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Radial Profile Angle

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Cousoulis, Paul

Radial Profile Angle

There are two different Plug-Ins for calculating Radial Profile they give the same results except for the first data point. The first data point is off by a factor of two. Does anyone know why and which one is correct? The two plugins are:

http://rsbweb.nih.gov/ij/plugins/radial-profile.html

http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html

Thanks
Paul

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This electronic message transmission and any attachments are
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Meso Scale Diagnostics, LLC. The information is intended for solely
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the intended recipient, you are hereby notified that any
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you should destroy this email immediately.

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please notify us by telephone (240-631-2522) or by electronic
mail to the sender of this email, Cousoulis, Paul ([hidden email]),
immediately.
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Kota Miura

Re: Radial Profile Angle

Hi Paul,

I did not know about the second plugin, but you probably could decide
the correct one by checking the actual pixel value at the (X0, Y0)
position and compare with the histogram value of the first bin in the
histogram. The value of the first bin position should be exactly same
as the intensity of that single pixel position.

Aside from that, I know that the first one (radial-profile.html) has a
problem with the last histogram bin since for that bin, the averaging
includes pixel intensities in the area between the circular ROI
boundary and its bounding square. Another problem might occur if you
are measuring NaN values (32bit images) because these pixels are
averaged as well (only for the number of counts ... so the results
becomes lower than the actual) in the results.

I fixed these problems a short while a go so please try the modified
plugin (jar file) in the following link. Details of modification are
written in the java file.

https://github.com/cmci/RadialProfileV2

Cheers,
Kota

On Wed, May 30, 2012 at 11:21 PM, Cousoulis, Paul
<[hidden email]> wrote:

> There are two different Plug-Ins for calculating Radial Profile they give the same results except for the first data point. The first data point is off by a factor of two. Does anyone know why and which one is correct? The two plugins are:
>
> http://rsbweb.nih.gov/ij/plugins/radial-profile.html
>
> http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html
>
> Thanks
> Paul
>
>
>
>
> ======================================================================
> This electronic message transmission and any attachments are
> confidential and/or proprietary and may constitute legally privileged information of
> Meso Scale Diagnostics, LLC. The information is intended for solely
> the use of [hidden email] ([hidden email]). If you are not
> the intended recipient, you are hereby notified that any
> disclosure, copying, distribution or the taking of any action in
> reliance of this information is strictly prohibited. You are not
> authorized to retain it in any form nor to re-transmit it, and
> you should destroy this email immediately.
>
> If you have received this electronic transmission in error,
> please notify us by telephone (240-631-2522) or by electronic
> mail to the sender of this email, Cousoulis, Paul ([hidden email]),
> immediately.
> =====================================================================
>
>
>
> _______________________________________________________
>
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Cousoulis, Paul

Re: Radial Profile Angle

In reply to this post by Cousoulis, Paul

Hi Kota

I don't know if the list will accept the attachment but I attached a pinhole image I'm trying to analyze. Both versions of Radial Profile skip the center pixel. The first point I get is a sum of the eight pixels surrounding the center pixel. Radial Profile divides this sum by something close to 9. Radial Profile-Ext divides this sum by something close to 18. I think they should divide by 8.

The new plugin you gave me a link to doesn't work in Fiji. I get the following error report.

C:\Fiji\FIJI-W~1\Fiji.app\plugins\Radial_ProfileV2.jar: java.util.zip.ZipException: error in opening zip file

C:\Fiji\FIJI-W~1\Fiji.app\plugins\Radial_ProfileV2.jar: java.util.zip.ZipException: error in opening zip file

Thanks

Paul

>Date: Thu, 31 May 2012 10:50:59 +0200

>From: Kota Miura <[hidden email]<mailto:[hidden email]>>

>Subject: Re: Radial Profile Angle

>Hi Paul,

>I did not know about the second plugin, but you probably could decide the correct one by checking the actual pixel value at the (X0, Y0) position and compare with the histogram value of the first bin in the histogram. The value of the first bin position should be exactly same as the intensity of that single pixel position.

>Aside from that, I know that the first one (radial-profile.html) has a problem with the last histogram bin since for that bin, the averaging includes pixel intensities in the area between the circular ROI boundary and its bounding square. Another problem might occur if you are measuring NaN values (32bit images) because these pixels are averaged as well (only for the number of counts ... so the results becomes lower than the actual) in the results.

>I fixed these problems a short while a go so please try the modified plugin (jar file) in the following link. Details of modification are written in the java file.

>https://github.com/cmci/RadialProfileV2

>Cheers,

>Kota

On Wed, May 30, 2012 at 11:21 PM, Cousoulis, Paul <[hidden email]<mailto:[hidden email]>> wrote:

> There are two different Plug-Ins for calculating Radial Profile they give the same results except for the first data point. The first data point is off by a factor of two. Does anyone know why and which one is correct? The two plugins are:

>

> http://rsbweb.nih.gov/ij/plugins/radial-profile.html

>

> http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html

>

> Thanks

> Paul

>

======================================================================
This electronic message transmission and any attachments are
confidential and/or proprietary and may constitute legally privileged information of
Meso Scale Diagnostics, LLC. The information is intended for solely
the use of [hidden email] ([hidden email]). If you are not
the intended recipient, you are hereby notified that any
disclosure, copying, distribution or the taking of any action in
reliance of this information is strictly prohibited. You are not
authorized to retain it in any form nor to re-transmit it, and
you should destroy this email immediately.

