how to know the location pixel

Dear all,

I done convert gray image to binary image. picture as attached.

my image name is spect128x128

I15 = dicomread('spect128x128', 'frame', 15);
T15 = graythresh(level);
BW15 = imbinarize(I15,T15);
figure
imshowpair(I15, BW15, 'montage')
CC = bwconncomp(BW16)

CC = 

  struct with fields:

    Connectivity: 8
       ImageSize: [130 130]
      NumObjects: 4
    PixelIdxList: {[6×1 double]  [22×1 double]  [35×1 double]  [59×1 double]}

>> numPixels = cellfun(@numel,CC.PixelIdxList)

numPixels =

     6    22    35    59

how to know the location for 16, 22, 35 56 it self?

Answer 1

[Image Analyst]

Try this well commented demo. It finds all the blobs, then gets their area, centroid, and list of all the pixels in each blob. It also colorizes each discrete blob so you know what blob is distinct.

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
imtool close all;  % Close all imtool figures if you have the Image Processing Toolbox.
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 16;
% Check that user has the Image Processing Toolbox installed.
hasIPT = license('test', 'image_toolbox');
if ~hasIPT
  % User does not have the toolbox installed.
  message = sprintf('Sorry, but you do not seem to have the Image Processing Toolbox.\nDo you want to try to continue anyway?');
  reply = questdlg(message, 'Toolbox missing', 'Yes', 'No', 'Yes');
  if strcmpi(reply, 'No')
    % User said No, so exit.
    return;
  end
end
%===============================================================================
% Read in gray scale image.
folder = pwd;
baseFileName = 'image.jpeg';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
if ~exist(fullFileName, 'file')
  % Didn't find it there.  Check the search path for it.
  fullFileName = baseFileName; % No path this time.
  if ~exist(fullFileName, 'file')
    % Still didn't find it.  Alert user.
    errorMessage = sprintf('Error: %s does not exist.', fullFileName);
    uiwait(warndlg(errorMessage));
    return;
  end
end
grayImage = imread(fullFileName);
% Get the dimensions of the image.  numberOfColorBands should be = 3.
[rows, columns, numberOfColorBands] = size(grayImage);
% If it's RGB instead of grayscale, convert it to gray scale.
if numberOfColorBands > 1
	grayImage = rgb2gray(grayImage);
end
% Display the original image.
subplot(2, 2, 1);
imshow(grayImage);
axis on;
caption = sprintf('Original Image : %s', baseFileName);
title(caption, 'FontSize', fontSize);
impixelinfo;
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'Outerposition', [0, 0.1, 1, 0.9]);

subplot(2, 2, 2);
imhist(grayImage);
grid on;
title('Histogram of Gray Scale Image', 'FontSize', fontSize);

% Get the binaryImage
mask = imbinarize(grayImage);
% Get rid of huge white frame
mask = imclearborder(mask); % Eliminate blobs touching the border.
% mask = grayImage > 44; % or whatever value works.
% Display the image.
subplot(2, 2, 3);
imshow(mask);
axis on;
title('Mask Image', 'FontSize', fontSize);

% Get areas, centroids, and pixel coordinates.
[labeledImage, numberOfBlobs] = bwlabel(mask);
props = regionprops(mask, 'Area', 'Centroid', 'PixelList');

% Colorize each blob.
% Let's assign each blob a different color to visually show the user the distinct blobs.
coloredLabels = label2rgb (labeledImage, 'hsv', 'k', 'shuffle'); % pseudo random color labels
% coloredLabels is an RGB image.  We could have applied a colormap instead (but only with R2014b and later)
subplot(2, 2, 4);
imshow(coloredLabels);
axis('on', 'image'); % Make sure image is not artificially stretched because of screen's aspect ratio.
caption = sprintf('Pseudo colored labels, from label2rgb().\nBlobs are numbered from top to bottom, then from left to right.');
title(caption, 'FontSize', fontSize);

% Print out the results.
for k = 1 : numberOfBlobs
	xy = props(k).PixelList; % Get an N by 2 array of (x,y) coordinates for this blob.
	fprintf('Blob #%d: Area = %d.  Centroid (x, y) = (%.4f, %.4f)\nPixels in blob #%d:\n    ', ...
		k, props(k).Area, props(k).Centroid(1), props(k).Centroid(2), k);
	for k2 = 1 : size(xy, 1) % For every pixel in this blob, print it's coordinates
		fprintf('(%d, %d), ', xy(k2, 1), xy(k2, 2));
	end
	fprintf('\n'); % Go to next line in command window.
end

In the command window you will see a list of all the measurements:

Blob #1: Area = 6. Centroid (x, y) = (151.1667, 83.1667)

Pixels in blob #1:

(150, 83), (151, 82), (151, 83), (151, 84), (152, 83), (152, 84),

Blob #2: Area = 14. Centroid (x, y) = (163.7143, 83.5000)

Pixels in blob #2:

(162, 83), (162, 84), (163, 82), (163, 83), (163, 84), (163, 85), (164, 82), (164, 83), (164, 84), (164, 85), (165, 82), (165, 83), (165, 84), (165, 85),

Blob #3: Area = 28. Centroid (x, y) = (169.7857, 94.5000)

Pixels in blob #3:

(167, 94), (167, 95), (168, 93), (168, 94), (168, 95), (168, 96), (169, 92), (169, 93), (169, 94), (169, 95), (169, 96), (169, 97), (170, 92), (170, 93), (170, 94), (170, 95), (170, 96), (170, 97), (171, 92), (171, 93), (171, 94), (171, 95), (171, 96), (171, 97), (172, 93), (172, 94), (172, 95), (172, 96),

Blob #4: Area = 6. Centroid (x, y) = (274.8333, 93.8333)

Pixels in blob #4:

(274, 93), (274, 94), (275, 93), (275, 94), (275, 95), (276, 94),

Blob #5: Area = 22. Centroid (x, y) = (281.0909, 83.0909)

Pixels in blob #5:

(279, 82), (279, 83), (279, 84), (280, 81), (280, 82), (280, 83), (280, 84), (280, 85), (281, 81), (281, 82), (281, 83), (281, 84), (281, 85), (282, 81), (282, 82), (282, 83), (282, 84), (282, 85), (283, 82), (283, 83), (283, 84), (283, 85),

Blob #6: Area = 35. Centroid (x, y) = (293.5714, 83.6286)

Pixels in blob #6:

(291, 82), (291, 83), (291, 84), (291, 85), (292, 81), (292, 82), (292, 83), (292, 84), (292, 85), (292, 86), (293, 81), (293, 82), (293, 83), (293, 84), (293, 85), (293, 86), (293, 87), (294, 81), (294, 82), (294, 83), (294, 84), (294, 85), (294, 86), (294, 87), (295, 81), (295, 82), (295, 83), (295, 84), (295, 85), (295, 86), (296, 81), (296, 82), (296, 83), (296, 84), (296, 85),

Blob #7: Area = 59. Centroid (x, y) = (299.6780, 94.6102)

Pixels in blob #7:

(296, 93), (296, 94), (296, 95), (296, 96), (296, 97), (297, 92), (297, 93), (297, 94), (297, 95), (297, 96), (297, 97), (297, 98), (298, 91), (298, 92), (298, 93), (298, 94), (298, 95), (298, 96), (298, 97), (298, 98), (299, 91), (299, 92), (299, 93), (299, 94), (299, 95), (299, 96), (299, 97), (299, 98), (300, 91), (300, 92), (300, 93), (300, 94), (300, 95), (300, 96), (300, 97), (300, 98), (301, 91), (301, 92), (301, 93), (301, 94), (301, 95), (301, 96), (301, 97), (301, 98), (302, 91), (302, 92), (302, 93), (302, 94), (302, 95), (302, 96), (302, 97), (302, 98), (303, 92), (303, 93), (303, 94), (303, 95), (303, 96), (303, 97), (304, 95),

[mohd akmal masud]

but my image is dicom

let say my image is spect128x128

then i want frame number 16,

then

I = dicomread('spect128x128', 'frame', 16)

then how to chane it in your code above?

because error pop up

[mohd akmal masud]

Error using imread>get_format_info (line 491)
Unable to determine the file format.
Error in imread (line 354)
        fmt_s = get_format_info(fullname);
Error in fromimageanalyst (line 36)
grayImage = imread(fullFileName); 

error

[mohd akmal masud]

can you give your email so i can send my dicom image

[Image Analyst]

I used imread() rather than dicomread() because I didn't have the dicom image. You can post the attach the dicom image here with the paperclip icon. Zip it up if it doesn't like that extension.

[mohd akmal masud]

here attached as request

[mohd akmal masud]

DO YOU HAVE ANY IDEA?

Answer 2

[Matt J]

If you mean you want the centroids of the different regions, it would be easier to use regionprops

stats=regionprops(BW16,'Centroid','Area')

[mohd akmal masud]

but i got this? i want the see at the picture.. please help me

stats = 

  4×1 struct array with fields:

    Area
    Centroid

[Matt J]

I15 = dicomread('spect128x128', 'frame', 15);
T15 = graythresh(level);
BW15 = imbinarize(I15,T15);
figure
imshowpair(I15, BW15, 'montage')

T = regionprops('table', BW16,'Area','Centroid')

[mohd akmal masud]

its work

  4×2 table
    Area                  Centroid              
    ____    ____________________________________
     6      52.8333333333333    62.8333333333333
    22      59.0909090909091    52.0909090909091
    35      71.5714285714286    52.6285714285714
    59      77.6779661016949    63.6101694915254

But for example, area 6, their centroid is 52.83 and 62.83. What actually this two number? because i go to center of area 6, the center is about 62. almost 62.83. But what is the value 52.83 means?

[Matt J]

52.83 and 62.83 are the X and Y coordinates of the region's centroid.

[mohd akmal masud]

yah, i got it. tq so much

Answer 3

[Ameer Hamza]

PixelIdxList property already contain the linear indexes of the pixels. If you want row and column number then you can try this

I15 = dicomread('spect128x128', 'frame', 15);
T15 = graythresh(level);
BW15 = imbinarize(I15,T15);
figure
imshowpair(I15, BW15, 'montage')
CC = bwconncomp(BW16)

[r, c] = cellfun(@(x) ind2sub(size(BW15), x), CC.PixelIdxList, 'UniformOutput', 0);

[mohd akmal masud]

ok, thank you so much sir.

then how to to fill the color in every object. lets say i want fill blue color in object no.4?