Problem with setCalibration() and getCalibration

[Dawid Krzempek]

Hello,
I am writing some Imagej plugin and have few problems with value calibration.
I am not experienced in writing programs like this one, so the solution can be very simple.

I try to calibrate ImagePlus. There is my code (img1 is ImagePlus object)

                float [] param={146494f,3.55146f,2079.82f};
                float cTable[]=new float[65536];
                Calibration calibr=new Calibration();
                float a=param[0];
                float b=param[1];
                float c=param[2];
                for (int i=0;i<65536;i++){
                    float value=-b+a/(i-c);
                    if (value>10) cTable[i]=10;
                    else if (value<0) cTable[i]=0;
                    else cTable[i]=value;
                }
                calibr.setCTable(cTable,"Gy");
                System.out.println(calibr.calibrated());
                img1.setCalibration(calibr);;
                System.out.println(img1.getCalibration().calibrated());

The output then:

true
false

setCalibration() seems not working. Image is not calibrated after using this method. I was expected "true true" output Could somebody tell me, where is my mistake?
The goal of calibration is working on calibrated (Gy) values, not on signal values. Is there any other way to achieve it?
Thanks for your help
David

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Dawid Krzempek]

Thanks for your reply. Now I understand, but it's not the end of my
problems. :)

As you can see from my code, I try to calibrate image using values (table),
not by function - my function is different than any of available in ImageJ.

But when I calibrate like this, image after display it is not calibrated. I
use *calib *in setCalibration() or setGlobalCalibration() - both are not
working.
When Global calibration is using, there are some "tracks" of calibration.
For example, when I am trying to open another Image, I get:
"The calibration of this image conflicts with the current global
calibration...."
But in fact image is not calibrated. Information about pixel doesn't seem
like that:
x=0, y=10 value=650 (6500)
It seems like that:
x=0, y=10 value=6500
So I don't have any information about calibrated value.
I have no idea, what I am doing wrong.
Maybe the function is obligatory to make ImageProcessor calibration
possible?
Thanks in advance
David

2014-11-13 18:32 GMT+01:00 Michael Schmid <[hidden email]>:

> Hi Wayne, David,
>
> looks like an unintended behavior in Calibration, currently calibrated()
> only checks for a function, not for a table (line 283...):
>
>     /** Returns true if this image is density calibrated. */
>     public boolean calibrated() {
>         return function!=NONE;
>     }
>
>
> I think that it should be
> ...
>         return function!=NONE || cTable != null;
>
>
> Best regards,
>
> Michael
> ________________________________________________________________
> Michael Schmid                    email: [hidden email]
> Institut für Angewandte Physik, Technische Universität Wien
> Wiedner Hauptstr. 8-10/E134, A 1040 Wien, Austria
> Tel. [phone] or -13453, Fax [phone]
> ________________________________________________________________
>
> On Nov 13, 2014, at 18:10, Dawid Krzempek wrote:
>
> > Hello,
> > I am writing some Imagej plugin and have few problems with value
> calibration.
> > I am not experienced in writing programs like this one, so the solution
> can be very simple.
> >
> > I try to calibrate ImagePlus. There is my code (img1 is ImagePlus object)
> >
> >                float [] param={146494f,3.55146f,2079.82f};
> >                float cTable[]=new float[65536];
> >                Calibration calibr=new Calibration();
> >                float a=param[0];
> >                float b=param[1];
> >                float c=param[2];
> >                for (int i=0;i<65536;i++){
> >                    float value=-b+a/(i-c);
> >                    if (value>10) cTable[i]=10;
> >                    else if (value<0) cTable[i]=0;
> >                    else cTable[i]=value;
> >                }
> >                calibr.setCTable(cTable,"Gy");
> >                System.out.println(calibr.calibrated());
> >                img1.setCalibration(calibr);;
> >                System.out.println(img1.getCalibration().calibrated());
> >
> > The output then:
> >
> > true
> > false
> >
> > setCalibration() seems not working. Image is not calibrated after using
> this method. I was expected "true true" output Could somebody tell me,
> where is my mistake?
> > The goal of calibration is working on calibrated (Gy) values, not on
> signal values. Is there any other way to achieve it?
> > Thanks for your help
> > David
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi David,

to me it looks like you can use the built-in RODBARD function in your case anyhow:

RODBARD:  y = d + (a-d)/(1+(x/c)^b) = d + (a-d)*c^b / (c^b+x^b)

You have  y = -b + a/(x-c)

If I got it right, the Rodbard parameters are

b = 1
d = -your_b
c = -your_c
a - d = your_a / c

Nevertheless, if you see something like 'value=650 (6500)' in the status line, it means that your image is calibrated, the calibrated value is 650, the raw pixel value is 6500.

Michael
________________________________________________________________


On Nov 13, 2014, at 18:59, Dawid Krzempek wrote:

> Thanks for your reply. Now I understand, but it's not the end of my problems. :)
>
> As you can see from my code, I try to calibrate image using values (table), not by function - my function is different than any of available in ImageJ.
>
> But when I calibrate like this, image after display it is not calibrated. I use calib in setCalibration() or setGlobalCalibration() - both are not working.
> When Global calibration is using, there are some "tracks" of calibration. For example, when I am trying to open another Image, I get:
> "The calibration of this image conflicts with the current global calibration...."
> But in fact image is not calibrated. Information about pixel doesn't seem like that:
> x=0, y=10 value=650 (6500)
> It seems like that:
> x=0, y=10 value=6500
> So I don't have any information about calibrated value.
> I have no idea, what I am doing wrong.
> Maybe the function is obligatory to make ImageProcessor calibration possible?
> Thanks in advance
> David
>
> 2014-11-13 18:32 GMT+01:00 Michael Schmid <[hidden email]>:
> Hi Wayne, David,
>
> looks like an unintended behavior in Calibration, currently calibrated() only checks for a function, not for a table (line 283...):
>
>     /** Returns true if this image is density calibrated. */
>     public boolean calibrated() {
>         return function!=NONE;
>     }
>
>
> I think that it should be
> ...
>         return function!=NONE || cTable != null;
>
>
> Best regards,
>
> Michael
> ________________________________________________________________
> Michael Schmid                    email: [hidden email]
> Institut für Angewandte Physik, Technische Universität Wien
> Wiedner Hauptstr. 8-10/E134, A 1040 Wien, Austria
> Tel. [phone] or -13453, Fax [phone]
> ________________________________________________________________
>
> On Nov 13, 2014, at 18:10, Dawid Krzempek wrote:
>
> > Hello,
> > I am writing some Imagej plugin and have few problems with value calibration.
> > I am not experienced in writing programs like this one, so the solution can be very simple.
> >
> > I try to calibrate ImagePlus. There is my code (img1 is ImagePlus object)
> >
> >                float [] param={146494f,3.55146f,2079.82f};
> >                float cTable[]=new float[65536];
> >                Calibration calibr=new Calibration();
> >                float a=param[0];
> >                float b=param[1];
> >                float c=param[2];
> >                for (int i=0;i<65536;i++){
> >                    float value=-b+a/(i-c);
> >                    if (value>10) cTable[i]=10;
> >                    else if (value<0) cTable[i]=0;
> >                    else cTable[i]=value;
> >                }
> >                calibr.setCTable(cTable,"Gy");
> >                System.out.println(calibr.calibrated());
> >                img1.setCalibration(calibr);;
> >                System.out.println(img1.getCalibration().calibrated());
> >
> > The output then:
> >
> > true
> > false
> >
> > setCalibration() seems not working. Image is not calibrated after using this method. I was expected "true true" output Could somebody tell me, where is my mistake?
> > The goal of calibration is working on calibrated (Gy) values, not on signal values. Is there any other way to achieve it?
> > Thanks for your help
> > David
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Dawid Krzempek]

Yes, you're right. It will be very useful for me, so thank you.

