Using Image Calculator with Virtual Stacks
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Dear All
I have 2 image stacks that are far too large to fit in memory. I would like to generate and save ratioed images of each pair of slices in the two stacks. I thought that Virtual Stacks and Process>Batch>Virtual Stack would do the job, but I am getting unexpected results. Each virtual stack has its own directory. Using the Batch Process Dialogue, I can identify the directory to contain the 32-bit ratioed images. Running Image Calculator in the code box provided in the dialogue produces the correct 32 bit result image. I can rename this result image "Result" and append the current Slice number of the virtual stacks to generate a unique filename, e.g. Result.001, Result.002... However, what ends up being saved by the Batch Process as "Result.*" is not the 32-bit result image, but the current slice of one of the virtual stacks used as input to the Image calculator. Furthermore, specifying the Output folder seems to serve no function, as an explicit SaveAs command requires a fully qualified path. The simple macro code I have written in the code box is run("Image Calculator...", "image1=[B 340 backsub] operation=Divide image2=[B 380 backsub] 32-bit"); // do the division with 32 bit result rename ("Result") ; selectWindow("B 340 backsub") ; // select one of the virtual stacks n = getSliceNumber() ; // get the current slice index nString = toString(n, 0); // convert the index to a string MyImage = "ratio." + nString ; // create a string for the output filename with the index as the extension selectWindow("Result") ; // select the result image SaveAsString = "Y:\\human brain\\june 28 2011 cold\\B ratio\\" + MyImage ; // create the string with the fully qualitifed path saveAs("Tiff", SaveAsString); // save the result image close() ; // close the result image Have I misunderstood how this batch functionality with Virtual Stacks is intended to be used? Any help would be very much appreciated. Jeremy Marks University of Chicago |
Re: Using Image Calculator with Virtual Stacks
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On Jul 1, 2011, at 7:02 PM, jmarks wrote:
> Dear All > I have 2 image stacks that are far too large to fit in memory. I would like > to generate and save ratioed images of each pair of slices in the two > stacks. > I thought that Virtual Stacks and Process>Batch>Virtual Stack would do the > job, but I am getting unexpected results. > Each virtual stack has its own directory. > Using the Batch Process Dialogue, I can identify the directory to contain > the 32-bit ratioed images. This is not working because Process>Batch>Virtual Stack only supports a single input stack, but the Image Calculator requires two. What you can do instead is use a macro like the one below. What the macro does is calculate the ratio of two virtual stacks, which are assumed to be open, saving the output in a directory, which is opened on completion as a third virtual stack. If you are running the 1.45k daily build, the last line of the macro can be replaced with run("Image Sequence...", "open=&dir sort use"); requires("1.45d"); if (nImages!=2) exit("Exactly 2 stacks required"); setBatchMode(true); dir = getDirectory("Select output directory"); for (i=1; i<=nSlices; i++) { showProgress(i, nSlices); selectImage(1); setSlice(i); selectImage(2); setSlice(i); imageCalculator("Divide create 32-bit", 1, 2); save(dir+IJ.pad(i, 5)+".tif"); close; } setBatchMode(false); run("Image Sequence...", "open=["+dir+"] sort use"); > Running Image Calculator in the code box provided in the dialogue produces > the correct 32 bit result image. I can rename this result image "Result" and > append the current Slice number of the virtual stacks to generate a unique > filename, e.g. Result.001, Result.002... > > However, what ends up being saved by the Batch Process as "Result.*" is not > the 32-bit result image, but the current slice of one of the virtual stacks > used as input to the Image calculator. Furthermore, specifying the Output > folder seems to serve no function, as an explicit SaveAs command requires a > fully qualified path. > > The simple macro code I have written in the code box is > > run("Image Calculator...", "image1=[B 340 backsub] operation=Divide > image2=[B 380 backsub] 32-bit"); // do the division with 32 bit result > rename ("Result") ; > selectWindow("B 340 backsub") ; // select one of the virtual stacks > n = getSliceNumber() ; // get the current slice index > nString = toString(n, 0); // convert the index to a > string > MyImage = "ratio." + nString ; // create a string for the > output filename with the index as the extension > selectWindow("Result") ; // select the result image > SaveAsString = "Y:\\human brain\\june 28 2011 cold\\B ratio\\" + > MyImage ; // create the string with the fully qualitifed path > saveAs("Tiff", SaveAsString); // save the result image > close() ; // close the result image > > > Have I misunderstood how this batch functionality with Virtual Stacks is > intended to be used? > Any help would be very much appreciated. > Jeremy Marks > University of Chicago > > -- > View this message in context: http://imagej.588099.n2.nabble.com/Using-Image-Calculator-with-Virtual-Stacks-tp6539611p6539611.html > Sent from the ImageJ mailing list archive at Nabble.com. |
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Thank you, Wayne! I will make sure I get the daily build. jm
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