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I'm trying to create a mask (or similar result) in order to erase pieces of a binary image that are not attached to the object surrounded by the boundary. I saw this thread (http://www.mathworks.com/matlabcentral/answers/120579-converting-boundary-to-mask) to do this from bwboundaries, but I'm having trouble making suitable changes to it. My goal is to use this code to isolate the part of this topography map that is connected, and get rid of the extra pieces. I need to retain the structure inside of the bounded area, as I was then going to use bwboundaries to create additional boundary lines of the main object's "interior" structure.
The following is my code to first create the single boundary line by searching for the bottom left pixel of the black area to begin the trace. It just looks for the first column of the image that isn't completely white and selects the last black pixel. The second section was then to create the inner boundary lines. Note that I am attempting this two step process, but if there is a way to do it with only one I'd like to hear that solution as well. Ultimately I just want boundaries for the main, large black area and the holes inside of it, while getting rid of the extra pieces hanging around.
figName='Images/BookTrace_1';
BW = imread([figName,'.png']);
BW=im2bw(BW);
imshow(BW,[]);
for j=1:size(BW,2)
if sum(BW(:,j))~=sum(BW(:,1))
corner=BW(:,j);
c=j-1;
break
end
end
r=find(corner==0);
r=r(end);
outline = bwtraceboundary(BW,[r c],'W',8,Inf,'counterclockwise');
hold on;
plot(outline(:,2),outline(:,1),'g','LineWidth',2);
[B,L] = bwboundaries(BW);
hold on
for k = 1:length(B)
boundary = B{k};
plot(boundary(:,2), boundary(:,1), 'g', 'LineWidth', 2)
end
Any suggestions or tips are greatly appreciated. If there are questions, please let me know and I'll update the post. Thank you!
EDIT: For clarification, my end goal is as in the below image. I need to trace all of the outer and inner boundaries attached to the main object, while eliminating any spare small pieces that are not attached to it.
It's very simple. I actually wouldn't use the code above and use the image processing toolbox instead. There's a built-in function to remove any white pixels that touch the border of the image. Use the imclearborder function.
The function will return a new binary image where any pixels that were touching the borders of the image will be removed. Given your code, it's very simply:
out = imclearborder(BW);
Using the above image as an example, I'm going to threshold it so that the green lines are removed... or rather merged with the other white pixels, and I'll call the above function:
BW = imread('http://i.stack.imgur.com/jhLOw.png'); %// Read from StackOverflow
BW = im2bw(BW); %// Convert to binary
out = imclearborder(BW); %// Remove pixels along border
imshow(out); %// Show image
We get:
If you want the opposite effect, where you want to retain the boundaries and remove everything else inside, simply create a new image by copying the original one and use the output from the above to null these pixel locations.
out2 = BW; %// Make copy
out2(out) = 0; %// Set pixels not belonging to boundary to 0
imshow(out2); %// Show image
We thus get:
Edit
Given the above desired output, I believe I know what you want now. You wish to fill in the holes for each group of pixels and trace along the boundary of the desired result. The fact that we have this split up into two categories is going to be useful. For those objects that are in the interior, use the imfill function and specify the holes option to fill in any of the black holes so that they're white. For the objects that exterior, this will need a bit of work. What I would do is invert the image so that pixels that are black become white and vice-versa, then use the bwareaopen function to clear away any pixels whose area is below a certain amount. This will remove those small isolated black regions that are along the border of the exterior regions. Once you're done, re-invert the image. The effect of this is that the small holes will be eliminated. I chose a threshold of 500 pixels for the area... seems to work well.
Therefore, using the above variables as reference, do this:
%// Fill holes for both regions separately
out_fill = imfill(out, 'holes');
out2_fill = ~bwareaopen(~out2, 500);
%// Merge together
final_out = out_fill | out2_fill;
This is what we get:
If you want a nice green border like in your example to illustrate this point, you can do this:
perim = bwperim(final_out);
red = final_out;
green = final_out;
blue = final_out;
red(perim) = 0;
blue(perim) = 0;
out_colour = 255*uint8(cat(3, red, green, blue));
imshow(out_colour);
The above code finds the perimeter of the objects, then we create a new image where the red and blue channels along the perimeter are set to 0, while setting the green channel to 255.
We get this:
You can ignore the green pixel border that surrounds the image. That's just a side effect with the way I'm finding the perimeter along the objects in the image. In fact, the image you supplied to me had a white pixel border that surrounds the whole region, so I'm not sure if that's intended or if that's part of the whole grand scheme of things.
