.pdf', height=20, width=50)
  178. 			par(mfrow=c(2,5), mar=c(0,0,10,0)+0.1, pch=16, cex.main=7)		
  179.  
  180. 			for(i in n.bins:1) {
  181. 				unit.temp <- units[units[,3]>time.scale[i,3] & units[,4]<time.scale[i,2],]
  182. 				cols.temp <- unique(unit.temp\$col_id)
  183. 				pbdb.temp <- unique(pbdb[is.element(pbdb\$unit_id, unit.temp\$unit_id),3:4])
  184.  
  185. 				plot(map.data, main=time.scale[i,1], axes=FALSE, frame.plot=TRUE, type='n', xlab='', ylab='')
  186.  
  187. 				# plot macrostrat units
  188. 				for(j in 1:length(cols.temp)) {
  189. 					top.units[counter] <- unit.temp[unit.temp\$col_id==cols.temp[j],1][1]
  190. 					color.temp <- rock.colors[match(unit.temp[unit.temp\$col_id==cols.temp[j],5][1], rock.colors[,1]),2]
  191.  
  192. 					poly.temp <- polygons[polygons[,1]==cols.temp[j],2:3]
  193. 					poly.proj <- mapproject(list(x=poly.temp[,1], y=poly.temp[,2]))
  194. 					polygon(poly.proj\$x, poly.proj\$y, col=paste(color.temp), border=paste(color.temp), lwd=0.5)
  195. 					counter <- counter + 1
  196. 				}
  197.  
  198. 				# plot pbdb
  199. 				if(nrow(pbdb.temp) > 0) {
  200. 					pbdb.proj <- mapproject(list(x=pbdb.temp[,2], y=pbdb.temp[,1]))
  201. 					points(pbdb.proj\$x, pbdb.proj\$y, cex=3, col=pbdb.color)
  202. 				}
  203. 				lines(map.data\$x, map.data\$y, col=map.color)
  204. 			}
  205. 			dev.off()
  206.  
  207. 			top.units <- top.units[top.units>0]
  208. 			rock.colors2 <- rock.colors[match(unique(units[is.element(units[,1], top.units), 5]),rock.colors[,1]),]
  209.  
  210. 			## make legend
  211. 			pdf(file='map_legend.pdf', height=6, width=10)
  212. 			layout(matrix(1:15, nrow=3, ncol=5, byrow=TRUE))
  213. 			for(i in 1:nrow(rock.colors2)) {
  214. 				par(mar=c(0.1,0.1,0.1,0.1))
  215. 				plot(1:10, xlim=c(0,10), ylim=c(0,10), type='n', axes=FALSE, frame.plot=TRUE, xlab='', ylab='')
  216. 				rect(1,1,9,4, col=paste(rock.colors2[i,2]))
  217. 				text(5,8, labels=rock.colors2[i,1], cex=1.5)
  218. 				text(5,6, labels=rock.colors2[i,3], cex=1.5)
  219. 			} 
  220. 			dev.off()
  221. 			";
  222.  
  223. 		fwrite($fh, $r_script);
  224.  
  225. 		$cmd = "echo 'rscript <- \"$r_file\"; source(rscript)' | " . "/usr/bin/R --slave 2>&1";
  226. 		exec($cmd, $r_ran); 
  227. 		if(count($r_ran)>0) {
  228. 			print_r($r_ran); echo "<br>";
  229. 		}
  230.  
  231. 		echo 'File <a href="map_figure.pdf" target="blank">map_figure.pdf</a> saved<BR>';
  232. 		echo 'File <a href="map_legend.pdf" target="blank">map_legend.pdf</a> saved<BR>';
  233.  
  234. 	}
  235.  
  236.  
  237. 	//////////////
  238. 	//
  239. 	// stuff at the end
  240. 	//
  241. 	//////////////
  242. 	if(isset($_POST['submit'])) {
  243. 		$t1 = microtime(true);
  244. 		$time_diff = $t1 - $t0;
  245. 		if ($time_diff/60 < 1) {
  246. 			$diff_seconds = round($time_diff, 3);
  247. 			echo "<br>This process took ".$diff_seconds." seconds";
  248. 		} else if ($time_diff>=1 & $time_diff<3600) {
  249. 			$diff_min = round($time_diff/60, 3);
  250. 			echo "<br>This process took ".$diff_min." minutes";
  251. 		} else {
  252. 			$diff_hour = round($time_diff/3600, 3);
  253. 			echo "<br>This process took ".$diff_hour." hours";
  254. 		}
  255. 	}
  256. ?>
  257.  
  258.  
  259.  
  260. <?php 
  261. 	require_once('../footer.html');
  262. 	exit();
  263. ?>
Runtime error #stdin #stdout 0.02s 13664KB
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Parse error: syntax error, unexpected T_ECHO in /home/g8NE3L/prog.php on line 119
https://ideone.com/pGCp2
language:
PHP (php 7.3.5)
created:
14 years ago
visibility:
public

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