Jazy_boundaries.ijm

//Version 0.0.4a
// Difference to Lazy grainboundareis: as black is 0, thicken lines must work with copy (AND)
// instead with copy (OR) and "max of stack" will be "min" of stack
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//-----------------------------------Grain-boundary-segmentation-helpers-------------------
//-----------------------------------------------------------------------------------------
macro"RGB to stack[0]"{
run("RGB Stack");
}

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macro "crop and scale - fast [1]"{
if (selectionType != -1){
 run("Crop");
//ask for scale factor
scalefactor = 2;
Dialog.create("scaling factor");
Dialog.addMessage("scaling factor");
Dialog.addNumber("   ", scalefactor);
Dialog.show();
scalefactor = Dialog.getNumber();
run("Scale...", "x="+scalefactor+" y="+scalefactor+" interpolation=None process create title="+getTitle+"scaled.tif");

}else{
showMessage("Selection required");
}		
}
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macro "crop and scale - smooth [2]"{
if (selectionType != -1){
 run("Crop");
//ask for scale factor
scalefactor = 2;
Dialog.create("scaling factor");
Dialog.addMessage("scaling factor");
Dialog.addNumber("   ", scalefactor);
Dialog.show();
scalefactor = Dialog.getNumber();
run("Scale...", "x="+scalefactor+" y="+scalefactor+" interpolation=Bicubic process create title="+getTitle+"scaled.tif");

}else{
showMessage("Selection required");
}		
}
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macro "Median filter [u]"{
radius = 1;
Dialog.create("median radius");
Dialog.addMessage("radius for median filter");
Dialog.addNumber("radius (pixel)= ", radius);
Dialog.show();
radius = Dialog.getNumber();	
run("Median...", "radius="+radius+" stack")
}
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macro "Sobel filter [o]"{
run("Find Edges", "stack");
}
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macro "Kompass filter [k]"{
for (i = 0; i < 7; i++) {
run("Duplicate...", " ");
}
run("Images to Stack", "use");
run("Convolve...", "text1=[-5 -5 -5\n3 0 3\n3 3 3\n] normalize");
run("Next Slice [>]");
run("Convolve...", "text1=[3 -5 -5\n3 0 -5\n3 3 3\n] normalize");
run("Next Slice [>]");
run("Convolve...", "text1=[3 3 -5\n3 0 -5\n3 3 -5\n] normalize");
run("Next Slice [>]");
run("Convolve...", "text1=[3 3 3\n3 0 -5\n3 -5 -5\n] normalize");
run("Next Slice [>]");
run("Convolve...", "text1=[3 3 3\n3 0 3\n-5 -5 -5\n] normalize");
run("Next Slice [>]");
run("Convolve...", "text1=[3 3 3\n-5 0 3\n-5 -5 3\n] normalize");
run("Next Slice [>]");
run("Convolve...", "text1=[-5 3 3\n-5 0 3\n-5 3 3\n] normalize");
run("Next Slice [>]");
run("Convolve...", "text1=[-5 -5 3\n-5 0 3\n3 3 3\n] normalize");
run("Z Project...", "projection=[Max Intensity]");
}
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macro "sharpen [s]"{
run("Sharpen", "stack");
}
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macro "enhance [c]"{
satur = 1;
Dialog.create("saturated pixels");
Dialog.addMessage("saturated pixels");
Dialog.addNumber("in % = ", satur);
Dialog.show();
satur = Dialog.getNumber();	
run("Enhance Contrast...", "saturated="+satur+" normalize process_all")
}
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macro "equalize [e]"{
satur = 0.4;
Dialog.create("saturated pixels");
Dialog.addMessage("saturated pixels");
Dialog.addNumber("in % = ", satur);
Dialog.show();
satur = Dialog.getNumber();	
run("Enhance Contrast...", "saturated="+satur+" equalize process_all")
}
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//http://fiji.sc/wiki/index.php/Auto_Threshold
macro "threshold/density slice ... [T]"{
run("Threshold...");
}
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//This assumes a bimodal histogram. The histogram is iteratively smoothed using a running 
//average of size 3, until there are only two local maxima: j and k. The threshold t is then
//computed as (j+k)/2. Images with histograms having extremely unequal peaks or a broad and 
//flat valley are unsuitable for this method.

macro "threshold Intermodes [I]"{
run("Convert to Mask", "method=Intermodes background=White calculate");
run("Invert LUT");
run("Invert");
}

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macro "threshold Mean [M]"{
run("Convert to Mask", "method=Mean background=White calculate");
run("Invert LUT");
run("Invert");
}

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macro "threshold Huang [H]"{
run("Convert to Mask", "method=Huang background=White calculate");
run("Invert LUT");
run("Invert");
}

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macro "average of stack [a]"{
if (nSlices >= 1){
run("Z Project...", "start=1 stop="+nSlices+" projection=[Average Intensity]");
}else{
showMessage("Stack required");}	
}

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macro "min of stack [z]"{ //
if (nSlices >= 1){
run("Z Project...", "start=1 stop="+nSlices+" projection=[Min Intensity]");
}else{
showMessage("Stack required");}	
}


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macro "thicken lines [t]"{
if (nSlices == 1){
run("Select All");
run("Copy");
setPasteMode("OR");
setSelectionLocation(1,0);
run("Paste");
setSelectionLocation(0,1);
run("Paste");
setPasteMode("COPY");
}else{
showMessage("single slice image required");}	
}
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macro "skeletonize [j]"{
run("Skeletonize", "stack");
}
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macro "prune [i]"{
run("Options...", "iterations=10 count=7 edm=Overwrite black do=Erode stack");
}
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macro "cut away rim (boundary map) [4]"{
	
xwidth = getWidth();
yheight = getHeight();
rimc = 5;
Dialog.create("width of rim");
Dialog.addMessage("width of rim");
Dialog.addNumber("in pixel",rimc);
Dialog.show();
rimc = Dialog.getNumber();

makeRectangle(rimc, rimc, xwidth-2*rimc, yheight-2*rimc);
run("Make Inverse")
run("Clear")
run("Select None");
setForegroundColor(0, 0, 0);
floodFill(1,1);

}

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macro "cut away rim (grain map) [5]"{
	
xwidth = getWidth();
yheight = getHeight();
rimc = 5;
Dialog.create("width of rim");
Dialog.addMessage("width of rim");
Dialog.addNumber("in pixel",rimc);
Dialog.show();
rimc = Dialog.getNumber();

makeRectangle(rimc, rimc, xwidth-2*rimc, yheight-2*rimc);
run("Make Inverse")
setForegroundColor(0, 0, 0);
fill();
run("Select None");
setForegroundColor(255, 255, 255);
floodFill(1,1);
}
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macro "invert image [y]"{
run("Invert");
}

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macro "scale to pixel  [x]"{
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
}

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