To consolidate into a working example so that you can copy and paste into MATLAB, here's all of the code in one code block:
%// Pre-processing
BW = imread('http://i.stack.imgur.com/jhLOw.png'); %// Read from StackOverflow
BW = im2bw(BW); %// Convert to binary
out = imclearborder(BW); %// Remove pixels along border
%// Obtain pixels that are along border
out2 = BW; %// Make copy
out2(out) = 0; %// Set pixels not belonging to boundary to 0
%// Fill holes for both regions separately
out_fill = imfill(out, 'holes');
out2_fill = ~bwareaopen(~out2, 500);
%// Merge together
final_out = out_fill | out2_fill;
%// Show final output
figure;
imshow(final_out);
%// Bonus - Show perimeter of output in green
perim = bwperim(final_out);
red = final_out;
green = final_out;
blue = final_out;
red(perim) = 0;
blue(perim) = 0;
out_colour = 255*uint8(cat(3, red, green, blue));
figure;
imshow(out_colour);
I know this thread about converting black color to white and white to black simultaneously.
I would like to convert only black to white.
I know this thread about doing this what I am asking but I do not understand what goes wrong.
Picture
Code
rgbImage = imread('ecg.png');
grayImage = rgb2gray(rgbImage); % for non-indexed images
level = graythresh(grayImage); % threshold for converting image to binary,
binaryImage = im2bw(grayImage, level);
% Extract the individual red, green, and blue color channels.
redChannel = rgbImage(:, :, 1);
greenChannel = rgbImage(:, :, 2);
blueChannel = rgbImage(:, :, 3);
% Make the black parts pure red.
redChannel(~binaryImage) = 255;
greenChannel(~binaryImage) = 0;
blueChannel(~binaryImage) = 0;
% Now recombine to form the output image.
rgbImageOut = cat(3, redChannel, greenChannel, blueChannel);
imshow(rgbImageOut);
Which gives
Where seems to be something wrong in red color channel.
The Black color is just (0,0,0) in RGB so its removal should mean to turn every (0,0,0) pixel to white (255,255,255).
Doing this idea with
redChannel(~binaryImage) = 255;
greenChannel(~binaryImage) = 255;
blueChannel(~binaryImage) = 255;
Gives
So I must have misunderstood something in Matlab. The blue color should not have any black. So this last image is strange.
How can you turn only black color to white?
I want to keep the blue color of the ECG.
If I understand you properly, you want to extract out the blue ECG plot while removing the text and axes. The best way to do that would be to examine the HSV colour space of the image. The HSV colour space is great for discerning colours just like the way humans do. We can clearly see that there are two distinct colours in the image.
We can convert the image to HSV using rgb2hsv and we can examine the components separately. The hue component represents the dominant colour of the pixel, the saturation denotes the purity or how much white light there is in the pixel and the value represents the intensity or strength of the pixel.
Try visualizing each channel doing:
im = imread('http://i.stack.imgur.com/cFOSp.png'); %// Read in your image
hsv = rgb2hsv(im);
figure;
subplot(1,3,1); imshow(hsv(:,:,1)); title('Hue');
subplot(1,3,2); imshow(hsv(:,:,2)); title('Saturation');
subplot(1,3,3); imshow(hsv(:,:,3)); title('Value');
Hmm... well the hue and saturation don't help us at all. It's telling us the dominant colour and saturation are the same... but what sets them apart is the value. If you take a look at the image on the right, we can tell them apart by the strength of the colour itself. So what it's telling us is that the "black" pixels are actually blue but with almost no strength associated to it.
We can actually use this to our advantage. Any pixels whose values are above a certain value are the values we want to keep.
Try setting a threshold... something like 0.75. MATLAB's dynamic range of the HSV values are from [0-1], so:
mask = hsv(:,:,3) > 0.75;
When we threshold the value component, this is what we get:
There's obviously a bit of quantization noise... especially around the axes and font. What I'm going to do next is perform a morphological erosion so that I can eliminate the quantization noise that's around each of the numbers and the axes. I'm going to make it the mask a bit large to ensure that I remove this noise. Using the image processing toolbox:
se = strel('square', 5);
mask_erode = imerode(mask, se);
We get this:
Great, so what I'm going to do now is make a copy of your original image, then set any pixel that is black from the mask I derived (above) to white in the final image. All of the other pixels should remain intact. This way, we can remove any text and the axes seen in your image:
im_final = im;
mask_final = repmat(mask_erode, [1 1 3]);
im_final(~mask_final) = 255;
I need to replicate the mask in the third dimension because this is a colour image and I need to set each channel to 255 simultaneously in the same spatial locations.
