Java Code Examples for ucar.nc2.Variable#getElementSize()
The following examples show how to use
ucar.nc2.Variable#getElementSize() .
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Example 1
Source File: GtopoIosp.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 6 votes |
public Array readData(Variable v2, Section wantSection) throws IOException, InvalidRangeException { // raf.seek(0); raf.order(RandomAccessFile.BIG_ENDIAN); int size = (int) wantSection.computeSize(); short[] arr = new short[size]; LayoutRegular indexer = new LayoutRegular(0, v2.getElementSize(), v2.getShape(), wantSection); while (indexer.hasNext()) { Layout.Chunk chunk = indexer.next(); raf.seek(chunk.getSrcPos()); raf.readShort(arr, (int) chunk.getDestElem(), chunk.getNelems()); // copy into primitive array } return Array.factory(v2.getDataType(), wantSection.getShape(), arr); }
Example 2
Source File: H5diagNew.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 6 votes |
public void showCompress(Variable v, H5headerNew.Vinfo vinfo, Size total, Formatter f) throws IOException { H5objects.MessageDataspace mdt = vinfo.mds; long total_elems = 1; f.format("%8s %-40s(", v.getDataType(), v.getShortName()); for (int len : mdt.dimLength) { f.format("%d ", len); total_elems *= len; } boolean sizeOk = total_elems == v.getSize(); total_elems = v.getSize(); long nominalSize = total_elems * v.getElementSize(); Size size = new Size(nominalSize, 1); countStorageSize(vinfo, size); total.storage += size.storage; total.nominal += nominalSize; total.count += size.count; float ratio = (size.storage == 0) ? 0 : (float) nominalSize / size.storage; f.format(") == %d nelems %s == %d bytes storage = %d (%f) nchunks = %d%n", total_elems, sizeOk ? "" : "*", nominalSize, size.storage, ratio, size.count); }
Example 3
Source File: H5diag.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 6 votes |
public void showCompress(Variable v, H5header.Vinfo vinfo, Size total, Formatter f) throws IOException { H5header.MessageDataspace mdt = vinfo.mds; long total_elems = 1; f.format("%8s %-40s(", v.getDataType(), v.getShortName()); for (int len : mdt.dimLength) { f.format("%d ", len); total_elems *= len; } boolean sizeOk = total_elems == v.getSize(); total_elems = v.getSize(); long nominalSize = total_elems * v.getElementSize(); Size size = new Size(nominalSize, 1); countStorageSize(vinfo, size); total.storage += size.storage; total.nominal += nominalSize; total.count += size.count; float ratio = (size.storage == 0) ? 0 : (float) nominalSize / size.storage; f.format(") == %d nelems %s == %d bytes storage = %d (%f) nchunks = %d%n", total_elems, sizeOk ? "" : "*", nominalSize, size.storage, ratio, size.count); }
Example 4
Source File: NcStream.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
private static Builder encodeVar(Variable var, int sizeToCache) throws IOException { Builder builder = NcStreamProto.Variable.newBuilder(); builder.setName(var.getShortName()); builder.setDataType(convertDataType(var.getDataType())); if (var.getDataType().isEnum()) { EnumTypedef enumType = var.getEnumTypedef(); if (enumType != null) builder.setEnumType(enumType.getShortName()); } for (Dimension dim : var.getDimensions()) { builder.addShape(encodeDim(dim)); } for (Attribute att : var.attributes()) { builder.addAtts(encodeAtt(att)); } // put small amounts of data in header "immediate mode" if (var.isCaching() && var.getDataType().isNumeric()) { if (var.isCoordinateVariable() || var.getSize() * var.getElementSize() < sizeToCache) { Array data = var.read(); ByteBuffer bb = data.getDataAsByteBuffer(); builder.setData(ByteString.copyFrom(bb.array())); } } return builder; }
Example 5
Source File: N3iospWriter.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
