How can I access to the whole stack?

[Juanjo Vega]

Hello,

I'm trying to process an entire stack, but I'm having some problems.

I wrote the code below in order to understand how to access to each one
of the stack slices. The idea is to copy the whole stack into a matrix
where each row is a slice and columns store the array of pixels for that
slice.

The code is very simple, but there's a problem is with "getProcessor()".
It doesn't work and I don't know what I'm doing wrong, or if there is
another way to get the slice without this method.

        ImagePlus imgSource;

        ...

        short inPixels[][] = new short[imgSource.getStack().getSize()][];
        for (int stack = 0; stack < inPixels.length; stack++) {
            IJ.write(" *** Stack : " + stack + " / " +
imgSource.getStack().getSize());
            inPixels[stack] = (short[])
imgSource.getStack().getProcessor(stack).convertToShort(true).getPixels();
        }

I also tried to look at:
http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Duplicater.java

Sincerelly,

Juanjo Vega.

--
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.uam.es

[phone]


"Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes.

[Fabrice Senger]

Juanjo Vega a écrit :

> Hello,
>
> I'm trying to process an entire stack, but I'm having some problems.
>
> I wrote the code below in order to understand how to access to each
> one of the stack slices. The idea is to copy the whole stack into a
> matrix where each row is a slice and columns store the array of pixels
> for that slice.
>
> The code is very simple, but there's a problem is with
> "getProcessor()". It doesn't work and I don't know what I'm doing
> wrong, or if there is another way to get the slice without this method.
>
>        ImagePlus imgSource;
>
>        ...
>
>        short inPixels[][] = new short[imgSource.getStack().getSize()][];
>        for (int stack = 0; stack < inPixels.length; stack++) {
>            IJ.write(" *** Stack : " + stack + " / " +
> imgSource.getStack().getSize());
>            inPixels[stack] = (short[])
> imgSource.getStack().getProcessor(stack).convertToShort(true).getPixels();
>
>        }
>
> I also tried to look at:
> http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Duplicater.java
>
> Sincerelly,
>
> Juanjo Vega.
>

... [show rest of quote]

Hi,

this might sound simplistic but, you can save your stack to a folder as
an image sequence, next you can process each image in that folder. Thus
you will access the information for each slice in the original stack...

Fabrice.

--
Senger Fabrice

[Juanjo Vega]

Hi,

Storing it to a file is not very useful. I need to perform some affine
transforms to the image so, after transforming each point, I get the new
one for each slice. That's because I need to have all the slices loaded
at the same time.

Thanks in anyway for the idea.

Sincerelly,

Juanjo.

Senger Fabrice escribió:

> Juanjo Vega a écrit :
>> Hello,
>>
>> I'm trying to process an entire stack, but I'm having some problems.
>>
>> I wrote the code below in order to understand how to access to each
>> one of the stack slices. The idea is to copy the whole stack into a
>> matrix where each row is a slice and columns store the array of
>> pixels for that slice.
>>
>> The code is very simple, but there's a problem is with
>> "getProcessor()". It doesn't work and I don't know what I'm doing
>> wrong, or if there is another way to get the slice without this method.
>>
>>        ImagePlus imgSource;
>>
>>        ...
>>
>>        short inPixels[][] = new short[imgSource.getStack().getSize()][];
>>        for (int stack = 0; stack < inPixels.length; stack++) {
>>            IJ.write(" *** Stack : " + stack + " / " +
>> imgSource.getStack().getSize());
>>            inPixels[stack] = (short[])
>> imgSource.getStack().getProcessor(stack).convertToShort(true).getPixels();
>>
>>        }
>>
>> I also tried to look at:
>> http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Duplicater.java
>>
>> Sincerelly,
>>
>> Juanjo Vega.
>>
> Hi,
>
> this might sound simplistic but, you can save your stack to a folder
> as an image sequence, next you can process each image in that folder.
> Thus you will access the information for each slice in the original
> stack...
>
> Fabrice.
>

... [show rest of quote]

--
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.uam.es

[phone]


"Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes.

[Du, Guanghua]

Hello, Juanjo,
I am also not very sure,  probably you should seperate   A.B.C.D to
(((A).B).C).D,


try it.


