bedmachine_3d documentation

bedmachine_3d creates a 3D map of BedMachine data.

Contents

Requirements

This function requires a set of Matlab tools and a Bedmachine dataset, and both will depend on where you're working. Get them here:

Syntax

bedmachine_3d(latlim,lonlim)
bedmachine_3d(xlim,ylim)
bedmachine_3d(...,'buffer',extrakm)
bedmachine_3d(...,'alpha',iceAlpha)
bedmachine_3d(...,'velocity',res_km)
bedmachine_3d(...,'greenland')
h = bedmachine_3d(...)

Description

bedmachine_3d(latlim,lonlim) creates a 3D map of the region specified by latitude and longitude limits. latlim and lonlin can be two-element arrays to specify just the min and max extents, or latlim,lonlim can be a range of values, and the resulting map will cover the entire range. Plotting might be slow for very large areas, so start small and see what your computer can handle.

bedmachine_3d(xlim,ylim) as above, but map extents are specified by polar stereographic meters.

bedmachine_3d(...,'buffer',extrakm) adds a buffer of specified width in kilometers around the region of interest.

bedmachine_3d(...,'alpha',iceAlpha) sets the transparency of the ice. By default, iceAlpha=1, meaning fully opaque. Use a value between 0 and 1 for semitransparent ice.

bedmachine_3d(...,'velocity',res_km) overlays ITS_LIVE velocity vectors at the specified spatial resolution res_km in kilometers. This option might be somewhat slow to render, especially for large regions. Requires ITS_LIVE Matlab toolbox (on File Exchange and GitHub).

bedmachine_3d(...,'greenland') plots Greenland instead of the default Antarctica.

h = bedmachine_3d(...) returns a structure of all the object graphical handles.

Example 1: Antarctic Peninsula

To make a map of any region of interest, you can simply enter the spatial extents of any region. You can enter coordinate in polar stereographic meters, or geographic (lat,lon). Here we'll use meters:

bedmachine_3d([-3000000 -1859450],[1881970 391935])

Setting view orientation

You can manually pan and rotate the map using the interactive figure tools, or you can use the view function to set the azimuth and elevation angles of the viewing angle, like this:

view(75,7)

Turn it into a 2D map like this:

view(2)

scalebarps('color','w')

Bathymetry colormap

By default, the bedmachine_3d function attempts to use the topo colormap from the cmocean function, which is available on the Mathworks File Exchange as a standalone function, or as part of the Climate Data Toolbox for Matlab. If you don't have the cmocean function, your default colormap will be used for bathymetry.

To set the extents of the bathymetry color axis, simply use the caxis command. Suggestion: Enter values that are symmetric about zero to sea level in the center of the color scale:

caxis([-1 1]*1500)

Example 2: Amery Ice Shelf

Instead of entering the spatial extents of your region of interest in polar stereographic meters, you may alternatively use geographic coordinates:

lat = [-75.36 -65.30];
lon = [63.64  65.18];

figure
bedmachine_3d(lat,lon);

Change the orientation to your liking:

view(70.5,11)

Vertical exaggeration

By default, bedmachine_3d plots at 20x vertical exaggeration. To change this, set the third value in the data aspect ratio using the daspect command. Here we'll change it to 100x exaggeration by specifying 1/100:

daspect([1 1 1/100])

Example 3: Pine Island Glacier

If you don't know the coordinates of the extents of the map you'd like to generate, but you know what feature you want at the center, use the scarloc function to get the center coordinates:

[piglatin,piglon] = scarloc('pine island glacier')
piglatin =
  -75.1667
piglon =
  -100

With just the center coordinates, you can add a buffer on all sides of the center coordinates. For example, adding 500 km buffer on all sides of the center location of PIG, we'll get a 1000x1000 km map:

figure

bedmachine_3d(piglatin,piglon,'buffer',500);

view(29,42)
caxis([-1 1]*2000)

Ice Transparency

You can make the ice semitransparent by specifying a value of alpha between 0 (invisible) and 1 (opaque):

[piglatin,piglon] = scarloc('pine island glacier');

figure
bedmachine_3d(piglatin,piglon,... % center coordinates
   'buffer',500,... % 500 km on all sides (a 1000x1000 km map)
   'alpha',0.5);    % semitransparent ice

view(29,42)
caxis([-1 1]*2000)

