Takes a bioformats compatible file and batch exports individual series, optionally Z Projected and rescaled #BIOP #Fiji #BigDataViewer

FijiMultiSeriesExporter.groovy

// You need to activate https://biop.epfl.ch/Fiji-Bdv-Playground/  for this script to function
// It takes a file and batch exports individual series, optionally Z Projected and rescaled
// Deals pretty correctly with Big dataset + saves multiresolution OME-TIFFs file, keeping the positional metadata
// Nicolas Chiaruttini, BIOP, EPFL, 2022

#@File(label="Dataset") image_file
#@boolean(label="Show advanced opening parameters") advanced
#@String(label="Give a name to your dataset") dataset_name
#@String( label = "Select a subset of channels (0 based, comma separated). Leave blank for all", value="") range_channels
#@String( label = "Selected slices (0 based, comma separated). Leave blank for all", required = false ) range_slices
#@String( label = "Selected frames (0 based, comma separated). Leave blank for all", required = false ) range_frames
#@Boolean( label = "Perform Z Projection") z_project
#@String(label="Z Projection Method", choices={"Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"}) z_project_method
#@Integer(label="Resize in (XY)", value=1) resize
#@File(label="Output directory", style="directory") output_directory
#@Boolean(label = "Show Images", value = false) show_images
#@Integer(label="Number of images processed in parallel", value=2) n_max_threads
#@Integer(label="Number of resolution levels", value=4) nResolutionLevels
#@Integer(label="Downscaling fator", value=2) downscaleFactor
#@String(label="Compression", choices={"LZW","Uncompressed"}) compression

#@SourceAndConverterService sac_service
#@CommandService command
#@ConvertService convert
#@TaskService taskService

def task = taskService.createTask("OME TIFF conversion "+image_file.getName())

task.setStatusMessage("Parsing file metadata...")

sac_service.remove(sac_service.getSourceAndConverters().toArray(new SourceAndConverter[0]))

if (advanced) {
	command.run(OpenFilesWithBigdataviewerBioformatsBridgeCommand.class,true, 
		"datasetname", dataset_name,
		"unit","MICROMETER",
		"files", [image_file] as File[]).get()
} else {
	command.run(BasicOpenFilesWithBigdataviewerBioformatsBridgeCommand.class,true, 
		"datasetname", dataset_name,
		"unit","MICROMETER",
		"files", [image_file] as File[],
		"splitrgbchannels", false).get()
}

def allSources = convert.convert(dataset_name, SourceAndConverter[].class)

IJ.log("Total number of sources="+allSources.length)

/**
 * Removing all z offsets to the image
 */

for (source: allSources) {
  center = SourceAndConverterHelper.getSourceAndConverterCenterPoint(source)
  AffineTransform3D zOffset = new AffineTransform3D()
  zOffset.translate(0,0,center.getDoublePosition(2))
  SourceTransformHelper.append(zOffset.inverse(), new SourceAndConverterAndTimeRange(source,0))
}


// Uses the Bdv UI to fetch the number of series ( how many nodes are there below dataset>SeriesNumber ?
def datasetPath = sac_service.getUI().getTreePathFromString(dataset_name+">SeriesNumber")
def int number_of_series = datasetPath.getLastPathComponent().getChildCount();


task.setProgressMaximum(number_of_series)

def iImage = new AtomicInteger()

def start = Instant.now();

task.setStatusMessage("Conversion in progress")

def lock = new Object()

GParsExecutorsPool.withPool(n_max_threads as int) {
	
	(0..number_of_series-1).eachParallel{ series_index ->  // 
		// Converts as virtual image plus
		def ij1_images=command.run(ExportToMultipleImagePlusCommand.class, false,
			"sacs", dataset_name+">Tile>"+series_index,
			"level", 0,
			"range_frames", range_frames,
			"range_channels", range_channels,
			"range_slices", range_slices,
			"export_mode", "Virtual no-cache", // Because we only read once!
			"parallel",Boolean.TRUE,
			"verbose",Boolean.TRUE,
		).get().getOutput("imps_out")

