Help to download and install Oval Profile Plugin
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Help to download and install Oval Profile Plugin
 
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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In reply to this post by Herbie
Hello,
Thanks so much for the prompt response. Much appreciate it. Unfortunately I am still unable to install the plug in. I am able to save the text file as you mentioned in 1 and 2 After I compile and run I get this following message. When I restart ImageJ I do not see the plugin Any suggestions? Thanks, Sushmitha I will respond to your question on directionality analysis in a following email On 4/10/19, 5:21 AM, "Herbie" <[hidden email]> wrote: Good day Sushmitha, you are right I was a bit too concise with the description of point 2. For plain ImageJ the following works for me: 1. Copy the Java source code to an empty text window (Plugins >> New >> Text Window...). 2. Save this file as "Oval_Profile.java" (the underscore is essential!) to the plugins-folder of your ImageJ installation. 3. Go to "Plugins >> Compile and Run..." and in the then opening file dialog search for the "Oval_Profile.java"-file in the plugins-folder and open it. 4. The plugin will be compiled and starts running. (It is automatically stored as "Oval_Profile.class"-file in the plugins-folder of your ImageJ installation.) 5. After restarting ImageJ you will find the plugin listed in the Plugins menu of ImageJ. HTH Herbie __________________________ PS: What is your opinion about the results I've provide concerning orientation analyses? ::::::::::::::::::::::::::: > Dear Herbie, > > I am unable to install this plugin > > I am able to do step1 > In step 2 - where do you save the java file? In macros? > Does this matter in Mac or PC. Tried on a Mac > > I think I am messing up in saving the coding file and therefore unable to run this code file. > > Next when I compile and run I cannot find the Oval Profile plug in at all. > > Thanks for the info > > Sushmitha > > On 3/30/19, 4:48 AM, "ImageJ Interest Group on behalf of Herbie" <[hidden email] on behalf of [hidden email]> wrote: > > Good day, > > please study the installation recommendations given here: > <https://imagej.nih.gov/ij/plugins/oval-profile.html> > > For plain ImageJ the following works for me: > > 1. > Copy the Java source code to an empty text window (Plugins >> New >> > Text Window...). > > 2. > Name this file Oval_Profile.java. (The underscore is essential!) > > 3. > Compile an run this code file (Plugins >> Compile and Run...). > > 4. The plugin starts. > > If you restart ImageJ the plugin will be listed in the Plugins menu. > > If you use Fiji, then there is no easy way to compile and run Java > source code. For whatever reasons the "Compile and Run..."-feature is > still missing in Fiji. > > HTH > > Herbie > > :::::::::::::::::::::::::::::::::::::::::::::::::: > Am 30.03.19 um 03:58 schrieb Durgam, Sushmitha S.: > > Hi. I am unable to install the Oval profile Plug in to obtain radial sum of FFT alignment > > > > > > Would appreciate help and any directions > > > > > > Thanks, > > > > Sushmitha > > > > > > [The Ohio State University] > > Sushmitha Durgam, BVSc, PhD, DACVS-LA > > Assistant Professor, Equine Surgery > > College of Veterinary Medicine Dept. of Veterinary Clinical Sciences > > 370 VMAB, 1900 Coffey Road, Columbus, OH 43210 > > 614-292-6661 (Ext - 2) Office / 248-909-6993 Mobile / 614-688-5642 Fax > > [hidden email]<mailto:[hidden email]> > > > > > > > > > > -- > > 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 |
Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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Hello. Finally have the oval profile plot working.
