forceRGB parameter

darwinjob · Aug 30, 2023 · 181ff99 · 181ff99
1 parent fb1a885
commit 181ff99
Show file tree

Hide file tree

Showing 10 changed files with 50 additions and 13 deletions.
diff --git a/generic-archiver/pom.xml b/generic-archiver/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>gov.nist.isg</groupId>
         <artifactId>pyramidio-parent</artifactId>
-        <version>1.1.5</version>
+        <version>1.1.6</version>
     </parent>
     <name>${project.groupId}:${project.artifactId}</name>
     <description>Generic library to write archives folders.</description>

diff --git a/hdfs-archiver/pom.xml b/hdfs-archiver/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>gov.nist.isg</groupId>
         <artifactId>pyramidio-parent</artifactId>
-        <version>1.1.5</version>
+        <version>1.1.6</version>
     </parent>
     <name>${project.groupId}:${project.artifactId}</name>
     <description>Library to read and write archives on HDFS.</description>

diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>gov.nist.isg</groupId>
     <artifactId>pyramidio-parent</artifactId>
-    <version>1.1.5</version>
+    <version>1.1.6</version>
     <packaging>pom</packaging>
     <name>${project.groupId}:${project.artifactId}</name>
     <description>Parent project of pyramidio, a Java tool to read and write image pyramids. Bio-Formats enhanced version.</description>

diff --git a/pyramidio-cli/pom.xml b/pyramidio-cli/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>gov.nist.isg</groupId>
         <artifactId>pyramidio-parent</artifactId>
-        <version>1.1.5</version>
+        <version>1.1.6</version>
     </parent>
     <name>${project.groupId}:${project.artifactId}</name>
     <description>Command line interface to build image pyramids.</description>

diff --git a/pyramidio-cli/src/main/java/gov/nist/isg/pyramidio/cli/FilesArchiverFactory.java b/pyramidio-cli/src/main/java/gov/nist/isg/pyramidio/cli/FilesArchiverFactory.java
@@ -42,7 +42,7 @@ public class FilesArchiverFactory {
     public static FilesArchiver createFromURI(String uri)
             throws IOException {
         try {
-            URI outputURI = new URI(uri);
+            URI outputURI = new URI(uri.replace(" ", "%20"));
             String scheme = outputURI.getScheme();
             logger.info("Got scheme " + scheme + " for URI " + uri);
 

diff --git a/pyramidio-cli/src/main/java/gov/nist/isg/pyramidio/cli/Main.java b/pyramidio-cli/src/main/java/gov/nist/isg/pyramidio/cli/Main.java
@@ -68,6 +68,10 @@ public static void main(String[] args) {
                 "Tile format such as jpg, png "
                 + "(default to the same format than the input)");
         options.addOption(tileFormatOption);
+
+        Option forceRgbOption = new Option("rgb", "forceRGB", false,
+                "The output will be forced to RGB888 discarding the input image properties.");
+        options.addOption(forceRgbOption);
 
         Option parallelismOption = new Option("p", "parallelism", true,
                 "Number of threads to use (default to number of cpu cores).");
@@ -139,13 +143,13 @@ public static void main(String[] args) {
 
             try {
                 long start = System.currentTimeMillis();
-                logger.info(inputFile + " - is about to start to build a pyramid.");
+                logger.info(inputFile + " - is about to start to build a pyramid. Output folder: " + outputFolder);
 
                 try (FilesArchiver archiver = FilesArchiverFactory
                         .createFromURI(outputFolder)) {
                     spb.buildPyramid(
                             //@darwinjob new DirectImageReader(inputFile),
-                    		new BioFormatsImageReader(inputFile),
+                    		new BioFormatsImageReader(inputFile, commandLine.hasOption(forceRgbOption.getOpt())),
                             inputFileBaseName,
                             archiver,
                             parallelism,
@@ -224,6 +228,6 @@ private static float getCalculatedPercentage(File inputFile) {
 	}
 
