Help with ImageJ macro code
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Hi all, I hope this is an appropriate place for this question. I'm writing a macro to put together a mask from three images with multiple channels. I am making progress on the macro, but as I test it, I'm running into a problem. When the 402nm image is opened, the windows "Z" and "W" are named properly. When the 488nm image is opened, the windows "A", "C", and "D" are named fine, but the "Z" and "W" windows are renamed to "1". This messes up the creation of the mask and will mess up the analysis that will come further down the line. I have even tried saving each image individually, but the names still get reset. This only occurs occasionally, though. Does anyone have any ideas? I can email the original images if it would help. Thanks in advance! BTW, this may not be the most elegant code, but go easy, I'm a beginner
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Chris //Selects directory to save files to dir = getDirectory("Select save directory"); //Prompt for 402nm image var violet = "Open a 402nm image"; requires("1.34m"); title = "Untitled"; width=512; height=512; Dialog.create("402nm"); Dialog.addMessage(violet); Dialog.show(); //Run ICS opener run("ICS/IDS... "); //Closes 402 unassigned, 402 background, and renames channel 2 as "Z" and channel 1 as "W" close(); close(); rename("Z"); run("Put Behind [tab]"); rename("W"); //Prompt for 488nm image var blue = "Open a 488nm image"; requires("1.34m"); title = "Untitled"; width=512; height=512; Dialog.create("488nm"); Dialog.addMessage(blue); Dialog.show(); //Run ICS opener run("ICS/IDS... "); //Converts stack to images run("Convert Stack to Images"); //Closes 488 unassigned, 488 background, E_488 and renames channel 3 as "D", channel 2 as "C", and channel 1 as "A" close(); close(); close(); rename("D"); run("Put Behind [tab]"); rename("C"); run("Put Behind [tab]"); rename("A"); //Prompt for 561nm image var green = "Open a 561nm image"; requires("1.34m"); title = "Untitled"; width=512; height=512; Dialog.create("561nm"); Dialog.addMessage(green); Dialog.show(); //Run ICS opener run("ICS/IDS... "); //Converts stack to images run("Convert Stack to Images"); //Closes 561 unassigned, 561 background, and renames channel 3 as "gamma", channel 2 as "F", and channel 1 as "E" close(); close(); rename("gamma"); run("Put Behind [tab]"); rename("F"); run("Put Behind [tab]"); rename("E"); //Create a mask run("Duplicate...", "title=Mask"); run("Paste Control..."); setPasteMode("OR"); selectWindow("F"); run("Copy"); selectWindow("Mask"); run("Paste"); selectWindow("gamma"); run("Copy"); selectWindow("Mask"); run("Paste"); selectWindow("D"); run("Copy"); selectWindow("Mask"); run("Paste"); selectWindow("C"); run("Copy"); selectWindow("Mask"); run("Paste"); selectWindow("A"); run("Copy"); selectWindow("Mask"); run("Paste"); selectWindow("Z"); run("Copy"); selectWindow("Mask"); run("Paste"); selectWindow("W"); run("Copy"); selectWindow("Mask"); run("Paste"); |
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To add more frustration, the images don't open the same way reproducibly. I tried rewriting the code so that all 3 raw images are opened, then the macro closes the certain channels I don't want and renames the channels I do want. The windows are still randomly reset to be named "1" and the channels do not come to the front the same way each time.
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Re: Help with ImageJ macro code
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In reply to this post by crieken
I do not know why your images get renamed, but I think the easiest way
to solve this is to use the getImageID() function, which returns a unique ID for the active image, and then use the selectImage(id) function to activate the image later. It has a few benefits: it's faster, the IDs are unique, and the IDs don't change throughout macro execution. I think you can just replace the rename() and selectWindow() statements you have now, and it should work. However, I believe imageCalculator("or", img1, img2) does the same thing as all of those select-copy-select-pastes, so you might use that in order to make the code more succinct. Justin On 1/30/08, crieken <[hidden email]> wrote: > Hi all, I hope this is an appropriate place for this question. I'm writing > a > macro to put together a mask from three images with multiple channels. I am > making progress on the macro, but as I test it, I'm running into a problem. > When the 402nm image is opened, the windows "Z" and "W" are named properly. > When the 488nm image is opened, the windows "A", "C", and "D" are named > fine, but the "Z" and "W" windows are renamed to "1". This messes up the > creation of the mask and will mess up the analysis that will come further > down the line. I have even tried saving each image individually, but the > names still get reset. This only occurs occasionally, though. Does anyone > have any ideas? I can email the original images if it would help. Thanks > in advance! BTW, this may not be the most elegant code, but go easy, I'm a > beginner :confused:. > Chris > > //Selects directory to save files to > dir = getDirectory("Select save directory"); > > //Prompt for 402nm image > var violet = "Open a 402nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("402nm"); > Dialog.addMessage(violet); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Closes 402 unassigned, 402 background, and renames channel 2 as "Z" and > channel 1 as "W" > close(); > close(); > rename("Z"); > run("Put Behind [tab]"); > rename("W"); > > //Prompt for 488nm image > var blue = "Open a 488nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("488nm"); > Dialog.addMessage(blue); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Converts stack to images > run("Convert Stack to Images"); > > //Closes 488 unassigned, 488 background, E_488 