save the data from Oval Profile Plot
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Hi,
I can use the Oval Profile Plot and download the list interactively. But I do not know how to do in a macro. getProfile() seems to require a rectangular selection or a straight line. thank you, Thomas ----- Thomas -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Thomas
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Good day Thomas,
this is in fact strange... Usually " *Plot.getValues(xpoints, ypoints)* Returns the values displayed by clicking on "List" in a plot or histogram window (example). " should do what you want. In case of the plot in question this doesn't work. I've briefly inspected the source code and it contains the usual plot calls* but I can't find the axis labels in the source code. Not sure what's going on. Perhaps someone else is able to lift the veil of secrecy. Regards Herbie ___________ * void createPlot() { String xLabel = ""; if(mode == 3) xLabel = "Circumference"; else xLabel = "Degrees"; Plot plot = new Plot(modes[mode], xLabel, "Gray Value", xValues, profile); plot.setLimits(getMin(xValues), getMax(xValues), getMin(profile), getMax(profile)); plot.setColor(Color.black); plot.show(); } In fact the actual y-label reads "Normalized Integrated Intensity" a string I can't find in the source code. Consequently, there must be another plot method. :::::::::::::::::::::::::::::::::::::: Am 20.06.20 um 23:18 schrieb foxtango: > Hi, > > I can use the Oval Profile Plot and download the list interactively. But I > do not know how to do in a macro. getProfile() seems to require a > rectangular selection or a straight line. > > thank you, Thomas > > > > ----- > Thomas > -- > 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 |
Re: save the data from Oval Profile Plot
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In reply to this post by foxtango
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> I can use the Oval Profile Plot and download the list interactively. But I > do not know how to do in a macro. getProfile() seems to require a > rectangular selection or a straight line. Plot.getValues works for me. Here is a runnable example: run("Blobs (25K)"); makeOval(77, 61, 123, 122); run("Oval Profile", "number=30 analysis=[Maximum Intensity]"); selectWindow("Maximum Intensity"); Plot.getValues(xpoints, ypoints); Array.show(xpoints,ypoints); The Oval Profile Plot plugin is available at https://imagej.nih.gov/ij/plugins/oval-profile.html -wayne -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Wayne,
thanks for testing and you are right! I was applying "Radial_Profile_Angle_Ext.jar": <https://imagej.nih.gov/ij/plugins/radial-profile-ext.html> Mea culpa! The data of the resulting plot can't be accessed because the plugin uses a special "multi_plot"-class. // run("Blobs (25K)"); makeOval(77, 61, 123, 122); run("Radial Profile Angle", "x_center=128 y_center=127 radius=127.50 starting_angle=0 integration_angle=180"); Plot.getValues(xpoints, ypoints); Array.show(xpoints,ypoints); // Sorry for the confusion! Kind regards Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 22.06.20 um 03:39 schrieb Wayne Rasband: >> I can use the Oval Profile Plot and download the list interactively. But I >> do not know how to do in a macro. getProfile() seems to require a >> rectangular selection or a straight line. > > Plot.getValues works for me. Here is a runnable example: > > run("Blobs (25K)"); > makeOval(77, 61, 123, 122); > run("Oval Profile", "number=30 analysis=[Maximum Intensity]"); > selectWindow("Maximum Intensity"); > Plot.getValues(xpoints, ypoints); > Array.show(xpoints,ypoints); > > The Oval Profile Plot plugin is available at > > https://imagej.nih.gov/ij/plugins/oval-profile.html > > -wayne > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Fwd: save the data from Oval Profile Plot
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Dear Herbie,
