I'm trying to smooth or interpolate away the "steps" building up to a intensity maximum, and at the same time preserving the shape of the surface so that the estimated width does not get shifted or changed. I have tried interpolating to a higher resolution using 2D spline, but the "steps" are still present and the estimated maxima region changes. Could someone please help me in smoothing/interpolating away those steps to make the surface look more continuous while conserving the surface shape?
As always, many thanks in advance for any advice or help!!
Uninterpolated
Interpolated
Attempt
conversion = 1/49.0196; % in mm/pixel
new_xData = linspace(xData(1), xData(end), 10*length(xData));
new_yData = linspace(yData(1), yData(end), 10*length(yData)).';
new_zData = interp2(xData, yData, zData, new_xData, new_yData, 'spline');
xData = new_xData; yData = new_yData; zData = new_zData;
h = figure();
surf(xData, yData, zData, 'LineStyle', 'none', 'FaceColor', 'interp');
xlim([xData(1) xData(end)])
ylim([yData(1) yData(end)])
zlim([0 ceil(max(zData(:)))]);
colormap(jet(4096))
xlabel('mm'); ylabel('mm'); zlabel('ln(Intensity)');
set(gca,'Ydir', 'reverse')
grid on
shading interp
view(3); axis vis3d; camlight;
% Change x and y tick labels from pixels to mm
addMM = #(x) sprintf('%.1f', x * conversion);
xticklabels(cellfun(addMM,num2cell(xticks'),'UniformOutput',false));
yticklabels(cellfun(addMM,num2cell(yticks'),'UniformOutput',false));
% Find maxium intensity region and plot it
hold on
maxValue = max(zData(:));
[rowsOfMaxes, colsOfMaxes] = find(zData == maxValue);
x_minind = min(colsOfMaxes(:));
x_maxind = max(colsOfMaxes(:));
p = zeros(1, 2);
p(1) = plot3(linspace(xData(x_minind), xData(x_minind), ...
length(yData)), yData, zData(:, x_minind), 'Linestyle', '-.', ...
'Color', 'black', 'LineWidth', 2.0);
p(2) = plot3(linspace(xData(x_maxind), xData(x_maxind), ...
length(yData)), yData, zData(:, x_maxind), 'Linestyle', '-.', ...
'Color', 'black', 'LineWidth', 2.0);
hold off
legend(p(1), 'Estimated width of maximum intensity', 'Location', 'North')
set(gca, 'FontSize', 14)
Related
I'm writing a code to plot the circular orbit of a satellite (created using comet3() function) around a 3d model of the Earth (created using surf() and set() functions). The problem is that I can't seem to find a way to get them together in the same plot. I have tried using hold on and hold off but that doesn't seem to work either. I'm pasting the MATLAB code below for reference.
Edit: All the other functions like sv_from_coe(), odeset, etc. are working perfectly, the only place I'm facing issue is combining the plots from comet3() and set().
G = 6.67E-11;
Me = 5.976E24;
coe = [6776, 0.0005638, 2.0543, 0.9, 5.549, 0];
[r, v] = sv_from_coe(coe);
rv = [r v];
opt = odeset('RelTol', 1e-6, 'AbsTol', 1e-6);
[t,X] = ode45(#rate, [0 2*1.5*3600], rv, opt);
[x,y,z] = sphere;
r_earth = 6378*1000;
figure
hs1 = surf(x*r_earth,y*r_earth,-z*r_earth);
cdata = imread('1024px-Land_ocean_ice_2048.jpg');
alpha = 1;
hold on
axis equal
comet3(X(:,1), X(:,2), X(:,3))
set(hs1, 'FaceColor', 'texturemap', 'CData', cdata, 'FaceAlpha', alpha, 'EdgeColor', 'none')
You just have to reverse the order, first plot the earth and set the texture. Then use comet3 to animate the trajectory:
% earth
[x,y,z] = sphere;
r_earth = 6378*1000;
% some simple trajectory
phi = 0:0.01:2*pi;
r_orbit = r_earth + 408*1e3; % ISS orbit height
xv = r_orbit * cos(phi);
yv = r_orbit * sin(phi);
zv = zeros(size(yv));
% draw figure
figure(1); clf;
ax = axes;
% first plot the earth and set texture
hs1 = surf(x*r_earth,y*r_earth,-z*r_earth);
alpha = 1;
cdata = imread("Land_ocean_ice_2048.jpg");
set(hs1, 'FaceColor', 'texturemap', 'CData', cdata, 'FaceAlpha', alpha, 'EdgeColor', 'none')
hold on
axis equal
% finally, animate using comet3
comet3(xv,yv,zv)
I have an isosurface I've plotted in MATLAB, e.g.:
And I'd like to extract the outline from this, for the given view settings that I currently have. The output I expect is like this (produced by GIMP):
Is there any way to programatically do this so I don't have to manually do it in GIMP?
