Getting the selected points
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Hi again!
The macro recorder is a very useful tool, but after placing two points in the image, I want to get their coordinates and I can't find a way to do this. I can't find even an option in the menu so I can get it from the macro recorder. Any idea? Thanks!, and sorry for inconvenience, but I'm just a begginner. -- Juanjo Vega ([hidden email]) Unidad de Biocomputación. Laboratorio B-13. Centro Nacional de Biotecnología. CNB-CSIC. C\ Darwin, 3. Campus de Cantoblanco. Universidad Autónoma de Madrid. 28049, Madrid, Spain. http://www.cnb.csic.es http://www.biocomp.cnb.uam.es +34 91 585 4510 "Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes. |
Re: Getting the selected points
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int[] ( PointRoi )ImagePlus.getRoi().getXCoordinates();
int[] ( PointRoi )ImagePlus.getRoi().getYCoordinates(); http://rsb.info.nih.gov/ij/developer/api/ij/gui/PolygonRoi.html#getXCoordinates() those are unfortunately relative to the bounding box of the Roi which you can get by ( PointRoi )ImagePlus.getRoi().getBounds() http://rsb.info.nih.gov/ij/developer/api/ij/gui/Roi.html#getBounds() I am looking forward to writing the next line of your Plugin ;) Best, Stephan On Tue, 2009-05-19 at 13:58 +0200, Juanjo Vega wrote: > Hi again! > > The macro recorder is a very useful tool, but after placing two > points > in the image, I want to get their coordinates and I can't find a way > to > do this. > > I can't find even an option in the menu so I can get it from the > macro > recorder. > > Any idea? > > Thanks!, and sorry for inconvenience, but I'm just a begginner. > |
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Haha, sorry, but there are not much samples or documents about
programming with imageJ, or at least I can't find them after two weeks looking over the internet. I had to discover some hard stuf like the underscore in jar files name ¬¬ I hope to learn as much as possible to become an useful list user too :) Thanks again, Stephan. Sincerely, Juanjo Stephan Saalfeld escribió: > int[] ( PointRoi )ImagePlus.getRoi().getXCoordinates(); > int[] ( PointRoi )ImagePlus.getRoi().getYCoordinates(); > > http://rsb.info.nih.gov/ij/developer/api/ij/gui/PolygonRoi.html#getXCoordinates() > > those are unfortunately relative to the bounding box of the Roi which > you can get by > > ( PointRoi )ImagePlus.getRoi().getBounds() > > http://rsb.info.nih.gov/ij/developer/api/ij/gui/Roi.html#getBounds() > > I am looking forward to writing the next line of your Plugin ;) > > Best, > Stephan > > > On Tue, 2009-05-19 at 13:58 +0200, Juanjo Vega wrote: > >> Hi again! >> >> The macro recorder is a very useful tool, but after placing two >> points >> in the image, I want to get their coordinates and I can't find a way >> to >> do this. >> >> I can't find even an option in the menu so I can get it from the >> macro >> recorder. >> >> Any idea? >> >> Thanks!, and sorry for inconvenience, but I'm just a begginner. >> >> > > -- Juanjo Vega ([hidden email]) Unidad de Biocomputación. Laboratorio B-13. Centro Nacional de Biotecnología. CNB-CSIC. C\ Darwin, 3. Campus de Cantoblanco. Universidad Autónoma de Madrid. 28049, Madrid, Spain. http://www.cnb.csic.es http://www.biocomp.cnb.uam.es +34 91 585 4510 "Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes. |
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There is a book from Burger and Burge Called "Digital Image Processing