and renames channel 3 as "D", > channel 2 as "C", and channel 1 as "A" > close(); > close(); > close(); > rename("D"); > run("Put Behind [tab]"); > rename("C"); > run("Put Behind [tab]"); > rename("A"); > > //Prompt for 561nm image > var green = "Open a 561nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("561nm"); > Dialog.addMessage(green); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Converts stack to images > run("Convert Stack to Images"); > > //Closes 561 unassigned, 561 background, and renames channel 3 as "gamma", > channel 2 as "F", and channel 1 as "E" > close(); > close(); > rename("gamma"); > run("Put Behind [tab]"); > rename("F"); > run("Put Behind [tab]"); > rename("E"); > > //Create a mask > run("Duplicate...", "title=Mask"); > run("Paste Control..."); > setPasteMode("OR"); > selectWindow("F"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("gamma"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("D"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("C"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("A"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("Z"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("W"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > > -- > View this message in context: > http://www.nabble.com/Help-with-ImageJ-macro-code-tp15195190p15195190.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
Antwort: Re: Help with ImageJ macro code
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Hi there,
I had a similar experience that somehow, when using a mcro together with plugins, the "front" window ist not always identical with the "active" resp. "selected" window. I did not look into that issue further, but also changed my code to use unique image IDs similar to what Justin suggests and from that on it worked as expected. Mit freundlichen Grüßen / Best regards Joachim Wesner Projektleiter Optik Technologiesysteme Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht Wetzlar HRB 2432 Geschäftsführer: Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy Martyr | Colin Davis [hidden email] Gesendet von: ImageJ Interest An Group [hidden email] <[hidden email]. Kopie GOV> Thema Re: Help with ImageJ macro code 31.01.2008 04:43 Bitte antworten an ImageJ Interest Group <[hidden email]. GOV> I do not know why your images get renamed, but I think the easiest way to solve this is to use the getImageID() function, which returns a unique ID for the active image, and then use the selectImage(id) function to activate the image later. It has a few benefits: it's faster, the IDs are unique, and the IDs don't change throughout macro execution. I think you can just replace the rename() and selectWindow() statements you have now, and it should work. However, I believe imageCalculator("or", img1, img2) does the same thing as all of those select-copy-select-pastes, so you might use that in order to make the code more succinct. Justin On 1/30/08, crieken <[hidden email]> wrote: > Hi all, I hope this is an appropriate place for this question. I'm writing > a > macro to put together a mask from three images with multiple channels. I am > making progress on the macro, but as I test it, I'm running into a problem. > When the 402nm image is opened, the windows "Z" and "W" are named properly. > When the 488nm image is opened, the windows "A", "C", and "D" are named > fine, but the "Z" and "W" windows are renamed to "1". This messes up the > creation of the mask and will mess up the analysis that will come further > down the line. I have even tried saving each image individually, but the > names still get reset. This only occurs occasionally, though. Does anyone > have any ideas? I can email the original images if it would help. Thanks > in advance! BTW, this may not be the most elegant code, but go easy, I'm a > beginner :confused:. > Chris > > //Selects directory to save files to > dir = getDirectory("Select save directory"); > > //Prompt for 402nm image > var violet = "Open a 402nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("402nm"); > Dialog.addMessage(violet); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Closes 402 unassigned, 402 background, and renames channel 2 as "Z" and > channel 1 as "W" > close(); > close(); > rename("Z"); > run("Put Behind [tab]"); > rename("W"); > > //Prompt for 488nm image > var blue = "Open a 488nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("488nm"); > Dialog.addMessage(blue); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Converts stack to images > run("Convert Stack to Images"); > > //Closes 488 unassigned, 488 background, E_488 and renames channel 3 as > channel 2 as "C", and channel 1 as "A" > close(); > close(); > close(); > rename("D"); > run("Put Behind [tab]"); > rename("C"); > run("Put Behind [tab]"); > rename("A"); > > //Prompt for 561nm image > var green = "Open a 561nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("561nm"); > Dialog.addMessage(green); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Converts stack to images > run("Convert Stack to Images"); > > //Closes 561 unassigned, 561 background, and renames channel 3 as > channel 2 as "F", and channel 1 as "E" > close(); > close(); > rename("gamma"); > run("Put Behind [tab]"); > rename("F"); > run("Put Behind [tab]"); > rename("E"); > > //Create a mask > run("Duplicate...", "title=Mask"); > run("Paste Control..."); > setPasteMode("OR"); > selectWindow("F"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("gamma"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("D"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("C"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("A"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("Z"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > selectWindow("W"); > run("Copy"); > selectWindow("Mask"); > run("Paste"); > > -- > View this message in context: > > Sent from the ImageJ mailing list archive at Nabble.com. > ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
