Merge branch 'ebremer:master' into master

README.md

@@ -1,4 +1,4 @@
-# Hatch 3.0.1
+# Hatch 3.0.2
 
 This tool converts the largest image in a VSI, SVS, or TIF image into a new TIFF image with a freshly created image pyramid with each scaling 1/2 dimensions each scale.
 
@@ -10,6 +10,17 @@ Features:
 
 3) image pyramid is re-created from original image
 
+Build with:
+
+Jar version
+```
+mvn -Phatchjar clean package
+```
+Native-image version (requires fully configured Graalvm native-image environment)
+```
+mvn -Phatch clean package
+```
+
 Usage:
 ```
 hatch -src <src> -dest <dest>

dependency-reduced-pom.xml

@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>edu.stonybrook.bmi</groupId>
   <artifactId>hatch</artifactId>
-  <version>3.0.1</version>
+  <version>3.0.2</version>
   <build>
     <resources>
       <resource>

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>edu.stonybrook.bmi</groupId>
 	<artifactId>hatch</artifactId>
-	<version>3.0.1</version>
+	<version>3.0.2</version>
 	<packaging>jar</packaging>
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

src/main/java/edu/stonybrook/bmi/hatch/Hatch.java

@@ -2,6 +2,7 @@
 
 import com.beust.jcommander.JCommander;
 import com.beust.jcommander.ParameterException;
+import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -19,7 +20,7 @@
  * @author erich
  */
 public class Hatch {    
-    public static String software = "hatch 3.0.1 by Wing-n-Beak";
+    public static String software = "hatch 3.0.2 by Wing-n-Beak";
     private static final String[] ext = new String[] {".vsi", ".svs", ".tif"};
     public static final String HELP = Hatch.software+"\n"+
         """
@@ -47,15 +48,14 @@ private static void Traverse(HatchParameters params) {
                     String frag = s.relativize(f).toString();
                     frag = frag.substring(0,frag.length()-4)+".tif";
                     Path t = Path.of(d.toString(), frag);
-                    t.toFile().getParentFile().mkdirs();
                     if (!t.toFile().exists()) {
                         System.out.println("PROCESSING FILE --> "+f);
-                        engine.submit(new FileProcessor(params, f.toString(), t.toString()));
+                        engine.submit(new FileProcessor(params, f, t));
                     } else if (t.toFile().length()==0) {
                         System.out.println("ZERO LENGTH FILE --> "+f);
                         t.toFile().delete();
                         System.out.println("RE-PROCESSING FILE --> "+f);
-                        engine.submit(new FileProcessor(params, f.toString(), t.toString()));
+                        engine.submit(new FileProcessor(params, f, t));
                     }
                 });
         } catch (IOException ex) {
@@ -124,18 +124,23 @@ public static void main(String[] args) {
 
 class FileProcessor implements Callable<String> {
     private final HatchParameters params;
-    private final String src;
-    private final String dest;
+    private final File src;
+    private final File dest;
 
-    public FileProcessor(HatchParameters params, String src, String dest) {
+    public FileProcessor(HatchParameters params, Path src, Path dest) {
         this.params = params;
-        this.src = src;
-        this.dest = dest;
+        this.src = src.toFile();
+        this.dest = dest.toFile();
     }
 
     @Override
     public String call() {
-        try (X2TIF v2t = new X2TIF(params, src, dest)) {
+        if (dest.exists()) {
+            dest.delete();
+        } else {
+            dest.getParentFile().mkdirs();
+        }
+        try (X2TIF v2t = new X2TIF(params, src.toString(), dest.toString())) {
             v2t.Execute();
         } catch (Exception ex) {
             System.out.println("FILE PROCESSOR ERROR --> "+src+" "+dest+" "+ex.toString());

src/main/java/edu/stonybrook/bmi/hatch/HatchWriter.java

@@ -31,6 +31,7 @@ public void nextImage() throws IOException {
     @Override
     public void close() {
         try (ros; writer) {
+            ros.flush();
             System.out.println("closing Writer....");
         } catch (IOException ex) {
             System.out.println("HatchWriter : "+ex);

src/main/java/edu/stonybrook/bmi/hatch/X2TIF.java

@@ -132,9 +132,6 @@ public X2TIF(HatchParameters params, String src, String dest) {
                 System.exit(0);
             }
             File fdest = new File(outputFile);
-            if (fdest.exists()) {
-                fdest.delete();
-            }
             int size = Math.max(width, height);
             int ss = (int) Math.ceil(Math.log(size)/Math.log(2));
             int tiless = (int) Math.ceil(Math.log(tileSizeX)/Math.log(2));
@@ -159,9 +156,11 @@ public X2TIF(HatchParameters params, String src, String dest) {
             meta.setPixelsSizeZ(new PositiveInteger(1), 0);
             meta.setPixelsSizeC(new PositiveInteger(3), 0);
             meta.setPixelsSizeT(new PositiveInteger(1), 0);
+            System.out.println("SRC : "+src+"   dest: "+fdest);
         } catch (DependencyException | ServiceException | FormatException | IOException ex) {
             Logger.getLogger(X2TIF.class.getName()).log(Level.SEVERE, null, ex);
         }
+
     }
 
     private int MaxImage(FormatReader reader) {