Problems running Versatile Wand in batch mode
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Problems running Versatile Wand in batch mode
 
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Hi,
I'm trying to use Versatile Wand in batch mode. The following macro works well in batch mode: setBatchMode(true); open(); makePoint(1854, 726); run("Gaussian Blur...", "sigma=2"); run("Set Scale...", "distance=0"); run("Versatile Wand", "value=60 color=-100 gradient=10 connectedness=8-connected x=2 y=2 do"); run("ROI Manager..."); roiManager("Add"); saveAs("Tiff"); However - when I try to work with multiple images, select the active image and then use the Versatile Wand, no selection is created: setBatchMode(true); open(); image1ID = getImageID(); open(); image2ID = getImageID(); selectImage(image1ID); if(isActive(image1ID)){ print("The first image is active"); } else { print("The first image isn't active"); } if(isActive(image2ID)){ print("The second image is active"); } else { print("The second image isn't active"); } makePoint(1854, 726); run("Gaussian Blur...", "sigma=2"); run("Set Scale...", "distance=0"); run("Versatile Wand", "value=60 color=-100 gradient=10 connectedness=8-connected x=2 y=2 do"); run("ROI Manager..."); roiManager("Add"); saveAs("Tiff"); Why wouldn't this script work? Only one image is active. Thank you, Avital -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Problems running Versatile Wand in batch mode
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Hi Avital,
sorry, I can't reproduce the problem. Your macro works; it blurs the first image and does the wand selection on it. I also get the selection in the ROI Manager. I tried with both 8-bit grayscale as well as RGB images. What I don't understand is the "makePoint(1854, 726)" command; Gaussian Blur does not care about point selections. So it blurs the whole image. I am using ImageJ 1.49u4, Java 1.6.0_45. Michael ________________________________________________________________ On May 19, 2015, at 17:01, Avital Steinberg wrote: > Hi, > I'm trying to use Versatile Wand in batch mode. The following macro works > well in batch mode: > > setBatchMode(true); > open(); > makePoint(1854, 726); > run("Gaussian Blur...", "sigma=2"); > run("Set Scale...", "distance=0"); > run("Versatile Wand", "value=60 color=-100 gradient=10 > connectedness=8-connected x=2 y=2 do"); > run("ROI Manager..."); > roiManager("Add"); > saveAs("Tiff"); > > However - when I try to work with multiple images, select the active image > and then use the Versatile Wand, no selection is created: > > setBatchMode(true); > open(); > image1ID = getImageID(); > open(); > image2ID = getImageID(); > selectImage(image1ID); > if(isActive(image1ID)){ > print("The first image is active"); > } > else { > print("The first image isn't active"); > } > > if(isActive(image2ID)){ > print("The second image is active"); > } > else { > print("The second image isn't active"); > } > makePoint(1854, 726); > run("Gaussian Blur...", "sigma=2"); > run("Set Scale...", "distance=0"); > run("Versatile Wand", "value=60 color=-100 gradient=10 connectedness=8-connected x=2 y=2 do"); > run("ROI Manager..."); > roiManager("Add"); > saveAs("Tiff"); > > Why wouldn't this script work? Only one image is active. > > Thank you, > Avital -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Problems running Versatile Wand in batch mode
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Thanks, but the problem isn't solved. Can anyone else check if they're
having similar problems running this code? Does this code create a selection in the saved image also for you? setBatchMode(true); open(); image1ID = getImageID(); open(); image2ID = getImageID(); selectImage(image1ID); if(isActive(image1ID)){ print("The first image is active"); } else { print("The first image isn't active"); } if(isActive(image2ID)){ print("The second image is active"); } else { print("The second image isn't active"); } makePoint(1854, 726); run("Gaussian Blur...", "sigma=2"); run("Set Scale...", "distance=0"); run("Versatile Wand", "value=60 color=-100 gradient=10 connectedness=8-connected x=2 y=2 do"); run("ROI Manager..."); roiManager("Add"); saveAs("Tiff"); I am using ImageJ 1.49t7, which came with Java 1.6.0_065 (64 bit). I am running it on a mac, but I had the same problems also on a Linux machine with ImageJ 1.49s and java 1.6.0_24. MakePoint isn't needed, but it's besides the point, since the bug has nothing to do with it and exists also without it. Thanks, Avital On Tue, May 19, 2015 at 6:25 PM, Michael Schmid <[hidden email]> wrote: > Hi Avital, > > sorry, I can't reproduce the