 	private static void printHelp(Options options) {
-        new HelpFormatter().printHelp("pyramidio", options);
+        new HelpFormatter().printHelp("java -jar pyramidio-cli-[version].jar -i my-image.jpg -o (my-output-folder || scheme:///path/file[.tar, .seq])", options);
     }
 }
diff --git a/pyramidio/pom.xml b/pyramidio/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>gov.nist.isg</groupId>
 		<artifactId>pyramidio-parent</artifactId>
-		<version>1.1.5</version>
+		<version>1.1.6</version>
 	</parent>
 	<name>${project.groupId}:${project.artifactId}</name>
 	<description>Library to read and write image pyramids.</description>

diff --git a/pyramidio/src/main/java/no/uio/nesys/pyramidio/BioFormatsImageReader.java b/pyramidio/src/main/java/no/uio/nesys/pyramidio/BioFormatsImageReader.java
@@ -1,5 +1,6 @@
 package no.uio.nesys.pyramidio;
 
+import java.awt.Graphics2D;
 import java.awt.Rectangle;
 import java.awt.image.BufferedImage;
 import java.io.File;
@@ -22,13 +23,32 @@ public class BioFormatsImageReader implements PartialImageReader {
 
 	private BufferedImageReader bufferedImageReader;
 	private ImageReader imageReader;
+	private boolean forceRGB;
 
 	private static final Logger logger = Logger.getLogger(
 			BioFormatsImageReader.class.getName());
-
+	/**
+	 * Processing non RGB888 image seems to be an issue. See https://github.com/darwinjob/pyramidio-bioformats/issues/13 
+	 * If you see any output artifacts try forceRGB=true
+	 * @param file
+	 * @throws FormatException
+	 * @throws IOException
+	 */
 	public BioFormatsImageReader(File file) throws FormatException, IOException {
+		this (file, false);
+	}
+
+	/**
+	 * 
+	 * @param file
+	 * @param forceRGB
+	 * @throws FormatException
+	 * @throws IOException
+	 */
+	public BioFormatsImageReader(File file, boolean forceRGB) throws FormatException, IOException {
 		imageReader = new ImageReader();
 		imageReader.setId(file.getPath());
+		this.forceRGB = forceRGB;
 		bufferedImageReader = new BufferedImageReader(imageReader);
 	}
 
@@ -46,12 +66,25 @@ public BufferedImage read() throws IOException {
 	public BufferedImage read(Rectangle rectangle) throws IOException {
 		try {
 			logger.fine("Reading rectangle: " + rectangle);
-			return bufferedImageReader.openImage(0, rectangle.x, rectangle.y, rectangle.width, rectangle.height);
+			BufferedImage bi = bufferedImageReader.openImage(0, rectangle.x, rectangle.y, rectangle.width, rectangle.height);
+
+			if (forceRGB) {
+				return convertToRGB(bi);
+			}
+			return bi;
 		} catch (FormatException e) {
 			throw new IOException(e);
 		}
 	}
 
+	private BufferedImage convertToRGB(BufferedImage src) {
+		BufferedImage img= new BufferedImage(src.getWidth(), src.getHeight(), BufferedImage.TYPE_INT_RGB);
+	    Graphics2D g2d= img.createGraphics();
+	    g2d.drawImage(src, 0, 0, null);
+	    g2d.dispose();
+	    return img;
+	}
+
 	@Override
 	public int getWidth() {
 		return imageReader.getSizeX();

diff --git a/s3-archiver/pom.xml b/s3-archiver/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>gov.nist.isg</groupId>
         <artifactId>pyramidio-parent</artifactId>
-        <version>1.1.5</version>
+        <version>1.1.6</version>
     </parent>
     <name>${project.groupId}:${project.artifactId}</name>
     <description>Library to read and write archives on Amazon S3.</description>

diff --git a/tar-archiver/pom.xml b/tar-archiver/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>gov.nist.isg</groupId>
         <artifactId>pyramidio-parent</artifactId>
-        <version>1.1.5</version>
+        <version>1.1.6</version>
     </parent>
     <name>${project.groupId}:${project.artifactId}</name>
     <description>Library to read and write archives in tar files.</description>