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Hi
I wrote a macro a while ago using the macro recorder and some additional lines of code. Its been great but I now need to write a description complete with pictures of the various steps. When I made the macro initially I also used a command that showed on the screen the progress of the macro, ie the individual steps but I have now forgotten what it was! Can anyone help? Hope this makes sense, and thanks in advance for your help, Rose |
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On Thu, Oct 25, 2012 at 11:29 AM, Rose Wilson <[hidden email]> wrote:
> When I made the macro initially I also used a command that showed on the > screen the progress of the macro, ie the individual steps but I have now > forgotten what it was! > Perhaps you were using IJ.log() or showProgress() > Rose Pariksheet -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Rose Wilson
Dear Rose,
Maybe you are looking for Plugins > Utilities > monitor events Best wishes Kees ________________________________________ From: ImageJ Interest Group [[hidden email]] On Behalf Of Rose Wilson [[hidden email]] Sent: 25 October 2012 16:29 To: [hidden email] Subject: Command to see whats happening in my macro? Hi I wrote a macro a while ago using the macro recorder and some additional lines of code. Its been great but I now need to write a description complete with pictures of the various steps. When I made the macro initially I also used a command that showed on the screen the progress of the macro, ie the individual steps but I have now forgotten what it was! Can anyone help? Hope this makes sense, and thanks in advance for your help, Rose -- View this message in context: http://imagej.1557.n6.nabble.com/Command-to-see-whats-happening-in-my-macro-tp5000523.html Sent from the ImageJ mailing list archive at Nabble.com. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Kees
thanks for the suggestion but I don't have that option under utilities... Rose |
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In reply to this post by Pariksheet Nanda
Hi Pariksheet,
I have tried both of these, but it comes up with the error; 'Number or numeric function expected in line 10' Is there a certain place it should go? I tried both at the top (as below) with the other general bits, but I did also try it before and after the run(Find Maxima .....) command too. Do you have any suggestions? Many thanks,Rose // Ask user for source and destination directories dir = getDirectory("Roses Source Directory"); dest1 = getDirectory("Roses Destination Directory"); dest2 = getDirectory("Roses Destination2 Directory"); list = getFileList(dir); setBatchMode(true); IJ.log() for (i=0; i<list.length; i++) { name = list[i]; path = dir + name; // Open image open(path); // Macro run("Find Maxima...", "noise=55 output=[Maxima Within Tolerance]"); run("Close-"); //run("Threshold..."); setThreshold(255, 255); run("Convert to Mask"); run("Analyze Particles...", "size=3000-Infinity pixel circularity=0.00-1.00 show=Outlines display exclude"); // saveAs("Tiff", dest1+name); close(); close(); Rosemary Wilson Department of Biology, University of York, Heslington, York, YO10 5YW Tel: +44 (0)1904 328569 Email: [hidden email] EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm On 26 Oct 2012, at 12:45, Pariksheet Nanda [via ImageJ] wrote: On Thu, Oct 25, 2012 at 11:29 AM, Rose Wilson <<a href="x-msg://28/user/SendEmail.jtp?type=node&node=5000543&i=0" target="_top" rel="nofollow" link="external">[hidden email]> wrote: ... [show rest of quote] |
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Hi Rose,
ImageJ text windows have a 'Debug' menu, where you can select 'Debug macro' and then step through the macro with ctrl-E (command-E on Macs). On Macs, you need to have the text window in the foreground; otherwise the menu is gone. In your case, the IJ.log() statement without any argument causes an error; to output a blank line, use IJ.log(""); Michael _______________________________________________________________________ On Fri, October 26, 2012 15:03, Rose Wilson wrote: > Hi Pariksheet, > I have tried both of these, but it comes up with the error; > 'Number or numeric function expected in line 10' > > Is there a certain place it should go? I tried both at the top (as below) > with the other general bits, but I did also try it before and after the > run(Find Maxima .....) command too. > > Do you have any suggestions? > Many thanks,Rose > > // Ask user for source and destination directories > dir = getDirectory("Roses Source Directory"); > dest1 = getDirectory("Roses Destination Directory"); > dest2 = getDirectory("Roses Destination2 Directory"); > > list = getFileList(dir); > setBatchMode(true); > IJ.log() > > for (i=0; i<list.length; i++) { > name = list[i]; > path = dir + name; > > // Open image > open(path); > // Macro > run("Find Maxima...", "noise=55 output=[Maxima Within