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In reply to this post by Justin McGrath
Great! Thanks for the assistance Justin. I'll let you know how it goes...
Chris
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In reply to this post by Justin McGrath
Hi Justin,
Unfortunately, it doesn't appear that each image is getting a unique ID... unless I'm not using the code correctly. In the end I need to have the windows named "A, C, D, E, F, gamma, W, Z" in order to do particle analysis. I keep getting errors, so I printed the image IDs and there is always a repeat, but it seems to vary. Are the image IDs usually expressed like"-10", "-71", etc.? Thanks for your advice. Chris //Selects directory to save files to dir = getDirectory("Select save directory"); //Prompt for 402nm image var violet = "Open a 402nm image"; requires("1.34m"); title = "Untitled"; width=512; height=512; Dialog.create("402nm"); Dialog.addMessage(violet); Dialog.show(); //Run ICS opener run("ICS/IDS... "); //Closes 402 unassigned, 402 background close(); close(); Z = getImageID(); run("Put Behind [tab]"); W = getImageID(); //Prompt for 488nm image var blue = "Open a 488nm image"; requires("1.34m"); title = "Untitled"; width=512; height=512; Dialog.create("488nm"); Dialog.addMessage(blue); Dialog.show(); //Run ICS opener run("ICS/IDS... "); //Converts stack to images run("Convert Stack to Images"); //Closes 488 unassigned, 488 background, E_488 close(); close(); close(); D = getImageID(); run("Put Behind [tab]"); C = getImageID(); run("Put Behind [tab]"); A = getImageID(); //Prompt for 561nm image var green = "Open a 561nm image"; requires("1.34m"); title = "Untitled"; width=512; height=512; Dialog.create("561nm"); Dialog.addMessage(green); Dialog.show(); //Run ICS opener run("ICS/IDS... "); //Converts stack to images run("Convert Stack to Images"); //Closes 561 unassigned, 561 background close(); close(); gamma = getImageID(); run("Put Behind [tab]"); F = getImageID(); run("Put Behind [tab]"); E = getImageID(); //Prints image IDs print(A); print(C); print(D); print(E); print(F); print(gamma); print(W); print(Z); //Renames windows selectWindow(A); rename("A"); selectWindow(C); rename("C"); selectWindow(D); rename("D"); selectWindow(E); rename("E"); selectWindow(F); rename("F"); selectWindow(gamma); rename("gamma"); selectWindow(W); rename("W"); selectWindow(Z); rename("Z");
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Re: Help with ImageJ macro code
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Hi Chris,
you are right that ImageIDs are negative numbers. They stay valid until an image is closed. A new image that you open gets a new ID that is the last ID used minus one. (strictly speaking, "image" means the ImagePlus class of ImageJ) See the selectImage(id) and getImageID entries on http://rsb.info.nih.gov/ij/developer/macro/functions.html It might be that your problems are caused by run("Put Behind [tab]"); since some operations on Windows happen in a different thread that may be slower than the thread executing the macro. Therefore, to access the images created I would simply try: Z = getImageID(); W = getImageID()+1; //the image created before Z Michael ________________________________________________________________ On 1 Feb 2008, at 01:42, crieken wrote: > Hi Justin, > Unfortunately, it doesn't appear that each image is getting a > unique ID... > unless I'm not using the code correctly. In the end I need to have > the > windows named "A, C, D, E, F, gamma, W, Z" in order to do particle > analysis. > I keep getting errors, so I printed the image IDs and there is > always a > repeat, but it seems to vary. Are the image IDs usually expressed > like"-10", "-71", etc.? Thanks for your advice. > Chris > > > //Selects directory to save files to > dir = getDirectory("Select save directory"); > > //Prompt for 402nm image > var violet = "Open a 402nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("402nm"); > Dialog.addMessage(violet); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Closes 402 unassigned, 402 background > close(); > close(); > Z = getImageID(); > run("Put Behind [tab]"); > W = getImageID(); > > //Prompt for 488nm image > var blue = "Open a 488nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("488nm"); > Dialog.addMessage(blue); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Converts stack to images > run("Convert Stack to Images"); > > //Closes 488 unassigned, 488 background, E_488 > close(); > close(); > close(); > D = getImageID(); > run("Put Behind [tab]"); > C = getImageID(); > run("Put Behind [tab]"); > A = getImageID(); > > > //Prompt for 561nm image > var green = "Open a 561nm image"; > requires("1.34m"); > title = "Untitled"; > width=512; height=512; > Dialog.create("561nm"); > Dialog.addMessage(green); > Dialog.show(); > > //Run ICS opener > run("ICS/IDS... "); > > //Converts stack to images > run("Convert Stack to Images"); > > //Closes 561 unassigned, 561 background > close(); > close(); > gamma = getImageID(); > run("Put Behind [tab]"); > F = getImageID(); > run("Put Behind [tab]"); > E = getImageID(); > > //Prints image IDs > print(A); > print(C); > print(D); > print(E); > print(F); > print(gamma); > print(W); > print(Z); > > > //Renames windows > selectWindow(A); > rename("A"); > selectWindow(C); > rename("C"); > selectWindow(D); > rename("D"); > selectWindow(E); > rename("E"); > selectWindow(F); > rename("F"); > selectWindow(gamma); > rename("gamma"); > selectWindow(W); > rename("W"); > selectWindow(Z); > rename("Z"); > > > Justin McGrath wrote: >> >> I do not know why your images get renamed, but I think the easiest >> way >> to solve this is to use the getImageID() function, which returns a >> unique ID for the active image, and then use the selectImage(id) >> function to activate the image later. It