Category Archives: Miscellaneous

Chinook salmon and southern resident killer whales occupy similar depths in the Salish Sea

New paper by UW colleagues entitled “Interpreting vertical movement behavior with holistic examination of depth distribution: a novel method reveals cryptic diel activity patterns of Chinook salmon in the Salish Sea” shows some results from Vemco receivers I deployed in the San Juan Islands. Young adult Chinook favor depths less than ~30 meters, with some seasonal variability in their diel activity patterns. Overall, they go deeper and vary more in the depths at night.

Dive profiles for two Salish Sea Chinook salmon during the summer and fall.

Dive profiles for two Salish Sea Chinook salmon during the summer and fall.

Interestingly, according to a report to NOAA/NWFSC by Baird et al, 2003 (STUDIES OF FORAGING IN “SOUTHERN RESIDENT” KILLER WHALES DURING JULY 2002: DIVE DEPTHS, BURSTS IN SPEED, AND THE USE OF A “CRITTERCAM” SYSTEM FOR EXAMINING SUB-SURFACE BEHAVIOR) SRKWs spend >97% of their time at depths of less than 30m.

This suggests any future deployment of horizontal echosounders should aim to ensonify a depth range centered on ~25m (e.g. 5-45m or 10-40 m).  Compared to the estimated orientation and surveyed depth range of our 2008-9 salmon-SRKW echosounder pilot studies, we may want to measure inclination more carefully to (a) center the survey on the mean summertime depth range of Chinook and (b) avoid ping reflections from surface waves, boats, and bubbles (which may have confused interpretations of targets >100 m from the transducer).  Here’s my diagram for the situation in 2008-9 in which we were centered on 15 m and ensonified a maximum depth range of ~0-30m (in other words, we may have been aiming a little high):

Screen grab from the 2009 ASA presentation showing echosounder geometry

Screen grab from the 2009 ASA presentation showing echosounder geometry



Basic R Studio and ggplot2 syntax

While I continue to try to get Sage to underpin the analysis stages of my open scientific workflow, a LOT of my colleagues and cohort use R these days.  So this week I installed R Studio and ggplot2 for OSX.

Here are notes from my first foray into plotting histograms.

First I took some date/time data in a Libre Office spreadsheet, converted it to decimal hour of day to keep things simple, renamed column headers to be simple single words (e.g. underscores to connect words), and then saved the active sheet as a tab-delimited .csv file (in this case named 2012-human.csv).

> lk2012<-read.table("/Users/scott/Documents/beamreach/research/pubs-in-progress/02a - ship SL/r-scott/2012-human.csv",header=T,sep="\t")
> png("/Users/scott/Documents/beamreach/research/pubs-in-progress/02a - ship SL/r-scott/lk-human-hr-hists.png")
> par(mfrow= c(3, 1))
> hist(lk2011$hour,breaks=24)
> hist(lk2012$hour,breaks=24)
> hist(lk2013$hour,breaks=24)

That reads the .csv file into lk2012, then prints this 3 panel plot of hour histograms —

Histograms of the hours in which reports were made to the Salish Sea hydrophone network's Google-spreadsheet-based observation log in 2011, 2012, & 2013.

Histograms of the hours in which reports were made to the Salish Sea hydrophone network’s Google-spreadsheet-based observation log in 2011, 2012, & 2013.

More on ggplot2 as I learn it… but know that it is making most of the plots for our current paper in progress regarding underwater noise from Salish Sea ships.

Revisiting GMT, perl, and proj

The time has come to make a site map for our ship source level paper.  I always love this stage of a project — map making — because it still takes me back to some of the geekiest open source Unix stuff my PhD advisor, Russ McDuff, taught me: using public bathymetric data in Generic Mapping Tools (GMT) and Proj within Perl to make awesome maps of the ocean for free!  It’s always a chore to get all these tools working within your Li/Un/*ix operating system, but below is an example of what they can do from this working directory

In my latest attempt (within a account), I had to remember (again) the syntax and commands for setting path variables…

  1. edit .bashrc to include a path to your proj and GMT binaries
  2. export PATH=~/bin:~/usr/local:~/usr/local/bin:~/$PATH
  3. execute: . .bashrc to reinitialize the PATH variable
  4. check PATH with env
  5. check all is well with which proj

Here’s the perl script for making the (above) rough draft map of Haro Strait and the San Juan Islands.


