Java Code Examples for ucar.ma2.DataType#STRUCTURE
The following examples show how to use
ucar.ma2.DataType#STRUCTURE .
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Example 1
Source File: GDVConvention.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 6 votes |
/** look for aliases. */ @Override protected void identifyCoordinateAxes() { for (VarProcess vp : varList) { if (vp.isCoordinateVariable) continue; if (vp.vb.dataType == DataType.STRUCTURE) continue; // cant be a structure String dimName = findAlias(vp.vb); if (dimName.isEmpty()) // none continue; rootGroup.findDimension(dimName).ifPresent(dim -> { vp.isCoordinateAxis = true; parseInfo.format(" Coordinate Axis added (GDV alias) = %s for dimension %s%n", vp.vb.getFullName(), dimName); }); } super.identifyCoordinateAxes(); // desperado identifyCoordinateAxesForce(); }
Example 2
Source File: Table.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 6 votes |
@Override public StructureDataIterator getStructureDataIterator(Cursor cursor) { StructureData parentStruct = cursor.getParentStructure(); StructureMembers members = parentStruct.getStructureMembers(); StructureMembers.Member m = members.findMember(nestedTableName); if (m.getDataType() == DataType.SEQUENCE) { ArraySequence seq = parentStruct.getArraySequence(m); return seq.getStructureDataIterator(); } else if (m.getDataType() == DataType.STRUCTURE) { ArrayStructure as = parentStruct.getArrayStructure(m); return as.getStructureDataIterator(); } throw new IllegalStateException("Cant find nested table member = " + nestedTableName); }
Example 3
Source File: NcDDS.java From tds with BSD 3-Clause "New" or "Revised" License | 6 votes |
private BaseType createScalarVariable(NetcdfFile ncfile, Variable v) { DataType dt = v.getDataType(); if (dt == DataType.DOUBLE) return new NcSDFloat64(v); else if (dt == DataType.FLOAT) return new NcSDFloat32(v); else if (dt == DataType.INT) return new NcSDInt32(v); else if (dt == DataType.UINT) return new NcSDUInt32(v); else if (dt == DataType.SHORT) return new NcSDInt16(v); else if (dt == DataType.USHORT) return new NcSDUInt16(v); else if ((dt == DataType.BYTE) || (dt == DataType.UBYTE)) return new NcSDByte(v); else if (dt == DataType.CHAR) return new NcSDString(v); else if (dt == DataType.STRING) return new NcSDString(v); else if (dt == DataType.STRUCTURE) return createStructure(ncfile, (Structure) v); else throw new UnsupportedOperationException("NcDDS Variable data type = " + dt); }
Example 4
Source File: CDMDSP.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
/** * Walk this variable, including fields, to construct sequence types * for any contained vlen dimensions * * @param cdmvar variable to walk */ protected void buildseqtypes(Variable cdmvar) throws DapException { if (CDMUtil.hasVLEN(cdmvar)) { buildseqtype(cdmvar); } if (cdmvar.getDataType() == DataType.STRUCTURE || cdmvar.getDataType() == DataType.SEQUENCE) { Structure struct = (Structure) cdmvar; List<Variable> fields = struct.getVariables(); for (int i = 0; i < fields.size(); i++) { Variable field = fields.get(i); buildseqtypes(field); // recurse for inner vlen dims } } }
Example 5
Source File: NcMLReaderNew.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
private StructureDS.Builder readStructureNew(Group.Builder groupBuilder, Element varElem) { String name = varElem.getAttributeValue("name"); String type = varElem.getAttributeValue("type"); DataType dtype = DataType.getType(type); // list of dimension names String dimNames = varElem.getAttributeValue("shape"); if (dimNames == null) { dimNames = ""; // deprecated, prefer explicit "" } List<Dimension> varDims = groupBuilder.makeDimensionsList(dimNames); StructureDS.Builder structBuilder; if (dtype == DataType.STRUCTURE) { structBuilder = StructureDS.builder().setName(name).addDimensions(varDims); } else { structBuilder = SequenceDS.builder().setName(name); } java.util.List<Element> varList = varElem.getChildren("variable", ncNS); for (Element vElem : varList) { readMemberVariable(groupBuilder, structBuilder, null, vElem); } // look for attributes java.util.List<Element> attList = varElem.getChildren("attribute", ncNS); for (Element attElem : attList) { readAtt(structBuilder.getAttributeContainer(), null, attElem); } return structBuilder; }
Example 6
Source File: TestPointDatasets.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 5 votes |
