Odd bUnwarpJ behavior -- help!

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Odd bUnwarpJ behavior -- help!

billo
I am trying to use bUnwarpJ from a macro in ImageJ (not Fiji) on a linux box running Fedora 25.  

My commands inthe macro are:

run("bUnwarpJ", "source_image=blueimage target_image=greenimage registration=Mono image_subsample_factor=0 initial_deformation=[Very Coarse] final_deformation=Coarse divergence_weight=0 curl_weight=0 landmark_weight=0 image_weight=1 consistency_weight=10 stop_threshold=0.01 save_transformations");
selectImage("Registered Source Image");
close();

call("bunwarpj.bUnwarpJ_.elasticTransformImageMacro", "/tmp/green.jpg", "/tmp/blue.jpg", "blueimage_direct_transf.txt", "/tmp/bluegreen.tif");

I get the error that "blueimage_direct_trans.txt" does not exist.

When I look for it, I note that the data is there, but it's in a file named "get_image=greenimage"!

Any help would be appreciated.

thanks,

billo
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Re: Odd bUnwarpJ behavior -- help!

Ignacio Arganda-Carreras-2
Hello Billo,

It looks like your path to "blueimage_direct_trans.txt" is not complete.
Have you tried using the whole path to the file?

On Sat, Apr 15, 2017 at 2:56 AM, billo <[hidden email]> wrote:

> I am trying to use bUnwarpJ from a macro in ImageJ (not Fiji) on a linux
> box
> running Fedora 25.
>
> My commands inthe macro are:
>
> run("bUnwarpJ", "source_image=blueimage target_image=greenimage
> registration=Mono image_subsample_factor=0 initial_deformation=[Very
> Coarse]
> final_deformation=Coarse divergence_weight=0 curl_weight=0
> landmark_weight=0
> image_weight=1 consistency_weight=10 stop_threshold=0.01
> save_transformations");
> selectImage("Registered Source Image");
> close();
>
> call("bunwarpj.bUnwarpJ_.elasticTransformImageMacro", "/tmp/green.jpg",
> "/tmp/blue.jpg", "blueimage_direct_transf.txt", "/tmp/bluegreen.tif");
>
> I get the error that "blueimage_direct_trans.txt" does not exist.
>
> When I look for it, I note that the data is there, but it's in a file named
> "get_image=greenimage"!
>
> Any help would be appreciated.
>
> thanks,
>
> billo
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Odd-bUnwarpJ-behavior-help-tp5018552.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Odd bUnwarpJ behavior -- help!

billo

Thanks for the reply!

That doesn't change anything, unfortunately. However, if I rename the file "get-image=greenimage" as blueimage_direct_transf.txt, it will read it, and move on. The transfer file is getting written. It's just misnamed a

I downloaded Fiji, and get the same error.

Two asides:

1) This works fine using an older version of bUnwarpJ , and ImageJ 1.48a. I don't know which version of bUnwarpJ I have installed on the old ImageJ, but it's a couple of years old, at least. I know that I invoked it using call("bUnwarpJ_.elasticTransformImageMacro",  ...) instead of call ("bunwarpj.bUnwarpJ_.elasticTransformImageMacro", ,,,)

2) This is part of an old script, er, macro, I wrote some time ago to clean up brightfield microscopy images. This part is an attempt to lessen chromatic aberration. It works by:

a) Split the rgb image into red, green and blue
b) Create edge strength images
c) Use the green edge image as the base, and warp the blue and red edge images to the green image
d) Apply the transformations to the "regular" red, green, and blue images
e) Restack them into a rgb image.

It works *farily* well. Or, rather, it worked fairly well before I upgraded ImageJ.

3) Since, as noted in #2 above, I run this on the blue and red images, I get the same error twice. However, the second incorrectly named transfer file is named, of all things, "et-image=greenimage" instead of "get-image-greenimage."

Thanks!

billo



On Sat, 2017-04-15 at 08:16 -0700, Ignacio Arganda-Carreras-2 [via ImageJ] wrote:
Hello Billo,

It looks like your path to "blueimage_direct_trans.txt" is not complete.
Have you tried using the whole path to the file?