Many thanks for all the help and info. Is there any way to assign the axes to the radial sum plot that comes about? Right now in picture 1 - the axes go up to 25000 Where as the one in picture 2 goes upto 6000 These are for comparative images. Would love to display them next to eachother and can see the peak and trough in pic 1 and relatively flat line (indicating lack of alignment) in pic 2 Any help would be appreciated. Best, Sushmitha On 4/12/19, 12:24 PM, "Herbie" <[hidden email]> wrote: Glen, according to a screenshot made available with an earlier post of Sushmitha, she uses plain ImageJ not Fiji. Regards Herbie Am 12.04.19 um 16:04 schrieb Glen MacDonald: > On the Mac, open the Applications folder and right-click on the Fiji.app icon. then select ’Show Package Contents’. > > Glen > >> On Apr 11, 2019, at 9:42 PM, Durgam, Sushmitha S. <[hidden email]> wrote: >> >> Hello, >> >> I am still unable to get Oval Profile installed on imageJ >> >> I was able to unzip the archive you sent. >> How do I copy the three class files into plugins folder on a Mac? >> Seems like I may be doing that step wrong. >> >> Thanks, >> Sushmitha >> >> On 4/11/19, 3:17 AM, "Herbie" <[hidden email]> wrote: >> >> Good day Sushmitha, >> >> this looks more like a problem with Java-versions. >> Do you have different versions of Java installed? >> Do you have more than one version of ImageJ installed? >> >> Attached please find a zip-Archive containing three files. >> >> 1. >> Unzip the archive. >> >> 2. >> Copy the three files to the "plugins"-folder of your ImageJ-installation. >> >> 3. >> Restart ImageJ. >> >> 4. >> Attached please find a screenshot of the "Plugins"-menu after the >> installation. >> >> HTH >> >> Herbie >> >> Oval_Profile.zip >> <http://imagej.1557.x6.nabble.com/file/t380516/Oval_Profile.zip> >> ScreenShot.png >> <http://imagej.1557.x6.nabble.com/file/t380516/ScreenShot.png> >> :::::::::::::::::::::::::::::::::::::::::::::::::: >> >> Durgam, Sushmitha S. wrote >>> Hello, >>> >>> Thanks so much for the prompt response. Much appreciate it. >>> >>> Unfortunately I am still unable to install the plug in. I am able to save >>> the text file as you mentioned in 1 and 2 >>> >>> After I compile and run I get this following message. >>> >>> When I restart ImageJ I do not see the plugin >>> >>> Any suggestions? >>> >>> Thanks, >>> Sushmitha >>> >>> I will respond to your question on directionality analysis in a following >>> >>> On 4/10/19, 5:21 AM, "Herbie" < >> >>> l16@ >> >>> > wrote: >>> >>> Good day Sushmitha, >>> >>> you are right I was a bit too concise with the description of point 2. >>> >>> For plain ImageJ the following works for me: >>> >>> 1. >>> Copy the Java source code to an empty text window (Plugins >> New >> >>> Text Window...). >>> >>> 2. >>> Save this file as "Oval_Profile.java" (the underscore is essential!) >>> to >>> the plugins-folder of your ImageJ installation. >>> >>> 3. >>> Go to "Plugins >> Compile and Run..." and in the then opening file >>> dialog search for the "Oval_Profile.java"-file in the plugins-folder >>> and >>> open it. >>> >>> 4. >>> The plugin will be compiled and starts running. >>> (It is automatically stored as "Oval_Profile.class"-file in the >>> plugins-folder of your ImageJ installation.) >>> >>> 5. >>> After restarting ImageJ you will find the plugin listed in the Plugins >>> menu of ImageJ. >>> >>> HTH >>> >>> Herbie >>> __________________________ >>> >>> PS: >>> What is your opinion about the results I've provide concerning >>> orientation analyses? >>> >>> ::::::::::::::::::::::::::: >>>> Dear Herbie, >>>> >>>> I am unable to install this plugin >>>> >>>> I am able to do step1 >>>> In step 2 - where do you save the