// Astrocyte Calcium Imaging Toolbox 
// by Wilson Adams, Vanderbilt Biophotonics Center

// Last Updated: 18 Sept 2018

// Bioformats Importer

macro "Bioformats Importer Action Tool - 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" {
	if (isKeyDown("shift")) {
		run("Image Sequence...")
	}
	else {
	run("Bio-Formats Importer");
	}
}

// B/C 
macro "Adjust Brightness and Contrast Action Tool - 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" {
    run("Brightness/Contrast...");
}

// LUT list
var luts = getLutMenu();
var lCmds = newMenu("LUT Menu Tool", luts);
macro "LUT Menu Tool - C037T0b11LT6b09UTcb09T" {
	cmd = getArgument();
	if (cmd!="-") run(cmd);
}
function getLutMenu() {
	list = getLutList();
	menu = newArray(16+list.length);
	menu[0] = "Invert LUT"; menu[1] = "Apply LUT"; menu[2] = "-";
	menu[3] = "Fire"; menu[4] = "Grays"; menu[5] = "Ice";
	menu[6] = "Spectrum"; menu[7] = "3-3-2 RGB"; menu[8] = "Red";
	menu[9] = "Green"; menu[10] = "Blue"; menu[11] = "Cyan";
	menu[12] = "Magenta"; menu[13] = "Yellow"; menu[14] = "Red/Green";
	menu[15] = "-";
	for (i=0; i<list.length; i++)
		menu[i+16] = list[i];
	return menu;
}

function getLutList() {
	lutdir = getDirectory("luts");
	list = newArray("No LUTs in /ImageJ/luts");
	if (!File.exists(lutdir))
		return list;
	rawlist = getFileList(lutdir);
	if (rawlist.length==0)
		return list;
	count = 0;
	for (i=0; i< rawlist.length; i++)
		if (endsWith(rawlist[i], ".lut")) count++;
	if (count==0)
		return list;
	list = newArray(count);
	index = 0;
	for (i=0; i< rawlist.length; i++) {
		if (endsWith(rawlist[i], ".lut"))
			list[index++] = substring(rawlist[i], 0, lengthOf(rawlist[i])-4);
	}
	return list;
}

// Flatfield Correction Tool
macro "Automated Flatfield Correction (+shift = Stacks) Action Tool - C037T0b11FT6b09FTcb09C" {
	runMacro("AutomatedFlatfieldCorrection")
}

// Z-project Tool (Default max)
macro "Maximum Intensity Projection (+space = Mean; +shift = StDev; +alt = Sum) Action Tool - C902T3f18Z" {
    if(isKeyDown("shift"))
	{	run("Z Project...", "projection=[Standard Deviation]");}
	if(isKeyDown("space"))
	{	run("Z Project...", "projection=[Average Intensity]");}
	if(isKeyDown("alt"))
	{	run("Z Project...", "projection=[Sum Slices]");}
	else
    {run("Z Project...", "start=1 stop="+nSlices+" projection=[Max Intensity]");}
}
// Plot Z projection
macro "Plot Z Axis Profile Action Tool - C000D0dD0eD13D14D15D16D17D18D19D1aD1bD1cD1dD20D21D22D23D24D25D26D27D28D29D2aD2bD2cD2fD33D34D35D36D37D38D39D3aD3bD3eD3fD47D48D49D4aD4dD4eD4fD5cD5dD5eD5fD6bD6cD6dD6eD6fD7dD7eD7fD8dD8eD8fD9dD9eD9fDaeDafDbeDbfDcfDdfDefDffC000C111C222C333C444D1fD2eD3dD4cD5bD6aD79D87D88D96Da5Db4Dc3Dd2De1Df0C444C555C666C777C888C999CaaaCbbbCcccD0fD1eD2dD3cD4bD5aD69D78D86D95Da4Db3Dc2Dd1De0CcccCdddCeeeCfff"{
	run("Plot Z-axis Profile")
}