Tolerance]"); > run("Close-"); > //run("Threshold..."); > setThreshold(255, 255); > run("Convert to Mask"); > run("Analyze Particles...", "size=3000-Infinity pixel > circularity=0.00-1.00 show=Outlines display exclude"); > // > saveAs("Tiff", dest1+name); > close(); > close(); > > Rosemary Wilson > Department of Biology, > University of York, > Heslington, > York, > YO10 5YW > Tel: +44 (0)1904 328569 > Email: [hidden email] > > EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm > > > > > On 26 Oct 2012, at 12:45, Pariksheet Nanda [via ImageJ] wrote: > >> On Thu, Oct 25, 2012 at 11:29 AM, Rose Wilson <[hidden email]> wrote: >> > When I made the macro initially I also used a command that showed on >> the >> > screen the progress of the macro, ie the individual steps but I have >> now >> > forgotten what it was! >> > >> >> Perhaps you were using IJ.log() or showProgress() >> >> >> > Rose >> >> Pariksheet >> >> -- >> 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.n6.nabble.com/Command-to-see-whats-happening-in-my-macro-tp5000523p5000543.html >> To unsubscribe from Command to see whats happening in my macro?, click >> here. >> NAML > > > > > > -- > View this message in context: > http://imagej.1557.n6.nabble.com/Command-to-see-whats-happening-in-my-macro-tp5000523p5000545.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Rose Wilson
On Fri, Oct 26, 2012 at 9:03 AM, Rose Wilson <[hidden email]> wrote:
> I have tried both of these, but it comes up with the error > As Michael explained, I neglected to point out that both the functions need a parameter. The macro function documentation page explains that IJ.log(string) needs a string, and showProgress(progress) uses a number between 0 and 1: http://imagej.nih.gov/ij/developer/macro/functions.html > Is there a certain place it should go? > You could put the progress indicator as the first statement in your "for" loop. To use showProgress you could add this 1 line right after the "for" statement (I'm redundantly including 1 statement before and after for context): for (i=0; i<list.length; i++) { showProgress((i+1) / list.length); name = list[i]; ...or if commands you are running in the loop are using their own progress bar clouding the progress of your macro, you could add this 1 line instead: IJ.log("Processing file " + i+1 + " of " + list.length); > Many thanks,Rose Pariksheet -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Pariksheet and Michael,
Thanks both for your help with this, its much appreciated. I'm not really a computer person so none of this is obvious for me! The IJ.log("Processing file " + i+1 + " of " + list.length); worked to show progress but I realise I have asked the wrong question! The piece of code I'm looking for is one which shows the pictures generated by the macro at each step, ie open image, find maxima, set threshold, etc as the macro progresses (like you would see if you were doing it manually) rather than it doing it in the background. Does that make sense? I need to check that my manual description is correct so I need to check the images that are generated at each step are the same. Thanks again for your help, Rose |
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Hi Rose,
> The piece of code I'm looking for is one which shows the pictures > generated by the macro at each step, ie open image, find maxima, set > threshold, etc as the macro progresses (like you would see if you were > doing it manually) rather than it doing it in the background. Did you try removing the line: setBatchMode(true); With batch mode off, images will pop up, etc., as though you were performing the commands manually. Once you are certain the macro works the way you expect, you can put the setBatchMode command back to make it run faster. Regards, Curtis On Tue, Oct 30, 2012 at 6:55 AM, Rose Wilson <[hidden email]> wrote: > Hi Pariksheet and Michael, > > Thanks both for your help with this, its much appreciated. I'm not really a > computer person so none of this is obvious for me! > > The IJ.log("Processing file " + i+1 + " of " + list.length); worked to show > progress but I realise I have asked the wrong question! > > The piece of code I'm looking for is one which shows the pictures generated > by the macro at each step, ie open image, find maxima, set threshold, etc > as the macro progresses (like you would see if you were doing it manually) > rather than it doing it in the background. Does that make sense? > > I need to check that my manual description is correct so I need to check > the > images that are generated at each step are the same. > > Thanks again for your help, > Rose > > > > -- > View this message in context: > http://imagej.1557.n6.nabble.com/Command-to-see-whats-happening-in-my-macro-tp5000523p5000584.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Curtis,
thats it! It does exactly what I wanted and works fine. Thank you very much, much appreciated! Rose |
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