how can i show my hyperspectral data in a two dimensional projection of hyperspectral cube?

i have a hyperspectral data in a .m file it is 984*740*224 how can i show it in a two dimensional projection of hyperspectral cube?

[Rik]

That depends on the range of values involved and how you would like to reduce your data to 1 dimension fewer. You might want to take a look at the medical image viewers on the file exchange, as those are often 3D.

[asmaa elyamany]

the data is a remote sensing and of type double

[Rik]

The source is not really relevant. It is a 3D volume with a specific value range. Most CT and MRI viewers should work if you don't have a specific way to reduce those dimensions.

[asmaa elyamany]

i used the VolumeViewer3D in the medical image viewer but it didn't view the image in a cube and it was somehow in greyscale but my data supose to be colorful

[Rik]

There are bound to be viewers that show the 3 directions and allow you to set a colormap to your liking.

Answer 1

[millercommamatt]

If your data is something like (x,y,spectra), you could try:

imagesc(your_data(:,:,1));

If your data is like (spectra, x, y) you could try:

imagesc(squeeze(your_data(10,:,:)));

[asmaa elyamany]

i have tried these two solutions and non of them gave me a cube shape i need to show the data like this

[millercommamatt]

You could use surf and plot each face of the hypercube as it's own surface plot.

i.e.

[Xdim,Ydim,Spectra_dim]=size(your_data);
[X Y Spectra]=meshgrid(1:Xdim,1:Ydim,1:Spectra_dim);
figure;
surf(squeeze(X(1,:,:)),squeeze(Y(1,:,:)),squeeze(Z(1,:,:)),squeeze(your_data(1,:,:)),'EdgeColor','none');
hold on;
surf(squeeze(X(end,:,:)),squeeze(Y(end,:,:)),squeeze(Z(end,:,:)),squeeze(your_data(end,:,:)),'EdgeColor','none');
surf(squeeze(X(:,1,:)),squeeze(Y(:,1,:)),squeeze(Z(:,1,:)),squeeze(your_data(:,1,:)),'EdgeColor','none');
surf(squeeze(X(:,end,:)),squeeze(Y(:,end,:)),squeeze(Z(:,end,:)),squeeze(your_data(:,end,:)),'EdgeColor','none');
surf(squeeze(X(:,:,1)),squeeze(Y(:,:,1)),squeeze(Z(:,:,1)),squeeze(your_data(:,:,1)),'EdgeColor','none');
surf(squeeze(X(:,:,end)),squeeze(Y(:,:,end)),squeeze(Z(:,:,end)),squeeze(your_data(:,:,end)),'EdgeColor','none');

Also, read through the Documentation on Volume Visulization and looks at the examples that use isosurface and isocaps. They're typically fed to the patch functions to create plots that look like you're cube example.

In my opinion, those cube plots are rarely useful. It's the 2-D slices that you really need. YMMV.

[asmaa elyamany]

i replaced the Spectra variable by Z in line 2 because it showed an error and it gave me an empty figuer and it showed a warning

Warning: Error creating or updating Surface

Error in value of property CData

Array is wrong shape or size

so i tried to swap Xdim by Ydim in line 2 and it gave me a figure but not what i am loking for not like the image above

[millercommamatt]

Have you tried the Volume Viewer App?

You said your data are 984*740*224. What are those dimensions? Which is x, y, and the spectra? Or are those dimensions something else? What is the range of your data? Are they brightness temperatures or reflectance or something else? Is the spectral dimension frequency or wavenumber or channel number?

[asmaa elyamany]

frist of all thanke very much for your attention;

the data is x,y and spectra the data is of type double and it is raw data (digital number)

the spectral dimension is channel number

[millercommamatt]

This should work. I tested it with random data that matched your description.

