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total pipeline
1 parent 1a8987b commit 462e9ff

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-5
lines changed

‎src/net/preibisch/dbio_headless/BlockExtractorUsingMetaBlocks.java

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@@ -47,7 +47,6 @@ public static void main(String[] args) {
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System.exit(0);
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}
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@Override
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public Void call() throws IncompatibleTypeException, IOException, SpimDataException {
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BufferedReader br;
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‎src/net/preibisch/dbio_headless/GenerateMetaBlocksFile.java

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@@ -40,15 +40,14 @@ public static void main(String[] args) {
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System.exit(0);
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}
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@Override
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public Void call() throws IncompatibleTypeException, SpimDataException, IOException {
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XMLFile<FloatType> inputData = XMLFile.XMLFile(input);
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long[] blocksizes = ArrayHelpers.fill(BasicBlockInfoGenerator.BLOCK_SIZE, inputData.getDims().length);
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Map<Integer, BasicBlockInfo> blocks = BasicBlockInfoGenerator.divideIntoBlockInfo(inputData.bb());
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Metadata md = new Metadata(Job.get().getId(),input,output,new BoundingBox(inputData.bb()),blocksizes,blocks);
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md.toJson(new File(metadata));
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md.toJson(metadata);
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return null;
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}
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‎src/net/preibisch/dbio_headless/SplitTiffImageIntoBlocksImages.java

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@@ -38,7 +38,6 @@ public static void main(String[] args) {
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System.exit(0);
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}
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@Override
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public Boolean call() throws Exception {
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long size = blockSize != null ? blockSize : BasicBlockInfoGenerator.BLOCK_SIZE;
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‎src/net/preibisch/dbio_headless/TestFusionSpimInBlocksN5.java

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@@ -72,7 +72,6 @@ public Task(int i, ImgFile input, N5File output, BasicBlockInfo binfo) {
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this.binfo = (BasicBlockInfo) binfo;
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}
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@Override
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public void run() {
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try {
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MyLogger.log().info("Started " + i);

‎src/net/preibisch/dbio_headless/TotalPipeline.java

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@@ -0,0 +1,99 @@
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package net.preibisch.dbio_headless;
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import java.io.File;
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import java.io.IOException;
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import java.util.Map;
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import java.util.concurrent.ExecutorService;
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import mpicbg.spim.data.SpimDataException;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.type.numeric.real.FloatType;
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import net.imglib2.util.Util;
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import net.preibisch.distribution.algorithm.blockmanagement.blockinfo.BasicBlockInfo;
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import net.preibisch.distribution.algorithm.blockmanagement.blockinfo.BasicBlockInfoGenerator;
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import net.preibisch.distribution.algorithm.blockmanagement.io.BlockFileManager;
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import net.preibisch.distribution.algorithm.controllers.items.Job;
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import net.preibisch.distribution.algorithm.controllers.items.Metadata;
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import net.preibisch.distribution.algorithm.errorhandler.logmanager.MyLogger;
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import net.preibisch.distribution.algorithm.multithreading.Threads;
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import net.preibisch.distribution.io.DataExtension;
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import net.preibisch.distribution.io.img.load.LoadTIFF;
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import net.preibisch.distribution.io.img.n5.N5File;
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import net.preibisch.distribution.io.img.xml.XMLFile;
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import net.preibisch.distribution.tools.helpers.ArrayHelpers;
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import net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox;
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public class TotalPipeline {
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static String inputFilePath = "/Users/Marwan/Desktop/Task/example_dataset/3d/dataset.xml";
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static String outputN5Path = "/Users/Marwan/Desktop/Task/example_dataset/3d/output.n5";
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static String metadataPath = "/Users/Marwan/Desktop/Task/example_dataset/3d/metadata.json";
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static String tiffFolderPath = "/Users/Marwan/Desktop/Task/example_dataset/3d/output/";
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public static void main(String[] args) throws SpimDataException, IOException {
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generateMetadata(inputFilePath, outputN5Path, metadataPath);
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splittoTiffs(inputFilePath, tiffFolderPath, metadataPath);
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mergeToN5(metadataPath, tiffFolderPath, outputN5Path);
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}
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public static void generateMetadata(String inputPath, String outputPath, String metadataPath)
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throws SpimDataException, IOException {
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XMLFile<FloatType> inputData = XMLFile.XMLFile(inputPath);
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long[] blocksizes = ArrayHelpers.fill(BasicBlockInfoGenerator.BLOCK_SIZE, inputData.getDims().length);
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Map<Integer, BasicBlockInfo> blocks = BasicBlockInfoGenerator.divideIntoBlockInfo(inputData.bb());
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MyLogger.log().info("Total blocks: " + blocks.size());
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Metadata md = new Metadata(Job.get().getId(), inputPath, outputPath, new BoundingBox(inputData.bb()),
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blocksizes, blocks);
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MyLogger.log().info(md.toString());
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md.toJson(metadataPath);
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}
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public static void splittoTiffs(String inputPath, String outputTiffPath, String metadataPath)
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throws SpimDataException, IOException {
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XMLFile<FloatType> inputData = XMLFile.XMLFile(inputPath);
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Metadata md = Metadata.fromJson(metadataPath);
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MyLogger.log().info(md.toString());
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MyLogger.log().info("Start process.. ");
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MyLogger.log().info("Block Generated.. ");
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ExecutorService service = Threads.createExService(Threads.numThreads());
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File file = new File(outputTiffPath);
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file.mkdir();
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BlockFileManager.saveAllBlocks(service, inputData.getImg(), md.getBlocksInfo(), outputTiffPath, DataExtension.TIF);
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MyLogger.log().info("Done !");
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}
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public static void mergeToN5(String metadataPath, String tiffFolderPath, String outputn5Path) throws IOException {
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Metadata md = Metadata.fromJson(metadataPath);
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long[] dims = md.getBb().getDimensions(1);
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N5File n5 = createOuptut(dims, outputn5Path);
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Map<Integer, BasicBlockInfo> blocks = md.getBlocksInfo();
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File folder = new File(tiffFolderPath);
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for (File f : folder.listFiles()) {
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if (DataExtension.fromURI(f.getName()) == DataExtension.TIF) {
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Integer x = Integer.valueOf(DataExtension.removeExtension(f.getName())) ;
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// File file = new File(outputPath, DataExtension.TIF.file(String.valueOf(x)));
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MyLogger.log().info("Image : " + f.getAbsolutePath());
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RandomAccessibleInterval<FloatType> blockImage = LoadTIFF.load(f);
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long[] gridOffset = blocks.get(x).getGridOffset();
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n5.saveBlock(blockImage, gridOffset);
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MyLogger.log().info("Block " + x + " saved in: " + Util.printCoordinates(gridOffset));
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}
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}
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n5.show("Result");
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}
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private static N5File createOuptut(long[] dims, String outputPath) throws IOException {
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N5File outputFile = new N5File(outputPath, dims);
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outputFile.create();
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MyLogger.log().info("N5 Generated");
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return outputFile;
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}
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}

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