convert matrix to jet colormap image and save as tiff

I'm working with hundreds of images that I need to convert to images using the jet colormap.

I work with tiff files.

I can import these in as matrices, but I can't seem to find a way to convert them to jet colormap images.

I wish to be able to convert them to jet colormap images and export them as a tiff file.

Answer 1

[Image Analyst]

Try ind2rgb

rgbImage = ind2rgb(grayImage, jet(256));

[Hosup Song]

that converts a certain colormap to rgb. I need to convert to jet, not rgb

[Image Analyst]

What are you talking about? I thought you wanted to convert a grayscale image to an RGB image using MATLAB's "jet" colormap, so that's what I gave you. Do you actually want to convert your image to a grayscale image of something like this:

[Hosup Song]

So the process is

1. import TIFF file
2. convert chosen layer of tiff file to matrix
3. convert that matrix to image with JET colormap

[Walter Roberson]

We still not understand what you mean about image with JET colormap, unless you mean what I gave in my Answer

[Image Analyst]

What do you mean by "layer"? Do you mean a page of a multi-page TIFF file, or do you mean one color channel of a full color RGB TIFF image? If you mean the latter and want to convert, say, the green channel, then the 3 steps are

originalImage = imread(fileName); % Import image.
grayImage = rgbImage(:, :, 2); % Extract green "layer".
rgbImage = ind2rgb(grayImage, jet(256));  % Pseudocolor with jet colormap.

By the way, the TIFF file after being read in by imread() is already an image. An image is a matrix, and vice versa, so there is no need to convert a "layer" (i.e. a color channel) to a matrix because it ALREADY IS a matrix. Nor is there any need to convert a matrix to an image because they're one and the same thing. But you can "pseudocolor an image" or "apply a colormap to a monochrome image" which basically assigns a color to every gray level in the image, turning it from a monochrome (gray scale) image into a full color image.

Answer 2

[Walter Roberson]

Choose the number of colors you want in your jet colormap.

numcolor = 27;

Then

cmap = jet(numcolor);

jetind = rgb2ind(YourRGBImage, cmap);

What would be returned is an array of indices into the jet colormap with the given number of colors, with each original RGB pixel having been converted into its closest match in the jet colormap.

[Walter Roberson]

You could then proceed with

jetted_image = ind2rgb(jetind, cmap);

and then jetted_image would be an RGB image in which all of the original colors had been approximated by their closest color in the JET colormap of the size you gave.

[Sarvagya]

Hi. I want to use this function. However, after normalizing my matrix using

normalize(matrix, 'range',[0,255])

I get the follwing error:

Array indices must be positive integers or logical values

I don't know why I would this error. Can you suggest what I should do here?

[Image Analyst]

@Sarvagya see the FAQ:

https://matlab.fandom.com/wiki/FAQ#%22Subscript_indices_must_either_be_real_positive_integers_or_logicals.%22

If you have any more questions, then attach your data and code to read it in with the paperclip icon after you read this:

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[Sarvagya]

Hi,

I do understand the error message. I can't have decimal or 0 (like python) as index in MATLAB. The reason why I asked it was because why would I get it in ind2rgb for a matrix? Specifically this line (line 23) of the function:

rgb(1:height, 1:width, 1) = reshape(cm(indexedImage, 1), [height width]);

This is where I get the error:

jetted_image = ind2rgb(gray, cmap);

And I get the following error:

Index in position 1 is invalid. Array indices must be positive integers or logical values.

Error in matlab.images.internal.ind2rgb (line 23)

rgb(1:height, 1:width, 1) = reshape(cm(indexedImage, 1), [height width]);

Error in ind2rgb (line 17)

r = matlab.images.internal.ind2rgb(a, cm);

Where

gray=squeeze(normalize(mat, 'range',[0,255]))

mat = rand(223,225)

and

cmap = jet(256)

However, it works for

gray = squeeze(normalize(mat, 'range',[0,1]))

I checked that matlab.images.internal.ind2rgbPreProcess is working fine for both the normalizations. So I don't know what's going wrong here.

[Image Analyst]

What function or variable is cm?

[Sarvagya]

It's defined in the function imd2rgb. I think it's the colormap variable.

[Image Analyst]

You could not pass an entire image as indexes into an N-by-3 colormap.

Please start a new thread of your own with your image and m-file attached.

If you have any more questions, then attach your data and code to read it in with the paperclip icon after you read this:

TUTORIAL: How to ask a question (on Answers) and get a fast answer