// Weka Segmentation tool STILL NEED TO ADD
macro "Trained Weka Segmentation Action Tool (+shift to train) - Cb7fD57D76Cc7fD00D01D02D03D04D05D06D07D08D09D0aD0dD0eD0fD10D11D12D13D14D15D16D17D18D19D1aD1dD1eD1fD20D21D22D23D24D25D26D27D28D29D2aD2dD2eD2fD30D31D32D33D34D35D36D37D38D39D3dD3eD3fD40D41D42D43D44D4eD4fD50D51D52D5aD5fD60D61D6fD70D7eD7fD80D8aD8fD90Da0Da1DaaDb0Db1Db2Db3Db7Db8Db9DbaDbbDc0Dc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcaDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdeDdfDe0De1De2De3De4De5De6De7DeeDefDf0Df1Df2Df3Df4Df5Df6DfbDfeDffCc7fCa43DbcCb42D85Cd48D3aD71De8C7d7D6dD82Cb43D92C8a8D6bD9eC984Cc42D5eDecCb7eD1cDcbDebCc52D45C9abD3cCc43Da6DfcCb43D2cD62DadDf7Cc6dDb4DdaDeaCc52D56C7d7C7c6D3bD4dDfdCc42D2bCb8eD73DdcDfaCb63D0cDa9De9C9acDedDf9Cb43D99Cb43D0bD8eD9fCb78Cc42D6eDb6DdbC7d8D1bDb5C8a5Cc7eCb63D5bD5cDa2Da5DccC7cbDacCb45DddCa9dCc52C7daDbdC7c7D9bDf8Cb9eD47DbeC9adD7cDa4Ca34D46Cd5aD53Cc43C7d8D72C985D91Cb8fCb53D81C8bbDabDcfCa73D9dDcdCa8dD63D8dCb52D48D49D4bD7bC7d9C7d7C8bcD55DceCb43Cb7bC7d8C8a6Da7Cc7fD4cDa8C8cbCc55D54Ca9eCc53DafC7daD8bD9cC7d7DaeCa9eCaadD7dCc68D4aC9aaC994Cb7fDbfC8bcCb53Cb7dC7d9Da3C7c7C9bcCb7aC7b5Cc7eC7daD8cCd46Ca9dC7daCd5cC7caC985Cc53D5dC9bcCa74Cb8dD9a" {
	
}

// ROI Multimeasure
macro "ROI Multimeasure Action Tool - C037T0b11RT6b09OTcb09I" {
	img = getTitle()
	run("Set Measurements...", "mean redirect=None decimal=6");
	roiManager("Multi Measure one");
	results = getTitle()
	rename(img+"_results")
}

// Stack Normalization Tool
macro "Stack Normalization Action Tool - 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" {
	runMacro("StackNormalizationTool");
}

// Difference Image Action Tool
macro "Difference Image Action Tool - 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" {
	runMacro("DifferenceImageTool");
}

// Calculator Plus Tool
macro "CalculatorPlus (+shift = imageCalculator) Action Tool - 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" {
	if (isKeyDown('shift')) {
		run("Image Calculator...")
	}
	else {
		run("Calculator Plus");
	}
}

// Export as GIF tool
macro "Export GIF Action Tool - C037T0b11GT6b09iTcb09F" {
	img = getTitle()
	path = getInfo("image.directory")
	n = nSlices
	run("Animation Options...", "speed=60 first=1 last=&n");
	run("Series Labeler", "stack_type=[time series or movie] label_format=[Custom Format] custom_suffix=sec custom_format=[] label_unit=[Custom Suffix] decimal_places=1 startup=0.000000000 interval=1.000000000 every_n-th=1 first=0 last=&n location_presets=[Lower Left] x_=0 y_=502");
	run("Duplicate...", "duplicate");
	run("RGB Color");
	saveAs("Gif", path+img+".gif");
}

// Scale Bar tool
macro "Scale Bar Action Tool - C902F02f3 -C902T1e0cu -C902T6e0cm" {
	run("Scale Bar...")
	}


macro "AstroProcessNDfile_fast Action Tool - 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" {
	runMacro("Bologna_AstroProcessNDfile_fast.ijm")
}

macro "theLime Action Tool - 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" {
	Dialog.create("Feature Pending")
	Dialog.addMessage("This feature isn't ready yet... check back soon")
	Dialog.show()	
}