diff --git a/README.md b/README.md
index 45f11ce..8c4d953 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # Hatch
 
-This tool converts VSI image format to TIFF.
+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.
 
 Features:
 1) Hatch transfers raw jpeg encodings from original image to new image to prevent any re-encoding image loss due to re-compression.
diff --git a/config/jni-config.json b/config/jni-config.json
index 73273d6..9924ee5 100644
--- a/config/jni-config.json
+++ b/config/jni-config.json
@@ -1,7 +1,4 @@
 [
-{
-  "name":"[Lsun.java2d.loops.GraphicsPrimitive;"
-},
 {
   "name":"com.sun.imageio.plugins.jpeg.JPEGImageReader",
   "methods":[
@@ -28,126 +25,8 @@
   ]
 },
 {
-  "name":"java.awt.AWTEvent",
-  "fields":[
-    {"name":"bdata"}, 
-    {"name":"consumed"}, 
-    {"name":"id"}
-  ]
-},
-{
-  "name":"java.awt.AlphaComposite",
-  "fields":[
-    {"name":"extraAlpha"}, 
-    {"name":"rule"}
-  ]
-},
-{
-  "name":"java.awt.Color",
-  "methods":[{"name":"getRGB","parameterTypes":[] }]
-},
-{
-  "name":"java.awt.Component",
-  "fields":[
-    {"name":"appContext"}, 
-    {"name":"background"}, 
-    {"name":"cursor"}, 
-    {"name":"enabled"}, 
-    {"name":"focusable"}, 
-    {"name":"foreground"}, 
-    {"name":"graphicsConfig"}, 
-    {"name":"height"}, 
-    {"name":"parent"}, 
-    {"name":"peer"}, 
-    {"name":"visible"}, 
-    {"name":"width"}, 
-    {"name":"x"}, 
-    {"name":"y"}
-  ],
-  "methods":[
-    {"name":"getFont_NoClientCode","parameterTypes":[] }, 
-    {"name":"getLocationOnScreen_NoTreeLock","parameterTypes":[] }, 
-    {"name":"getToolkitImpl","parameterTypes":[] }, 
-    {"name":"isEnabledImpl","parameterTypes":[] }
-  ]
-},
-{
-  "name":"java.awt.Container",
-  "fields":[{"name":"layoutMgr"}]
-},
-{
-  "name":"java.awt.Dimension",
-  "fields":[
-    {"name":"height"}, 
-    {"name":"width"}
-  ]
-},
-{
-  "name":"java.awt.Font",
-  "fields":[
-    {"name":"name"}, 
-    {"name":"pData"}, 
-    {"name":"size"}, 
-    {"name":"style"}
-  ],
-  "methods":[
-    {"name":"getFont","parameterTypes":["java.lang.String"] }, 
-    {"name":"getFontPeer","parameterTypes":[] }
-  ]
-},
-{
-  "name":"java.awt.Insets",
-  "fields":[
-    {"name":"bottom"}, 
-    {"name":"left"}, 
-    {"name":"right"}, 
-    {"name":"top"}
-  ],
-  "methods":[{"name":"<init>","parameterTypes":["int","int","int","int"] }]
-},
-{
-  "name":"java.awt.Toolkit",
-  "methods":[
-    {"name":"getDefaultToolkit","parameterTypes":[] }, 
-    {"name":"getFontMetrics","parameterTypes":["java.awt.Font"] }
-  ]
-},
-{
-  "name":"java.awt.desktop.UserSessionEvent$Reason",
-  "fields":[
-    {"name":"CONSOLE"}, 
-    {"name":"LOCK"}, 
-    {"name":"REMOTE"}, 
-    {"name":"UNSPECIFIED"}
-  ]
-},
-{
-  "name":"java.awt.event.InputEvent",
-  "fields":[{"name":"modifiers"}],
-  "methods":[{"name":"getButtonDownMasks","parameterTypes":[] }]
-},
-{
-  "name":"java.awt.geom.AffineTransform",
-  "fields":[
-    {"name":"m00"}, 
-    {"name":"m01"}, 
-    {"name":"m02"}, 
-    {"name":"m10"}, 
-    {"name":"m11"}, 
-    {"name":"m12"}
-  ]
-},
-{
-  "name":"java.awt.geom.Path2D",
-  "fields":[
-    {"name":"numTypes"}, 
-    {"name":"pointTypes"}, 
-    {"name":"windingRule"}
-  ]
-},
-{
-  "name":"java.awt.geom.Path2D$Float",
-  "fields":[{"name":"floatCoords"}]
+  "name":"java.awt.GraphicsEnvironment",
+  "methods":[{"name":"isHeadless","parameterTypes":[] }]
 },
 {
   "name":"java.awt.image.BufferedImage",
@@ -176,22 +55,6 @@
   ],
   "methods":[{"name":"getRGBdefault","parameterTypes":[] }]
 },
-{
-  "name":"java.awt.image.ComponentColorModel"
-},
-{
-  "name":"java.awt.image.IndexColorModel",
-  "fields":[
-    {"name":"allgrayopaque"}, 
-    {"name":"colorData"}, 
-    {"name":"map_size"}, 
-    {"name":"rgb"}, 
-    {"name":"transparent_index"}
-  ]
-},
-{
-  "name":"java.awt.image.PackedColorModel"
-},
 {
   "name":"java.awt.image.Raster",
   "fields":[
@@ -218,19 +81,17 @@
     {"name":"setPixels","parameterTypes":["int","int","int","int","int[]","java.awt.image.DataBuffer"] }
   ]
 },
-{
-  "name":"java.awt.image.SinglePixelPackedSampleModel",
-  "fields":[
-    {"name":"bitMasks"}, 
-    {"name":"bitOffsets"}, 
-    {"name":"bitSizes"}, 
-    {"name":"maxBitSize"}
-  ]
-},
 {
   "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":[
@@ -242,19 +103,6 @@
   "name":"javax.imageio.plugins.jpeg.JPEGQTable",
   "fields":[{"name":"qTable"}]
 },
-{
-  "name":"sun.awt.SunHints",
-  "fields":[{"name":"INTVAL_STROKE_PURE"}]
-},
-{
-  "name":"sun.awt.Win32GraphicsEnvironment",
-  "methods":[{"name":"dwmCompositionChanged","parameterTypes":["boolean"] }]
-},
-{
-  "name":"sun.awt.image.BufImgSurfaceData$ICMColorData",
-  "fields":[{"name":"pData"}],
-  "methods":[{"name":"<init>","parameterTypes":["long"] }]
-},
 {
   "name":"sun.awt.image.ByteComponentRaster",
   "fields":[
@@ -265,268 +113,8 @@
     {"name":"type"}
   ]
 },
-{
-  "name":"sun.awt.image.BytePackedRaster",
-  "fields":[
-    {"name":"data"}, 
-    {"name":"dataBitOffset"}, 
-    {"name":"pixelBitStride"}, 
-    {"name":"scanlineStride"}, 
-    {"name":"type"}
-  ]
-},
-{
-  "name":"sun.awt.image.IntegerComponentRaster",
-  "fields":[
-    {"name":"data"}, 
-    {"name":"dataOffsets"}, 
-    {"name":"pixelStride"}, 
-    {"name":"scanlineStride"}, 
-    {"name":"type"}
-  ]
-},
-{
-  "name":"sun.awt.image.ShortComponentRaster",
-  "fields":[
-    {"name":"data"}, 
-    {"name":"dataOffsets"}, 
-    {"name":"pixelStride"}, 
-    {"name":"scanlineStride"}, 
-    {"name":"type"}
-  ]
-},
-{
-  "name":"sun.awt.image.SunVolatileImage",
-  "fields":[{"name":"volSurfaceManager"}]
-},
-{
-  "name":"sun.awt.image.VolatileSurfaceManager",
-  "fields":[{"name":"sdCurrent"}]
-},
-{
-  "name":"sun.awt.windows.WComponentPeer",
-  "fields":[
-    {"name":"hwnd"}, 
-    {"name":"winGraphicsConfig"}
-  ],
-  "methods":[
-    {"name":"disposeLater","parameterTypes":[] }, 
-    {"name":"replaceSurfaceData","parameterTypes":[] }, 
-    {"name":"replaceSurfaceDataLater","parameterTypes":[] }
-  ]
-},
-{
-  "name":"sun.awt.windows.WDesktopPeer",
-  "methods":[
-    {"name":"systemSleepCallback","parameterTypes":["boolean"] }, 
-    {"name":"userSessionCallback","parameterTypes":["boolean","java.awt.desktop.UserSessionEvent$Reason"] }
-  ]
-},
-{
-  "name":"sun.awt.windows.WObjectPeer",
-  "fields":[
-    {"name":"createError"}, 
-    {"name":"destroyed"}, 
-    {"name":"pData"}, 
-    {"name":"target"}
-  ],
-  "methods":[{"name":"getPeerForTarget","parameterTypes":["java.lang.Object"] }]
-},
-{
-  "name":"sun.awt.windows.WToolkit",
-  "methods":[
-    {"name":"displayChanged","parameterTypes":[] }, 
-    {"name":"windowsSettingChange","parameterTypes":[] }
-  ]
-},
 {
   "name":"sun.java2d.Disposer",
   "methods":[{"name":"addRecord","parameterTypes":["java.lang.Object","long","long"] }]
