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Search found 8 results on 1 pages for 'imagej'.

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  • Overlay of multiple colors in ImageJ

    - by nico
    Hi everyone, I'm writing a little plugin for imageJ and I am drawing several regions as an overlay on the image. I'm using this code: ImagePlus imp = getImage(); Overlay ov = new Overlay(); for (int r=0; r<regions.length; r++) { ov.add(regions[r]); } imp.setOverlay(ov); Where regions is an array of Roi. This works as intended and draws the regions in the (hurting to my eyes) standard ImageJ cyan used for overlays. I would like to draw one particular region in another colour, but I cannot seem to find a way to do it. I found that you can change the colour of the whole overlay, but I need two colours in the same overlay. Any ideas? Thanks in advance nico

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  • How can I do batch image processing with ImageJ in Java or clojure?

    - by Robert McIntyre
    I want to use ImageJ to do some processing of several thousand images. Is there a way to take any general imageJ plugin and apply it to hundreds of images automatically? For example, say I want to take my thousand images and apply a polar transformation to each--- A polar transformation plugin for ImageJ can be found here: http://rsbweb.nih.gov/ij/plugins/polar-transformer.html Great! Let's use it. From: [http://albert.rierol.net/imagej_programming_tutorials.html#How%20to%20automate%20an%20ImageJ%20dialog] I find that I can apply a plugin using the following: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" ""))) This is good because it suppresses the dialog which would otherwise pop up for every image. But running this always brings up a window containing the transformed image, when what I want is to simply return the transformed image. The stupidest way to do what I want is to just close the window that comes up and return the image which it was displaying. Does what I want but is absolutely retarded: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" "") (let [return-image (IJ/getImage)] (.hide return-image) return-image))) I'm obviously missing something about how to use imageJ plugins in a programming context. Does anyone know the right way to do this? Thanks, --Robert McIntyre

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  • How can I do batch image processing with ImageJ in clojure?

    - by Robert McIntyre
    I want to use ImageJ to do some processing of several thousand images. Is there a way to take any general imageJ plugin and apply it to hundreds of images automatically? For example, say I want to take my thousand images and apply a polar transformation to each--- A polar transformation plugin for ImageJ can be found here: http://rsbweb.nih.gov/ij/plugins/polar-transformer.html Great! Let's use it. From: [http://albert.rierol.net/imagej_programming_tutorials.html#How%20to%20automate%20an%20ImageJ%20dialog] I find that I can apply a plugin using the following: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" ""))) This is good because it suppresses the dialog which would otherwise pop up for every image. But running this always brings up a window containing the transformed image, when what I want is to simply return the transformed image. The stupidest way to do what I want is to just close the window that comes up and return the image which it was displaying. Does what I want but is absolutely retarded: (defn x-polar [imageP] (let [thread (Thread/currentThread) options ""] (.setName thread "Run$_polar-transform") (Macro/setOptions thread options) (IJ/runPlugIn imageP "Polar_Transformer" "") (let [return-image (IJ/getImage)] (.hide return-image) return-image))) I'm obviously missing something about how to use imageJ plugins in a programming context. Does anyone know the right way to do this? Thanks, --Robert McIntyre

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  • Bandpass filter of FFT applied image. (Like ImageJ bandpass filter algorithm)

    - by maximus
    There is a good function that I need, which is implemented in Java program: ImageJ I need to understand the algorithm used there. The function has several parameters: link text And before using FFT it converts image to a special one: The Bandpass Filter uses a special algorithm to reduce edge artifacts (before the Fourier transform, the image is extended in size by attaching mirrored copies of image parts outside the original image, thus no jumps occur at the edges) Can you tell me more about this special transform? Actually tiling mirrored image. I am writing on C++ and wish to rewrite that part of the program on C++.

