problem using R-Plot

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problem using R-Plot

Aryeh Weiss
The first time that I use R-Plot after starting Fiji, it works. After
that, it throws an error saying

Unsupported format not file not found
/tmp/ in line 6

here is a minimal macro that demonstrates the problem:

run("Blobs (25K)");
run("Grays");
setAutoThreshold("Default dark no-reset");
run("Analyze Particles...", "display exclude clear summarize add");
run("R Histogram", "data_column=Area title=[] x-axis_label=Area
y-axis_label=Frequency fit=[log-normal fit] show");

The first time that this is run, it works. Then I get the error stated
above.

I presume that if ti works once, then my R is ok. I did export
RPATH="/usr/bin/R" , but that had no effect on the problem.

Thanks in advance for any advice.

--aryeh

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

Ph:  972-3-5317638
FAX: 972-3-7384051

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: problem using R-Plot

Curtis Rueden-2
Hi Aryeh,

> run("R Histogram", "data_column=Area title=[] x-axis_label=Area
> y-axis_label=Frequency fit=[log-normal fit] show");

Which plugin is this? I don't have an "R Histogram" in my Fiji, and I'm
unfamiliar with it.

If you type "r histogram" into the search bar, what does it say for
"Location" in the right-hand pane?

Thanks,
Curtis

--
Curtis Rueden
Software architect, LOCI/Eliceiri lab - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Have you tried the Image.sc Forum? https://forum.image.sc/

On Mon, Aug 24, 2020 at 1:33 PM Aryeh Weiss <[hidden email]> wrote:

> The first time that I use R-Plot after starting Fiji, it works. After
> that, it throws an error saying
>
> Unsupported format not file not found
> /tmp/ in line 6
>
> here is a minimal macro that demonstrates the problem:
>
> run("Blobs (25K)");
> run("Grays");
> setAutoThreshold("Default dark no-reset");
> run("Analyze Particles...", "display exclude clear summarize add");
> run("R Histogram", "data_column=Area title=[] x-axis_label=Area
> y-axis_label=Frequency fit=[log-normal fit] show");
>
> The first time that this is run, it works. Then I get the error stated
> above.
>
> I presume that if ti works once, then my R is ok. I did export
> RPATH="/usr/bin/R" , but that had no effect on the problem.
>
> Thanks in advance for any advice.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: 972-3-7384051
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: problem using R-Plot

Aryeh Weiss
Hi Curtis,

Thank you for your reply.

On 24/08/2020 22:12, Curtis Rueden wrote:
> Hi Aryeh,
>
> > run("R Histogram", "data_column=Area title=[] x-axis_label=Area
> > y-axis_label=Frequency fit=[log-normal fit] show");
>
> Which plugin is this? I don't have an "R Histogram" in my Fiji, and
> I'm unfamiliar with it.

It is part of the Particle Sizer package https://imagej.net/ParticleSizer

It appears in the Analyze menu. I installed it using the update site.

Best regards
--aryeh


> If you type "r histogram" into the search bar, what does it say for
> "Location" in the right-hand pane?
>
> Thanks,
> Curtis
>
> --
> Curtis Rueden
> Software architect, LOCI/Eliceiri lab - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Have you tried the Image.sc Forum? https://forum.image.sc/
>
> On Mon, Aug 24, 2020 at 1:33 PM Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     The first time that I use R-Plot after starting Fiji, it works. After
>     that, it throws an error saying
>
>     Unsupported format not file not found
>     /tmp/ in line 6
>
>     here is a minimal macro that demonstrates the problem:
>
>     run("Blobs (25K)");
>     run("Grays");
>     setAutoThreshold("Default dark no-reset");
>     run("Analyze Particles...", "display exclude clear summarize add");
>     run("R Histogram", "data_column=Area title=[] x-axis_label=Area
>     y-axis_label=Frequency fit=[log-normal fit] show");
>
>     The first time that this is run, it works. Then I get the error
>     stated
>     above.
>
>     I presume that if ti works once, then my R is ok. I did export
>     RPATH="/usr/bin/R" , but that had no effect on the problem.
>
>     Thanks in advance for any advice.
>
>     --aryeh
>
>     --
>     Aryeh Weiss
>     Faculty of Engineering
>     Bar Ilan University
>     Ramat Gan 52900 Israel
>
>     Ph:¬† 972-3-5317638
>     FAX: 972-3-7384051
>
>     --
>     ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Ph:  972-3-5317638
FAX: 972-3-7384051


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: problem using R-Plot

Rocco D'Antuono
Hi Aryeh, just as confirmation I get the same error, the following is not yet
a solution.
I have tried the plugin and my guess is that the "tmp" folder doesn't have a
file .png that the plugin expects to find in it.
The error seems produced by the last line in this excerpt from "RPlot.java"
on GitHub:

/...
String tmp = IJ.getDirectory("temp");
tmp = tmp.replace("\\", "\\\\");
...
String filename = "density_"+getStamp()+".png";
IJ.open(tmp+filename);/

I think the plugin stops when it doesn't find "filename" or cannot access
the folder.
As check, what do you get if you run as beanshell script the following
lines?:

/import ij.IJ;
tmp = IJ.getDirectory("temp");
tmp = tmp.replace("\\", "\\\\");
print(tmp);/

Is that folder visible/accessible for you?

Best,
Rocco






-----
Senior Microscopist
Crick Advanced Light Microscopy facility (CALM)
The Francis Crick Institute
1 Midland Road, NW1 1AT, London (UK)
--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Senior Microscopist
Crick Advanced Light Microscopy facility (CALM)
The Francis Crick Institute
1 Midland Road, NW1 1AT, London (UK)
https://roccodant.github.io/
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Re: problem using R-Plot

Aryeh Weiss
Hi Rocco and thank you for your reply.

On 25/08/2020 13:42, Rocco D'Antuono wrote:

> Hi Aryeh, just as confirmation I get the same error, the following is not yet
> a solution.
> I have tried the plugin and my guess is that the "tmp" folder doesn't have a
> file .png that the plugin expects to find in it.
> The error seems produced by the last line in this excerpt from "RPlot.java"
> on GitHub:
>
> /...
> String tmp = IJ.getDirectory("temp");
> tmp = tmp.replace("\\", "\\\\");
> ...
> String filename = "density_"+getStamp()+".png";
> IJ.open(tmp+filename);/
>
> I think the plugin stops when it doesn't find "filename" or cannot access
> the folder.
> As check, what do you get if you run as beanshell script the following
> lines?:
>
> /import ij.IJ;
> tmp = IJ.getDirectory("temp");
> tmp = tmp.replace("\\", "\\\\");
> print(tmp);/
>
> Is that folder visible/accessible for you?

When I run this script, it print out:

/tmp/

BTW, import does not work for me. I used auto-imports.
I used  instead: importClass(Packages.ij.IJ)

Best regards

--aryeh

>
> Best,
> Rocco
>
>
>
>
>
>
> -----
> Senior Microscopist
> Crick Advanced Light Microscopy facility (CALM)
> The Francis Crick Institute
> 1 Midland Road, NW1 1AT, London (UK)
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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

Ph:  972-3-5317638
FAX: 972-3-7384051

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