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PIKAL Petr | 21 Feb 2013 16:26
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package ReadImages

Dear all

I prepared some image processing routine which depended on package ReadImages. Basically I imported
image to R, changed rgb to grayscale, normalised an image made some selections and changed to image by imagematrix.

Recently I learned that this package was removed from CRAN and can not be used in R 3.0.0.

What options I have now to import image to R, change it to grayscale, make some computation or selection,
change it back to image and plot for visual inspection.

Thanks
Petr
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Greg Snow | 22 Feb 2013 06:44
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Re: package ReadImages

Some possibilities:  The EBImage package on Bioconductor; the jpeg and png
packages read jpeg and png images.

On Thu, Feb 21, 2013 at 8:26 AM, PIKAL Petr <petr.pikal <at> precheza.cz> wrote:

> Dear all
>
> I prepared some image processing routine which depended on package
> ReadImages. Basically I imported image to R, changed rgb to grayscale,
> normalised an image made some selections and changed to image by
> imagematrix.
>
> Recently I learned that this package was removed from CRAN and can not be
> used in R 3.0.0.
>
> What options I have now to import image to R, change it to grayscale, make
> some computation or selection, change it back to image and plot for visual
> inspection.
>
> Thanks
> Petr
>
> ______________________________________________
> R-help <at> r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
(Continue reading)

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Prof Brian Ripley | 22 Feb 2013 08:17
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Re: package ReadImages

On 22/02/2013 05:44, Greg Snow wrote:
> Some possibilities:  The EBImage package on Bioconductor; the jpeg and png
> packages read jpeg and png images.

Almost everyone using ReadImages was using it to read TIFF images, which 
package tiff can do.  See the 'Data Import/Export Manual',
http://cran.r-project.org/doc/manuals/r-devel/R-data.html#Image-files .

> On Thu, Feb 21, 2013 at 8:26 AM, PIKAL Petr <petr.pikal <at> precheza.cz> wrote:
>
>> Dear all
>>
>> I prepared some image processing routine which depended on package
>> ReadImages. Basically I imported image to R, changed rgb to grayscale,
>> normalised an image made some selections and changed to image by
>> imagematrix.
>>
>> Recently I learned that this package was removed from CRAN and can not be
>> used in R 3.0.0.

It was archived, already being orphaned.  When R 3.0.0 is released you 
can see if it works there: I expect it to.

>>
>> What options I have now to import image to R, change it to grayscale, make
>> some computation or selection, change it back to image and plot for visual
>> inspection.
>>
>> Thanks
>> Petr
(Continue reading)

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PIKAL Petr | 22 Feb 2013 09:36
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Re: package ReadImages

Hi

> -----Original Message-----
> From: r-help-bounces <at> r-project.org [mailto:r-help-bounces <at> r-
> project.org] On Behalf Of Prof Brian Ripley
> Sent: Friday, February 22, 2013 8:17 AM
> To: r-help <at> r-project.org
> Subject: Re: [R] package ReadImages
> 
> On 22/02/2013 05:44, Greg Snow wrote:
> > Some possibilities:  The EBImage package on Bioconductor; the jpeg
> and
> > png packages read jpeg and png images.
> 
> Almost everyone using ReadImages was using it to read TIFF images,
> which package tiff can do.  See the 'Data Import/Export Manual',
> http://cran.r-project.org/doc/manuals/r-devel/R-data.html#Image-files .

Thanks, I will try.

> 
> > On Thu, Feb 21, 2013 at 8:26 AM, PIKAL Petr <petr.pikal <at> precheza.cz>
> wrote:
> >
> >> Dear all
> >>
> >> I prepared some image processing routine which depended on package
> >> ReadImages. Basically I imported image to R, changed rgb to
> >> grayscale, normalised an image made some selections and changed to
> >> image by imagematrix.
(Continue reading)

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PIKAL Petr | 22 Feb 2013 09:57
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Re: package ReadImages

Thanks.

I tried EBImage several years ago for another problem, but Bioconductor packages have some difficulties
to install in our network/firewall environment and I am not in a position to change it. It seems to me also an
overkill for such simple task.

jpeg and png seems to me a bit too much simple, without direct possibility to transform from rgb to grayscale
and normalisation.

Anyway, I will give it a try.

Petr

From: Greg Snow [mailto:538280 <at> gmail.com]
Sent: Friday, February 22, 2013 6:45 AM
To: PIKAL Petr
Cc: r-help
Subject: Re: [R] package ReadImages

Some possibilities:  The EBImage package on Bioconductor; the jpeg and png packages read jpeg and png images.