When I do that, this is what I get:
Now you'll notice that there are gaps in the graph.... which is to be expected due to quantization noise. We can do something further by converting this image to grayscale and thresholding the image, then filling joining the edges together by a morphological dilation. This is safe because we have already eliminated the axies and text. We can then use this as a mask to index into the original image to obtain our final graph.
Something like this:
im2 = rgb2gray(im_final);
thresh = im2 < 200;
se = strel('line', 10, 90);
im_dilate = imdilate(thresh, se);
mask2 = repmat(im_dilate, [1 1 3]);
im_final_final = 255*ones(size(im), class(im));
im_final_final(mask2) = im(mask2);
I threshold the previous image that we got without the text and axes after I convert it to grayscale, and then I perform dilation with a line structuring element that is 90 degrees in order to connect those lines that were originally disconnected. This thresholded image will contain the pixels that we ultimately need to sample from the original image so that we can get the graph data we need.
I then take this mask, replicate it, make a completely white image and then sample from the original image and place the locations we want from the original image in the white image.
This is our final image:
Very nice! I had to do all of that image processing because your image basically has quantization noise to begin with, so it's going to be a bit harder to get the graph entirely. Ander Biguri in his answer explained in more detail about colour quantization noise so certainly check out his post for more details.
However, as a qualitative measure, we can subtract this image from the original image and see what is remaining:
imshow(rgb2gray(abs(double(im) - double(im_final_final))));
We get:
So it looks like the axes and text are removed fine, but there are some traces in the graph that we didn't capture from the original image and that makes sense. It all has to do with the proper thresholds you want to select in order to get the graph data. There are some trouble spots near the beginning of the graph, and that's probably due to the morphological processing that I did. This image you provided is quite tricky with the quantization noise, so it's going to be very difficult to get a perfect result. Also, these thresholds unfortunately are all heuristic, so play around with the thresholds until you get something that agrees with you.
Good luck!
What's the problem?
You want to detect all black parts of the image, but they are not really black
Example:
Your idea (or your code):
You first binarize the image, selecting the pixels that ARE something against the pixels that are not. In short, you do: if pixel>level; pixel is something
Therefore there is a small misconception you have here! when you write
% Make the black parts pure red.
it should read
% Make every pixel that is something (not background) pure red.
Therefore, when you do
redChannel(~binaryImage) = 255;
greenChannel(~binaryImage) = 255;
blueChannel(~binaryImage) = 255;
You are doing
% Make every pixel that is something (not background) white
% (or what it is the same in this case, delete them).
Therefore what you should get is a completely white image. The image is not completely white because there has been some pixels that were labelled as "not something, part of the background" by the value of level, in case of your image around 0.6.
A solution that one could think of is manually setting the level to 0.05 or similar, so only black pixels will be selected in the gray to binary threholding. But this will not work 100%, as you can see, the numbers have some very "no-black" values.
How would I try to solve the problem:
I would try to find the colour you want, extract just that colour from the image, and then delete outliers.
Extract blue using HSV (I believe I answered you somewhere else how to use HSV).
rgbImage = imread('ecg.png');
hsvImage=rgb2hsv(rgbImage);
I=rgbImage;
R=I(:,:,1);
G=I(:,:,2);
B=I(:,:,3);
th=0.1;
R((hsvImage(:,:,1)>(280/360))|(hsvImage(:,:,1)<(200/360)))=255;
G((hsvImage(:,:,1)>(280/360))|(hsvImage(:,:,1)<(200/360)))=255;
B((hsvImage(:,:,1)>(280/360))|(hsvImage(:,:,1)<(200/360)))=255;
I2= cat(3, R, G, B);
imshow(I2)
Once here we would like to get the biggest blue part, and that would be our signal. Therefore the best approach seems to first binarize the image taking all blue pixels
% Binarize image, getting all the pixels that are "blue"
bw=im2bw(rgb2gray(I2),0.9999);
And then using bwlabel, label all the independent pixel "islands".
