hyper-spectral image displays in not true color it shows in blue

hello !. i am new to matlab ,

i used multibandread to display specific bands of a hyperspectral image and its spectral profile ( used raw or fla or int) ,

my problems is

1:the image displays but not in its normal color, it displays in blue ( adding photos and code related)

2:i want to get the spectral profile of each band ( i did already plot in the code but the spectrum i get seems not like the z-profile i get from envi)

3: can i display it in colors ?

( note iam using Matlab R2016a ,R2018a)

here is the code i made

I editied the code thanks to Guillaume to make it easier to read /cheers

thanks very much

filename = 'fvf01.fla';
lines = 1040;
samples = 1392;
bands = 31;
datatype = 'uint16';
offset = 0;
interleave = 'bsq';
byteorder = 'ieee-le';
bandtoread = 10;
bandname = sprintf('Band %d', bandtoread);
img = multibandread(filename, [lines, samples, bands], ...
                    datatype, offset, interleave, byteorder, ...
                    {'Band', 'Direct', bandtoread});
imagesc(img);
title(bandname);

[Guillaume]

Not related to your problem, but I'm always surprised when people write:

img = multibandread(a, [b,c,d], ...
                    e, f, g, h, ...
                    {'Band','Direct',[i]} );

Reading that line of code on its own, and not looking up the documentation of multibandread can you tell me what a, b, c, d, e, f, g, h and i represent? None of the variable names have any meaning. Why not write:

filename = 'fvf01.fla';
lines = 1040;
samples = 1392;
bands = 31;
datatype = 'uint16';
offset = 0;
interleave = 'bsq';
byteorder = 'ieee-le';
bandtoread = 10;
bandname = sprintf('Band %d', bandtoread);
img = multibandread(filename, [lines, samples, bands], ...
                    datatype, offset, interleave, byteorder, ...
                    {'Band', 'Direct', bandtoread});
imagesc(img);
title(bandname);

which is instantly more understandable simply because the variable names have meaning.

Now with regards to your question:

1.the image displays but not in true color

I'm not sure what you mean by true colour. A single band is simply a range of intensity, the colour information is not part of the band. You could display it as you have with a range of dark blue to light blue, or in greyscale from black to white. It would still display the same information. You could also use false colours (a la rainbow) which is rarely a good idea as it creates visual artifacts.

2.i want to get the spectral profile of each band

You explicitly ask for only one band in your code, with your last 3 arguments to multibandread. Again I'm not really sure what you're asking.

[Adam]

Surely if you have time to write a question and put utterly useless tags in the 'tag' list you have time to put intelligent tags in too, otherwise why would you expect anyone to spend their time to read your question if you don't consider it important enough to put proper tags that will help guide people who may be able to help towards your question?!

[kefo]

@ Adam thanks for ur nice comment , in fact iam totaly new for programing and matlab . i can imagine my experience here . just by miss understanding what is taging u are talking about. this what i understood to put tag about where is the question . maybe little clearfication would help . thanks

[Adam]

When you ask a question the 'tags' box asks for 'Create one or two-word tags that help you quickly locate related questions.' You entered "1" and "2". You might as well have just left it empty instead of that. Far better add words that are relevant to the question you are asking, e.g. multibandread, imagesc. Then people who know about multibandread may see the tag and look at your question to try to help.

[kefo]

@Guillaume

thanks for ur patience . i have little experience in programing . and i meant by it as variable , but as u said up there its easier to type directly the name as variables . so its my bad iam still learning and such nice person like u is doing giving me some nice notes to fix how i write the code . thanks very much ( i will refix it and re edit it there )

1:about a true color one ( i mean RGB ) or at least as envi is showing ( if u choose specific band it would show a grey image . so for an example i did try ( i did try something like ex. imagesc (img, [low high]) ; , img= 'fvf01.fla' and imshow doesnt work at all for me too and it did give me range of color ( by changing the values of high and low ) without showing the photo it self

2:what i mix up here . on evni when i load one band . i can still get spectral profile ( z-profile ) on each pixel ( as i know each pixel should have full spectrum ) , can u clearfiy for me if i can if i want to show spectral profile to each band i may choose . it should be full spectrum ? or how it should looks like ? and is plot command right to be used here to show it ? ( note i know there is diff between raidence and reflectance hyperspectral images and its spectral profile )

i hope iam clear this time and easier to express the problem :( and sorry for my bad way of asking the question and thanks for ur patience really )

[kefo]

@Adam

thanks very much again , i will take write it down from this time on right :D . its more clearfiy now as u did just explain . /highfive

[Guillaume]

@kefo, I realise you're not a native english speaker and you're doing your best but it's difficult to understand what you wrote.

If you're displaying a single band, then using RGB is probably not a good idea. You're better off displaying that band in greyscale.

If you want to display multiple bands at once, I'm not sure how you'd do that. RGB is effectively a 3 band image and that's all your monitor can display. So if you want to display more than 3 bands at once, you'd have to somehow define a mapping from many bands to 3 to display it.

[kefo]

@Guillaume, yes iam not native english speaker . thanks much again for ur patience

iam trying to display single band yes and yes it seems not good idea to convert it to RGB or display it in RGB , greyscale could be better idea as already on envi when u choose single bands it shows grey but when u load whole image bands it be RGB ( normal real colors) , as i tried alot of codes to make it display in grey but seems it failed either cause lack of my exp. or it doesnt work . can u give me an example of how to display it in grey on same code ?

about the spectral profile on envi i do just can get z-profile of each pixel on image , which each pixel should include whole complete spectrum , but on matlab idk how it works , can i get spectral profile of a band photo " which i guess it will be like each pixel in the photo will have spectrum . which mean at end it would be an avarage of whole spectrum that the band photo have , so i used igure;

plot(img,'Color',[0 0.1 0]);

and it gave me a graph but iam not sure 100% if that a spectral profile for one band or what ?

thanks much again . bless u

[Walter Roberson]

Guide to Tags

[kefo]

@Walter Roberson thanks very much . thats very helpful and useful link

sorry again for the mess up with my tags , didn't understand exactly how it works :D

Answer 1

[Guillaume]

I'm sorry to say I'm struggling to understand what you're asking so my answer may be completely off the mark.

