I use function pcolor3 to draw a volume rendering result like the following one.
And I want to plot a base map:
The question is I can do the two images separately. But when I combine them together, both of them are missing:
Can anyone help me find a solution? Thanks.
Sorry for not attaching the code. Here it is.
#data is a 3d matrix. S is a shapefile.
[X,Y,Z]=meshgrid(xgr,ygr,zgr);
S = shaperead(filename);
hold on;
pcolor3(X,Y,Z,data); # show the 3d matrix
mapshow(S,'FaceColor',[0.5 0.5 0.5]); # show the base map
hold off;
I'm not sure if the problem is in function mapshow. When I use mapshow in a 3d scatterplot, it is good. However, this time, it's bad.
Related
I drew a mesh in Matlab. The data for the mesh was supplied with a filled 3d Matrix. Nothing special with that.
I saved the created figure and came back to it now.
I want to create a different plot with the same data. Is there a way to extract the matrix data from the mesh so I can reuse it?
With some luck, following solution could work:
Load the figure file:
fig = openfig('fig_file_name.fig');
Get the surface data from the axes of the figure (assuming surface is the first "children"):
s = fig.CurrentAxes.Children(1);
Look for your data in s.XData, s.YData and s.ZData.
Better solution is using findobj (instead of fig.CurrentAxes.Children(1)) use:
s = findobj(fig, 'type', 'Surface');
I have 3D cloud of dots. I need to plot them as a surface. I tried variant with meshdrid, griddata, scatteredInterpolant,trisurf-delaunay. Nothing works. I know that this question was discussed a lot, but it seems I don't understand some important details. The code which i have now:
load('coords.mat')
figure()
subplot(1,2,1)
plot3(x,y,z,'.')
axis off
view(3)
subplot(1,2,2)
C=gray(numel(x)); % unsuccessful attempt
[~,idx]=sort(z); % to have
C=C(idx,:); % illumination
scatter3(x,y,z,50,C,'filled')
axis off
view(3)
produces the following image:
Could you help me:
1) to find a way to draw it with surface function.
and as some dots may be inside the surface (may be it is my problem)
2) How to remove 'invisible' dots?
I need solution for different cases, picture and data presents just an example.
Mat file may be downloaded here.
P.S.
In case it is important – I obtain coordinates of this dots as a rotation of random bezier curve.
UPDATE
In case data above is too big I generate another set with smaller amount of dots:
Coordinates are here.
where do you get this data from? It is represented as vectors but if you reshape it to matrices you can use the surf function. Try this code:
z=reshape(z,100,100);
y=reshape(y,100,100);
x=reshape(x,100,100);
surf(x,y,z)
I have a 24 dimensional dataset of 100,000 data points which are mapped onto 2d plane using sammon mapping (a method ro reduce dimensionality and visualize). The scatter plot is shown below! Doesn't look too interesting..
But when i tilted my screen an looked at the figure, a square array of points appeared. I am not a matlab user and i am confused whether there is some meaning
to this for example are the points forming a clusters etc ? or is this just some sorcery.
Please use the scatter command and change the scatter properties.
fig = figure('Color','white');
sc = scatter(y_stacked(:,1), y_stacked(:,2));
sc.Marker = '.';
sc.SizeData = 1;
Then, make the figure window as big as possible and/or zoom in to examine your data points more closely.
I have got a data of size 13558x100 and I am trying to plot it. For 2D, I could use:
plot(X(:,1), X(:,2))
How can I plot this big data? Can I just use surf to visualize the data or is there any other way?
As others have mentioned imagesc is the better way to go about this. It allows you to see a field of 2D data without a 3D plot using colour mapping. The toy example code is here.
Y = randn(13558,100);
figure; imagesc( Y );
This code generates the image as follows.
Furthermore, you can use the function colorbar to get a bar legend for your data.
colorbar;
After using the colorbar function, it generates the figure below.
I am trying to plot a 3d view of a very large CT dataset. My data is in a 3d matrix of 2000x2000x1000 dimension. The object is surrounded by air, which is set to NaN in my matrix.
I would like to be able to see the greyscale value of the surface of the object (no isosurface) but I cannot quite work out how to do that in Matlab. Can anyone help me please?
Given that I a dealing with a huge matrix and I am only interested in the surface of the object, does anyone know a good trick how to reduce the size of my dataset?
The function surf(X,Y,Z) allows you to plot 3d data, where (X,Y) gives the coordinates in the x-y-plane while Z gives the z-coordinate and the surface color.
By default the function does not plot anything for the NaN entries, so you should be good to go with the surf function.
To set the surf-function to use a grayscale plotting use:
surf(matrix3d);
colormap(gray);
This plots the matrix in a surface plot and sets the colormap to grayscale.
In addition, as I understand your data, you might be able to eliminate entire plane-segments in your matrix. If for instance the plane A(1,1:2000,1:1000) is NaN in all entries you could eliminate all those entries (thus the entire Y,Z-plane in entry X=1). This will however require some heavy for loops, which might be over the top. This depends on how many data matrices you have compared to how many different plot you want for each matrix.
I will try to give you some ideas. I assume lack of a direct 3D "surface detector".
Since you have a 3D matrix where XY-planes are CT scan slices and each slice is an image, I would try to find edges of each slice say with edge. This would require some preprocessing like first thresholding each slice image. Then I can either use scatter3 to display the edge data as a 3D point cloud or delaunay3 to display the edge data as a surface.
I hope this will help you achieve what you are asking for.
I managed to get it working:
function [X,Y,Z,C] = extract_surface(file_name,slice_number,voxel_size)
LT = imread(file_name);%..READ THE 2D MAP
BW = im2bw(LT,1);%..THRESHOLD TO BINARY
B = bwboundaries(BW,8,'noholes');%..FIND THE OUTLINE OF THE IMAGE
X = B{1}(:,1);%..EXTRACT X AND Y COORDINATES
Y = B{1}(:,2);
indices = sub2ind(size(LT),X,Y);%..FIND THE CORRESPONDING LINEAR INDICES
C = LT(indices);%..NOW READ THE VALUES AT THE OUTLINE POSITION
Z = ones(size(X))*slice_number;
I can then plot this with
figure
scatter3(X,Y,Z,2,C)
Now the only thing I could improve is to have all these points in the scatter plot connected with a surface. #upperBound you suggested delaunay3 for this purpose - I cannot quite figure out how to do this. Do you have a tip?