Introduced NetCDF SEAGrid

calvalus-portal/src/main/java/com/bc/calvalus/portal/client/OrderL3ProductionView.java

@@ -113,7 +113,8 @@ public void onChange(ChangeEvent event) {
         l3ConfigForm.compositingPeriodLength.setValue(30);
 
         outputParametersForm = new OutputParametersForm(portalContext);
-        outputParametersForm.setAvailableOutputFormats("BEAM-DIMAP", "NetCDF", "NetCDF4", "GeoTIFF", "BigGeoTiff");
+        outputParametersForm.setAvailableOutputFormats("BEAM-DIMAP", "NetCDF", "NetCDF4", "NetCDF4-SEAGrid",
+                                                       "GeoTIFF", "BigGeoTiff");
 
         l2ConfigForm.setProductSet(productSetSelectionForm.getSelectedProductSet());
         updateTemporalParameters(productSetFilterForm.getValueMap());
@@ -279,4 +280,4 @@ public void setProductionParameters(Map<String, String> parameters) {
         l3ConfigForm.setValues(parameters);
         outputParametersForm.setValues(parameters);
     }
-}
+}

calvalus-processing/src/main/java/com/bc/calvalus/processing/l2/ProductFormatter.java

@@ -46,6 +46,8 @@
  */
 public class ProductFormatter {
 
+    public static final String FORMAT_NETCDF4_SEAGRID = "NetCDF4-SEAGrid";
+
     private static final Logger LOG = CalvalusLogger.getLogger();
 
     private final String outputFormat;
@@ -91,6 +93,12 @@ public ProductFormatter(String productName, String outputFormat, String desiredO
             outputExtension = ".nc";
             outputCompression = ""; // no further compression required
             outputFormat = "NetCDF4-BEAM"; // use NetCDF with BEAM extensions
+        } else if (outputFormat.equalsIgnoreCase(FORMAT_NETCDF4_SEAGRID)) {
+            outputExtension = ".nc";
+            outputCompression = ""; // already written as NetCDF-4
+            // L3Formatter uses the dedicated binning FormatterPlugin; ProductFormatter
+            // only provides the temporary file and HDFS copy, so no ProductWriterPlugIn
+            // is required.
         } else if (outputFormat.equals("GeoTIFF")) {
             outputExtension = ".tif";
             outputCompression = desiredOutputCompression;
@@ -107,20 +115,22 @@ public ProductFormatter(String productName, String outputFormat, String desiredO
         } else {
             outputCompression = desiredOutputCompression;
         }
-        // test if writer for output format exists
-        ProductIOPlugInManager registry = ProductIOPlugInManager.getInstance();
-        Iterator it = registry.getWriterPlugIns(outputFormat);
-        if(it.hasNext()) {
-            ProductWriterPlugIn plugIn = (ProductWriterPlugIn) it.next();
-            if (outputExtension.isEmpty()) {
-                // get output extension from writer
-                String[] defaultFileExtensions = plugIn.getDefaultFileExtensions();
-                if (defaultFileExtensions != null && defaultFileExtensions.length > 0) {
-                    outputExtension = defaultFileExtensions[0];
+        if (!FORMAT_NETCDF4_SEAGRID.equalsIgnoreCase(outputFormat)) {
+            // test if writer for output format exists
+            ProductIOPlugInManager registry = ProductIOPlugInManager.getInstance();
+            Iterator it = registry.getWriterPlugIns(outputFormat);
+            if(it.hasNext()) {
+                ProductWriterPlugIn plugIn = (ProductWriterPlugIn) it.next();
+                if (outputExtension.isEmpty()) {
+                    // get output extension from writer
+                    String[] defaultFileExtensions = plugIn.getDefaultFileExtensions();
+                    if (defaultFileExtensions != null && defaultFileExtensions.length > 0) {
+                        outputExtension = defaultFileExtensions[0];
+                    }
                 }
+            } else {
+                throw new IllegalArgumentException("Unsupported output format: " + outputFormat);
             }
-        } else {
-            throw new IllegalArgumentException("Unsupported output format: " + outputFormat);
         }
 
