ParticleAnalyzer class and stacks

[Aryeh Weiss]

I am trying to use the particle analyzer in python. I found an example
for use of the PA on stacks, in which the PA is run on each slice
individually within a loop. Is there a way to run the PA on the entire
stack, without having to loop over each slice?
I looked for an example of this, and I am sure there must be many such
examples, but I did not find it.

Thanks in advance
--aryeh

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Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


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

On Jul 6, 2014, at 6:24 AM, Aryeh Weiss wrote:

> I am trying to use the particle analyzer in python. I found an example for use of the PA on stacks, in which the PA is run on each slice individually within a loop. Is there a way to run the PA on the entire stack, without having to loop over each slice?
> I looked for an example of this, and I am sure there must be many such examples, but I did not find it.

Try using the command recorder (Plugins>Macros>Record). The following is what is recorded when I open the "Bat Cochlea Volume" sample stack, threshold it and run the particle analyzer, with the recorder running in "JavaScript" mode.

  IJ.run("Set Measurements...", "area centroid stack decimal=3");
  imp = IJ.openImage("http://imagej.nih.gov/ij/images/bat-cochlea-volume.zip");
  IJ.setAutoThreshold(imp, "Default dark");
  IJ.run(imp, "Analyze Particles...", "size=10 display clear summarize stack");

-wayne
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[Aryeh Weiss]

On 7/6/14, 11:57 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Jul 6, 2014, at 6:24 AM, Aryeh Weiss wrote:
>
>> I am trying to use the particle analyzer in python. I found an example for use of the PA on stacks, in which the PA is run on each slice individually within a loop. Is there a way to run the PA on the entire stack, without having to loop over each slice?
>> I looked for an example of this, and I am sure there must be many such examples, but I did not find it.
> Try using the command recorder (Plugins>Macros>Record). The following is what is recorded when I open the "Bat Cochlea Volume" sample stack, threshold it and run the particle analyzer, with the recorder running in "JavaScript" mode.
>
>    IJ.run("Set Measurements...", "area centroid stack decimal=3");
>    imp = IJ.openImage("http://imagej.nih.gov/ij/images/bat-cochlea-volume.zip");
>    IJ.setAutoThreshold(imp, "Default dark");
>    IJ.run(imp, "Analyze Particles...", "size=10 display clear summarize stack");
>
> -wayne
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

Thank yo for your reply.

I was trying to do it using the the ParticleAnalyzer class without  IJ.run .
Is there a way to do that? For that matter, is it generally better to
use the API rather than use
  IJ.run ?

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


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[Aryeh Weiss]

On 7/7/14, 9:14 AM, Paul van Schayck wrote:

> Dear Aryeh,
>
> On Mon, Jul 7, 2014 at 4:43 AM, Aryeh Weiss <[hidden email]> wrote:
>> I was trying to do it using the the ParticleAnalyzer class without  IJ.run .
>> Is there a way to do that? For that matter, is it generally better to use
>> the API rather than use
>>   IJ.run ?
> That's certainly possible. And probably as you already found in your
> example. You can do something like this (this is Javascript, but can
> be adapted to Python
>
>      table = new ResultsTable()
>      pa = ParticleAnalyzer(0, Measurements.CENTER_OF_MASS, table,
> 300,Number.POSITIVE_INFINITY, 0.4, 1.0)
>      pa.analyze(imp)
>
>      // Loop through objects and store them in list object
>      r = []
>      for (i=0; i < table.getCounter(); i++)  {
>           r[i] = { "XM": table.getValue("XM",i), "YM": table.getValue("YM",i) }
>      }
>
> I'm not sure what drawback you find with looping through the stacks.
> Internally, this is what Analyze Particle plugin is doing internally
> as well AFAIK.
>
> Kind regards,
>
> Paul
>

Hi Paul,


Thank you for your reply.
I have a student who is converting some algorithms which I implemented
as macros to python.
I thought that it would be cleaner (and maybe more efficient) to have
the analyzer operate on the stack,
just as in the macro I have a "stack" keyword.
Also, if I generate a mask, I prefer that a stack be generated, rather
then get each slice, and append it to a stack
(although that can certainly be done).

The API docs mention processStack, which appears to be a flag that tell
it to process a stack (just a guess), but I dont know how to use it.

Best regards,
--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


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[Paul van Schayck]

Dear Aryeh,

On Mon, Jul 7, 2014 at 8:57 AM, Aryeh Weiss <[hidden email]> wrote:

> Thank you for your reply.
> I have a student who is converting some algorithms which I implemented as
> macros to python.
> I thought that it would be cleaner (and maybe more efficient) to have the
> analyzer operate on the stack,
> just as in the macro I have a "stack" keyword.
> Also, if I generate a mask, I prefer that a stack be generated, rather then
> get each slice, and append it to a stack
> (although that can certainly be done).
>
> The API docs mention processStack, which appears to be a flag that tell it
> to process a stack (just a guess), but I dont know how to use it.
>

As far as I can tell from the ParticleAnalyzer code [1], this really
an internal option for the run() method. But maybe someone more
familiar with that code should comment on that.

Paul

[1] https://github.com/imagej/imagej1/blob/master/ij/plugin/filter/ParticleAnalyzer.java

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