I am interested in extracting the objects inside the region.
For example,
Fig1 showed the intensity profile of my laser profile. According to the laser intensity, I divide the profile into 2 region of interest (ROI1 and ROI2).
Fig2 showed the overlap of my exp result of positive responses and the laser intensity profile. The positive response data file is composed of x and y coordinates. As you can see the results are scattered over the laser profile image.
Here is what I want to do, I want to extract the spots within the ROI2 and discard all the rest as shown in Fig3. How can I do it? Specifically, how can I define a irregular shape ROI2 in matlab and extract the coordinates of positive response data.
Thanks for the help.
As eykanal says, you can use the impoly function to create any sort of ROI you want in your image. A general solution for extracting coordiantes is to create the ROI you want, and the use find to extract the coordinates and some set operation to remove unwanted points. Like this:
imshow(image)
h = impoly() ; %# draw ROI1
ROI1 = createMask(h); %# create binary mask of ROI1
h2 = impoly(); %# draw dummy_ROI consisting of ROI1+ROI2
dummy_ROI = createMask(h2); %# create binary mask
ROI2 = dummy_ROI-ROI1; %# create ROI2
p = find(ROI2); %# find all coordinates of ROI2
points = intersect(ind,p); %# find all points with linear index ind that are
%# part of ROI2
I think this problem is easier than you think, provided you always segment the image along (what appear to be) contour lines. You want to select all points which have a value greater than contour line 1 and less than contour line 2. I'm not sure how you specified the contour lines, but the selection command should simply be:
#% let laserData be the image data (it looks like it should
#% be 512x256, so I'll assume that)
highBound = mean(contour1points);
lowBound = mean(contour2points);
selectedData = laserData(laserData > lowBound & laserData < highBound);
If, as it appears, you're simply setting contours based on value, then the mean(contour1points) could be replaced by a user-defined value, using the function to get the value of the pixel under the cursor which I can't happen to recall right now. If you want to define a polygon, check out the impoly function.
I don't know what representation you use for your ROIs, but I would suggest some methods:
If your ROI is an ellipse and you know its equation just apply it to the results coordinates. Use the sign to decide if whether it is inside or not
If your ROI is a polygon of some kind you can use the function inpolygon
You could render the ROIs to black and white images and easily test hit/miss.
Please provide more details regarding the ROI representation.
Related
I have the follow code in matlab which is supposed to draw a polygon on a image (has to be a 2d image, be just a patch).
numCorners=8;
dotPos=[];
for rr=1:numCorners
dotPos(end+1)=(cos(rr/numCorners*2*pi))*100;
dotPos(end+1)=(sin(rr/numCorners*2*pi))*100;
end
BaseIm=zeros(1000,1000);
dotpos=[500,500];
imageMatrix =drawpolygon(BaseIm, dotPos, 1); or how else do draw a white polygon here?
imshow(imageMatrix);
This doesn't work as drawpolygon does not appear to exist in this way any idea how to do this?
Note that the resulting data must be an image of equal size of baseIM and must be an array of doubles (ints can be converted) as this is test data for another algorithm.
I have since found the inpolygon(xi,yi,xv,yv); function which I could combine with a for loop if I knew how to properly call it.
If you just need to plot two polygons, you can use the fill function.
t=0:2*pi;
x=cos(t)*2;
y=sin(t)*2
fill(x,y,'r')
hold on
fill(x/2,y/2,'g')
As an alternative, you can use the patch function:
figure
t=0:2*pi;
x=cos(t)*2;
y=sin(t)*2
patch(x,y,'c')
hold on
patch(x/2,y/2,'k')
Edit
The fill and patch functions allow to add polygons also over an actual image too.
% Load an image on the axes
imshow('Jupiter_New_Horizons.jpg')
hold on
% Get the axis limits (just to center the polygons
x_lim=get(gca,'xlim')
y_lim=get(gca,'ylim')
% Create the polygon's coords
t=0:2*pi;
x=cos(t)*50+x_lim(2)/2;
y=sin(t)*50+y_lim(2)/2
% Add the two polygons to the image
f1_h=fill(x,y,'r')
hold on
f1_h=fill(x/2,y/2,'g')
Hope this helps.
