Dear all,
I'm using the Extended Depth of Field (EDF) plugin (see http://bigwww.epfl.ch/demo/edf/index.html for details). Can someone tell me how to use this plugin in batch mode, i.e. without the parameter window showing up? I'd like to use it in a macro. Or otherwise, is there any alternative to this nice plugin? Thanks, jan -- Jan Eglinger PhD Student, Eckhard Lammert group Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse 108 01307 Dresden Germany +49 351 210 2722 |
Hi,
if this plugin uses ImageJ GenericDialog for the parameter window it should even work in macro, the macro (recorder) knows how to handle this! It will remember what input was used and not show the window. Use it once to see how the parameter syntax is if you need this functionality in your own (non-recorder)macros. However, in some earlier ImageJ version there was an issue with nonunique "parameter names" that is now fixed already some time ago, so you might need to upgrade. Cheers JW Jan Eglinger <eglinger@MPI-CBG .DE> An Gesendet von: [hidden email] ImageJ Interest Kopie Group <[hidden email]. Thema GOV> Extended Depth of Field (EDF) plugin with batch mode 04.01.2007 14:41 Bitte antworten an ImageJ Interest Group <[hidden email]. GOV> Dear all, I'm using the Extended Depth of Field (EDF) plugin (see http://bigwww.epfl.ch/demo/edf/index.html for details). Can someone tell me how to use this plugin in batch mode, i.e. without the parameter window showing up? I'd like to use it in a macro. Or otherwise, is there any alternative to this nice plugin? Thanks, jan -- Jan Eglinger PhD Student, Eckhard Lammert group Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse 108 01307 Dresden Germany +49 351 210 2722 ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
I'm interested in doing the same, however, the macro recorder only outputs the string "Run("Easy mode...")" which does not let you to tune the parameters of the plugin for the projection.
Any idea as how to do that? |
On 10/2/14, 10:16 PM, Pulceblue wrote:
> I'm interested in doing the same, however, the macro recorder only outputs > the string "Run("Easy mode...")" which does not let you to tune the > parameters of the plugin for the projection. > Any idea as how to do that? > > > > This is an example of something that worked for me: run("Extended Depth of Field (Easy mode)...", "quality='0' topology='0' show-topology='off' show-view='off'"); I think that I found it documented in the EDF documentation. I needed a way to force the macro to wait for EDF to finish and return an image. Here is the entire code segment that does this: // the following block is executed if the Extended Depth of Focus plugin is selected if (matches(processingMethod, "EDF")) { run("Extended Depth of Field (Easy mode)...", "quality='0' topology='0' show-topology='off' show-view='off'"); // The following code is required in order to wait for the the EDF plugin to finish, and open the expected image. // We must wait for a window called "Output" . Batch mode cannot be true, because if so the window will not open. initTime = getTime(); oldTime = initTime; while (!isOpen("Output")) { elapsedTime = getTime() - initTime; newTime = getTime() - oldTime; // print something every 10 seconds so that we will know it is still alive if (newTime > 10000) { oldTime = getTime(); newTime = 0; print(elapsedTime/1000, " seconds elapsed"); } } wait(1000); // let's really make sure that window is open -- give it another second selectImage("Output"); rename("edfImage"); edfTitle = getTitle(); } --aryeh -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Thanks Aryeh! You put me on the right track.
The solution was very easy. I somehow overlooked the documentation. Thanks a lot! Claudio |
Hi Claudio,
I am trying to do the same thing right now but using the code given above just gives me the error "Unrecognized command: "Extended Depth of Field (Easy mode)..." " Any idea what I have to change? Alternatively: For some reason I cannot find the documenation of the EDF plugin. Can someone please let me know where to find it? Thanks, Ulrike -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Servus Claudio,
I'm not sure whether I completely understand your question. Nevertheless if it is how to use the Extended Depth of Field (EDF) within a macro or plugin, you can (for example) do it this way: IJ.run("Easy mode...", "quality='4' topology='0' show-topology='off' show-view='off'"); And the plugin website is the following: http://bigwww.epfl.ch/demo/edf/ My best regards, Philippe Philippe CARL Laboratoire de Bioimagerie et Pathologies UMR 7021 CNRS - Université de Strasbourg Faculté de Pharmacie 74 route du Rhin 67401 ILLKIRCH Tel : +33(0)3 68 85 42 89 ----- Mail original ----- De: "Ulrike" <[hidden email]> À: "imagej" <[hidden email]> Envoyé: Jeudi 23 Juillet 2020 22:03:16 Objet: Re: Antwort: Extended Depth of Field (EDF) plugin with batch mode Hi Claudio, I am trying to do the same thing right now but using the code given above just gives me the error "Unrecognized command: "Extended Depth of Field (Easy mode)..." " Any idea what I have to change? Alternatively: For some reason I cannot find the documenation of the EDF plugin. Can someone please let me know where to find it? Thanks, Ulrike -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
In reply to this post by Ulrike
Try this line instead:
run("EDF Easy ", "quality='0' topology='1' show-topology='off' show-view='off'"); Taken from the Demo text: // EDF Demo Macro // // http://bigwww.epfl.ch/demo/edf/ // // Daniel Sage // Biomedical Imaging Group (BIG) // Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland // // 14 June 2007 // run("EDF Easy ", "quality='0' topology='1' show-topology='off' show-view='off'"); // // Description of the arguments // // argument quality: Speed/Quality trade-off. // 0 for fast // 1 for intermediate speed // 2 for medium quality / medium speed // 3 for intermediate quality // 4 for high quality // // argument topology: Topology smoothness // 0 for no smoothing of the topology // 1 for weak smoothing // 2 for medium smoothing // 3 for strong smoothing // 4 for very strong smoothing // // argument show-topology: Show the topology map // on // off // // argument show-view: Show the 3D view // on // off -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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