But even when I use setFunction() and write analogous code:

*                float [] param={146494f,3.55146f,2079.82f};*
*                Calibration calibr=new Calibration();*
*                float a=param[0];*
*                float b=param[1];*
*                float c=param[2];*
*                double b0=1.0;                double c0=-c;
double d0=-b;                double a0=-d0+a/c0;                double []
coef={a0,b0,c0,d0};
calibr.setFunction(Calibration.RODBARD,coef,"Gy");
img.setCalibration(calibr);
System.out.println(calibr.calibrated());
System.out.println(img.getCalibration().calibrated());*

the output is still 'true false'. So there is no problem in calibration
method, but with setCalibration(). *calib* seems to be not associated with
img.

img.setGlobalCalibration(calib) is not working properly too. I still dont
see 'value=650 (6500)'.

I still have to calibrate from code level, not from GUI level, because via
GUI I can't enforce values of coefficients, ImageJ requires fitting.
Best regards
David

2014-11-13 19:36 GMT+01:00 Michael Schmid <[hidden email]>:

> Hi David,
>
> to me it looks like you can use the built-in RODBARD function in your case
> anyhow:
>
> RODBARD:  y = d + (a-d)/(1+(x/c)^b) = d + (a-d)*c^b / (c^b+x^b)
>
> You have  y = -b + a/(x-c)
>
> If I got it right, the Rodbard parameters are
>
> b = 1
> d = -your_b
> c = -your_c
> a - d = your_a / c
>
> Nevertheless, if you see something like 'value=650 (6500)' in the status
> line, it means that your image is calibrated, the calibrated value is 650,
> the raw pixel value is 6500.
>
> Michael
> ________________________________________________________________
>
>
> On Nov 13, 2014, at 18:59, Dawid Krzempek wrote:
>
> > Thanks for your reply. Now I understand, but it's not the end of my
> problems. :)
> >
> > As you can see from my code, I try to calibrate image using values
> (table), not by function - my function is different than any of available
> in ImageJ.
> >
> > But when I calibrate like this, image after display it is not
> calibrated. I use calib in setCalibration() or setGlobalCalibration() -
> both are not working.
> > When Global calibration is using, there are some "tracks" of
> calibration. For example, when I am trying to open another Image, I get:
> > "The calibration of this image conflicts with the current global
> calibration...."
> > But in fact image is not calibrated. Information about pixel doesn't
> seem like that:
> > x=0, y=10 value=650 (6500)
> > It seems like that:
> > x=0, y=10 value=6500
> > So I don't have any information about calibrated value.
> > I have no idea, what I am doing wrong.
> > Maybe the function is obligatory to make ImageProcessor calibration
> possible?
> > Thanks in advance
> > David
> >
> > 2014-11-13 18:32 GMT+01:00 Michael Schmid <[hidden email]>:
> > Hi Wayne, David,
> >
> > looks like an unintended behavior in Calibration, currently calibrated()
> only checks for a function, not for a table (line 283...):
> >
> >     /** Returns true if this image is density calibrated. */
> >     public boolean calibrated() {
> >         return function!=NONE;
> >     }
> >
> >
> > I think that it should be
> > ...
> >         return function!=NONE || cTable != null;
> >
> >
> > Best regards,
> >
> > Michael
> > ________________________________________________________________
> > Michael Schmid                    email: [hidden email]
> > Institut für Angewandte Physik, Technische Universität Wien
> > Wiedner Hauptstr. 8-10/E134, A 1040 Wien, Austria
> > Tel. [phone] or -13453, Fax [phone]
> > ________________________________________________________________
> >
> > On Nov 13, 2014, at 18:10, Dawid Krzempek wrote:
> >
> > > Hello,
> > > I am writing some Imagej plugin and have few problems with value
> calibration.
> > > I am not experienced in writing programs like this one, so the
> solution can be very simple.
> > >
> > > I try to calibrate ImagePlus. There is my code (img1 is ImagePlus
> object)
> > >
> > >                float [] param={146494f,3.55146f,2079.82f};
> > >                float cTable[]=new float[65536];
> > >                Calibration calibr=new Calibration();
> > >                float a=param[0];
> > >                float b=param[1];
> > >                float c=param[2];
> > >                for (int i=0;i<65536;i++){
> > >                    float value=-b+a/(i-c);
> > >                    if (value>10) cTable[i]=10;
> > >                    else if (value<0) cTable[i]=0;
> > >                    else cTable[i]=value;
> > >                }
> > >                calibr.setCTable(cTable,"Gy");
> > >                System.out.println(calibr.calibrated());
> > >                img1.setCalibration(calibr);;
> > >                System.out.println(img1.getCalibration().calibrated());
> > >
> > > The output then:
> > >
> > > true
> > > false
> > >
> > > setCalibration() seems not working. Image is not calibrated after
> using this method. I was expected "true true" output Could somebody tell
> me, where is my mistake?
> > > The goal of calibration is working on calibrated (Gy) values, not on
> signal values. Is there any other way to achieve it?
> > > Thanks for your help
> > > David
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> >
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi David,

