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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)
This is the link to the dataset. I have this contour plot which has a bit rough edges. My question is, how can I smooth these edges these edges correspond to Nan. I filled in the Z matrix with Nan so as to remove unwanted values.
I also wanted to ask that why shading flat and interp is not working on this contour.
I have set shading to flat and in Matlab2013b I get proper flat figure but in Matlab 2014b and 2015b I am getting this figure.
MATLAB 2015b:
MATLAB 2013b
How can I obtain perfectly meshed plot in Matlab 2015b, I checked for shading options in the documentation and there are only 3 faceted, interp and flat.
shading flat works in 2013b but not in subsequent versions. Can someone tell me why is it so?
This is the sample code which I am using right now:
clear all; close all; clc;
load temperature.txt;
time = temperature(:,1); % This column contains the time
x = temperature(:,2); % This column contains the x values.
temperature_system = temperature(:,3); % This column contains the temperatures.
% Rejecting the outliers
pos = (temperature_system > prctile(temperature_system,97));
time(pos) = [];
x(pos) = [];
temperature_system(pos) = [];
X1 = [time x];
F = scatteredInterpolant(X1,temperature_system);
x1 = linspace(min(x),max(x),100);
x2 = linspace(min(time),max(time),100);
[X,Y] = meshgrid(x2,x1);
Z = F(X,Y);
% Is the data below the criteria for all points in space at a specific time
emptyTime = all(Z<10,1);
emptySpace = all(Z<10,2);
[emptyTime, emptySpace] = meshgrid(emptyTime, emptySpace);
Z(emptyTime | emptySpace) = nan;
% Replacing the remaining zeros with nan
pos = find(Z<1);
Z(pos) = nan;
f1 = figure(1);
%set(f1,'renderer','zbuffer');
%surf(X,Y,Z);
[C,h] = contourf(X,Y,Z, 'Linestyle', 'none');
shading flat;
colormap(jet);
q = colorbar;
set(q,'direction','reverse');
q.Label.String = 'Temperature';
xlabel('Time (ps)','FontSize', 16, 'FontWeight', 'bold',...
'FontName', 'Helvetica', 'Color', 'Black');
ylabel('Length of box (A)','FontSize', 16, 'FontWeight', 'bold',...
'FontName', 'Helvetica', 'Color', 'Black');
set(gca,'LineWidth',3,'TickLength',[0.02 0.02]);
set(gca,'XMinorTick','on');
set(gca,'YMinorTick','on','XTicksBetween', 5);
set(gca,'FontSize',12,'FontName','Helvetica');
It's difficult to test the issue without having your data. I got rid of the lines by means of the LineStyle property:
Code:
Z = peaks(20);
subplot(2,1,1);
contourf(Z,10);
colorbar;
subplot(2,1,2);
contourf(Z,10, 'LineStyle', 'none');
colorbar;
There is example of the web that shows how to do animated plot in a single figure.
However, I want to do two subplots in a single figure, such that they will show animation in a first subplot, and then the animation ina second subplot.
Using 'figure(1)' or 'figure (2)' and 'hold on', I can do the animation plot as follows. However, How do I call the subplot to do the similiar things?
So the effect I am looking for is: 1) figure that is opened and has two subplot. 2) plot the animated curve in the 1st subplot, then plot the animated curve in the 2nd subplot. 3) I want to go back to the 1st subplot to plot more things, and also go to 2nd subplot to plot more things.