On Sat, Apr 15, 2017 at 2:56 AM, billo <[hidden email]> wrote:

> I am trying to use bUnwarpJ from a macro in ImageJ (not Fiji) on a linux
> box
> running Fedora 25.
>
> My commands inthe macro are:
>
> run("bUnwarpJ", "source_image=blueimage target_image=greenimage
> registration=Mono image_subsample_factor=0 initial_deformation=[Very
> Coarse]
> final_deformation=Coarse divergence_weight=0 curl_weight=0
> landmark_weight=0
> image_weight=1 consistency_weight=10 stop_threshold=0.01
> save_transformations");
> selectImage("Registered Source Image");
> close();
>
> call("bunwarpj.bUnwarpJ_.elasticTransformImageMacro", "/tmp/green.jpg",
> "/tmp/blue.jpg", "blueimage_direct_transf.txt", "/tmp/bluegreen.tif");
>
> I get the error that "blueimage_direct_trans.txt" does not exist.
>
> When I look for it, I note that the data is there, but it's in a file named
> "get_image=greenimage"!
>
> Any help would be appreciated.
>
> thanks,
>
> billo
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Odd-bUnwarpJ-behavior-help-tp5018552.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>


--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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


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Re: Odd bUnwarpJ behavior -- help!

billo
In reply to this post by Ignacio Arganda-Carreras-2

Here's a little bit more info. I took out everything from the macro except reading the files and running bUnwarpJ. The problem persists.

First, here's the linux bash script that invokes ImageJ:

% cat jnk.sh

#!/bin/sh
command='./jre/bin/java -Xmx2048m -jar ij.jar -macro billo1.txt "/home/oliver/micros/baby_micros/orig/DSC_2261.JPG /home/oliver/micros/baby_micros/orig/DSC_22
63.JPG"'
eval $command


Here's the modified macro in its entirety:



%cat billo1.txt

position=indexOf(tmpfiles," ");
firstfile=substring(tmpfiles,0,position);
endpos=lengthOf(tmpfiles);
secondfile=substring(tmpfiles,position+1,endpos);
open(firstfile);
open(secondfile);

run("bUnwarpJ", "source_image=firstfile target_image=secondfile registration=Mono image_subsample_factor=0 initial_deformation=[Very Coarse] final_deformation
=Coarse divergence_weight=0 curl_weight=0 landmark_weight=0 image_weight=1 consistency_weight=10 stop_threshold=0.01 save_transformations");
close();
run("Quit");


Running this results in the writing of a file named "'get_image=secondfile'" that has the information that should be in firstfile_direct_transf.txt.


billo




On Sat, 2017-04-15 at 08:16 -0700, Ignacio Arganda-Carreras-2 [via ImageJ] wrote:
Hello Billo,

It looks like your path to "blueimage_direct_trans.txt" is not complete.
Have you tried using the whole path to the file?

On Sat, Apr 15, 2017 at 2:56 AM, billo <[hidden email]> wrote:

> I am trying to use bUnwarpJ from a macro in ImageJ (not Fiji) on a linux
> box
> running Fedora 25.
>
> My commands inthe macro are:
>
> run("bUnwarpJ", "source_image=blueimage target_image=greenimage
> registration=Mono image_subsample_factor=0 initial_deformation=[Very
> Coarse]
> final_deformation=Coarse divergence_weight=0 curl_weight=0
> landmark_weight=0
> image_weight=1 consistency_weight=10 stop_threshold=0.01
> save_transformations");
> selectImage("Registered Source Image");
> close();
>
> call("bunwarpj.bUnwarpJ_.elasticTransformImageMacro", "/tmp/green.jpg",
> "/tmp/blue.jpg", "blueimage_direct_transf.txt", "/tmp/bluegreen.tif");
>
> I get the error that "blueimage_direct_trans.txt" does not exist.
>
> When I look for it, I note that the data is there, but it's in a file named
> "get_image=greenimage"!
>
> Any help would be appreciated.
>
> thanks,
>
> billo
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Odd-bUnwarpJ-behavior-help-tp5018552.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>


--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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



If you reply to this email, your message will be added to the discussion below:
http://imagej.1557.x6.nabble.com/Odd-bUnwarpJ-behavior-help-tp5018552p5018553.html
To unsubscribe from Odd bUnwarpJ behavior -- help!, click here.
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