ok, I found it now: You need

    Calibration calibr=new Calibration(img);

If you don't give the ImagePlus as an argument, the calibration will assume it's for an 8-bit image. Then, 16-bit calibration won't work.

Wayne, sorry for the false alarm concerning the calibrated() function!

Michael
________________________________________________________________
On Nov 13, 2014, at 20:49, Dawid Krzempek wrote:

> Yes, you're right. It will be very useful for me, so thank you.
>
> But even when I use setFunction() and write analogous code:
>
> *                float [] param={146494f,3.55146f,2079.82f};*
> *                Calibration calibr=new Calibration();*
> *                float a=param[0];*
> *                float b=param[1];*
> *                float c=param[2];*
> *                double b0=1.0;                double c0=-c;
> double d0=-b;                double a0=-d0+a/c0;                double []
> coef={a0,b0,c0,d0};
> calibr.setFunction(Calibration.RODBARD,coef,"Gy");
> img.setCalibration(calibr);
> System.out.println(calibr.calibrated());
> System.out.println(img.getCalibration().calibrated());*
>
> the output is still 'true false'. So there is no problem in calibration
> method, but with setCalibration(). *calib* seems to be not associated with
> img.
>
> img.setGlobalCalibration(calib) is not working properly too. I still dont
> see 'value=650 (6500)'.
>
> I still have to calibrate from code level, not from GUI level, because via
> GUI I can't enforce values of coefficients, ImageJ requires fitting.
> Best regards
> David
>
> 2014-11-13 19:36 GMT+01:00 Michael Schmid <[hidden email]>:
>
>> Hi David,
>>
>> to me it looks like you can use the built-in RODBARD function in your case
>> anyhow:
>>
>> RODBARD:  y = d + (a-d)/(1+(x/c)^b) = d + (a-d)*c^b / (c^b+x^b)
>>
>> You have  y = -b + a/(x-c)
>>
>> If I got it right, the Rodbard parameters are
>>
>> b = 1
>> d = -your_b
>> c = -your_c
>> a - d = your_a / c
>>
>> Nevertheless, if you see something like 'value=650 (6500)' in the status
>> line, it means that your image is calibrated, the calibrated value is 650,
>> the raw pixel value is 6500.
>>
>> Michael
>> ________________________________________________________________
>>
>>
>> On Nov 13, 2014, at 18:59, Dawid Krzempek wrote:
>>
>>> Thanks for your reply. Now I understand, but it's not the end of my
>> problems. :)
>>>
>>> As you can see from my code, I try to calibrate image using values
>> (table), not by function - my function is different than any of available
>> in ImageJ.
>>>
>>> But when I calibrate like this, image after display it is not
>> calibrated. I use calib in setCalibration() or setGlobalCalibration() -
>> both are not working.
>>> When Global calibration is using, there are some "tracks" of
>> calibration. For example, when I am trying to open another Image, I get:
>>> "The calibration of this image conflicts with the current global
>> calibration...."
>>> But in fact image is not calibrated. Information about pixel doesn't
>> seem like that:
>>> x=0, y=10 value=650 (6500)
>>> It seems like that:
>>> x=0, y=10 value=6500
>>> So I don't have any information about calibrated value.
>>> I have no idea, what I am doing wrong.
>>> Maybe the function is obligatory to make ImageProcessor calibration
>> possible?
>>> Thanks in advance
>>> David
>>>
>>> 2014-11-13 18:32 GMT+01:00 Michael Schmid <[hidden email]>:
>>> Hi Wayne, David,
>>>
>>> looks like an unintended behavior in Calibration, currently calibrated()
>> only checks for a function, not for a table (line 283...):
>>>
>>>    /** Returns true if this image is density calibrated. */
>>>    public boolean calibrated() {
>>>        return function!=NONE;
>>>    }
>>>
>>>
>>> I think that it should be
>>> ...
>>>        return function!=NONE || cTable != null;
>>>
>>>
>>> Best regards,
>>>
>>> Michael
>>> ________________________________________________________________
>>>
>>>
>>> On Nov 13, 2014, at 18:10, Dawid Krzempek wrote:
>>>
>>>> Hello,
>>>> I am writing some Imagej plugin and have few problems with value
>> calibration.
>>>> I am not experienced in writing programs like this one, so the
>> solution can be very simple.
>>>>
>>>> I try to calibrate ImagePlus. There is my code (img1 is ImagePlus
>> object)
>>>>
>>>>               float [] param={146494f,3.55146f,2079.82f};
>>>>               float cTable[]=new float[65536];
>>>>               Calibration calibr=new Calibration();
>>>>               float a=param[0];
>>>>               float b=param[1];
>>>>               float c=param[2];
>>>>               for (int i=0;i<65536;i++){
>>>>                   float value=-b+a/(i-c);
>>>>                   if (value>10) cTable[i]=10;
>>>>                   else if (value<0) cTable[i]=0;
>>>>                   else cTable[i]=value;
>>>>               }
>>>>               calibr.setCTable(cTable,"Gy");
>>>>               System.out.println(calibr.calibrated());
>>>>               img1.setCalibration(calibr);;
>>>>               System.out.println(img1.getCalibration().calibrated());
>>>>
>>>> The output then:
>>>>
>>>> true
>>>> false
>>>>
>>>> setCalibration() seems not working. Image is not calibrated after
>> using this method. I was expected "true true" output Could somebody tell
>> me, where is my mistake?
>>>> The goal of calibration is working on calibrated (Gy) values, not on
>> signal values. Is there any other way to achieve it?
>>>> Thanks for your help
>>>> David
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>>
>>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Dawid Krzempek]