figure(1); hold on; x = 1:1000;
y = x.^2;
%// Plot starts here
figure,hold on
%// Set x and y limits of the plot
xlim([min(x(:)) max(x(:))])
ylim([min(y(:)) max(y(:))])
%// Plot point by point
for k = 1:numel(x)
plot(x(k),y(k),'-') %// Choose your own marker here
%// MATLAB pauses for 0.001 sec before moving on to execue the next
%%// instruction and thus creating animation effect
pause(0.001);
end
Just do the subplot's in the loop:
for k = 1:numel(x)
subplot(1,2,1)
plot(x(k),y(k),'-') %// Choose your own marker here
subplot(1,2,2)
plot(x(1:k),y(1:k))
%// MATLAB pauses for 0.001 sec before moving on to execue the next
%%// instruction and thus creating animation effect
pause(0.001);
end
% Easiest way
x = rand(1, 11); y = rand(1, 11);
z = rand(1, 11); a = rand(1, 11);
figure
for i = 1 : 10
subplot(211)
plot(x(i : i+1), y(i : i+1), '.-k');
hold on; % include this if you want to show plot history
subplot(212)
plot(z(i : i+1), a(i : i+1), '.-k');
drawnow;
pause(0.1);
end
% If you don't want to call "plot" interatively
x = rand(1, 11); y = rand(1, 11);
z = rand(1, 11); a = rand(1, 11);
figure
subplot(211)
p1 = plot(NaN, NaN, 'marker', 'o');
subplot(212)
p2 = plot(NaN, NaN, 'marker', 'd');
for i = 1 : 10
set(p1, 'xdata', x(i : i+1), 'ydata', y(i : i+1));
set(p2, 'xdata', z(i : i+1), 'ydata', a(i : i+1));
drawnow;
pause(0.1);
end
First define your plot as a construct, so p1 = plot(x,y). Then you set up your loop and in the loop your write
set(p1,'YData',y);
This will update the plot p1s YData which is y. If you want to see it in an animated form just add a pause(0.1) %seconds after the set.
I am trying to program scatterplot with specific errorbars. The only build in function i found is
errorbar()
but this only enables me to make a 2d plot with errorbars in y direction. What i am asking for is a method to plot this with errorbars in x and y direction.
At the end my goal is to make a 3D-scatter-plot with 3 errorbars.
Perfect would be if the resulting image would be a 3d-plot with 3d geometric shapes (coordinate x,y,z with expansion in the dimension proportional to the errorbars) as 'marker'.
I found this page while searching the internet: http://code.izzid.com/2007/08/19/How-to-make-a-3D-plot-with-errorbars-in-matlab.html
But unfortunately they use only one errorbar.
My data is set of 6 arrays each containing either the x,y or z coordinate or the specific standard derivation i want to show as errorbar.
The code you posted looks very easy to adapt to draw all three error bars. Try this (note that I adapted it also so that you can change the shape and colour etc of the plots as you normally would by using varargin, e.g. you can call plot3d_errorbars(...., '.r'):
function [h]=plot3d_errorbars(x, y, z, ex, ey, ez, varargin)
% create the standard 3d scatterplot
hold off;
h=plot3(x, y, z, varargin{:});
% looks better with large points
set(h, 'MarkerSize', 25);
hold on
% now draw the vertical errorbar for each point
for i=1:length(x)
xV = [x(i); x(i)];
yV = [y(i); y(i)];
zV = [z(i); z(i)];
xMin = x(i) + ex(i);
xMax = x(i) - ex(i);
yMin = y(i) + ey(i);
yMax = y(i) - ey(i);
zMin = z(i) + ez(i);
zMax = z(i) - ez(i);
xB = [xMin, xMax];
yB = [yMin, yMax];
zB = [zMin, zMax];
% draw error bars
h=plot3(xV, yV, zB, '-k');
set(h, 'LineWidth', 2);
h=plot3(xB, yV, zV, '-k');
set(h, 'LineWidth', 2);
h=plot3(xV, yB, zV, '-k');
set(h, 'LineWidth', 2);
end
Example of use:
x = [1, 2];
y = [1, 2];
z = [1, 2];
ex = [0.1, 0.1];
ey = [0.1, 0.5];
ez = [0.1, 0.3];
plot3d_errorbars(x, y, z, ex, ey, ez, 'or')
I would like to give the subplots I make a simple label. Unfortunately I'm getting an ugly behavior. Consider the following function:
function h = set_label1(label)
tlh = get(gca, 'Title');
if strcmp(get(tlh, 'String'), '')
title(' ');
end
ylh = get(gca, 'YLabel');
if strcmp(get(ylh, 'String'), '')
ylabel(' ');
end
ylp = get(ylh, 'Position');
x = ylp(1);
tlp = get(tlh, 'Position');
y = tlp(2);
h = text('String', label, ...
'HorizontalAlignment', 'right',...
'VerticalAlignment', 'Baseline', ...
