$study_min && $row['top']<$study_max) $my_pkg[] = $temp_pkg[$i];
mysqli_free_result($result);
}
$all_units = implode(",",$my_pkg);
//////////////
//
// units saved as O_S_units.csv
//
//////////////
$units_file = "O_S_units.csv";
$fh = fopen($units_file, 'w') or die("can't open file");
chmod($units_file, 0777);
$file_row = "unit_id, col_id, age_bottom, age_top, color\n";
fwrite($fh, $file_row);
$q = "SELECT units.id, col_id, b.age_bottom, t.age_top, color FROM units
INNER JOIN intervals b ON b.id=FO
INNER JOIN intervals t ON t.id=LO
WHERE units.id IN (".$all_units.") and b.age_bottom>$study_min AND t.age_top<$study_max"; //echo $q."
";
$result=mysqli_query($connect_macrostrat, $q);
while($row=mysqli_fetch_assoc($result)) {
$file_row = $row['id'].",".$row['col_id'].",".$row['age_bottom'].",".$row['age_top'].",".$row['color']."\n";
fwrite($fh, $file_row);
}
fclose($fh);
mysqli_free_result($result);
echo 'File '.$units_file.' saved
';
//////////////
//
// pbdb_collections saved as O_S_collections.csv
//
//////////////
$fh = fopen("collections.csv", "r");
$my_collections = fgetcsv($fh, 100000, ",")
echo "There are ".count($data)." collections
";
fclose($fh);
$pbdb_file = "O_S_collections.csv";
$fh = fopen($pbdb_file, 'w') or die("can't open file");
chmod($pbdb_file, 0777);
$file_row = "collection_no, unit_id, lat, lng\n";
fwrite($fh, $file_row);
$q = "SELECT collection_no, unit_id, lat, lng FROM pbdb_matches
WHERE collection_no IN (".implode(",",$my_collections).")";
$result=mysqli_query($connect_macrostrat, $q);
while($row=mysqli_fetch_assoc($result)) {
$file_row = $row['collection_no'].",".$row['unit_id'].",".$row['lat'].",".$row['lng']."\n";
fwrite($fh, $file_row);
}
fclose($fh);
mysqli_free_result($result);
echo 'File '.$pbdb_file.' saved
';
//////////////
//
// draw map in R
//
//////////////
$r_file = "temp.r";
$fh = fopen($r_file, 'w') or die("can't open file");
chmod($r_file, 0777);
$r_script = "
source('myFunctions.r')
library(maps)
library(mapproj)
time.scale <- read.csv(file='time_scale.csv', header=TRUE); n.bins <- nrow(time.scale)
units <- read.csv(file='O_S_units.csv', header=TRUE)
polygons <- read.csv(file='column_polygons.csv', header=TRUE)
pbdb <- read.csv(file='O_S_collections.csv', header=TRUE)
## make maps
lon.limit <- c(-172,-50)
lat.limit <- c(25,83)
map.orient <- c(54,-103,0)
map.data <- map('world', c('USA', 'Canada'), xlim=lon.limit, ylim=lat.limit, proj='azequalarea',orient=map.orient, plot=FALSE, interior=FALSE)
map.color <- 'gray25' # solid dark gray
pbdb.color <- rgb(1,0,0,0.3) # transparent red
rock.colors <- matrix(NA, nrow=15, ncol=3)
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')
rock.colors[,2] <- c('#6BA1FF','#7C7C7C','#9A9469','#FF8400','#FFFF00','#00FFFF','#FF80A8','#55432F','#008800','#55432F','#008800','#55432F','#3838FF','#7C7C7C','#008800')
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')
rock.colors <- rock.colors[order(rock.colors[,1]),]
top.units <- vector(mode='numeric', length=nrow(units)); counter <- 1
pdf(file='map_figure.pdf', height=20, width=50)
par(mfrow=c(2,5), mar=c(0,0,10,0)+0.1, pch=16, cex.main=7)
for(i in n.bins:1) {
unit.temp <- units[units[,3]>time.scale[i,3] & units[,4] 0) {
pbdb.proj <- mapproject(list(x=pbdb.temp[,2], y=pbdb.temp[,1]))
points(pbdb.proj\$x, pbdb.proj\$y, cex=3, col=pbdb.color)
}
lines(map.data\$x, map.data\$y, col=map.color)
}
dev.off()
top.units <- top.units[top.units>0]
rock.colors2 <- rock.colors[match(unique(units[is.element(units[,1], top.units), 5]),rock.colors[,1]),]
## make legend
pdf(file='map_legend.pdf', height=6, width=10)
layout(matrix(1:15, nrow=3, ncol=5, byrow=TRUE))
for(i in 1:nrow(rock.colors2)) {
par(mar=c(0.1,0.1,0.1,0.1))
plot(1:10, xlim=c(0,10), ylim=c(0,10), type='n', axes=FALSE, frame.plot=TRUE, xlab='', ylab='')
rect(1,1,9,4, col=paste(rock.colors2[i,2]))
text(5,8, labels=rock.colors2[i,1], cex=1.5)
text(5,6, labels=rock.colors2[i,3], cex=1.5)
}
dev.off()
";
fwrite($fh, $r_script);
$cmd = "echo 'rscript <- \"$r_file\"; source(rscript)' | " . "/usr/bin/R --slave 2>&1";
exec($cmd, $r_ran);
if(count($r_ran)>0) {
print_r($r_ran); echo "
";
}
echo 'File map_figure.pdf saved
';
echo 'File map_legend.pdf saved
';
}
//////////////
//
// stuff at the end
//
//////////////
if(isset($_POST['submit'])) {
$t1 = microtime(true);
$time_diff = $t1 - $t0;
if ($time_diff/60 < 1) {
$diff_seconds = round($time_diff, 3);
echo "
This process took ".$diff_seconds." seconds";
} else if ($time_diff>=1 & $time_diff<3600) {
$diff_min = round($time_diff/60, 3);
echo "
This process took ".$diff_min." minutes";
} else {
$diff_hour = round($time_diff/3600, 3);
echo "
This process took ".$diff_hour." hours";
}
}
?>