Fix BTree1data bug.

core/src/commonMain/kotlin/com/sunya/netchdf/NetchdfFile.kt

@@ -22,7 +22,7 @@ fun openNetchdfFile(filename : String, strict : Boolean = false) : Netchdf? {
             NetchdfFileFormat.NC_FORMAT_NETCDF4_CLASSIC  -> Hdf5File(useFilename, strict)
             NetchdfFileFormat.HDF5  -> Hdf5File(useFilename, strict)
             NetchdfFileFormat.HDF4  -> Hdf4File(useFilename)
-            else  -> null // throw RuntimeException(" unsupported NetcdfFileFormat $format")
+            else  -> null
         }
     }
 }
@@ -38,7 +38,7 @@ fun openNetchdfFileWithFormat(filename : String, format : NetchdfFileFormat) : N
             NetchdfFileFormat.NC_FORMAT_NETCDF4_CLASSIC  -> Hdf5File(useFilename, false)
             NetchdfFileFormat.HDF5  -> Hdf5File(useFilename, false)
             NetchdfFileFormat.HDF4  -> Hdf4File(useFilename)
-            else  -> null // throw RuntimeException(" unsupported NetcdfFileFormat $format")
+            else  -> null
         }
     }
 }

core/src/commonMain/kotlin/com/sunya/netchdf/NetchdfFileFormat.kt

@@ -185,7 +185,7 @@ enum class NetchdfFileFormat(private val version: Int, private val formatName: S
             val h5type = searchForwardHdf5(raf, magic)
             if (h5type != null) return h5type
 
-            val h4type = searchForwardHdf4(raf, magic)
+            val h4type = searchForwardHdf4(raf)
             return h4type ?: INVALID
         }
 
@@ -284,7 +284,7 @@ enum class NetchdfFileFormat(private val version: Int, private val formatName: S
             return null
         }
 
-        private fun searchForwardHdf4(raf: OpenFileIF, want: ByteArray): NetchdfFileFormat? {
+        private fun searchForwardHdf4(raf: OpenFileIF): NetchdfFileFormat? {
             val size: Long = raf.size()
             val state = OpenFileState(0L, true)
             var startPos = 0L

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

@@ -79,7 +79,6 @@ internal class LinkedByteSource(val h4 : H4builder,
     private val state : OpenFileState
     private var segno = -1
     private var segSize = 0
-    private var buffer = ByteArray(0)
     private var exhausted = false
     val totalSize: Int
 

core/src/commonMain/kotlin/com/sunya/netchdf/hdf4/H4builder.kt

@@ -65,7 +65,7 @@ class H4builder(val raf: OpenFileIF, val valueCharset: Charset) {
             val ndd: Int = raf.readShort(state).toUShort().toInt() // number of DD blocks
             link = raf.readInt(state).toUInt().toLong() // point to the next DDH; link == 0 means no more
             var pos = state.pos
-            for (i in 0 until ndd) {
+            repeat (ndd) {
                 val tag: Tag = readTag(raf, state)
                 pos += 12
                 state.pos = pos // tag usually changed the file pointer
@@ -425,7 +425,7 @@ class H4builder(val raf: OpenFileIF, val valueCharset: Charset) {
         }
 
         // compute the vb and add to the group
-        val vb = SDread(tagNDG!!, vgroup.name, group, dims) ?: return
+        val vb = SDread(tagNDG, vgroup.name, group, dims) ?: return
 