% Label each "blob"
lbl=bwlabel(~bw);
The label most repeated will be the signal. So we find it and separate the background from the signal using that label.
% Find the blob with the highes amount of data. That will be your signal.
r=histc(lbl(:),1:max(lbl(:)));
[~,idxmax]=max(r);
% Profit!
signal=rgbImage;
signal(repmat((lbl~=idxmax),[1 1 3]))=255;
background=rgbImage;
background(repmat((lbl==idxmax),[1 1 3]))=255;
Here there is a plot with the signal, background and difference (using the same equation as #rayryang used)
Here is a variation on #rayryeng's solution to extract the blue signal:
%// retrieve picture
imgRGB = imread('http://i.stack.imgur.com/cFOSp.png');
%// detect axis lines and labels
imgHSV = rgb2hsv(imgRGB);
BW = (imgHSV(:,:,3) < 1);
BW = imclose(imclose(BW, strel('line',40,0)), strel('line',10,90));
%// clear those masked pixels by setting them to background white color
imgRGB2 = imgRGB;
imgRGB2(repmat(BW,[1 1 3])) = 255;
%// show extracted signal
imshow(imgRGB2)
To get a better view, here is the detected mask overlayed on top of the original image (I'm using imoverlay function from the File Exchange):
figure
imshow(imoverlay(imgRGB, BW, uint8([255,0,0])))
Here is a code for this:
rgbImage = imread('ecg.png');
redChannel = rgbImage(:, :, 1);
greenChannel = rgbImage(:, :, 2);
blueChannel = rgbImage(:, :, 3);
black = ~redChannel&~greenChannel&~blueChannel;
redChannel(black) = 255;
greenChannel(black) = 255;
blueChannel(black) = 255;
rgbImageOut = cat(3, redChannel, greenChannel, blueChannel);
imshow(rgbImageOut);
black is the area containing the black pixels. These pixels are set to white in each color channel.
In your code you use a threshold and a grayscale image so of course you have much bigger area of pixels that is set to white resp. red color. In this code only pixel that contain absolutly no red, green and blue are set to white.
The following code does the same with a threshold for each color channel:
rgbImage = imread('ecg.png');
redChannel = rgbImage(:, :, 1);
greenChannel = rgbImage(:, :, 2);
blueChannel = rgbImage(:, :, 3);
black = (redChannel<150)&(greenChannel<150)&(blueChannel<150);
redChannel(black) = 255;
greenChannel(black) = 255;
blueChannel(black) = 255;
rgbImageOut = cat(3, redChannel, greenChannel, blueChannel);
imshow(rgbImageOut);
i am mechanical engineering student working on a project to automatically detect the weld seam (The seam is a edge that is to be welded) present in a workshop. This gives a basic terminology involved in welding (http://i.imgur.com/Hfwjq0w.jpg).
To separate the weldment from the other objects, i have taken the background image and subtracted the foreground image having the weldment to obatin only the weldment(http://i.imgur.com/v7yBWs1.jpg). After image subtraction,there are the shadow ,glare and remnant noises of subtracted background are still present.
As i want to automatically identify only the weld seam without the outer boundary of weldment, i have tried to detect the edges in the weldment image using canny algorithm and tried to eliminate the isolated noises using the function bwareopen.I have somehow obtained the approximate boundary of weldment and weld seam. The threshold i have used are purely on trial and error approach as dont know a way to automatically set a threshold to detect them.
The problem now i am facing is that i cant specify an definite threshold as this algorithm should be able to identify the seam of any material regardless of its surface texture,glare and shadow present there. I need some assistance to remove the glare,shadow and isolated points from the background subtracted image.
Also i need help to get rid of the outer boundary and obtain only smooth weld seam from starting point to end point.