Is this good enough? Edge detection taken from the bwboundaries documentation.
clear, close all
[x y z v] = flow;
figure(1)
p = patch(isosurface(x, y, z, v, -3));
set(p, 'FaceColor', 'red', 'EdgeColor', 'none');
daspect([1 1 1])
view(3)
grid off
axis off
print -dbmp test
I=imread('test.bmp');
G = im2bw(I, graythresh(I));
[B,L] = bwboundaries(~G,'noholes');
for k = 1:length(B)
boundary = B{k};
plot(boundary(:,2), -boundary(:,1), 'k', 'LineWidth', 2)
hold on
end
hold off
Which results in:
I am plotting two maps next to each other using subplot. However, now, the image is turning out like this:
Is there any way to make the map part of the image larger? I would like to plot the maps side by side, by in this image, the resolution is low and the size is small.
%% Graph one site at a time
nFrames = 6240; % Number of frames.
for k = 94:nFrames
h11 = subplot(1,2,1); % PM2.5
% Map of conterminous US
ax = figure(1);
set(ax, 'visible', 'off', 'units','normalized','outerposition',[0 0 1 1]);
ax = usamap('conus');
set(ax,'Position',get(h11,'Position'));
delete(h11);
states = shaperead('usastatelo', 'UseGeoCoords', true,...
'Selector',...
{#(name) ~any(strcmp(name,{'Alaska','Hawaii'})), 'Name'});
faceColors = makesymbolspec('Polygon',...
{'INDEX', [1 numel(states)], 'FaceColor', 'none'}); % NOTE - colors are random
geoshow(ax, states, 'DisplayType', 'polygon', ...
'SymbolSpec', faceColors)
framem off; gridm off; mlabel off; plabel off
hold on
% Plot data
scatterm(ax,str2double(Lat_PM25{k})', str2double(Lon_PM25{k})', 25, str2double(data_PM25{k})', 'filled');
% Colorbar
caxis([5 30]);
h = colorbar;
ylabel(h,'ug/m3');
% Title
title(['PM2.5 24-hr Concentration ', datestr(cell2mat(date_PM25(k)), 'mmm dd yyyy')]);
%%%%
h22 = subplot(1,2,2); % O3
% Map of conterminous US
ax2 = usamap('conus');
set(ax2,'Position',get(h22,'Position'));
delete(h22);
states = shaperead('usastatelo', 'UseGeoCoords', true,...
'Selector',...
{#(name) ~any(strcmp(name,{'Alaska','Hawaii'})), 'Name'});
faceColors = makesymbolspec('Polygon',...
{'INDEX', [1 numel(states)], 'FaceColor', 'none'}); % NOTE - colors are random
geoshow(ax2, states, 'DisplayType', 'polygon', ...
'SymbolSpec', faceColors)
framem off; gridm off; mlabel off; plabel off
hold on
% Plot data
scatterm(ax2,str2double(Lat_O3{k})', str2double(Lon_O3{k})', 25, str2double(data_O3{k})'*1000, 'filled');
hold on
% Colorbar
caxis([10 90]);
h = colorbar;
ylabel(h,'ppb');
% Title
title(['O3 MDA8 Concentration ', datestr(cell2mat(date_O3(k)), 'mmm dd yyyy')]); % Title changes every daytitle(str);
% Capture the frame
mov(k) = getframe(gcf); % Makes figure window pop up
% Save as jpg
eval(['print -djpeg map_US_' datestr(cell2mat(date_PM25(k)),'yyyy_mm_dd') '_PM25_24hr_O3_MDA8.jpg']);
clf
end
close(gcf)
To change the amount of space the data occupies in the figure, you can use this command:
set(gca,'Position',[0.1 .1 0.75 0.85])
You'll have to play with the numbers a bit, to get things look nice. Note that Matlab rescales everything when you resize the figure window, so the optimal numbers depend on the window size you want to use.
On the other hand, you want to make the map bigger in comparison to the colorbar. You cannot make it without changing your window size, because your maps are already as high as the color bars. I would suggest to:
Set caxis to the same range in both plots.
Remove the colorbar on the left one.
Increase the height of your figure window to make the maps occupy as much width as possible.
Put the two images nicelye side by side using the command above.
For more information, see Matlab Documentation on Axes Properties.