has a few benefits: it's >> faster, the IDs are unique, and the IDs don't change throughout macro >> execution. >> >> I think you can just replace the rename() and selectWindow() >> statements you have now, and it should work. However, I believe >> imageCalculator("or", img1, img2) does the same thing as all of those >> select-copy-select-pastes, so you might use that in order to make the >> code more succinct. >> >> Justin >> >> >> >> On 1/30/08, crieken <[hidden email]> wrote: >>> Hi all, I hope this is an appropriate place for this question. I'm >>> writing >>> a >>> macro to put together a mask from three images with multiple >>> channels. I >>> am >>> making progress on the macro, but as I test it, I'm running into a >>> problem. >>> When the 402nm image is opened, the windows "Z" and "W" are named >>> properly. >>> When the 488nm image is opened, the windows "A", "C", and "D" are >>> named >>> fine, but the "Z" and "W" windows are renamed to "1". This >>> messes up the >>> creation of the mask and will mess up the analysis that will come >>> further >>> down the line. I have even tried saving each image individually, >>> but the >>> names still get reset. This only occurs occasionally, though. Does >>> anyone >>> have any ideas? I can email the original images if it would help. >>> Thanks >>> in advance! BTW, this may not be the most elegant code, but go >>> easy, I'm >>> a >>> beginner :confused:. >>> Chris >>> >>> //Selects directory to save files to >>> dir = getDirectory("Select save directory"); >>> >>> //Prompt for 402nm image >>> var violet = "Open a 402nm image"; >>> requires("1.34m"); >>> title = "Untitled"; >>> width=512; height=512; >>> Dialog.create("402nm"); >>> Dialog.addMessage(violet); >>> Dialog.show(); >>> >>> //Run ICS opener >>> run("ICS/IDS... "); >>> >>> //Closes 402 unassigned, 402 background, and renames channel 2 as >>> "Z" and >>> channel 1 as "W" >>> close(); >>> close(); >>> rename("Z"); >>> run("Put Behind [tab]"); >>> rename("W"); >>> >>> //Prompt for 488nm image >>> var blue = "Open a 488nm image"; >>> requires("1.34m"); >>> title = "Untitled"; >>> width=512; height=512; >>> Dialog.create("488nm"); >>> Dialog.addMessage(blue); >>> Dialog.show(); >>> >>> //Run ICS opener >>> run("ICS/IDS... "); >>> >>> //Converts stack to images >>> run("Convert Stack to Images"); >>> >>> //Closes 488 unassigned, 488 background, E_488 and renames >>> channel 3 as >>> "D", >>> channel 2 as "C", and channel 1 as "A" >>> close(); >>> close(); >>> close(); >>> rename("D"); >>> run("Put Behind [tab]"); >>> rename("C"); >>> run("Put Behind [tab]"); >>> rename("A"); >>> >>> //Prompt for 561nm image >>> var green = "Open a 561nm image"; >>> requires("1.34m"); >>> title = "Untitled"; >>> width=512; height=512; >>> Dialog.create("561nm"); >>> Dialog.addMessage(green); >>> Dialog.show(); >>> >>> //Run ICS opener >>> run("ICS/IDS... "); >>> >>> //Converts stack to images >>> run("Convert Stack to Images"); >>> >>> //Closes 561 unassigned, 561 background, and renames channel 3 as >>> "gamma", >>> channel 2 as "F", and channel 1 as "E" >>> close(); >>> close(); >>> rename("gamma"); >>> run("Put Behind [tab]"); >>> rename("F"); >>> run("Put Behind [tab]"); >>> rename("E"); >>> >>> //Create a mask >>> run("Duplicate...", "title=Mask"); >>> run("Paste Control..."); >>> setPasteMode("OR"); >>> selectWindow("F"); >>> run("Copy"); >>> selectWindow("Mask"); >>> run("Paste"); >>> selectWindow("gamma"); >>> run("Copy"); >>> selectWindow("Mask"); >>> run("Paste"); >>> selectWindow("D"); >>> run("Copy"); >>> selectWindow("Mask"); >>> run("Paste"); >>> selectWindow("C"); >>> run("Copy"); >>> selectWindow("Mask"); >>> run("Paste"); >>> selectWindow("A"); >>> run("Copy"); >>> selectWindow("Mask"); >>> run("Paste"); >>> selectWindow("Z"); >>> run("Copy"); >>> selectWindow("Mask"); >>> run("Paste"); >>> selectWindow("W"); >>> run("Copy"); >>> selectWindow("Mask"); >>> run("Paste"); >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Help-with-ImageJ-macro-code- >>> tp15195190p15195190.html >>> Sent from the ImageJ mailing list archive at Nabble.com. >>> >> >> > > -- > View this message in context: http://www.nabble.com/Help-with- > ImageJ-macro-code-tp15195190p15218299.html > Sent from the ImageJ mailing list archive at Nabble.com. |
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Hi Michael,
Thanks for the advice. I have rewritten the code as you have suggested, but I'm still getting errors. The good news is, I think I know why, but the bad is that I have no idea how to solve it. When I run the macro and open my images, I notice that the active image window (the one on top) will not remain consistent from run to run. I therefore believe that ImageJ is closing some of the channels I want to retain (A, C, D, etc...) and keeping some of the junk channels I want to discard, thus causing errors in the back end because the imageID that I direct ImageJ to no longer exists. I will try rewriting the code so that no channels are closed, but how can I be sure that I'm getting the correct imageID when I don't know how to control which window is active? I could try to identify the windows based on their original window names using a string search (ie 402nm ch:1), but then I run back into the problem that these window names are being reset to "1". Aaargh! Sorry to be such a bother, but does anyone have a good fix for this? Many thanks! Chris
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Re: Help with ImageJ macro code
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Hi Chris,
