diff --git a/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEM.java b/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEM.java index 45961801..faf6817b 100644 --- a/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEM.java +++ b/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEM.java @@ -10,6 +10,7 @@ import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.janelia.saalfeldlab.hotknife.util.Grid; +import org.janelia.saalfeldlab.hotknife.util.N5PathSupplier; import org.janelia.saalfeldlab.hotknife.util.Transform; import org.janelia.saalfeldlab.hotknife.util.Util; import org.janelia.saalfeldlab.n5.DataType; @@ -44,6 +45,8 @@ import net.imglib2.util.Intervals; import net.imglib2.view.Views; +import static org.janelia.saalfeldlab.n5.spark.downsample.scalepyramid.N5ScalePyramidSpark.downsampleScalePyramid; + public class SparkMaskedCLAHEMultiSEM { @SuppressWarnings({"FieldMayBeFinal", "unused"}) @@ -325,7 +328,19 @@ public static void main(final String... args) throws IOException, InterruptedExc final JavaSparkContext sparkContext = new JavaSparkContext(conf); sparkContext.setLogLevel("ERROR"); - process( sparkContext, options.n5PathInput, options.n5DatasetInput, options.n5DatasetOutput, options.blockFactorXY, options.blockFactorZ, options.overwrite ); + final String fullScaleInputDataset = options.n5DatasetInput + "/s0"; + final String outputDataset = options.n5DatasetInput + "_clahe"; + final String fullScaleOutputDataset = outputDataset + "/s0"; + final int[] downsampleFactors = new int[] { 2, 2, 1 }; + + process( sparkContext, options.n5PathInput, fullScaleInputDataset, fullScaleOutputDataset, options.blockFactorXY, options.blockFactorZ, options.overwrite ); + + downsampleScalePyramid(sparkContext, + new N5PathSupplier(options.n5PathInput), + fullScaleOutputDataset, + outputDataset, + downsampleFactors); + sparkContext.close(); } diff --git a/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEMBatch.java b/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEMBatch.java index 8549ab2f..828ec5fa 100644 --- a/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEMBatch.java +++ b/src/main/java/org/janelia/saalfeldlab/hotknife/SparkMaskedCLAHEMultiSEMBatch.java @@ -84,7 +84,6 @@ public static void main(final String... args) throws Exception { options.n5PathInput, n5DatasetInput, n5DatasetOutput, - n5FieldMax, options.blockFactorXY, options.blockFactorZ, options.overwrite);