-},
-{
-  "name":"sun.java2d.InvalidPipeException"
-},
-{
-  "name":"sun.java2d.NullSurfaceData"
-},
-{
-  "name":"sun.java2d.SunGraphics2D",
-  "fields":[
-    {"name":"clipRegion"}, 
-    {"name":"composite"}, 
-    {"name":"eargb"}, 
-    {"name":"lcdTextContrast"}, 
-    {"name":"pixel"}, 
-    {"name":"strokeHint"}
-  ]
-},
-{
-  "name":"sun.java2d.SurfaceData",
-  "fields":[
-    {"name":"pData"}, 
-    {"name":"valid"}
-  ]
-},
-{
-  "name":"sun.java2d.loops.Blit",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.BlitBg",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.CompositeType",
-  "fields":[
-    {"name":"AnyAlpha"}, 
-    {"name":"Src"}, 
-    {"name":"SrcNoEa"}, 
-    {"name":"SrcOver"}, 
-    {"name":"SrcOverNoEa"}, 
-    {"name":"Xor"}
-  ]
-},
-{
-  "name":"sun.java2d.loops.DrawGlyphList",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.DrawGlyphListAA",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.DrawGlyphListLCD",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.DrawLine",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.DrawParallelogram",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.DrawPath",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.DrawPolygons",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.DrawRect",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.FillParallelogram",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.FillPath",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.FillRect",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.FillSpans",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.GraphicsPrimitive",
-  "fields":[{"name":"pNativePrim"}]
-},
-{
-  "name":"sun.java2d.loops.GraphicsPrimitiveMgr",
-  "methods":[{"name":"register","parameterTypes":["sun.java2d.loops.GraphicsPrimitive[]"] }]
-},
-{
-  "name":"sun.java2d.loops.MaskBlit",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.MaskFill",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.ScaledBlit",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.SurfaceType",
-  "fields":[
-    {"name":"Any3Byte"}, 
-    {"name":"Any4Byte"}, 
-    {"name":"AnyByte"}, 
-    {"name":"AnyColor"}, 
-    {"name":"AnyInt"}, 
-    {"name":"AnyShort"}, 
-    {"name":"ByteBinary1Bit"}, 
-    {"name":"ByteBinary2Bit"}, 
-    {"name":"ByteBinary4Bit"}, 
-    {"name":"ByteGray"}, 
-    {"name":"ByteIndexed"}, 
-    {"name":"ByteIndexedBm"}, 
-    {"name":"FourByteAbgr"}, 
-    {"name":"FourByteAbgrPre"}, 
-    {"name":"Index12Gray"}, 
-    {"name":"Index8Gray"}, 
-    {"name":"IntArgb"}, 
-    {"name":"IntArgbBm"}, 
-    {"name":"IntArgbPre"}, 
-    {"name":"IntBgr"}, 
-    {"name":"IntRgb"}, 
-    {"name":"IntRgbx"}, 
-    {"name":"OpaqueColor"}, 
-    {"name":"ThreeByteBgr"}, 
-    {"name":"Ushort4444Argb"}, 
-    {"name":"Ushort555Rgb"}, 
-    {"name":"Ushort555Rgbx"}, 
-    {"name":"Ushort565Rgb"}, 
-    {"name":"UshortGray"}, 
-    {"name":"UshortIndexed"}
-  ]
-},
-{
-  "name":"sun.java2d.loops.TransformHelper",
-  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]
-},
-{
-  "name":"sun.java2d.loops.XORComposite",
-  "fields":[
-    {"name":"alphaMask"}, 
-    {"name":"xorColor"}, 
-    {"name":"xorPixel"}
-  ]
-},
-{
-  "name":"sun.java2d.pipe.Region",
-  "fields":[
-    {"name":"bands"}, 
-    {"name":"endIndex"}, 
-    {"name":"hix"}, 
-    {"name":"hiy"}, 
-    {"name":"lox"}, 
-    {"name":"loy"}
-  ]
-},
-{
-  "name":"sun.java2d.pipe.RegionIterator",
-  "fields":[
-    {"name":"curIndex"}, 
-    {"name":"numXbands"}, 
-    {"name":"region"}
-  ]
-},
-{
-  "name":"sun.java2d.windows.WindowsFlags",
-  "fields":[
-    {"name":"d3dEnabled"}, 
-    {"name":"d3dSet"}, 
-    {"name":"offscreenSharingEnabled"}, 
-    {"name":"setHighDPIAware"}
-  ]
 }
 ]
diff --git a/config/reflect-config.json b/config/reflect-config.json
index 2f97972..69f6f7f 100644
--- a/config/reflect-config.json
+++ b/config/reflect-config.json
@@ -1,18 +1,53 @@
 [
+    {
+    "name": "sun.awt.image.BufImgSurfaceData",
+    "methods": [
+      {"name": "getSolidLoops", "parameterTypes": ["sun.java2d.loops.SurfaceType"]}
+    ],
+    "allDeclaredConstructors": true,
+    "allPublicConstructors": true,
+    "allDeclaredMethods": true,
+    "allPublicMethods": true
+  },
 {
-  "name":"[[I"
+  "name":"boolean",
+  "allDeclaredFields":true
 },
 {
-  "name":"[[J"
+  "name":"com.beust.jcommander.converters.BooleanConverter",
+  "queryAllDeclaredConstructors":true,
+  "methods":[{"name":"<init>","parameterTypes":["java.lang.String"] }]
 },
 {
-  "name":"java.awt.image.AffineTransformOp"
+  "name":"com.beust.jcommander.converters.FileConverter",
+  "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":[] }]
+},
+{
+  "name":"com.beust.jcommander.validators.NoValueValidator",
+  "methods":[{"name":"<init>","parameterTypes":[] }]
 },
 {
-  "name":"java.awt.image.ConvolveOp"
+  "name":"edu.stonybrook.bmi.hatch.HatchParameters",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true
 },
 {
-  "name":"java.awt.image.LookupOp"
+  "name":"int",
+  "allDeclaredFields":true
+},
+{
+  "name":"java.io.File",
+  "allDeclaredFields":true
 },
 {
   "name":"java.security.SecureRandomParameters"
@@ -35,9 +70,6 @@
   "name":"loci.common.Log4jTools",
   "methods":[{"name":"setRootLevel","parameterTypes":["java.lang.String"] }]
 },
-{
-  "name":"[Lloci.formats.tiff.OnDemandLongArray;"
-},
 {
   "name":"loci.common.LogbackTools"
 },
@@ -133,19 +165,11 @@
   "name":"ome.codecs.services.LuraWaveServiceImpl"
 },
 {
-  "name":"sun.java2d.marlin.DMarlinRenderingEngine",
+  "name":"sun.security.provider.NativePRNG",
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
-{
-  "name":"sun.security.provider.DRBG",
-  "methods":[{"name":"<init>","parameterTypes":["java.security.SecureRandomParameters"] }]
-},
 {
   "name":"sun.security.provider.SHA",
   "methods":[{"name":"<init>","parameterTypes":[] }]
-},
-{
-  "name":"sun.security.provider.SHA2$SHA256",
-  "methods":[{"name":"<init>","parameterTypes":[] }]
 }
 ]
diff --git a/config/resource-config.json b/config/resource-config.json
index da4ea41..4120960 100644
--- a/config/resource-config.json
+++ b/config/resource-config.json
@@ -19,6 +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"
     }
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
index 09f31c6..2742a53 100644
--- 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>2.1.0</version>
+  <version>2.2.0</version>
   <build>
     <resources>
       <resource>
@@ -19,43 +19,6 @@
         </excludes>
       </resource>
     </resources>
-    <plugins>
-      <plugin>
-        <artifactId>maven-shade-plugin</artifactId>
-        <version>3.4.1</version>
-        <executions>
-          <execution>
-            <phase>package</phase>
-            <goals>
-              <goal>shade</goal>