Hi Michael,
your email made my day (night). :) I am very grateful for your help.
Thanks to you, I have some work for yesterday. So for now it's all.
Thank you once again
Best regards
David

2014-11-13 21:04 GMT+01:00 Michael Schmid <[hidden email]>:

> Hi David,
>
> ok, I found it now: You need
>
>     Calibration calibr=new Calibration(img);
>
> If you don't give the ImagePlus as an argument, the calibration will
> assume it's for an 8-bit image. Then, 16-bit calibration won't work.
>
> Wayne, sorry for the false alarm concerning the calibrated() function!
>
> Michael
> ________________________________________________________________
> On Nov 13, 2014, at 20:49, Dawid Krzempek wrote:
>
> > Yes, you're right. It will be very useful for me, so thank you.
> >
> > But even when I use setFunction() and write analogous code:
> >
> > *                float [] param={146494f,3.55146f,2079.82f};*
> > *                Calibration calibr=new Calibration();*
> > *                float a=param[0];*
> > *                float b=param[1];*
> > *                float c=param[2];*
> > *                double b0=1.0;                double c0=-c;
> > double d0=-b;                double a0=-d0+a/c0;                double []
> > coef={a0,b0,c0,d0};
> > calibr.setFunction(Calibration.RODBARD,coef,"Gy");
> > img.setCalibration(calibr);
> > System.out.println(calibr.calibrated());
> > System.out.println(img.getCalibration().calibrated());*
> >
> > the output is still 'true false'. So there is no problem in calibration
> > method, but with setCalibration(). *calib* seems to be not associated
> with
> > img.
> >
> > img.setGlobalCalibration(calib) is not working properly too. I still dont
> > see 'value=650 (6500)'.
> >
> > I still have to calibrate from code level, not from GUI level, because
> via
> > GUI I can't enforce values of coefficients, ImageJ requires fitting.
> > Best regards
> > David
> >
> > 2014-11-13 19:36 GMT+01:00 Michael Schmid <[hidden email]>:
> >
> >> Hi David,
> >>
> >> to me it looks like you can use the built-in RODBARD function in your
> case
> >> anyhow:
> >>
> >> RODBARD:  y = d + (a-d)/(1+(x/c)^b) = d + (a-d)*c^b / (c^b+x^b)
> >>
> >> You have  y = -b + a/(x-c)
> >>
> >> If I got it right, the Rodbard parameters are
> >>
> >> b = 1
> >> d = -your_b
> >> c = -your_c
> >> a - d = your_a / c
> >>
> >> Nevertheless, if you see something like 'value=650 (6500)' in the status
> >> line, it means that your image is calibrated, the calibrated value is
> 650,
> >> the raw pixel value is 6500.
> >>
> >> Michael
> >> ________________________________________________________________
> >>
> >>
> >> On Nov 13, 2014, at 18:59, Dawid Krzempek wrote:
> >>
> >>> Thanks for your reply. Now I understand, but it's not the end of my
> >> problems. :)
> >>>
> >>> As you can see from my code, I try to calibrate image using values
> >> (table), not by function - my function is different than any of
> available
> >> in ImageJ.
> >>>
> >>> But when I calibrate like this, image after display it is not
> >> calibrated. I use calib in setCalibration() or setGlobalCalibration() -
