i know the scale but when i use imagesc function the image doesnt show me the right size of my spot. what am i doing wrong?

clear all;
close all;

Scale = 29.4/64;                                            % Pixelscale of the image

[FileName, PathName] = uigetfile({'*.txt','PHASICS Txt File';'*.*', 'All Files (*.*)'},'Pick a file');
PhaseFile = fullfile(PathName,FileName);
PhaseData=importdata(PhaseFile,'\t');           % Read header less tab delimited txt file[Ny, Nx] = size(PhaseData);

[Nx, Ny] = size(PhaseData);

figure
imagesc(PhaseData);                                  % Plot the data

Answer 1

[Image Analyst]

PhaseData is structure. you need the Data field

theImage = PhaseData.Data;

[Sobia Rehman]

It gives an error

[Image Analyst]

You keep forgetting to attach a sample data file.

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

[Sobia Rehman]

I have not got your point

[Image Analyst]

When you browsed to a file and selected it, what was the name of that file? Please attach that file with the paperclip icon.

[Sobia Rehman]

Here the file is attached. And Thank you very much for your help.

[Image Analyst]

This seems to work

Scale = 29.4/64;  % Pixelscale of the image
% [FileName, PathName] = uigetfile({'*.txt','PHASICS Txt File';'*.*', 'All Files (*.*)'},'Pick a file');
% PhaseFile = fullfile(PathName,FileName);
PhaseFile = 'EXPORT PHA 170,0.5C,100,110,120 nJ, 20mmmin_0001.txt'
PhaseData=importdata(PhaseFile,'\t') % Read header less tab delimited txt file[Ny, Nx] = size(PhaseData);
[Nx, Ny] = size(PhaseData)
figure
imagesc(PhaseData);  % Display the data

Is there still a problem?

[Sobia Rehman]

The height of my structure shown here is 30, although actual height is 10 and the scale along x axis and y axis is the pixel count? or micrometer etc?

[Image Analyst]

It's the pixel count. If you want the axes to show some other units, you can change the tick labels with 'XData' and 'YData' in imshow().

PhaseFile = 'EXPORT PHA 170,0.5C,100,110,120 nJ, 20mmmin_0001.txt'
PhaseData=importdata(PhaseFile,'\t'); % Read header less tab delimited txt file[Ny, Nx] = size(PhaseData);

[rows, columns] = size(PhaseData)
fovy = 10;
fovx = fovy * columns / rows
imshow(PhaseData, [], 'XData', [0, fovx], 'YData', [0, fovy]);  % Display the data
caption = sprintf('Micrometers (%d pixels along x)', columns);
xlabel(caption)
caption = sprintf('Micrometers (%d pixels along y)', rows);
ylabel(caption)
axis ('on')

[Sobia Rehman]

Its working.

But this image shows it is 1.5 um but actually its around 14-15 um.

What can be the reason?

[Image Analyst]

I guess your scale (calibration factor) is wrong. See attached spatial calibration demo and integrate it into your code.

[Sobia Rehman]

Thanks Heaps!!

I will work on that but I want do one more task at the end. Once I get the image with exact dimentions I want to plot a grapgh for those dimentions (x and y) with third variable (Refractive index) in Imagesc to get a colored image at the end. Can you please guide how to assign x and y for dimentions and then tis specific plot?

[Image Analyst]

To get a line plot of x vs your third variable (let's call it z), you can use hold on. Then use rescale() to scale your third variable between 1 and the number of rows. Basically it would overlay a line plot over the image so you'd have z vs x and y would not be involved.

I'm not exactly sure what you want. So do you have a z value for every (x,y) pair? That would be an image or a surface. You can't put that over your original image without obscuring your original image. I suggest you use surf() or imshow() to show your z vs. (x,y) data.

[Sobia Rehman]

Hi again,

I want know one point.

I want to get the simplest method for this. If we have an image in pixel count and we know the scale of pixel and we want to assign the pixel along x axis as x cordinates and the pixel along y axis as y cordinates and then want to plot it according to the scale. what can be the simplest code for that?

[Image Analyst]

@Sobia Rehman not sure what you mean but let me reqord it more precisely and see if that's what you mean. You have a distance in pixels, and you have a spatial calibration factor in (real world units) per pixel. Now you want to plot the x and y, which you have in pixels, in real world units. Is that it? If so, lets say your units are millimeters and you have a variable called mmPerPixel, and vectors xInPixels and yInPixels in units of pixels. So you'd just convert and then plot

xInMm = xInPixels * mmPerPixel;
yInMm = yInPixels * mmPerPixel;
plot(xInMm, yInMm, 'b-', 'LineWidth', 2);
grid on;
xlabel('X in mm', 'FontSize', 20);
ylabel('Y in mm', 'FontSize', 20);
title('Y vs X in mm', 'FontSize', 20);

[Sobia Rehman]

I have attavhed two files.

when i start with

clear all;

close all;

Scale = 29.4/64; % Pixelscale of the image

[FileName, PathName] = uigetfile({'*.txt','PHASICS Txt File';'*.*', 'All Files (*.*)'},'Pick a file');

PhaseFile = fullfile(PathName,FileName);

PhaseData=importdata(PhaseFile,'\t');

The above lines of the code is to call the file and scale is mentioned.

Then I start with

[Nx, Ny] = size(PhaseData); This is to find the number of rows and columns

If i write next in code

imagesc(PhaseData); This displays me the image of PhaseData and along x axis and y axis numbers are shown which is actually xcordinates and ycordinates in pixel count. My question is how to assign the x cordinates and y cordinates in pixels first and then convert it to mm according to the scale.

In last comment you have mentioned xInPixels but i dont know how to assign values to this xInPixels.

I hope my question is clear. I am stuck with this issue from many days. It will be great if you can help me out from this.

Many Thanks

[Image Analyst]

You can use imshow():

XData = [0, Nx] * Scale;
YData = [0, Ny] * Scale;
imshow(PhaseData, 'XData', XData, 'YData', YData);
axis('on', 'image')

This will make the axis read out in calibrated, real world units instead of pixels.

[Sobia Rehman]

This gives me an image like this

Can you please have a look. Thanks for your time and efforts.

[Sobia Rehman]

Finally I have got this using this code

clear all;

close all;

%nBulk = 1.4536;

Scale = 29.4/64; % Pixelscale of the image

[FileName, PathName] = uigetfile({'*.txt','PHASICS Txt File';'*.*', 'All Files (*.*)'},'Pick a file');

PhaseFile = fullfile(PathName,FileName);

PhaseData=importdata(PhaseFile,'\t'); % Read header less tab delimited txt file[Ny, Nx] = size(PhaseData);

[Nx, Ny] = size(PhaseData);

XData = [0, Nx] * Scale;

YData = [0, Ny] * Scale;

imagesc(XData, YData, PhaseData);

This shows me the picture now in real life units.

Thanks heaps for your help.

[Image Analyst]

You must have floating point image outside the range of 0-1. So try it this way:

XData = [0, Nx] * Scale;
YData = [0, Ny] * Scale;
imshow(PhaseData, [], 'XData', XData, 'YData', YData);
axis('on', 'image')