move GDAL GeoTiff reader to adapter so that it can be used for comman…

…dline ingest

extensions/adapters/raster/pom.xml

@@ -9,7 +9,32 @@
 	<artifactId>geowave-adapter-raster</artifactId>
 	<name>Geowave Raster Adapter</name>
 	<description>Geowave Data Adapter for Raster Data</description>
-	<dependencies>
+	<dependencies><dependency>
+			<groupId>it.geosolutions.imageio-ext</groupId>
+			<artifactId>imageio-ext-gdalgeotiff</artifactId>
+			<version>1.1.13</version>
+			<exclusions>
+				<exclusion>
+					<groupId>com.vividsolutions</groupId>
+					<artifactId>jts</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.geotools</groupId>
+			<artifactId>gt-imageio-ext-gdal</artifactId>
+			<version>${geotools.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>com.vividsolutions</groupId>
+					<artifactId>jts</artifactId>
+				</exclusion>
+				<exclusion>
+					<artifactId>gt-epsg-hsql</artifactId>
+					<groupId>org.geotools</groupId>
+				</exclusion>
+			</exclusions>
+		</dependency>
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>

extensions/cli/landsat8/src/main/java/mil/nga/giat/geowave/format/landsat8/GDALGeoTiffFormat.java → extensions/adapters/raster/src/main/java/mil/nga/giat/geowave/adapter/raster/plugin/GDALGeoTiffFormat.java

@@ -1,4 +1,4 @@
-package mil.nga.giat.geowave.format.landsat8;
+package mil.nga.giat.geowave.adapter.raster.plugin;
 
 import java.util.Collections;
 import java.util.HashMap;

extensions/adapters/raster/src/main/java/mil/nga/giat/geowave/adapter/raster/plugin/GDALGeoTiffFormatFactory.java

@@ -0,0 +1,45 @@
+package mil.nga.giat.geowave.adapter.raster.plugin;
+
+import java.awt.RenderingHints.Key;
+import java.util.Map;
+
+import org.geotools.coverage.grid.io.AbstractGridFormat;
+import org.geotools.coverageio.BaseGridFormatFactorySPI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import it.geosolutions.imageio.plugins.geotiff.GeoTiffImageReaderSpi;
+
+public class GDALGeoTiffFormatFactory extends
+		BaseGridFormatFactorySPI
+{
+	private final static Logger LOGGER = LoggerFactory.getLogger(GDALGeoTiffFormatFactory.class);
+
+	@Override
+	public boolean isAvailable() {
+		boolean available = true;
+
+		// if these classes are here, then the runtime environment has
+		// access to JAI and the JAI ImageI/O toolbox.
+		try {
+			Class.forName("it.geosolutions.imageio.plugins.geotiff.GeoTiffImageReaderSpi");
+			available = new GeoTiffImageReaderSpi().isAvailable();
+
+		}
+		catch (final ClassNotFoundException cnf) {
+			if (LOGGER.isDebugEnabled()) {
+				LOGGER.debug("GDALGeoTiffFormatFactory is not availaible.");
+			}
+
+			available = false;
+		}
+
+		return available;
+	}
+
+	@Override
+	public AbstractGridFormat createFormat() {
+		return new GDALGeoTiffFormat();
+	}
+
+}

extensions/cli/landsat8/src/main/java/mil/nga/giat/geowave/format/landsat8/GDALGeoTiffReader.java → extensions/adapters/raster/src/main/java/mil/nga/giat/geowave/adapter/raster/plugin/GDALGeoTiffReader.java

@@ -1,4 +1,4 @@
-package mil.nga.giat.geowave.format.landsat8;
+package mil.nga.giat.geowave.adapter.raster.plugin;
 
 import org.geotools.coverageio.gdal.BaseGDALGridCoverage2DReader;
 import org.geotools.data.DataSourceException;

extensions/adapters/raster/src/main/resources/META-INF/services/org.geotools.coverage.grid.io.GridFormatFactorySpi

@@ -1 +1,2 @@
 mil.nga.giat.geowave.adapter.raster.plugin.GeoWaveGTRasterFormatFactory
+mil.nga.giat.geowave.adapter.raster.plugin.GDALGeoTiffFormatFactory

extensions/cli/geoserver/src/main/java/mil/nga/giat/geowave/cli/geoserver/GeoServerConfig.java

@@ -104,7 +104,7 @@ public GeoServerConfig() {
 	}
 
 	public String getUrl() {
-		if (!url.contains("//")) {
+		if (url.contains("//")) {
 			// assume exact URL
 			return url;
 		}

extensions/cli/landsat8/src/main/java/mil/nga/giat/geowave/format/landsat8/RasterIngestRunner.java

