Background substraction and LUT inconsitent on a folder

[Eric Denarier]

Hi All,
With the following code several of the images (image size 356ko) of a
folder are saved with their original color instead of beeing all orange.
Any suggestion ?


It may seem that adding a wait(100); after run ("Orange Hot"); is working

but then how to know what should be the "wait" value???

Is there an other way to fix the problem ??


enclosed two files for a test.

Thanks for your help


I used Both FIJI : image2 2.0.0-rc-56/1.51h
and ImageJ 1.51i5
on Windows7 with the same problems


Thank you


/////////// Code here //////////

inputDir = getDirectory("Choose Source Directory ");
outputDir = getDirectory("Choose Destination Directory ");
list = getFileList(inputDir);

for (k=0; k<list.length; k++) {
open(inputDir +list[k]);

run ("Subtract Background...", "rolling=100");
run( "Orange Hot", "");
saveAs("Jpeg", outputDir +list[k]);
close(); }

--

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U1216
Chemin Fortuné Ferrini
38700 La Tronche
France

Tél :[phone]

http://neurosciences.ujf-grenoble.fr/


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

[Krs5]

I noticed that there is an overlay on your images. If I remove the overlay I can save with the new LUT or for example as 16-bit, what also does not seem to work for your images.

Not sure if this is intended behaviour...

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Eric Denarier
Sent: 20 February 2017 13:34
To: [hidden email]
Subject: Background substraction and LUT inconsitent on a folder

Hi All,
With the following code several of the images (image size 356ko) of a folder are saved with their original color instead of beeing all orange.
Any suggestion ?


It may seem that adding a wait(100); after run ("Orange Hot"); is working

but then how to know what should be the "wait" value???

Is there an other way to fix the problem ??


enclosed two files for a test.

Thanks for your help


I used Both FIJI : image2 2.0.0-rc-56/1.51h
and ImageJ 1.51i5
on Windows7 with the same problems


Thank you


/////////// Code here //////////

inputDir = getDirectory("Choose Source Directory ");
outputDir = getDirectory("Choose Destination Directory ");
list = getFileList(inputDir);

for (k=0; k<list.length; k++) {
open(inputDir +list[k]);

run ("Subtract Background...", "rolling=100");
run( "Orange Hot", "");
saveAs("Jpeg", outputDir +list[k]);
close(); }

--

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U1216
Chemin Fortuné Ferrini
38700 La Tronche
France

Tél :[phone]

http://neurosciences.ujf-grenoble.fr/


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

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

[Cammer, Michael]

I tried opening the LUT and then saving, then reopening, and it worked fine remembering the new LUT with the overlays intact.

I'm using ImageJ 1.51j9 Java 1.6.0_20 on Win7

=*===========================================================*=
 Michael Cammer, DART Microscopy Laboratory, NYU Langone Medical Center
    Cell:  914-309-3270     Office: Skirball 2nd Floor main office, back right
      http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/


-----Original Message-----
From: Straatman, Kees (Dr.) [mailto:[hidden email]]
Sent: Monday, February 20, 2017 11:58 AM
To: [hidden email]
Subject: Re: Background substraction and LUT inconsitent on a folder

I noticed that there is an overlay on your images. If I remove the overlay I can save with the new LUT or for example as 16-bit, what also does not seem to work for your images.



Not sure if this is intended behaviour...



Kees



-----Original Message-----

From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Eric Denarier

Sent: 20 February 2017 13:34

To: [hidden email]

Subject: Background substraction and LUT inconsitent on a folder



Hi All,

With the following code several of the images (image size 356ko) of a folder are saved with their original color instead of beeing all orange.

Any suggestion ?





It may seem that adding a wait(100); after run ("Orange Hot"); is working



but then how to know what should be the "wait" value???



Is there an other way to fix the problem ??





enclosed two files for a test.



Thanks for your help





I used Both FIJI : image2 2.0.0-rc-56/1.51h

and ImageJ 1.51i5

on Windows7 with the same problems





Thank you





/////////// Code here //////////



inputDir = getDirectory("Choose Source Directory ");

outputDir = getDirectory("Choose Destination Directory ");

list = getFileList(inputDir);



for (k=0; k<list.length; k++) {

open(inputDir +list[k]);



run ("Subtract Background...", "rolling=100");

run( "Orange Hot", "");

saveAs("Jpeg", outputDir +list[k]);

close(); }



--



Eric Denarier

Grenoble Institut des Neurosciences

Inserm U1216

Chemin Fortuné Ferrini

38700 La Tronche

France



Tél :[phone]



https://urldefense.proofpoint.com/v2/url?u=http-3A__neurosciences.ujf-2Dgrenoble.fr_&d=DQIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=CRjlD1ZNrMIrv-70EprXtKWHOKKsHF_9UoC3-JGLy5o&s=2SuIGmsoc1VOfuiQzlM2DVUsXOxv0PGAN5WrCivVnXU&e= 





--

ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DQIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=CRjlD1ZNrMIrv-70EprXtKWHOKKsHF_9UoC3-JGLy5o&s=zE6JLvQua52AAfwPBzEoApfU5sMgC5V8pVPkTyaKDiI&e= 



--

ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DQIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=CRjlD1ZNrMIrv-70EprXtKWHOKKsHF_9UoC3-JGLy5o&s=zE6JLvQua52AAfwPBzEoApfU5sMgC5V8pVPkTyaKDiI&e= 


------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================


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

[Eric Denarier]

I also removed the overlays but it does the same. Strange behavior !!!

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U1216
Chemin Fortuné Ferrini
38700 La Tronche
France

Tél :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 20/02/2017 17:57, Straatman, Kees (Dr.) a écrit :

> I noticed that there is an overlay on your images. If I remove the overlay I can save with the new LUT or for example as 16-bit, what also does not seem to work for your images.
>
> Not sure if this is intended behaviour...
>
> Kees
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Eric Denarier
> Sent: 20 February 2017 13:34
> To: [hidden email]
> Subject: Background substraction and LUT inconsitent on a folder
>
> Hi All,
> With the following code several of the images (image size 356ko) of a folder are saved with their original color instead of beeing all orange.
> Any suggestion ?
>
>
> It may seem that adding a wait(100); after run ("Orange Hot"); is working
>
> but then how to know what should be the "wait" value???
>
> Is there an other way to fix the problem ??
>
>
> enclosed two files for a test.
>
> Thanks for your help
>
>
> I used Both FIJI : image2 2.0.0-rc-56/1.51h
> and ImageJ 1.51i5
> on Windows7 with the same problems
>
>
> Thank you
>
>
> /////////// Code here //////////
>
> inputDir = getDirectory("Choose Source Directory ");
> outputDir = getDirectory("Choose Destination Directory ");
> list = getFileList(inputDir);
>
> for (k=0; k<list.length; k++) {
> open(inputDir +list[k]);
>
> run ("Subtract Background...", "rolling=100");
> run( "Orange Hot", "");
> saveAs("Jpeg", outputDir +list[k]);
> close(); }
>

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