-            </goals>
-          </execution>
-        </executions>
-        <configuration>
-          <shadedArtifactAttached>false</shadedArtifactAttached>
-          <transformers>
-            <transformer>
-              <mainClass>edu.stonybrook.bmi.hatch.X2TIF</mainClass>
-            </transformer>
-            <transformer />
-            <transformer />
-            <transformer>
-              <addHeader>false</addHeader>
-            </transformer>
-          </transformers>
-          <filters>
-            <filter>
-              <artifact>*:*</artifact>
-              <excludes>
-                <exclude>META-INF/*.SF</exclude>
-                <exclude>META-INF/*.DSA</exclude>
-                <exclude>META-INF/*.RSA</exclude>
-              </excludes>
-            </filter>
-          </filters>
-        </configuration>
-      </plugin>
-    </plugins>
   </build>
   <profiles>
     <profile>
@@ -65,7 +28,7 @@
         <plugins>
           <plugin>
             <artifactId>maven-enforcer-plugin</artifactId>
-            <version>3.2.1</version>
+            <version>3.3.0</version>
             <configuration>
               <rules>
                 <dependencyConvergence />
@@ -81,13 +44,35 @@
                 <goals>
                   <goal>shade</goal>
                 </goals>
+                <configuration>
+                  <shadedArtifactAttached>false</shadedArtifactAttached>
+                  <transformers>
+                    <transformer>
+                      <mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
+                      <manifestEntries>
+                        <Multi-Release>true</Multi-Release>
+                      </manifestEntries>
+                    </transformer>
+                    <transformer />
+                  </transformers>
+                  <filters>
+                    <filter>
+                      <artifact>*:*</artifact>
+                      <excludes>
+                        <exclude>META-INF/*.SF</exclude>
+                        <exclude>META-INF/*.DSA</exclude>
+                        <exclude>META-INF/*.RSA</exclude>
+                      </excludes>
+                    </filter>
+                  </filters>
+                </configuration>
               </execution>
             </executions>
             <configuration>
               <shadedArtifactAttached>false</shadedArtifactAttached>
               <transformers>
                 <transformer>
-                  <mainClass>edu.stonybrook.bmi.hatch.X2TIF</mainClass>
+                  <mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
                   <manifestEntries>
                     <Multi-Release>true</Multi-Release>
                   </manifestEntries>
@@ -116,7 +101,7 @@
           <plugin>
             <groupId>org.graalvm.buildtools</groupId>
             <artifactId>native-maven-plugin</artifactId>
-            <version>0.9.20</version>
+            <version>0.9.21</version>
             <extensions>true</extensions>
             <executions>
               <execution>
@@ -125,25 +110,11 @@
                 <goals>
                   <goal>build</goal>
                 </goals>
-                <configuration>
-                  <imageName>hatch</imageName>
-                  <mainClass>edu.stonybrook.bmi.hatch.X2TIF</mainClass>
-                  <debug>true</debug>
-                  <skipNativeBuild>true</skipNativeBuild>
-                  <skipNativeTests>true</skipNativeTests>
-                  <verbose>true</verbose>
-                  <buildArgs>
-                    <buildArg>--no-fallback</buildArg>
-                    <buildArg>-H:ConfigurationFileDirectories=config</buildArg>
-                    <buildArg>--enable-url-protocols=https</buildArg>
-                    <buildArg>-H:+AddAllCharsets</buildArg>
-                  </buildArgs>
-                </configuration>
               </execution>
             </executions>
             <configuration>
               <imageName>hatch</imageName>
-              <mainClass>edu.stonybrook.bmi.hatch.X2TIF</mainClass>
+              <mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
               <debug>true</debug>
               <skipNativeBuild>true</skipNativeBuild>
               <skipNativeTests>true</skipNativeTests>
@@ -153,6 +124,7 @@
                 <buildArg>-H:ConfigurationFileDirectories=config</buildArg>
                 <buildArg>--enable-url-protocols=https</buildArg>
                 <buildArg>-H:+AddAllCharsets</buildArg>
+                <buildArg>--static</buildArg>
               </buildArgs>
             </configuration>
           </plugin>
diff --git a/nbactions-hatch.xml b/nbactions-hatch.xml
index ff172c1..921e6fa 100644
--- a/nbactions-hatch.xml
+++ b/nbactions-hatch.xml
@@ -13,7 +13,7 @@
                 <exec.vmArgs></exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.appArgs></exec.appArgs>
-                <exec.mainClass>edu.stonybrook.bmi.hatch.X2TIF</exec.mainClass>
+                <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
             </properties>
         </action>
@@ -30,7 +30,7 @@
                 <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.appArgs></exec.appArgs>
-                <exec.mainClass>edu.stonybrook.bmi.hatch.X2TIF</exec.mainClass>
+                <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
             </properties>
@@ -47,7 +47,7 @@
             <properties>
                 <exec.vmArgs></exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.mainClass>edu.stonybrook.bmi.hatch.X2TIF</exec.mainClass>
+                <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
                 <exec.appArgs></exec.appArgs>
             </properties>
diff --git a/nbactions-hatchjar.xml b/nbactions-hatchjar.xml
index 5166f49..28a6694 100644
--- a/nbactions-hatchjar.xml
+++ b/nbactions-hatchjar.xml
@@ -10,10 +10,10 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
             </goals>
             <properties>
-                <exec.vmArgs>-Xmx20G -Xms20G -XX:+UseZGC</exec.vmArgs>
+                <exec.vmArgs></exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.appArgs>-v \HalcyonStorage\tcga\paad\TCGA-2J-AAB1-01Z-00-DX1.F3B4818F-9C3B-4C66-8241-0570B2873EC9.svs \HalcyonStorage\tcga\paad\profile.tif</exec.appArgs>
-                <exec.mainClass>edu.stonybrook.bmi.hatch.X2TIF</exec.mainClass>
+                <exec.appArgs>-v -src \vsi\tk\7-24-20 -dest \vsi\tk\wow</exec.appArgs>
+                <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
             </properties>
         </action>
@@ -27,10 +27,10 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
             </goals>
             <properties>