I am currently doing some seismic modelling and processing in MATLAB, and would like to come up with an easy way of muting parts of various datasets. If I plot the frequency-wavenumber spectrum of some of my data, for instance, I obtain the following result:
Now, say that I want to mute some of the data present here. I could of course attempt to run through the entire matrix represented here and specify a threshold value where everything above said value should be set equal to zero, but this will be very difficult and time-consuming when I later will work with more complicated fk-spectra. I recently learned that MATLAB has an inbuilt function called impoly which allows me to interactively draw a polygon in plots. So say I, for instance, draw the following polygon in my plot with the impoly-function:
Is there anything I can do now to set all points within this polygon equal to zero? After defining the polygon as illustrated above I haven't found out how to proceed in order to mute the information contained in the polygon, so if anybody can give me some help here, then i would greatly appreciate it!
Yes, you can use the createMask function that's part of the impoly interface once you delineate the polygon in your figure. Once you use create this mask, you can use the mask to index into your data and set the right regions to zero.
Here's a quick example using the pout.tif image in MATLAB:
im = imread('pout.tif');
figure; imshow(im);
h = impoly;
I get this figure and I draw a polygon inside this image:
Now, use the createMask function with the handle to the impoly call to create a binary mask that encapsulates this polygon:
mask = createMask(h);
I get this mask:
imshow(mask);
You can then use this mask to index into your data and set the right regions to 0. First make a copy of the original data then set the data accordingly.
im_zero = im;
im_zero(mask) = 0;
I now get this:
imshow(im_zero);
Note that this only applies to single channel (2D) data. If you want to apply this to multi-channel (3D) data, then perhaps a multiplication channel-wise with the opposite of the mask may be prudent.
Something like this:
im_zero = bsxfun(#times, im, cast(~mask, class(im)));
The above code takes the opposite of the polygon mask, converts it into the same class as the original input im, then performs an element-wise multiplication of this mask with each channel of the input separately. The result will zero each spatial location that's defined in the mask over all channels.
Let's say i have an image like that one:
After some quick messing around, i got a binary image of the axe, like that:
What is the easiest/fastest way to get the contour of that image using GNU/Octave?
In Octave you can use bwboundaries (but I will welcome patches that implement bwtraceboundaries)
octave:1> pkg load image;
octave:2> bw = logical (imread ("http://i.stack.imgur.com/BoQPe.jpg"));
octave:3> boundaries = bwboundaries (bw);
octave:4> boundaries = cell2mat (boundaries);
octave:5> imshow (bw);
octave:6> hold on
octave:7> plot (boundaries(:,2), boundaries(:,1), '.g');
There are a couple of differences here from #Benoit_11 answer:
here we get the boundaries for all the objects in the image. bwboundaries will also accept coordinates as input argument to pick only a single object but I believe that work should be done by further processing your mask (may be due to the jpeg artifacts)
because we get boundaries for all objects, so you get a cell array with the coordinates. This is why we are using dots to plot the boundaries (the default is lines and it will be all over the image as it jumps from one object to other). Also, it is not documented whether the coordinates given are for the continuous boundary, so you should not assume it (again, why we plot dots).
the image that is read seems to have some artifacts, I will guess that is from saving in jpeg.
You can use bwtraceboundary in the Image package. Here is the Matlab implementation but that should be pretty similar using Octave:
First estimate starting pixel to look for boundary and then plot (BW is the image). (Check here )
dim = size(BW);
col = round(dim(2)/2)-90;
row = min(find(BW(:,col)));
boundary = bwtraceboundary(BW,[row, col],'N');
imshow(BW)
hold on;
plot(boundary(:,2),boundary(:,1),'g','LineWidth',3);
Output:
I have a original gray scale image(I m using mammogram image with labels outside image).
