Add command line option to apply raw tile stitching parameters to dec…

…onvolved tiles (#38) * added parameters for flatfield images * fixed the default correction images paths * use same style * add option to apply raw tile stitching parameters to deconvolved tiles * update file naming for new version * add ability to use json specifying tif inputs Co-authored-by: Cristian Goina <[email protected]>
saalfeldlab · Apr 5, 2022 · e118564 · e118564
1 parent e578943
commit e118564
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Showing 2 changed files with 53 additions and 3 deletions.
diff --git a/src/main/java/org/janelia/stitching/StitchingArguments.java b/src/main/java/org/janelia/stitching/StitchingArguments.java
@@ -1,6 +1,12 @@
 package org.janelia.stitching;
 
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
 import java.io.Serializable;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
@@ -10,6 +16,10 @@
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 
+import com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+
 /**
  * Command line arguments parser for a stitching job.
  *
@@ -104,11 +114,15 @@ public static enum RematchingMode implements Serializable
 	@Option(name = "--fusestage", required = false,
 			usage = "Allow fusing tiles using their stage coordinates (when there is no '-final' suffix in the tile configuration filename), i.e. when exporting initial tile configuration.")
 	private boolean allowFusingStage = false;
+
+	@Option(name = "--applyRawStitchingToDecon", required = false,
+		usage = "Apply stitching parameters obtained from raw tiles to deconvolved tiles.")
+	private boolean applyRawStitchingToDecon = false;
 
 
 	private boolean parsedSuccessfully = false;
 
-	public StitchingArguments( final String[] args ) throws IllegalArgumentException
+	public StitchingArguments( final String[] args ) throws IllegalArgumentException, IOException
 	{
 		final CmdLineParser parser = new CmdLineParser( this );
 		try {
@@ -139,7 +153,40 @@ else if ( rematchingModeStr.equalsIgnoreCase( "incremental" ) )
 		for ( int i = 0; i < inputTileConfigurations.size(); ++i )
 			if ( !CloudURI.isCloudURI( inputTileConfigurations.get( i ) ) )
 				inputTileConfigurations.set( i, Paths.get( inputTileConfigurations.get( i ) ).toAbsolutePath().toString() );
-
+
+		if ( applyRawStitchingToDecon )
+		{
+		    	for ( int channel = 0; channel < inputTileConfigurations.size(); channel++ )
+		    	{
+		    	    	// need to replace eg. /base/path/tiles.n5/488nm/Tile.tif with /base/path/matlab_decon/Tile.tif
+		    		String inputTileConfiguration = inputTileConfigurations.get( channel );
+			    	JsonArray jsonArray = (JsonArray) new JsonParser().parse( new FileReader( inputTileConfiguration ) );
+			    	JsonObject firstTile = (JsonObject) jsonArray.get( 0 );
+			    	File firstTileFile = new File( firstTile.get( "file" ).toString() );
+			    	String parentDir = firstTileFile.getParent();
+			    	String greatGrandparentDirectory = firstTileFile.getParentFile().getParentFile().getParent();
+
+		    		String content = new String( Files.readAllBytes( Paths.get( inputTileConfiguration ) ), StandardCharsets.UTF_8);
+		    		content = content.replaceAll( ".tif", "_decon.tif" );
+		    		String outputTileConfiguration;
+		    		if ( inputTileConfiguration.contains( "-n5-final.json" ) )
+		    		{
+			    		content = content.replaceAll( parentDir, greatGrandparentDirectory + "/matlab_decon" );
+		    			outputTileConfiguration = inputTileConfiguration.replace( "-n5-final.json", "-rawToDecon-final.json" );
+		    		}
+		    		else
+		    		{	// then it contains references to tifs not n5s
+			    		content = content.replaceAll( parentDir, parentDir + "/matlab_decon" );
+			    		if ( inputTileConfiguration.contains( "final.json" ) )
+			    			outputTileConfiguration = inputTileConfiguration.replace( "-final.json", "-rawToDecon-final.json" );
+			    		else
+			    			outputTileConfiguration = inputTileConfiguration.replace( ".json", "-rawToDecon.json" );
+		    		}
+		    		Files.write( Paths.get( outputTileConfiguration ), content.getBytes( StandardCharsets.UTF_8 ) );
+		    		inputTileConfigurations.set(channel, outputTileConfiguration);
+		    	}
+		}
+
 		if (correctionImagesPaths != null && correctionImagesPaths.size() > 0)
 		{
 			if (correctionImagesPaths.size() != inputTileConfigurations.size())
@@ -189,6 +236,8 @@ public long[] maxCoord()
 
 	public boolean stitchOnly() { return stitchOnly; }
 	public boolean fuseOnly() { return fuseOnly; }
+
+	public boolean applyRawStitchingToDecon() { return applyRawStitchingToDecon; }
 
 	public RematchingMode rematchingMode() { return rematchingMode; }
 

diff --git a/src/main/java/org/janelia/stitching/StitchingSpark.java b/src/main/java/org/janelia/stitching/StitchingSpark.java
@@ -1,5 +1,6 @@
 package org.janelia.stitching;
 
+import java.io.IOException;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -19,7 +20,7 @@
 
 public class StitchingSpark implements Serializable, AutoCloseable
 {
-	public static void main( final String[] args )
+	public static void main( final String[] args ) throws IllegalArgumentException, IOException
 	{
 		final StitchingArguments stitchingArgs = new StitchingArguments( args );
 		if ( !stitchingArgs.parsedSuccessfully() )