GMT symbols for Whale-watchers and marine biologists¶

What’s this?¶

This is a collection of custom symbols for the Generic Mapping Tools (GMT) software that may be of interest mainly to whale-watchers or whale researchers. With this, you can show your data in a map created with GMT as fine and detailed marine mammal’s icons instead the usual circles or squares. GMT is a very complete GIS software so you could add also bathymetric and coastal lines, the locations of the main cities and ports in your area, or other useful data like plankton concentration or water temperatures in your map.

The collection currently comprises symbols for 8 species of Baleen Whales, 16 of Toothed Whales, 2 species of seals and 4 more for “unidentified” seals, beaked whales, dolphins or whales. Several versions (low/normal/high) of most symbols are also available, and you can change easily between color or gray symbols in 57 of the 90 symbols provided, therefore you can choose really between more than 150 different symbols.

Author of the symbols: Pablo Valdés <marine.biol@arsystel.com> (Spanish preferred, but you can use also English or French). In the future I hope to create gradually more symbols for other species. I greatly appreciate your suggestions and feedback.

These symbols are freely available under a GNU Library General Public Licence (version 2, or later).

How to use the symbols?¶

Before to start, think in the type of map you want to obtain and prepare your data. If you want to create a 2D map (most common situation) you need plot, if you want a 3D map you should use plot3d instead. Think also in how many different symbols you want to show in each individual map. You should have at least a different .xy file for each species that you want to show. You could want also to show separately males and females or adults/youngs/calfs. In this case, you will either need to give a different size to each group or place the data for each group in a different .xy (or .xyz) file and provide different symbols.

A valid input datafile.xy is simply a text file containing several lines like this:

#common dolphin data, file: cdolphin.xy
#longitude latitude (symbolsize) (symboltype) (...others)
-5:40:44   30:30:01  0.10    k
6:45.70   -43       0.12     k
355.707   42.7543   0.17     k
...

plot can deal with several lon/lat formats. All of this are accepted. The symbolsize field is optional, but if not provided you must specify a common size (used for all observations in this file) in the script with -Sksymbolname/simbolsize

The symboltype field is also optional, k means custom symbol. Currently I can’t pass different symbols to plot in the same file (I need split first the file) and must provide a unique symbolname in the script for all lines, so the interest of having this field is reduced. Probably I’m missing something. You can also add other fields like font, angle, position or a last field with a short remembering note in a text line, they are ignored by plot but you could pass it to text.

Take a look at the pics (.png) and choose the symbols that you want. No installation needed, simply browse the directory symbols and copy the files with extension .def having the same name as the desired pic to your working directory. This is the list of symbols available:

English name (scientific name) - symbols available

Cetacea

Toothed Whales, SubO. Odontoceti

Common dolphin (Delphinus delphis) - ddelphis_low.def - ddelphis_midlow.def - ddelphis.def - ddelphis_midhigh.def - ddelphis_high.def
Stripped dolphin (Stenella coeruleoalba) - stripped_low.def, stripped.def, stripped_high.def
Bottlenose dolphin (Tursiops truncatus) - bottlenose_low.def, bottlenose.def, bottlenose_high.def
Atlantic White-sided dolphin (Lagenorhynchus acutus) - atlanticwhitesided_low.def, atlanticwhitesided.def, atlanticwhitesided_high.def
Killer whale (Orcinus orca) - killerwhale_low.def, killerwhale.def, killerwhale_high.def
Risso’s dolphin (Grampus griseus) - rissosdolphin_low.def, rissosdolphin.def, rissosdolphin_high.def
Short-Finned Pilot whale (Globicephala macrorhynchus) - shortfinnnedpilotwhale_low.def, shortfinnnedpilotwhale.def - shortfinnnedpilotwhale_low.def
Long-Finned Pilot whale (Globicephala melaena) - longfinnedpilotwhale_low.def, longfinnedpilotwhale.def - longfinnedpilotwhale_low.def
Southern Rightwhale Dolphin (Lagenodelphis peronii)
- srightwhaledolphin_low.def, srightwhaledolphin.def
- srightwhaledolphin_high.def
Common porpoise (Phocoena phocoena) - commonporpoise_low.def, commonporpoise.def, commonporpoise_high.def
Burmeister’s porpoise (Phocoena spinipinnis) - burmeistersporpoise_low.def, burmeistersporpoise.def, burmeistersporpoise_high.def
Spectacled porpoise (Australophocaena dioptrica) - spectacledporpoise_low.def, spectacledporpoise.def, spectacledporpoise_high.def
Beluga (Delphinaterus leucas) - beluga_low.def, beluga.def, beluga_high.def
Cuvier’s beaked whale (Ziphius cavirostris) - cuviersbeaked_low.def, cuviersbeaked.def, cuviersbeaked_high.def
Unidentified beaked whale (Mesoplodon spp.) - unidentifiedbeakedwhale_low.def, unidentifiedbeakedwhale.def, unidentifiedbeakedwhale_high.def
Sperm whale (Physeter macrocephalus) - spermwhale_low.def, spermwhale.def, spermwhale_high.def - spermwhaletail_low.def, spermwhaletail.def, spermwhaletail_high.def
Pygmy sperm whale (Kogia breviceps) - pigmyspermwhale_low.def, pigmyspermwhale.def, pigmyspermwhale_high.def
A dolphin (gen. unknown) - unidentifieddolphin_low.def, unidentifieddolphin.def, unidentifieddolphin_high.def