Example:
% Default dimenstions
figure
x = 1:.1:4;
y = x;
[X, Y] = meshgrid(x,y);
subplot(1,2,1)
h = pcolor(X, Y, sin(X).*cos(Y)*2);
set(h, 'EdgeAlpha', 0);
axis square
colorbar
subplot(1,2,2)
h = pcolor(X, Y, sin(Y).*cos(X));
set(h, 'EdgeAlpha', 0);
axis square
colorbar
% adjust dimensions
subplot(1,2,1)
set(gca, 'Position', [0.1 0.1 0.3 0.85])
subplot(1,2,2)
set(gca, 'Position', [0.55 0.1 0.3 0.85])
This blog post has many great examples of FileExchange scripts dealing with size of subplots.
subplot_tight works very well and makes the subplots larger. Instead of writing in subplot(1,2,1), use subplot_tight(1,2,1)
My problem was similar -> scaling subplots in a figure a bit more up. Important for me though, was to maintain the aspect ratio that I've set before.
Enhancing the answer from #texnic in order to not have to set the values manually, one might use the following:
scale = 1.1; % Subplot scale
subplot(1,2,1)
% Your plotting here ...
pos = get(gca, 'Position'); % Get positions of the subplot [left bottom width height]
set(gca, 'Position', [pos(1) pos(2) pos(3)*scale pos(4)*scale]); % Scale width and height
Understanding this, one can also easily implement a parametric move of the subplot.
The properties of my figure I want to build are the following:
The figure shows 200 points. The points above the diagonal should be shown with red stars and the one below the diagonal, with blue triangles.
This is what I've managed to do so far
x=[0 1];
y=[0 1];
line(x,y, 'linewidth', 1);
hggroup = scatter(rand(100,1),rand(100,1));
axis tight;
axis square;
title('Scatterplot')
Could you help me with that? Thanks in advance.
How about this:
line([0 1],[0 1], 'linewidth', 1);
hold on
x = rand(100,1);
y = rand(100,1);
idx = y>x;
scatter(x(idx),y(idx),'r*');
scatter(x(~idx),y(~idx),'b^');
axis tight;
axis square;
title('Scatterplot')
I have little or no experience with volumetric data in MATLAB,
I need to complete next task:
I have 3 vectors ( rows ):
x_ = vector(1:smpl:max_row,1);
y_ = vector(1:smpl:max_row,2);
z_ = vector(1:smpl:max_row,3);
that are samples from large 3 columns array vector with height max_row.
x_ , y_ , z_ are points of 3D figure - surface points of the figure ( volume ). They represent 3D body that should be drawn in matlab.
I created linear grid:
%linear grid
a = -1.1:step:(-1.1+step*(length(x_)-1));
b = -1.1:step:(-1.1+step*(length(y_)-1));
c = -1.1:step:(-1.1+step*(length(z_)-1));
[x,y,z] = meshgrid(-1.1:step:(-1.1+step*(length(x_)-1)));
and also I create array v length(x_)*length(x_)*length(x_) that contains '1' in cells that are of 3D body representation function points and '0' another.
I tryied to make interpolation:
vi = interp3(x,y,z,v,x,y,z,'nearest');
but then vi = v that I've already created.
Now I need to plot the v array on 3D and form 3D body like in
http://www.mathworks.com/help/techdoc/ref/isonormals.html
for example.
I make that next way:
%plotting:
figure
p = patch(isosurface(x,y,z,v,1e-5,'verbose'),'FaceColor','green','EdgeColor','none');
grid on;
isonormals(v,p);
daspect([1 1 1])
view(3);
axis tight;
camproj perspective;
camlight
lighting gouraud
colormap(hsv)
but I get then only small rectangles in place of function '1' that are not connected like in picture that is attached.
I expect solid body enclosed by that points to be plotted.
Does anybody know what is the problem , how to draw 3D body from the x,y,z,v arrays ?
Thanks in advance.
image:
http://imgur.com/Ulegj
Try this, which will be a nice plot (it interpolates a bit though):
x = vector(1:smpl:max_row,1);
y = vector(1:smpl:max_row,2);
z = vector(1:smpl:max_row,3);
% Settings
displaySurface = 1;
displayPoints = 0;
xres = 800; % Resolution, the higher, the smoother
yres = 800;
cm = 'default'; % Colormap
% Axes Limits
xmin = min(x);
ymin = min(y);
xmax = max(x);
ymax = max(y);
xi = linspace(xmin, xmax, xres);
yi = linspace(ymin, ymax, yres);
% Figure
myfig = figure('Position', [200 200 800 600]);
rotate3d off
[XI, YI] = meshgrid(xi, yi);
ZI = griddata(x, y, z, XI, YI, 'cubic');
mesh(XI,YI,ZI);
colormap(cm)
if(displaySurface == 1)
hold on;
surf(XI, YI, ZI, 'EdgeColor', 'none');
end
hold on;
xlabel('x');
ylabel('y');
zlabel('z');
title('Title', 'FontWeight', 'bold');
xlim([xmin xmax])
ylim([ymin ymax])
grid off;
if(displayPoints == 1)
hold on
plot3(x, y, z,'marker','p','markerfacecolor','w','linestyle','none')
hidden off
end