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update with params
1 parent f1c6c5b commit 7864a17

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4 files changed

+169
-81
lines changed

4 files changed

+169
-81
lines changed

‎pom.xml‎

Lines changed: 1 addition & 1 deletion
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@@ -252,7 +252,7 @@
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<!-- MainClass in mainfest make a executable jar -->
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<archive>
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<manifest>
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<mainClass>net.preibisch.fusiontask.task.MainJob</mainClass>
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<mainClass>net.preibisch.fusiontask.task.FusionV2</mainClass>
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</manifest>
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</archive>
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‎src/net/preibisch/fusiontask/task/Fusion.java‎

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This file was deleted.

src/net/preibisch/fusiontask/task/MainJob.java renamed to src/net/preibisch/fusiontask/task/FusionV1.java

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@@ -29,7 +29,7 @@
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import picocli.CommandLine;
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import picocli.CommandLine.Option;
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public class MainJob implements Callable<Void> {
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public class FusionV1 implements Callable<Void> {
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@Option(names = { "-t", "--task" }, required = false, description = "The path of the Data")
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private String task;
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@@ -50,7 +50,7 @@ public class MainJob implements Callable<Void> {
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@Option(names = { "-id" }, required = false, description = "The id of block")
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private Integer id;
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public MainJob() {
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public FusionV1() {
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// TODO Auto-generated constructor stub
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}
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@@ -166,6 +166,6 @@ public static void main(String[] args) {
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// /Users/Marwan/Desktop/Task/output.n5 -m
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// /Users/Marwan/Desktop/Task/metadata.json -id 1";
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// System.out.println(String.join(" ", args));
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CommandLine.call(new MainJob(), args);
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CommandLine.call(new FusionV1(), args);
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}
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}

