Hi all,
I am trying to use the Batch macro function with this line of code : run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); Output format is tiff The files are saved in the correct folder but still as stacks and not as projections. Any comments ? -- Eric Denarier Grenoble Institut des Neurosciences Inserm U836 Chemin Fortuné Ferrini 38700 La Tronche France Tél :33 (0)4 56 52 05 38 Fax :33 (0)4 56 52 06 57 http://neurosciences.ujf-grenoble.fr/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
On Wednesday 03 Oct 2012 11:03:06 you wrote:
> Hi all, > I am trying to use the Batch macro function with this line of code : > run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); > Output format is tiff > The files are saved in the correct folder but still as stacks and not as > projections. > Any comments ? Probably because you have not "selected" the image to save, so it saves the one which is currently selected. Cheers Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
On Wed, Oct 3, 2012 at 12:19 PM, Gabriel Landini <[hidden email]>wrote:
> On Wednesday 03 Oct 2012 11:03:06 you wrote: > > Hi all, > > I am trying to use the Batch macro function with this line of code : > > run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); > > Output format is tiff > > The files are saved in the correct folder but still as stacks and not as > > projections. > > Any comments ? > > Probably because you have not "selected" the image to save, so it saves the > one which is currently selected. > > Cheers > Gabriel > ... which would look something like orgID = getImageID(); run("Z Project...", "start=1 stop=72 projection=[Max Intensity]"); projID = getImageID(); selectImage(orgID); close(); selectImage(projID); Kota > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- -------------------------------------------------------------*Dr. Kota Miura* Scientist & IT Engineer Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg GERMANY Tel +49 6221 387 404 Mobile +49 160 95001177 Fax +49 6221 387 512 http://cmci.embl.de ------------------------------------------------------------- -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
In reply to this post by Gabriel Landini
I tried Kota's code (see below). It doesn't work.
A precision maybe : I am working with composite stacks (2 channels, 9 z) I tried with 1 channel stack and it does the same. orgID = getImageID(); run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); projID = getImageID(); selectImage(orgID); close(); selectImage(projID); Eric Denarier Grenoble Institut des Neurosciences Inserm U836 Chemin Fortuné Ferrini 38700 La Tronche France Tél :33 (0)4 56 52 05 38 Fax :33 (0)4 56 52 06 57 http://neurosciences.ujf-grenoble.fr/ Le 03/10/2012 12:19, Gabriel Landini a écrit : > On Wednesday 03 Oct 2012 11:03:06 you wrote: >> Hi all, >> I am trying to use the Batch macro function with this line of code : >> run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); >> Output format is tiff >> The files are saved in the correct folder but still as stacks and not as >> projections. >> Any comments ? > Probably because you have not "selected" the image to save, so it saves the > one which is currently selected. > > Cheers > Gabriel > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Eric,
On Wed, 3 Oct 2012, Eric Denarier wrote: > I tried Kota's code (see below). It doesn't work. > A precision maybe : I am working with composite stacks (2 channels, 9 z) > I tried with 1 channel stack and it does the same. > > orgID = getImageID(); > run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); > projID = getImageID(); > selectImage(orgID); > close(); > selectImage(projID); Rather than letting Kota and Gabriel guess, why not making available your macro and some example files? It takes such a needlessly long time to try to reproduce problems... Ciao, Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
In reply to this post by Kota Miura
To clarify : the problem is only when I use the Process/Batch/macro.
If I use the macro directly on one stack it works great. Maybe I do not use the function Process/Batch/macro correctly. In the Batch Process windows output format is : tif and Add Macro Code is : [Select from list] I join a stack (reduced in size) I upgraded imageJ to 1.47c : it is still not working Here is the macro I used original = getTitle(); run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); proj = getTitle(); selectImage(original); close(); selectImage(proj); Eric Denarier Grenoble Institut des Neurosciences Inserm U836 Chemin Fortuné Ferrini 38700 La Tronche France Tél :33 (0)4 56 52 05 38 Fax :33 (0)4 56 52 06 57 http://neurosciences.ujf-grenoble.fr/ Le 03/10/2012 12:25, Kota Miura a écrit : > > > On Wed, Oct 3, 2012 at 12:19 PM, Gabriel Landini <[hidden email] > <mailto:[hidden email]>> wrote: > > On Wednesday 03 Oct 2012 11:03:06 you wrote: > > Hi all, > > I am trying to use the Batch macro function with this line of code : > > run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); > > Output format is tiff > > The files are saved in the correct folder but still as stacks > and not as > > projections. > > Any comments ? > > Probably because you have not "selected" the image to save, so it > saves the > one which is currently selected. > > Cheers > Gabriel > > > ... which would look something like > > orgID = getImageID(); > run("Z Project...", "start=1 stop=72 projection=[Max Intensity]"); > projID = getImageID(); > selectImage(orgID); > close(); > selectImage(projID); > > Kota > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > -- > ------------------------------------------------------------- > *Dr. Kota Miura* > > Scientist & IT Engineer > Centre for Molecular and Cellular Imaging, > European Molecular Biology Laboratory > Meyerhofstr. 1 > 69117 Heidelberg > GERMANY > > Tel +49 6221 387 404 > Mobile +49 160 95001177 > Fax +49 6221 387 512 > http://cmci.embl.de <http://cmci.embl.de/> > ------------------------------------------------------------- > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Eric,
