help with closing binary image
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From: us on 30 Mar 2010 10:54 "M Ladderman" <mirresimons(a)gmail.com> wrote in message <hot214$21p$1(a)fred.mathworks.com>... > "M Ladderman" <mirresimons(a)gmail.com> wrote in message <hot13j$fm7$1(a)fred.mathworks.com>... > > That looks promising, I will try and implement it. So I can set more or less how flexible the convex hull is, that is would I think I need. I had tried it a while ago this code but I did not succeed in implementing it. I will try again. It will work with binary images? Thanks! > > > > ImageAnalyst <imageanalyst(a)mailinator.com> wrote in message <88de8fa6-05f5-46f7-8707-0a2c0f29f205(a)e7g2000yqf.googlegroups.com>... > > > I think this might be a good situation for alpha shapes. us, don't > > > you agree? us has uploaded an alpha shape program to the File > > > Exchange: > > > http://www.mathworks.com/matlabcentral/fileexchange/6760-ashape-a-pedestrian-alpha-shape-extractor > > > > > > It's sort of like a flexible convex hull - one that can more or less > > > follow nooks and crannies rather than being strictly convex. > Stupid question maybe but I cannot remember how to get x,y from a binary image (so two vectors that describe where the 1 of the binary image are at), to use that for the input in Ashape. > firstly: thanks, IA, to allude to the pedestrian ashaper(!)... one of the solutions img=[ 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 0 0 1 1 1 1 1 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 ]; bp=bwperim(img); [y,x]=find(bp); ashape(x,y,1); % <- select your ALPHA... NOTE: - if you use r2010a, there will be an annoying warning message due to the fact that DELAUNAY now has a different syntax... - i will change this asap... - sorry for this... us
From: ImageAnalyst on 30 Mar 2010 12:14 us I thought this fish image wold be a good one for me to practice on with your ashaper. I got this far but something's not right. I thought I'd try something quick and dirty but I guess I need to really dig into the options to figure it out. I need to get going now - maybe I can pick it up later in the day. clc; % Clear the command window. close all; % Close all figures (except those of imtool.) clear all; % Erase all existing variables. workspace; % Make sure the workspace panel is showing. fontSize = 18; % Read in and crop image. filename = 'C:\Documents and Settings\username\My Documents\Temporary stuff\fishexample.jpg'; imageArray = imread(filename); % Convert to grayscale. imageArray = imageArray(:,:,1); % Crop off the border. imageArray = imcrop(imageArray, [145 27 1127 425]); % convert to binary. imageArray = imageArray > 128; subplot(2,2,1); imshow(imageArray, []); title('Original Image', 'FontSize', fontSize); set(gcf, 'Position', get(0,'Screensize')); % Maximize figure. % Get the perimeter. perimeterImage = bwperim(imageArray); subplot(2,2,2); imshow(perimeterImage, []); title('Perimeter Image', 'FontSize', fontSize); % Create a new axes for the alpha shapes result, % since ashape() seems to want to automatically % put results into the current axes object. subplot(2,2,3); set(gca,'YDir','reverse') % Flip upside down. title('Alpha Shape Image', 'FontSize', fontSize); [y, x] = find(perimeterImage); aslibStructure = ashape(x, y, 2.5); % <- select your ALPHA... subplot(2,2,4); % set(gca,'YDir','reverse') % Flip upside down. plot(aslibStructure.x, aslibStructure.y); axis 'equal'; title('Alpha Shape Image2', 'FontSize', fontSize);
From: M Ladderman on 9 Apr 2010 09:28 Hi, I have been working on this with same adjustments to the alpha but, with very low alphas I still get a small (but significant) hole in the belly that is not covered. Any ideas on how to improve this? Thanks! Mirre ImageAnalyst <imageanalyst(a)mailinator.com> wrote in message <f2d1b2ac-4e40-4f6c-83ed-3ff92fb98eb4(a)b30g2000yqd.googlegroups.com>... > us > I thought this fish image wold be a good one for me to practice on > with your ashaper. I got this far but something's not right. I > thought I'd try something quick and dirty but I guess I need to really > dig into the options to figure it out. I need to get going now - > maybe I can pick it up later in the day. > > clc; % Clear the command window. > close all; % Close all figures (except those of imtool.) > clear all; % Erase all existing variables. > workspace; % Make sure the workspace panel is showing. > fontSize = 18; > > % Read in and crop image. > filename = 'C:\Documents and Settings\username\My Documents\Temporary > stuff\fishexample.jpg'; > imageArray = imread(filename); > % Convert to grayscale. > imageArray = imageArray(:,:,1); > % Crop off the border. > imageArray = imcrop(imageArray, [145 27 1127 425]); > % convert to binary. > imageArray = imageArray > 128; > subplot(2,2,1); > imshow(imageArray, []); > title('Original Image', 'FontSize', fontSize); > set(gcf, 'Position', get(0,'Screensize')); % Maximize figure. > > % Get the perimeter. > perimeterImage = bwperim(imageArray); > subplot(2,2,2); > imshow(perimeterImage, []); > title('Perimeter Image', 'FontSize', fontSize); > > % Create a new axes for the alpha shapes result, > % since ashape() seems to want to automatically > % put results into the current axes object. > subplot(2,2,3); > set(gca,'YDir','reverse') % Flip upside down. > title('Alpha Shape Image', 'FontSize', fontSize); > [y, x] = find(perimeterImage); > aslibStructure = ashape(x, y, 2.5); % <- select your ALPHA... > > subplot(2,2,4); > % set(gca,'YDir','reverse') % Flip upside down. > plot(aslibStructure.x, aslibStructure.y); > axis 'equal'; > title('Alpha Shape Image2', 'FontSize', fontSize);
From: ImageAnalyst on 9 Apr 2010 18:51 Not from me - I haven't had a chance to return to looking at this. Maybe if you've taken my code further, you can post it and us can help us out (no pun intended)
From: M Ladderman on 12 Apr 2010 07:26
Hi, Stupid me I tried lower alphas, which result of course in smaller structuring disks. Stupid sorry. So I got my alpha up and get a nice segmentation image from ashape, I want to use the x and y now to get them connected in the way ashape does it. In ashape my whole fish is enclosed by connected dots (by lines). But when I use plot there is still a part missing probably because the polygon plot draws is not the same as ashape displays? I hope this is more or less clear what I mean. Cheers ImageAnalyst <imageanalyst(a)mailinator.com> wrote in message <aa8ee488-d330-4ad2-97a3-7807707b857c(a)h27g2000yqm.googlegroups.com>... > Not from me - I haven't had a chance to return to looking at this. > Maybe if you've taken my code further, you can post it and us can help > us out (no pun intended) |