Merge branch 'ebremer:master' into master

SBU-BMI · May 19, 2023 · 1ab584c · 1ab584c
2 parents c5e12ca + 505e0f1
commit 1ab584c
Show file tree

Hide file tree

Showing 13 changed files with 51 additions and 280 deletions.
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Hatch 3.0.0
+# Hatch 3.0.1
 
 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.
 

diff --git a/config/jni-config.json b/config/jni-config.json
@@ -1,120 +1,10 @@
 [
 {
-  "name":"com.sun.imageio.plugins.jpeg.JPEGImageReader",
-  "methods":[
-    {"name":"acceptPixels","parameterTypes":["int","boolean"] }, 
-    {"name":"passComplete","parameterTypes":[] }, 
-    {"name":"passStarted","parameterTypes":["int"] }, 
-    {"name":"pushBack","parameterTypes":["int"] }, 
-    {"name":"readInputData","parameterTypes":["byte[]","int","int"] }, 
-    {"name":"setImageData","parameterTypes":["int","int","int","int","int","byte[]"] }, 
-    {"name":"skipInputBytes","parameterTypes":["long"] }, 
-    {"name":"skipPastImage","parameterTypes":["int"] }, 
-    {"name":"warningOccurred","parameterTypes":["int"] }, 
-    {"name":"warningWithMessage","parameterTypes":["java.lang.String"] }
-  ]
-},
-{
-  "name":"com.sun.imageio.plugins.jpeg.JPEGImageWriter",
-  "methods":[
-    {"name":"grabPixels","parameterTypes":["int"] }, 
-    {"name":"warningOccurred","parameterTypes":["int"] }, 
-    {"name":"warningWithMessage","parameterTypes":["java.lang.String"] }, 
-    {"name":"writeMetadata","parameterTypes":[] }, 
-    {"name":"writeOutputData","parameterTypes":["byte[]","int","int"] }
-  ]
-},
-{
-  "name":"java.awt.GraphicsEnvironment",
-  "methods":[{"name":"isHeadless","parameterTypes":[] }]
-},
-{
-  "name":"java.awt.image.BufferedImage",
-  "fields":[
-    {"name":"colorModel"}, 
-    {"name":"imageType"}, 
-    {"name":"raster"}
-  ],
-  "methods":[
-    {"name":"getRGB","parameterTypes":["int","int","int","int","int[]","int","int"] }, 
-    {"name":"setRGB","parameterTypes":["int","int","int","int","int[]","int","int"] }
-  ]
-},
-{
-  "name":"java.awt.image.ColorModel",
-  "fields":[
-    {"name":"colorSpace"}, 
-    {"name":"colorSpaceType"}, 
-    {"name":"isAlphaPremultiplied"}, 
-    {"name":"is_sRGB"}, 
-    {"name":"nBits"}, 
-    {"name":"numComponents"}, 
-    {"name":"pData"}, 
-    {"name":"supportsAlpha"}, 
-    {"name":"transparency"}
-  ],
-  "methods":[{"name":"getRGBdefault","parameterTypes":[] }]
-},
-{
-  "name":"java.awt.image.Raster",
-  "fields":[
-    {"name":"dataBuffer"}, 
-    {"name":"height"}, 
-    {"name":"minX"}, 
-    {"name":"minY"}, 
-    {"name":"numBands"}, 
-    {"name":"numDataElements"}, 
-    {"name":"sampleModel"}, 
-    {"name":"sampleModelTranslateX"}, 
-    {"name":"sampleModelTranslateY"}, 
-    {"name":"width"}
-  ]
-},
-{
-  "name":"java.awt.image.SampleModel",
-  "fields":[
-    {"name":"height"}, 
-    {"name":"width"}
-  ],
-  "methods":[
-    {"name":"getPixels","parameterTypes":["int","int","int","int","int[]","java.awt.image.DataBuffer"] }, 
-    {"name":"setPixels","parameterTypes":["int","int","int","int","int[]","java.awt.image.DataBuffer"] }
-  ]
+  "name":"java.io.IOException",
+  "methods":[{"name":"<init>","parameterTypes":["java.lang.String"] }]
 },
 {
   "name":"java.lang.Boolean",
   "methods":[{"name":"getBoolean","parameterTypes":["java.lang.String"] }]
-},
-{
-  "name":"java.lang.System",