maybe also this is a multithreading problem with the foreground image not being set fast enough? There was a bug in ImageJ versions before 1.39f that has caused such problems - maybe you have an old version? Otherwise, adding a short delay before close() could help, e.g. wait(200); It's not an elegant solution, only a workaround... Michael ________________________________________________________________ On 1 Feb 2008, at 13:16, crieken wrote: > Hi Michael, > Thanks for the advice. I have rewritten the code as you have > suggested, but > I'm still getting errors. The good news is, I think I know why, > but the bad > is that I have no idea how to solve it. When I run the macro and > open my > images, I notice that the active image window (the one on top) will > not > remain consistent from run to run. I therefore believe that ImageJ is > closing some of the channels I want to retain (A, C, D, etc...) and > keeping > some of the junk channels I want to discard, thus causing errors in > the back > end because the imageID that I direct ImageJ to no longer exists. > I will > try rewriting the code so that no channels are closed, but how can > I be sure > that I'm getting the correct imageID when I don't know how to > control which > window is active? I could try to identify the windows based on their > original window names using a string search (ie 402nm ch:1), but > then I run > back into the problem that these window names are being reset to "1". > Aaargh! Sorry to be such a bother, but does anyone have a good fix > for > this? Many thanks! > Chris > > > > Michael Schmid-3 wrote: >> >> Hi Chris, >> >> you are right that ImageIDs are negative numbers. They stay >> valid until an image is closed. A new image that you open gets >> a new ID that is the last ID used minus one. >> (strictly speaking, "image" means the ImagePlus class of ImageJ) >> >> See the selectImage(id) and getImageID entries on >> http://rsb.info.nih.gov/ij/developer/macro/functions.html >> >> It might be that your problems are caused by >> run("Put Behind [tab]"); >> since some operations on Windows happen in a different thread >> that may be slower than the thread executing the macro. >> >> Therefore, to access the images created I would simply try: >> Z = getImageID(); >> W = getImageID()+1; //the image created before Z >> >> >> Michael >> ________________________________________________________________ >> >> On 1 Feb 2008, at 01:42, crieken wrote: >> >>> Hi Justin, >>> Unfortunately, it doesn't appear that each image is getting a >>> unique ID... >>> unless I'm not using the code correctly. In the end I need to have >>> the >>> windows named "A, C, D, E, F, gamma, W, Z" in order to do particle >>> analysis. >>> I keep getting errors, so I printed the image IDs and there is >>> always a >>> repeat, but it seems to vary. Are the image IDs usually expressed >>> like"-10", "-71", etc.? Thanks for your advice. >>> Chris >>> >>> >>> //Selects directory to save files to >>> dir = getDirectory("Select save directory"); >>> >>> //Prompt for 402nm image >>> var violet = "Open a 402nm image"; >>> requires("1.34m"); >>> title = "Untitled"; >>> width=512; height=512; >>> Dialog.create("402nm"); >>> Dialog.addMessage(violet); >>> Dialog.show(); >>> >>> //Run ICS opener >>> run("ICS/IDS... "); >>> >>> //Closes 402 unassigned, 402 background >>> close(); >>> close(); >>> Z = getImageID(); >>> run("Put Behind [tab]"); >>> W = getImageID(); >>> >>> //Prompt for 488nm image >>> var blue = "Open a 488nm image"; >>> requires("1.34m"); >>> title = "Untitled"; >>> width=512; height=512; >>> Dialog.create("488nm"); >>> Dialog.addMessage(blue); >>> Dialog.show(); >>> >>> //Run ICS opener >>> run("ICS/IDS... "); >>> >>> //Converts stack to images >>> run("Convert Stack to Images"); >>> >>> //Closes 488 unassigned, 488 background, E_488 >>> close(); >>> close(); >>> close(); >>> D = getImageID(); >>> run("Put Behind [tab]"); >>> C = getImageID(); >>> run("Put Behind [tab]"); >>> A = getImageID(); >>> >>> >>> //Prompt for 561nm image >>> var green = "Open a 561nm image"; >>> requires("1.34m"); >>> title = "Untitled"; >>> width=512; height=512; >>> Dialog.create("561nm"); >>> Dialog.addMessage(green); >>> Dialog.show(); >>> >>> //Run ICS opener >>> run("ICS/IDS... "); >>> >>> //Converts stack to images >>> run("Convert Stack to Images"); >>> >>> //Closes 561 unassigned, 561 background >>> close(); >>> close(); >>> gamma = getImageID(); >>> run("Put Behind [tab]"); >>> F = getImageID(); >>> run("Put Behind [tab]"); >>> E = getImageID(); >>> >>> //Prints image IDs >>> print(A); >>> print(C); >>> print(D); >>> print(E); >>> print(F); >>> print(gamma); >>> print(W); >>> print(Z); >>> >>> >>> //Renames windows >>> selectWindow(A); >>> rename("A"); >>> selectWindow(C); >>> rename("C"); >>> selectWindow(D); >>> rename("D"); >>> selectWindow(E); >>> rename("E"); >>> selectWindow(F); >>> rename("F"); >>> selectWindow(gamma); >>> rename("gamma"); >>> selectWindow(W); >>> rename("W"); >>> selectWindow(Z); >>> rename("Z"); >>> |
Re: Help with ImageJ macro code
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In reply to this post by crieken
Maybe use setSlice() instead of splitting the stack into different windows.
You can't close unwanted channels, and you'll need more code, but as long as your channels are always in the same order in the stack, then it should work correctly. Justin On Feb 1, 2008 6:16 AM, crieken <[hidden email]> wrote: > Hi Michael, > Thanks for the advice. I have rewritten the code as you have suggested, > but > I'm still getting errors. The good news is, I think I know why, but the > bad > is that I have no idea how to solve it. When I run the macro and open my > images, I notice that the active image window (the one on top) will not > remain consistent from run to run. I therefore believe that ImageJ is > closing some of the channels I want to retain (A, C, D, etc...) and > keeping > some of the junk channels I want to discard, thus causing errors in the > back > end because the imageID that I direct ImageJ to no longer exists. I will > try rewriting the code so that no channels are closed, but how can I be > sure > that I'm getting the correct imageID when I don't know how to control > which > window is active? I