add downsample hack to SparkMaskedCLAHEMultiSEM, remove max parameter…

… from batch call
saalfeldlab · Nov 22, 2024 · 5cdfd83 · 5cdfd83
1 parent a11f40f
commit 5cdfd83
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Showing 2 changed files with 16 additions and 2 deletions.
diff --git 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
@@ -84,7 +84,6 @@ public static void main(final String... args) throws Exception {
 											 options.n5PathInput,
 											 n5DatasetInput,
 											 n5DatasetOutput,
-											 n5FieldMax,
 											 options.blockFactorXY,
 											 options.blockFactorZ,
 											 options.overwrite);