i have tried to use the following code:
a=imread('imageofworkpiece.jpg'); %http://i.imgur.com/3ngu235.jpg
b=imread('background.jpg'); %http://i.imgur.com/DrF6wC2.jpg
Ip = imsubtract(b,a);
imshow(Ip) % weldment separated %http://i.imgur.com/v7yBWs1.jpg
BW = rgb2gray(Ip);
c=edge(BW,'canny',0.05); % by trial and error
figure;imshow(c) % %http://i.imgur.com/1UQ8E3D.jpg
bw = bwareaopen(c, 100); % by trial and error
figure;imshow(bw) %http://i.imgur.com/Gnjy2aS.jpg
Can anybody please suggest me a adaptive way to set a threhold and remove the outer boundary to detect only the seam? Thank you
Well this doesn't solve your problem of finding an automatic thresholding algorithm. but I can help with isolation the seam. The seam is along the y axis (will this always be the case?) so I used hough transform to isolate only near vertical lines. Normally it finds all lines but I restricted the theta search parameter. The code I'm using now happens to highlight the longest line segment (I got it directly from the matlab website) and it is coincidentally the weld seam. This was purely coincidental. But using your bwareaopened image as input the hough line detector is able to find the seam. Of course it required a bit of playing around to work, so you are stuck at your original problem of finding optimal settings somehow
Maybe this can be a springboard for someone else
a=imread('weldment.jpg'); %http://i.imgur.com/3ngu235.jpg
b=imread('weld_bg.jpg'); %http://i.imgur.com/DrF6wC2.jpg
Ip = imsubtract(b,a);
imshow(Ip) % weldment separated %http://i.imgur.com/v7yBWs1.jpg
BW = rgb2gray(Ip);
c=edge(BW,'canny',0.05); % by trial and error
bw = bwareaopen(c, 100); % by trial and error
figure(1);imshow(c) ;title('canny') % %http://i.imgur.com/1UQ8E3D.jpg
figure(2);imshow(bw);title('bw area open') %http://i.imgur.com/Gnjy2aS.jpg
[H,T,R] = hough(bw,'RhoResolution',1,'Theta',-15:5:15);
figure(3)
imshow(H,[],'XData',T,'YData',R,...
'InitialMagnification','fit');
xlabel('\theta'), ylabel('\rho');
axis on, axis normal, hold on;
P = houghpeaks(H,5,'threshold',ceil(0.5*max(H(:))));
x = T(P(:,2)); y = R(P(:,1));
plot(x,y,'s','color','white');
% Find lines and plot them
lines = houghlines(BW,T,R,P,'FillGap',2,'MinLength',30);
figure(4), imshow(BW), hold on
max_len = 0;
for k = 1:length(lines)
xy = [lines(k).point1; lines(k).point2];
plot(xy(:,1),xy(:,2),'LineWidth',2,'Color','green');
% Plot beginnings and ends of lines
plot(xy(1,1),xy(1,2),'x','LineWidth',2,'Color','yellow');
plot(xy(2,1),xy(2,2),'x','LineWidth',2,'Color','red');
% Determine the endpoints of the longest line segment
len = norm(lines(k).point1 - lines(k).point2);
if ( len > max_len)
max_len = len;
xy_long = xy;
end
end
% highlight the longest line segment
plot(xy_long(:,1),xy_long(:,2),'LineWidth',2,'Color','blue');
from your image it looks like the weld seam will be usually very dark with sharp intensity edge so why don't you use that ?
do not use background
create derivation image
dx[y][x]=pixel[y][x]-pixel[y][x-1]
do this for whole image (if on place then x must decrease in loop!!!)
filter out all derivations lower then thresholds
if (|dx[y][x]|<threshold) dx[y][x]=0; else pixel[y][x]=255;` // or what ever values you use
how to obtain threshold value ?
compute min and max intensity and set threshold as (max-min)*scale where scale is value lower then 1.0 (start with 0.02 or 0.1 for example ...
do this also for y axis
so compute dy[][]... and combine dx[][] and dy[][] together. Either with OR or by AND logical functions
filter out artifacts
you can use morphologic filters or smooth threshold for this. After all this you will have mask of pixels of weld seam
if you need boundig box then just loop through all pixels and remember min,max x,y coords ...
[Notes]
if your images will have good lighting then you can ignore the derivation and threshold the intensity directly with something like:
threshold = 0.5*(average_intensity+lowest_intensity)
if you want really fully automate this then you have to use adaptive thresholds. So try more thresholds in a loop and remember result closest to desired output based on geometry size,position etc ...
