Merge remote-tracking branch 'origin/master'

seadas · Dec 8, 2014 · f59bcc9 · f59bcc9
2 parents 2fe790c + 7bd565f
commit f59bcc9
Show file tree

Hide file tree

Showing 10 changed files with 37 additions and 45 deletions.
diff --git a/pom.xml b/pom.xml
@@ -80,6 +80,7 @@
         <module>../beam/beam-cluster-analysis</module>
         <module>../beam/beam-collocation</module>
         <module>../beam/beam-envisat-reader</module>
+        <module>../beam/beam-envi-reader</module>
         <module>../beam/beam-geotiff</module>
         <module>../beam/beam-getasse30-reader</module>
         <module>../beam/beam-hdf5-writer</module>
@@ -253,6 +254,11 @@
                  <artifactId>beam-envisat-reader</artifactId>
                  <version>${beam.versionRange}</version>
              </dependency>
+             <dependency>
+                 <groupId>org.esa.beam</groupId>
+                 <artifactId>beam-envi-reader</artifactId>
+                 <version>5.0.1</version>
+             </dependency>
             <dependency>
                  <groupId>org.esa.beam</groupId>
                  <artifactId>beam-geotiff</artifactId>

diff --git a/seadas-bootstrap/pom.xml b/seadas-bootstrap/pom.xml
@@ -81,6 +81,10 @@
             <groupId>org.esa.beam</groupId>
             <artifactId>beam-envisat-reader</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.esa.beam</groupId>
+            <artifactId>beam-envi-reader</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.esa.beam</groupId>
             <artifactId>beam-geotiff</artifactId>

diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/AquariusL2FileReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/AquariusL2FileReader.java
@@ -1,14 +1,11 @@
 package gov.nasa.gsfc.seadas.dataio;
 
-import com.bc.ceres.core.ProgressMonitor;
 import org.esa.beam.framework.dataio.ProductIOException;
 import org.esa.beam.framework.datamodel.Band;
-import org.esa.beam.framework.datamodel.PixelGeoCoding;
+import org.esa.beam.framework.datamodel.PixelGeoCoding2;
 import org.esa.beam.framework.datamodel.Product;
 import org.esa.beam.framework.datamodel.ProductData;
 
-import java.io.IOException;
-
 /**
  * Created by IntelliJ IDEA.
  * User: seadas
@@ -97,13 +94,8 @@ public void addGeocoding(final Product product) throws ProductIOException {
             latBand = product.getBand(latitude);
             lonBand = product.getBand(longitude);
         }
-        try {
-            if (latBand != null && lonBand != null) {
-                product.setGeoCoding(new PixelGeoCoding(latBand, lonBand, null, 5, ProgressMonitor.NULL));
-            }
-        } catch (IOException e) {
-            throw new ProductIOException(e.getMessage());
+        if (latBand != null && lonBand != null) {
+            product.setGeoCoding(new PixelGeoCoding2(latBand, lonBand, null));
         }
-
     }
 }
diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L1ASeawifsFileReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L1ASeawifsFileReader.java
@@ -1,13 +1,10 @@
 package gov.nasa.gsfc.seadas.dataio;
 
-import com.bc.ceres.core.ProgressMonitor;
 import org.esa.beam.framework.dataio.ProductIOException;
 import org.esa.beam.framework.datamodel.*;
 import ucar.ma2.InvalidRangeException;
-import ucar.nc2.Attribute;
 import ucar.nc2.Variable;
 
-import java.io.IOException;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -66,12 +63,8 @@ public Product createProduct() throws ProductIOException {
         latBand.setData(lats);
         ProductData lons = ProductData.createInstance(longitudes);
         lonBand.setData(lons);
-        try {
-            product.setGeoCoding(new PixelGeoCoding(latBand, lonBand, null, 10, ProgressMonitor.NULL));
-        } catch (IOException e) {
-            throw new ProductIOException(e.getMessage());
-        }
-
+        product.setGeoCoding(new PixelGeoCoding2(latBand, lonBand,null));
+
         addFlagsAndMasks(product);
 
         return product;

diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L1BHicoFileReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L1BHicoFileReader.java
@@ -1,6 +1,5 @@
 package gov.nasa.gsfc.seadas.dataio;
 
-import com.bc.ceres.core.ProgressMonitor;
 import org.esa.beam.framework.dataio.ProductIOException;
 import org.esa.beam.framework.datamodel.*;
 import ucar.ma2.Array;
@@ -333,6 +332,7 @@ public void addGeocoding(final Product product) throws ProductIOException {
 
         Variable latVar = ncFile.findVariable(navGroup + "/" + latitude);
         Variable lonVar = ncFile.findVariable(navGroup + "/" + longitude);
+
         if (latVar != null && lonVar != null ) {
             final ProductData lonRawData;
             final ProductData latRawData;
@@ -353,11 +353,8 @@ public void addGeocoding(final Product product) throws ProductIOException {
             latBand.setData(latRawData);
             lonBand.setData(lonRawData);
 
