Analyze/Analyze Particles...

[Jarek Grodek]

hello IJ group,

i work on images containing elongated and round particles with different
angles. however particles oriented vertically are not desired because they
are mostly artifacts.
"Analyze Particles" in Analyze Menu may be more fit for my needs, if it
will offer option of choice of angle range for particle, just like "Area"
and "Circularity". Is it possible to enhance this Analyzer for this
feature?
till now i try to apply macro:

<<<

// This macro removes particles
// with orientation criterion.

requires("1.33f");

run("Skeletonize");
run("Set Measurements...", "area centroid fit decimal=3");
run("Analyze Particles...", "size=1-999999999 circularity=0.00-1
show=Nothing clear record");

setJustification("center");
for (i=0; i<nResults; i++) {
    x = getResult('XStart', i);
    y = getResult('YStart', i);

    doWand(x,y);
    major = getResult("Major",i);
    minor = getResult("Minor",i);
    angle = getResult("Angle",i);
    area = getResult("Area",i);
    x = getResult('X',i);
    y = getResult('Y',i);

   if (major >= minor*1.2 && (angle >20 && angle<160)) {
     run("Clear");
   }
}
run("Select None");

      run("Set Measurements...", "area centroid fit display redirect=None
decimal=3")
      Height=getHeight();
      Width=getWidth();
      x=0;
      y=Height/3;
      b=Height/3;
      dx = 0;
      dy = b;
      moveSelection(dx, dy);
  }

  function moveSelection(dx, dy) {
      requires("1.31b");

rename("oryginal");
makeRectangle(x,y-y,Width,y);
run("Duplicate...", "title=brodka");
run("Analyze Particles...", "size=3-Infinity circularity=0.00-1.00
show=Nothing display");
close;
selectWindow("oryginal");
makeRectangle(x, y, Width, y);
run("Duplicate...", "title=srodek");
run("Analyze Particles...", "size=3-Infinity circularity=0.00-1.00
show=Nothing display");
close;
selectWindow("oryginal");
makeRectangle(x, y+y, Width, y);
run("Duplicate...", "title=zarodek");
run("Analyze Particles...", "size=3-Infinity circularity=0.00-1.00
show=Nothing display");
close;
selectWindow("oryginal");
close;

>>>

however when i try to combine this macro with other macros it doesn't work
as well as i would like to.

Please send me back any help is appreaciated.



MSc Eng. Jaroslaw Grodek
Institute of Agrophysics
Polish Academy of Sciences in Lublin
Doswiadczalna 4
20-290 Lublin
Poland

[Jarek Grodek]

Hello
I've posted a question of particle analyzing by mean of Analyze/Analyze
Partciles. maybe you've missed it so I decided to repeat this question, as
follows:

On Pt Marca 14 2008, 10:02, Jarosław Grodek napisał(a):
> hello IJ group,
>
> i work on images containing elongated and round particles with different
> angles. however particles oriented vertically are not desired because they
> are mostly artifacts.
> "Analyze Particles" in Analyze Menu may be more fit for my needs, if it
> will offer option of choice of angle range for particle, just like "Area"
> and "Circularity". Is it possible to enhance this Analyzer for this
> feature?

>
> Please send me back any help is appreaciated.

MSc Eng. Jaroslaw Grodek
Institute of Agrophysics
Polish Academy of Sciences in Lublin
Doswiadczalna 4
20-290 Lublin
Poland

[Sami Badawi-2]

Hi Jarosław,

I have a little OSS project, ShapeLogic, that is investigating the use
of declarative programming techniques in image processing.

I am currently working on an automatic color and gray scale particle
counter. The first version of the particle counter should be out in
ShapeLogic 1.1. Judging from previous releases this is probably going
to have pretty rudimentary functionality, but hopefully ShapeLogic 1.2
should be more useful. The goal is for the particle counter is to be
good enough to handle 3 of the sample particle images that comes with
ImageJ: http://www.shapelogic.org/particle.html

If you would like to send me some sample images I will try to see if
ShapeLogic can do what you asked for.

-Sami Badawi
http://www.shapelogic.org


2008/3/18 Jarosław Grodek <[hidden email]>:

> Hello
>  I've posted a question of particle analyzing by mean of Analyze/Analyze
>  Partciles. maybe you've missed it so I decided to repeat this question, as
>  follows:
>
>  On Pt Marca 14 2008, 10:02, Jarosław Grodek napisał(a):
>  > hello IJ group,
>  >
>  > i work on images containing elongated and round particles with different
>  > angles. however particles oriented vertically are not desired because they
>  > are mostly artifacts.
>  > "Analyze Particles" in Analyze Menu may be more fit for my needs, if it
>  > will offer option of choice of angle range for particle, just like "Area"
>  > and "Circularity". Is it possible to enhance this Analyzer for this
>  > feature?
>
>  >
>  > Please send me back any help is appreaciated.
>
>  MSc Eng. Jaroslaw Grodek
>  Institute of Agrophysics
>  Polish Academy of Sciences in Lublin
>  Doswiadczalna 4
>  20-290 Lublin
>  Poland
>

[Joachim Wesner]

Hi list,

I know this is more a general Java question, but as it appears in
connection with an IJ plugin that I want to write....