could try to identify the windows based on their > original window names using a string search (ie 402nm ch:1), but then I > run > back into the problem that these window names are being reset to "1". > Aaargh! Sorry to be such a bother, but does anyone have a good fix for > this? Many thanks! > Chris > > > > Michael Schmid-3 wrote: > > > > Hi Chris, > > > > you are right that ImageIDs are negative numbers. They stay > > valid until an image is closed. A new image that you open gets > > a new ID that is the last ID used minus one. > > (strictly speaking, "image" means the ImagePlus class of ImageJ) > > > > See the selectImage(id) and getImageID entries on > > http://rsb.info.nih.gov/ij/developer/macro/functions.html > > > > It might be that your problems are caused by > > run("Put Behind [tab]"); > > since some operations on Windows happen in a different thread > > that may be slower than the thread executing the macro. > > > > Therefore, to access the images created I would simply try: > > Z = getImageID(); > > W = getImageID()+1; //the image created before Z > > > > > > Michael > > ________________________________________________________________ > > > > On 1 Feb 2008, at 01:42, crieken wrote: > > > >> Hi Justin, > >> Unfortunately, it doesn't appear that each image is getting a > >> unique ID... > >> unless I'm not using the code correctly. In the end I need to have > >> the > >> windows named "A, C, D, E, F, gamma, W, Z" in order to do particle > >> analysis. > >> I keep getting errors, so I printed the image IDs and there is > >> always a > >> repeat, but it seems to vary. Are the image IDs usually expressed > >> like"-10", "-71", etc.? Thanks for your advice. > >> Chris > >> > >> > >> //Selects directory to save files to > >> dir = getDirectory("Select save directory"); > >> > >> //Prompt for 402nm image > >> var violet = "Open a 402nm image"; > >> requires("1.34m"); > >> title = "Untitled"; > >> width=512; height=512; > >> Dialog.create("402nm"); > >> Dialog.addMessage(violet); > >> Dialog.show(); > >> > >> //Run ICS opener > >> run("ICS/IDS... "); > >> > >> //Closes 402 unassigned, 402 background > >> close(); > >> close(); > >> Z = getImageID(); > >> run("Put Behind [tab]"); > >> W = getImageID(); > >> > >> //Prompt for 488nm image > >> var blue = "Open a 488nm image"; > >> requires("1.34m"); > >> title = "Untitled"; > >> width=512; height=512; > >> Dialog.create("488nm"); > >> Dialog.addMessage(blue); > >> Dialog.show(); > >> > >> //Run ICS opener > >> run("ICS/IDS... "); > >> > >> //Converts stack to images > >> run("Convert Stack to Images"); > >> > >> //Closes 488 unassigned, 488 background, E_488 > >> close(); > >> close(); > >> close(); > >> D = getImageID(); > >> run("Put Behind [tab]"); > >> C = getImageID(); > >> run("Put Behind [tab]"); > >> A = getImageID(); > >> > >> > >> //Prompt for 561nm image > >> var green = "Open a 561nm image"; > >> requires("1.34m"); > >> title = "Untitled"; > >> width=512; height=512; > >> Dialog.create("561nm"); > >> Dialog.addMessage(green); > >> Dialog.show(); > >> > >> //Run ICS opener > >> run("ICS/IDS... "); > >> > >> //Converts stack to images > >> run("Convert Stack to Images"); > >> > >> //Closes 561 unassigned, 561 background > >> close(); > >> close(); > >> gamma = getImageID(); > >> run("Put Behind [tab]"); > >> F = getImageID(); > >> run("Put Behind [tab]"); > >> E = getImageID(); > >> > >> //Prints image IDs > >> print(A); > >> print(C); > >> print(D); > >> print(E); > >> print(F); > >> print(gamma); > >> print(W); > >> print(Z); > >> > >> > >> //Renames windows > >> selectWindow(A); > >> rename("A"); > >> selectWindow(C); > >> rename("C"); > >> selectWindow(D); > >> rename("D"); > >> selectWindow(E); > >> rename("E"); > >> selectWindow(F); > >> rename("F"); > >> selectWindow(gamma); > >> rename("gamma"); > >> selectWindow(W); > >> rename("W"); > >> selectWindow(Z); > >> rename("Z"); > >> > >> > >> Justin McGrath wrote: > >>> > >>> I do not know why your images get renamed, but I think the easiest > >>> way > >>> to solve this is to use the getImageID() function, which returns a > >>> unique ID for the active image, and then use the selectImage(id) > >>> function to activate the image later. It has a few benefits: it's > >>> faster, the IDs are unique, and the IDs don't change throughout macro > >>> execution. > >>> > >>> I think you can just replace the rename() and selectWindow() > >>> statements you have now, and it should work. However, I believe > >>> imageCalculator("or", img1, img2) does the same thing as all of those > >>> select-copy-select-pastes, so you might use that in order to make the > >>> code more succinct. > >>> > >>> Justin > >>> > >>> > >>> > >>> On 1/30/08, crieken <[hidden email]> wrote: > >>>> Hi all, I hope this is an appropriate place for this question. I'm > >>>> writing > >>>> a > >>>> macro to put together a mask from three images with multiple > >>>> channels. I > >>>> am > >>>> making progress on the macro, but as I test it, I'm running into a > >>>> problem. > >>>> When the 402nm image is opened, the windows "Z" and "W" are named > >>>> properly. > >>>> When the 488nm image is opened, the windows "A", "C", and "D" are > >>>> named > >>>> fine, but the "Z" and "W" windows are renamed to "1". This > >>>> messes up the > >>>> creation of the mask and will mess up the analysis that will come > >>>> further > >>>> down the line. I have even tried saving each image individually, > >>>> but the > >>>> names still get reset. This only occurs occasionally, though. Does > >>>> anyone > >>>> have any ideas? I can email the original images if it would help. > >>>> Thanks > >>>> in advance! BTW, this may not be the most elegant code, but go > >>>> easy, I'm > >>>> a > >>>> beginner :confused:. > >>>> Chris > >>>> > >>>> //Selects directory to save files to > >>>> dir = getDirectory("Select save directory"); > >>>> > >>>> //Prompt for 402nm