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topotools_first_steps_SCI.m
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topotools_first_steps_SCI.m
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%% First steps with topotools
%Download most recent version of topotools from github: https://github.com/wschwanghart/topotoolbox
%on Linux systems, you can do:
%git clone https://github.com/wschwanghart/topotoolbox
%Make sure to add the correct path to where you have downloaded and
%unzipped topotools:
addpath(genpath('/home/bodo/topotoolbox'))
rmpath(genpath('/home/bodo/topotoolbox\.git'));
%%
%For a detailed introduction to the stream channel theory and chi values,
%see Neely et al., 2017 (PDF in Matlab-Topotools/Neely17_KZPicker_SCI.pdf)
%and github repository: https://github.com/UP-RS-ESP/DEM-KZP
%% Load a DEM
dem_fname='Pozo_USGS_UTM11_NAD83_cl2_DEM_1m.tif';
SCI_dem = GRIDobj(dem_fname);
imagesc(SCI_dem)
imageschs(SCI_dem, SCI_dem)
SCI_dem_FIL = fillsinks(SCI_dem)
SCI_FD = FLOWobj(SCI_dem_FIL,'preprocess','carve');
SCI_FAC = flowacc(SCI_FD);
%dem_FAC_fname="Pozo_USGS_UTM11_NAD83_all_color_cl2_DEM_1m_FAC.tif";
%GRIDobj2geotiff(SCI_FAC,DEM_FAC_fname);
dem_resolution = SCI_dem.refmat(2,1);
% get the DEM resolution, used to convert area threshold to meters squared
area_threshold = 1e4
minApix = area_threshold/(dem_resolution*dem_resolution);
minApix = ceil(minApix); % convert area threshold to meters specified above
SCI_FAC_w = SCI_FAC > minApix; % masks flow accum grid (above threshold)
min_drainage_area_to_process = 1e4;
SCI_rivers_w = SCI_FAC.*(SCI_FAC.cellsize.^2) > ...
area_threshold;
SCI_STR_w = STREAMobj(SCI_FD, SCI_FAC_w);
SCI_rivers_STR = STREAMobj(SCI_FD, SCI_rivers_w);
%extract largest catchment
SCI_rivers_STR = klargestconncomps(SCI_rivers_STR, 1);
figure(1)
imageschs(SCI_dem, SCI_dem, ...
'ticklabels','nice','colorbar',true)
ylabel('UTM-Northing (m)', 'Fontsize', 12);
xlabel('UTM-Easting (m)', 'Fontsize', 12);
hold on
plot(SCI_rivers_STR, 'k')
[SCI_dbasins, SCI_dbasins_outlet] = drainagebasins(SCI_FD);
%Plot longitudinal river profile
figure(2)
plotdz(SCI_rivers_STR,SCI_dem, 'color', 'k', 'linewidth', 0.5)
hold on
plotdz(trunk(SCI_rivers_STR),SCI_dem, 'color', 'b', 'linewidth', 3)
%calculatuate relief
SCI_DEM_rel_200m = ...
localtopography(SCI_dem, 200);
figure
imageschs(SCI_dem, SCI_DEM_rel_200m)
colorbar
GRIDobj2geotiff(SCI_DEM_rel_200m,'filename2save.tif');
% calculate slope and area from DEM
% set a minimum gradient (no place in DEM has a slope of 0)
min_str_gradient = 0.0001
SCI_mg = imposemin(SCI_FD,SCI_dem,min_str_gradient);
SCI_rivers_slope = ...
gradient(SCI_rivers_STR,SCI_mg,...
'unit','tangent');
SCI_rivers_area = ...
SCI_FAC.Z(SCI_rivers_STR.IXgrid).*...
(SCI_FAC.cellsize).^2;
figure;
loglog(SCI_rivers_area, ...
SCI_rivers_slope, '+')
xlabel('Drainage Area [m^2]')
ylabel('Slope [m/m]')
grid on
%Better approach:
theta=-0.45
SCI_ksn045 = SCI_FAC;
SCI_ksn045 = SCI_dem_gradient8 ./ (SCI_FAC.*...
(SCI_FAC.cellsize^2)).^theta;
SCI_ksn045.name = 'ksn045';
SCI_ksn045.zunit = 'm^0.9';
%calculate area-slope relation for entire area (may not be useful)
SCI_slopearea = slopearea(SCI_rivers_STR,...
SCI_mg,...
SCI_FAC, ...
'areabinlocs', 'median', ...