-  "methods":[
-    {"name":"load","parameterTypes":["java.lang.String"] }, 
-    {"name":"setProperty","parameterTypes":["java.lang.String","java.lang.String"] }
-  ]
-},
-{
-  "name":"javax.imageio.plugins.jpeg.JPEGHuffmanTable",
-  "fields":[
-    {"name":"lengths"}, 
-    {"name":"values"}
-  ]
-},
-{
-  "name":"javax.imageio.plugins.jpeg.JPEGQTable",
-  "fields":[{"name":"qTable"}]
-},
-{
-  "name":"sun.awt.image.ByteComponentRaster",
-  "fields":[
-    {"name":"data"}, 
-    {"name":"dataOffsets"}, 
-    {"name":"pixelStride"}, 
-    {"name":"scanlineStride"}, 
-    {"name":"type"}
-  ]
-},
-{
-  "name":"sun.java2d.Disposer",
-  "methods":[{"name":"addRecord","parameterTypes":["java.lang.Object","long","long"] }]
 }
 ]
diff --git a/config/reflect-config.json b/config/reflect-config.json
@@ -1,14 +1,13 @@
 [
-    {
-    "name": "sun.awt.image.BufImgSurfaceData",
-    "methods": [
-      {"name": "getSolidLoops", "parameterTypes": ["sun.java2d.loops.SurfaceType"]}
-    ],
-    "allDeclaredConstructors": true,
-    "allPublicConstructors": true,
-    "allDeclaredMethods": true,
-    "allPublicMethods": true
-  },
+{
+  "name":"[[I"
+},
+{
+  "name":"[[J"
+},
+{
+  "name":"[[Lloci.formats.tiff.TiffRational;"
+},
 {
   "name":"boolean",
   "allDeclaredFields":true
@@ -23,11 +22,6 @@
   "queryAllDeclaredConstructors":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
-{
-  "name":"com.beust.jcommander.converters.IntegerConverter",
-  "queryAllDeclaredConstructors":true,
-  "methods":[{"name":"<init>","parameterTypes":["java.lang.String"] }]
-},
 {
   "name":"com.beust.jcommander.validators.NoValidator",
   "methods":[{"name":"<init>","parameterTypes":[] }]
@@ -41,31 +35,10 @@
   "allDeclaredFields":true,
   "queryAllDeclaredMethods":true
 },
-{
-  "name":"int",
-  "allDeclaredFields":true
-},
 {
   "name":"java.io.File",
   "allDeclaredFields":true
 },
-{
-  "name":"java.security.SecureRandomParameters"
-},
-{
-  "name":"javax.imageio.spi.ImageReaderSpi"
-},
-{
-  "name":"javax.imageio.spi.ImageReaderWriterSpi",
-  "methods":[
-    {"name":"getFileSuffixes","parameterTypes":[] }, 
-    {"name":"getFormatNames","parameterTypes":[] }, 
-    {"name":"getMIMETypes","parameterTypes":[] }
-  ]
-},
-{
-  "name":"javax.imageio.spi.ImageWriterSpi"
-},
 {
   "name":"loci.common.Log4jTools",
   "methods":[{"name":"setRootLevel","parameterTypes":["java.lang.String"] }]
@@ -163,13 +136,5 @@
 },
 {
   "name":"ome.codecs.services.LuraWaveServiceImpl"
-},
-{
-  "name":"sun.security.provider.NativePRNG",
-  "methods":[{"name":"<init>","parameterTypes":[] }]
-},
-{
-  "name":"sun.security.provider.SHA",
-  "methods":[{"name":"<init>","parameterTypes":[] }]
 }
 ]
diff --git a/config/resource-config.json b/config/resource-config.json
@@ -19,15 +19,9 @@
     {
       "pattern":"\\Qorg/joda/time/tz/data/America/New_York\\E"
     }, 
-    {
-      "pattern":"\\Qorg/joda/time/tz/data/Etc/UTC\\E"
-    }, 
     {
       "pattern":"\\Qorg/joda/time/tz/data/ZoneInfoMap\\E"
     }
   ]},
-  "bundles":[{
-      "name":"sun.awt.resources.awt",
-      "classNames":["sun.awt.resources.awt"]
-    }]
+  "bundles":[]
 }
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>edu.stonybrook.bmi</groupId>
   <artifactId>hatch</artifactId>
-  <version>3.0.0</version>
+  <version>3.0.1</version>
   <build>
     <resources>
       <resource>