If you have received this electronic transmission in error,
please notify us by telephone (240-631-2522) or by electronic
mail to the sender of this email, Cousoulis, Paul ([hidden email]),
immediately.
=====================================================================

_______________________________________________________

ImageJ mailing list: http://imagej.nih.gov/ij/list.html

120531_Lens009pinhole15um200msDiff.tif (700K) Download Attachment

Kota Miura

Re: Radial Profile Angle

Hi Paul,

could you download the file using the link below (downloads starts by clicking)?
https://github.com/cmci/RadialProfileV2/blob/master/Radial_ProfileV2.jar?raw=true

cheers,
Kota

On Fri, Jun 1, 2012 at 6:57 PM, Cousoulis, Paul
<[hidden email]> wrote:

> Hi Kota
>
>
>
> I don't know if the list will accept the attachment but I attached a pinhole image I'm trying to analyze. Both versions of Radial Profile skip the center pixel. The first point I get is a sum of the eight pixels surrounding the center pixel. Radial Profile divides this sum by something close to 9. Radial Profile-Ext divides this sum by something close to 18. I think they should divide by 8.
>
>
>
> The new plugin you gave me a link to doesn't work in Fiji. I get the following error report.
>
>
>
> C:\Fiji\FIJI-W~1\Fiji.app\plugins\Radial_ProfileV2.jar: java.util.zip.ZipException: error in opening zip file
>
> C:\Fiji\FIJI-W~1\Fiji.app\plugins\Radial_ProfileV2.jar: java.util.zip.ZipException: error in opening zip file
>
>
>
> Thanks
>
> Paul

>>Date: Thu, 31 May 2012 10:50:59 +0200
>
>>From: Kota Miura <[hidden email]<mailto:[hidden email]>>
>
>>Subject: Re: Radial Profile Angle
>
>
>
>>Hi Paul,
>
>
>
>>I did not know about the second plugin, but you probably could decide the correct one by checking the actual pixel value at the (X0, Y0) position and compare with the histogram value of the first bin in the histogram. The value of the first bin position should be exactly same as the intensity of that single pixel position.
>
>
>
>>Aside from that, I know that the first one (radial-profile.html) has a problem with the last histogram bin since for that bin, the averaging includes pixel intensities in the area between the circular ROI boundary and its bounding square. Another problem might occur if you are measuring NaN values (32bit images) because these pixels are averaged as well (only for the number of counts ... so the results becomes lower than the actual) in the results.
>
>
>
>>I fixed these problems a short while a go so please try the modified plugin (jar file) in the following link. Details of modification are written in the java file.
>
>
>
>>https://github.com/cmci/RadialProfileV2
>
>
>
>>Cheers,
>
>>Kota
>
>
>
> On Wed, May 30, 2012 at 11:21 PM, Cousoulis, Paul <[hidden email]<mailto:[hidden email]>> wrote:
>
>> There are two different Plug-Ins for calculating Radial Profile they give the same results except for the first data point. The first data point is off by a factor of two. Does anyone know why and which one is correct? The two plugins are:
>
>>
>
>> http://rsbweb.nih.gov/ij/plugins/radial-profile.html
>
>>
>
>> http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html
>
>>
>
>> Thanks
>
>> Paul
>
>>
>
>
>
> ======================================================================
> This electronic message transmission and any attachments are
> confidential and/or proprietary and may constitute legally privileged information of
> Meso Scale Diagnostics, LLC. The information is intended for solely
> the use of [hidden email] ([hidden email]). If you are not
> the intended recipient, you are hereby notified that any
> disclosure, copying, distribution or the taking of any action in
> reliance of this information is strictly prohibited. You are not
> authorized to retain it in any form nor to re-transmit it, and
> you should destroy this email immediately.
>
> If you have received this electronic transmission in error,
> please notify us by telephone (240-631-2522) or by electronic
> mail to the sender of this email, Cousoulis, Paul ([hidden email]),
> immediately.
> =====================================================================
>
>
>
> _______________________________________________________
>
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Cousoulis, Paul

Re: Radial Profile Angle

In reply to this post by Cousoulis, Paul

Hi Kota

I figured out what was going wrong. After I put the file in the plugin directory and started Fiji, I couldn't find the command in the plugins menu, so I ran Install Plugin. That gave me the error messages and changes the size of the plug in file from 6kB to 0kB. I don't know if that is another bug. Deleting the 0kB and putting the new Radial_ProfileV2.jar file back in the plugin directory, this time I found it in the EMBLtools>Measure Submenu. The plugin is working correctly and is giving me the expected values.