: An algorithmic introduction using Java" that is good to start programming plugins (if only I had some time to study it...) Christophe On Tue, May 19, 2009 at 3:28 PM, Juanjo Vega <[hidden email]> wrote: > Haha, sorry, but there are not much samples or documents about programming > with imageJ, or at least I can't find them after two weeks looking over the > internet. > > I had to discover some hard stuf like the underscore in jar files name ¬¬ > > I hope to learn as much as possible to become an useful list user too :) > > Thanks again, Stephan. > > Sincerely, > > Juanjo > > Stephan Saalfeld escribió: >> >> int[] ( PointRoi )ImagePlus.getRoi().getXCoordinates(); >> int[] ( PointRoi )ImagePlus.getRoi().getYCoordinates(); >> >> >> http://rsb.info.nih.gov/ij/developer/api/ij/gui/PolygonRoi.html#getXCoordinates() >> >> those are unfortunately relative to the bounding box of the Roi which >> you can get by >> >> ( PointRoi )ImagePlus.getRoi().getBounds() >> >> http://rsb.info.nih.gov/ij/developer/api/ij/gui/Roi.html#getBounds() >> >> I am looking forward to writing the next line of your Plugin ;) >> >> Best, >> Stephan >> >> >> On Tue, 2009-05-19 at 13:58 +0200, Juanjo Vega wrote: >> >>> >>> Hi again! >>> >>> The macro recorder is a very useful tool, but after placing two >>> points in the image, I want to get their coordinates and I can't find a >>> way >>> to do this. >>> >>> I can't find even an option in the menu so I can get it from the >>> macro recorder. >>> >>> Any idea? >>> >>> Thanks!, and sorry for inconvenience, but I'm just a begginner. >>> >>> >> >> > > -- > Juanjo Vega ([hidden email]) > > Unidad de Biocomputación. Laboratorio B-13. > Centro Nacional de Biotecnología. CNB-CSIC. > C\ Darwin, 3. Campus de Cantoblanco. > Universidad Autónoma de Madrid. > 28049, Madrid, Spain. > > http://www.cnb.csic.es > http://www.biocomp.cnb.uam.es > > +34 91 585 4510 > > > "Las mejores almas son capaces de los mayores vicios como de las mayores > virtudes, y aquellos que caminan despacio por el camino recto pueden llegar > más lejos que los que corren pero se apartan de él." - Discurso del Método, > René Descartes. > |
Re: Getting the selected points
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In reply to this post by Juanjo Vega
Juanjo,
I'm sorry you feel this way. I'm also new to ImageJ and find the wiki page is very helpful. http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:the_imagej_eclipse_howto Hope this help. Regards, -Thai -----Original Message----- From: Juanjo Vega [mailto:[hidden email]] Sent: Tuesday, May 19, 2009 9:28 AM To: List IMAGEJ Subject: Re: Getting the selected points Haha, sorry, but there are not much samples or documents about programming with imageJ, or at least I can't find them after two weeks looking over the internet. I had to discover some hard stuf like the underscore in jar files name ¬¬ I hope to learn as much as possible to become an useful list user too :) Thanks again, Stephan. Sincerely, Juanjo Stephan Saalfeld escribió: > int[] ( PointRoi )ImagePlus.getRoi().getXCoordinates(); > int[] ( PointRoi )ImagePlus.getRoi().getYCoordinates(); > > http://rsb.info.nih.gov/ij/developer/api/ij/gui/PolygonRoi.html#getXCo > ordinates() > > those are unfortunately relative to the bounding box of the Roi which > you can get by > > ( PointRoi )ImagePlus.getRoi().getBounds() > > http://rsb.info.nih.gov/ij/developer/api/ij/gui/Roi.html#getBounds() > > I am looking forward to writing the next line of your Plugin ;) > > Best, > Stephan > > > On Tue, 2009-05-19 at 13:58 +0200, Juanjo Vega wrote: > >> Hi again! >> >> The macro recorder is a very useful tool, but after placing two >> points in the image, I want to get their coordinates and I can't find >> a way to do this. >> >> I can't find even an option in the menu so I can get it from the >> macro recorder. >> >> Any idea? >> >> Thanks!, and sorry for inconvenience, but I'm just a begginner. >> >> > > -- Juanjo Vega ([hidden email]) Unidad de Biocomputación. Laboratorio B-13. Centro Nacional de Biotecnología. CNB-CSIC. C\ Darwin, 3. Campus de Cantoblanco. Universidad Autónoma de Madrid. 28049, Madrid, Spain. http://www.cnb.csic.es http://www.biocomp.cnb.uam.es +34 91 585 4510 "Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes. |