I have a protocol file with thousand of measurements (~ 4000). I want to
read the file into (virtual) memory and show the user a window with colums
that include the most basic data of the measurements (short description
string, date, time, some specific info). It should be possible to sort the
data based on
individual columns by clicking on the top line or similar, it should be
also possible to do a basic string search in that window etc.

Finally, clicking on a single or multiple entries will finally activate my
plugin code to retrive the full measurement and show results, reconstructed
images etc.

This kind of interface is pretty common today, is there any Java class that
I could use to implement this?

Sincerely

Joachim


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[ctrueden]

Hi Joachim,

If you are using Java 1.6, you can use a JTable with a TableRowSorter and a
RowFilter for enabling the functionality you want.

-Curtis

On Tue, Mar 18, 2008 at 10:58 AM, Joachim Wesner <
[hidden email]> wrote:

> Hi list,
>
> I know this is more a general Java question, but as it appears in
> connection with an IJ plugin that I want to write....
>
> I have a protocol file with thousand of measurements (~ 4000). I want to
> read the file into (virtual) memory and show the user a window with colums
> that include the most basic data of the measurements (short description
> string, date, time, some specific info). It should be possible to sort the
> data based on
> individual columns by clicking on the top line or similar, it should be
> also possible to do a basic string search in that window etc.
>
> Finally, clicking on a single or multiple entries will finally activate my
> plugin code to retrive the full measurement and show results,
> reconstructed
> images etc.
>
> This kind of interface is pretty common today, is there any Java class
> that
> I could use to implement this?
>
> Sincerely
>
> Joachim
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>

[Gwen Barnes]

Hi, I guess I'm not 100% sure what you want, but if you only want to measure
horizontal distances, without worrying about making your line perfectly
horizontal every time, you could run a macro like this:

macro "horizontal component" {
run ("Measure");
n=nResults-1;
getLine(x1,y1,x2,y2,lineWidth);
HorizComp=abs(x2-x1);
gLength=sqrt((x1-x2)*(x1-x2)+(y1-y2)*(y1-y2));
gAngle=acos(HorizComp/gLength)*180/3.14;
setResult("Angle",n,gAngle);
setResult("Length",n,gLength);
setResult("HorizComp",n,HorizComp);
updateResults();
}

-Gwen

2008/3/18 Jarosław Grodek <[hidden email]>:

> Hello
> I've posted a question of particle analyzing by mean of Analyze/Analyze
> Partciles. maybe you've missed it so I decided to repeat this question, as
> follows:
>
> On Pt Marca 14 2008, 10:02, Jarosław Grodek napisał(a):
> > hello IJ group,
> >
> > i work on images containing elongated and round particles with different
> > angles. however particles oriented vertically are not desired because
> they
> > are mostly artifacts.
> > "Analyze Particles" in Analyze Menu may be more fit for my needs, if it
> > will offer option of choice of angle range for particle, just like
> "Area"
> > and "Circularity". Is it possible to enhance this Analyzer for this
> > feature?
>
> >
> > Please send me back any help is appreaciated.
>
> MSc Eng. Jaroslaw Grodek
> Institute of Agrophysics
> Polish Academy of Sciences in Lublin
> Doswiadczalna 4
> 20-290 Lublin
> Poland
>

[Jarek Grodek]

hello thanks for reply.
What i really want to do is enhancement of Particle Remover plugin
http://rsb.info.nih.gov/ij/plugins/particle-remover.html to enable
removing particles of which the angle of orientation is for example
between 45 and 135 degree and and leave on image only particles which
angle of orientation is 0-45 and 135-180 degree.
And wouldn't it be nice to have a possibility of input of range of angles
of particles which should be removed just like it is with area and
circularity in the mentioned plugin?
greetings
Jarek


On Wt Marca 18 2008, 17:56, Gwen Barnes napisał(a):