         // tagVH's on the group tag (TagVGroup) might be attributes
         tagVHs.forEach {
@@ -558,7 +558,7 @@ class H4builder(val raf: OpenFileIF, val valueCharset: Charset) {
             println("   **** NO dimensions found for SD ${dataGroup.refCode()}")
             return null
         }
-        val dimSDD = dimSDDout!!
+        val dimSDD = dimSDDout
 
         val nt: TagNT = tagidMap[tagid(dimSDD.data_nt_ref, TagEnum.NT.code)] as TagNT?
             ?: throw IllegalStateException("   **** NO nt tag found for SD ${dataGroup.refCode()}")

core/src/commonMain/kotlin/com/sunya/netchdf/hdf4/H4chunkIterator.kt

@@ -14,7 +14,6 @@ internal class H4chunkIterator<T>(h4 : H4builder, val v2: Variable<*>, val wantS
 
     private val vinfo = v2.spObject as Vinfo
     private val elemSize = vinfo.elemSize
-    private val datatype = v2.datatype
     private val wantSpace = IndexSpace(wantSection)
 
     private val tiledData : H4tiledData = H4tiledData(h4, v2.shape, vinfo.chunkLengths, vinfo.chunks!!)

core/src/commonMain/kotlin/com/sunya/netchdf/hdf4/H4tiledData.kt

@@ -43,7 +43,7 @@ internal class H4tiledData(val h4 : H4builder, varShape : LongArray, chunk : Int
 
 internal class H4CompressedDataChunk(
     val h4 : H4builder,
-    val offsets: IntArray,  // offset index of this chunk, reletive to entire array
+    val offsets: IntArray,  // offset index of this chunk, relative to entire array
     private val compress: SpecialComp?
 ) {
     fun isMissing() = (compress == null)

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

@@ -126,7 +126,7 @@ private fun transform(org: ODLgroup, trans: ODLgroup) {
     }
 
     if (wantName != null) {
-        val nestedTrans = ODLgroup(wantName!!, trans)
+        val nestedTrans = ODLgroup(wantName, trans)
         trans.nested.add(nestedTrans)
         if (org.variables.isNotEmpty()) {
             nestedTrans.variables.add(transformVariables(org))
@@ -234,7 +234,7 @@ internal fun ODLparseFromString(text: String): ODLgroup {
         } else if (line.startsWith("END")) {
             // noop
         } else if (currentObject != null) {
-            addFieldToObject(currentObject as ODLobject, line)
+            addFieldToObject(currentObject, line)
         } else {
             addFieldToGroup(currentStruct, line)
         }
@@ -399,7 +399,7 @@ class ODLparser(val rootGroup: Group.Builder, val show : Boolean = false) {
                             return false
                         }
                     } catch (ex : Exception) {
-                        logger.warn{" *** ODL cant parse dimension ${att.component1()} length ${att.component2()}"}
+                        logger.warn{" *** ODL cant parse dimension ${att.component1()} length ${att.component2()} message=${ex.message}"}
                         return false
                     }
                 }

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

@@ -657,7 +657,7 @@ internal class TagVH(icode: Int, refno: Int, offset : Long, length : Int) : Tag(
         fld_isize = IntArray(nfields) { h4.raf.readShort(state).toUShort().toInt() }
         fld_offset = IntArray(nfields) { h4.raf.readShort(state).toUShort().toInt() }
         fld_nelems = IntArray(nfields) { h4.raf.readShort(state).toUShort().toInt() } // "Order of the nth field of the Vdata (16-bit integer)"
-        for (i in 0 until nfields) {
+        repeat (nfields) {
             val slen = h4.raf.readShort(state).toInt()
             fld_name.add(h4.raf.readString(state, slen))
         }

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

@@ -102,7 +102,7 @@ enum class TagEnum(val desc: String, val code: Int) {
         fun byCode(code: Int): TagEnum {
             if (hashCodes == null) { // LOOK may fail when multithreading
                 val mapit = mutableMapOf<Int, TagEnum>()
-                values().forEach { mapit[it.code] = it}
+                entries.forEach { mapit[it.code] = it}
                 hashCodes = mapit
             }
             val te = hashCodes!![code]

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

@@ -75,7 +75,7 @@ internal class Vinfo(val refno: Int) : Comparable<Vinfo?> {
         return this
     }
 
-    // make sure needed info is present : call this when variable needs to be read
+    // make sure that the needed info is present: call this when variable needs to be read
     // this allows us to defer getting layout info until then
     fun setLayoutInfo(header: H4builder) {
         if (tagData == null) return

