I was wondering if anyone knows where I can find the Reslice algorithm
description/explanation. I am learning image processing and analysis on my own and I find ImageJ extrimly helpful. Now, I am trying to understand the inner workings of some of the functions. I greatly appreciate the help. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Dear Ronny,
Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press "l") and then type the tool name you are looking for. In your case, just type "resl" will already be enough to locate the "reslice" tool. From there you will see that the tool path within ImageJ is "Image>Stacks" and that it's code with within the class "ij.plugin.Slicer". Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/) then go to "Developer Resources->Browsable Source" (https://imagej.nih.gov/ij/developer/source/index.html) and locate "ij.plugin.Slicer".to find the "Slicer.java" file and there you can enjoy the source code you are looking for!!! My best regards, Philippe Philippe CARL Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS - Université de Strasbourg Faculté de Pharmacie 74 route du Rhin 67401 ILLKIRCH Tel : +33(0)3 68 85 41 84 -----Message d'origine----- De : ImageJ Interest Group [mailto:[hidden email]] De la part de Ronny Shalev Envoyé : jeudi 28 septembre 2017 00:22 À : [hidden email] Objet : ImageJ Reslice command (Image-Stacks->Reslice) I was wondering if anyone knows where I can find the Reslice algorithm description/explanation. I am learning image processing and analysis on my own and I find ImageJ extrimly helpful. Now, I am trying to understand the inner workings of some of the functions. I greatly appreciate the help. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Phillipe and everyone,
In the Command Finder, you can also click the "Source" button to jump directly to the source code on the ImageJ 1.x web site. The source can also be browsed on GitHub: https://github.com/imagej/imagej1 Press the T key to search for specific files. Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Thu, Sep 28, 2017 at 2:36 AM, Philippe CARL <[hidden email]> wrote: > Dear Ronny, > Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press > "l") and then type the tool name you are looking for. > In your case, just type "resl" will already be enough to locate the > "reslice" tool. > From there you will see that the tool path within ImageJ is "Image>Stacks" > and that it's code with within the class "ij.plugin.Slicer". > Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/) then > go to "Developer Resources->Browsable Source" (https://imagej.nih.gov/ij/ > developer/source/index.html) and locate "ij.plugin.Slicer".to find the > "Slicer.java" file and there you can enjoy the source code you are looking > for!!! > My best regards, > Philippe > > Philippe CARL > Laboratoire de Biophotonique et Pharmacologie > UMR 7213 CNRS - Université de Strasbourg > Faculté de Pharmacie > 74 route du Rhin > 67401 ILLKIRCH > Tel : +33(0)3 68 85 41 84 > > -----Message d'origine----- > De : ImageJ Interest Group [mailto:[hidden email]] De la part de > Ronny Shalev > Envoyé : jeudi 28 septembre 2017 00:22 > À : [hidden email] > Objet : ImageJ Reslice command (Image-Stacks->Reslice) > > I was wondering if anyone knows where I can find the Reslice algorithm > description/explanation. > > I am learning image processing and analysis on my own and I find ImageJ > extrimly helpful. Now, I am trying to understand the inner workings of some > of the functions. > > I greatly appreciate the help. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Thanks for the input, Philippe and Curtis,
I was wondering if there exists a paper discussing the algorithm as a concept (and, maybe pseudo code). If I need to understand the algorithm via reading the code, I will need to learn Java, which might take sometime as I am working on Python right now. Regards Ronny On Thu, Sep 28, 2017 at 5:37 PM, Curtis Rueden <[hidden email]> wrote: > Hi Phillipe and everyone, > > In the Command Finder, you can also click the "Source" button to jump > directly to the source code on the ImageJ 1.x web site. > > The source can also be browsed on GitHub: > https://github.com/imagej/imagej1 > > Press the T key to search for specific files. > > Regards, > Curtis > > -- > Curtis Rueden > LOCI software architect - https://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > > On Thu, Sep 28, 2017 at 2:36 AM, Philippe CARL <[hidden email]> > wrote: > > > Dear Ronny, > > Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press > > "l") and then type the tool name you are looking for. > > In your case, just type "resl" will already be enough to locate the > > "reslice" tool. > > From there you will see that the tool path within ImageJ is > "Image>Stacks" > > and that it's code with within the class "ij.plugin.Slicer". > > Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/) then > > go to "Developer Resources->Browsable Source" ( > https://imagej.nih.gov/ij/ > > developer/source/index.html) and locate "ij.plugin.Slicer".to find the > > "Slicer.java" file and there you can enjoy the source code you are > looking > > for!!! > > My best regards, > > Philippe > > > > Philippe CARL > > Laboratoire de Biophotonique et Pharmacologie > > UMR 7213 CNRS - Université de Strasbourg > > Faculté de Pharmacie > > 74 route du Rhin > > 67401 ILLKIRCH > > Tel : +33(0)3 68 85 41 84 > > > > -----Message d'origine----- > > De : ImageJ Interest Group [mailto:[hidden email]] De la part de > > Ronny Shalev > > Envoyé : jeudi 28 septembre 2017 00:22 > > À : [hidden email] > > Objet : ImageJ Reslice command (Image-Stacks->Reslice) > > > > I was wondering if anyone knows where I can find the Reslice algorithm > > description/explanation. > > > > I am learning image processing and analysis on my own and I find ImageJ > > extrimly helpful. Now, I am trying to understand the inner workings of > some > > of the functions. > > > > I greatly appreciate the help. > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Ronny Shalev, PhD Cell: 216-543-6596 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Ronny,
> I was wondering if there exists a paper discussing the algorithm as a > concept There is user documentation in the ImageJ user manual: https://imagej.net/docs/guide/146-28.html#sub:Reslice...[/] No paper though. > If I need to understand the algorithm via reading the code, I will > need to learn Java, which might take sometime as I am working on > Python right now. Fortunately, Java syntax is quite similar to Python. Reading the source code will be your best bet to understand the algorithm here. Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Thu, Sep 28, 2017 at 4:54 PM, Ronny Shalev <[hidden email]> wrote: > Thanks for the input, Philippe and Curtis, > > I was wondering if there exists a paper discussing the algorithm as a > concept (and, maybe pseudo code). If I need to understand the algorithm via > reading the code, I will need to learn Java, which might take sometime as I > am working on Python right now. > > Regards > > Ronny > > On Thu, Sep 28, 2017 at 5:37 PM, Curtis Rueden <[hidden email]> wrote: > > > Hi Phillipe and everyone, > > > > In the Command Finder, you can also click the "Source" button to jump > > directly to the source code on the ImageJ 1.x web site. > > > > The source can also be browsed on GitHub: > > https://github.com/imagej/imagej1 > > > > Press the T key to search for specific files. > > > > Regards, > > Curtis > > > > -- > > Curtis Rueden > > LOCI software architect - https://loci.wisc.edu/software > > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden > > Did you know ImageJ has a forum? http://forum.imagej.net/ > > > > > > On Thu, Sep 28, 2017 at 2:36 AM, Philippe CARL <[hidden email] > > > > wrote: > > > > > Dear Ronny, > > > Within ImageJ, just do "Plugins->Utilites->Find Commands..." (or press > > > "l") and then type the tool name you are looking for. > > > In your case, just type "resl" will already be enough to locate the > > > "reslice" tool. > > > From there you will see that the tool path within ImageJ is > > "Image>Stacks" > > > and that it's code with within the class "ij.plugin.Slicer". > > > Thus you go then to the ImageJ website (https://imagej.nih.gov/ij/) > then > > > go to "Developer Resources->Browsable Source" ( > > https://imagej.nih.gov/ij/ > > > developer/source/index.html) and locate "ij.plugin.Slicer".to find the > > > "Slicer.java" file and there you can enjoy the source code you are > > looking > > > for!!! > > > My best regards, > > > Philippe > > > > > > Philippe CARL > > > Laboratoire de Biophotonique et Pharmacologie > > > UMR 7213 CNRS - Université de Strasbourg > > > Faculté de Pharmacie > > > 74 route du Rhin > > > 67401 ILLKIRCH > > > Tel : +33(0)3 68 85 41 84 > > > > > > -----Message d'origine----- > > > De : ImageJ Interest Group [mailto:[hidden email]] De la part de > > > Ronny Shalev > > > Envoyé : jeudi 28 septembre 2017 00:22 > > > À : [hidden email] > > > Objet : ImageJ Reslice command (Image-Stacks->Reslice) > > > > > > I was wondering if anyone knows where I can find the Reslice algorithm > > > description/explanation. > > > > > > I am learning image processing and analysis on my own and I find ImageJ > > > extrimly helpful. Now, I am trying to understand the inner workings of > > some > > > of the functions. > > > > > > I greatly appreciate the help. > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > Ronny Shalev, PhD > > Cell: 216-543-6596 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Dear list