@@ -45,6 +45,7 @@
 import mil.nga.giat.geowave.adapter.raster.RasterUtils;
 import mil.nga.giat.geowave.adapter.raster.adapter.RasterDataAdapter;
 import mil.nga.giat.geowave.adapter.raster.adapter.merge.nodata.NoDataMergeStrategy;
+import mil.nga.giat.geowave.adapter.raster.plugin.GDALGeoTiffReader;
 import mil.nga.giat.geowave.adapter.raster.plugin.GeoWaveGTRasterFormat;
 import mil.nga.giat.geowave.adapter.vector.plugin.ExtractGeometryFilterVisitor;
 import mil.nga.giat.geowave.adapter.vector.plugin.GeoWaveGTDataStore;

extensions/formats/geotools-raster/src/main/java/mil/nga/giat/geowave/format/geotools/raster/GeoToolsRasterDataStoreIngestPlugin.java

@@ -6,15 +6,20 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.apache.log4j.Logger;
 import org.geotools.coverage.grid.GridCoverage2D;
 import org.geotools.coverage.grid.io.AbstractGridFormat;
 import org.geotools.coverage.grid.io.GridCoverage2DReader;
 import org.geotools.coverage.grid.io.GridFormatFinder;
+import org.geotools.factory.Hints;
+import org.geotools.referencing.CRS;
 import org.opengis.coverage.grid.GridCoverage;
+import org.opengis.referencing.crs.CoordinateReferenceSystem;
 
 import mil.nga.giat.geowave.adapter.raster.RasterUtils;
 import mil.nga.giat.geowave.adapter.raster.adapter.RasterDataAdapter;
@@ -38,7 +43,8 @@
 public class GeoToolsRasterDataStoreIngestPlugin implements
 		LocalFileIngestPlugin<GridCoverage>
 {
-	private final static Logger LOGGER = Logger.getLogger(GeoToolsRasterDataStoreIngestPlugin.class);
+	private final static Logger LOGGER = Logger.getLogger(
+			GeoToolsRasterDataStoreIngestPlugin.class);
 	private final RasterOptionProvider optionProvider;
 
 	public GeoToolsRasterDataStoreIngestPlugin() {
@@ -63,48 +69,134 @@ public void init(
 	@Override
 	public boolean supportsFile(
 			final File file ) {
-
-		final AbstractGridFormat format = GridFormatFinder.findFormat(file);
+		AbstractGridFormat format = null;
+		try {
+			format = GridFormatFinder.findFormat(
+					file);
+		}
+		catch (final Exception e) {
+			LOGGER.info(
+					"Unable to support as raster file",
+					e);
+		}
 		// the null check is enough and we don't need to check the format
 		// accepts this file because the finder should have previously validated
 		// this
 		return (format != null);
 	}
 
+	private static AbstractGridFormat prioritizedFindFormat(
+			final File input ) {
+		final AbstractGridFormat format = null;
+		try {
+			final Set<AbstractGridFormat> formats = GridFormatFinder.findFormats(
+					input);
+			if ((formats == null) || formats.isEmpty()) {
+				LOGGER.warn(
+						"Unable to support raster file " + input.getAbsolutePath());
+				return null;
+			}
+			// world image and geotiff can both open tif files, give
+			// priority to gdalgeotiff, followed by geotiff
+			for (final AbstractGridFormat f : formats) {
+				if ("GDALGeoTiff".equals(
+						f.getName())) {
+					return f;
+				}
+			}
+			for (final AbstractGridFormat f : formats) {
+				if ("GeoTIFF".equals(
+						f.getName())) {
+					return f;
+				}
+			}
+
+			// otherwise just pick the first
+			final Iterator<AbstractGridFormat> it = formats.iterator();
+			if (it.hasNext()) {
+				return it.next();
+			}
+		}
+		catch (final Exception e) {
+			LOGGER.warn(
+					"Error while trying read raster file",
+					e);
+			return null;
+		}
+		return format;
+	}
+
 	@Override
 	public CloseableIterator<GeoWaveData<GridCoverage>> toGeoWaveData(
 			final File input,
 			final Collection<ByteArrayId> primaryIndexIds,
 			final String globalVisibility ) {
-
-		final AbstractGridFormat format = GridFormatFinder.findFormat(input);
-		final GridCoverage2DReader reader = format.getReader(input);
+		final AbstractGridFormat format = prioritizedFindFormat(
+				input);
+		if (format == null) {
+			return new Wrapper(
+					Collections.emptyIterator());
+		}
+		Hints hints = null;
+		if ((optionProvider.getCrs() != null) && !optionProvider.getCrs().trim().isEmpty()) {
+			try {
+				final CoordinateReferenceSystem crs = CRS.decode(
+						optionProvider.getCrs());
+				if (crs != null) {
+					hints = new Hints();
+					hints.put(
+							Hints.DEFAULT_COORDINATE_REFERENCE_SYSTEM,
+							crs);
+				}
+			}
+			catch (final Exception e) {
+				LOGGER.warn(
+						"Unable to find coordinate reference system, continuing without hint",
+						e);
+			}
+		}
+		final GridCoverage2DReader reader = format.getReader(
+				input, hints);
 		if (reader == null) {
-			LOGGER.error("Unable to get reader instance, getReader returned null");
+			LOGGER.error(
+					"Unable to get reader instance, getReader returned null");
 			return new Wrapper(
 					Collections.emptyIterator());
 		}
 		try {
-			final GridCoverage2D coverage = reader.read(null);
+			final GridCoverage2D coverage = reader.read(
+					null);
 			if (coverage != null) {
 				final Map<String, String> metadata = new HashMap<String, String>();
 				final String coverageName = coverage.getName().toString();
-				final String[] mdNames = reader.getMetadataNames(coverageName);
-				if ((mdNames != null) && (mdNames.length > 0)) {
-					for (final String mdName : mdNames) {
-						metadata.put(
-								mdName,
-								reader.getMetadataValue(
-										coverageName,
-										mdName));
+				try {
+					// wrapping with try-catch block because often the reader
+					// does not support operations on coverage name
+					// if not, we just don't have metadata, and continue
+					final String[] mdNames = reader.getMetadataNames(
+							coverageName);
+					if ((mdNames != null) && (mdNames.length > 0)) {
+						for (final String mdName : mdNames) {
+							metadata.put(
+									mdName,
+									reader.getMetadataValue(
+											coverageName,
+											mdName));
+						}
 					}
 				}
+				catch (final Exception e) {
+					LOGGER.debug(
+							"Unable to find metadata from coverage reader",
+							e);
+				}
 				final List<GeoWaveData<GridCoverage>> coverages = new ArrayList<GeoWaveData<GridCoverage>>();
 