Example 4: Getz Ice Shelf

Another way to enter the location of interest is simply to enter all of the coordinates of the area you want to plot. For example, if you want a map that fully encompasses the Getz Ice Shelf, use antbounds_data to get the outline of the ice shelf:

[lat,lon] = antbounds_data('getz');

figure
plotps(lat,lon)

With the coordinates of the outline of Getz, we can now make a 3D map of Getz Ice Shelf. Add a buffer of 100 km on all sides for good measure:

figure
bedmachine_3d(lat,lon,'buffer',100);

And again, we can change the transparency:

figure
bedmachine_3d(lat,lon,'buffer',100,'alpha',0.6);
caxis([-1 1]*2500)

Example 5: Greenland

Greenland works the same way as Antarctica, but a word of caution: Although Greenland is smaller than Antarctica, the Greenland BedMachine dataset is much higher resolution, so plotting large areas might be slow!

Here let's start by getting oriented. Assuming you have Arctic Mapping Tools, draw an outline of Greenland, and then add a yline at top of the map we'll generate, and a place a vertical line to demark the left side of our region of interest:

figure
greenland

yline(-3e6)
xline(-0.5e6)

With the x and y coordinates shown as straight lines in the map above, enter the extents of the bottom right quadrant of that map. Use Inf to say we want all the data to the edge of the BedMachine dataset.

I reiterate, this a small portion of Greenland, but due to the high resolution, this takes about 10 seconds for my laptop to render:

figure
bedmachine_3d([-0.5e6 Inf],[-Inf -3e6],'greenland')

Get a different perspective:

view(-143,32)

Example 6: Denman Glacier

In this example, we'll explore how to set specific properties of the graphics objects. Start by plotting 3D map of Denman Glacier, and return a handle h of the graphics objects:

[lat,lon] = scarloc('denman glacier');

figure
h = bedmachine_3d(lat,lon,'bufer',300,'alpha',0.6);

Take a look at the contents of h:

h
h = 
  struct with fields:

          bed: [1×1 Surface]
         base: [1×1 Surface]
          sfz: [1×1 Surface]
      iceside: [1×1 Surface]
      bedside: [1×1 Surface]
     oceansfz: [1×1 Patch]
    oceanside: [1×1 Surface]
       corner: [1×4 Graphics]

Above, you see that the bed is plotted as a surface object, the top and sides of the ice sheet are plotted as surfaces, the top of the ocean is plotted as a patch object, and there are four vertical lines that mark the corners of the ocean.

You can query or change the properties of each object however you'd like. For example, if you'd like to know how transparent the ocean surface is, check the FaceAlpha value, like this:

h.oceansfz.FaceAlpha
ans =
    0.1000

Specifying object properties

To change any object property, simply set it to your liking. Here we'll make the top and sides of the ocean more opaque, and we'll use my rgb function (available on File Exchange; also part of the Climate Data Toolbox) to make the ocean orange:

h.oceansfz.FaceAlpha = 0.6;
h.oceanside.FaceAlpha = 0.6;
h.oceansfz.FaceColor = rgb('orange');
h.oceanside.FaceColor = rgb('orange');

Example 7: Advanced options

In this example, we'll start with a map of the Filchner Ice Shelf:

[lat,lon] = antbounds_data('filchner');

figure
h = bedmachine_3d(lat,lon,'bufer',50,'alpha',0.4);
view(-122,37)
caxis([-1 1]*1400)

% Make the base of the ice shelf extra transparent:
h.base.FaceAlpha = 0.2;

Looks pretty good. Now what if we wanted to depict basal melt rates? That data should be shown nowhere else but the base of the ice shelf, right? The good news is the base of the ice shelf is plotted as a surface object, so it's easy to add melt rates as CData.

Unfortunately, Matlab only lets us use one active colormap at a time, so plotting color-scaled bed topography along with color-scaled melt rates will be difficult. One solution: Convert either the color scaling of the basal topography or the melt rates to a static RGB image.

Start by converting basal topography colormap to a static image:

% Get the bed elevation data:
bed = h.bed.ZData;

% Convert to a grayscale matrix:
bed_gray = mat2gray(bed,[-1 1]*1400);

% Index the grayscale matrix to the topo colormap:
cmap = cmocean('topo');
ind = gray2ind(bed_gray,size(cmap,1));
bed_RGB = reshape(cmap(ind+1,:),[size(bed,1) size(bed,2) 3]);

% Change the bed color data to a static texturemap:
h.bed.CData = bed_RGB;
h.bed.FaceColor = 'texturemap';

Now the bed color is no longer tied to the current colormap. You can change the color axis limits or the colormap without affecting how the bed looks. And that's what we will do.

