Help to download and install Oval Profile Plugin

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Help to download and install Oval Profile Plugin

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]>




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Re: Help to download and install Oval Profile Plugin

Herbie
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
>

--
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Re: Help to download and install Oval Profile Plugin

Durgam, Sushmitha S.
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
   


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Re: Help to download and install Oval Profile Plugin

CARL Philippe (LBP)
Dear Sushmitha,
I would rather replace the points 1 and 2 by just:
Save the following file within the ImageJ plugin folder:
https://imagej.nih.gov/ij/plugins/download/Oval_Profile.java
And for your other questions:
> In step 2 - where do you save the java file? In macros?
In the plugin folder of ImageJ (or a subfolder of the plugin folder).
> Does this matter in Mac or PC. Tried on a Mac
No it doesn't matter PC or Mac...
I hope this helps you to go further.
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 41 84

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Durgam, Sushmitha S.
Envoyé : mercredi 10 avril 2019 05:14
À : [hidden email]
Objet : Re: Help to download and install Oval Profile Plugin

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
   


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Re: Help to download and install Oval Profile Plugin

Herbie
In reply to this post by Durgam, Sushmitha S.
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
>      
>

--
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Re: Help to download and install Oval Profile Plugin

Curtis Rueden
In reply to this post by Durgam, Sushmitha S.
Hi everyone,

> If you use Fiji, then there is no easy way to compile and run Java
> source code.

That is not the case. Fiji comes bundled with the SciJava Script Editor (
https://imagej.net/Script_Editor), which supports compiling and running
Java code.

> the "Compile and Run..."-feature is still missing in Fiji.

For those who want to read about the technical issues surreounding "Compile
and Run" and other dynamic classpath features of IJ1, see these links:

* https://github.com/imagej/imagej-ui-swing/issues/48
* https://github.com/imagej/imagej-legacy/issues/98

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Have you tried the Image.sc Forum? https://forum.image.sc/



On Sat, Mar 30, 2019 at 3:48 AM Herbie <[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
>

--
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Re: Help to download and install Oval Profile Plugin

Herbie
I'm unable to compile and run "Oval_Profile.java" from the Fiji Script
Editor (fresh download) after having entered the code to the editor.

With the menu command "Compile and Run" I get:
"Oval_Profile not up-to-date because 1 source files are not up-to-date
(/var/folders/7g/9r90_ps92r72prt3_d3v52l80000gn/T/java3585174238626278361/src/main/java/Oval_Profile.java)"
etc.

Can't even find a corresponding compiled ".class"-file.

With plain ImageJ I encounter no problems when using "Compile and Run...".

That's why I wrote:
"If you use Fiji, then there is no easy way to compile and run Java
source code."

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 10.04.19 um 16:06 schrieb Curtis Rueden:

> Hi everyone,
>
>> If you use Fiji, then there is no easy way to compile and run Java
>> source code.
>
> That is not the case. Fiji comes bundled with the SciJava Script Editor (
> https://imagej.net/Script_Editor), which supports compiling and running
> Java code.
>
>> the "Compile and Run..."-feature is still missing in Fiji.
>
> For those who want to read about the technical issues surreounding "Compile
> and Run" and other dynamic classpath features of IJ1, see these links:
>
> * https://github.com/imagej/imagej-ui-swing/issues/48
> * https://github.com/imagej/imagej-legacy/issues/98
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Have you tried the Image.sc Forum? https://forum.image.sc/
>
>
>
> On Sat, Mar 30, 2019 at 3:48 AM Herbie <[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
>

--
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Re: Help to download and install Oval Profile Plugin

Durgam, Sushmitha S.
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
    >      
    >
   


--
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Re: Help to download and install Oval Profile Plugin

Herbie
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
> email
>
> On 4/10/19, 5:21 AM, "Herbie" &lt;

> l16@

> &gt; 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"
> &lt;

> IMAGEJ@.NIH

>  on behalf of

> l16@

> &gt; wrote:
>     >
>     >      Good day,
>     >      
>     >      please study the installation recommendations given here:
>     >      &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
>     >      
>     >      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@

> &lt;mailto:

> durgam.3@

> &gt;
>     >      >
>     >      >
>     >      >
>     >      >
>     >      > --
>     >      > 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)
> &lt;http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png&gt;





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Re: Help to download and install Oval Profile Plugin

Durgam, Sushmitha S.
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
    > email
    >
    > On 4/10/19, 5:21 AM, "Herbie" &lt;
   
    > l16@
   
    > &gt; 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"
    > &lt;
   
    > IMAGEJ@.NIH
   
    >  on behalf of
   
    > l16@
   
    > &gt; wrote:
    >     >
    >     >      Good day,
    >     >      
    >     >      please study the installation recommendations given here:
    >     >      &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
    >     >      
    >     >      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@
   
    > &lt;mailto:
   
    > durgam.3@
   
    > &gt;
    >     >      >
    >     >      >
    >     >      >
    >     >      >
    >     >      > --
    >     >      > 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)
    > &lt;http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png&gt;
   
   
   
   
   
    --
    Sent from: http://imagej.1557.x6.nabble.com/
   
    --
    ImageJ mailing list: http://imagej.nih.gov/ij/list.html
   


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Re: Help to download and install Oval Profile Plugin

Herbie
Good day!

Your "ImageJ"-installation, actually a folder named "ImageJ", should
reside in your Mac "Applications"-folder.

In this "ImageJ"-folder you should find a folder named "plugins" and
this is the folder where all those ImageJ-plugins should reside that you
like to use and that, after a restart of ImageJ, are listed in the
"Plugins"-menu.

In essence, copy the three files to the "plugins"-folder that is in the
"ImageJ"-folder.

