http://imagej.273.s1.nabble.com/Help-with-ImageJ-macro-code-tp3697312p3697323.html
Maybe use setSlice() instead of splitting the stack into different windows.
> 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:
>
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>