java file? In macros? >>>> Does this matter in Mac or PC. Tried on a Mac >>>> >>>> I think I am messing up in saving the coding file and therefore >>> unable to run this code file. >>>> >>>> Next when I compile and run I cannot find the Oval Profile plug in >>> at all. >>>> >>>> Thanks for the info >>>> >>>> Sushmitha >>>> >>>> On 3/30/19, 4:48 AM, "ImageJ Interest Group on behalf of Herbie" >>> < >> >>> IMAGEJ@.NIH >> >>> on behalf of >> >>> l16@ >> >>> > wrote: >>>> >>>> Good day, >>>> >>>> please study the installation recommendations given here: >>>> <https://imagej.nih.gov/ij/plugins/oval-profile.html> >>>> >>>> For plain ImageJ the following works for me: >>>> >>>> 1. >>>> Copy the Java source code to an empty text window (Plugins >> >>> New >> >>>> Text Window...). >>>> >>>> 2. >>>> Name this file Oval_Profile.java. (The underscore is >>> essential!) >>>> >>>> 3. >>>> Compile an run this code file (Plugins >> Compile and Run...). >>>> >>>> 4. The plugin starts. >>>> >>>> If you restart ImageJ the plugin will be listed in the Plugins >>> menu. >>>> >>>> If you use Fiji, then there is no easy way to compile and run >>> Java >>>> source code. For whatever reasons the "Compile and >>> Run..."-feature is >>>> still missing in Fiji. >>>> >>>> HTH >>>> >>>> Herbie >>>> >>>> :::::::::::::::::::::::::::::::::::::::::::::::::: >>>> Am 30.03.19 um 03:58 schrieb Durgam, Sushmitha S.: >>>>> Hi. I am unable to install the Oval profile Plug in to obtain >>> radial sum of FFT alignment >>>>> >>>>> >>>>> Would appreciate help and any directions >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Sushmitha >>>>> >>>>> >>>>> [The Ohio State University] >>>>> Sushmitha Durgam, BVSc, PhD, DACVS-LA >>>>> Assistant Professor, Equine Surgery >>>>> College of Veterinary Medicine Dept. of Veterinary Clinical >>> Sciences >>>>> 370 VMAB, 1900 Coffey Road, Columbus, OH 43210 >>>>> 614-292-6661 (Ext - 2) Office / 248-909-6993 Mobile / >>> 614-688-5642 Fax >>>>> >> >>> durgam.3@ >> >>> <mailto: >> >>> durgam.3@ >> >>> > >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>> >>> >>> Screen Shot 2019-04-11 at 2.30.31 AM.png (558K) >>> <http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png> >> >> >> >> >> >> -- >> 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 > > -- > 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 |
Re: Help to download and install Oval Profile Plugin
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Re: Help to download and install Oval Profile Plugin
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In reply to this post by Durgam, Sushmitha S.
Good day Sushmitha,
attached please find two pairs of results (Orientation Salience Functions: *OSF*) obtained from the sample images (Image A and Image B) that you've provided earlier. ____________________________________________________________________ For a reasonable comparison of the two sample images it is recommended... ...to bring their sizes into line with each other. For this purpose I've considered the central 630x630 portion of Image A. ...to use a sensible normalization of the OSFs. For this purpose I've normalized the integral of the OSFs to one which means that the ordinate may be regarded as "relative frequency" of the orientations. ____________________________________________________________________ 1. Results pair "OrientationSalience_ImagesAB_PS1-HP00.png" These are the OSFs I get from analyzing the Power Spectra (PS) of the windowed DC-free images with an angular resolution of about 0.182deg. (This is the simplest approach.) ____________________________________________________________________ 2. Results pair "OrientationSalience_ImagesAB_ACF4-HP02.png" These are the