'gradaggfun', 'median', ...
'streamgradient', 'robust', ...
'plot', false);
%% Figures
figure;
loglog(SCI_rivers_area, SCI_rivers_slope, ...
'.', 'color', [0.5 0.5 0.5])
xlabel('Drainage Area [m^2]')
ylabel('Slope [m/m]')
grid on
hold on
loglog(SCI_slopearea.a, SCI_slopearea.g, 'ks', 'markersize' ,5)
aeval = logspace(log10(min(SCI_slopearea.a)),log10(max(SCI_slopearea.a)),10);
geval = SCI_slopearea.ks(1)*aeval.^SCI_slopearea.theta;
loglog(aeval, geval, 'k-', 'linewidth', 2)
figure;
loglog(SCI_rivers_area, SCI_rivers_slope, '.', 'color', [0.9 0.9 0.9])
xlabel('Drainage Area [m^2]')
ylabel('Slope [m/m]')
grid on
hold on
SCI_slopearea = ...
slopearea(SCI_rivers_STR, SCI_mg,...
SCI_FAC, ...
'areabinlocs', 'median', ...
'gradaggfun', 'median', ...
'streamgradient', 'robust', ...
'plot', false, ...
'theta', 0.45);
loglog(SCI_slopearea.a, SCI_slopearea.g, 'ks', 'markersize' ,5)
aeval = logspace(log10(min(SCI_slopearea.a)),log10(max(SCI_slopearea.a)),10);
geval = SCI_slopearea.ks(1)*aeval.^SCI_slopearea.theta;
loglog(aeval, geval, 'k-', 'linewidth', 2)
%% Compare different theta
figure;
loglog(SCI_rivers_area, SCI_rivers_slope, '.', 'color', [0.7 0.7 0.7])
xlabel('Drainage Area [m^2]')
ylabel('Slope [m/m]')
grid on
hold on
SCI_slopearea = ...
slopearea(SCI_rivers_STR, SCI_mg,...
SCI_FAC, ...
'areabinlocs', 'median', ...
'gradaggfun', 'median', ...
'streamgradient', 'robust', ...
'plot', false, ...
'theta', 0.45);
loglog(SCI_slopearea.a, SCI_slopearea.g, 'ks', 'markersize' ,5)
aeval = logspace(log10(min(SCI_slopearea.a)),log10(max(SCI_slopearea.a)),10);
geval = SCI_slopearea.ks(1)*aeval.^SCI_slopearea.theta;
loglog(aeval, geval, 'k-', 'linewidth', 2)
title('Steepness Index with \theta=0.45')
figure;
loglog(SCI_rivers_area, SCI_rivers_slope, '.', 'color', [0.7 0.7 0.7])
xlabel('Drainage Area [m^2]')
ylabel('Slope [m/m]')
grid on
hold on
SCI_slopearea = ...
slopearea(SCI_rivers_STR, SCI_mg,...
SCI_FAC, ...
'areabinlocs', 'median', ...
'gradaggfun', 'median', ...
'streamgradient', 'robust', ...
'plot', false, ...
'theta', 0.4);
loglog(SCI_slopearea.a, SCI_slopearea.g, 'ks', 'markersize' ,5)
aeval = logspace(log10(min(SCI_slopearea.a)),log10(max(SCI_slopearea.a)),10);
geval = SCI_slopearea.ks(1)*aeval.^SCI_slopearea.theta;
loglog(aeval, geval, 'k-', 'linewidth', 2)
title('Steepness Index with \theta=0.4')
figure;
loglog(SCI_rivers_area, SCI_rivers_slope, '.', 'color', [0.7 0.7 0.7])
xlabel('Drainage Area [m^2]')
ylabel('Slope [m/m]')
grid on
hold on
SCI_slopearea = ...
slopearea(SCI_rivers_STR, SCI_mg,...
SCI_FAC, ...
'areabinlocs', 'median', ...
'gradaggfun', 'median', ...
'streamgradient', 'robust', ...
'plot', false, ...
'theta', 0.5);
loglog(SCI_slopearea.a, SCI_slopearea.g, 'ks', 'markersize' ,5)
aeval = logspace(log10(min(SCI_slopearea.a)),log10(max(SCI_slopearea.a)),10);
geval = SCI_slopearea.ks(1)*aeval.^SCI_slopearea.theta;
loglog(aeval, geval, 'k-', 'linewidth', 2)
title('Steepness Index with \theta=0.5')
figure;
loglog(SCI_rivers_area, SCI_rivers_slope, '.', 'color', [0.7 0.7 0.7])
xlabel('Drainage Area [m^2]')
ylabel('Slope [m/m]')
grid on
hold on
SCI_slopearea = ...
slopearea(SCI_rivers_STR, SCI_mg,...