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  • pdflatex reads .eps files saved in OS/X, but not in Ubuntu

    - by David B Borenstein
    Sorry if this is a stupid question; I'm a newbie. I am preparing a manuscript in LaTeX. The journal (Physical Biology, an IOP publication) requires that figures be saved in .eps format, so I am trying to do that. However, I cannot get my LaTeX file to build when I have generated the .eps files on my Ubuntu computer. If I save the images on my Mac, the file build just fine. So far, I have tried saving images in ImageJ, FIJI and Inkscape. The same problem occurs in all three. When using kile, I get the following error: /usr/share/texmf-texlive/tex/latex/oberdiek/epstopdf-base.sty:0: Shell escape feature is not enabled. In TexWorks, the error is different, but still there: Package pdftex.def Error: File `./figures4/figure4a-eps-converted-to.pdf' not found. Now, if I fire up Inkscape, FIJI or ImageJ on OS/X, everything works fine. The Mac also can't build with the Ubuntu-saved images. The images generated on the Ubuntu machine open fine using Document Viewer. I am building the same LaTeX file on both computers, with the exact same results. The header of my LaTeX file is: \documentclass[12pt]{iopart} \usepackage{graphicx} \usepackage{epstopdf} \usepackage{parskip} \usepackage{color} \usepackage{iopams} And then the code for the figure is: \begin{figure} \center{\includegraphics[width=4in] {./figures4/figure4a.eps}} \footnotesize{\caption{ \label{fig:4a} (4a) lorem ipsum dolor sic amet.}} \end{figure} I'd be happy to send an example of both .eps files. Again, sorry if this is a dumb question. I tried everything I could think of before posting here. Thanks, David

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  • Reading serialised object from file

    - by nico
    Hi everyone. I'm writing a little Java program (it's an ImageJ plugin, but the problem is not specifically ImageJ related) and I have some problem, most probably due to the fact that I never really programmed in Java before... So, I have a Vector of Vectors and I'm trying to save it to a file and read it. The variable is defined as: Vector <Vector <myROI> > ROIs = new Vector <Vector <myROI> >(); where myROI is a class that I previously defined. Now, to write the vector to a file I use: void saveROIs() { SaveDialog save = new SaveDialog("Save ROIs...", imp.getTitle(), ".xroi"); String name = save.getFileName(); if (name == null) return; String dir = save.getDirectory(); try { FileOutputStream fos = new FileOutputStream(dir+name); ObjectOutputStream oos = new ObjectOutputStream(fos); oos.writeObject(ROIs); oos.close(); } catch (Exception e) { IJ.log(e.toString()); } } This correctly generates a binary file containing (I suppose) the object ROIs. Now, I use a very similar code to read the file: void loadROIs() { OpenDialog open = new OpenDialog("Load ROIs...", imp.getTitle(), ".xroi"); String name = open.getFileName(); if (name == null) return; String dir = open.getDirectory(); try { FileInputStream fin = new FileInputStream(dir+name); ObjectInputStream ois = new ObjectInputStream(fin); ROIs = (Vector <Vector <myROI> >) ois.readObject(); // This gives error ois.close(); } catch (Exception e) { IJ.log(e.toString()); } } But this function does not work. First, I get a warning: warning: [unchecked] unchecked cast found : java.lang.Object required: java.util.Vector<java.util.Vector<myROI>> ROIs = (Vector <Vector <myROI> >) ois.readObject(); ^ I Googled for that and see that I can suppress by prepending @SuppressWarnings("unchecked"), but this just makes things worst, as I get an error: <identifier> expected ROIs = (Vector <Vector <myROI> >) ois.readObject(); ^ In any case, if I omit @SuppressWarnings and ignore the warning, the object is not read and an exception is thrown java.io.WriteAbortedException: writing aborted; java.io.NotSerializableException: myROI Again Google tells me myROI needs to implements Serializable. I tried just adding implements Serializable to the class definition, but it is not sufficient. Can anyone give me some hints on how to procede in this case? Also, how to get rid of the typecast warning?

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  • Stripe suppression algorithm needed

    - by maximus
    I have images with text. There are dark stripes in image that still exists in binary image too. That makes characters connected with that stripe - it can be vertical or horizontal (or at some angle) I need to remove them from image at first, and then to binarize. I've seen bandpass filter in ImageJ program that have some options like - suppress horizontal stripes, and it works good, but it also apply a bandpass filtering. So any idea please how to do it. I think it should be done in frequency domain.

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  • Count the number of objects in an Image

    - by kunjaan
    I am investigating the possibility of image processing to identify certain objects and also count them in an image. I will be given a picture and I need to identify the number of boxes present in that image. Does anybody have any experience with any Machine Vision/ Image Processing libraries like ImageJ, Fiji, JAI, jMagick ,Java Vision Toolkit? Which do you think is best suited for the job? What do you guys suggest? If the APIs can be used from Java, it would be better. Thank you. Edit: I am dealing with warehouse brown boxes. Yes I am talking about regular photos. The source is usually a mobile phone picture.

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