Re: Getting the selected points
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In reply to this post by Juanjo Vega
Juanjo Vega wrote:
> Haha, sorry, but there are not much samples or documents about > programming with imageJ, or at least I can't find them after two weeks > looking over the internet. General introduction to ImageJ programming: http://albert.rierol.net/imagej_programming_tutorials.html#ImageJ%20programming%20basics Numerous examples for scripting: http://pacific.mpi-cbg.de/Scripting http://pacific.mpi-cbg.de/wiki/index.php/Scripting_comparisons http://pacific.mpi-cbg.de/wiki/index.php/Javascript_Scripting http://pacific.mpi-cbg.de/wiki/index.php/Jython_Scripting http://pacific.mpi-cbg.de/wiki/index.php/Clojure_Scripting The above is just stuff I've written, with some help from others. Checkout as well the ImageJ documentation wiki: http://imagejdocu.tudor.lu/doku.php Albert -- Albert Cardona http://albert.rierol.net |
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In reply to this post by Le, Thai (NIH/NCI) [C]
Thanks to all of you!
I'll have a look to the samples. Sincerelly, Juanjo. Le, Thai (NIH/NCI) [C] escribió: > Juanjo, > > I'm sorry you feel this way. I'm also new to ImageJ and find the wiki page is very helpful. > http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:the_imagej_eclipse_howto > > Hope this help. > > Regards, > -Thai > > -----Original Message----- > From: Juanjo Vega [mailto:[hidden email]] > Sent: Tuesday, May 19, 2009 9:28 AM > To: List IMAGEJ > Subject: Re: Getting the selected points > > Haha, sorry, but there are not much samples or documents about programming with imageJ, or at least I can't find them after two weeks looking over the internet. > > I had to discover some hard stuf like the underscore in jar files name ¬¬ > > I hope to learn as much as possible to become an useful list user too :) > > Thanks again, Stephan. > > Sincerely, > > Juanjo > > Stephan Saalfeld escribió: > >> int[] ( PointRoi )ImagePlus.getRoi().getXCoordinates(); >> int[] ( PointRoi )ImagePlus.getRoi().getYCoordinates(); >> >> http://rsb.info.nih.gov/ij/developer/api/ij/gui/PolygonRoi.html#getXCo >> ordinates() >> >> those are unfortunately relative to the bounding box of the Roi which >> you can get by >> >> ( PointRoi )ImagePlus.getRoi().getBounds() >> >> http://rsb.info.nih.gov/ij/developer/api/ij/gui/Roi.html#getBounds() >> >> I am looking forward to writing the next line of your Plugin ;) >> >> Best, >> Stephan >> >> >> On Tue, 2009-05-19 at 13:58 +0200, Juanjo Vega wrote: >> >> >>> Hi again! >>> >>> The macro recorder is a very useful tool, but after placing two >>> points in the image, I want to get their coordinates and I can't find >>> a way to do this. >>> >>> I can't find even an option in the menu so I can get it from the >>> macro recorder. >>> >>> Any idea? >>> >>> Thanks!, and sorry for inconvenience, but I'm just a begginner. >>> >>> >>> >> >> > > -- > Juanjo Vega ([hidden email]) > > Unidad de Biocomputación. Laboratorio B-13. > Centro Nacional de Biotecnología. CNB-CSIC. > C\ Darwin, 3. Campus de Cantoblanco. > Universidad Autónoma de Madrid. > 28049, Madrid, Spain. > > http://www.cnb.csic.es > http://www.biocomp.cnb.uam.es > > +34 91 585 4510 > > > "Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes. > > -- Juanjo Vega ([hidden email]) Unidad de Biocomputación. Laboratorio B-13. Centro Nacional de Biotecnología. CNB-CSIC. C\ Darwin, 3. Campus de Cantoblanco. Universidad Autónoma de Madrid. 28049, Madrid, Spain. http://www.cnb.csic.es http://www.biocomp.cnb.uam.es +34 91 585 4510 "Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes. |
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In reply to this post by Stephan Saalfeld
Dear list,