-            try {
-                product.setGeoCoding(new PixelGeoCoding(latBand, lonBand, null, 5, ProgressMonitor.NULL));
-            } catch (IOException e) {
-                throw new ProductIOException(e.getMessage());
-            }
+            product.setGeoCoding(new PixelGeoCoding2(latBand, lonBand,null));
+
         }
     }
 }
diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L1BOcm2FileReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L1BOcm2FileReader.java
@@ -1,14 +1,11 @@
 package gov.nasa.gsfc.seadas.dataio;
 
-import com.bc.ceres.core.ProgressMonitor;
 import org.esa.beam.framework.dataio.ProductIOException;
 import org.esa.beam.framework.datamodel.Band;
-import org.esa.beam.framework.datamodel.PixelGeoCoding;
+import org.esa.beam.framework.datamodel.PixelGeoCoding2;
 import org.esa.beam.framework.datamodel.Product;
 import org.esa.beam.framework.datamodel.ProductData;
 import ucar.nc2.Variable;
-
-import java.io.IOException;
 import java.util.List;
 
 /**
@@ -97,11 +94,7 @@ public void addGeocoding(final Product product) throws ProductIOException {
         latBand.setNoDataValueUsed(true);
         lonBand.setNoDataValueUsed(true);
 
-        try {
-            product.setGeoCoding(new PixelGeoCoding(latBand, lonBand, null, 5, ProgressMonitor.NULL));
-        } catch (IOException e) {
-            throw new ProductIOException(e.getMessage());
-        }
+        product.setGeoCoding(new PixelGeoCoding2(latBand, lonBand,null));
     }
 }
 
diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L2FileReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/L2FileReader.java
@@ -314,13 +314,8 @@ public void addPixelGeocoding(final Product product) throws ProductIOException {
                 }
             }
         }
-        try {
-            if (latBand != null) {
-                product.setGeoCoding(new PixelGeoCoding(latBand, lonBand, null, 5, ProgressMonitor.NULL));
-            }
-        } catch (IOException e) {
-            throw new ProductIOException(e.getMessage());
+        if (latBand != null) {
+            product.setGeoCoding(new PixelGeoCoding2(latBand, lonBand,null));
         }
-
     }
 }
diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/SeadasFileReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/SeadasFileReader.java
@@ -68,6 +68,11 @@ public synchronized void  readBandData(Band destBand, int sourceOffsetX, int sou
             sourceOffsetX = destBand.getSceneRasterWidth() - (sourceOffsetX + sourceWidth);
         }
         sourceOffsetY += leadLineSkip;
+        int widthRemainder = destBand.getSceneRasterWidth() - (sourceOffsetX + sourceWidth);
+
+        if (widthRemainder < 0){
+            sourceWidth += widthRemainder;
+        } 
         start[0] = sourceOffsetY;
         start[1] = sourceOffsetX;
         stride[0] = sourceStepY;
@@ -100,7 +105,12 @@ public synchronized void  readBandData(Band destBand, int sourceOffsetX, int sou
                 storage = array.copyTo1DJavaArray();
             }
 
-            arraycopy(storage, 0, buffer, 0, destBuffer.getNumElems());
+            if (widthRemainder < 0){
+                arraycopy(storage, 0, buffer, 0, destBuffer.getNumElems() + widthRemainder);
+            }else{
+                arraycopy(storage, 0, buffer, 0, destBuffer.getNumElems());
+
+            }
         } finally {
             pm.done();
         }

diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/SeadasProductReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/SeadasProductReader.java
@@ -162,7 +162,10 @@ protected Product readProductNodesImpl() throws IOException {
 
             }
 
-            return seadasFileReader.createProduct();
+            Product product = seadasFileReader.createProduct();
+
+            configurePreferredTileSize(product);
+            return product;
 
         } catch (IOException e) {
             throw new ProductIOException(e.getMessage());

diff --git a/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/ViirsXDRFileReader.java b/seadas-reader/src/main/java/gov/nasa/gsfc/seadas/dataio/ViirsXDRFileReader.java
@@ -356,7 +356,6 @@ else if (shortName.contains("VIIRS-DualGain")){
                 ProductData lons = ProductData.createInstance(longitudes);
                 lonBand.setData(lons);
 
-                //product.setGeoCoding(new PixelGeoCoding(latBand, lonBand, null, 5, ProgressMonitor.NULL));
                 product.setGeoCoding(new BowtiePixelGeoCoding(latBand, lonBand, detectorsInScan));
             } else {
                 product.setGeoCoding(new BowtiePixelGeoCoding(product.getBand(latitude), product.getBand(longitude), detectorsInScan));