Juanjo Vega schrieb:

> Hi,
>
> Storing it to a file is not very useful. I need to perform some affine
> transforms to the image so, after transforming each point, I get the new
> one for each slice. That's because I need to have all the slices loaded
> at the same time.
>
> Thanks in anyway for the idea.
>
> Sincerelly,
>
> Juanjo.
>
> Senger Fabrice escribió:
>> Juanjo Vega a écrit :
>>> Hello,
>>>
>>> I'm trying to process an entire stack, but I'm having some problems.
>>>
>>> I wrote the code below in order to understand how to access to each
>>> one of the stack slices. The idea is to copy the whole stack into a
>>> matrix where each row is a slice and columns store the array of
>>> pixels for that slice.
>>>
>>> The code is very simple, but there's a problem is with
>>> "getProcessor()". It doesn't work and I don't know what I'm doing
>>> wrong, or if there is another way to get the slice without this method.
>>>
>>>        ImagePlus imgSource;
>>>
>>>        ...
>>>
>>>        short inPixels[][] = new short[imgSource.getStack().getSize()][];
>>>        for (int stack = 0; stack < inPixels.length; stack++) {
>>>            IJ.write(" *** Stack : " + stack + " / " +
>>> imgSource.getStack().getSize());
>>>            inPixels[stack] = (short[])
>>> imgSource.getStack().getProcessor(stack).convertToShort(true).getPixels();
>>>
>>>        }
>>>
>>> I also tried to look at:
>>> http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Duplicater.java
>>>
>>> Sincerelly,
>>>
>>> Juanjo Vega.
>>>
>> Hi,
>>
>> this might sound simplistic but, you can save your stack to a folder
>> as an image sequence, next you can process each image in that folder.
>> Thus you will access the information for each slice in the original
>> stack...
>>
>> Fabrice.
>>
>

... [show rest of quote]

--
best wishes!
**************************************
Guanghua Du, PhD
James-Franck Str. 1
Physik Dept, E12, TUM
85748, Garching b. Muenchen
Germany

Tel:[phone]
E-mail: [hidden email]
**************************************

[Gabriel Lapointe]

Hello Juanjo,
This is part of a small plugin where I created a 3D array. Pixels get
mapped in a Array[z][x][y] format. I hope it help.
Gabriel Lapointe

public void run(ImageProcessor orig)
    {
        int w = orig.getWidth();
        int h = orig.getHeight();
        int z = stack.getSize();
        int [][][] Aori = new int[z][w][h];
        for (int s = 1; s <= z; s++)
        {
            imp.setSlice(s);
            Aori[s-1]=orig.getIntArray();
        }
        CleanB(Aori, 0, 255, w, h, z);
        CleanW(Aori, 255, 0, w, h, z);
        CleanE(Aori, 255, 0, w, h, z);
        for (int s = 1; s <= z; s++)
        {
            imp.setSlice(s);
            orig.setIntArray(Aori[s-1]);
        }
    }  



Juanjo Vega wrote:

> Hello,
>
> I'm trying to process an entire stack, but I'm having some problems.
>
> I wrote the code below in order to understand how to access to each
> one of the stack slices. The idea is to copy the whole stack into a
> matrix where each row is a slice and columns store the array of pixels
> for that slice.
>
> The code is very simple, but there's a problem is with
> "getProcessor()". It doesn't work and I don't know what I'm doing
> wrong, or if there is another way to get the slice without this method.
>
>        ImagePlus imgSource;
>
>        ...
>
>        short inPixels[][] = new short[imgSource.getStack().getSize()][];
>        for (int stack = 0; stack < inPixels.length; stack++) {
>            IJ.write(" *** Stack : " + stack + " / " +
> imgSource.getStack().getSize());
>            inPixels[stack] = (short[])
> imgSource.getStack().getProcessor(stack).convertToShort(true).getPixels();
>
>        }
>
> I also tried to look at:
> http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Duplicater.java
>
> Sincerelly,
>
> Juanjo Vega.
>

... [show rest of quote]

[Michael Schmid]

Hi Juanjo,

one not so intuitive point that you seem to have missed:

Stack slices are not numbered 0...(n-1) but 1...n.

So it should be
   ...getProcessor(stack+1)...