[edit1] finally have some time/mood for this so
Intensity image threshold
you provided just single image which is far from enough to make reliable algorithm. This is the result
as you can see without further processing this is not good approach
Derivation image threshold
threshold derivation by x (10%)
threshold derivation by y (5%)
AND combination of both 10% di/dx and 1.5% di/dy
The code in C++ looks like this (sorry do not use Matlab):
int x,y,i,i0,i1,tr2,tr3;
pic1=pic0; // copy input image pic0 to pic1
pic2=pic0; // copy input image pic0 to pic2 (just to resize to desired size for derivation)
pic3=pic0; // copy input image pic0 to pic3 (just to resize to desired size for derivation)
pic1.rgb2i(); // RGB -> grayscale
// abs derivate by x
for (y=pic1.ys-1;y>0;y--)
for (x=pic1.xs-1;x>0;x--)
{
i0=pic1.p[y][x ].dd;
i1=pic1.p[y][x-1].dd;
i=i0-i1; if (i<0) i=-i;
pic2.p[y][x].dd=i;
}
// compute min,max derivation
i0=pic2.p[1][1].dd; i1=i0;
for (y=1;y<pic1.ys;y++)
for (x=1;x<pic1.xs;x++)
{
i=pic2.p[y][x].dd;
if (i0>i) i0=i;
if (i1<i) i1=i;
}
tr2=i0+((i1-i0)*100/1000);
// abs derivate by y
for (y=pic1.ys-1;y>0;y--)
for (x=pic1.xs-1;x>0;x--)
{
i0=pic1.p[y ][x].dd;
i1=pic1.p[y-1][x].dd;
i=i0-i1; if (i<0) i=-i;
pic3.p[y][x].dd=i;
}
// compute min,max derivation
i0=pic3.p[1][1].dd; i1=i0;
for (y=1;y<pic1.ys;y++)
for (x=1;x<pic1.xs;x++)
{
i=pic3.p[y][x].dd;
if (i0>i) i0=i;
if (i1<i) i1=i;
}
tr3=i0+((i1-i0)*15/1000);
// threshold the derivation images and combine them
for (y=1;y<pic1.ys;y++)
for (x=1;x<pic1.xs;x++)
{
// copy original (pic0) pixel for non thresholded areas the rest fill with green color
if ((pic2.p[y][x].dd>=tr2)&&(pic3.p[y][x].dd>=tr3)) i=0x00FF00;
else i=pic0.p[y][x].dd;
pic1.p[y][x].dd=i;
}
pic0 is input image
pic1 is output image
pic2,pic3 are just temporary storage for derivations
pic?.xy,pic?.ys is the size of pic?
pic.p[y][x].dd is pixel axes (dd means access pixel as DWORD ...)
as you can see there is a lot of stuff around (nod visible in the first image you provided) so you need to process this further
segmentate and separate...,
use hough transform ...
filter out small artifacts ...
identify object by expected geometry properties (aspect ratio,position,size)
Adaptive thresholds:
you need for this to know the desired output image properties (not possible to reliably deduce from single image input) then create function that do the above processing with variable tr2,tr3. Try in loop more options of tr2,tr3 (loop through all values or iterate to better results and remember the best output (so you also need some function that detects the quality of output) for example:
quality=0.0; param=0.0;
for (a=0.2;a<=0.8;a+=0.1)
{
pic1=process_image(pic0,a);
q=detect_quality(pic1);
if (q>quality) { quality=q; param=a; pico=pic1; }
}
after this the pic1 should hold the relatively best threshold image ... You should process like this all threshold separately inside the process_image the targeted threshold must be scaled by a for example tr2=i0+((i1-i0)*a);
I have a hard problem that need your help. I have a binary image that maintains some unwanted region (small white dot) and hole regions (in figure 1).My idea is that the first I will remove unwanted region by calculating area these region and then filter with small area value.At the second step, I fill in hole region to make clear image.What do you think best method to fill in hole region. Do you have any idea to resolve it. Could you help me implement it by matlab. Thank you so much. This is my reference code for remove unwanted region. But it need threshold term. You can download image test at here
function exImage=rmUnwantedRegion(Img,threshold)
lb = bwlabel(Img);
st = regionprops(lb, 'Area', 'PixelIdxList' );
toRemove = [st.Area] <threshold; % fix your threshold here
exImage = Img;
exImage( vertcat(st(toRemove).PixelIdxList ) ) = 0; % remove
end
Here is an example implementation based on my comment:
subplot(1,3,1), imshow(input);
title('Original Image');
Calculating the opening of the image:
openInput=bwareaopen(input, 20);
subplot(1,3,2), imshow(bwareaopen(input, 20));
title('Opened Image');
And the subsequent closing:
ClosedInput = imclose(openInput,ones(10));
subplot(1,3,3), imshow(ClosedInput);
title('Closed Image');
Result:
Assuming white pixel is 1
Black is 0
Step 1:
Use convultion matrix (http://en.wikipedia.org/wiki/Kernel_%28image_processing%29)
with blur filter
Step 2:
Treshold each pixel with some static value (for example 0.5)
if pixel is >0.5 pixel = 1
else pixel = 0
This looks like a job for binary dilation and erosion. Generally an erosion is done first to remove unwanted noise and then dilation is performed with the same structuring element to fill in the gaps left by the erosion. Matlab uses strel to create structuring elements for morphological operations. You can also read about morphological operators here
Example:
SE=strel('square',5);
im_eroded=imerode(im,SE);
im_dilated=imdilate(im_eroded,SE);
You need to do an erosion (Wikipedia or Matlab) followed by a dilation (Wikipedia or Matlab). This is done using the imerode and the imdilate functions in Matlab.