Now we will use melt_interp_adusumilli (available on File Exchange) to interpolate melt rates published by Adusumilli et al. 2020:

% Get surface grid coordinates:
x = h.base.XData;
y = h.base.YData;

% Convert arrays to grids:
[X,Y] = meshgrid(x,y);

% Get melt rates corresponding to the grid:
melt = melt_interp_adusumilli(X,Y);

Now we can set the color data of the ice shelf to the basal melt rates, and change the colormap accordingly:

h.base.CData = melt;
h.base.FaceColor = 'texturemap';
h.base.FaceAlpha = .9;

caxis([-3 3])
cmocean balance
cb = colorbar;
ylabel(cb,'basal melt rate (m/yr)')

Or of course you can always change it to a 2D view:

view(2)

Example 8: ITS_LIVE velocity vectors

If you have the ITS_LIVE toolbox (on GitHub and File Exchange), you can easily overlay velocity vectors on the surface. Just use the 'velocity' option, and specify the spatial resolution (in kilometers) of the velocity vectors you'd like to plot. Here's Drygalski Ice Tongue, with a 50 km buffer around it, and velocity vectors plotted at 2 km resolution.

% Get the outline of Drygalski Ice Tongue:
[lat,lon] = antbounds_data('drygalski');

figure
h = bedmachine_3d(lat,lon,'buffer',50,'velocity',2);

caxis([-1 1]*1100) % bed topography color limits
daspect([1 1 1/15]) % 15x vertical exaggeration
view(-47,20) % viewing angle

% Make the ocean a little more opaque:
h.oceansfz.FaceAlpha = 0.3;
h.oceanside.FaceAlpha = 0.3;

Changing the properties of the vectors is pretty straightforward. Set the color and linewidth, etc to your liking. Also, in addition to setting the spatial resolution of the velocity vectors, note that you can also lengthen the arrows by changing the AutoScaleFactor. The default AutoScaleFactor is 0.9, so below we set it to 2, which more than doubles the length of each arrow.

h.vel.Color = rgb('purple');
h.vel.AutoScaleFactor = 2;

Extra tips

lighting phong

which I find gives a more natural feel. However, phong lighting is slow when graphics are complex, especially if the region you're plotting is large. If you use phong lighting set it at the very end, just before you save the image. That way you won't have to deal with its sluggishness while you tinker with the viewing angle or whatnot.

Known issues

Citing this dataset

If you use BedMachine data, please cite the Morlighem paper listed below. And if this function is useful for you, please do me a kindness and cite my Antarctic Mapping Tools paper.

Morlighem M. et al., (2017), BedMachine v3: Complete bed topography and ocean bathymetry mapping of Greenland from multi-beam echo sounding combined with mass conservation, Geophys. Res. Lett., 44, doi:10.1002/2017GL074954.

Morlighem, M., E. Rignot, T. Binder, D. D. Blankenship, R. Drews, G. Eagles, O. Eisen, F. Ferraccioli, R. Forsberg, P. Fretwell, V. Goel, J. S. Greenbaum, H. Gudmundsson, J. Guo, V. Helm, C. Hofstede, I. Howat, A. Humbert, W. Jokat, N. B. Karlsson, W. Lee, K. Matsuoka, R. Millan, J. Mouginot, J. Paden, F. Pattyn, J. L. Roberts, S. Rosier, A. Ruppel, H. Seroussi, E. C. Smith, D. Steinhage, B. Sun, M. R. van den Broeke, T. van Ommen, M. van Wessem, and D. A. Young. 2019. Deep glacial troughs and stabilizing ridges unveiled beneath the margins of the Antarctic ice sheet, Nature Geoscience. doi:10.1016/j.cageo.2016.08.003.

Greene, C. A., Gwyther, D. E., & Blankenship, D. D. Antarctic Mapping Tools for Matlab. Computers & Geosciences. 104 (2017) pp.151-157. doi:10.1016/j.cageo.2016.08.003.

Author Info

This function and supporting documentation were written by Chad A. Greene of NASA Jet Propulsion Laboratory, April 2021.