Re: ImageJ Delaunay Plugin

[dscho]

Hi Eva,

On Mon, 28 Jan 2013, Wagner, Eva wrote:

> Dear Mr. Schindelin,

Heh... on this list, we usually address each other using our first names...

> my friend Daniel Gereg wrote an E-Mail to you last friday asking for the
> download-link for the newest version of the
> Delaunay-Voronoi-Triangulation-Plugin for ImageJ.
>
> First of all: thank you for fixing the download link.

My pleasure, thanks for reporting the issue!

> I'm writing to you, hoping you could maybe help me with some issues I
> have with the plugin.
>
> I wanted to ask, if there is any way of exporting the mean distance and
> variance score, that appears at the bottom of the results table, into
> the summary table if I want to run several pictures in a row using a
> batch.
>

Right now, the mean distance and variance were intended to be written to
the Log window, but are written to the Log window, but wrote to the
Results window instead (and that line was lost upon the next update to the
Results window) when you check the showMeanDistance checkbox.

For the moment, you can easily fix that (putting the informations in the
correct columns) by running this macro:

-- snip --
selectWindow("Results");
list = split(getInfo("window.contents"), "\n");
if (list.length > 0) {
        line = list[list.length - 1];
        if (matches(line, "mean distance: .*, variance: .*")) {
                fields = split(line, " ");
                meanDistance = replace(fields[2], ",", "");
                variance = fields[4];
                index = nResults();
                setResult("Mean Distance", index, meanDistance);
                setResult("Variance", index, variance);
                updateResults();
        }
}
-- snap --

> It would be realy great, if you could help me, or maybe just give me a
> hint, since I have more than 4500 pictures I want to analize with your
> plugin and I want to avoid having to export every result separately.

I will try to find some time soon to fix the issue and upload a fixed
Delaunay_Voronoi plugin.

Ciao,
Johannes

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[dscho]

Hi Eva,

On Mon, 28 Jan 2013, Johannes Schindelin wrote:

> On Mon, 28 Jan 2013, Wagner, Eva wrote:
>
> > I wanted to ask, if there is any way of exporting the mean distance
> > and variance score, that appears at the bottom of the results table,
> > into the summary table if I want to run several pictures in a row
> > using a batch.
>
> Right now, the mean distance and variance were intended to be written to
> the Log window, but are written to the Log window, but wrote to the
> Results window instead (and that line was lost upon the next update to the
> Results window) when you check the showMeanDistance checkbox.
>
> I will try to find some time soon to fix the issue and upload a fixed
> Delaunay_Voronoi plugin.

I uploaded a new version of VIB_.jar to the update site; after a fresh
update, your Fiji should output the mean distance and variance into the
respective columns of the results table.

Ciao,
Johannes

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[Eva Wagner]

Hi!

I'm really sorry, I have to bug you again, but I'm really hoping, you can help me again...

I've been using the Delaunay Plugin I wrote to you about some weeks ago.
I recorded the following Macro:

 run("Make Binary");
run("Analyze Particles...", "size=25-Infinity circularity=0.00-1.00 show=Nothing display summarize");
run("Delaunay Voronoi", "mode=Delaunay interactive showmeandistance inferselectionfromparticles");

I then used this Macro with the Batch-Option to Process sveral Pictures in one step.

The problem I've been encountering ist, that the Batch doesnt measure one picture at a time, instead, it stacks the information of the images (the images consist of simple dots), so that with every additional picture, that is processes, more points are measured and the mean distance - obviously - decreases.
is there anything I can do to avoid this problem?

I hope, I explained myself clearly and maybe you can give me any hint...

[dscho]

Hi Eva,

On Sun, 3 Mar 2013, Eva Wagner wrote:

> I'm really sorry, I have to bug you again, but I'm really hoping, you
> can help me again...
>
> I've been using the Delaunay Plugin I wrote to you about some weeks ago.
> I recorded the following Macro:
>
>  run("Make Binary");
> run("Analyze Particles...", "size=25-Infinity circularity=0.00-1.00
> show=Nothing display summarize");
> run("Delaunay Voronoi", "mode=Delaunay interactive showmeandistance
> inferselectionfromparticles");
>
> I then used this Macro with the Batch-Option to Process sveral Pictures in
> one step.
>
> The problem I've been encountering ist, that the Batch doesnt measure one
> picture at a time, instead, it stacks the information of the images (the
> images consist of simple dots), so that with every additional picture, that
> is processes, more points are measured and the mean distance - obviously -
> decreases.
> is there anything I can do to avoid this problem?

I think the problem is that the way you called the particle analyzer, it
only adds to the results instead of replacing them.

Most likely, the problem goes away when you insert a "clean" into the
parameters of the particle analyzer, a good place would be between
"display" and "summarize".

Ciao,
Johannes

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[Jan Eglinger]

Hi,

On 04.03.2013 6:44 PM, Johannes Schindelin wrote:
> Most likely, the problem goes away when you insert a "clean" into the
> parameters of the particle analyzer, a good place would be between
> "display" and "summarize".

however, the missing parameter should be "clear", not "clean". The macro
recorder would have recorded this if you crossed "Clear results" in the
"Analyze Particles" dialog.

Cheers,
Jan

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[Eva Wagner]

Hey!
I just tried putting in the "clear" in the macro.
It solves the "measuring-problem", but the problem now is, that for every picture a new window with the measurements appears (as far as I can see, the numbers ar correct now), but it is closed automatically, when the picture is finished. So that in the end I wind up with only the calculated values of the last picture... Any ideas?

[dscho]

Hi Jan,

On Mon, 4 Mar 2013, Jan Eglinger wrote:

> On 04.03.2013 6:44 PM, Johannes Schindelin wrote:
> > Most likely, the problem goes away when you insert a "clean" into the
> > parameters of the particle analyzer, a good place would be between
> > "display" and "summarize".
>
> however, the missing parameter should be "clear", not "clean". The macro
> recorder would have recorded this if you crossed "Clear results" in the
> "Analyze Particles" dialog.

But of course! I should remember to use copy/paste where appropriate.

Thanks, Jan!
Johannes

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[dscho]

Hi Eva,

On Mon, 4 Mar 2013, Eva Wagner wrote:

> I just tried putting in the "clear" in the macro.
> It solves the "measuring-problem", but the problem now is, that for every
> picture a new window with the measurements appears (as far as I can see, the
> numbers ar correct now), but it is closed automatically, when the picture is
> finished. So that in the end I wind up with only the calculated values of
> the last picture... Any ideas?

You probably want to save the results into a file for later inspection
anyway. I would probably go about it like this:

        saveAs("Results", "/<path>/Results-" + getTitle() + ".txt");

Ciao,
Johannes

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