         if ("zip".equals(outputCompression)) {

calvalus-processing/src/main/java/com/bc/calvalus/processing/l3/L3Formatter.java

@@ -27,6 +27,7 @@
 import com.bc.ceres.binding.ConversionException;
 import com.bc.ceres.binding.Converter;
 import com.bc.ceres.binding.ConverterRegistry;
+import org.esa.snap.binning.operator.formatter.Formatter;
 import org.esa.snap.binning.operator.formatter.FormatterFactory;
 import org.esa.snap.binning.support.IsinPlanetaryGrid;
 import org.locationtech.jts.geom.Geometry;
@@ -36,7 +37,6 @@
 import org.esa.snap.binning.PlanetaryGrid;
 import org.esa.snap.binning.TemporalBinSource;
 import org.esa.snap.binning.operator.BinningConfig;
-import org.esa.snap.binning.operator.formatter.Formatter;
 import org.esa.snap.binning.operator.formatter.FormatterConfig;
 import org.esa.snap.core.datamodel.MetadataElement;
 import org.esa.snap.core.datamodel.Product;
@@ -89,25 +89,39 @@ private L3Formatter(String dateStart, String dateStop, String outputFile, String
         metadataSerializer = new MetadataSerializer();
     }
 
-    private void format(TemporalBinSource temporalBinSource, String regionName, String regionWKT) throws Exception {
-        Geometry regionGeometry = GeometryUtils.createGeometry(regionWKT);
-        final String processingHistoryXml = configuration.get(JobConfigNames.PROCESSING_HISTORY);
-        final MetadataElement processingGraphMetadata = metadataSerializer.fromXml(processingHistoryXml);
-        // TODO maybe replace region information in metadata if overwritten in formatting request
-        org.esa.snap.binning.operator.formatter.Formatter formatter;
-        if (planetaryGrid instanceof IsinPlanetaryGrid) {
+    private void format(TemporalBinSource temporalBinSource,
+                        String regionName,
+                        String regionWKT) throws Exception {
+        boolean useSeaGridNetcdfFormatter =
+                usesSeaGridNetcdfFormatter(formatterConfig.getOutputFormat());
+        Formatter formatter;
+        if (useSeaGridNetcdfFormatter) {
+            // SNAP's default formatter maps planetary grids to rectangular raster products.
+            // Select the Calvalus plugin by output format, not just by grid type, because
+            // existing SEA-grid requests may still require a standard raster product.
+            formatter = FormatterFactory.get(SeaGridFormatterPlugin.NAME);
+        } else if (planetaryGrid instanceof IsinPlanetaryGrid) {
             formatter = FormatterFactory.get("isin");
         } else {
             formatter = FormatterFactory.get("default");
         }
+
+        Geometry regionGeometry = null;
+        if (!useSeaGridNetcdfFormatter) {
+            regionGeometry = GeometryUtils.createGeometry(regionWKT);
+        }
+        final String processingHistoryXml = configuration.get(JobConfigNames.PROCESSING_HISTORY);
+        final MetadataElement processingGraphMetadata = metadataSerializer.fromXml(processingHistoryXml);
+        // TODO maybe replace region information in metadata if overwritten in formatting request
+        MetadataElement[] metadataElements = new MetadataElement[]{processingGraphMetadata};
         formatter.format(planetaryGrid,
                 temporalBinSource,
                 featureNames,
                 formatterConfig,
                 regionGeometry,
                 startTime,
                 endTime,
-                processingGraphMetadata);
+                metadataElements);
     }
 
     private static ProductData.UTC parseTime(String timeString) {
@@ -174,6 +188,10 @@ public static void write(TaskInputOutputContext context, TemporalBinSource tempo
         }
     }
 