I reproduced your problem here. I think you better write a full macro for that. In the macro textbook I wrote, http://cmci.embl.de/documents/ijcourses#macro_programming_in_imagej you could refer to p68. 2.5.2 Batch Processing of Files and modify the code 23 in p71 to do your job. Cheers, Kota On Wed, Oct 3, 2012 at 4:51 PM, Eric Denarier <[hidden email] > wrote: > To clarify : the problem is only when I use the Process/Batch/macro. > If I use the macro directly on one stack it works great. > Maybe I do not use the function Process/Batch/macro correctly. > In the Batch Process windows output format is : tif > and Add Macro Code is : [Select from list] > I join a stack (reduced in size) > I upgraded imageJ to 1.47c : it is still not working > > Here is the macro I used > > original = getTitle(); > > run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); > proj = getTitle(); > selectImage(original); > close(); > selectImage(proj); > > > Eric Denarier > Grenoble Institut des Neurosciences > Inserm U836 > Chemin Fortuné Ferrini > 38700 La Tronche > France > > > Tél :33 (0)4 56 52 05 38 > Fax :33 (0)4 56 52 06 57 > > http://neurosciences.ujf-**grenoble.fr/<http://neurosciences.ujf-grenoble.fr/> > > Le 03/10/2012 12:25, Kota Miura a écrit : > >> >> >> On Wed, Oct 3, 2012 at 12:19 PM, Gabriel Landini <[hidden email]<mailto: >> [hidden email]>> wrote: >> >> On Wednesday 03 Oct 2012 11:03:06 you wrote: >> > Hi all, >> > I am trying to use the Batch macro function with this line of code : >> > run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); >> > Output format is tiff >> > The files are saved in the correct folder but still as stacks >> and not as >> > projections. >> > Any comments ? >> >> Probably because you have not "selected" the image to save, so it >> saves the >> one which is currently selected. >> >> Cheers >> Gabriel >> >> >> ... which would look something like >> >> orgID = getImageID(); >> run("Z Project...", "start=1 stop=72 projection=[Max Intensity]"); >> projID = getImageID(); >> selectImage(orgID); >> close(); >> selectImage(projID); >> >> Kota >> >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> >> >> >> >> >> -- >> ------------------------------**------------------------------**- >> *Dr. Kota Miura* >> >> >> Scientist & IT Engineer >> Centre for Molecular and Cellular Imaging, >> European Molecular Biology Laboratory >> Meyerhofstr. 1 >> 69117 Heidelberg >> GERMANY >> >> Tel +49 6221 387 404 >> Mobile +49 160 95001177 >> Fax +49 6221 387 512 >> http://cmci.embl.de <http://cmci.embl.de/> >> ------------------------------**------------------------------**- >> >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html> > -- -------------------------------------------------------------*Dr. Kota Miura* Scientist & IT Engineer Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg GERMANY Tel +49 6221 387 404 Mobile +49 160 95001177 Fax +49 6221 387 512 http://cmci.embl.de ------------------------------------------------------------- -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
In reply to this post by ERIC
On Oct 3, 2012, at 6:03 AM, Eric Denarier wrote:
> Hi all, > I am trying to use the Batch macro function with this line of code : > run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); > Output format is tiff > The files are saved in the correct folder but still as stacks and not as > projections. > Any comments ? Upgrade to the ImageJ 1.47d daily build and this line of macro code will work as expected using the Process>Batch>Macro command. Change the code to run("Z Project...", "projection=[Max Intensity]"); and it will work with stacks of any size. -wayne -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Thanks Wayne,
It works nicely !!! Eric Denarier Grenoble Institut des Neurosciences Inserm U836 Chemin Fortuné Ferrini 38700 La Tronche France Tél :33 (0)4 56 52 05 38 Fax :33 (0)4 56 52 06 57 http://neurosciences.ujf-grenoble.fr/ Le 05/10/2012 04:41, Rasband, Wayne (NIH/NIMH) [E] a écrit : > On Oct 3, 2012, at 6:03 AM, Eric Denarier wrote: > >> Hi all, >> I am trying to use the Batch macro function with this line of code : >> run("Z Project...", "start=1 stop=9 projection=[Max Intensity]"); >> Output format is tiff >> The files are saved in the correct folder but still as stacks and not as >> projections. >> Any comments ? > Upgrade to the ImageJ 1.47d daily build and this line of macro code will work as expected using the Process>Batch>Macro command. Change the code to > > run("Z Project...", "projection=[Max Intensity]"); > > and it will work with stacks of any size. > > -wayne > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Free forum by Nabble | Edit this page |