I'm the author of the "Radial_Profile_Angle_Ext" plugin. And it's first versions indeed implemented a special "multi_plot"-class since at that time multi-plotting wasn't implemented within the native Plot class. But since then the native ImageJ Plot class has really evolved and became even way more powerful than the "multi_plot"-class I was using within the plugin. So I have modified the plugin so that it is using the native ImageJ Plot class. Thus all what you have to do is to update your "Radial_Profile_Angle_Ext" plugin to it's last version and you should be all set. Kindest 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: "l16" <[hidden email]> À: "imagej" <[hidden email]> Envoyé: Lundi 22 Juin 2020 10:40:22 Objet: Re: save the data from Oval Profile Plot Dear Wayne, thanks for testing and you are right! I was applying "Radial_Profile_Angle_Ext.jar": <https://imagej.nih.gov/ij/plugins/radial-profile-ext.html> Mea culpa! The data of the resulting plot can't be accessed because the plugin uses a special "multi_plot"-class. // run("Blobs (25K)"); makeOval(77, 61, 123, 122); run("Radial Profile Angle", "x_center=128 y_center=127 radius=127.50 starting_angle=0 integration_angle=180"); Plot.getValues(xpoints, ypoints); Array.show(xpoints,ypoints); // Sorry for the confusion! Kind regards Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 22.06.20 um 03:39 schrieb Wayne Rasband: >> I can use the Oval Profile Plot and download the list interactively. But I >> do not know how to do in a macro. getProfile() seems to require a >> rectangular selection or a straight line. > > Plot.getValues works for me. Here is a runnable example: > > run("Blobs (25K)"); > makeOval(77, 61, 123, 122); > run("Oval Profile", "number=30 analysis=[Maximum Intensity]"); > selectWindow("Maximum Intensity"); > Plot.getValues(xpoints, ypoints); > Array.show(xpoints,ypoints); > > The Oval Profile Plot plugin is available at > > https://imagej.nih.gov/ij/plugins/oval-profile.html > > -wayne > > -- > 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 |
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Hi Herbie and Wayne,
thank you for your help. The two lines work as expected. Regards, Thomas Am Mo., 22. Juni 2020 um 11:14 Uhr schrieb CARL Philippe (LBP) < [hidden email]>: > Dear Herbie, > I'm the author of the "Radial_Profile_Angle_Ext" plugin. > And it's first versions indeed implemented a special "multi_plot"-class > since at that time multi-plotting wasn't implemented within the native Plot > class. > But since then the native ImageJ Plot class has really evolved and became > even way more powerful than the "multi_plot"-class I was using within the > plugin. > So I have modified the plugin so that it is using the native ImageJ Plot > class. > Thus all what you have to do is to update your "Radial_Profile_Angle_Ext" > plugin to it's last version and you should be all set. > Kindest 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: "l16" <[hidden email]> > À: "imagej" <[hidden email]> > Envoyé: Lundi 22 Juin 2020 10:40:22 > Objet: Re: save the data from Oval Profile Plot > > Dear Wayne, > > thanks for testing and you are right! > > I was applying "Radial_Profile_Angle_Ext.jar": > <https://imagej.nih.gov/ij/plugins/radial-profile-ext.html> > > Mea culpa! > > The data of the resulting plot can't be accessed because the plugin uses > a special "multi_plot"-class. > > // > run("Blobs (25K)"); > makeOval(77, 61, 123, 122); > run("Radial Profile Angle", "x_center=128 y_center=127 radius=127.50 > starting_angle=0 integration_angle=180"); > Plot.getValues(xpoints, ypoints); > Array.show(xpoints,ypoints); > // > > Sorry for the confusion! > > Kind regards > > Herbie > > ::::::::::::::::::::::::::::::::::::::::::: > Am 22.06.20 um 03:39 schrieb Wayne Rasband: > >> I can use the Oval Profile Plot and download the list interactively. > But I > >> do not know how to do in a macro. getProfile() seems to require a > >> rectangular selection or a straight line. > > > > Plot.getValues works for me. Here is a runnable example: > > > > run("Blobs (25K)"); > > makeOval(77, 61, 123, 122); > > run("Oval Profile", "number=30 analysis=[Maximum Intensity]"); > > selectWindow("Maximum Intensity"); > > Plot.getValues(xpoints, ypoints); > > Array.show(xpoints,ypoints); > > > > The Oval Profile Plot plugin is available at > > > > https://imagej.nih.gov/ij/plugins/oval-profile.html > > > > -wayne > > > > -- > > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Thomas
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