@Override public void writeData(Variable v2, Section section, Array values) throws java.io.IOException, InvalidRangeException { N3headerNew.Vinfo vinfo = (N3headerNew.Vinfo) v2.getSPobject(); DataType dataType = v2.getDataType(); if (v2.isUnlimited()) { Range firstRange = section.getRange(0); setNumrecs(firstRange.last() + 1); } if (v2 instanceof Structure) { if (!(values instanceof ArrayStructure)) throw new IllegalArgumentException("writeData for Structure: data must be ArrayStructure"); if (v2.getRank() == 0) throw new IllegalArgumentException("writeData for Structure: must have rank > 0"); Dimension d = v2.getDimension(0); if (!d.isUnlimited()) throw new IllegalArgumentException("writeData for Structure: must have unlimited dimension"); writeRecordData((Structure) v2, section, (ArrayStructure) values); } else { Layout layout = (!v2.isUnlimited()) ? new LayoutRegular(vinfo.begin, v2.getElementSize(), v2.getShape(), section) : new LayoutRegularSegmented(vinfo.begin, v2.getElementSize(), header.recsize, v2.getShape(), section); writeData(values, layout, dataType); } }
Example 6
Source File: N3iospWriter.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
private void writeRecordData(ucar.nc2.Structure s, int recnum, StructureData sdata) throws java.io.IOException, ucar.ma2.InvalidRangeException { StructureMembers members = sdata.getStructureMembers(); // loop over members for (Variable vm : s.getVariables()) { StructureMembers.Member m = members.findMember(vm.getShortName()); if (null == m) continue; // this means that the data is missing from the ArrayStructure // convert String member data into CHAR data Array data = sdata.getArray(m); if (data instanceof ArrayObject && vm.getDataType() == DataType.CHAR && vm.getRank() > 0) { int strlen = vm.getShape(vm.getRank() - 1); data = ArrayChar.makeFromStringArray((ArrayObject) data, strlen); // turn it into an ArrayChar } // layout of the destination N3headerNew.Vinfo vinfo = (N3headerNew.Vinfo) vm.getSPobject(); long begin = vinfo.begin + recnum * header.recsize; // this assumes unlimited dimension Section memberSection = vm.getShapeAsSection(); Layout layout = new LayoutRegular(begin, vm.getElementSize(), vm.getShape(), memberSection); try { writeData(data, layout, vm.getDataType()); } catch (Exception e) { log.error("Error writing member=" + vm.getShortName() + " in struct=" + s.getFullName(), e); throw new IOException(e); } } }
Example 7
Source File: Nc4ChunkingStrategyGrib.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
@Override public boolean isChunked(Variable v) { if (v.isUnlimited()) return true; // if (getChunkAttribute(v) != null) return true; int n = v.getRank(); return n >= 2 && v.getSize() * v.getElementSize() > getMinVariableSize(); }
Example 8
Source File: Nc4ChunkingDefault.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
@Override public boolean isChunked(Variable v) { if (v.isUnlimited()) return true; // if (getChunkAttribute(v) != null) return true; long size = v.getSize() * v.getElementSize(); return (size > minVariableSize); }
Example 9
Source File: NetcdfCopier.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
private void copyVariableData(NetcdfFormatWriter ncwriter, Group groupIn, Group groupOut, Count counter, CancelTask cancel) throws IOException { for (Variable oldVar : groupIn.getVariables()) { if (cancel.isCancel()) { break; } Variable newVar = groupOut.findVariableLocal(oldVar.getShortName()); if (debug) { System.out.format("write var= %s size = %d type = %s%n", oldVar.getFullName(), oldVar.getSize(), oldVar.getDataType()); } cancel.setProgress("writing " + oldVar.getFullName(), counter.countVars++); long size = oldVar.getSize() * oldVar.getElementSize(); counter.bytes += size; if (size <= maxSize) { copyAll(ncwriter, oldVar, newVar); } else { copySome(ncwriter, oldVar, newVar, maxSize, cancel); } } for (Group nestedIn : groupIn.getGroups()) { if (cancel.isCancel()) { break; } Group nestedOut = groupOut.findGroupLocal(nestedIn.getShortName()); copyVariableData(ncwriter, nestedIn, nestedOut, counter, cancel); } }
Example 10
Source File: NetcdfFormatWriter.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
private long calcSize(Group group) { long totalSizeOfVars = 0; for (Variable var : group.getVariables()) { totalSizeOfVars += Dimensions.getSize(var.getDimensions()) * var.getElementSize(); } for (Group nested : group.getGroups()) { totalSizeOfVars += calcSize(nested); } return totalSizeOfVars; }
Example 11