Doing this require to specify the size of the element eroding and dilating using the strel function with a shape ('square', 'disk', 'octagon', etc.) and a size.
SE=strel('disk',5);
im_eroded=imerode(im,SE);
im_dilated=imdilate(im_eroded,SE);
A biologist friend of mine asked me if I could help him make a program to count the squama (is this the right translation?) of lizards.
He sent me some images and I tried some things on Matlab. For some images it's much harder than other, for example when there are darker(black) regions. At least with my method. I'm sure I can get some useful help here. How should I improve this? Have I taken the right approach?
These are some of the images.
I got the best results by following Image Processing and Counting using MATLAB. It's basically turning the image into Black and white and then threshold it. But I did add a bit of erosion.
Here's the code:
img0=imread('C:...\pic.png');
img1=rgb2gray(img0);
%The output image BW replaces all pixels in the input image with luminance greater than level with the value 1 (white) and replaces all other pixels with the value 0 (black). Specify level in the range [0,1].
img2=im2bw(img1,0.65);%(img1,graythresh(img1));
imshow(img2)
figure;
%erode
se = strel('line',6,0);
img2 = imerode(img2,se);
se = strel('line',6,90);
img2 = imerode(img2,se);
imshow(img2)
figure;
imshow(img1, 'InitialMag', 'fit')
% Make a truecolor all-green image. I use this later to overlay it on top of the original image to show which elements were counted (with green)
green = cat(3, zeros(size(img1)),ones(size(img1)), zeros(size(img1)));
hold on
h = imshow(green);
hold off
%counts the elements now defined by black spots on the image
[B,L,N,A] = bwboundaries(img2);
%imshow(img2); hold on;
set(h, 'AlphaData', img2)
text(10,10,strcat('\color{green}Objects Found:',num2str(length(B))))
figure;
%this produces a new image showing each counted element and its count id on top of it.
imshow(img2); hold on;
colors=['b' 'g' 'r' 'c' 'm' 'y'];
for k=1:length(B),
boundary = B{k};
cidx = mod(k,length(colors))+1;
plot(boundary(:,2), boundary(:,1), colors(cidx),'LineWidth',2);
%randomize text position for better visibility
rndRow = ceil(length(boundary)/(mod(rand*k,7)+1));
col = boundary(rndRow,2); row = boundary(rndRow,1);
h = text(col+1, row-1, num2str(L(row,col)));
set(h,'Color',colors(cidx),'FontSize',14,'FontWeight','bold');
end
figure;
spy(A);
And these are some of the results. One the top-left corner you can see how many were counted.
Also, I think it's useful to have the counted elements marked in green so at least the user can know which ones have to be counted manually.
There is one route you should consider: watershed segmentation. Here is a quick and dirty example with your first image (it assumes you have the IP toolbox):
raw=rgb2gray(imread('lCeL8.jpg'));
Icomp = imcomplement(raw);
I3 = imhmin(Icomp,20);
L = watershed(I3);
%%
imagesc(L);
axis image
Result shown with a colormap:
You can then count the cells as follows:
count = numel(unique(L));
One of the advantages is that it can be directly fed to regionprops and give you all the nice details about the individual 'squama':
r=regionprops(L, 'All');
imshow(raw);
for k=2:numel(r)
if r(k).Area>100 % I chose 100 to filter out the objects with a small are.
rectangle('Position',r(k).BoundingBox, 'LineWidth',1, 'EdgeColor','b', 'Curvature', [1 1]);
end
end
Which you could use to monitor over/under segmentation:
Note: special thanks to #jucestain for helping with the proper access to the fields in the r structure here