> >> both are not working.
> >>> When Global calibration is using, there are some "tracks" of
> >> calibration. For example, when I am trying to open another Image, I get:
> >>> "The calibration of this image conflicts with the current global
> >> calibration...."
> >>> But in fact image is not calibrated. Information about pixel doesn't
> >> seem like that:
> >>> x=0, y=10 value=650 (6500)
> >>> It seems like that:
> >>> x=0, y=10 value=6500
> >>> So I don't have any information about calibrated value.
> >>> I have no idea, what I am doing wrong.
> >>> Maybe the function is obligatory to make ImageProcessor calibration
> >> possible?
> >>> Thanks in advance
> >>> David
> >>>
> >>> 2014-11-13 18:32 GMT+01:00 Michael Schmid <[hidden email]>:
> >>> Hi Wayne, David,
> >>>
> >>> looks like an unintended behavior in Calibration, currently
> calibrated()
> >> only checks for a function, not for a table (line 283...):
> >>>
> >>>    /** Returns true if this image is density calibrated. */
> >>>    public boolean calibrated() {
> >>>        return function!=NONE;
> >>>    }
> >>>
> >>>
> >>> I think that it should be
> >>> ...
> >>>        return function!=NONE || cTable != null;
> >>>
> >>>
> >>> Best regards,
> >>>
> >>> Michael
> >>> ________________________________________________________________
> >>>
> >>>
> >>> On Nov 13, 2014, at 18:10, Dawid Krzempek wrote:
> >>>
> >>>> Hello,
> >>>> I am writing some Imagej plugin and have few problems with value
> >> calibration.
> >>>> I am not experienced in writing programs like this one, so the
> >> solution can be very simple.
> >>>>
> >>>> I try to calibrate ImagePlus. There is my code (img1 is ImagePlus
> >> object)
> >>>>
> >>>>               float [] param={146494f,3.55146f,2079.82f};
> >>>>               float cTable[]=new float[65536];
> >>>>               Calibration calibr=new Calibration();
> >>>>               float a=param[0];
> >>>>               float b=param[1];
> >>>>               float c=param[2];
> >>>>               for (int i=0;i<65536;i++){
> >>>>                   float value=-b+a/(i-c);
> >>>>                   if (value>10) cTable[i]=10;
> >>>>                   else if (value<0) cTable[i]=0;
> >>>>                   else cTable[i]=value;
> >>>>               }
> >>>>               calibr.setCTable(cTable,"Gy");
> >>>>               System.out.println(calibr.calibrated());
> >>>>               img1.setCalibration(calibr);;
> >>>>               System.out.println(img1.getCalibration().calibrated());
> >>>>
> >>>> The output then:
> >>>>
> >>>> true
> >>>> false
> >>>>
> >>>> setCalibration() seems not working. Image is not calibrated after
> >> using this method. I was expected "true true" output Could somebody tell
> >> me, where is my mistake?
> >>>> The goal of calibration is working on calibrated (Gy) values, not on
> >> signal values. Is there any other way to achieve it?
> >>>> Thanks for your help
> >>>> David
> >>>>
> >>>> --
> >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>
> >>>
> >>
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Rasband, Wayne (NIH/NIMH) [E]]

