Merge pull request #195 from JohnLCaron/removeBtree1

Remove BTree1, H5TiledData1, H5chunkIterator.

Author: JohnLCaron

cli/build.gradle.kts

@@ -3,7 +3,7 @@
 }
 
 dependencies {
-    implementation(project(":core"))
+    api(project(":core"))
 
     implementation(libs.lzf)
     implementation(libs.lz4)
@@ -33,4 +33,4 @@ tasks.register<Jar>("uberJar") {
     })
 }
 
-project.tasks["compileJava"].dependsOn(":core:allMetadataJar")
+// project.tasks["compileJava"].dependsOn(":core:allMetadataJar")

core/src/commonMain/kotlin/com/sunya/cdm/api/Variable.kt

@@ -51,6 +51,10 @@ data class Variable<T>(
         return "$datatype ${fullname()}${shape.contentToString()}"
     }
 
+    override fun toString(): String {
+        return "Variable(${nameAndShape()}, group=${group.fullname()}, nelems=$nelems, spObject=$spObject)"
+    }
+
     @InternalLibraryApi
     class Builder<T>(val name : String, val datatype : Datatype<T>) {
         val dimensions = mutableListOf<Dimension>()

core/src/commonMain/kotlin/com/sunya/cdm/array/StructureMember.kt

@@ -1,3 +1,5 @@
+@file:OptIn(ExperimentalUnsignedTypes::class)
+
 package com.sunya.cdm.array
 
 import com.sunya.cdm.api.Datatype

core/src/commonMain/kotlin/com/sunya/netchdf/hdf4/Hdf4File.kt

@@ -46,17 +46,17 @@ class Hdf4File(val filename : String) : Netchdf {
         }
     }
 
-    override fun <T> chunkIterator(v2: Variable<T>, section: SectionPartial?, maxElements : Int?): Iterator<ArraySection<T>> {
+    override fun <T> chunkIterator(v2: Variable<T>, wantSection: SectionPartial?, maxElements : Int?): Iterator<ArraySection<T>> {
         if (v2.nelems == 0L) {
             return listOf<ArraySection<T>>().iterator()
         }
-        val wantSection = SectionPartial.fill(section, v2.shape)
+        val section = SectionPartial.fill(wantSection, v2.shape)
         val vinfo = v2.spObject as Vinfo
 
         return if (vinfo.isChunked) {  // LOOK isLinked?
-            H4chunkIterator(header, v2, wantSection)
+            H4chunkIterator(header, v2, section)
         } else {
-            H4maxIterator(v2, wantSection, maxElements ?: 100_000)
+            H4maxIterator(v2, section, maxElements ?: 100_000)
         }
     }
 

core/src/commonMain/kotlin/com/sunya/netchdf/hdf5/BTree1.kt

@@ -6,7 +6,7 @@ import com.sunya.cdm.iosp.OpenFileState
 import com.sunya.cdm.layout.Tiling
 import com.sunya.cdm.util.InternalLibraryApi
 
-/** B-tree, version 1, used for data (node type 1) */
+/** B-tree, version 1, used for data (node type 1)
 internal class BTree1(
     val h5: H5builder,
     val rootNodeAddress: Long,
@@ -130,7 +130,7 @@ internal class BTree1(
                 ", tile= ${tiling.tile(key.offsets).contentToString()}  idx=$idx"
     }
 
-}
+} */
 
 
 interface DataChunkIF {

core/src/commonMain/kotlin/com/sunya/netchdf/hdf5/BTree1data.kt

@@ -118,7 +118,7 @@ internal class BTree1data(
         override fun chunkSize() = key.chunkSize
         override fun filterMask() = key.filterMask
 
-        override fun show(tiling : Tiling) : String = "chunkSize=${key.chunkSize}, chunkStart=${offsets().contentToString()}" +
+        override fun show(tiling : Tiling) : String = "order=$key, chunkSize=${key.chunkSize}, chunkStart=${offsets().contentToString()}" +
                 ", tile= ${tiling.tile(offsets() ).contentToString()}"
 
         fun show() = show(tiling)

core/src/commonMain/kotlin/com/sunya/netchdf/hdf5/BTree2data.kt

@@ -306,6 +306,7 @@ internal class BTree2data(private val h5: H5builder, owner: String, address: Lon
         }
     }
 
+    // TODO this is probably not handling missing chunks correctly. See BTree1data, which iterates over tiles.
     fun chunkIterator() : Iterator<ChunkImpl> = ChunkIterator()
 
     private inner class ChunkIterator : AbstractIterator<ChunkImpl>() {

core/src/commonMain/kotlin/com/sunya/netchdf/hdf5/H5TiledData1.kt

@@ -4,7 +4,7 @@ import com.sunya.cdm.layout.IndexSpace
 import com.sunya.cdm.layout.IndexND
 import com.sunya.cdm.layout.Tiling
 
-/** wraps BTree1 to handle iterating through tiled data (aka chunked data) */
+/** wraps BTree1 to handle iterating through tiled data (aka chunked data)
 internal class H5TiledData1(val btree : BTree1, val varShape: LongArray, val chunkShape: LongArray) {
     private val check = true
     private val debug = false
@@ -104,4 +104,4 @@ internal class H5TiledData1(val btree : BTree1, val varShape: LongArray, val chu
         return "TiledData(chunk=${chunkShape.contentToString()}, readHit=$readHit, readMiss=$readMiss)"
     }
 
-}
+} */

core/src/commonMain/kotlin/com/sunya/netchdf/hdf5/H5cdmBuilder.kt

@@ -280,6 +280,11 @@ internal class DataContainerVariable(
             else -> throw RuntimeException()
         }
     }
+
+    override fun toString(): String {
+        return "DataContainerVariable(mdl=$mdl, mfp=$mfp, onlyFillValue=$onlyFillValue)"
+    }
+
 }
 
 internal fun getFillValue(h5 : H5builder, v5 : H5Variable, h5type: H5TypeInfo): ByteArray {

core/src/commonMain/kotlin/com/sunya/netchdf/hdf5/H5chunkIterator.kt

@@ -8,9 +8,7 @@ import com.sunya.cdm.layout.IndexSpace
 import com.sunya.cdm.layout.transferMissingNelems
 import com.sunya.cdm.util.InternalLibraryApi
 
-// TODO assumes BTree1, could it include BTree2? any chunked reader ?
-//   only used in Netchdf.readChunksConcurrent
-
+/*  (to be removed)
 @OptIn(InternalLibraryApi::class)
 internal class H5chunkIterator<T>(val h5 : H5builder, val v2: Variable<T>, val wantSection : Section) : AbstractIterator<ArraySection<T>>() {
     private val debugChunking = false
@@ -86,5 +84,5 @@ internal class H5chunkIterator<T>(val h5 : H5builder, val v2: Variable<T>, val w
 
         return ArraySection(array, intersectSpace.section(v2.shape)) // LOOK use space instead of Section ??
     }
-}
+} */