Computational photography with ImageJ

[Benedito Benes Timoteo]

Good afternoon !

 I am trying to do computational photography and I wonder if I can use libtiff or LibTiff.NET in ImageJ.

 If yes, is it possible for you to give some kind of roadmap?

I already have tried various products ( Octave, FreeMat and Scilab) and couldn´t achieve what I want.

What I´m trying to do is this:

1 - open a .tif image, get rid of all tags ( saving them for possible further use ) and produce a matrice like:

                                             [(RGB)1,1 (RGB)1,2 ...............................(RGB)1,m
                                              (RGB)2,1 (RGB)2,2 ...............................(RGB)2,m
                                                                           ...............................
                                                                           ...............................
                                              (RGB)n,1 (RGB)n,2 ...............................(RGB)n,m]

    This requires some libtiff ( the only solution that I know of ).

2 - I will, then, use functions on this matrice geting another n x m matrice. If not in ImageJ, I can do this in Octave or

 Scilab.

3 - Finally I will write another .tif file. If  1-  is possible in ImageJ than this phase will most probably be possible too.

I have a Windows 7 64-bit machine. I will send whatever additional information is necessary if you feel that my idea is

 viable.

I´m waiting for your kind reply  and am

Sincerely yours

Benedito Benes Timoteo
       

[David Gene Morgan]

Benedito,

        I don't know how to connect libtiff to imageJ, but I can suggest that
you try using the statistical software package called R instead.  There
is great documentation for it, starting in places like:

                http://cran.r-project.org/

and I have used their image reading/writing tools to manipulate files of
various sorts.  I don't know that this will solve your problem, but it
is worth examining.

On 05/24/2012 11:14 AM, Benedito Benes Timoteo wrote:

> Good afternoon !
>
>   I am trying to do computational photography and I wonder if I can use libtiff or LibTiff.NET in ImageJ.
>
>   If yes, is it possible for you to give some kind of roadmap?
>
> I already have tried various products ( Octave, FreeMat and Scilab) and couldn´t achieve what I want.
>
> What I´m trying to do is this:
>
> 1 - open a .tif image, get rid of all tags ( saving them for possible further use ) and produce a matrice like:
>
>                                               [(RGB)1,1 (RGB)1,2 ...............................(RGB)1,m
>                                                (RGB)2,1 (RGB)2,2 ...............................(RGB)2,m
>                                                                             ...............................
>                                                                             ...............................
>                                                (RGB)n,1 (RGB)n,2 ...............................(RGB)n,m]
>
>      This requires some libtiff ( the only solution that I know of ).
>
> 2 - I will, then, use functions on this matrice geting another n x m matrice. If not in ImageJ, I can do this in Octave or
>
>   Scilab.
>
> 3 - Finally I will write another .tif file. If  1-  is possible in ImageJ than this phase will most probably be possible too.
>
> I have a Windows 7 64-bit machine. I will send whatever additional information is necessary if you feel that my idea is
>
>   viable.
>
> I´m waiting for your kind reply  and am
>
> Sincerely yours
>
> Benedito Benes Timoteo
>

--
                  David Gene Morgan
                   cryoEM Facility
                   320C Simon Hall
            Indiana University Bloomington
                812 856 1457 (office)
                812 856 3221 (EM lab)
             http://bio.indiana.edu/~cryo

[Jim Passmore-2]

Benedito,

On Thu, May 24, 2012 at 11:14 AM, Benedito Benes Timoteo
<[hidden email]>wrote:

>  I am trying to do computational photography and I wonder if I can use
> libtiff or LibTiff.NET in ImageJ.
>
Not sure you would need to explicitly use libtiff, as ImageJ already has
capability of reading & writing many tif variations.


> I already have tried various products ( Octave, FreeMat and Scilab) and
> couldn´t achieve what I want.
>
If you're looking at different options, I'd look at python.


>
> What I´m trying to do is this:
> 1 - open a .tif image, get rid of all tags ( saving them for possible
> further use ) and produce a matrice like:
>
As mentioned above, ImageJ can already read/write tif files out of the
box.    If trying Python, the Python Imaging Library (PIL) has support for
several image formats, including tif.  So either package would likely be
able to handle this.

2 - I will, then, use functions on this matrice geting another n x m
> matrice. If not in ImageJ, I can do this in Octave or Scilab.
>
ImageJ supports writing your own plugins in Java, so you should be able to
do anything you want with the data once the file is read.  I'm sure there
are Java libraries for matrix manipulation.  On the python front, the Numpy
and Scipy projects (www.scipy.org) add FANTASTIC support for matrix
manipulation to python.  I'm working on a project to do some data
manipulation & measurement using python in this way.  (Now if I could just
get the time to spend on the project!)


> 3 - Finally I will write another .tif file. If  1-  is possible in ImageJ
> than this phase will most probably be possible too.
>
See #1 above.

If you're interested in python, I recommend the Python(x,y) (
www.pythonxy.com) package that has been put together specifically for
scientific applications.  It packages a python install with Numpy, Scipy,
PIL, and many other libraries of interest to scientific programming, as
well as tools to build GUI applications.  Included is Spyder, which can be
used as a nice python code editor, but also has interactive features
similar to Matlab or Octave.  The nice thing about this package is all the
version dependencies have been taken care of--much easier than installing
python everything separately.

Good luck!


*Jim Passmore*
Research Associate
Sealed Air Corporation

[Marcel]

Hello,

i've implemented a R bridge in my application to transfer images (as different datatypes) easily from ImageJ to R and vice versa from R to ImageJ. In R you can apply all kind of functions to that data, transfer the image data back to ImageJ and finally store the data as e.g. a *.tiff file. In the Windows version the R application is bundled with the app so you don't need to install anything else.

You can find video tutorials here:

http://bio7.org/flash/imageDataTransfer.htm

and a blog entry about the R to ImageJ bridge:

http://bio7.org/?p=894

Maybee that works for you.

[Benedito Benes Timoteo]

Hello Jim
Thanks for your tip. As I have both apps I´ll certainlly try it and let you
know.

best regards

On Thu, May 24, 2012 at 2:41 PM, Bio7 <[hidden email]>wrote:

> Hello,
>
> i've implemented a R bridge in my  http://bio7.org application  to
> transfer
> images (as different datatypes) easily from ImageJ to R and vice versa from
> R to ImageJ. In R you can apply all kind of functions to that data,
> transfer
> the image data back to ImageJ and finally store the data as e.g. a *.tiff
> file. In the Windows version the R application is bundled with the app so
> you don't need to install anything else.
>
> You can find video tutorials here:
>
> http://bio7.org/flash/imageDataTransfer.htm
> http://bio7.org/flash/imageDataTransfer.htm
>
> and a blog entry about the R to ImageJ bridge:
>
> http://bio7.org/?p=894 http://bio7.org/?p=894
>
> Maybee that works for you.
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/Computational-photography-with-ImageJ-tp4998788p4998793.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>