-                <exec.vmArgs>-Xmx20G -Xms20G -XX:+UseZGC -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
+                <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.appArgs>-v \HalcyonStorage\tcga\paad\TCGA-2J-AAB1-01Z-00-DX1.F3B4818F-9C3B-4C66-8241-0570B2873EC9.svs \HalcyonStorage\tcga\paad\profile.tif</exec.appArgs>
-                <exec.mainClass>edu.stonybrook.bmi.hatch.X2TIF</exec.mainClass>
+                <exec.appArgs>-v -src \vsi\tk\7-24-20 -dest \vsi\tk\wow</exec.appArgs>
+                <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
             </properties>
@@ -45,11 +45,11 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
             </goals>
             <properties>
-                <exec.vmArgs>-Xmx20G -Xms20G -XX:+UseZGC</exec.vmArgs>
+                <exec.vmArgs></exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.mainClass>edu.stonybrook.bmi.hatch.X2TIF</exec.mainClass>
+                <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
-                <exec.appArgs>-v \HalcyonStorage\tcga\paad\TCGA-2J-AAB1-01Z-00-DX1.F3B4818F-9C3B-4C66-8241-0570B2873EC9.svs \HalcyonStorage\tcga\paad\profile.tif</exec.appArgs>
+                <exec.appArgs>-v -src \vsi\tk\7-24-20 -dest \vsi\tk\wow</exec.appArgs>
             </properties>
         </action>
     </actions>
diff --git a/pom.xml b/pom.xml
index 9fe58d4..33eed24 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>edu.stonybrook.bmi</groupId>
 	<artifactId>hatch</artifactId>
-	<version>2.1.0</version>
+	<version>2.2.0</version>
 	<packaging>jar</packaging>
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -24,47 +24,20 @@
                     </exclusion>
                 </exclusions>
             </dependency>
+            <dependency>
+                <groupId>com.beust</groupId>
+                <artifactId>jcommander</artifactId>
+                <version>1.82</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.jena</groupId>
+                <artifactId>jena-core</artifactId>
+                <version>4.7.0</version>
+                <type>jar</type>
+            </dependency>
 	</dependencies>
 	<build>
-            <plugins>
-		<plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-shade-plugin</artifactId>
-                    <version>3.4.1</version>
-                    <configuration>
-                        <shadedArtifactAttached>false</shadedArtifactAttached>
-                        <transformers>
-                            <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                                <mainClass>edu.stonybrook.bmi.hatch.X2TIF</mainClass>
-                            </transformer>
-                            <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
-                            <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer"/>
-                            <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
-                                <addHeader>false</addHeader>
-                            </transformer>
-                        </transformers>
-                        <filters>
-                            <filter>
-                                <artifact>*:*</artifact>
-                                <excludes>
-                                    <exclude>META-INF/*.SF</exclude>
-                                    <exclude>META-INF/*.DSA</exclude>
-                                    <exclude>META-INF/*.RSA</exclude>
-                                </excludes>
-                            </filter>
-                        </filters>
-                    </configuration>
-                    <executions>
-                        <execution>
-                            <phase>package</phase>
-                                <goals>
-                                    <goal>shade</goal>
-                                </goals>
-                        </execution>
-                    </executions>
-                </plugin>
-            </plugins>
-            <resources>
+              <resources>
                 <resource>
                     <filtering>false</filtering>
                     <directory>src/main/resources</directory>
@@ -102,7 +75,7 @@
                         <plugin>
                             <groupId>org.apache.maven.plugins</groupId>
                             <artifactId>maven-enforcer-plugin</artifactId>
-                            <version>3.2.1</version>
+                            <version>3.3.0</version>
                             <configuration>
                                 <rules><dependencyConvergence/></rules>
                             </configuration>
@@ -115,7 +88,7 @@
                                 <shadedArtifactAttached>false</shadedArtifactAttached>
                                 <transformers>
                                     <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                                        <mainClass>edu.stonybrook.bmi.hatch.X2TIF</mainClass>
+                                        <mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
                                         <manifestEntries>
                                             <Multi-Release>true</Multi-Release>
                                         </manifestEntries>
@@ -152,7 +125,7 @@
                         <plugin>
                             <groupId>org.graalvm.buildtools</groupId>
                             <artifactId>native-maven-plugin</artifactId>
-                            <version>0.9.20</version>
+                            <version>0.9.21</version>
                             <extensions>true</extensions>
                             <executions>
                                 <execution>
@@ -165,7 +138,7 @@
                             </executions>
                             <configuration>
                                 <imageName>hatch</imageName>
-                                <mainClass>edu.stonybrook.bmi.hatch.X2TIF</mainClass>
+                                <mainClass>edu.stonybrook.bmi.hatch.Hatch</mainClass>
                                 <debug>true</debug>
                                 <skipNativeBuild>true</skipNativeBuild>
                                 <skipNativeTests>true</skipNativeTests>
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/CellSensReader.java b/src/main/java/edu/stonybrook/bmi/hatch/CellSensReader.java
index 91639c1..4d3eaae 100644
--- a/src/main/java/edu/stonybrook/bmi/hatch/CellSensReader.java
+++ b/src/main/java/edu/stonybrook/bmi/hatch/CellSensReader.java
@@ -2503,6 +2503,11 @@ public byte[] getRawBytes(IFD ifd, int no, int row, int col) {
         throw new UnsupportedOperationException("Not supported yet."); // Generated from nbfs://nbhost/SystemFileSystem/Templates/Classes/Code/GeneratedMethodBody
     }
 