'FontUnits', 'pixels', ...
'FontSize', 16, ...
'FontWeight', 'bold', ...
'FontName', 'Arial', ...
'Position', [x y 0]);
end
Here is a simple test run:
figure;
h1 = axes('OuterPosition', [0,0,.5 1]);
set(h1,'LooseInset',get(h1,'TightInset'));
h2 = axes('OuterPosition', [.5,0,.5 1]);
set(h2,'LooseInset',get(h2,'TightInset'));
axes(h1);
plot([0 1], [4 5]);
set_label1('A');
axes(h2);
plot([0 1], [4 5]);
set_label1('B');
The picture I obtain is:
If you resize the figure the labels will not be in the right position anymore. That is fine, I expected it (If you know how to put them back where they belong and you tell us that would make me very happy).
THe problem I'm facing is that I do not want to specify the position of the label in 'data' units.
Instead, I want to use normalized units. So I used modified form of function. Now let us use this:
function h = set_label2(label)
tlh = get(gca, 'Title');
if strcmp(get(tlh, 'String'), '')
title(' ');
end
ylh = get(gca, 'YLabel');
if strcmp(get(ylh, 'String'), '')
ylabel(' ');
end
oldUnits = replace_prop(ylh, 'Units', 'normalized');
ylp = get(ylh, 'Position');
x = ylp(1);
set(ylh, 'Units', oldUnits);
oldUnits = replace_prop(tlh, 'Units', 'normalized');
tlp = get(tlh, 'Position');
y = tlp(2);
set(ylh, 'Units', oldUnits);
h = text('String', label, ...
'HorizontalAlignment', 'right',...
'VerticalAlignment', 'Baseline', ...
'FontUnits', 'pixels', ...
'FontSize', 16, ...
'FontWeight', 'bold', ...
'FontName', 'Arial', ...
'Units', 'normalized',...
'Position', [x y 0]);
end
function oldvalue = replace_prop(handle, propName, newvalue)
oldvalue = get(handle, propName);
set(handle, propName, newvalue);
end
Running the same test:
figure;
h1 = axes('OuterPosition', [0,0,.5 1]);
set(h1,'LooseInset',get(h1,'TightInset'));
h2 = axes('OuterPosition', [.5,0,.5 1]);
set(h2,'LooseInset',get(h2,'TightInset'));
axes(h1);
plot([0 1], [4 5]);
set_label2('A');
axes(h2);
plot([0 1], [4 5]);
set_label2('B');
We obtain the exact same picture as before. The only problem is that when we resize it now something bad happens:
The labels are actually in the correct position. But it seems that the 'LooseInset' and 'TightInset' property I used make the axes act as if there is no labels.
Is there any fix for this? Really all I am doing is getting the position of the title and ylabel in normalized units as opposed in data units and this seems to mess it up.
The reason I need to get it in normalized units is so that when we get a 3D plot I can position the label with respect to the title and the zlabel.
For posterity's sake here is the version I decided to go with. It does what I expect it to do, but now I have a problem which I have no idea how to solve. OK, first the good news, here is the function called axes_label.
function c = axes_label(varargin)
if isa(varargin{1}, 'char')
axesHandle = gca;
else
axesHandle = get(varargin{1}{1}, 'Parent');
end
if strcmp(get(get(axesHandle, 'Title'), 'String'), '')
title(axesHandle, ' ');
end
if strcmp(get(get(axesHandle, 'YLabel'), 'String'), '')
ylabel(axesHandle, ' ');
end
if strcmp(get(get(axesHandle, 'ZLabel'), 'String'), '')
zlabel(axesHandle, ' ');
end
if isa(varargin{1}, 'char')
label = varargin{1};
if nargin >=2
dx = varargin{2};
if nargin >= 3
dy = varargin{3};
else
dy = 0;
end
else
dx = 3;
dy = 3;
end
h = text('String', label, ...
'HorizontalAlignment', 'left',...
'VerticalAlignment', 'top', ...
'FontUnits', 'pixels', ...
'FontSize', 16, ...
'FontWeight', 'bold', ...
'FontName', 'Arial', ...