I think you may be better off loading the whole hyperspectral image as a 3D matrix, and then if you want to look at a specific band, just select the relevant slice of the 3d matrix. This would go like this:

filename = 'fvf01.fla';
lines = 1040;
samples = 1392;
bands = 31;
datatype = 'uint16';
offset = 0;
interleave = 'bsq';
byteorder = 'ieee-le';
img = multibandread(filename, [lines, samples, bands], ...
                    datatype, offset, interleave, byteorder);  %read whole image
%img should be a 1040 x 1392 x 31 matrix
%to view a specific band
bandtoshow = 10;
imshow(img(:, :, bandtoshow));
title(sprintf('band %d', bandtoshow));

Note that I use imshow to display the band instead of imagesc. imshow defaults to a greyscale colourmap whereas imagesc uses pareto. You could always change the colourmap if you use imagesc:

imagesc(img(:, :, bandtoshow));
colormap(gray);

I don't think there is a function to display multispectral images in matlab (but I don't work with multispectral images). You could make a simple gui that allows you to see each band individually:

figure;
himg = imshow(img(:, :, 1));
hcontrol = uicontrol('style', 'popupmenu', 'String', compose('band %d', 1:bands), 'Position', [50 20 80 20], 'Callback', @(hcontrol, ~) set(himg, 'CData', img(:, :, hcontrol.Value)));

If you want to see the profile of a pixel along the bands, simply index your 3D matrix:

pixelrow = 50;
pixelcolumn = 20;
figure;
plot(squeeze(img(pixelrow, pixelcolumn, :)));
title(sprintf('Spectrum at x = %d, y = %d', pixelcolumn, pixelrow));

And this is how you'd plot all the spectrums along a given row:

row = 100;
figure;
plot(squeeze(img(row, :, :)));
legend(compose('band %d', 1:bands));
title(sprintf('Spectrum along row %d', row));

Hopefuly, this helps you do what you want.

[kefo]

@Guillaume thanks very much my friend , you are such amazing and generous person bless you ,

1- the first code workd perfect just with little twist , at the imshow part ( it gave me an error ) and all i did is switching to imagesc and it worked instantly, there could be another solution but that what came first to my mind

2- the greyscale code worked like charm . thanks very much

3- the profile for each pixel code worked nicely on ur code ( 3d matrix load method) and worked on my old code , just didnt want to load both the band and the profile of the pixel together . its either this or that , so iam very greatful for u

4- last code worked on ur code fine , but by saying "this is how you'd plot all the spectrums along a given row" , a whole row of the 3d matrix or what row , iam sorry if i didnt understand cause the result of the profile looks very weird :D

i would love to thank you dearly for all ur effort and generousity , you are helping me alot and guiding me ( i have learned form u ) so all my respect to you

[Guillaume]

1- You're seeing a warning that the image is not displayed at a scale of 1:1. It's not an error. I think it's a stupid warning, You can turn it off with

warning('off', 'images:initSize:adjustingMag');

4- The idea is to plot the intensities along a single row of the image (2D) for each band. It may not be useful to you. Another way to visualise the same data which you may understand better:

row = 100;
figure;
ribbon(squeeze(img(row, :, :)));
xlabel('band');
ylabel('column');
title(sprintf('intensities at row %d', row));

[kefo]

@Guillaume good i got most of it now , and btw every thing works now fully combined ( image loaded, band selected and displayed in greyscale , dsplaying pixel spectrum , either single band on same and spectrum per figure or 4 bands and 4 plots in same figure with subplot

something like that

there is no words i can express with my gratitude and admire for your generosity, kindness, knowlage and patience , i have learned alot from you and looking forward for more cooperations later.

we learn from the masters of the profession

so thanks very much again and again . its really was nice to meet you and to keep as friend . /friendship highfive

figure ;
subplot(2, 2, 1)
plot(squeeze(image(pixelrow1, pixelcolumn1, :)));
title(sprintf('Spectrum at x = %d, y = %d', pixelcolumn1, pixelrow1));

Answer 2

[R Akshay]

Hi

I am trying to plot a spectrum of the hyperspectral image captured using SpecimIQ camera. On using the above mentioned code to plot the spectrum profile of the i could not get any output.

Used this same code as mentioned above.

figure ;
plot(squeeze(image(pixelrow1, pixelcolumn1, :)));
title(sprintf('Spectrum at x = %d, y = %d', pixelcolumn1, pixelrow1));

my image size is 512*512 and has 204 bands in it.

but output of spectrum profile shows blank output.

[Image Analyst]

What does this produce in the command window

spectrum = YourImage(pixelrow1, pixelcolumn1, :) % Don't use a semicolon.

Also, don't use image as the name of your variable. When you say plot(squeeze(image(pixelrow1, pixelcolumn1, :))); it might be calling the function called image() instead of referencing your variable. Probably not if you defined image beforehand, but still, it's very bad practice to name your function after built-in functions.

[Walter Roberson]

nnz(~isfinite(image(pixelrow1, pixelcolumn1, :)))

would help