+    @Override
+    public byte[] getRawBytesMeta(int no, int row, int col) {
+        throw new UnsupportedOperationException("Not supported yet."); // Generated from nbfs://nbhost/SystemFileSystem/Templates/Classes/Code/GeneratedMethodBody
+    }
+
   // -- Helper class --
 
   class TileCoordinate {
@@ -2586,11 +2591,9 @@ class Pyramid {
     public ArrayList<String> deviceIDs = new ArrayList<String>();
     public ArrayList<String> deviceManufacturers = new ArrayList<String>();
 
-    public Hashtable<String, Object> originalMetadata =
-      new Hashtable<String, Object>();
+    public Hashtable<String, Object> originalMetadata = new Hashtable<String, Object>();
 
-    public HashMap<String, Integer> dimensionOrdering =
-      new HashMap<String, Integer>();
+    public HashMap<String, Integer> dimensionOrdering = new HashMap<String, Integer>();
 
     public transient Double zStart;
     public transient Double zIncrement;
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/FormatReader.java b/src/main/java/edu/stonybrook/bmi/hatch/FormatReader.java
index 4e82552..0b40f11 100644
--- a/src/main/java/edu/stonybrook/bmi/hatch/FormatReader.java
+++ b/src/main/java/edu/stonybrook/bmi/hatch/FormatReader.java
@@ -1821,6 +1821,7 @@ protected Pulse getPulse(String value) throws FormatException {
    * Construct an {@link ome.xml.model.AffineTransform} corresponding to
    * the given angle.
    * @param theta the angle of rotation in radians
+     * @return 
    */
   protected AffineTransform getRotationTransform(double theta) {
     AffineTransform transform = new AffineTransform();
@@ -1838,6 +1839,7 @@ private boolean isOmero(String id) {
     id.indexOf("\n") > 0;
   }
   