Baleen Whales, SubO. Misticeti:

Minke whale (Balaenoptera acutorostrata)
- minkewhale.def, minkewhale_low.def, minkewhale_high.def
Fin Whale (Balaenoptera physalus) - finwhale.def, finwhale_low.def, finwhale_high.def
Sei Whale (Balaenoptera borealis) - seiwhale_low.def, seiwhale.def, seiwhale_high.def
Humpback Whale (Megaptera novaeangliae) - humpbacktail_one_low.def, humpbacktail_one.def - humpbacktail_two_low.def, humpbacktail_two.def - jumpback_low.def (yes, with j, look at the pic ;-)) - jumpback.def, jumpback_high.def
Gray Whale (Eschrichtius robustus) - graywhale_low.def, graywhale.def, graywhale_high.def
Right Whales (Eubalaena glacialis, Eubalaena australis) - southernrightwhale_low.def, southernrightwhale.def, southernrightwhale_high.def - northernrightwhale_low.def, northernrightwhale.def, northernrightwhale_high.def
A whale (unknown species) - unidentifiedwhale_low.def, unidentifiedwhale.def, unidentifiedwhale_high.def

3: Call them including the corresponding plot or plot3d lines in a GMT script like this:

#!/usr/bin/env bash
gmt coast -JM20c -R-10/6/33/36 -K -W0.5pt/0 -P -Gblack > myfile.ps
gmt plot cdolphin.xy -Skcommondolphin/ -JM20c -R-10/6/33/36 -P -K -O >> myfile.ps
gmt plot bottlenose_dolphin.xy -Skbottlenose_high/0.5 -K -O ...etc >> myfile.ps
gmt plot killerwhale_data.xy   -Skkillerwhale_low/0.5 -O ...etc >> myfile.ps

In our examples we will place all the .xy and .def files in our working directory, but you can find more convenient to move them to several subdirectories named, for instance, data and symbols:

gmt plot data/killer_whale.xy -Sksymbols/Cetacea/killerwhale/0.5 -O ...etc >> myfile.ps

In this case, please read also the points 1.2-1.3 of the file FAQ.txt

4: Run the bash script, print/open the output postscript file myfile.ps, or convert to PDF or rasters with gmt psconvert.

FAQ and Troubleshoting¶

The symbols are not drawn¶

When In run the script I obtain GMT ERROR: plot:

Could not find custom symbol symbolname.def!¶

Probably you had wrote something like: -Sksymbolname.def/0.5 Please note that this is incorrect, you should remove .def and use -Sksymbolname/0.5 instead in your script.

Could not find custom symbol mydirsymbolname!, Cannot open file mydirmyfile.xy!¶

Probably you had placed your symbols in a subdirectory and are using the wrong directory notation for your operative system. Please note that Linux use “/” for directories whereas Microsoft Windows use “”, so check if you had wrote something like -Skmydirkillerwhale when you want to say -Skmydir/killerwhale or mydirkillerwhale.xy instead mydir/killerwhale.xy This error could also occur if you try to run a script created in Windows in a Linux OS or vice versa. Try to intercange / and and run again the script.

Symbol customization¶

The symbols are to much big!, What size should I use?¶

In your script you’ll need to reduce the normal size of the symbols. A range of sizes between 0.12 and 0.18, (rarely more than 0.2) should be OK. Some symbols are a little bigger than others, so play with the size in the script until you obtain the right for you. Remember that you can easily modify the size of the symbol directly in your GMT script (-Skoorca/0.8 -Skoorca/0.2) or in your file xy. I recommend to use different sizes for males, females and calfs.

I don’t want color symbols!¶

You can easily obtain the same symbol in graytones editing the def file with your favourite text editor. Follow the instructions you will find inside the .def files. Some symbols like the killerwhale have only a b/w version for obvious reasons.

How can I change the colour of the symbols?¶

The colour of each area is specified inside the def file, so you can’t simply specify a colour directly in your GMT script or you will obtain strange results. You should open and edit the -W and -G in the def file.

After editing the def file I obtain strange polygonal patches instead the desired symbol but all points are the same than in the original .def!

Check that you don’t have deleted the pt specification in a line with -W. This (-W100) is erroneous, (width line 100 pt) while this (-W025.pt/100) is ok.