#`gmtset X_AXIS_LENGTH 8.5i X_AXIS_LENGTH 11i`;
#`gmtset ANOT_FONT_SIZE 8 ANOT_OFFSET 0.037`;
#$gxscl=4; $gyscl=4;
#`gmtset GLOBAL_X_SCALE $gxscl  GLOBAL_Y_SCALE $gyscl`;

# Haro Strait region
#$prj=6;        # inches/degree
$lonmin=-123.5; $lonmax=-123; $latmin=48.25; $latmax=48.75;
#$xoff=2.5;  $yoff=4;
$xoff=2;  $yoff=2;
#$xoff=0;  $yoff=0;



`psbasemap $proj $bound -K -P -V -X$xoff -Y$yoff $tick > $out_ps`;
`grdimage $basemap -C$cptfile $proj $bound -P -O -K -V >> $out_ps`;
`grdcontour $basemap -C50 $proj $bound -W.05p -Q10 -P -O -K -V >> $out_ps`;
#`grdcontour $basemap -Cfig1cnt $proj $bound -W1p/255/255/255 -Q10 -P -O -K -V >> $out_ps`;
#`grdcontour $basemap -C10 $proj $bound -W.05p -Q10 -P -O -K -V >> $out_ps`;
#`grdcontour $basemap -C20 -A100f3 $proj $bound -W1p -Q10 -P -O -K -V >> $out_ps`;
#`grdcontour $basemap -C500 $proj $bound -W$cntpen -Q10 -P -O -K -V >> $out_ps`;
#`grdcontour $basemap -C0 $proj $bound -W$cntpen -Q10 -P -O -K -V >> $out_ps`;
#`grdcontour $basemap -C2000 -Af3 $proj $bound -W0.5p/50/50/50 -Q10 -P -O -K -V >> $out_ps`;

#`pscoast $proj $bound -Dh -A9 -W -G255/255/255 -S240/240/240 -N1 -N2 -O -K -V >> $out_ps`;
#`pscoast $proj $bound -Dh -A9 -W -N1 -N2 -O -K -V >> $out_ps`;
# Land grey:
#`pscoast $proj $bound -Dh -A20 -W0.5p/10/10/10 -G200/200/200 -O -K -V >> $out_ps`;
`pscoast $proj $bound -Dh -A20 -W0.5p/10/10/10 -O -K -V >> $out_ps`;

# Label pertinent features...
open (WORDS, ">labels");
print (WORDS "-123.75  48.445    $wfont 0 0 2 Victoria\n");
#print (WORDS "-124.690  48.245    $nodefont 0 0 TL Neah Bay\n");
#print (WORDS "-122.750  48.060    $nodefont 0 0 TR Marine Science Center\n");
#print (WORDS "-123.300  48.550    $nodefont 0 0 BR Orcasound lab\n");
print (WORDS "-123.065  48.525    $nodefont 0 0 TL Lime Kiln\n");
#print (WORDS "-122.700  48.425    $nodefont 0 0 TL State Park\n");
print (WORDS "-122.700  47.635    $nodefont 0 0 TC Seattle\n");
#`pstext -Jm -R -G0/0/0 -Dj$xtoff/$ytoff-O -K -V < labels >> $out_ps`;
# No background rectangles
#`pstext -Jm -R -G0/0/0 -O -K -V < labels >> $out_ps`;
# Background rectangles with rounded corners: [ -W[color,][o|O|c|C[pen]]
#`pstext -Jm -R -G0/0/0 -W255/255/255,Othick,255/0/0 -O -K -V < labels >> $out_ps`;
`rm labels`;

# Put symbols on nodes
open(SYM, ">nodes.lonlat") || die "Can't open nodes.lonlat!\n";
# print SYM "-124.675  48.390\n";  # Neah Bay
# print SYM "-122.750  48.125\n"; # Port Townsend
# print SYM "-123.200  48.550\n"; # Orcasound
 print SYM "-123.150  48.500\n"; # Lime Kiln
# print SYM "-122.350  47.600\n"; # Seattle
`psxy nodes.lonlat -Jm -R -P -Sc0.5/0/0/0 -G255/0/0 -V -O -K >> $out_ps`;

