save 16 bit tif

[alessandra griffa]

Good morning!

I have an ImagePlus stack ('impoutstack'), 32 bit, and I would like to save
it as a 16 bit tif stack.
I did this:

*ImageProcessor ip = impoutstack.getProcessor();
impoutstack.setProcessor(null, ip.convertToShort(true)); // conversion
impoutstack.setCalibration(impoutstack.getCalibration()); // update
calibration
FileSaver saverstack = new FileSaver(impoutstack);*
*saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*

but at run time I get the exception

*java.lang.ClassCastExceprion at ij.io.ImageWriter.write16BitStack*

Does anyone know how to easily save as 16 bit tif stack?

Thanks a lot,
Alessandra

[Thomas Boudier]

Hi Alessandra,

Why not use the imageConverter class :

import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.filter.*;

public class Filter_Plugin implements PlugInFilter {
        ImagePlus imp;

        public int setup(String arg, ImagePlus imp) {
                this.imp = imp;
                return DOES_ALL;
        }

        public void run(ImageProcessor ip) {
                ImageConverter c=new ImageConverter(imp);
                c.convertToGray16();
        }

}

Do not forget to adjust the contrast before converting to 16 bits.

Thomas



>
> I have an ImagePlus stack ('impoutstack'), 32 bit, and I would like to save
> it as a 16 bit tif stack.
> I did this:
>
> *ImageProcessor ip = impoutstack.getProcessor();
> impoutstack.setProcessor(null, ip.convertToShort(true)); // conversion
impoutstack.setCalibration(impoutstack.getCalibration()); // update
calibration

> FileSaver saverstack = new FileSaver(impoutstack);*
> *saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*
>
> but at run time I get the exception
>
> *java.lang.ClassCastExceprion at ij.io.ImageWriter.write16BitStack*
>
> Does anyone know how to easily save as 16 bit tif stack?
>
> Thanks a lot,
> Alessandra
>
>

[alessandra griffa]

I tried this too, but the problem is at the point of the instruction
*saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*
I get the image converted, but I am not able to save it?
Am i missing something?
Is there another class to save?

2008/6/6 Thomas Boudier <[hidden email]>:

> Hi Alessandra,
>
> Why not use the imageConverter class :
>
> import ij.*;
> import ij.process.*;
> import ij.gui.*;
> import java.awt.*;
> import ij.plugin.filter.*;
>
> public class Filter_Plugin implements PlugInFilter {
>        ImagePlus imp;
>
>        public int setup(String arg, ImagePlus imp) {
>                this.imp = imp;
>                return DOES_ALL;
>        }
>
>        public void run(ImageProcessor ip) {
>                ImageConverter c=new ImageConverter(imp);
>                c.convertToGray16();
>        }
>
> }
>
> Do not forget to adjust the contrast before converting to 16 bits.
>
> Thomas
>
>
>
> >
> > I have an ImagePlus stack ('impoutstack'), 32 bit, and I would like to
> save
> > it as a 16 bit tif stack.
> > I did this:
> >
> > *ImageProcessor ip = impoutstack.getProcessor();
> > impoutstack.setProcessor(null, ip.convertToShort(true)); // conversion
> impoutstack.setCalibration(impoutstack.getCalibration()); // update
> calibration
> > FileSaver saverstack = new FileSaver(impoutstack);*
> > *saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*
> >
> > but at run time I get the exception
> >
> > *java.lang.ClassCastExceprion at ij.io.ImageWriter.write16BitStack*
> >
> > Does anyone know how to easily save as 16 bit tif stack?
> >
> > Thanks a lot,
> > Alessandra
> >
> >
>

[Thomas Boudier]

Hi,

Use StackConverter instead of ImageConverter :

StackConverter c = new StackConverter(imp);
c.convertToGray16();

Thomas


alessandra griffa a écrit :

> I tried this too, but the problem is at the point of the instruction
> *saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*
> I get the image converted, but I am not able to save it?
> Am i missing something?
> Is there another class to save?
>
> 2008/6/6 Thomas Boudier <[hidden email]>:
>
>> Hi Alessandra,
>>
>> Why not use the imageConverter class :
>>
>> import ij.*;
>> import ij.process.*;
>> import ij.gui.*;
>> import java.awt.*;
>> import ij.plugin.filter.*;
>>
>> public class Filter_Plugin implements PlugInFilter {
>>        ImagePlus imp;
>>
>>        public int setup(String arg, ImagePlus imp) {
>>                this.imp = imp;
>>                return DOES_ALL;
>>        }
>>
>>        public void run(ImageProcessor ip) {
>>                ImageConverter c=new ImageConverter(imp);
>>                c.convertToGray16();
>>        }
>>
>> }
>>
>> Do not forget to adjust the contrast before converting to 16 bits.
>>
>> Thomas
>>
>>
>>
>>> I have an ImagePlus stack ('impoutstack'), 32 bit, and I would like to
>> save
>>> it as a 16 bit tif stack.
>>> I did this:
>>>
>>> *ImageProcessor ip = impoutstack.getProcessor();
>>> impoutstack.setProcessor(null, ip.convertToShort(true)); // conversion
>> impoutstack.setCalibration(impoutstack.getCalibration()); // update
>> calibration
>>> FileSaver saverstack = new FileSaver(impoutstack);*
>>> *saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*
>>>
>>> but at run time I get the exception
>>>
>>> *java.lang.ClassCastExceprion at ij.io.ImageWriter.write16BitStack*
>>>
>>> Does anyone know how to easily save as 16 bit tif stack?
>>>
>>> Thanks a lot,
>>> Alessandra
>>>
>>>
>
>

