How do you select an image from set of slices to change pixel intensity
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Hello
I wrote the following macro to make a 10 slices. I need to add a white box in certain location in all the images. I used the macro command setSlice, then setpixel to select slice then change the pixel intensity to 256.
his seems to work for slice 1 only. I am not sure why. Is their a different commad o do this?
The code:
// This macro generate 10 image.
width = 500; height = 500;
xc = width/2; yc = height/2;
newImage("Math", "16-bit black", width, height, 10);
//setVoxelSize(width, height, depth, unit)
for(z=1; z |
Re: How do you select an image from set of slices to change pixel intensity
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You should use nSlices() instead of nImages() to return the number of slices
in your stack. nImages() gives you the number of images (i.e. one in your example, the stack). Christophe On Wed, Oct 19, 2011 at 21:56, mtamimi <[hidden email]> wrote: > Hello > I wrote the following macro to make a 10 slices. I need to add a white box > in certain location in all the images. I used the macro command setSlice, > then setpixel to select slice then change the pixel intensity to 256. > his seems to work for slice 1 only. I am not sure why. Is their a different > commad o do this? > > The code: > > // This macro generate 10 image. > > width = 500; height = 500; > xc = width/2; yc = height/2; > newImage("Math", "16-bit black", width, height, 10); > //setVoxelSize(width, height, depth, unit) > for(z=1; z<nImages+1;z++){ > > for (y= 100; y<250; y++) { > for (x= 100; x<250; x++) { > setSlice(z); > setPixel(x, y,256); > } > } > resetMinAndMax(); > exit; > > Thank you in advance for all your input. > Sincerely, > Mat M. Al-Tamimi > > -- > View this message in context: > http://imagej.588099.n2.nabble.com/How-do-you-select-an-image-from-set-of-slices-to-change-pixel-intensity-tp6910289p6910289.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
Re: How do you select an image from set of slices to change pixel intensity
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In reply to this post by mtamimi
Hi,
There are several small mistakes in your code. 1. you should use nSlices instead of nImages. 2. you forgot the close curly braces for the z loop. 3. you'd rather setSlice(z) outside the x and y loops. 4. white is 255. So it would look like this. for(z=1; z<=nSlices;z++){ setSlice(z); for (y= 100; y<250; y++) { for (x= 100; x<250; x++) { setPixel(x, y,255); } } } // this was missing You could also replace this code by this faster version: makeRectangle(100, 100, 149, 149); setForegroundColor(255,255,255); run("Fill","stack"); Sincerely, Jerome. On Wed, Oct 19, 2011 at 9:56 PM, mtamimi <[hidden email]> wrote: > Hello > I wrote the following macro to make a 10 slices. I need to add a white box > in certain location in all the images. I used the macro command setSlice, > then setpixel to select slice then change the pixel intensity to 256. > his seems to work for slice 1 only. I am not sure why. Is their a different > commad o do this? > > The code: > > // This macro generate 10 image. > > width = 500; height = 500; > xc = width/2; yc = height/2; > newImage("Math", "16-bit black", width, height, 10); > //setVoxelSize(width, height, depth, unit) > for(z=1; z<nImages+1;z++){ > > for (y= 100; y<250; y++) { > for (x= 100; x<250; x++) { > setSlice(z); > setPixel(x, y,256); > } > } > resetMinAndMax(); > exit; > > Thank you in advance for all your input. > Sincerely, > Mat M. Al-Tamimi > > -- > View this message in context: > http://imagej.588099.n2.nabble.com/How-do-you-select-an-image-from-set-of-slices-to-change-pixel-intensity-tp6910289p6910289.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
Re: How do you select an image from set of slices to change pixel intensity
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In reply to this post by mtamimi
Dear Mat,
first, the nImages returned the number of open images. If you 3 open images your macro would create 4 ROIs. the correct function was nSlices. Second, the Exit was redundant, since the macro will exit on completion. I replaced it with a closing '}" for the initial for statement. Another option is to create the initial ROI and add it to the ROI Manager // This macro generate 10 image. width = 500; height = 500; xc = width/2; yc = height/2; newImage("Math", "16-bit black", width, height, 10); //setVoxelSize(width, height, depth, unit) //for(z=1; z<nImages+1;z++){ for(z=1; z<nSlices+1;z++){ for (y= 100; y<250; y++) { for (x= 100; x<250; x++) { setSlice(z); setPixel(x, y,256); } } resetMinAndMax(); //exit; } Regards, Glen Glen MacDonald Core for Communication Research Virginia Merrill Bloedel Hearing Research Center Box 357923 University of Washington Seattle, WA 98195-7923 (206) 616-4156 On Wed, 19 Oct 2011, mtamimi wrote: > Hello > I wrote the following macro to make a 10 slices. I need to add a white box > in certain location in all the images. I used the macro command setSlice, > then setpixel to select slice then change the pixel intensity to 256. > his seems to work for slice 1 only. I am not sure why. Is their a different > commad o do this? > > The code: > > // This macro generate 10 image. > > width = 500; height = 500; > xc = width/2; yc = height/2; > newImage("Math", "16-bit black", width, height, 10); > //setVoxelSize(width, height, depth, unit) > for(z=1; z<nImages+1;z++){ > > for (y= 100; y<250; y++) { > for (x= 100; x<250; x++) { > setSlice(z); > setPixel(x, y,256); > } > } > resetMinAndMax(); > exit; > > Thank you in advance for all your input. > Sincerely, > Mat M. Al-Tamimi > > -- > View this message in context: http://imagej.588099.n2.nabble.com/How-do-you-select-an-image-from-set-of-slices-to-change-pixel-intensity-tp6910289p6910289.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
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Hello When I use
this it does not work Do you know why? The code: ========= // This
macro generate 10 image.
width = 500; height = 500; xc =
width/2; yc = height/2;
newImage("Math", "16-bit black", width, height, 10);
//id=getImageID; //setVoxelSize(width,
height, depth, unit)
for(z=1; z<nSlices+1;z++){ for
(y= 100; y<250; y++) { for
(x= 100; x<250; x++) { //selectImage(id); setSlice(z); setPixel(x,
y,256); } } resetMinAndMax(); } From: Glen MacDonald-2
[via ImageJ] [mailto:[hidden email]] Dear Mat,
If
you reply to this email, your message will be added to the discussion below: To unsubscribe from
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In reply to this post by lechristophe
Thank you.
It worked. From: lechristophe
[via ImageJ] [mailto:[hidden email]] You should use nSlices() instead of nImages() to return the number of
slices
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In reply to this post by Jerome Mutterer-3
Hello Mat From: Jerome
Mutterer-3 [via ImageJ] [mailto:[hidden email]] Hi,
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