Image Processing packages

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Image Processing packages

Thomas Roth (geb. Kaliwe)
Hi,
 
I've been looking for Image Processing packages. Thresholding, Edge
Filters, Dct, Segmentation, Restoration. I'm aware, that Octave, Matlab
etc. would be a good address but then I'm missing the "statistical
power"  of R. Does anybody know of packages, projects etc. Comments on
wether the use of R for such matters is useful are welcome.
 
Greetings
 
Thomas Kaliwe

        [[alternative HTML version deleted]]

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Re: Image Processing packages

Philippe Grosjean
Hello,

There are a couple of things for image processing in R (look at pixmap
and Rimage, for instance). However, R is *not* a good software for
processing images (nor is Matlab, Octave, IDL: they use to have specific
packages for image processing and analysis, but resulting applications
are way to slow in comparison to dedicated software).

A good approach is to mix ImageJ and R, if you are looking for an Open
Source solution. You could look at ZooImage for an example application
using these two software (analysis of digital zooplankton images, see:
http://www.sciviews.org/zooimage).

Best,

Philippe Grosjean


Thomas Kaliwe wrote:

> Hi,
>  
> I've been looking for Image Processing packages. Thresholding, Edge
> Filters, Dct, Segmentation, Restoration. I'm aware, that Octave, Matlab
> etc. would be a good address but then I'm missing the "statistical
> power"  of R. Does anybody know of packages, projects etc. Comments on
> wether the use of R for such matters is useful are welcome.
>  
> Greetings
>  
> Thomas Kaliwe
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>

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Re: Image Processing packages

Philippe Grosjean
[hidden email] wrote:
> Philippe, I am trying to get there but I keep on receiving a blank file after 5
> minutes, is there something wrong with the site?
> H.Ghezzo
> McGill University
> Montreal - Canada

Well, I am trying myself. Indded, it seems that my server is down, or
very busy. I will look at this tomorrow.
Best,

Philippe Grosjean

> Quoting Philippe Grosjean <[hidden email]>:
>
>
>>Hello,
>>
>>There are a couple of things for image processing in R (look at pixmap
>>and Rimage, for instance). However, R is *not* a good software for
>>processing images (nor is Matlab, Octave, IDL: they use to have specific
>>packages for image processing and analysis, but resulting applications
>>are way to slow in comparison to dedicated software).
>>
>>A good approach is to mix ImageJ and R, if you are looking for an Open
>>Source solution. You could look at ZooImage for an example application
>>using these two software (analysis of digital zooplankton images, see:
>>http://www.sciviews.org/zooimage).
>>
>>Best,
>>
>>Philippe Grosjean
>>
>>
>>Thomas Kaliwe wrote:
>>
>>>Hi,
>>>
>>>I've been looking for Image Processing packages. Thresholding, Edge
>>>Filters, Dct, Segmentation, Restoration. I'm aware, that Octave, Matlab
>>>etc. would be a good address but then I'm missing the "statistical
>>>power"  of R. Does anybody know of packages, projects etc. Comments on
>>>wether the use of R for such matters is useful are welcome.
>>>
>>>Greetings
>>>
>>>Thomas Kaliwe
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>______________________________________________
>>>[hidden email] mailing list
>>>https://stat.ethz.ch/mailman/listinfo/r-help
>>>PLEASE do read the posting guide!
>>
>>http://www.R-project.org/posting-guide.html
>>
>>>
>>______________________________________________
>>[hidden email] mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>
>
>
>
>
>

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Re: Image Processing packages

Kort, Eric
In reply to this post by Thomas Roth (geb. Kaliwe)
Thomas Kaliwe wrote:
> Hi,
>  
> I've been looking for Image Processing packages. Thresholding, Edge
> Filters, Dct, Segmentation, Restoration. I'm aware, that Octave,
Matlab
> etc. would be a good address but then I'm missing the "statistical
> power"  of R. Does anybody know of packages, projects etc. Comments on
> wether the use of R for such matters is useful are welcome.
>  

See also my package rtiff for reading tiff images.

I routinely do image analysis in R.  Yes, it is relatively slow compared
to dedicated solutions, but I like the smooth integration with the
associated statistical analysis and the ability to have a single script
that performs the image analysis and multiple files and subsequent
statistical analysis, and with modern computing equipment R is fast
enough for my purposes.  

I have a variety of standard image processing functions written in R,
but have yet to distribute them because most people choose not to
perform image analysis in R for the previously stated reasons.  