On Thu, Feb 21, 2013 at 8:26 AM, PIKAL Petr <petr.pikal <at> precheza.cz<mailto:petr.pikal <at> precheza.cz>> wrote:
Dear all

I prepared some image processing routine which depended on package ReadImages. Basically I imported
image to R, changed rgb to grayscale, normalised an image made some selections and changed to image by imagematrix.

Recently I learned that this package was removed from CRAN and can not be used in R 3.0.0.

What options I have now to import image to R, change it to grayscale, make some computation or selection,
(Continue reading)

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Greg Snow | 22 Feb 2013 17:53
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Re: package ReadImages

For some of the fancier transforms it may be easier to use an outside tool
such as Imagemagick which will do a lot of these things.  There is even a
C++ interface to imagemagick that may work nicely with packages like Rcpp
if you don't want to use an intermediate file.

But jobs like converting to grayscale can be very simple using R itself.
 Many of the functions that read in images store them as 3 dimensional
arrays and you would just need an apply command to change the 3 values for
each pixel to a grayscale value (see col2gray in the TeachingDemos package
for one way to do this, though loading in the whole package is probably
overkill for something this simple).

On Fri, Feb 22, 2013 at 1:57 AM, PIKAL Petr <petr.pikal <at> precheza.cz> wrote:

>  Thanks. ****
>
> ** **
>
> I tried EBImage several years ago for another problem, but Bioconductor
> packages have some difficulties to install in our network/firewall
> environment and I am not in a position to change it. It seems to me also an
> overkill for such simple task.****
>
> ** **
>
> jpeg and png seems to me a bit too much simple, without direct possibility
> to transform from rgb to grayscale and normalisation.****
>
> ** **
>
(Continue reading)

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PIKAL Petr | 25 Feb 2013 07:50
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Re: package ReadImages

Thanks to all.

For the time being due to urgency I will stay with a copy of R 2.15.x with which ReadImages works. It is
simplest solution which I can adopt immediately without much additional effort.
However I will need to elaborate another solution in future, for which I will consider various suggested options.
Regards
Petr

From: Greg Snow [mailto:538280 <at> gmail.com]
Sent: Friday, February 22, 2013 5:54 PM
To: PIKAL Petr
Cc: r-help
Subject: Re: [R] package ReadImages

For some of the fancier transforms it may be easier to use an outside tool such as Imagemagick which will do a
lot of these things.  There is even a C++ interface to imagemagick that may work nicely with packages like
Rcpp if you don't want to use an intermediate file.

But jobs like converting to grayscale can be very simple using R itself.  Many of the functions that read in
images store them as 3 dimensional arrays and you would just need an apply command to change the 3 values for
each pixel to a grayscale value (see col2gray in the TeachingDemos package for one way to do this, though
loading in the whole package is probably overkill for something this simple).

On Fri, Feb 22, 2013 at 1:57 AM, PIKAL Petr <petr.pikal <at> precheza.cz<mailto:petr.pikal <at> precheza.cz>> wrote:
Thanks.

I tried EBImage several years ago for another problem, but Bioconductor packages have some difficulties
to install in our network/firewall environment and I am not in a position to change it. It seems to me also an
overkill for such simple task.
(Continue reading)

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Uwe Ligges | 25 Feb 2013 13:49
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Re: package ReadImages

Note that ReadImages has been orphaned and is under the BSD license, so 
you can become maintainer and re-establish the package on CRAN.

Best,
Uwe Ligges

On 25.02.2013 07:50, PIKAL Petr wrote:
> Thanks to all.
>
> For the time being due to urgency I will stay with a copy of R 2.15.x with which ReadImages works. It is
simplest solution which I can adopt immediately without much additional effort.
> However I will need to elaborate another solution in future, for which I will consider various suggested options.
> Regards
> Petr
>
> From: Greg Snow [mailto:538280 <at> gmail.com]
> Sent: Friday, February 22, 2013 5:54 PM
> To: PIKAL Petr
> Cc: r-help
> Subject: Re: [R] package ReadImages
>
> For some of the fancier transforms it may be easier to use an outside tool such as Imagemagick which will do a
lot of these things.  There is even a C++ interface to imagemagick that may work nicely with packages like
Rcpp if you don't want to use an intermediate file.
>
> But jobs like converting to grayscale can be very simple using R itself.  Many of the functions that read in
images store them as 3 dimensional arrays and you would just need an apply command to change the 3 values for
each pixel to a grayscale value (see col2gray in the TeachingDemos package for one way to do this, though
loading in the whole package is probably overkill for something this simple).
>
(Continue reading)

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John | 23 Feb 2013 06:49

Re: package ReadImages

Petr,

Another program that may be useful is ImageJ which has a great many
useful analytic plugins.  The program is written in Java and it
supports a good many different image file formats.  You should also be
able to use Octave to normalize an image.

JWDougherty
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