+  public abstract byte[] getRawBytesMeta(int no, int row, int col);
   public abstract byte[] getRawBytes(byte[] rawbuffer, int no, int row, int col);
   public abstract byte[] getRawBytes(IFD ifd, int no, int row, int col);
   public abstract byte[] getDecodedTile(byte[] rawbuffer, int no, int row, int col);
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/Hatch.java b/src/main/java/edu/stonybrook/bmi/hatch/Hatch.java
new file mode 100644
index 0000000..0df2049
--- /dev/null
+++ b/src/main/java/edu/stonybrook/bmi/hatch/Hatch.java
@@ -0,0 +1,149 @@
+package edu.stonybrook.bmi.hatch;
+
+import com.beust.jcommander.JCommander;
+import com.beust.jcommander.ParameterException;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Objects;
+import java.util.concurrent.Callable;
+import java.util.concurrent.LinkedBlockingQueue;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import java.util.stream.Stream;
+import org.apache.jena.rdf.model.Model;
+
+/**
+ *
+ * @author erich
+ */
+public class Hatch {    
+    public static String software = "hatch 2.2.0 by Wing-n-Beak";
+    private static final String[] ext = new String[] {".vsi", ".svs", ".tif"};
+    public static final String HELP = Hatch.software+"\n"+
+        """
+        usage: hatch <src> <dest>
+        -v : verbose
+        """;
+    
+    private static void Traverse(HatchParameters params) {
+        Path s = params.src.toPath();
+        Path d = params.dest.toPath();
+        ThreadPoolExecutor engine = new ThreadPoolExecutor(params.fp,params.fp,0L,TimeUnit.MILLISECONDS,new LinkedBlockingQueue<>());
+        engine.prestartAllCoreThreads();
+        try (Stream<Path> X = Files.walk(params.src.toPath())) {
+            X
+                .filter(Objects::nonNull)
+                .filter(fff -> {
+                    for (String ext1 : ext) {
+                        if (fff.toFile().toString().toLowerCase().endsWith(ext1)) {
+                            return true;
+                        }
+                    } 
+                    return false;
+                })    
+                .forEach(f->{
+                    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()));
+                    } 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()));
+                    }
+                });
+        } catch (IOException ex) {
+            Logger.getLogger(Hatch.class.getName()).log(Level.SEVERE, null, ex);
+        }
+        int cc = engine.getActiveCount()+engine.getQueue().size();
+        while ((engine.getActiveCount()+engine.getQueue().size())>0) {
+            int curr = engine.getActiveCount()+engine.getQueue().size();
+            if (cc!=curr) {
+                cc=curr;
+                if (params.verbose) System.out.println("All jobs submitted...waiting for "+curr);
+            }
+        }
+        System.out.println("Engine shutdown");
+        engine.shutdown();
+    }
+    
+    public static void main(String[] args) {
+        loci.common.DebugTools.setRootLevel("WARN");
+        HatchParameters params = new HatchParameters();
+        JCommander jc = JCommander.newBuilder().addObject(params).build();
+        jc.setProgramName(Hatch.software+"\nhatch");    
+        try {
+            jc.parse(args);
+            if (params.isHelp()) {
+                jc.usage();
+                System.exit(0);
+            } else if (params.src.exists()) {
+                if (params.src.isDirectory()) {
+                    System.out.println(params.src+" is directory");
+                    if (!params.dest.exists()) {
+                        params.dest.mkdir();
+                    }
+                    if (!params.dest.isDirectory()) {
+                        jc.usage();
+                    } else {
+                        Traverse(params);
+                    }
+                } else {
+                    System.out.println(params.src+" is not a directory");
+                    if (params.dest.exists()) {
+                        System.out.println(params.dest+" does exist");
+                        if (!params.dest.isDirectory()) {
+                            System.out.println(params.dest+" is not a directory");
+                            X2TIF v2t = new X2TIF(params, params.src.toString(), params.dest.toString());
+                            v2t.Execute();
+                            try {
+                                v2t.close();
+                            } catch (Exception ex) {
+                                Logger.getLogger(Hatch.class.getName()).log(Level.SEVERE, null, ex);
+                            }
+                        } else {
+                            jc.usage();
+                        }
+                    } else {
+                        System.out.println(params.dest+" does not exist");
+                        X2TIF v2t = new X2TIF(params, params.src.toString(), params.dest.toString());
+                        v2t.Execute();
+                    }
+                }
+            } else {
+                System.out.println(params.src.toString()+" does not exist!");
+            }  
+        } catch (ParameterException ex) {
+            System.out.println(ex.getMessage());
+        }
+    }
+}
+
+class FileProcessor implements Callable<Model> {
+    private final HatchParameters params;
+    private final String src;
+    private final String dest;
+
+    public FileProcessor(HatchParameters params, String src, String dest) {
+        this.params = params;
+        this.src = src;
+        this.dest = dest;
+    }
+    
+    @Override
+    public Model call() {
+        try (X2TIF v2t = new X2TIF(params, src, dest)) {
+            v2t.Execute();
+        } catch (Exception ex) {
+            System.out.println("FILE PROCESSOR ERROR --> "+src+" "+dest+" "+ex.toString());
+        }
+        return null;
+    }    
+}
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/HatchParameters.java b/src/main/java/edu/stonybrook/bmi/hatch/HatchParameters.java
new file mode 100644
index 0000000..f535da5
--- /dev/null
+++ b/src/main/java/edu/stonybrook/bmi/hatch/HatchParameters.java
@@ -0,0 +1,40 @@
+package edu.stonybrook.bmi.hatch;
+
+import com.beust.jcommander.Parameter;
+import com.beust.jcommander.internal.Lists;
+import java.io.File;
+import java.util.List;
+
+/**
+ *
+ * @author erich
+ */
+public class HatchParameters {
+    @Parameter(names = {"-help","-h"}, help = true)
+    private boolean help;
+    
+    public boolean isHelp() {
+        return help;
+    }
+    
+    @Parameter(names = "-src", description = "Source Folder or File", required = true)
+    public File src;
+
+    @Parameter(names = "-dest", description = "Destination Folder or File", required = true)
+    public File dest;  
+    
+    @Parameter(names = "-fp", description = "# of file processors")
+    public int fp = 1;  
+
+    @Parameter(names = "-cores", description = "# of cores for processing")
+    public int cores = 1;  
+    
+    @Parameter
+    public List<String> parameters = Lists.newArrayList();
+    
+    @Parameter(names = {"-v","-verbose"})
+    public boolean verbose = false;
+    
+    @Parameter(names = "-meta")
+    public boolean meta = false;
+}
\ No newline at end of file
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/JPEGTools.java b/src/main/java/edu/stonybrook/bmi/hatch/JPEGTools.java
index 4ce7aec..4acbac8 100644
--- a/src/main/java/edu/stonybrook/bmi/hatch/JPEGTools.java
+++ b/src/main/java/edu/stonybrook/bmi/hatch/JPEGTools.java
@@ -61,7 +61,6 @@ public static byte[] FindFirstEOI(RandomAccessInputStream ets, byte[] r) throws
     