+    static boolean usesSeaGridNetcdfFormatter(String outputFormat) {
+        return ProductFormatter.FORMAT_NETCDF4_SEAGRID.equalsIgnoreCase(outputFormat);
+    }
+
     private static class ProductConverter implements Converter<Product> {
 
         private final Configuration conf;

calvalus-processing/src/main/java/com/bc/calvalus/processing/l3/SeaGridFormatter.java

@@ -0,0 +1,67 @@
+/*
+ * Copyright (C) 2010 Brockmann Consult GmbH (info@brockmann-consult.de)
+ *
+ * This program is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License as published by the Free
+ * Software Foundation; either version 3 of the License, or (at your option)
+ * any later version.
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program; if not, see http://www.gnu.org/licenses/
+ */
+
+package com.bc.calvalus.processing.l3;
+
+import com.bc.calvalus.commons.CalvalusLogger;
+import com.bc.calvalus.processing.l2.ProductFormatter;
+import org.esa.snap.binning.PlanetaryGrid;
+import org.esa.snap.binning.TemporalBinSource;
+import org.esa.snap.binning.operator.formatter.Formatter;
+import org.esa.snap.binning.operator.formatter.FormatterConfig;
+import org.esa.snap.binning.support.SEAGrid;
+import org.esa.snap.core.datamodel.MetadataElement;
+import org.esa.snap.core.datamodel.ProductData;
+import org.locationtech.jts.geom.Geometry;
+
+import java.io.File;
+import java.util.logging.Logger;
+
+/**
+ * Formats a SNAP {@link SEAGrid} as the flattened NetCDF layout required by
+ * {@link ProductFormatter#FORMAT_NETCDF4_SEAGRID}.
+ */
+final class SeaGridFormatter implements Formatter {
+
+    private static final Logger LOG = CalvalusLogger.getLogger();
+
+    @Override
+    public void format(PlanetaryGrid planetaryGrid,
+                       TemporalBinSource temporalBinSource,
+                       String[] featureNames,
+                       FormatterConfig formatterConfig,
+                       Geometry regionGeometry,
+                       ProductData.UTC startTime,
+                       ProductData.UTC endTime,
+                       MetadataElement... metadataElements) throws Exception {
+        if (!(planetaryGrid instanceof SEAGrid)) {
+            throw new IllegalArgumentException(
+                    ProductFormatter.FORMAT_NETCDF4_SEAGRID +
+                    " requires org.esa.snap.binning.support.SEAGrid, but the request uses " +
+                    planetaryGrid.getClass().getName());
+        }
+
+        LOG.info("Using flattened SEAGrid NetCDF formatter for output format " +
+                 ProductFormatter.FORMAT_NETCDF4_SEAGRID + '.');
+        SeaGridNetcdfFormatter.write(new File(formatterConfig.getOutputFile()),
+                                     (SEAGrid) planetaryGrid,
+                                     temporalBinSource,
+                                     featureNames,
+                                     startTime,
+                                     endTime,
+                                     metadataElements);
+    }
+}

calvalus-processing/src/main/java/com/bc/calvalus/processing/l3/SeaGridFormatterPlugin.java

@@ -0,0 +1,39 @@
+/*
+ * Copyright (C) 2010 Brockmann Consult GmbH (info@brockmann-consult.de)
+ *
+ * This program is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License as published by the Free
+ * Software Foundation; either version 3 of the License, or (at your option)
+ * any later version.
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ * more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program; if not, see http://www.gnu.org/licenses/
+ */
+
+package com.bc.calvalus.processing.l3;
+
+import org.esa.snap.binning.operator.formatter.Formatter;
+import org.esa.snap.binning.operator.formatter.FormatterPlugin;
+
+/**
+ * Makes the Calvalus flattened SEA-grid formatter available to SNAP's
+ * {@code FormatterFactory}.
+ */
+public final class SeaGridFormatterPlugin implements FormatterPlugin {
+
+    static final String NAME = "seagrid";
+
+    @Override
+    public String getName() {
+        return NAME;
+    }
+
+    @Override
+    public Formatter create() {
+        return new SeaGridFormatter();
+    }
+}