[Xdim,Ydim,Spectra_dim]=size(your_data);
[X Y Spectra]=meshgrid(1:Xdim,1:Ydim,1:Spectra_dim);
figure;
surf(squeeze(X(1,:,:)),squeeze(Y(1,:,:)),squeeze(Spectra(1,:,:)),squeeze(your_data(1,:,:)),'EdgeColor','none');
hold on;
surf(squeeze(X(end,:,:)),squeeze(Y(end,:,:)),squeeze(Spectra(end,:,:)),squeeze(your_data(end,:,:)),'EdgeColor','none');
surf(squeeze(X(:,1,:)),squeeze(Y(:,1,:)),squeeze(Spectra(:,1,:)),squeeze(your_data(:,1,:)),'EdgeColor','none');
surf(squeeze(X(:,end,:)),squeeze(Y(:,end,:)),squeeze(Spectra(:,end,:)),squeeze(your_data(:,end,:)),'EdgeColor','none');
surf(squeeze(X(:,:,1)),squeeze(Y(:,:,1)),squeeze(Spectra(:,:,1)),squeeze(your_data(:,:,1)),'EdgeColor','none');
surf(squeeze(X(:,:,end)),squeeze(Y(:,:,end)),squeeze(Spectra(:,:,end)),squeeze(your_data(:,:,end)),'EdgeColor','none');

[asmaa elyamany]

when running this code it gave me this

Warning: Error creating or updating Surface

Error in value of property CData

Array is wrong shape or size

and an empty 3D grid with nothing in it

[millercommamatt]

You said that your data are a 3-D array of size 984x740x224 where the dimensions represent the X-coordinate, the Y-coordinate, and the spectral channel number respectively. You said that the data points in this array are of type double and that the numbers represent some numeric value from the sensor.

The error you posted suggests that the array you're using is a different shape that what I reiterated above. Did you copy and paste the code or transcribe it by hand? Maybe you left out a squeeze function or made in error in the indexing?

Please post the output of just this line. Note that I've removed the semicolon so that the output will be displayed on the screen. The output should be: Xdim = 984, Ydim=740, Spectra_dim=224.

[Xdim,Ydim,Spectra_dim]=size(your_data)

Posting your specific code would also help with troublshooting. Including full error text with the reported line numbers would also help.

[asmaa elyamany]

the output of my data was like this

[Xdim,Ydim,Spectra_dim]=size(HypeRvieW)

Xdim =

984

Ydim =

740

Spectra_dim =

224

somehow when i run your code the X ,Y and Spectra is 740*984*224

[millercommamatt]

We just need to switch what's being labeled as x and y in the code I gave you remember that matlab uses row-major dimension ordering.

[Ydim,Xdim,Spectra_dim]=size(your_data);%should be Ydim = 984, Xdim=740, Spectra_dim=224.
[X Y Spectra]=meshgrid(1:Xdim,1:Ydim,1:Spectra_dim);%each array shoudl be 984x740x224
figure;
surf(squeeze(X(1,:,:)),squeeze(Y(1,:,:)),squeeze(Spectra(1,:,:)),squeeze(your_data(1,:,:)),'EdgeColor','none');
hold on;
surf(squeeze(X(end,:,:)),squeeze(Y(end,:,:)),squeeze(Spectra(end,:,:)),squeeze(your_data(end,:,:)),'EdgeColor','none');
surf(squeeze(X(:,1,:)),squeeze(Y(:,1,:)),squeeze(Spectra(:,1,:)),squeeze(your_data(:,1,:)),'EdgeColor','none');
surf(squeeze(X(:,end,:)),squeeze(Y(:,end,:)),squeeze(Spectra(:,end,:)),squeeze(your_data(:,end,:)),'EdgeColor','none');
surf(squeeze(X(:,:,1)),squeeze(Y(:,:,1)),squeeze(Spectra(:,:,1)),squeeze(your_data(:,:,1)),'EdgeColor','none');
surf(squeeze(X(:,:,end)),squeeze(Y(:,:,end)),squeeze(Spectra(:,:,end)),squeeze(your_data(:,:,end)),'EdgeColor','none');

[asmaa elyamany]

the code is very helpful but the image displayed is blue while i want it to be coloful and may i ask you how to ratate it to make the image in the front not in the top

Answer 2

[millercommamatt]

To control the orientation of the image, read the documentation for 3-D camera control:

https://www.mathworks.com/help/matlab/views.html

Specifically read the documentation for view:

https://www.mathworks.com/help/matlab/ref/view.html

There's also a button in the graphic windows to manually orbit the camera around.

As for the color, please study the documentation for colormap and caxis

https://www.mathworks.com/help/matlab/ref/colormap.html

https://www.mathworks.com/help/matlab/ref/caxis.html

As always when reading the documentation, pay attention to links to other function and the see also section to see related functions. Following these links will lead you to examples of related tasks and provide a broader view of the tools you have at your disposal.