problem. Your macro works; it blurs the first > image and does the wand selection on it. I also get the selection in the > ROI Manager. > I tried with both 8-bit grayscale as well as RGB images. > > What I don't understand is the "makePoint(1854, 726)" command; Gaussian > Blur does not care about point selections. So it blurs the whole image. > > I am using ImageJ 1.49u4, Java 1.6.0_45. > > Michael > ________________________________________________________________ > On May 19, 2015, at 17:01, Avital Steinberg wrote: > > > Hi, > > I'm trying to use Versatile Wand in batch mode. The following macro works > > well in batch mode: > > > > setBatchMode(true); > > open(); > > makePoint(1854, 726); > > run("Gaussian Blur...", "sigma=2"); > > run("Set Scale...", "distance=0"); > > run("Versatile Wand", "value=60 color=-100 gradient=10 > > connectedness=8-connected x=2 y=2 do"); > > run("ROI Manager..."); > > roiManager("Add"); > > saveAs("Tiff"); > > > > However - when I try to work with multiple images, select the active > image > > and then use the Versatile Wand, no selection is created: > > > > setBatchMode(true); > > open(); > > image1ID = getImageID(); > > open(); > > image2ID = getImageID(); > > selectImage(image1ID); > > if(isActive(image1ID)){ > > print("The first image is active"); > > } > > else { > > print("The first image isn't active"); > > } > > > > if(isActive(image2ID)){ > > print("The second image is active"); > > } > > else { > > print("The second image isn't active"); > > } > > makePoint(1854, 726); > > run("Gaussian Blur...", "sigma=2"); > > run("Set Scale...", "distance=0"); > > run("Versatile Wand", "value=60 color=-100 gradient=10 > connectedness=8-connected x=2 y=2 do"); > > run("ROI Manager..."); > > roiManager("Add"); > > saveAs("Tiff"); > > > > Why wouldn't this script work? Only one image is active. > > > > Thank you, > > Avital > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Sorry, cannot reproduce the problem. An image is saved with a selection included.
Running Fiji on Windows 7 Kees -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Avital Steinberg Sent: 20 May 2015 10:36 To: [hidden email] Subject: Re: Problems running Versatile Wand in batch mode Thanks, but the problem isn't solved. Can anyone else check if they're having similar problems running this code? Does this code create a selection in the saved image also for you? setBatchMode(true); open(); image1ID = getImageID(); open(); image2ID = getImageID(); selectImage(image1ID); if(isActive(image1ID)){ print("The first image is active"); } else { print("The first image isn't active"); } if(isActive(image2ID)){ print("The second image is active"); } else { print("The second image isn't active"); } makePoint(1854, 726); run("Gaussian Blur...", "sigma=2"); run("Set Scale...", "distance=0"); run("Versatile Wand", "value=60 color=-100 gradient=10 connectedness=8-connected x=2 y=2 do"); run("ROI Manager..."); roiManager("Add"); saveAs("Tiff"); I am using ImageJ 1.49t7, which came with Java 1.6.0_065 (64 bit). I am running it on a mac, but I had the same problems also on a Linux machine with ImageJ 1.49s and java 1.6.0_24. MakePoint isn't needed, but it's besides the point, since the bug has nothing to do with it and exists also without it. Thanks, Avital On Tue, May 19, 2015 at 6:25 PM, Michael Schmid <[hidden email]> wrote: > Hi Avital, > > sorry, I can't reproduce the problem. Your macro works; it blurs the > first image and does the wand selection on it. I also get the > selection in the ROI Manager. > I tried with both 8-bit grayscale as well as RGB images. > > What I don't understand is the "makePoint(1854, 726)" command; > Gaussian Blur does not care about point selections. So it blurs the whole image. > > I am using ImageJ 1.49u4, Java 1.6.0_45. > > Michael > ________________________________________________________________ > On May 19, 2015, at 17:01, Avital Steinberg wrote: > > > Hi, > > I'm trying to use Versatile Wand in batch mode. The following macro > > works well in batch mode: > > > > setBatchMode(true); > > open(); > > makePoint(1854, 726); > > run("Gaussian Blur...", "sigma=2"); > > run("Set Scale...", "distance=0"); > > run("Versatile Wand", "value=60 color=-100 gradient=10 > > connectedness=8-connected x=2 y=2 do"); run("ROI Manager..."); > > roiManager("Add"); saveAs("Tiff"); > > > > However - when I try to work with multiple images, select the active > image > > and then use the Versatile Wand, no selection is created: > > > > setBatchMode(true); > > open(); > > image1ID = getImageID(); > > open(); > > image2ID = getImageID(); > > selectImage(image1ID); > > if(isActive(image1ID)){ > > print("The first image is active"); } else { > > print("The first image isn't active"); } > > > > if(isActive(image2ID)){ > > print("The second image is active"); } else { > > print("The second image isn't active"); } makePoint(1854, 726); > > run("Gaussian Blur...", "sigma=2"); run("Set Scale...", > > "distance=0"); run("Versatile Wand", "value=60 color=-100 > > gradient=10 > connectedness=8-connected x=2 y=2 do"); > > run("ROI Manager..."); > > roiManager("Add"); > > saveAs("Tiff"); > > > > Why wouldn't this script work? Only one image is active. > > > > Thank you, > > Avital > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Problems running Versatile Wand in batch mode
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Thanks - I updated ImageJ to the latest daily build (since Michael seemed
to be using a version of ImageJ which was up to date), but I still have the same problem, Avital On Wed, May 20, 2015 at 12:53 PM, Straatman, Kees (Dr.) < [hidden email]> wrote: > Sorry, cannot reproduce the problem. An image is saved with a selection > included. > > Running Fiji on Windows 7 > > Kees > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Avital Steinberg > Sent: 20 May 2015 10:36 > To: [hidden email] > Subject: Re: Problems running Versatile Wand in batch mode > > Thanks, but the problem isn't solved. Can anyone else check if they're > having similar problems running this code? Does this code create a > selection in the saved image also for you? > > setBatchMode(true); > open(); > image1ID = getImageID(); > open(); > image2ID = getImageID(); > selectImage(image1ID); > if(isActive(image1ID)){ > print("The first image is active"); > } > else { > print("The first image isn't active"); } > > if(isActive(image2ID)){ > print("The second image is active"); } else { > print("The second image isn't active"); } makePoint(1854, 726); > run("Gaussian Blur...", "sigma=2"); run("Set Scale...", "distance=0"); > run("Versatile Wand", "value=60 color=-100 gradient=10 > connectedness=8-connected x=2 y=2 do"); run("ROI Manager..."); > roiManager("Add"); saveAs("Tiff"); > > > I am using ImageJ 1.49t7, which came with Java 1.6.0_065 (64 bit). I am > running it on a mac, but I had the same problems also on a Linux machine > with ImageJ 1.49s and java 1.6.0_24. > > MakePoint isn't needed, but it's besides the point, since the bug has > nothing to do with it and exists also without it. > > Thanks, > Avital > > On Tue, May 19, 2015 at 6:25 PM, Michael Schmid <[hidden email]> > wrote: > > > Hi Avital, > > > > sorry, I can't reproduce the problem. Your macro works; it blurs the > > first image and does the wand selection on it. I also get the > > selection in the ROI Manager. > > I tried with both 8-bit grayscale as well as RGB images. > > > > What I don't understand is the "makePoint(1854, 726)" command; > > Gaussian Blur does not care about point selections. So it blurs the > whole image. > > > > I am using ImageJ 1.49u4, Java 1.6.0_45. > > > > Michael > > ________________________________________________________________ > > On May 19, 2015, at 17:01, Avital Steinberg wrote: > > > > > Hi, > > > I'm trying to use Versatile Wand in batch mode. The following macro > > > works well in batch mode: > > > > > > setBatchMode(true); > > > open(); > > > makePoint(1854, 726); > > > run("Gaussian Blur...", "sigma=2"); > > > run("Set Scale...", "distance=0"); > > > run("Versatile Wand", "value=60 color=-100 gradient=10 > > > connectedness=8-connected x=2 y=2 do"); run("ROI Manager..."); > > > roiManager("Add"); saveAs("Tiff"); > > > > > > However - when I try to work with multiple images, select the active > > image > > > and then use the Versatile Wand, no selection is created: > > > > > > setBatchMode(true); > > > open(); > > > image1ID = getImageID(); > > > open(); > > > image2ID = getImageID(); > > > selectImage(image1ID); > > > if(isActive(image1ID)){ > > > print("The first image is active"); } else { > > > print("The first image isn't active"); } > > > > > > if(isActive(image2ID)){ > > > print("The second image is active"); } else { > > > print("The second image isn't active"); } makePoint(1854, 726); > > > run("Gaussian Blur...", "sigma=2"); run("Set Scale...", > > > "distance=0"); run("Versatile Wand", "value=60 color=-100 > > > gradient=10 > > connectedness=8-connected x=2 y=2 do"); > > > run("ROI Manager..."); > > > roiManager("Add"); > > > saveAs("Tiff"); > > > > > > Why wouldn't this script work? Only one image is active. > > > > > > Thank you, > > > Avital > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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