OSFs I get from analyzing the 4-fold over-sampled Auto-Correlation Functions (ACF) of the windowed and slightly highpass-filtered images with an angular resolution of about 0.182deg. (This appears being the optimum approach for the images in question.) ____________________________________________________________________ As mentioned earlier, both sample images show severe clipping at gray-value 85 and should not be used for scientific analyses. HTH Herbie :::::::::::::::::::::::::::::::::::::::::::::::::: Am 19.04.19 um 20:48 schrieb Durgam, Sushmitha S.: > Hello. Finally have the oval profile plot working. > > Many thanks for all the help and info. > > Is there any way to assign the axes to the radial sum plot that comes about? > > Right now in picture 1 - the axes go up to 25000 > Where as the one in picture 2 goes upto 6000 > > These are for comparative images. > Would love to display them next to eachother and can see the peak and trough in pic 1 and relatively flat line (indicating lack of alignment) in pic 2 > > Any help would be appreciated. > > Best, > Sushmitha > > On 4/12/19, 12:24 PM, "Herbie" <[hidden email]> wrote: > > Glen, > > according to a screenshot made available with an earlier post of > Sushmitha, she uses plain ImageJ not Fiji. > > Regards > > Herbie > > > Am 12.04.19 um 16:04 schrieb Glen MacDonald: > > On the Mac, open the Applications folder and right-click on the Fiji.app icon. then select ’Show Package Contents’. > > > > Glen > > > >> On Apr 11, 2019, at 9:42 PM, Durgam, Sushmitha S. <[hidden email]> wrote: > >> > >> Hello, > >> > >> I am still unable to get Oval Profile installed on imageJ > >> > >> I was able to unzip the archive you sent. > >> How do I copy the three class files into plugins folder on a Mac? > >> Seems like I may be doing that step wrong. > >> > >> Thanks, > >> Sushmitha > >> > >> On 4/11/19, 3:17 AM, "Herbie" <[hidden email]> wrote: > >> > >> Good day Sushmitha, > >> > >> this looks more like a problem with Java-versions. > >> Do you have different versions of Java installed? > >> Do you have more than one version of ImageJ installed? > >> > >> Attached please find a zip-Archive containing three files. > >> > >> 1. > >> Unzip the archive. > >> > >> 2. > >> Copy the three files to the "plugins"-folder of your ImageJ-installation. > >> > >> 3. > >> Restart ImageJ. > >> > >> 4. > >> Attached please find a screenshot of the "Plugins"-menu after the > >> installation. > >> > >> HTH > >> > >> Herbie > >> > >> Oval_Profile.zip > >> <http://imagej.1557.x6.nabble.com/file/t380516/Oval_Profile.zip> > >> ScreenShot.png > >> <http://imagej.1557.x6.nabble.com/file/t380516/ScreenShot.png> > >> :::::::::::::::::::::::::::::::::::::::::::::::::: > >> > >> Durgam, Sushmitha S. wrote > >>> Hello, > >>> > >>> Thanks so much for the prompt response. Much appreciate it. > >>> > >>> Unfortunately I am still unable to install the plug in. I am able to save > >>> the text file as you mentioned in 1 and 2 > >>> > >>> After I compile and run I get this following message. > >>> > >>> When I restart ImageJ I do not see the plugin > >>> > >>> Any suggestions? > >>> > >>> Thanks, > >>> Sushmitha > >>> > >>> I will respond to your question on directionality analysis in a following > >>> > >>> On 4/10/19, 5:21 AM, "Herbie" < > >> > >>> l16@ > >> > >>> > wrote: > >>> > >>> Good day Sushmitha, > >>> > >>> you are right I was a bit too concise with the description of point 2. > >>> > >>> For plain ImageJ the following works for me: > >>> > >>> 1. > >>> Copy the Java source code to an empty text window (Plugins >> New >> > >>> Text Window...). > >>> > >>> 2. > >>> Save this file as "Oval_Profile.java" (the underscore is essential!) > >>> to > >>> the plugins-folder of your ImageJ installation. > >>> > >>> 3. > >>> Go to "Plugins >> Compile and Run..." and in the then opening file > >>> dialog search for the "Oval_Profile.java"-file in the plugins-folder > >>> and > >>> open it. > >>> > >>> 4. > >>> The plugin will be compiled and starts running. > >>> (It is automatically stored as "Oval_Profile.class"-file in the > >>> plugins-folder of your ImageJ installation.) > >>> > >>> 5. > >>> After restarting ImageJ you will find the plugin listed in the Plugins > >>> menu of ImageJ. > >>> > >>> HTH > >>> > >>> Herbie > >>> __________________________ > >>> > >>> PS: > >>> What is your opinion about the results I've provide concerning > >>> orientation analyses? > >>> > >>> ::::::::::::::::::::::::::: > >>>> Dear Herbie, > >>>> > >>>> I am unable to install this plugin > >>>> > >>>> I am able to do step1 > >>>> In step 2 - where do you save the java file? In macros? > >>>> Does this matter in Mac or PC. Tried on a Mac > >>>> > >>>> I think I am messing up in saving the coding file and therefore > >>> unable to run this code file. > >>>> > >>>> Next when I compile and run I cannot find the Oval Profile plug in > >>> at all. > >>>> > >>>> Thanks for the info > >>>> > >>>> Sushmitha > >>>> > >>>> On 3/30/19, 4:48 AM, "ImageJ Interest Group on behalf of Herbie" > >>> < > >> > >>> IMAGEJ@.NIH > >> > >>> on behalf of > >> > >>> l16@ > >> > >>> > wrote: > >>>> > >>>> Good day, > >>>> > >>>> please study the installation recommendations given here: > >>>> <https://imagej.nih.gov/ij/plugins/oval-profile.html> > >>>> > >>>> For plain ImageJ the following works for me: > >>>> > >>>> 1. > >>>> Copy the Java source code to an empty text window (Plugins >> > >>> New >> > >>>> Text Window...). > >>>> > >>>> 2. > >>>> Name this file Oval_Profile.java. (The underscore is > >>> essential!) > >>>> > >>>> 3. > >>>> Compile an run this code file (Plugins >> Compile and Run...). > >>>> > >>>> 4. The plugin starts. > >>>> > >>>> If you restart ImageJ the plugin will be listed in the Plugins > >>> menu. > >>>> > >>>> If you use Fiji, then there is no easy way to compile and run > >>> Java > >>>> source code. For whatever reasons the "Compile and > >>> Run..."-feature is > >>>> still missing in Fiji. > >>>> > >>>> HTH > >>>> > >>>> Herbie > >>>> > >>>> :::::::::::::::::::::::::::::::::::::::::::::::::: > >>>> Am 30.03.19 um 03:58 schrieb Durgam, Sushmitha S.: > >>>>> Hi. I am unable to install the Oval profile Plug in to obtain > >>> radial sum of FFT alignment > >>>>> > >>>>> > >>>>> Would appreciate help and any directions > >>>>> > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Sushmitha > >>>>> > >>>>> > >>>>> [The Ohio State University] > >>>>> Sushmitha Durgam, BVSc, PhD, DACVS-LA > >>>>> Assistant Professor, Equine Surgery > >>>>> College of Veterinary Medicine Dept. of Veterinary Clinical > >>> Sciences > >>>>> 370 VMAB, 1900 Coffey Road, Columbus, OH 43210 > >>>>> 614-292-6661 (Ext - 2) Office / 248-909-6993 Mobile / > >>> 614-688-5642 Fax > >>>>> > >> > >>> durgam.3@ > >> > >>> <mailto: > >> > >>> durgam.3@ > >> > >>> > > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> 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 > >>> > >>> > >>> Screen Shot 2019-04-11 at 2.30.31 AM.png (558K) > >>> <http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png> > >> > >> > >> > >> > >> > >> -- > >> 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 > > > > -- > > 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  OrientationSalience_ImagesAB_PS1-HP00.png (39K) Download Attachment OrientationSalience_ImagesAB_ACF4-HP02.png (40K) Download Attachment |
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