‎src/net/preibisch/fusiontask/task/FusionV2.java‎

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@@ -0,0 +1,165 @@
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package net.preibisch.fusiontask.task;
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import java.io.IOException;
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import java.util.List;
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import java.util.concurrent.Callable;
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import org.janelia.saalfeldlab.n5.N5FSWriter;
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import org.janelia.saalfeldlab.n5.N5Writer;
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import org.janelia.saalfeldlab.n5.RawCompression;
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import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
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import com.google.gson.JsonIOException;
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import com.google.gson.JsonSyntaxException;
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import mpicbg.spim.data.SpimDataException;
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import mpicbg.spim.data.sequence.ViewId;
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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.preibisch.distribution.algorithm.blockmanager.block.BasicBlockInfo;
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import net.preibisch.distribution.algorithm.clustering.kafka.KafkaManager;
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import net.preibisch.distribution.algorithm.clustering.kafka.KafkaProperties;
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import net.preibisch.distribution.algorithm.clustering.scripting.TaskType;
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import net.preibisch.distribution.algorithm.controllers.items.BlocksMetaData;
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import net.preibisch.distribution.algorithm.task.FusionParams;
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import net.preibisch.distribution.io.img.XMLFile;
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import net.preibisch.distribution.io.img.n5.N5File;
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import net.preibisch.distribution.tools.Tools;
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import net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox;
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import picocli.CommandLine;
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import picocli.CommandLine.Option;
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public class FusionV2 implements Callable<Void> {
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@Option(names = { "-t", "--task" }, required = false, description = "The path of the Data")
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private String task;
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@Option(names = { "-o", "--output" }, required = false, description = "The path of the Data")
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private String output;
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@Option(names = { "-i", "--input" }, required = false, description = "The path of the Data")
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private String input;
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@Option(names = { "-m", "--meta" }, required = false, description = "The path of the MetaData file")
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private String metadataPath;
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@Option(names = { "-p", "--param" }, required = false, description = "The path of the MetaData file")
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private String paramPath;
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@Option(names = { "-v","-view" }, required = false, description = "The id of block")
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private int view;
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@Option(names = { "-id" }, required = false, description = "The id of block")
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private Integer id;
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public FusionV2() {
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// TODO Auto-generated constructor stub
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}
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@Override
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public Void call() throws Exception {
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try {
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try {
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id = id - 1;
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} catch (Exception e) {
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KafkaManager.error(-1, e.toString());
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System.out.println("Error id");
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throw new Exception("Specify id!");
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}
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TaskType type = TaskType.of(task);
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switch (type) {
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case PREPARE:
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generateN5(input, metadataPath,paramPath, output, id,view);
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return null;
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case PROCESS:
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blockTask(input, metadataPath, paramPath, output, id,view);
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return null;
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default:
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KafkaManager.error(id, "Specify task");
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System.out.println("Error");
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throw new Exception("Specify task!");
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}
82+
} catch (Exception e) {
83+
KafkaManager.error(id, e.toString());
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System.out.println("Error");
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throw new Exception("Specify task!");
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}
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// MyLogger.log.info("Block " + id + " saved !");
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}
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public static void blockTask(String inputPath, String metadataPath, String paramPath, String outputPath, int id,int view) {
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try {
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KafkaManager.log(id, "Start process");
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// XMLFile inputFile = XMLFile.XMLFile(inputPath);
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BlocksMetaData md = BlocksMetaData.fromJson(metadataPath);
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FusionParams params = FusionParams.fromJson(paramPath);
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String jobId = md.getJobId();
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KafkaProperties.setJobId(jobId);
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KafkaManager.log(id, "Got metadata !");
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BasicBlockInfo binfo = md.getBlocksInfo().get(id);
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KafkaManager.log(id, "Got block info !");
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// BoundingBox bb = new BoundingBox(Util.long2int(binfo.getMin()), Util.long2int(binfo.getMax()));
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KafkaManager.log(id, "Bounding box created: " + params.getBb().toString());
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List<ViewId> viewIds = params.getViewIds().get(view);
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KafkaManager.log(id, "Got view ids ");
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XMLFile inputFile = XMLFile.XMLFile(inputPath, params.getBb(), params.getDownsampling(), viewIds);
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KafkaManager.log(id, "Input loaded. ");
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// XMLFile inputFile = XMLFile.XMLFile(inputPath);
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RandomAccessibleInterval<FloatType> block = inputFile.fuse(params.getBb(),view);
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KafkaManager.log(id, "Got block. ");
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N5File outputFile = N5File.open(outputPath);
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outputFile.saveBlock(block, binfo.getGridOffset());
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KafkaManager.log(id, "Task finished " + id);
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KafkaManager.done(id, "Task finished " + id);
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} catch (SpimDataException | IOException e) {
118+
KafkaManager.error(id, e.toString());
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e.printStackTrace();
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}
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}
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public static void generateN5(String inputPath, String metadataPath,String paramPath, String outputPath, int id,int view) {
124+
try {
125+
KafkaManager.log(id, "Start generate n5");
126+
BlocksMetaData md = BlocksMetaData.fromJson(metadataPath);
127+
FusionParams params = FusionParams.fromJson(paramPath);
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BoundingBox bb = new BoundingBox(params.getBb());
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long[] dims = bb.getDimensions((int)params.getDownsampling());
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int blockUnit = md.getBlockUnit();
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N5File outputFile = new N5File(outputPath, dims, blockUnit);
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outputFile.create();
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KafkaManager.log(id, "N5 Generated");
134+
KafkaManager.done(id, "N5 Generated");
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} catch (JsonSyntaxException | JsonIOException | IOException e) {
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137+
KafkaManager.error(id, e.toString());
138+
e.printStackTrace();
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}
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}
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142+
public static void generateN5fromXML(String inputPath, String metadataPath, String outputPath, int id) {
143+
try {
144+
System.out.println("Start generating output");
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XMLFile inputFile = XMLFile.XMLFile(inputPath);
146+
RandomAccessibleInterval<FloatType> virtual = inputFile.fuse();
147+
String dataset = "/volumes/raw";
148+
N5Writer writer = new N5FSWriter(outputPath);
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BlocksMetaData md = BlocksMetaData.fromJson(metadataPath);
150+
// long[] dims = md.getDimensions();
151+
int blockUnit = md.getBlockUnit();
152+
int[] blocks = Tools.array(blockUnit, virtual.numDimensions());
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154+
N5Utils.save(virtual, writer, dataset, blocks, new RawCompression());
155+
System.out.println("Ouptut generated");
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} catch (SpimDataException | IOException e1) {
157+
// TODO Auto-generated catch block
158+
e1.printStackTrace();
159+
}
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}
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public static void main(String[] args) {
163+
CommandLine.call(new FusionV2(), args);
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}
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}

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