we implemented the Contrast Limited Adaptive Histogram Equalization http://portal.acm.org/citation.cfm?id=180940 as an ImageJ plugin and put it into Fiji. There is a manual page at the Fiji-Wiki http://pacific.mpi-cbg.de/wiki/index.php/Enhance_Local_Contrast_(CLAHE) that references the source code which, stripped off the package declaration, compiles and runs in bare ImageJ as well. The implemented technique is about enhancing the local contrast in an image by equalizing the histogram in that region. The maximal desired contrast stretch can be limited. Best regards, Stephan |
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On Nov 13, 2009, at 7:04 PM, Stephan Saalfeld wrote:
> Dear list, > > we implemented the Contrast Limited Adaptive Histogram Equalization > > http://portal.acm.org/citation.cfm?id=180940 > > as an ImageJ plugin and put it into Fiji. There is a manual page at > Fiji-Wiki > > http://pacific.mpi-cbg.de/wiki/index.php/Enhance_Local_Contrast_ > (CLAHE) > > that references the source code which, stripped off the package > declaration, compiles and runs in bare ImageJ as well. > > The implemented technique is about enhancing the local contrast > in an image by equalizing the histogram in that region. The > maximal desired contrast stretch can be limited. > > Best regards, > Stephan There is a version of this plugin at http://rsb.info.nih.gov/ij/plugins/clahe/index.html that works with ImageJ. -wayne |
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In reply to this post by Stephan Saalfeld
All,
I don't understand the phrase "compiles and runs in bare ImageJ as well". Does this imply that plugins written for Fiji don't necessarily work for ImageJ David Webster |
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D
On Fri, Nov 13, 2009 at 8:15 PM, David William Webster <[hidden email]> wrote: > All, > > I don't understand the phrase "compiles and runs in bare ImageJ as well". > Does this imply that plugins written for Fiji don't necessarily work for > ImageJ Wrong. Fiji is Just ImageJ, there isn't any magic. Only pre-packaged jars, namespaced plugins and lots of documentation. All Stephan said is that the source .java file for the CLAHE plugin contains a package declaration--a java language feature to create namespaces and avoid name collisions. Wayne removed that package declaration and posted the new .java and .class files online at http://rsb.info.nih.gov/ij/plugins/clahe/index.html Compare the two .java files to help you understand the difference. Search for the word "package". Albert -- http://albert.rierol.net |
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In reply to this post by David Webster
On Nov 13, 2009, at 8:15 PM, David William Webster wrote:
> All, > > I don't understand the phrase "compiles and runs in bare > ImageJ as well". Does this imply that plugins written for > Fiji don't necessarily work for ImageJ They work with a little effort. Here is what you need to do get the CLAHE plugin on the Fiji website to run in ImageJ: 1. Find and downloaded a version of the source without line numbers. 2. Change the file name from mpicbg-ij-CLAHE.java to CLAHE_.java. 3. Change the class name from CLAHE to CLAHE_. 4. Remove the package statement. 5. Remove the "import mpicbg.util.Util;" statement. 6. Find the source for the mpicbg.util.Util class. 7. Copy the round() function from Util.java and paste it into CLAHE_.java. 9. Change "Util.round()" to "round()" in nine places. 10. Use Plugins>Compile and Run to compile and run the plugin. -wayne |
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Hi,
thank you very much, Wayne, for providing the ImageJ version. > 1. Find and downloaded a version of the source without line numbers. > The gitweb interface offers that: http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=mpicbg.git;a=blob_plain;f=mpicbg/ij/CLAHE.java Just go a step up in the package browser and click `raw'---this is the bare file. Best regards, Stephan |
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