I need to remove some objects(Labels) in that image, So i converted that grayscale image to a binary image. Then i followed the answer method provided in
How to Select Object with Largest area
Finally i extracted an Object with largest area as binary image. I want that region in gray scale for accessing and segmenting small objects within that. For example. Minor tissues in region and also should detect its edge.
**
How can i get that separated object region as grayscale image or
anyway to get the largest object region from gray scale directly
without converting to binary or any other way.?
**
(I am new to matlab. I dono whether i explained it correctly or not. If u cant get, I ll provide more detail)
If I understood you correctly, you are looking to have a gray image with only the biggest blob being highlighted.
Code
img = imread(IMAGE_FILEPATH);
BW = im2bw(img,0.2); %%// 0.2 worked to get a good area for the biggest blob
%%// Biggest blob
[L, num] = bwlabel(BW);
counts = sum(bsxfun(#eq,L(:),1:num));
[~,ind] = max(counts);
BW = (L==ind);
%%// Close the biggest blob
[L,num] = bwlabel( ~BW );
counts = sum(bsxfun(#eq,L(:),1:num));
[~,ind] = max(counts);
BW = ~(L==ind);
%%// Original image with only the biggest blob highlighted
img1 = uint8(255.*bsxfun(#times,im2double(img),BW));
%%// Display input and output images
figure,
subplot(121),imshow(img)
subplot(122),imshow(img1)
Output
If I understand your question correctly, you want to use the binary map and access the corresponding pixel intensities in those regions.
If that's the case, then it's very simple. You can use the binary map to identify the spatial co-ordinates of where you want to access the intensities in the original image. Create a blank image, then copy over these intensities over to the blank image using those spatial co-ordinates.
Here's some sample code that you can play around with.
% Assumptions:
% im - Original image
% bmap - Binary image
% Where the output image will be stored
outImg = uint8(zeros(size(im)));
% Find locations in the binary image that are white
locWhite = find(bmap == 1);
% Copy over the intensity values from these locations from
% the original image to the output image.
% The output image will only contain those pixels that were white
% in the binary image
outImg(locWhite) = im(locWhite);
% Show the original and the result side by side
figure;
subplot(1,2,1);
imshow(im); title('Original Image');
subplot(1,2,2);
imshow(outImg); title('Extracted Result');
Let me know if this is what you're looking for.
Method #2
As suggested by Rafael in his comments, you can skip using find all together and use logical statements:
outImg = img;
outImg(~bmap) = 0;
I decided to use find as it less obfuscated for a beginner, even though it is less efficient to do so. Either method will give you the correct result.
Some food for thought
The extracted region that you have in your binary image has several holes. I suspect you would want to grab the entire region without any holes. As such, I would recommend that you fill in these holes before you use the above code. The imfill function from MATLAB works nicely and it accepts binary images as input.
Check out the documentation here: http://www.mathworks.com/help/images/ref/imfill.html
As such, apply imfill on your binary image first, then go ahead and use the above code to do your extraction.
I am trying to generate the following "effect" from a basic shape in MATLAB:
But I don't even know how this process is called. Let's say I have an image containing the brown shape, what I want is generate the contours outside of it, that get smoother as they get bigger.
Is there either a name for this effect, a function to do this in MATLAB or an algorithm that does it from scratch?
thanks
I think you are looking for bwdist.
The image you are displaying looks like the positive part of a distance function from the boundary of your shape. You can perform this easily in Matlab using the examples on the aforementioned manual page.
Try this:
I = imread('brown_image.png');
I_bw = (rgb2gray(I) > 0); % or whatever, just so I_bw is 1 in the 'brown' region
r = 10;
se1 = strel('disk', r);
se2 = strel('disk', r-1);
imshow(imdilate(I_bw, se1) - imdilate(I_bw, se2))
Requires image processing toolbox, but the basic idea is to dilate the image twice with dilation elements that differ by 1 (or however thick you want the contours to be) and subtract the result of the smaller one from the bigger one. You could then color them however you want.