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version that recreates lookup-tables for zvi files - Volker Baecker, 11/21/2011 11:26 AM

 
/**
* MRI Image Conversion Tools
* Tools for batch-converting lsm or lif images to tif
*
* Work on a folder containing lif or lsm files
* For each file and for each image it contains:
* - save the channels each as a tif file
* - save the overlay as an RGB tif file
* - optional: save stacks as projections
*
* written 2011 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr)
*
* The Lif2Tif macro is based on the Leica LIF Extractor macro by Christophe LETERRIER (http://christopheleterrier.com/LeterrierSOFT.html)
* which is based on the ZStacks Projector macro version 1.1 14/05/2008
*/

var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Image_Conversion_Tools"
var DO_PROJECTION = false;
var USE_ALL_SLICES_FOR_PROJECTION = false;
var PROJECTION_START_SLICE = 1;
var PROJECTION_END_SLICE = 3;
var PROJECTION_METHOD = "Max Intensity";
var CHANNELS_STRING = "1111";

var OUTPUT_SUBFOLDER = "tif"

macro "Unused Tool - C037" { }

macro "MRI Image Conversion Tools Help Action Tool - C000T4b12?" {
run('URL...', 'url='+helpURL);
}
macro "Lif2Tif Action Tool - C037T0b11LT7b09iTcb09f" {

DIR_PATH=getDirectory("Select a directory");
OUTPUT_DIR = DIR_PATH + "/" + OUTPUT_SUBFOLDER;
File.makeDirectory(OUTPUT_DIR);

print("\\Clear");
print("converting lif file in folder: "+DIR_PATH);

// Get all file names
ALL_NAMES=getFileList(DIR_PATH);
ALL_EXT=newArray(ALL_NAMES.length);
// Create extensions array
for (i=0; i<ALL_NAMES.length; i++) {
LENGTH=lengthOf(ALL_NAMES[i]);
ALL_EXT[i]=substring(ALL_NAMES[i],LENGTH-4,LENGTH);
}

setBatchMode(true);

// Loop on all .lei and .lif extensions
fileIndex = 0;
numberOfLifFiles = 0;
for (n=0; n<ALL_EXT.length; n++) {
if (ALL_EXT[n]==".lei" || ALL_EXT[n]==".lif") numberOfLifFiles++;
}

for (n=0; n<ALL_EXT.length; n++) {
if (ALL_EXT[n]==".lei" || ALL_EXT[n]==".lif") {
fileIndex++;
// Get the file path
FILE_PATH=DIR_PATH+ALL_NAMES[n];
FILE_NAME=File.getName(FILE_PATH);

// Start BioFormats and get series number in file.
run("Bio-Formats Macro Extensions");
Ext.setId(FILE_PATH);
Ext.getSeriesCount(SERIES_COUNT);
SERIES_NAMES=newArray(SERIES_COUNT);

seriesIndex = 0;
for (i=0; i<SERIES_COUNT; i++) {
seriesIndex++;
print("\\Update2:converting image " + (fileIndex) + " of " + numberOfLifFiles + " / series " + seriesIndex + " of " + SERIES_COUNT);
Ext.setSeries(i);
Ext.getEffectiveSizeC(CHANNEL_COUNT);
Ext.getSizeZ(SLICE_COUNT);
SERIES_NAMES[i]="";
Ext.getSeriesName(SERIES_NAMES[i]);
TEMP_NAME=toLowerCase(SERIES_NAMES[i]);
run("Bio-Formats Importer", "open=["+ FILE_PATH + "] " + " color_mode=Default view=Hyperstack" + " stack_order=Default " + "series_"+d2s(i+1,0));
Stack.setDisplayMode("composite");
title = getTitle();
Stack.setActiveChannels(CHANNELS_STRING);
run("Stack to RGB", "slices keep");
rename(title + "-1");
if (SLICE_COUNT>1 && DO_PROJECTION) doProjection();
currentTitle = getTitle();
index = lastIndexOf(currentTitle, ".lif - ");
name = substring(currentTitle, index+7, lengthOf(currentTitle)-2);
save(OUTPUT_DIR + "/" + name + " - RGB.tif");
close();
run("Split Channels");
// Loop on each channel (each opened window)
for(j=1; j<CHANNEL_COUNT+1; j++) {
selectImage("C"+j+"-"+title);
if (SLICE_COUNT>1 && DO_PROJECTION) doProjection();
currentTitle = getTitle();
index = lastIndexOf(currentTitle, ".lif - ");
name = substring(currentTitle, index+7, lengthOf(currentTitle));
save(OUTPUT_DIR + "/" + name + " - C" + j + ".tif");
close();
}
}
}
}
setBatchMode("exit and display");
showStatus("finished converting lif to tif");
print("finished converting lif to tif");
}