Thanks
Paul

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Kota Miura
Sent: Monday, June 04, 2012 5:48 AM
To: ImageJ Interest Group
Cc: Cousoulis, Paul
Subject: [SPAM] - Re: Radial Profile Angle - Found word(s) list error in the Text body

Hi Paul,

could you download the file using the link below (downloads starts by clicking)?
https://github.com/cmci/RadialProfileV2/blob/master/Radial_ProfileV2.jar?raw=true

cheers,
Kota

On Fri, Jun 1, 2012 at 6:57 PM, Cousoulis, Paul <[hidden email]> wrote:

> Hi Kota
>
>
>
> I don't know if the list will accept the attachment but I attached a pinhole image I'm trying to analyze. Both versions of Radial Profile skip the center pixel. The first point I get is a sum of the eight pixels surrounding the center pixel. Radial Profile divides this sum by something close to 9. Radial Profile-Ext divides this sum by something close to 18. I think they should divide by 8.
>
>
>
> The new plugin you gave me a link to doesn't work in Fiji. I get the following error report.
>
>
>
> C:\Fiji\FIJI-W~1\Fiji.app\plugins\Radial_ProfileV2.jar:
> java.util.zip.ZipException: error in opening zip file
>
> C:\Fiji\FIJI-W~1\Fiji.app\plugins\Radial_ProfileV2.jar:
> java.util.zip.ZipException: error in opening zip file
>
>
>
> Thanks
>
> Paul

>>Date: Thu, 31 May 2012 10:50:59 +0200
>
>>From: Kota Miura <[hidden email]<mailto:[hidden email]>>
>
>>Subject: Re: Radial Profile Angle
>
>
>
>>Hi Paul,
>
>
>
>>I did not know about the second plugin, but you probably could decide the correct one by checking the actual pixel value at the (X0, Y0) position and compare with the histogram value of the first bin in the histogram. The value of the first bin position should be exactly same as the intensity of that single pixel position.
>
>
>
>>Aside from that, I know that the first one (radial-profile.html) has a problem with the last histogram bin since for that bin, the averaging includes pixel intensities in the area between the circular ROI boundary and its bounding square. Another problem might occur if you are measuring NaN values (32bit images) because these pixels are averaged as well (only for the number of counts ... so the results becomes lower than the actual) in the results.
>
>
>
>>I fixed these problems a short while a go so please try the modified plugin (jar file) in the following link. Details of modification are written in the java file.
>
>
>
>>https://github.com/cmci/RadialProfileV2
>
>
>
>>Cheers,
>
>>Kota
>
>
>
> On Wed, May 30, 2012 at 11:21 PM, Cousoulis, Paul <[hidden email]<mailto:[hidden email]>> wrote:
>
>> There are two different Plug-Ins for calculating Radial Profile they give the same results except for the first data point. The first data point is off by a factor of two. Does anyone know why and which one is correct? The two plugins are:
>
>>
>
>> http://rsbweb.nih.gov/ij/plugins/radial-profile.html
>
>>
>
>> http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html
>
>>
>
>> Thanks
>
>> Paul
>
>>
>
>
>
> ======================================================================
> This electronic message transmission and any attachments are
> confidential and/or proprietary and may constitute legally privileged
> information of
> Meso Scale Diagnostics, LLC. The information is intended for solely
> the use of [hidden email] ([hidden email]). If you are not
> the intended recipient, you are hereby notified that any
> disclosure, copying, distribution or the taking of any action in
> reliance of this information is strictly prohibited. You are not
> authorized to retain it in any form nor to re-transmit it, and
> you should destroy this email immediately.
>
> If you have received this electronic transmission in error,
> please notify us by telephone (240-631-2522) or by electronic
> mail to the sender of this email, Cousoulis, Paul
> ([hidden email]),
> immediately.
> =====================================================================
>
>
>
> _______________________________________________________
>
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
-------------------------------------------------------------
Dr. Kota Miura

Scientist & IT Engineer
Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory Meyerhofstr. 1
69117 Heidelberg
GERMANY

Tel +49 6221 387 404

Mobile +49 160 95001177

Fax +49 6221 387 512

http://cmci.embl.de
-------------------------------------------------------------

======================================================================
This electronic message transmission and any attachments are
confidential and/or proprietary and may constitute legally privileged information of
Meso Scale Diagnostics, LLC. The information is intended for solely
the use of recipient (recipient). If you are not
the intended recipient, you are hereby notified that any
disclosure, copying, distribution or the taking of any action in
reliance of this information is strictly prohibited. You are not
authorized to retain it in any form nor to re-transmit it, and
you should destroy this email immediately.

If you have received this electronic transmission in error,
please notify us by telephone (240-631-2522) or by electronic
mail to the sender of this email, Cousoulis, Paul ([hidden email]),
immediately.
=====================================================================

____________________________________________
ImageJ mailing list: http://imagej.nih.gov/ij/list.html