On Nov 13, 2014, at 12:10 PM, Dawid Krzempek <[hidden email]> wrote:

>
> Hello,
> I am writing some Imagej plugin and have few problems with value calibration.
> I am not experienced in writing programs like this one, so the solution can be very simple.
>
> I try to calibrate ImagePlus. There is my code (img1 is ImagePlus object)
>
>                float [] param={146494f,3.55146f,2079.82f};
>                float cTable[]=new float[65536];
>                Calibration calibr=new Calibration();
>                float a=param[0];
>                float b=param[1];
>                float c=param[2];
>                for (int i=0;i<65536;i++){
>                    float value=-b+a/(i-c);
>                    if (value>10) cTable[i]=10;
>                    else if (value<0) cTable[i]=0;
>                    else cTable[i]=value;
>                }
>                calibr.setCTable(cTable,"Gy");
>                System.out.println(calibr.calibrated());
>                img1.setCalibration(calibr);;
>                System.out.println(img1.getCalibration().calibrated());
>
> The output then:
>
> true
> false
>
> setCalibration() seems not working. Image is not calibrated after using this method. I was expected "true true" output Could somebody tell me, where is my mistake?

You did not make a mistake. You encountered a bug that is fixed in the latest ImageJ daily build (1.49m3). You can upgrade by using the Help>Update ImageJ command and selecting “daily build” from the drop down menu.

-wayne


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Dawid Krzempek]

Hi Wayne,
thanks a lot. I wouldn't get by without your help.
Best regards
David

2014-11-14 0:20 GMT+01:00 Rasband, Wayne (NIH/NIMH) [E] <
[hidden email]>:

> On Nov 13, 2014, at 12:10 PM, Dawid Krzempek <[hidden email]>
> wrote:
> >
> > Hello,
> > I am writing some Imagej plugin and have few problems with value
> calibration.
> > I am not experienced in writing programs like this one, so the solution
> can be very simple.
> >
> > I try to calibrate ImagePlus. There is my code (img1 is ImagePlus object)
> >
> >                float [] param={146494f,3.55146f,2079.82f};
> >                float cTable[]=new float[65536];
> >                Calibration calibr=new Calibration();
> >                float a=param[0];
> >                float b=param[1];
> >                float c=param[2];
> >                for (int i=0;i<65536;i++){
> >                    float value=-b+a/(i-c);
> >                    if (value>10) cTable[i]=10;
> >                    else if (value<0) cTable[i]=0;
> >                    else cTable[i]=value;
> >                }
> >                calibr.setCTable(cTable,"Gy");
> >                System.out.println(calibr.calibrated());
> >                img1.setCalibration(calibr);;
> >                System.out.println(img1.getCalibration().calibrated());
> >
> > The output then:
> >
> > true
> > false
> >
> > setCalibration() seems not working. Image is not calibrated after using
> this method. I was expected "true true" output Could somebody tell me,
> where is my mistake?
>
> You did not make a mistake. You encountered a bug that is fixed in the
> latest ImageJ daily build (1.49m3). You can upgrade by using the
> Help>Update ImageJ command and selecting “daily build” from the drop down
> menu.
>
> -wayne
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html