So in general I would agree that R is sub-optimal for image processing
(and this is certainly outside the realm of things R was intended to do
if I read the early mailing list archives correctly).  However, it can
be done and it might be desirable to do so from a work-flow perspective.

-Eric

> Greetings
>  
> Thomas Kaliwe
This email message, including any attachments, is for the so...{{dropped}}

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Re: Image Processing packages

Stephan Matthiesen
Hi,

Am Donnerstag, 26. Januar 2006 19:39 schrieb Kort, Eric:
> I have a variety of standard image processing functions written in R,
> but have yet to distribute them because most people choose not to
> perform image analysis in R for the previously stated reasons.

I encourage you to distribute them. I work with satellite imagery, where you
need both statistical tools for data analysis and versatile image
processing/visualization tools.

> So in general I would agree that R is sub-optimal for image processing
> (and this is certainly outside the realm of things R was intended to do
> if I read the early mailing list archives correctly).  However, it can
> be done and it might be desirable to do so from a work-flow perspective.

I agree. Actually, it seems to me that an increasing number of people use R
for tasks that are not strictly statistical analyses, often as a replacement
for Matlab.

Thanks for your good work!

Stephan

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Re: Image Processing packages

Charles Annis, P.E.
In reply to this post by Kort, Eric
Eric:

I use R to quantify the efficacy of ultrasonic inspections of metal
components (e.g. looking for nonmetallic inclusions in forgings) and use R
for image processing, but my methods have been rather a kluge.  I am
interested in your R functions, if you will make them available.
Unfortunately, making a package for CRAN is (in my opinion) WAY too hard on
Windows, and I've given up, but I hope that you do not.  I second Stephan
Matthiesen's recent suggestion that you make your image processing functions
available to fellow R users, if not on CRAN, then perhaps as ascii files
from your website.

Thanks.

Charles Annis, P.E.

[hidden email]
phone: 561-352-9699
eFax:  614-455-3265
http://www.StatisticalEngineering.com
 
-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Kort, Eric
Sent: Thursday, January 26, 2006 2:39 PM
To: Thomas Kaliwe; [hidden email]
Subject: Re: [R] Image Processing packages

Thomas Kaliwe wrote:
> Hi,
>  
> I've been looking for Image Processing packages. Thresholding, Edge
> Filters, Dct, Segmentation, Restoration. I'm aware, that Octave,
Matlab
> etc. would be a good address but then I'm missing the "statistical
> power"  of R. Does anybody know of packages, projects etc. Comments on
> wether the use of R for such matters is useful are welcome.
>  

See also my package rtiff for reading tiff images.

I routinely do image analysis in R.  Yes, it is relatively slow compared
to dedicated solutions, but I like the smooth integration with the
associated statistical analysis and the ability to have a single script
that performs the image analysis and multiple files and subsequent
statistical analysis, and with modern computing equipment R is fast
enough for my purposes.  

I have a variety of standard image processing functions written in R,
but have yet to distribute them because most people choose not to
perform image analysis in R for the previously stated reasons.  

So in general I would agree that R is sub-optimal for image processing
(and this is certainly outside the realm of things R was intended to do
if I read the early mailing list archives correctly).  However, it can
be done and it might be desirable to do so from a work-flow perspective.

-Eric

> Greetings
>  
> Thomas Kaliwe
This email message, including any attachments, is for the so...{{dropped}}

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http://www.R-project.org/posting-guide.html

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Re: Image Processing packages

Kort, Eric
In reply to this post by Thomas Roth (geb. Kaliwe)
Charles Annis, P.E. writes...
> Eric:
>
> I use R to quantify the efficacy of ultrasonic inspections of metal
> components (e.g. looking for nonmetallic inclusions in forgings) and
use R
> for image processing, but my methods have been rather a kluge.  I am
> interested in your R functions, if you will make them available.
> Unfortunately, making a package for CRAN is (in my opinion) WAY too
hard
> on
> Windows, and I've given up, but I hope that you do not.  I second
Stephan
> Matthiesen's recent suggestion that you make your image processing
> functions
> available to fellow R users, if not on CRAN, then perhaps as ascii
files
> from your website.

I knew I was asking for trouble when I sent that post. =)

Ok, I will clean up my code and put together a package, hopefully in the
next couple of weeks.