     public static byte[] FindFirstEOI(byte[] ets) throws IOException {
         int c=0;
-//        Files.write((new File("dump.jpg")).toPath(), ets);
         while(c<ets.length) {
             c++;
             if (Byte.compare(ets[c-1],FF)==0) {
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/MinimalTiffReader.java b/src/main/java/edu/stonybrook/bmi/hatch/MinimalTiffReader.java
index d1e36af..3714809 100644
--- a/src/main/java/edu/stonybrook/bmi/hatch/MinimalTiffReader.java
+++ b/src/main/java/edu/stonybrook/bmi/hatch/MinimalTiffReader.java
@@ -778,4 +778,9 @@ protected void initTiffParser() {
     tiffParser.setUse64BitOffsets(use64Bit);
   }
 
+    @Override
+    public byte[] getRawBytesMeta(int no, int row, int col) {
+        throw new UnsupportedOperationException("Not supported yet."); // Generated from nbfs://nbhost/SystemFileSystem/Templates/Classes/Code/GeneratedMethodBody
+    }
+
 }
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/TiffParser.java b/src/main/java/edu/stonybrook/bmi/hatch/TiffParser.java
index c61c52d..782666f 100644
--- a/src/main/java/edu/stonybrook/bmi/hatch/TiffParser.java
+++ b/src/main/java/edu/stonybrook/bmi/hatch/TiffParser.java
@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package edu.stonybrook.bmi.hatch;
 
 import java.io.Closeable;
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/TiffSaver.java b/src/main/java/edu/stonybrook/bmi/hatch/TiffSaver.java
index bb4c791..14441b1 100644
--- a/src/main/java/edu/stonybrook/bmi/hatch/TiffSaver.java
+++ b/src/main/java/edu/stonybrook/bmi/hatch/TiffSaver.java
@@ -1,6 +1,5 @@
 package edu.stonybrook.bmi.hatch;
 
-import static edu.stonybrook.bmi.hatch.X2TIF.software;
 import java.io.ByteArrayOutputStream;
 import java.io.Closeable;
 import java.io.DataOutputStream;
@@ -449,8 +448,7 @@ private void writeImageIFD(IFD ifd, int no, byte[][] strips, int nChannels, bool
         defaultByteCount = strips[0].length;
       }
       writeIFDStrips(ifd, no, strips, nChannels, last, x, y, defaultByteCount);
-    }
-    finally {
+    } finally {
       if (in != null) {
         in.close();
       }
@@ -978,7 +976,7 @@ private void makeValidIFD(IFD ifd, int pixelType, int nChannels) {
       ifd.putIFDValue(IFD.Y_RESOLUTION, 512);
     }*/
     if (ifd.get(IFD.SOFTWARE) == null) {
-      ifd.putIFDValue(IFD.SOFTWARE, software);
+      ifd.putIFDValue(IFD.SOFTWARE, Hatch.software);
     }
     if (ifd.get(IFD.ROWS_PER_STRIP) == null && ifd.get(IFD.TILE_WIDTH) == null && ifd.get(IFD.TILE_LENGTH) == null) {
       ifd.putIFDValue(IFD.ROWS_PER_STRIP, new long[] {1});
@@ -1004,8 +1002,7 @@ private void writeIFDStrips(IFD ifd, int no, byte[][] strips, int nChannels, boo
     }
 
     if (ifd.containsKey(IFD.STRIP_BYTE_COUNTS) || ifd.containsKey(IFD.TILE_BYTE_COUNTS)) {
-      long[] ifdByteCounts = isTiled ?
-        ifd.getIFDLongArray(IFD.TILE_BYTE_COUNTS) : ifd.getStripByteCounts();
+      long[] ifdByteCounts = isTiled ? ifd.getIFDLongArray(IFD.TILE_BYTE_COUNTS) : ifd.getStripByteCounts();
       for (long stripByteCount : ifdByteCounts) {
         byteCounts.add(stripByteCount);
       }
diff --git a/src/main/java/edu/stonybrook/bmi/hatch/X2TIF.java b/src/main/java/edu/stonybrook/bmi/hatch/X2TIF.java
index fe99ab3..6ec9ce5 100644
--- a/src/main/java/edu/stonybrook/bmi/hatch/X2TIF.java
+++ b/src/main/java/edu/stonybrook/bmi/hatch/X2TIF.java
@@ -32,15 +32,17 @@
 import ome.xml.model.enums.DimensionOrder;
 import ome.xml.model.enums.PixelType;
 import ome.xml.model.primitives.PositiveInteger;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
 
 /**
  *
  * @author erich
  */
-public class X2TIF {
+public class X2TIF implements AutoCloseable {
     private FormatReader reader;
-    private String inputFile;
-    private String outputFile;
+    private final String inputFile;
+    private final String outputFile;
     private int tileSizeX;
     private int tileSizeY;
     private int height;
@@ -48,7 +50,6 @@ public class X2TIF {
     private int maximage;
     private Pyramid pyramid;
     private OMETiffWriter writer;
-    private boolean verbose = false;
     private final StopWatch time;
     private int depth;
     private Length ppx;
@@ -57,15 +58,19 @@ public class X2TIF {
     private TiffRational py;
     private int TileSize;
     private IMetadata meta;
-    public static String software = "hatch 2.1.0 by Wing-n-Beak";
+    private final HatchParameters params;
+    private final Model m;
     