> Hi, I guess I'm not 100% sure what you want, but if you only want to
> measure
> horizontal distances, without worrying about making your line perfectly
> horizontal every time, you could run a macro like this:
>
> macro "horizontal component" {
> run ("Measure");
> n=nResults-1;
> getLine(x1,y1,x2,y2,lineWidth);
> HorizComp=abs(x2-x1);
> gLength=sqrt((x1-x2)*(x1-x2)+(y1-y2)*(y1-y2));
> gAngle=acos(HorizComp/gLength)*180/3.14;
> setResult("Angle",n,gAngle);
> setResult("Length",n,gLength);
> setResult("HorizComp",n,HorizComp);
> updateResults();
> }
>
> -Gwen
>
> 2008/3/18 Jarosław Grodek <[hidden email]>:
>
>> Hello
>> I've posted a question of particle analyzing by mean of Analyze/Analyze
>> Partciles. maybe you've missed it so I decided to repeat this question,
>> as
>> follows:
>>
>> On Pt Marca 14 2008, 10:02, Jarosław Grodek napisał(a):
>> > hello IJ group,
>> >
>> > i work on images containing elongated and round particles with
>> different
>> > angles. however particles oriented vertically are not desired because
>> they
>> > are mostly artifacts.
>> > "Analyze Particles" in Analyze Menu may be more fit for my needs, if
>> it
>> > will offer option of choice of angle range for particle, just like
>> "Area"
>> > and "Circularity". Is it possible to enhance this Analyzer for this
>> > feature?
>>
>> >
>> > Please send me back any help is appreaciated.
>>
>> MSc Eng. Jaroslaw Grodek
>> Institute of Agrophysics
>> Polish Academy of Sciences in Lublin
>> Doswiadczalna 4
>> 20-290 Lublin
>> Poland
>>
>

MSc Eng. Jaroslaw Grodek
Institute of Agrophysics
Polish Academy of Sciences in Lublin
Doswiadczalna 4
20-290 Lublin
Poland

[Gabriel Landini]

On Wednesday 19 March 2008 13:48:06 Jarosław Grodek wrote:
> What i really want to do is enhancement of Particle Remover plugin
> http://rsb.info.nih.gov/ij/plugins/particle-remover.html to enable
> removing particles of which the angle of orientation is for example
> between 45 and 135 degree and and leave on image only particles which
> angle of orientation is 0-45 and 135-180 degree.
> And wouldn't it be nice to have a possibility of input of range of angles
> of particles which should be removed just like it is with area and
> circularity in the mentioned plugin?

I think that this may do what you want.
http://www.dentistry.bham.ac.uk/landinig/software/classify/classify.html

Cheers,

G.

[GCH-2]

Jarek,

Try the Shape descriptor plugin which has been modified to quantify  
particles with given angles.

http://www.gcsca.net/IJ/Shapes.html

Regards,

Gary.


On Mar 19, 2008, at 2:48 PM, Jarosław Grodek wrote:

> hello thanks for reply.
> What i really want to do is enhancement of Particle Remover plugin
> http://rsb.info.nih.gov/ij/plugins/particle-remover.html to enable
> removing particles of which the angle of orientation is for example
> between 45 and 135 degree and and leave on image only particles which
> angle of orientation is 0-45 and 135-180 degree.
> And wouldn't it be nice to have a possibility of input of range of  
> angles
> of particles which should be removed just like it is with area and
> circularity in the mentioned plugin?
> greetings
> Jarek
>
>
> On Wt Marca 18 2008, 17:56, Gwen Barnes napisał(a):
>> Hi, I guess I'm not 100% sure what you want, but if you only want to
>> measure
>> horizontal distances, without worrying about making your line  
>> perfectly
>> horizontal every time, you could run a macro like this:
>>
>> macro "horizontal component" {
>> run ("Measure");
>> n=nResults-1;
>> getLine(x1,y1,x2,y2,lineWidth);
>> HorizComp=abs(x2-x1);
>> gLength=sqrt((x1-x2)*(x1-x2)+(y1-y2)*(y1-y2));
>> gAngle=acos(HorizComp/gLength)*180/3.14;
>> setResult("Angle",n,gAngle);
>> setResult("Length",n,gLength);
>> setResult("HorizComp",n,HorizComp);
>> updateResults();
>> }
>>
>> -Gwen
>>
>> 2008/3/18 Jarosław Grodek <[hidden email]>:
>>
>>> Hello
>>> I've posted a question of particle analyzing by mean of Analyze/
>>> Analyze
>>> Partciles. maybe you've missed it so I decided to repeat this  
>>> question,
>>> as
>>> follows:
>>>
>>> On Pt Marca 14 2008, 10:02, Jarosław Grodek napisał(a):
>>>> hello IJ group,
>>>>
>>>> i work on images containing elongated and round particles with
>>> different
>>>> angles. however particles oriented vertically are not desired  
>>>> because
>>> they
>>>> are mostly artifacts.
>>>> "Analyze Particles" in Analyze Menu may be more fit for my  
>>>> needs, if
>>> it
>>>> will offer option of choice of angle range for particle, just like
>>> "Area"
>>>> and "Circularity". Is it possible to enhance this Analyzer for this
>>>> feature?
>>>
>>>>
>>>> Please send me back any help is appreaciated.
>>>
>>> MSc Eng. Jaroslaw Grodek
>>> Institute of Agrophysics
>>> Polish Academy of Sciences in Lublin
>>> Doswiadczalna 4
>>> 20-290 Lublin
>>> Poland
>>>
>>
>
>
> MSc Eng. Jaroslaw Grodek
> Institute of Agrophysics
> Polish Academy of Sciences in Lublin
> Doswiadczalna 4
> 20-290 Lublin
> Poland