macro "Lsm2Tif Action Tool - C037T0b11LT7b09sTcb09m" {
DIR_PATH=getDirectory("Select a directory");
OUTPUT_DIR = DIR_PATH + "/" + OUTPUT_SUBFOLDER;
File.makeDirectory(OUTPUT_DIR);

print("\\Clear");
print("converting lsm file in folder: "+DIR_PATH);

// Get all file names
ALL_NAMES=getFileList(DIR_PATH);
ALL_EXT=newArray(ALL_NAMES.length);
// Create extensions array
for (i=0; i<ALL_NAMES.length; i++) {
LENGTH=lengthOf(ALL_NAMES[i]);
ALL_EXT[i]=substring(ALL_NAMES[i],LENGTH-4,LENGTH);
}

setBatchMode(true);

// Loop on all .lei and .lsm extensions
fileIndex = 0;
numberOfLifFiles = 0;
for (n=0; n<ALL_EXT.length; n++) {
if (ALL_EXT[n]==".lsm" ) numberOfLifFiles++;
}

for (n=0; n<ALL_EXT.length; n++) {
if (ALL_EXT[n]==".lsm") {
fileIndex++;
// Get the file path
FILE_PATH=DIR_PATH+ALL_NAMES[n];
FILE_NAME=File.getName(FILE_PATH);
print("\\Update2:converting image " + (fileIndex) + " of " + numberOfLifFiles);
open(FILE_PATH);
Stack.setDisplayMode("composite");
title = getTitle();
getDimensions(width, height, colors, slices, frames);
SLICE_COUNT = slices;
Stack.setActiveChannels(CHANNELS_STRING);
run("Stack to RGB", "slices keep");
rename(title + "-1");
if (slices>1 && DO_PROJECTION) doProjection();
currentTitle = getTitle();
name = substring(currentTitle, 0, lengthOf(currentTitle)-6);
save(OUTPUT_DIR + "/" + name + " - RGB.tif");
close();
run("Split Channels");
// Loop on each channel (each opened window)
for(j=1; j<colors+1; j++) {
selectImage("C"+j+"-"+title);
if (slices>1 && DO_PROJECTION) doProjection();
currentTitle = getTitle();
name = substring(currentTitle, 3, lengthOf(currentTitle)-4);
save(OUTPUT_DIR + "/" + name + " - C" + j + ".tif");
close();
}
close();
}
}
setBatchMode("exit and display");
showStatus("finished converting lsm to tif");
print("finished converting lsm to tif");
}

macro "Zvi2Tif Action Tool - C037T0b11ZT7b09vTcb09i" {
DIR_PATH=getDirectory("Select a directory");
OUTPUT_DIR = DIR_PATH + "/" + OUTPUT_SUBFOLDER;
File.makeDirectory(OUTPUT_DIR);

print("\\Clear");
print("converting zvi file in folder: "+DIR_PATH);

// Get all file names
ALL_NAMES=getFileList(DIR_PATH);
ALL_EXT=newArray(ALL_NAMES.length);
// Create extensions array
for (i=0; i<ALL_NAMES.length; i++) {
LENGTH=lengthOf(ALL_NAMES[i]);
ALL_EXT[i]=substring(ALL_NAMES[i],LENGTH-4,LENGTH);
}

setBatchMode(true);