		if (ij1_images.size()!=1) IJ.log("ERROR : ONE IMAGE EXPECTED, MULTIPLE ONES FOUND")
		def image = ij1_images.get(0)
		IJ.log("Processing "+image.getTitle())
		// Z Project
		if (z_project) {
			def iniTitle = image.getTitle();
			def cal = image.getCalibration().copy();
			ZProjector zp = new ZProjector();
    		zp.setImage(image);
    		zp.setMethod(Arrays.asList(ZProjector.METHODS).indexOf(z_project_method));
    		zp.setStopSlice(image.getNSlices());
    		if (image.getNSlices() > 1 || image.getNFrames() > 1) {
        		zp.doHyperStackProjection(true);
    		}
    		def initialBitDepth = image.getBitDepth()
    		image = zp.getProjection();
			image.setTitle(iniTitle+"_ZProj_"+z_project_method)
			cal.zOrigin = 0 // remove z offset when projecting
			image.setCalibration(cal)
			// Restores bit depth
			if (image.getBitDepth() != initialBitDepth) {
				def ic = new ImageConverter(image) 
				ic.setDoScaling(false)
				switch (initialBitDepth) {
					case 8:
						ic.convertToGray8()
					break
					case 16:
						ic.convertToGray16()
					break
					default:
					IJ.log("Conversion from "+image.getBitDepth()+" to "+initialBitDepth+" unsupported")
				}
			}
		} 
		// Resizes the image if set by the user
		if (resize!=1) {
			def iniTitle = image.getTitle();
			def cal = image.getCalibration().copy()
			cal.pixelWidth = cal.pixelWidth * resize as double
			cal.pixelHeight = cal.pixelHeight * resize as double
			cal.xOrigin = cal.xOrigin / resize as double
			cal.yOrigin = cal.yOrigin / resize as double
			image = Scaler.resize(
				image, image.getWidth()/resize as int, 
				image.getHeight()/resize as int, 
				image.getNSlices() as int, 
				"bilinear")
			image.setTitle(iniTitle+"_RescaledXY_"+resize)
			image.setCalibration(cal)
		}
		if(show_images) {image.show()}
		def totalPath =  output_directory.getAbsolutePath()+File.separator+image_file.getName()+"_"+image.getTitle()+".ome.tiff"
		new Thread(() -> {
			ImagePlusToOMETiff.writeToOMETiff(image, new File(totalPath), nResolutionLevels, downscaleFactor, compression);
			synchronized (lock) {
				printTimingMessage(start, ((double)(iImage.incrementAndGet())/(double)(number_of_series))*100)	
				long currentProgress = iImage.get();
				task.setProgressValue(currentProgress);
				if (currentProgress==number_of_series) {
					task.run(() -> {}) // finished task
				}
			}
		}).start();
	}
}

return "Done"

void printTimingMessage(Instant start, double percentageCompleteness) {
    long s = Duration.between(start, Instant.now()).getSeconds();
    String elapsedTime = String.format("%d:%02d:%02d", (s / 3600) as int, ((s % 3600) / 60) as int, (s % 60) as int);
    double sPerPC = s / percentageCompleteness;
    long sRemaining = (long) ((100 - percentageCompleteness) * sPerPC);
    String remainingTime = String.format("%d:%02d:%02d", (sRemaining / 3600) as int, ((sRemaining % 3600) / 60) as int, (sRemaining % 60) as int);
    LocalDateTime estimateDoneJob = LocalDateTime.now().plus(Duration.ofSeconds(sRemaining));
    DateTimeFormatter formatter = DateTimeFormatter.ofPattern("HH:mm");
    long nDays = sRemaining / (3600 * 24);
    String daysMessage = "";
    if (nDays == 1) {
        daysMessage += " tomorrow.";
    }
    if (nDays == 1) {
        daysMessage += " in " + nDays + " days.";
    }
    String formatDateTime = estimateDoneJob.format(formatter)
    if ((percentageCompleteness as int)== 100) {
	    String message = ' -  Task completed. Elapsed time:' + elapsedTime + '.'
	    IJ.log(message);    	
    } else {
	    String message = ' -  Task ' + (percentageCompleteness as int) + ' % completed. Elapsed time:' + elapsedTime + '. Estimated remaining time: ' + remainingTime + '. Job done at around ' + formatDateTime + daysMessage
	    IJ.log(message);
    }
}


import ch.epfl.biop.scijava.command.source.ExportToMultipleImagePlusCommand
import ch.epfl.biop.bdv.bioformats.command.OpenFilesWithBigdataviewerBioformatsBridgeCommand
import ch.epfl.biop.bdv.bioformats.command.BasicOpenFilesWithBigdataviewerBioformatsBridgeCommand
import sc.fiji.bdvpg.scijava.command.source.BasicTransformerCommand
import bdv.viewer.SourceAndConverter
import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper
import sc.fiji.bdvpg.sourceandconverter.transform.SourceTransformHelper
import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterAndTimeRange
import net.imglib2.realtransform.AffineTransform3D
import ij.plugin.ZProjector
import ij.plugin.Scaler
import groovyx.gpars.GParsPool.*
import groovyx.gpars.*
import java.util.concurrent.atomic.AtomicInteger
import ij.IJ
import org.apache.commons.io.FilenameUtils

import java.time.Duration
import java.time.Instant
import java.time.LocalDateTime
import java.time.format.DateTimeFormatter
import ch.epfl.biop.ImagePlusToOMETiff
import ij.process.ImageConverter