I noticed some strange behaviour when using different Set Measurements together with the ROI manager in a macro. example code run("Blobs (25K)"); setAutoThreshold("Default"); setOption("BlackBackground", false); run("Convert to Mask"); run("Set Measurements...", "display redirect=None decimal=0"); run("Analyze Particles...", "size=1-Infinity summarize add"); run("Set Measurements...", "feret's display redirect=None decimal=3"); roiManager("Measure"); As soon as the second Set Measurements runs area data is already displayed in the Results window, even before anything is measured, labelled as blobs.gif. The last line adds a second series of data to the Results table now labelled as ROIs but still the results are for area and not feret's data. Strangely enough the first few times the values for area were the correct values but after I moved some code around they now show zeros. Also hitting "Measure" in the ROI menu after running the macro still gives the same result. Checking the settings under Analyze > Set Measurements shows however that Feret's diameter is selected and not Area. I have tested it on several PCs, all Windows 7 using the latest updated version of Fiji. So it seems to be that there is somewhere a bug. Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging Facility Centre for Core Biotechnology Services University of Leicester www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Good day Kees,
after running your macro I think I see what you mean... My impression is, that "Set Measurements..." was intended to be used only once (at the beginning) of a macro but I may be wrong and others may confirm that the described behavior appears at least as strange. Regards Herbie ::::::::::::::::::::::::::::::::::::::::::::::::::: Am 05.10.17 um 21:50 schrieb Straatman, Kees (Dr.): > Dear list > > > I noticed some strange behaviour when using different Set > Measurements together with the ROI manager in a macro. > > > example code > > > run("Blobs (25K)"); setAutoThreshold("Default"); > setOption("BlackBackground", false); run("Convert to Mask"); run("Set > Measurements...", "display redirect=None decimal=0"); run("Analyze > Particles...", "size=1-Infinity summarize add"); run("Set > Measurements...", "feret's display redirect=None decimal=3"); > roiManager("Measure"); > > As soon as the second Set Measurements runs area data is already > displayed in the Results window, even before anything is measured, > labelled as blobs.gif. The last line adds a second series of data to > the Results table now labelled as ROIs but still the results are for > area and not feret's data. Strangely enough the first few times the > values for area were the correct values but after I moved some code > around they now show zeros. > > Also hitting "Measure" in the ROI menu after running the macro still > gives the same result. Checking the settings under Analyze > Set > Measurements shows however that Feret's diameter is selected and not > Area. > > I have tested it on several PCs, all Windows 7 using the latest > updated version of Fiji. > > So it seems to be that there is somewhere a bug. > > Best wishes > > Kees > > Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging > Facility Centre for Core Biotechnology Services University of > Leicester > www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility> > > > > -- 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 Krs5
> On Oct 5, 2017, at 3:50 PM, Straatman, Kees (Dr.) <[hidden email]> wrote:
> > Dear list > > I noticed some strange behaviour when using different Set Measurements together with the ROI manager in a macro. > > example code > > run("Blobs (25K)"); > setAutoThreshold("Default"); > setOption("BlackBackground", false); > run("Convert to Mask"); > run("Set Measurements...", "display redirect=None decimal=0"); > run("Analyze Particles...", "size=1-Infinity summarize add"); > run("Set Measurements...", "feret's display redirect=None decimal=3"); > roiManager("Measure"); > > As soon as the second Set Measurements runs area data is already displayed in the Results window, even before anything is measured, labelled as blobs.gif. The last line adds a second series of data to the Results table now labelled as ROIs but still the results are for area and not feret's data. Strangely enough the first few times the values for area were the correct values but after I moved some code around they now show zeros. > > Also hitting "Measure" in the ROI menu after running the macro still gives the same result. Checking the settings under Analyze > Set Measurements shows however that Feret's diameter is selected and not Area. > > I have tested it on several PCs, all Windows 7 using the latest updated version of Fiji. > > So it seems to be that there is somewhere a bug. Dear Kees, This bug is fixed in the latest ImageJ daily build (1.51r18). Or work around it by adding run("Clear Results”); after running the particle analyzer, as in this version of your test macro: run("Blobs (25K)"); setAutoThreshold("Default"); setOption("BlackBackground", false); run("Convert to Mask"); run("Set Measurements...", "display redirect=None decimal=0"); run("Analyze Particles...", "size=1-Infinity summarize add"); run("Clear Results"); run("Set Measurements...", "feret's display redirect=None decimal=3"); roiManager("Measure”); -wayne -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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