diff --git a/ha.txt b/ha.txt
diff --git a/nbactions-hatchjar.xml b/nbactions-hatchjar.xml
@@ -12,7 +12,7 @@
             <properties>
                 <exec.vmArgs></exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.appArgs>-v -src \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.svs -dest \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.tif</exec.appArgs>
+                <exec.appArgs>-jp2 -v -src \hatchtest\src -dest \hatchtest\dest</exec.appArgs>
                 <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
             </properties>
@@ -29,7 +29,7 @@
             <properties>
                 <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.appArgs>-v -src \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.svs -dest \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.tif</exec.appArgs>
+                <exec.appArgs>-jp2 -v -src \hatchtest\src -dest \hatchtest\dest</exec.appArgs>
                 <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
@@ -49,7 +49,7 @@
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
-                <exec.appArgs>-v -src \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.svs -dest \boom\TCGA-AC-A2QJ-01Z-00-DX1.48C303BB-5A23-4037-BD28-77629A8CD9DA.tif</exec.appArgs>
+                <exec.appArgs>-jp2 -v -src \hatchtest\src -dest \hatchtest\dest</exec.appArgs>
             </properties>
         </action>
     </actions>
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>edu.stonybrook.bmi</groupId>
 	<artifactId>hatch</artifactId>
-	<version>3.0.0</version>
+	<version>3.0.1</version>
 	<packaging>jar</packaging>
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

diff --git a/src/main/java/edu/stonybrook/bmi/hatch/CellSensReader.java b/src/main/java/edu/stonybrook/bmi/hatch/CellSensReader.java
@@ -1,5 +1,7 @@
 package edu.stonybrook.bmi.hatch;
 
+import java.awt.Color;
+import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
@@ -1010,11 +1012,13 @@ public byte[] getRaw(byte[] rawbuffer, int no, int row, int col) throws FormatEx
         }
       }
       BufferedImage bi = AWTImageTools.makeImage(tile, 512, 512, 3, true, 8/8, false, true, false);
+      Graphics2D graphics = bi.createGraphics();
+      graphics.setColor(Color.BLACK);
+      graphics.fillRect(0, 0, 512, 512);
       ByteArrayOutputStream baos = new ByteArrayOutputStream();
       ImageIO.write(bi, "jpg", baos );
       tile = baos.toByteArray();
-      throw new Error("BUFFER UNDER");
-      //return tile;
+      return tile;
     }
     Long offset = tileOffsets.get(getCoreIndex())[index];
     byte[] buf = null;

diff --git a/src/main/java/edu/stonybrook/bmi/hatch/Hatch.java b/src/main/java/edu/stonybrook/bmi/hatch/Hatch.java
@@ -19,7 +19,7 @@
  * @author erich
  */
 public class Hatch {    
-    public static String software = "hatch 3.0.0 by Wing-n-Beak";
+    public static String software = "hatch 3.0.1 by Wing-n-Beak";
     private static final String[] ext = new String[] {".vsi", ".svs", ".tif"};
     public static final String HELP = Hatch.software+"\n"+
         """

diff --git a/src/main/java/edu/stonybrook/bmi/hatch/HatchWriter.java b/src/main/java/edu/stonybrook/bmi/hatch/HatchWriter.java
@@ -1,8 +1,6 @@
 package edu.stonybrook.bmi.hatch;
 
 import java.io.IOException;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 import loci.common.RandomAccessOutputStream;
 import loci.formats.FormatException;
 import loci.formats.codec.CodecOptions;
@@ -29,16 +27,13 @@ public HatchWriter(String file) throws IOException {
     public void nextImage() throws IOException {
         ros.seek(ros.length());
     }
-
 
     @Override
-    public void close() throws Exception {
-        try {
-            try (ros; writer) {
-                System.out.println("closing Writer....");
-            }
+    public void close() {
+        try (ros; writer) {
+            System.out.println("closing Writer....");
         } catch (IOException ex) {
-            Logger.getLogger(HatchWriter.class.getName()).log(Level.SEVERE, null, ex);
+            System.out.println("HatchWriter : "+ex);
         }
     }