[Jarek Grodek]

hello again,
Thanks to Gabriel and Gary for direct information about their plugins.
Both suply my purpose.
greetings, and i think the post is closed
with best regards
Jarek

On Śr Marca 19 2008, 23:00, GCH napisał(a):

> Jarek,
>
> Try the Shape descriptor plugin which has been modified to quantify
> particles with given angles.
>
> http://www.gcsca.net/IJ/Shapes.html
>
> Regards,
>
> Gary.
>
>
> On Mar 19, 2008, at 2:48 PM, JarosĹ&#65533;aw Grodek wrote:
>
>> hello thanks for reply.
>> What i really want to do is enhancement of Particle Remover plugin
>> http://rsb.info.nih.gov/ij/plugins/particle-remover.html to enable
>> removing particles of which the angle of orientation is for example
>> between 45 and 135 degree and and leave on image only particles which
>> angle of orientation is 0-45 and 135-180 degree.
>> And wouldn't it be nice to have a possibility of input of range of
>> angles
>> of particles which should be removed just like it is with area and
>> circularity in the mentioned plugin?
>> greetings
>> Jarek
>>
>>
>> On Wt Marca 18 2008, 17:56, Gwen Barnes napisaĹ&#65533;(a):
>>> Hi, I guess I'm not 100% sure what you want, but if you only want to
>>> measure
>>> horizontal distances, without worrying about making your line
>>> perfectly
>>> horizontal every time, you could run a macro like this:
>>>
>>> macro "horizontal component" {
>>> run ("Measure");
>>> n=nResults-1;
>>> getLine(x1,y1,x2,y2,lineWidth);
>>> HorizComp=abs(x2-x1);
>>> gLength=sqrt((x1-x2)*(x1-x2)+(y1-y2)*(y1-y2));
>>> gAngle=acos(HorizComp/gLength)*180/3.14;
>>> setResult("Angle",n,gAngle);
>>> setResult("Length",n,gLength);
>>> setResult("HorizComp",n,HorizComp);
>>> updateResults();
>>> }
>>>
>>> -Gwen
>>>
>>> 2008/3/18 JarosĹ&#65533;aw Grodek <[hidden email]>:
>>>
>>>> Hello
>>>> I've posted a question of particle analyzing by mean of Analyze/
>>>> Analyze
>>>> Partciles. maybe you've missed it so I decided to repeat this
>>>> question,
>>>> as
>>>> follows:
>>>>
>>>> On Pt Marca 14 2008, 10:02, JarosĹ&#65533;aw Grodek napisaĹ&#65533;(a):
>>>>> hello IJ group,
>>>>>
>>>>> i work on images containing elongated and round particles with
>>>> different
>>>>> angles. however particles oriented vertically are not desired
>>>>> because
>>>> they
>>>>> are mostly artifacts.
>>>>> "Analyze Particles" in Analyze Menu may be more fit for my
>>>>> needs, if
>>>> it
>>>>> will offer option of choice of angle range for particle, just like
>>>> "Area"
>>>>> and "Circularity". Is it possible to enhance this Analyzer for this
>>>>> feature?
>>>>
>>>>>
>>>>> Please send me back any help is appreaciated.
>>>>
>>>> MSc Eng. Jaroslaw Grodek
>>>> Institute of Agrophysics
>>>> Polish Academy of Sciences in Lublin
>>>> Doswiadczalna 4
>>>> 20-290 Lublin
>>>> Poland
>>>>
>>>
>>
>>
>> MSc Eng. Jaroslaw Grodek
>> Institute of Agrophysics
>> Polish Academy of Sciences in Lublin
>> Doswiadczalna 4
>> 20-290 Lublin
>> Poland
>
>

MSc Eng. Jaroslaw Grodek
Institute of Agrophysics
Polish Academy of Sciences in Lublin
Doswiadczalna 4
20-290 Lublin
Poland