// Loop on all .lei and .lsm extensions
fileIndex = 0;
numberOfLifFiles = 0;
for (n=0; n<ALL_EXT.length; n++) {
if (ALL_EXT[n]==".zvi" ) numberOfLifFiles++;
}

for (n=0; n<ALL_EXT.length; n++) {
if (ALL_EXT[n]==".zvi") {
fileIndex++;
// Get the file path
FILE_PATH=DIR_PATH+ALL_NAMES[n];
FILE_NAME=File.getName(FILE_PATH);
print("\\Update2:converting image " + (fileIndex) + " of " + numberOfLifFiles);

run("Bio-Formats Importer", "open=["+FILE_PATH+"] open=["+FILE_PATH+"] autoscale color_mode=Composite view=Hyperstack stack_order=XYCZT");

Stack.setDisplayMode("composite");
title = getTitle();
getDimensions(width, height, colors, slices, frames);
SLICE_COUNT = slices;
run("Bio-Formats Macro Extensions");
Ext.setId(FILE_PATH);
for (j=1; j<colors+1; j++) {
Ext.getMetadataValue("MultiChannel Color "+(j-1), colorCode);
colorCode = parseInt(colorCode,10);
Stack.setChannel(j);
blueColor = (colorCode&0xff0000)>> 16;
greenColor = (colorCode & 0xff00)>>8;
redColor = colorCode&0xff;
reds = newArray(256);
greens = newArray(256);
blues = newArray(256);
for (i=0; i<256; i++) {
reds[i] = round((i / 255.0) * redColor);
greens[i] = round((i / 255.0) * greenColor);
blues[i] = round((i / 255.0) * blueColor);
}
setLut(reds,greens,blues);
}
Stack.setChannel(1);

Stack.setActiveChannels(CHANNELS_STRING);
run("Stack to RGB", "slices keep");
rename(title + "-1");
if (slices>1 && DO_PROJECTION) doProjection();
currentTitle = getTitle();
name = substring(currentTitle, 0, lengthOf(currentTitle)-6);
save(OUTPUT_DIR + "/" + name + " - RGB.tif");
close();
run("Split Channels");
// Loop on each channel (each opened window)
for(j=1; j<colors+1; j++) {
selectImage("C"+j+"-"+title);
if (slices>1 && DO_PROJECTION) doProjection();
currentTitle = getTitle();
name = substring(currentTitle, 3, lengthOf(currentTitle)-4);
save(OUTPUT_DIR + "/" + name + " - C" + j + ".tif");
close();
}
}
}
setBatchMode("exit and display");
showStatus("finished converting zvi to tif");
print("finished converting zvi to tif");
}

function doProjection() {
currentTitle = getTitle();
startSlice = PROJECTION_START_SLICE;
endSlice = PROJECTION_END_SLICE;
if (USE_ALL_SLICES_FOR_PROJECTION) {
startSllice = 1;
endSlice = SLICE_COUNT;
}
run("Z Project...", "start=" + startSlice + " stop=" + endSlice +" projection=" + "[" + PROJECTION_METHOD + "]");
selectImage(currentTitle);
close();
rename(currentTitle);
}

macro 'Lif2Tif Action Tool Options' {
showOptionsDialog()
}

macro 'Lsm2Tif Action Tool Options' {
showOptionsDialog()
}

macro 'Zvi2Tif Action Tool Options' {
showOptionsDialog()
}

function showOptionsDialog() {
Dialog.create("Tif Export Options");
Dialog.addMessage("Projection Options");
Dialog.addCheckbox("do z-projection", DO_PROJECTION);
Dialog.addCheckbox("use all slices for projection", USE_ALL_SLICES_FOR_PROJECTION);
Dialog.addNumber("start slice for projection", PROJECTION_START_SLICE);
Dialog.addNumber("end slice for projection", PROJECTION_END_SLICE);
Dialog.addChoice("projection method", newArray("Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"), PROJECTION_METHOD);
Dialog.addMessage("Colour Options");
Dialog.addString("Channels for RGB-overlay (1-use, 0-skip):", CHANNELS_STRING);
Dialog.show();
DO_PROJECTION = Dialog.getCheckbox();
USE_ALL_SLICES_FOR_PROJECTION = Dialog.getCheckbox();
PROJECTION_START_SLICE = Dialog.getNumber();
PROJECTION_END_SLICE = Dialog.getNumber();
PROJECTION_METHOD = Dialog.getChoice();
CHANNELS_STRING = Dialog.getString();
}
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