-    public X2TIF() {
+    public X2TIF(HatchParameters params, String src, String dest) {
         time = new StopWatch();
-    }
-    
-    public void SetSrcDest(String src, String dest) {
         inputFile = src;
         outputFile = dest;
+        this.params = params;
+        if (params.meta) {
+            m = ModelFactory.createDefaultModel();
+        } else {
+            m = null;
+        }
     }
     
     public int MaxImage(FormatReader reader) {
@@ -79,7 +84,7 @@ public int MaxImage(FormatReader reader) {
             }
             ii++;
         }
-        System.out.println("MAX IMAGE SIZE IS SERIES : "+maxseries);
+        if (params.verbose) System.out.println("MAX IMAGE SIZE IS SERIES : "+maxseries);
         return maxseries;
     }
     
@@ -130,7 +135,7 @@ private void SetupWriter() {
                 } else {
                     h = wholenumytiles * tileSizeY + (fractiony/2);
                 }
-                if (verbose) {
+                if (params.verbose) {
                     System.out.println("Pyramid : "+w+" "+ h +" "+((int) (1+ Math.ceil(w/tileSizeX)))+" "+((int) (1+ Math.ceil(h/tileSizeX))));
                 }
                 ((OMEPyramidStore) meta).setResolutionSizeX(new PositiveInteger(w), 0, j);
@@ -181,14 +186,16 @@ private void initialize() {
             ppx = retrieve.getPixelsPhysicalSizeX(maximage);
             ppy = retrieve.getPixelsPhysicalSizeY(maximage);
             SetPPS();
-            if (verbose) {
+            if (params.verbose) {
                 System.out.println("Image Size   : "+width+"x"+height);
                 System.out.println("Tile size    : "+tileSizeX+"x"+tileSizeY);
                 System.out.println("Compression  : "+reader.metadata.get("Compression"));
             }
             try {
                 if (reader.metadata.get("Compression")==null) {
-                    System.out.println("NULL compression specified...trying JPEG...no promises...");
+                    if (params.verbose) {
+                        System.out.println("NULL compression specified...trying JPEG...no promises...");
+                    }
                 } else if (reader.metadata.get("Compression")!="JPEG") {
                     throw new Error("Hatch can only convert images that have JPEG compression.");
                 }
@@ -205,7 +212,7 @@ private void initialize() {
             int tiless = (int) Math.ceil(Math.log(tileSizeX)/Math.log(2));
             depth = ss-tiless+2;
             TileSize = reader.getOptimalTileHeight() * reader.getOptimalTileWidth() * 24;
-            if (verbose) {
+            if (params.verbose) {
                 System.out.println("# of scales to be generated : "+depth);
             }
             SetupWriter();
@@ -282,7 +289,7 @@ public void DumpBI2File3(BufferedImage bi, int a, int b) {
     }
         
     public void readWriteTiles() throws FormatException, IOException {
-        if (verbose) {
+        if (params.verbose) {
             System.out.println("transferring image data...");
         }
         reader.setSeries(maximage);
@@ -295,7 +302,7 @@ public void readWriteTiles() throws FormatException, IOException {
         writer.setResolution(0);
         byte[] rawbuffer = new byte[TileSize+20];
         for (int y=0; y<nYTiles; y++) {
-            if (verbose) {
+            if (params.verbose) {
                 float perc = 100f*y/nYTiles;
                 System.out.println(perc+"%");
             }
@@ -316,20 +323,18 @@ public void readWriteTiles() throws FormatException, IOException {
                     ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION, PhotoInterp.RGB.getCode());
                 }
                 ifd.put(777, raw);
-               // Dump2File(raw,x,y);
                 writer.saveBytes(0, buf, ifd, tileX, tileY, effTileSizeX, effTileSizeY);
                 BufferedImage bi = ImageIO.read(new ByteArrayInputStream(raw));
-                //DumpBI2File(bi,x,y);
                 bi = bi.getSubimage(0, 0, effTileSizeX, effTileSizeY);
                 pyramid.put(bi, x, y);
             }
         }
-        if (verbose) {
+        if (params.verbose) {
             time.Cumulative();
             System.out.println("Generate image pyramid...");
         }
         for (int s=1;s<depth;s++) {
-            if (verbose) {
+            if (params.verbose) {
                 System.out.println("Level : "+s+" of "+depth);
             }
             System.out.println("Lump...");
@@ -343,7 +348,7 @@ public void readWriteTiles() throws FormatException, IOException {
             System.out.println("Resolution S="+s+" "+pyramid.getWidth()+"x"+pyramid.getHeight());
             writer.setSeries(0);
             writer.setResolution(s);
-            if (verbose) {
+            if (params.verbose) {
                 System.out.println("Writing level "+s+"...");
             }
             for (int y=0; y<pyramid.gettilesY(); y++) {
@@ -372,21 +377,10 @@ public void readWriteTiles() throws FormatException, IOException {
         }
     }
     
-    public void SetVerbose(boolean x) {
-        verbose = x;
-    }
-    
-    public void DisplayHelp() {
-        System.out.println(software);
-        System.out.println("usage: hatch <src> <dest>");
-        System.out.println("-v : verbose");
-    }
-    
-    public void Execute(String src, String dest) {
-        if (verbose) {
+    public void Execute() {
+        if (params.verbose) {
             System.out.println("initializing...");
         }
-        SetSrcDest(src,dest);
         initialize();
         try {
             readWriteTiles();
@@ -396,22 +390,9 @@ public void Execute(String src, String dest) {
         }
     }
 
-    public static void main(String[] args) {
-        loci.common.DebugTools.setRootLevel("WARN");
-        X2TIF v2t = new X2TIF();
-        if ((args.length<2)||args.length>3) {
-            v2t.DisplayHelp();
-        } else {
-            if (args.length==3) {
-                if (args[0].equals("-v")) {
-                    v2t.SetVerbose(true);
-                    v2t.Execute(args[1],args[2]);
-                } else {
-                    v2t.DisplayHelp();
-                }
-            } else {
-                v2t.Execute(args[0],args[1]);
-            }
-        }
+    @Override
+    public void close() throws Exception {
+        reader.close();
+        writer.close();
     }
 }