#Put more symbols on...
`psxy catscradle.lonlat -Jm -R -P -Sc0.05/0/0/0 -G255/0/0 -V -O -K >> $out_ps`;

# Good offset if using WS lat/lon labels
#$locyoff=1.8; $locxoff=2.8;
$locyoff=0.75; $locxoff=0.75;
#`psbasemap -Jm0.2 -R-135/-105/35/55 -O -K -X$locxoff -Y$locyoff -P -Ba10f5/a5f5WeSn >> $out_ps`;
#`psbasemap -Jm0.2 -R-135/-105/35/55 -O -K -X$locxoff -Y$locyoff -P -Ba10f5/a5f5wesn >> $out_ps`;
`psbasemap -Jm2.5 -R-125/-122/47/48.5 -O -K -X$locxoff -Y$locyoff -P -Ba10f5/a5f5wesn >> $out_ps`;
# plot the coast line
#`pscoast -Jm -R -O -K -W -G210/180/140 -S135/206/250 -N1 -N2 >> $out_ps`;
#`pscoast -Jm -R -Di -A200 -O -K -W -G216/242/254 -S148/191/139 -N1 -N2 -V >> $out_ps`;
# Seattle Aquarium Kiosk colors
#`pscoast -Jm -R -Di -A200 -O -K -W -G172/208/165 -S186/232/254 -N1 -N2 -V >> $out_ps`;
`pscoast -Jm -R -Di -A200 -O -K -W -G200/200/200 -S255/255/255 -N1 -N2 -V >> $out_ps`;

# Put symbols on key cities
open(SYM, ">cities.lonlat") || die "Can't open cities.lonlat!\n";
# print SYM "-123.45 48.45\n";
`psxy cities.lonlat -Jm -R -P -Sc0.5/0/0/0 -G0/0/0 -V -O -K >> $out_ps`;

# Small box around the zoomed area
$lonboxmax=$lonmax; $lonboxmin=$lonmin;
$latboxmax=$latmax; $latboxmin=$latmin;
open(BOX, ">magbox.lonlat") || die "Can't open magbox.lonlat!\n";
print BOX "$lonboxmax-$marg   $latboxmax+$marg\n";
print BOX "$lonboxmax-$marg      $latboxmin-$marg\n";
print BOX "$lonboxmin+$marg      $latboxmin-$marg\n";
print BOX "$lonboxmin+$marg      $latboxmax+$marg\n";
print BOX "$lonboxmax-$marg      $latboxmax+$marg\n";
`psxy magbox.lonlat -Jm -R -P -W4p/0/0/0 -V -O >> $out_ps`;
`rm magbox.lonlat`;

`convert $out_ps $out_nm.png`;

Ship source level work with Val in Seattle

Working together in Seattle, we are still struggling to understand and compute how loud commercial ships are at high-frequencies (1-100 kHz).  In pursuit of the optimal way to convert our receive levels into source levels, we are considering spherical spreading vs a frequency-dependent model informed in part by our tonal transmission loss experiments at Lime Kiln.  We also MUST tackle how to apply the physics of sound absorption in sea water, at least for those ships for which we have measured a signal above noise in the 10-100 kHz frequency range.

Today Val is working on comparing 1/3 octave band levels for a few key ships with measurements made by JASCO.  He is also comparing our transmission loss experimental results with theirs, ideally seeing whether we have similar frequency-dependent spreading models and assessing how different they are from a simple assumption of spherical spreading with or without absorption.

I continue scouring the literature (some of it rooted in WWII Naval measurements) for comparable measurements of surface ship noise.  I’m also trying to understand cavitation better, including searching for any measurements of noise from cavitating propellers and/or ships.  Thus far the best recent examples are Kipple and Hildebrand’s single ship (among many measurements of noise below ~1 kHz), but I’ve just found some declassified measurements of surface ships and submarines that appear to extend up into the 10-100 kHz range.

On a procedural note, I need to add Zotpress to this blog so I can insert citations properly…