-Eric

>
> Thanks.
>
> Charles Annis, P.E.
This email message, including any attachments, is for the so...{{dropped}}

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Re: Image Processing packages

Thomas Roth (geb. Kaliwe)
In reply to this post by Charles Annis, P.E.
Hi,

Is it possible that I could see some of your functions and/or results of
those functions(Eric, Charles, Stephan). It's more about that I'd like
to see what already has been accomplished and the way that was chosen
thus circumventing reinvention and getting an overview.


Cheers

Thomas

-----Urspr√ľngliche Nachricht-----
Von: [hidden email]
[mailto:[hidden email]] Im Auftrag von Charles Annis,
P.E.
Gesendet: Freitag, 27. Januar 2006 16:36
An: 'Kort, Eric'
Cc: [hidden email]; [hidden email]
Betreff: Re: [R] Image Processing packages

Eric:

I use R to quantify the efficacy of ultrasonic inspections of metal
components (e.g. looking for nonmetallic inclusions in forgings) and use
R
for image processing, but my methods have been rather a kluge.  I am
interested in your R functions, if you will make them available.
Unfortunately, making a package for CRAN is (in my opinion) WAY too hard
on
Windows, and I've given up, but I hope that you do not.  I second
Stephan
Matthiesen's recent suggestion that you make your image processing
functions
available to fellow R users, if not on CRAN, then perhaps as ascii files
from your website.

Thanks.

Charles Annis, P.E.

[hidden email]
phone: 561-352-9699
eFax:  614-455-3265
http://www.StatisticalEngineering.com
 
-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Kort, Eric
Sent: Thursday, January 26, 2006 2:39 PM
To: Thomas Kaliwe; [hidden email]
Subject: Re: [R] Image Processing packages

Thomas Kaliwe wrote:
> Hi,
>  
> I've been looking for Image Processing packages. Thresholding, Edge
> Filters, Dct, Segmentation, Restoration. I'm aware, that Octave,
Matlab
> etc. would be a good address but then I'm missing the "statistical
> power"  of R. Does anybody know of packages, projects etc. Comments on
> wether the use of R for such matters is useful are welcome.
>  

See also my package rtiff for reading tiff images.

I routinely do image analysis in R.  Yes, it is relatively slow compared
to dedicated solutions, but I like the smooth integration with the
associated statistical analysis and the ability to have a single script
that performs the image analysis and multiple files and subsequent
statistical analysis, and with modern computing equipment R is fast
enough for my purposes.  

I have a variety of standard image processing functions written in R,
but have yet to distribute them because most people choose not to
perform image analysis in R for the previously stated reasons.  

So in general I would agree that R is sub-optimal for image processing
(and this is certainly outside the realm of things R was intended to do
if I read the early mailing list archives correctly).  However, it can
be done and it might be desirable to do so from a work-flow perspective.

-Eric

> Greetings
>  
> Thomas Kaliwe
This email message, including any attachments, is for the\ s...{{dropped}}

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Re: Image Processing packages

Kort, Eric
In reply to this post by Thomas Roth (geb. Kaliwe)

> From: [hidden email] [mailto:[hidden email]]
> Hi,
>
> Is it possible that I could see some of your functions and/or results
of
> those functions(Eric, Charles, Stephan). It's more about that I'd like
> to see what already has been accomplished and the way that was chosen
> thus circumventing reinvention and getting an overview.
>

Yes.  I sent some examples to you off list (didn't want to clog the
mailing list with the images).

>
> Cheers
>
> Thomas
>
This email message, including any attachments, is for the so...{{dropped}}

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Re: Image Processing packages

Kort, Eric
In reply to this post by Thomas Roth (geb. Kaliwe)

Nice.  May I incorporate these into the collection I am packaging up for redistribution?

-Eric

-----Original Message-----
From: Vincent Zoonekynd [mailto:[hidden email]]
Sent: Mon 1/30/2006 6:48 PM
To: [hidden email]
Cc: [hidden email]; Kort, Eric; [hidden email]; Thomas Kaliwe
Subject: Re: [R] Image Processing packages
 
A couple of years ago, I was using R as a first step before
implementing image analysis algorithms on a portable biochip
reader. Here is the code I had written at the time, should
someone find it useful (it mainly contains "morphological
operations"):
  http://zoonek2.free.fr/UNIX/48_R/morphology.R

There are a few examples (commented in French) at the end of
  http://zoonek.free.fr/Ecrits/2004_BioRet.pdf.bz2

The code of those examples:
  http://zoonek2.free.fr/UNIX/48_R/Rapport_final_morphologie.Rnw

-- Vincent

This email message, including any attachments, is for the so...{{dropped}}

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