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

@@ -71,28 +71,19 @@ internal class BTree1data(
                         keyValues.add(Pair(order, DataChunk(key, childPointer)))
                         lastOrder = order
                     } else {
-                        children.add(BTreeNode(childPointer, this))
+                        children.add( BTreeNode(childPointer, this) )
                     }
                 }
+                if (children.isNotEmpty()) {
+                    lastOrder = children.last().lastOrder
+                }
             }
 
             // note there may be unused entries, "All nodes of a particular type of tree have the same maximum degree,
             // but most nodes will point to less than that number of children""
         }
 
-        // this does not have missing data. Use iterator on the Btree1data class
-        /*  return only the leaf nodes, in depth-first order
-        fun asSequence(): Sequence<Pair<Int, DataChunkIF>> = sequence {
-            // Handle child nodes recursively (in-order traversal)
-            if (children.isNotEmpty()) {
-                children.forEachIndexed { index, childNode ->
-                    yieldAll(childNode.asSequence()) // Yield all elements from the child
-                }
-            } else {  // If it's a leaf node (no children)
-                keyValues.forEach { yield(it) }
-            }
-        } */
-
+        // uses a tree search = O(log n)
         fun findDataChunk(wantOrder: Int): DataChunk? {
             if (children.isNotEmpty()) { // search tree; assumes that chunks are ordered
                 children.forEach { childNode ->
@@ -106,6 +97,10 @@ internal class BTree1data(
             return null
         }
 
+        override fun toString(): String {
+            return "BTreeNode(address=$address, level=$level, nentries=$nentries, lastOrder=$lastOrder)"
+        }
+
     }
 
     data class DataChunkKey(val order: Int, val chunkSize: Int, val filterMask : Int)
@@ -129,3 +124,13 @@ internal class BTree1data(
     }
 }
 
+interface DataChunkIF {
+    fun childAddress(): Long
+    fun offsets(): LongArray
+    fun isMissing(): Boolean
+    fun chunkSize(): Int
+    fun filterMask(): Int?
+
+    fun show(tiling : Tiling): String
+}
+

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

@@ -311,7 +311,6 @@ internal class BTree2data(private val h5: H5builder, owner: String, address: Lon
 
     private inner class ChunkIterator : AbstractIterator<ChunkImpl>() {
         var count = 0
-        var first = true
 
         override fun computeNext() {
             if (count >= records.size) {

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

@@ -7,6 +7,7 @@ import com.sunya.cdm.iosp.OpenFileState
 import com.sunya.cdm.util.InternalLibraryApi
 import java.util.*
 
+// DataLayoutExtensibleArray4
 class ExtensibleArrayIndex(val h5: H5builder, address: Long, datasetDimensions: IntArray, chunkDimensions: IntArray) {
     val raf = h5.raf
 

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

@@ -11,6 +11,7 @@ import kotlin.math.min
 
 val UNDEFINED_ADDRESS = -1L
 
+// the start of a port of jfhf FractalHeap. May not need it.
 class FractalHeapJ(val h5: H5builder, forWho: String, val fractalHeapAddress: Long) {
 
     val raf = h5.raf

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

@@ -28,7 +28,7 @@ internal class GroupSymbolTable(val btreeAddress : Long) {
         val nentries = h5.raf.readShort(state)
 
         var posEntry = state.pos
-        for (i in 0 until nentries) {
+        repeat (nentries.toInt()) {
             val entry = h5.readSymbolTable(state)
             posEntry += entry.dataSize
             if (entry.objectHeaderAddress != 0L) { // skip zeroes, probably a bug in HDF5 file format or docs, or me
@@ -58,7 +58,6 @@ internal fun H5builder.readSymbolTable(state : OpenFileState) : SymbolTableEntry
         }
     if (debugGroup) rootEntry.show()
 
-    // may be btree or symbolic link
     var btreeAddress : Long? = null
     var nameHeapAddress : Long? = null
     var linkOffset : Int? = null