/* * Copyright (C), 2023, Jan Brocher / BioVoxxel. All rights reserved. * * Original macro written by Jan Brocher/BioVoxxel. * * BSD-3 License * * Redistribution and use in source and binary forms of all plugins and macros, * with or without modification, are permitted provided that the following conditions are met: * 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer * in the documentation and/or other materials provided with the distribution. * 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived * from this software without specific prior written permission. * * DISCLAIMER: * * THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE * ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE * USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #@File (label = "Choose directory", required=false, style="directory", persist=false, description="Only folders can be specified, not individual images") inputFolder #@String(value="All images in the specified folder need to be of RGB type and of the same size", visibility="MESSAGE", required="false") info #@Boolean (label = "Run on active open image", value=false, description="Runs on the actively selected single image, ONLY, but works on stacks") runOnOpen #@Float (label = "Pixel saturation (%)", value="0.01", min="0.00", max="1.00", style="format:0.00", stepSize="0.01", description="Avoid too much oversaturation. Best stay below 0.10 %") saturation #@File (label = "Save in subfolder", required=false, style="directory", description="If empty, images will not be saved, otherwise end up as .tif images in the specified folder") rgbTargetFolder #@Boolean (label = "Print used limits", value=false, description="prints the used contrast limits into the log window") printExtremes #@Boolean (label = "Close saved images", value=false, description="Closes the images after processing.") closeImages #@String (label = "Usage", value="This tool applies the maximum possible contrast inside good scientific practice limits
equally to all images in the specified folder.
Keep saturation values between 0.01-0.10. Higher values oversaturate too many pixels!
This is different from normal auto contrast since all images stay optically comparable.
All images which later should be optically compared need to be processed here together in one step!", visibility="MESSAGE", required="false") rgb_contrast_optimizer_usage inputFolder += File.separator; if (!runOnOpen) { setBatchMode(true); File.openSequence(inputFolder, "scale=100"); } originalStack = getTitle(); getDimensions(width, height, channels, slices, frames); labels = newArray(slices); for (i = 1; i <= slices; i++) { Stack.setSlice(i); if (bitDepth() != 24) { exit("Close all non RGB color images"); } labels[i-1] = getInfo("slice.label"); } min = 0; max = 0; absoluteMin = 1e30; absoluteMax = 0; run("HSB Stack"); //setBatchMode("show"); getDimensions(width, height, channels, slices, frames); absoluteMin = 1e30; absoluteMax = 0; Stack.setChannel(3); for (s = 1; s <= slices; s++) { Stack.setSlice(s); run("Enhance Contrast...", "saturated=" + saturation); getMinAndMax(min, max); absoluteMin = Math.min(absoluteMin, min); absoluteMax = Math.max(absoluteMax, max); } if (printExtremes) { print("Contrast adjustment with --> min = " + absoluteMin + " / max = " + absoluteMax + " (saturation = " + saturation + " %)"); } for (s2 = 1; s2 <= slices; s2++) { Stack.setSlice(s2); setMinAndMax(absoluteMin, absoluteMax); getMinAndMax(min2, max2); run("Apply LUT", "slice"); } run("RGB Color", "slices"); resultStack = getTitle(); setBatchMode("show"); getDimensions(width, height, channels, slices, frames); for (s = 1; s <= slices; s++) { Stack.setSlice(s); if (runOnOpen) { rename(resultStack + "_contr-adj"); } else { setMetadata("Label", labels[s-1] + "_contr-adj"); } } metadata = getMetadata("Info"); existingAdjustmentMetadataIndex = lastIndexOf(metadata, "\nContrast adjustment"); if (existingAdjustmentMetadataIndex > 0) { metadata = substring(metadata, 0, existingAdjustmentMetadataIndex); } metadata = metadata + "\nContrast adjustment:\nmin=" + absoluteMin + " / max=" + absoluteMax + " (saturation = " + saturation + " %)\n"; setMetadata("Info", metadata); setBatchMode(false); //run("Stack to Images"); if (rgbTargetFolder != 0) { run("Image Sequence... ", "dir=[" + rgbTargetFolder + File.separator + "] format=TIFF name=[] use"); if (closeImages) { close(resultStack); } }