image > >>>> var violet = "Open a 402nm image"; > >>>> requires("1.34m"); > >>>> title = "Untitled"; > >>>> width=512; height=512; > >>>> Dialog.create("402nm"); > >>>> Dialog.addMessage(violet); > >>>> Dialog.show(); > >>>> > >>>> //Run ICS opener > >>>> run("ICS/IDS... "); > >>>> > >>>> //Closes 402 unassigned, 402 background, and renames channel 2 as > >>>> "Z" and > >>>> channel 1 as "W" > >>>> close(); > >>>> close(); > >>>> rename("Z"); > >>>> run("Put Behind [tab]"); > >>>> rename("W"); > >>>> > >>>> //Prompt for 488nm image > >>>> var blue = "Open a 488nm image"; > >>>> requires("1.34m"); > >>>> title = "Untitled"; > >>>> width=512; height=512; > >>>> Dialog.create("488nm"); > >>>> Dialog.addMessage(blue); > >>>> Dialog.show(); > >>>> > >>>> //Run ICS opener > >>>> run("ICS/IDS... "); > >>>> > >>>> //Converts stack to images > >>>> run("Convert Stack to Images"); > >>>> > >>>> //Closes 488 unassigned, 488 background, E_488 and renames > >>>> channel 3 as > >>>> "D", > >>>> channel 2 as "C", and channel 1 as "A" > >>>> close(); > >>>> close(); > >>>> close(); > >>>> rename("D"); > >>>> run("Put Behind [tab]"); > >>>> rename("C"); > >>>> run("Put Behind [tab]"); > >>>> rename("A"); > >>>> > >>>> //Prompt for 561nm image > >>>> var green = "Open a 561nm image"; > >>>> requires("1.34m"); > >>>> title = "Untitled"; > >>>> width=512; height=512; > >>>> Dialog.create("561nm"); > >>>> Dialog.addMessage(green); > >>>> Dialog.show(); > >>>> > >>>> //Run ICS opener > >>>> run("ICS/IDS... "); > >>>> > >>>> //Converts stack to images > >>>> run("Convert Stack to Images"); > >>>> > >>>> //Closes 561 unassigned, 561 background, and renames channel 3 as > >>>> "gamma", > >>>> channel 2 as "F", and channel 1 as "E" > >>>> close(); > >>>> close(); > >>>> rename("gamma"); > >>>> run("Put Behind [tab]"); > >>>> rename("F"); > >>>> run("Put Behind [tab]"); > >>>> rename("E"); > >>>> > >>>> //Create a mask > >>>> run("Duplicate...", "title=Mask"); > >>>> run("Paste Control..."); > >>>> setPasteMode("OR"); > >>>> selectWindow("F"); > >>>> run("Copy"); > >>>> selectWindow("Mask"); > >>>> run("Paste"); > >>>> selectWindow("gamma"); > >>>> run("Copy"); > >>>> selectWindow("Mask"); > >>>> run("Paste"); > >>>> selectWindow("D"); > >>>> run("Copy"); > >>>> selectWindow("Mask"); > >>>> run("Paste"); > >>>> selectWindow("C"); > >>>> run("Copy"); > >>>> selectWindow("Mask"); > >>>> run("Paste"); > >>>> selectWindow("A"); > >>>> run("Copy"); > >>>> selectWindow("Mask"); > >>>> run("Paste"); > >>>> selectWindow("Z"); > >>>> run("Copy"); > >>>> selectWindow("Mask"); > >>>> run("Paste"); > >>>> selectWindow("W"); > >>>> run("Copy"); > >>>> selectWindow("Mask"); > >>>> run("Paste"); > >>>> > >>>> -- > >>>> View this message in context: > >>>> http://www.nabble.com/Help-with-ImageJ-macro-code- > >>>> tp15195190p15195190.html > >>>> Sent from the ImageJ mailing list archive at Nabble.com. > >>>> > >>> > >>> > >> > >> -- > >> View this message in context: http://www.nabble.com/Help-with- > >> ImageJ-macro-code-tp15195190p15218299.html > >> Sent from the ImageJ mailing list archive at Nabble.com. > > > > > > -- > View this message in context: > http://www.nabble.com/Help-with-ImageJ-macro-code-tp15195190p15225608.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
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In reply to this post by Michael Schmid
Aha! I'm using 1.38x - I'll check for a newer version and let you know how it goes. Thanks!
Chris
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1.39q is confused and telling me that I've run out of memory (63MB) when I have it set to 1500MB. Hmmm, maybe I'll try a version that's a bit older...
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Now the whole thing is messed up and when I try to open ImageJ.exe, I get an error message that says, "Could not create the java virtual machine". I can run the ij.jar, but then I get the 63MB error.
Chris
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Re: Help with ImageJ macro code
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On Windows, try deleting the configuration file (ImageJ.cfg) and
restarting ImageJ. The ImageJ launcher (ImageJ.exe) will detect that ImageJ.cfg is missing and generate a replacement. If the ImageJ/jre directory is missing, it will detect the latest installed Java and setup ImageJ.cfg to use that instead. It will set the memory limit to 2/3 of installed memory or 640MB, whichever is lower. You will only be able to use 63MB of you launch ImageJ by double clicking on ij.jar. -wayne On Feb 1, 2008, at 1:13 PM, crieken wrote: > Now the whole thing is messed up and when I try to open ImageJ.exe, I > get an > error message that says, "Could not create the java virtual machine". > I can > run the ij.jar, but then I get the 63MB error. > Chris > > > crieken wrote: >> >> 1.39q is confused and telling me that I've run out of memory (63MB) >> when I >> have it set to 1500MB. Hmmm, maybe I'll try a version that's a bit >> older... >> >> >> crieken wrote: >>> >>> Aha! I'm using 1.38x - I'll check for a newer version and let you >>> know >>> how it goes. Thanks! >>> Chris >>> >>> >>> Michael Schmid-3 wrote: >>>> >>>> Hi Chris, >>>> >>>> maybe also this is a multithreading problem with the >>>> foreground image not being set fast enough? >>>> >>>> There was a bug in ImageJ versions before 1.39f that has caused >>>> such problems - maybe you have an old version? >>>> >>>> Otherwise, adding a short delay before close() could help, e.g. >>>> wait(200); >>>> It's not an elegant solution, only a workaround... >>>> >>>> >>>> Michael >>>> ________________________________________________________________ >>>> >>>> On 1 Feb 2008, at 13:16, crieken wrote: >>>> >>>>> Hi Michael, >>>>> Thanks for the advice. I have rewritten the code as you have >>>>> suggested, but >>>>> I'm still getting errors. The good news is, I think I know why, >>>>> but