feat: add slice suport when going to-paintera

Author: cmhulbert

pom.xml

@@ -45,6 +45,8 @@
 
         <label-utilities-spark.version>1.2.0-SNAPSHOT</label-utilities-spark.version>
         <n5-spark.version>4.1.0-SNAPSHOT</n5-spark.version>
+        <n5-universe.version>3.1.0-SNAPSHOT</n5-universe.version>
+        <n5.version>4.0.2-SNAPSHOT</n5.version>
         <spark.version>3.5.4</spark.version>
         <spark-core_2.12.version>${spark.version}</spark-core_2.12.version>
         <jackson.version>2.15.4</jackson.version>

src/main/kotlin/org/janelia/saalfeldlab/conversion/to/scalar/ToScalar.kt

@@ -174,12 +174,23 @@ class ToScalar : Callable<Int> {
 				}
 			}
 
-			val chunksPerShard = this.chunksPerShard?.let { cps ->
-				when (cps.size) {
-					1 -> IntArray(3) { cps[0] }
-					3 -> cps.clone()
-					else -> throw InvalidBlockSize(cps, "chunks-per-shard has to be specified with one or three entries but got ${cps.joinToString(", ", "[", "]")}")
+			val chunksPerShard = this.chunksPerShard?.let { chunksPerShard ->
+				val argString = chunksPerShard.joinToString(", ", "[", "]")
+				val chunks = when (chunksPerShard.size) {
+					1 -> IntArray(3) { chunksPerShard[0] }
+					3 -> chunksPerShard.clone()
+					else -> throw InvalidBlockSize(chunksPerShard, "chunks-per-shard has to be specified with one or three entries but got $argString")
 				}
+
+				val zeroChunksAnyDim = chunks.any { it < 1 }
+				if (zeroChunksAnyDim)
+					throw InvalidBlockSize(chunksPerShard, "chunks-per-shard entries have to be positive but got $argString")
+
+				val oneChunkPerShard = chunks.all { it == 1 }
+				if (oneChunkPerShard)
+					throw InvalidBlockSize(chunksPerShard, "chunks-per-shard has to be greater than 1 in at least one dimension but got $argString")
+
+				chunks
 			}
 
 			val xyzUnit = this.xyzUnit.let { units ->

src/test/kotlin/org/janelia/saalfeldlab/conversion/NDSlicingToPainteraTest.kt

@@ -43,7 +43,7 @@ class NDSlicingToPainteraTest {
 				"-d", "labels",
 				"--type=label",
 				"--target-dataset=seg",
-				"--slice-positions", "x,y,z,1", // axis0→x, axis1→y, axis2→z, channel axis fixed at 1
+				"--slice-positions", "x,y,z,1", // axis0→x, axis1→y, axis2→z, channel axis sliced at 1
 				"--dataset-resolution", "1,1,1"
 			)
 		)
@@ -53,11 +53,11 @@ class NDSlicingToPainteraTest {
 		val s0 = reader.getDatasetAttributes("seg/data/s0")
 		assertEquals(listOf(6L, 7L, 8L), s0.dimensions.toList(), "s0 is the 3D sliced shape (x,y,z)")
 
-		/* the indices are derived from s0, so they must carry the sliced shape too */
+		/* the indices are derived from s0, so they have the sliced shape too */
 		assertTrue(reader.datasetExists("seg/unique-labels/s0"), "unique-labels index exists")
 		assertEquals(listOf(6L, 7L, 8L), reader.getDatasetAttributes("seg/unique-labels/s0").dimensions.toList(), "unique-labels has sliced shape")
 
-		/* the LMT round-trips the c=1 slice voxel-for-voxel */
+		/* the LMT matches the c=1 slice voxel-for-voxel */
 		val lmt = N5LabelMultisets.openLabelMultiset(reader, "seg/data/s0")
 		val ra = lmt.randomAccess()
 		for (x in 0 until 6) for (y in 0 until 7) for (z in 0 until 8) {

src/test/kotlin/org/janelia/saalfeldlab/conversion/ToScalarZarr3OutputTest.kt

@@ -160,7 +160,7 @@ class ToScalarZarr3OutputTest {
 			.count { it.isFile && it.name != "zarr.json" }
 		assertEquals(1, shardFiles)
 
-		/* the 3 skipped shards read back as the fill value (0); the one voxel round-trips */
+		/* the 3 skipped shards read back as the fill value (0); the one voxel reads back unchanged */
 		val reader = createReader(outputPath)
 		LoopBuilder.setImages(sparseImg, N5Utils.open<UnsignedLongType>(reader, outputDataset))
 			.forEachPixel(BiConsumer { e: UnsignedLongType, a: UnsignedLongType -> assertTrue(e.valueEquals(a)) })
@@ -196,7 +196,7 @@ class ToScalarZarr3OutputTest {
 	@Test
 	fun `to-scalar sharded zarr3 keeps within-shard chunk sparsity`() {
 		/* one whole shard of 2x2x2 chunks (block 3, chunks-per-shard 2 -> shard 6); chunk (1,1,1) is all fill (0)
-		 * while the other seven carry data, so the shard is written but that chunk must be omitted, not materialized */
+		 * while the other seven hold data, so the shard is written but that chunk must be omitted, not written out */
 		val chunkDims = longArrayOf(6, 6, 6)
 		val img = ArrayImgs.unsignedLongs(LongArray((6 * 6 * 6)) { 7L }, *chunkDims)
 		val ra = img.randomAccess()
@@ -230,7 +230,7 @@ class ToScalarZarr3OutputTest {
 		assertNull(reader.readChunk<LongArray>(outputDataset, attrs, *longArrayOf(1, 1, 1)), "all-fill inner chunk should be omitted")
 		assertNotNull(reader.readChunk<LongArray>(outputDataset, attrs, *longArrayOf(0, 0, 0)), "data inner chunk should be present")
 
-		/* and it still round-trips: the omitted chunk reads back as fill 0 */
+		/* the omitted chunk still reads back as fill 0 */
 		LoopBuilder.setImages(img, N5Utils.open<UnsignedLongType>(reader, outputDataset))
 			.forEachPixel(BiConsumer { e: UnsignedLongType, a: UnsignedLongType -> assertTrue(e.valueEquals(a)) })
 	}