Good luck

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::::
Am 12.04.19 um 06:42 schrieb Durgam, Sushmitha S.:

> 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
>      > email
>      >
>      > On 4/10/19, 5:21 AM, "Herbie" &lt;
>      
>      > l16@
>      
>      > &gt; 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"
>      > &lt;
>      
>      > IMAGEJ@.NIH
>      
>      >  on behalf of
>      
>      > l16@
>      
>      > &gt; wrote:
>      >     >
>      >     >      Good day,
>      >     >
>      >     >      please study the installation recommendations given here:
>      >     >      &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
>      >     >
>      >     >      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@
>      
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>      
>      > durgam.3@
>      
>      > &gt;
>      >     >      >
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>      >     >      >
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Re: Help to download and install Oval Profile Plugin

Glen MacDonald-3
In reply to this post by Durgam, Sushmitha S.
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
>> email
>>
>> On 4/10/19, 5:21 AM, "Herbie" &lt;
>
>> l16@
>
>> &gt; 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"
>> &lt;
>
>> IMAGEJ@.NIH
>
>> on behalf of
>
>> l16@
>
>> &gt; wrote:
>>>
>>>     Good day,
>>>
>>>     please study the installation recommendations given here:
>>>     &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
>>>
>>>     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@
>
>> &lt;mailto:
>
>> durgam.3@
>
>> &gt;
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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)
>> &lt;http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png&gt;
>
>
>
>
>
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Re: Help to download and install Oval Profile Plugin

Herbie
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
>>> email
>>>
>>> On 4/10/19, 5:21 AM, "Herbie" &lt;
>>
>>> l16@
>>
>>> &gt; 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"
>>> &lt;
>>
>>> IMAGEJ@.NIH
>>
>>> on behalf of
>>
>>> l16@
>>
>>> &gt; wrote:
>>>>
>>>>      Good day,
>>>>
>>>>      please study the installation recommendations given here:
>>>>      &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
>>>>
>>>>      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@
>>
>>> &lt;mailto:
>>
>>> durgam.3@
>>
>>> &gt;
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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)
>>> &lt;http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png&gt;
>>
>>
>>
>>
>>
>>     --
>>     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
>
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Re: Help to download and install Oval Profile Plugin

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
    >>> email
    >>>
    >>> On 4/10/19, 5:21 AM, "Herbie" &lt;
    >>
    >>> l16@
    >>
    >>> &gt; 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"
    >>> &lt;
    >>
    >>> IMAGEJ@.NIH
    >>
    >>> on behalf of
    >>
    >>> l16@
    >>
    >>> &gt; wrote:
    >>>>
    >>>>      Good day,
    >>>>
    >>>>      please study the installation recommendations given here:
    >>>>      &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
    >>>>
    >>>>      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@
    >>
    >>> &lt;mailto:
    >>
    >>> durgam.3@
    >>
    >>> &gt;
    >>>>>
    >>>>>
    >>>>>
    >>>>>
    >>>>> --
    >>>>> 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)
    >>> &lt;http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png&gt;
    >>
    >>
    >>
    >>
    >>
    >>     --
    >>     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
   


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Re: Help to download and install Oval Profile Plugin

Herbie
Good day!

Be careful with plots that show suppressed zero for the ordinate dimension!

Furthermore, I doubt that you are displaying orientations because
orientation angles run from 0deg to 180deg not to 360deg.

Finally and once more:
Please be aware of the fact that professional orientation analyses
aren't trivial.

Regards

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
>      >>> email
>      >>>
>      >>> On 4/10/19, 5:21 AM, "Herbie" &lt;
>      >>
>      >>> l16@
>      >>
>      >>> &gt; 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"
>      >>> &lt;
>      >>
>      >>> IMAGEJ@.NIH
>      >>
>      >>> on behalf of
>      >>
>      >>> l16@
>      >>
>      >>> &gt; wrote:
>      >>>>
>      >>>>      Good day,
>      >>>>
>      >>>>      please study the installation recommendations given here:
>      >>>>      &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
>      >>>>
>      >>>>      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@
>      >>
>      >>> &lt;mailto:
>      >>
>      >>> durgam.3@
>      >>
>      >>> &gt;
>      >>>>>
>      >>>>>
>      >>>>>
>      >>>>>
>      >>>>> --
>      >>>>> 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)
>      >>> &lt;http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png&gt;
>      >>
>      >>
>      >>
>      >>
>      >>
>      >>     --
>      >>     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
>      
>

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Re: Help to download and install Oval Profile Plugin

Herbie
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
>      >>> email
>      >>>
>      >>> On 4/10/19, 5:21 AM, "Herbie" &lt;
>      >>
>      >>> l16@
>      >>
>      >>> &gt; 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"
>      >>> &lt;
>      >>
>      >>> IMAGEJ@.NIH
>      >>
>      >>> on behalf of
>      >>
>      >>> l16@
>      >>
>      >>> &gt; wrote:
>      >>>>
>      >>>>      Good day,
>      >>>>
>      >>>>      please study the installation recommendations given here:
>      >>>>      &lt;https://imagej.nih.gov/ij/plugins/oval-profile.html&gt;
>      >>>>
>      >>>>      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@
>      >>
>      >>> &lt;mailto:
>      >>
>      >>> durgam.3@
>      >>
>      >>> &gt;
>      >>>>>
>      >>>>>
>      >>>>>
>      >>>>>
>      >>>>> --
>      >>>>> 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)
>      >>> &lt;http://imagej.1557.x6.nabble.com/attachment/5022051/0/Screen%20Shot%202019-04-11%20at%202.30.31%20AM.png&gt;
>      >>
>      >>
>      >>
>      >>
>      >>
>      >>     --
>      >>     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

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