the bad >>>>> is that I have no idea how to solve it. When I run the macro and >>>>> open my >>>>> images, I notice that the active image window (the one on top) will >>>>> not >>>>> remain consistent from run to run. I therefore believe that >>>>> ImageJ is >>>>> closing some of the channels I want to retain (A, C, D, etc...) and >>>>> keeping >>>>> some of the junk channels I want to discard, thus causing errors in >>>>> the back >>>>> end because the imageID that I direct ImageJ to no longer exists. >>>>> I will >>>>> try rewriting the code so that no channels are closed, but how can >>>>> I be sure >>>>> that I'm getting the correct imageID when I don't know how to >>>>> control which >>>>> window is active? I could try to identify the windows based on >>>>> their >>>>> original window names using a string search (ie 402nm ch:1), but >>>>> then I run >>>>> back into the problem that these window names are being reset to >>>>> "1". >>>>> Aaargh! Sorry to be such a bother, but does anyone have a good fix >>>>> for >>>>> this? Many thanks! >>>>> Chris >>>>> >>>>> >>>>> >>>>> Michael Schmid-3 wrote: >>>>>> >>>>>> Hi Chris, >>>>>> >>>>>> you are right that ImageIDs are negative numbers. They stay >>>>>> valid until an image is closed. A new image that you open gets >>>>>> a new ID that is the last ID used minus one. >>>>>> (strictly speaking, "image" means the ImagePlus class of ImageJ) >>>>>> >>>>>> See the selectImage(id) and getImageID entries on >>>>>> http://rsb.info.nih.gov/ij/developer/macro/functions.html >>>>>> >>>>>> It might be that your problems are caused by >>>>>> run("Put Behind [tab]"); >>>>>> since some operations on Windows happen in a different thread >>>>>> that may be slower than the thread executing the macro. >>>>>> >>>>>> Therefore, to access the images created I would simply try: >>>>>> Z = getImageID(); >>>>>> W = getImageID()+1; //the image created before Z >>>>>> >>>>>> >>>>>> Michael >>>>>> ________________________________________________________________ >>>>>> >>>>>> On 1 Feb 2008, at 01:42, crieken wrote: >>>>>> >>>>>>> Hi Justin, >>>>>>> Unfortunately, it doesn't appear that each image is getting a >>>>>>> unique ID... >>>>>>> unless I'm not using the code correctly. In the end I need to >>>>>>> have >>>>>>> the >>>>>>> windows named "A, C, D, E, F, gamma, W, Z" in order to do >>>>>>> particle >>>>>>> analysis. >>>>>>> I keep getting errors, so I printed the image IDs and there is >>>>>>> always a >>>>>>> repeat, but it seems to vary. Are the image IDs usually >>>>>>> expressed >>>>>>> like"-10", "-71", etc.? Thanks for your advice. >>>>>>> Chris >>>>>>> >>>>>>> >>>>>>> //Selects directory to save files to >>>>>>> dir = getDirectory("Select save directory"); >>>>>>> >>>>>>> //Prompt for 402nm image >>>>>>> var violet = "Open a 402nm image"; >>>>>>> requires("1.34m"); >>>>>>> title = "Untitled"; >>>>>>> width=512; height=512; >>>>>>> Dialog.create("402nm"); >>>>>>> Dialog.addMessage(violet); >>>>>>> Dialog.show(); >>>>>>> >>>>>>> //Run ICS opener >>>>>>> run("ICS/IDS... "); >>>>>>> >>>>>>> //Closes 402 unassigned, 402 background >>>>>>> close(); >>>>>>> close(); >>>>>>> Z = getImageID(); >>>>>>> run("Put Behind [tab]"); >>>>>>> W = getImageID(); >>>>>>> >>>>>>> //Prompt for 488nm image >>>>>>> var blue = "Open a 488nm image"; >>>>>>> requires("1.34m"); >>>>>>> title = "Untitled"; >>>>>>> width=512; height=512; >>>>>>> Dialog.create("488nm"); >>>>>>> Dialog.addMessage(blue); >>>>>>> Dialog.show(); >>>>>>> >>>>>>> //Run ICS opener >>>>>>> run("ICS/IDS... "); >>>>>>> >>>>>>> //Converts stack to images >>>>>>> run("Convert Stack to Images"); >>>>>>> >>>>>>> //Closes 488 unassigned, 488 background, E_488 >>>>>>> close(); >>>>>>> close(); >>>>>>> close(); >>>>>>> D = getImageID(); >>>>>>> run("Put Behind [tab]"); >>>>>>> C = getImageID(); >>>>>>> run("Put Behind [tab]"); >>>>>>> A = getImageID(); >>>>>>> >>>>>>> >>>>>>> //Prompt for 561nm image >>>>>>> var green = "Open a 561nm image"; >>>>>>> requires("1.34m"); >>>>>>> title = "Untitled"; >>>>>>> width=512; height=512; >>>>>>> Dialog.create("561nm"); >>>>>>> Dialog.addMessage(green); >>>>>>> Dialog.show(); >>>>>>> >>>>>>> //Run ICS opener >>>>>>> run("ICS/IDS... "); >>>>>>> >>>>>>> //Converts stack to images >>>>>>> run("Convert Stack to Images"); >>>>>>> >>>>>>> //Closes 561 unassigned, 561 background >>>>>>> close(); >>>>>>> close(); >>>>>>> gamma = getImageID(); >>>>>>> run("Put Behind [tab]"); >>>>>>> F = getImageID(); >>>>>>> run("Put Behind [tab]"); >>>>>>> E = getImageID(); >>>>>>> >>>>>>> //Prints image IDs >>>>>>> print(A); >>>>>>> print(C); >>>>>>> print(D); >>>>>>> print(E); >>>>>>> print(F); >>>>>>> print(gamma); >>>>>>> print(W); >>>>>>> print(Z); >>>>>>> >>>>>>> >>>>>>> //Renames windows >>>>>>> selectWindow(A); >>>>>>> rename("A"); >>>>>>> selectWindow(C); >>>>>>> rename("C"); >>>>>>> selectWindow(D); >>>>>>> rename("D"); >>>>>>> selectWindow(E); >>>>>>> rename("E"); >>>>>>> selectWindow(F); >>>>>>> rename("F"); >>>>>>> selectWindow(gamma); >>>>>>> rename("gamma"); >>>>>>> selectWindow(W); >>>>>>> rename("W"); >>>>>>> selectWindow(Z); >>>>>>> rename("Z"); >>>>>>> >>>> >>>> >>> >>> >> >> > > -- > View this message in context: > http://www.nabble.com/Help-with-ImageJ-macro-code- > tp15195190p15231843.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
Plot profile for multiple ROIs
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In reply to this post by crieken
Hi all,
I need to obtain plot profiles from several lines in a number of images. If I create all the lines for an image with the ROI Multimeasure or the ROI manager, would be possible to get automatically all the corresponding plot profiles? Thanks in advance -- Dr Pedro J Camello Dpt Physiology Faculty of Veterinary Sciences University of Extremadura 10071 Caceres Spain Ph: 927257100 Extension 1321 Fax:927257110 |
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