'Units', 'normalized');
el = addlistener(axesHandle, 'Position', 'PostSet', #(o, e) posChanged(o, e, h, dx, dy));
c = {h, el};
else
h = varargin{1}{1};
delete(varargin{1}{2});
if nargin >= 2
if isa(varargin{2}, 'char')
set(h, 'String', varargin{2});
if nargin >=3
dx = varargin{3};
dy = varargin{4};
else
dx = 3;
dy = 3;
end
else
dx = varargin{2};
dy = varargin{3};
end
else
error('Needs more arguments. Type help axes_label');
end
el = addlistener(axesHandle, 'Position', 'PostSet', #(o, e) posChanged(o, e, h, dx, dy));
c = {h, el};
end
posChanged(0, 0, h, dx, dy);
end
function posChanged(~, ~, h, dx, dy)
axh = get(h, 'Parent');
p = get(axh, 'Position');
o = get(axh, 'OuterPosition');
xp = (o(1)-p(1))/p(3);
yp = (o(2)-p(2)+o(4))/p(4);
set(h, 'Units', get(axh, 'Units'),'Position', [xp yp]);
set(h, 'Units', 'pixels');
p = get(h, 'Position');
set(h, 'Position', [p(1)+dx, p(2)+5-dy]);
set(h, 'Units', 'normalized');
end
Ok, so how do we use this crappy function? I made it so that we can have these uses:
% c = axes_label('label')
% Places the text object with the string 'label' on the upper-left
% corner of the current axes and returns a cell containing the handle
% of the text and an event listener.
%
% c = axes_label('label', dx, dy)
% Places the text object dx pixels from the left side of the axes
% and dy pixels from the top. These values are set to 3 by default.
%
% c = axes_label(c, ...)
% Peforms the operations mentioned above on cell c containing the
% handle of the text and the event listener.
%
% c = axes_label(c, dx, dy)
% Adjusts the current label to the specifed distance from the
% upper-left corner of the current axes.
If we perform the same test as before:
figure;
h1 = axes('OuterPosition', [0,0,.5 1]);
set(h1,'LooseInset',get(h1,'TightInset'));
h2 = axes('OuterPosition', [.5,0,.5 1]);
set(h2,'LooseInset',get(h2,'TightInset'));
axes(h1);
plot([0 1], [4 5]);
axes_label('A');
axes(h2);
plot([0 1], [4 5]);
axes_label('B', 250, 250);
Now we obtain what I wanted. Label 'A' is set at the upper-left corner of the axes's Outerbox. And label B I explicitly set it to be 250 pixels from its upper-left corner. Here is a plot:
What I like about this function is that if I were to store the cell returned from it and then I put back I can change the position. For instance if label = axes_label('A'); Then on the command prompt I can do label = axes_label(label, 10, 20); and I will see my label move.
The problem I'm facing now is ralated to the function export_fig
If I try to use this:
export_fig('testing.png', '-nocrop', '-painters');
Then this is the figure I obtain.
This is the reason why I exaggerated with label B. Before I added the event listeners export_fig would do an OK job at printing the labels where I had positioned them. But somehow now export_fig doesn't do what it claims it does. Mainly exporting an image with
Figure/axes reproduced as it appears on screen
If instead we remove the option -painters then we get this:
There is probably a bug in code since I'm not experienced with listeners, so if anyone can fix this behavior and/or can improve on this code please feel free to do so and share it as an answer.
First of all, I like your idea of using the title/y-label to position the text on the upper left corner, clever :)
Now, instead of using normalized units, keep using data units and create an event listener for whenever the title or the y-label change their positions, and use their new values to re-adjust the created text.
So add the following to the end of your set_label1 function:
addlistener(ylh, 'Position', 'PostSet', #(o,e) posChanged(o,e,h,1))
addlistener(tlh, 'Position', 'PostSet', #(o,e) posChanged(o,e,h,2))
and here is the callback function used for both cases (we use the last argument idx to control whether to set x or y coordinate):
function posChanged(src,evt,hTxt,idx)
posLabel = evt.NewValue; %# new position of either title/y-label
posText = get(hTxt, 'Position'); %# current text position
posText(idx) = posLabel(idx); %# update x or y position (based on idx)
set(hTxt, 'Position',posText) %# adjust the text position
end