SCI_FAC, ...
'areabinlocs', 'median', ...
'gradaggfun', 'median', ...
'streamgradient', 'robust', ...
'plot', false, ...
'theta', 0.6);
loglog(SCI_slopearea.a, SCI_slopearea.g, 'ks', 'markersize' ,5)
aeval = logspace(log10(min(SCI_slopearea.a)),log10(max(SCI_slopearea.a)),10);
geval = SCI_slopearea.ks(1)*aeval.^SCI_slopearea.theta;
loglog(aeval, geval, 'k-', 'linewidth', 2)
title('Steepness Index with \theta=0.6')
%% Generate a map of steepness indices
SCI_slopearea = ...
slopearea(SCI_rivers_STR, SCI_mg,...
SCI_FAC, ...
'areabinlocs', 'median', ...
'gradaggfun', 'median', ...
'streamgradient', 'robust', ...
'plot', false, ...
'theta', 0.45);
g = gradient(SCI_rivers_STR,SCI_dem);
a = getnal(SCI_rivers_STR,SCI_FAC)*SCI_FAC.cellsize^2;
SCI_ksn = g./(a.^SCI_slopearea.theta);
%% Map view:
figure;
plotc(SCI_rivers_STR,SCI_ksn)
colormap(jet)
caxis([0 50])
h = colorbar;
h.Label.String = 'KSn';
box on
axis image
%% aggregate into larger segments
figure;
SCI_ksna = aggregate(SCI_rivers_STR,...
SCI_ksn,'seglength',100);
imageschs(SCI_dem, SCI_dem, ...
'colormap', 'gray')
hold on
plotc(SCI_rivers_STR,SCI_ksna, ...
'linewidth', 2)
caxis([0 60])
h = colorbar;
colormap(jet)
h.Label.String = 'KSn';
box on
axis image
%% smooth steepness indices
SCI_ksnsmooth = smooth(SCI_rivers_STR,...
SCI_ksn);
figure;
plotc(SCI_rivers_STR,SCI_ksnsmooth)
caxis([0 80])
h = colorbar;
colormap(jet)
h.Label.String = 'KSn';
box on
axis image
%% Export as shapefile
S = STREAMobj2mapstruct(SCI_rivers_STR,...
'seglength',50,'attributes',...
{'ksn' SCI_ksnsmooth @mean ...
'uparea' a @mean ...
'gradient' g @mean});
shapewrite(S,'ksn_testshape.shp');
%% CHIPLOT
c = chiplot(SCI_rivers_STR,SCI_dem,SCI_FAC)
%% MORE FANCY STUFF for plotting
symbolspec_ksn045 = makesymbolspec('line',...
{'ksn045' [prctile([AOI_STR_MS.ksn045], 5) ...
prctile([AOI_STR_MS.ksn045], 95)] 'color' jet(6)});
symbolspec_ksnadj = makesymbolspec('line',...
{'ksnadj' [prctile([AOI_STR_MS.ksnadj], 5) ...
prctile([AOI_STR_MS.ksnadj], 95)] 'color' jet(6)});
clf
set(gcf,'units','normalized','position',[0 0 1 1]);
set(gcf, 'PaperOrientation', 'landscape');
set(gcf, 'PaperType', PaperType_size);
subplot(2,1,1,'align')
imageschs(AOI_DEM, AOI_DEM, 'caxis', ...
[floor(min(AOI_DEM(:))) ceil(max(AOI_DEM(:)))], ...
'colormap',gray,'colorbar',false)
hold on
mapshow(AOI_STR_MS,'SymbolSpec',symbolspec_ksn045, 'Linewidth', 2);
ylabel('UTM-Northing (m)', 'Fontsize', 12);
xlabel('UTM-Easting (m)', 'Fontsize', 12);
title_string = sprintf('%s: K_{sn} -0.45 ', DEM_basename_no_underscore);
title(title_string, 'Fontsize', 14), grid;
colorbar
caxis([prctile([AOI_STR_MS.ksn045], 5) prctile([AOI_STR_MS.ksn045], 95)])
hold off
%save a processed DEM to a geotiff:
%GRIDobj2geotiff(dem_fname);