--
/*****************************************************/
     Thomas Boudier, MCU Université Paris 6,
     UMR 7101 / IFR 83. Bat A 328, Jussieu.
     Tel : [phone]  Fax : [phone]
/****************************************************/

[alessandra griffa]

Hi!

I tried with that, and also I tried to use IJ.save instead of
FileSaver.saveAsTiffStack, but I always get the exception:

java.lang.ClassCastException: [F cannot be cast to [S
 at ij.io.ImageWriter.write16BitStack(ImageWriter.java:78)
 at ij.io.ImageWriter.write(ImageWriter.java:213)
 at ij.io.TiffEncoder.write(TiffEncoder.java:116)
 at ij.io.FileSaver.saveAsTiffStack(FileSaver.java:109)
 at ij.io.FileSaver.saveAsTiff(FileSaver.java:69)
 at ij.plugin.filter.Writer.run(Writer.java:20)
 at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:243)
 at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
 at ij.IJ.runPlugIn(IJ.java:133)
 at ij.Executer.runCommand(Executer.java:95)
 at ij.Executer.run(Executer.java:49)
 at ij.IJ.run(IJ.java:230)
 at ij.IJ.saveAs(IJ.java:1162)
 at ij.IJ.save(IJ.java:1095)
 at Detect_.run(Detect_.java:447)
 at java.lang.Thread.run(Unknown Source)

Alessandra



2008/6/6 Thomas Boudier <[hidden email]>:

> Hi,
>
> Use StackConverter instead of ImageConverter :
>
> StackConverter c = new StackConverter(imp);
> c.convertToGray16();
>
> Thomas
>
>
> alessandra griffa a écrit :
>
> I tried this too, but the problem is at the point of the instruction
>> *saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*
>> I get the image converted, but I am not able to save it?
>> Am i missing something?
>> Is there another class to save?
>>
>> 2008/6/6 Thomas Boudier <[hidden email]>:
>>
>> Hi Alessandra,
>>>
>>> Why not use the imageConverter class :
>>>
>>> import ij.*;
>>> import ij.process.*;
>>> import ij.gui.*;
>>> import java.awt.*;
>>> import ij.plugin.filter.*;
>>>
>>> public class Filter_Plugin implements PlugInFilter {
>>>       ImagePlus imp;
>>>
>>>       public int setup(String arg, ImagePlus imp) {
>>>               this.imp = imp;
>>>               return DOES_ALL;
>>>       }
>>>
>>>       public void run(ImageProcessor ip) {
>>>               ImageConverter c=new ImageConverter(imp);
>>>               c.convertToGray16();
>>>       }
>>>
>>> }
>>>
>>> Do not forget to adjust the contrast before converting to 16 bits.
>>>
>>> Thomas
>>>
>>>
>>>
>>> I have an ImagePlus stack ('impoutstack'), 32 bit, and I would like to
>>>>
>>> save
>>>
>>>> it as a 16 bit tif stack.
>>>> I did this:
>>>>
>>>> *ImageProcessor ip = impoutstack.getProcessor();
>>>> impoutstack.setProcessor(null, ip.convertToShort(true)); // conversion
>>>>
>>> impoutstack.setCalibration(impoutstack.getCalibration()); // update
>>> calibration
>>>
>>>> FileSaver saverstack = new FileSaver(impoutstack);*
>>>> *saverstack.saveAsTiffStack(pathout + "/" + filename + ".tif");*
>>>>
>>>> but at run time I get the exception
>>>>
>>>> *java.lang.ClassCastExceprion at ij.io.ImageWriter.write16BitStack*
>>>>
>>>> Does anyone know how to easily save as 16 bit tif stack?
>>>>
>>>> Thanks a lot,
>>>> Alessandra
>>>>
>>>>
>>>>
>>
>>
> --
> /*****************************************************/
>    Thomas Boudier, MCU Université Paris 6,
>    UMR 7101 / IFR 83. Bat A 328, Jussieu.
>    Tel : [phone]  Fax : [phone]
> /****************************************************/
>