 				if (optionProvider.isSeparateBands() && (coverage.getNumSampleDimensions() > 1)) {
 					final String baseName = optionProvider.getCoverageName() != null ? optionProvider.getCoverageName()
 							: input.getName();
-					final double[][] nodata = optionProvider.getNodata(coverage.getNumSampleDimensions());
+					final double[][] nodata = optionProvider.getNodata(
+							coverage.getNumSampleDimensions());
 					for (int b = 0; b < coverage.getNumSampleDimensions(); b++) {
 						final RasterDataAdapter adapter = new RasterDataAdapter(
 								baseName + "_B" + b,
@@ -120,10 +212,11 @@ public CloseableIterator<GeoWaveData<GridCoverage>> toGeoWaveData(
 								new double[][] {
 									nodata[b]
 								});
-						coverages.add(new GeoWaveData<GridCoverage>(
-								adapter,
-								primaryIndexIds,
-								coverage));
+						coverages.add(
+								new GeoWaveData<GridCoverage>(
+										adapter,
+										primaryIndexIds,
+										coverage));
 					}
 				}
 				else {
@@ -135,11 +228,13 @@ public CloseableIterator<GeoWaveData<GridCoverage>> toGeoWaveData(
 							optionProvider.getTileSize(),
 							optionProvider.isBuildPyramid(),
 							optionProvider.isBuildHistogream(),
-							optionProvider.getNodata(coverage.getNumSampleDimensions()));
-					coverages.add(new GeoWaveData<GridCoverage>(
-							adapter,
-							primaryIndexIds,
-							coverage));
+							optionProvider.getNodata(
+									coverage.getNumSampleDimensions()));
+					coverages.add(
+							new GeoWaveData<GridCoverage>(
+									adapter,
+									primaryIndexIds,
+									coverage));
 				}
 				return new Wrapper(
 						coverages.iterator()) {
@@ -152,8 +247,9 @@ public void close()
 				};
 			}
 			else {
-				LOGGER.warn("Null grid coverage from file '" + input.getAbsolutePath()
-						+ "' for discovered geotools format '" + format.getName() + "'");
+				LOGGER.warn(
+						"Null grid coverage from file '" + input.getAbsolutePath()
+								+ "' for discovered geotools format '" + format.getName() + "'");
 			}
 		}
 		catch (final IOException e) {

extensions/formats/geotools-raster/src/main/java/mil/nga/giat/geowave/format/geotools/raster/RasterOptionProvider.java

@@ -14,10 +14,13 @@ public class RasterOptionProvider implements
 {
 
 	@Parameter(names = "--pyramid", description = "Build an image pyramid on ingest for quick reduced resolution query")
-	private boolean buildPyramid = RasterDataAdapter.DEFAULT_BUILD_PYRAMID;
+	private boolean buildPyramid = false;
 
+	@Parameter(names = "--crs", description = "A CRS override for the provided raster file")
+	private String crs = null;
+
 	@Parameter(names = "--histogram", description = "Build a histogram of samples per band on ingest for performing band equalization")
-	private boolean buildHistogream = RasterDataAdapter.DEFAULT_BUILD_HISTOGRAM;
+	private boolean buildHistogream = false;
 
 	@Parameter(names = "--tileSize", description = "Optional parameter to set the tile size stored (default is 256)")
 	private int tileSize = RasterDataAdapter.DEFAULT_TILE_SIZE;
@@ -45,6 +48,10 @@ public boolean isSeparateBands() {
 		return separateBands;
 	}
 
+	public String getCrs() {
+		return crs;
+	}
+
 	public String getCoverageName() {
 		if ((coverageName == null) || coverageName.trim().isEmpty()) {
 			return null;