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macro:autofocus_hyperstack
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macro:autofocus_hyperstack [2019/04/12 13:13] |
macro:autofocus_hyperstack [2019/04/12 13:13] (current) |
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| + | <code> | ||
| + | // Autofocus hyperstack macro | ||
| + | // Select the in focus frame from each slice of a hyperstack and create a new stack | ||
| + | // of just the in focus frames | ||
| + | // Based on algorithm F-11 "Normalized Variance" | ||
| + | // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. | ||
| + | // And the original macro by Andy Weller http://imagejdocu.tudor.lu/doku.php?id=macro:normalized_variance | ||
| + | |||
| + | setBatchMode(true); | ||
| + | |||
| + | //Get image type | ||
| + | type = bitDepth(); | ||
| + | if (type==8) {type="8-bit";} else {if(type==16) {type="16-bit";} else{if(type==32) {type="32-bit";} else {if(type==24) {type="RGB";}}}} | ||
| + | |||
| + | StackID=getTitle(); | ||
| + | Stack.getDimensions(width, height, channels, slices, frames); | ||
| + | |||
| + | if (channels>1) {exit("The hyperstack has 2-channels please reduce dimensionality")} else{} | ||
| + | |||
| + | |||
| + | for (k=1; k<=frames; k++) { Stack.setFrame(k); | ||
| + | m=0; | ||
| + | normVar = 0; // Set to 0 which is out of focus | ||
| + | for (l=1; l<=slices; l++){ | ||
| + | selectWindow(StackID); | ||
| + | Stack.setSlice(l); | ||
| + | |||
| + | getRawStatistics(nPixels, mean); | ||
| + | W = getWidth(); | ||
| + | H = getHeight(); | ||
| + | b = 0; | ||
| + | |||
| + | for (j=0; j<H; j++) { | ||
| + | for (i=0; i<W; i++) { | ||
| + | p = getPixel(i,j); | ||
| + | t = (p-mean)*(p-mean); | ||
| + | b += t; | ||
| + | } | ||
| + | } | ||
| + | |||
| + | if ((b/(H*W*mean))>normVar) {normVar = (b/(H*W*mean)); m++;} else {normVar=normVar;} | ||
| + | |||
| + | } | ||
| + | |||
| + | Stack.setSlice(m); | ||
| + | run("Select All"); | ||
| + | run("Copy"); | ||
| + | if (isOpen("Output")){ | ||
| + | selectWindow("Output"); | ||
| + | run("Add Slice"); | ||
| + | } | ||
| + | else{ | ||
| + | newImage("Output", type, width, height, 1); | ||
| + | } | ||
| + | run("Paste"); | ||
| + | selectWindow(StackID); | ||
| + | Stack.setSlice(l); | ||
| + | |||
| + | } | ||
| + | setBatchMode("exit and display"); | ||
| + | //Richard Mort 27/09/2018 | ||
| + | </code> | ||
macro/autofocus_hyperstack.txt · Last modified: 2019/04/12 13:13 (external edit)
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