(for whatever reason you name the silces 'stack', not 'slice' - this
obfuscates the code somewhat)

Michael

_________________________________________________________

On Tue, July 7, 2009 14:30, Juanjo Vega wrote:

> Hello,
>
> I'm trying to process an entire stack, but I'm having some problems.
>
> I wrote the code below in order to understand how to access to each one
> of the stack slices. The idea is to copy the whole stack into a matrix
> where each row is a slice and columns store the array of pixels for that
> slice.
>
> The code is very simple, but there's a problem is with "getProcessor()".
> It doesn't work and I don't know what I'm doing wrong, or if there is
> another way to get the slice without this method.
>
>         ImagePlus imgSource;
>
>         ...
>
>         short inPixels[][] = new short[imgSource.getStack().getSize()][];
>         for (int stack = 0; stack < inPixels.length; stack++) {
>             IJ.write(" *** Stack : " + stack + " / " +
> imgSource.getStack().getSize());
>             inPixels[stack] = (short[])
> imgSource.getStack().getProcessor(stack).convertToShort(true).getPixels();
>         }
>
> I also tried to look at:
> http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Duplicater.java
>
> Sincerelly,
>
> Juanjo Vega.
>
> --
> Juanjo Vega ([hidden email])
>
> Unidad de Biocomputación. Laboratorio B-13.
> Centro Nacional de Biotecnología. CNB-CSIC.
> C\ Darwin, 3. Campus de Cantoblanco.
> Universidad Autónoma de Madrid.
> 28049, Madrid, Spain.
>
> http://www.cnb.csic.es
> http://www.biocomp.cnb.uam.es
>
> [phone]
>
>
> "Las mejores almas son capaces de los mayores vicios como de las mayores
> virtudes, y aquellos que caminan despacio por el camino recto pueden
> llegar más lejos que los que corren pero se apartan de él." - Discurso del
> Método, René Descartes.
>

... [show rest of quote]

[Juanjo Vega]

Your plugin looks nice. Is easier to access data in that way.

But finally I was able to manage with the slices :)

Thank you!

Juanjo

Gabriel Lapointe escribió:

> Hello Juanjo,
> This is part of a small plugin where I created a 3D array. Pixels get
> mapped in a Array[z][x][y] format. I hope it help.
> Gabriel Lapointe
>
> public void run(ImageProcessor orig)
>     {
>         int w = orig.getWidth();
>         int h = orig.getHeight();
>         int z = stack.getSize();
>         int [][][] Aori = new int[z][w][h];
>         for (int s = 1; s <= z; s++)
>         {
>             imp.setSlice(s);
>             Aori[s-1]=orig.getIntArray();
>         }
>         CleanB(Aori, 0, 255, w, h, z);
>         CleanW(Aori, 255, 0, w, h, z);
>         CleanE(Aori, 255, 0, w, h, z);
>         for (int s = 1; s <= z; s++)
>         {
>             imp.setSlice(s);
>             orig.setIntArray(Aori[s-1]);
>         }
>     }  
>
>
>
> Juanjo Vega wrote:
>  
>> Hello,
>>
>> I'm trying to process an entire stack, but I'm having some problems.
>>
>> I wrote the code below in order to understand how to access to each
>> one of the stack slices. The idea is to copy the whole stack into a
>> matrix where each row is a slice and columns store the array of pixels
>> for that slice.
>>
>> The code is very simple, but there's a problem is with
>> "getProcessor()". It doesn't work and I don't know what I'm doing
>> wrong, or if there is another way to get the slice without this method.
>>
>>        ImagePlus imgSource;
>>
>>        ...
>>
>>        short inPixels[][] = new short[imgSource.getStack().getSize()][];
>>        for (int stack = 0; stack < inPixels.length; stack++) {
>>            IJ.write(" *** Stack : " + stack + " / " +
>> imgSource.getStack().getSize());
>>            inPixels[stack] = (short[])
>> imgSource.getStack().getProcessor(stack).convertToShort(true).getPixels();
>>
>>        }
>>
>> I also tried to look at:
>> http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Duplicater.java
>>
>> Sincerelly,
>>
>> Juanjo Vega.
>>
>>    
>
>  

... [show rest of quote]

--
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.uam.es

[phone]


"Las mejores almas son capaces de los mayores vicios como de las mayores virtudes, y aquellos que caminan despacio por el camino recto pueden llegar más lejos que los que corren pero se apartan de él." - Discurso del Método, René Descartes.