Source File: TestHttpOpen.java From tds with BSD 3-Clause "New" or "Revised" License | 5 votes |
private long readAllData(NetcdfFile ncfile) throws IOException { System.out.println("------Open " + ncfile.getLocation()); long total = 0; for (Variable v : ncfile.getVariables()) { long nbytes = v.getSize() * v.getElementSize(); System.out.println(" Try to read variable " + v.getFullName() + " " + nbytes); v.read(); total += v.getSize() * v.getElementSize(); } ncfile.close(); return total; }
Example 12
Source File: CFGridWriter.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
private long processTransformationVars(ArrayList<Variable> varList, ArrayList<String> varNameList, NetcdfDataset ncd, ucar.nc2.dt.GridDataset gds, GridDatatype grid, Range timeRange, Range zRangeUse, Range yRange, Range xRange, int z_stride, int y_stride, int x_stride) throws InvalidRangeException { long varsSize = 0L; List<CoordinateTransform> cctt = grid.getCoordinateSystem().getCoordinateTransforms(); for (CoordinateTransform ct : cctt) { Parameter param = ct.findParameterIgnoreCase(CF.FORMULA_TERMS); if (param != null) { String[] varStrings = param.getStringValue().split(" "); for (int i = 1; i < varStrings.length; i += 2) { Variable paramVar = ncd.findVariable(varStrings[i].trim()); if (!varNameList.contains(varStrings[i]) && (null != paramVar)) { if (gds.findGridDatatype(paramVar.getFullName()) != null) { // Subset if needed if ((null != timeRange) || (zRangeUse != null) || (x_stride > 1 && y_stride > 1) || (yRange != null || xRange != null)) { GridDatatype complementaryGrid = gds.findGridDatatype(paramVar.getFullName()); complementaryGrid = complementaryGrid.makeSubset(null, null, timeRange, zRangeUse, yRange, xRange); paramVar = complementaryGrid.getVariable(); } } else { // Also have to subset the var if it is not a grid but has vertical dimension (the dimensionless vars in // the formula) and zRangeUse != null if (zRangeUse != null && paramVar.getRank() == 1) { List<Range> ranges = new ArrayList<Range>(); ranges.add(zRangeUse); paramVar = paramVar.section(ranges); } } varNameList.add(paramVar.getFullName()); varsSize += paramVar.getSize() * paramVar.getElementSize(); varList.add(paramVar); } } } } return varsSize; }
Example 13
Source File: NetcdfCopier.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
/** * Copies data from {@code oldVar} to {@code newVar}. The writes are done in a series of chunks no larger than * {@code maxChunkSize} * bytes. * * @param oldVar a variable from the original file to copy data from. * @param newVar a variable from the original file to copy data from. * @param maxChunkSize the size, <b>in bytes</b>, of the largest chunk to write. * @param cancel allow user to cancel, may be null. * @throws IOException if an I/O error occurs. */ private void copySome(NetcdfFormatWriter ncwriter, Variable oldVar, Variable newVar, long maxChunkSize, CancelTask cancel) throws IOException { long maxChunkElems = maxChunkSize / oldVar.getElementSize(); long byteWriteTotal = 0; ChunkingIndex index = new ChunkingIndex(oldVar.getShape()); while (index.currentElement() < index.getSize()) { try { int[] chunkOrigin = index.getCurrentCounter(); int[] chunkShape = index.computeChunkShape(maxChunkElems); cancel.setProgress( "Reading chunk " + new Section(chunkOrigin, chunkShape) + " from variable: " + oldVar.getShortName(), -1); Array data = oldVar.read(chunkOrigin, chunkShape); if (!getOutputFormat().isNetdf4format() && oldVar.getDataType() == DataType.STRING) { data = convertDataToChar(newVar, data); } if (data.getSize() > 0) { // zero when record dimension = 0 cancel.setProgress( "Writing chunk " + new Section(chunkOrigin, chunkShape) + " from variable: " + oldVar.getShortName(), -1); ncwriter.write(newVar, chunkOrigin, data); if (debugWrite) { System.out.println(" write " + data.getSize() + " bytes at " + new Section(chunkOrigin, chunkShape)); } byteWriteTotal += data.getSize(); } index.setCurrentCounter(index.currentElement() + (int) Index.computeSize(chunkShape)); if (cancel.isCancel()) { return; } } catch (InvalidRangeException e) { e.printStackTrace(); throw new IOException(e.getMessage()); } } }