static private void checkData(StructureData sdata) { for (StructureMembers.Member member : sdata.getMembers()) { DataType dt = member.getDataType(); if (dt == DataType.FLOAT) { sdata.getScalarFloat(member); sdata.getJavaArrayFloat(member); } else if (dt == DataType.DOUBLE) { sdata.getScalarDouble(member); sdata.getJavaArrayDouble(member); } else if (dt == DataType.BYTE) { sdata.getScalarByte(member); sdata.getJavaArrayByte(member); } else if (dt == DataType.SHORT) { sdata.getScalarShort(member); sdata.getJavaArrayShort(member); } else if (dt == DataType.INT) { sdata.getScalarInt(member); sdata.getJavaArrayInt(member); } else if (dt == DataType.LONG) { sdata.getScalarLong(member); sdata.getJavaArrayLong(member); } else if (dt == DataType.CHAR) { sdata.getScalarChar(member); sdata.getJavaArrayChar(member); sdata.getScalarString(member); } else if (dt == DataType.STRING) { sdata.getScalarString(member); } if ((dt != DataType.STRING) && (dt != DataType.CHAR) && (dt != DataType.STRUCTURE) && (dt != DataType.SEQUENCE)) { sdata.convertScalarFloat(member.getName()); } } }
Example 7
Source File: CDMTypeFcns.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
public static DataType daptype2cdmtype(DapType type) { assert (type != null); switch (type.getTypeSort()) { case Char: return DataType.CHAR; case UInt8: return DataType.UBYTE; case Int8: return DataType.BYTE; case Int16: return DataType.SHORT; case UInt16: return DataType.USHORT; case Int32: return DataType.INT; case UInt32: return DataType.UINT; case Int64: return DataType.LONG; case UInt64: return DataType.ULONG; case Float32: return DataType.FLOAT; case Float64: return DataType.DOUBLE; case String: case URL: return DataType.STRING; case Opaque: return DataType.OPAQUE; case Enum: // Coverity[FB.BC_UNCONFIRMED_CAST] DapEnumeration dapenum = (DapEnumeration) type; switch (dapenum.getBaseType().getTypeSort()) { case Char: case UInt8: case Int8: return DataType.ENUM1; case Int16: case UInt16: return DataType.ENUM2; case Int32: case UInt32: return DataType.ENUM4; case Int64: case UInt64: // since there is no ENUM8, use ENUM4 return DataType.ENUM4; default: break; } break; case Structure: return DataType.STRUCTURE; case Sequence: return DataType.SEQUENCE; default: break; } return null; }
Example 8
Source File: NcStream.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
public static DataType convertDataType(ucar.nc2.stream.NcStreamProto.DataType dtype) { switch (dtype) { case CHAR: return DataType.CHAR; case BYTE: return DataType.BYTE; case SHORT: return DataType.SHORT; case INT: return DataType.INT; case LONG: return DataType.LONG; case FLOAT: return DataType.FLOAT; case DOUBLE: return DataType.DOUBLE; case STRING: return DataType.STRING; case STRUCTURE: return DataType.STRUCTURE; case SEQUENCE: return DataType.SEQUENCE; case ENUM1: return DataType.ENUM1; case ENUM2: return DataType.ENUM2; case ENUM4: return DataType.ENUM4; case OPAQUE: return DataType.OPAQUE; case UBYTE: return DataType.UBYTE; case USHORT: return DataType.USHORT; case UINT: return DataType.UINT; case ULONG: return DataType.ULONG; } throw new IllegalStateException("illegal data type " + dtype); }
Example 9
Source File: NcMLReaderNew.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
/** * Read the NcML variable element, and nested elements. * * @param groupBuilder put dimension into this group * @param refGroup parent Group in referenced dataset, may be null * @param varElem ncml variable element */ private void readVariable(Group.Builder groupBuilder, @Nullable Group refGroup, Element varElem) { String name = varElem.getAttributeValue("name"); if (name == null) { errlog.format("NcML Variable name is required (%s)%n", varElem); return; } String nameInFile = Optional.ofNullable(varElem.getAttributeValue("orgName")).orElse(name); DataType dtype = null; String typeS = varElem.getAttributeValue("type"); if (typeS != null) { dtype = DataType.getType(typeS); } // see if it already exists Variable refv = (refGroup == null) ? null : refGroup.findVariableLocal(nameInFile); Optional<Variable.Builder<?>> addedFromAgg = groupBuilder.findVariableLocal(nameInFile); if (refv == null && !addedFromAgg.isPresent()) { // new if (dtype == null) { errlog.format("NcML Variable dtype is required for new variable (%s)%n", name); return; } if (dtype == DataType.STRUCTURE || dtype == DataType.SEQUENCE) { groupBuilder.addVariable(readStructureNew(groupBuilder, varElem)); } else { groupBuilder.addVariable(readVariableNew(groupBuilder, dtype, varElem)); } return; } // refv exists if (refv != null) { if (dtype == null) { dtype = refv.getDataType(); } if (dtype == DataType.STRUCTURE || dtype == DataType.SEQUENCE) { readStructureExisting(groupBuilder, null, dtype, (Structure) refv, varElem) .ifPresent(groupBuilder::addVariable); } else { readVariableExisting(groupBuilder, null, dtype, refv, varElem).ifPresent(groupBuilder::addVariable); } return; } // refv does not exist, but addedFromAgg may be present DataType finalDtype = dtype; addedFromAgg.ifPresent(agg -> { if (agg instanceof VariableDS.Builder<?>) { VariableDS.Builder<?> aggDs = (VariableDS.Builder<?>) agg; aggDs.setOriginalName(nameInFile); } DataType reallyFinalDtype = finalDtype != null ? finalDtype : agg.dataType; augmentVariableNew(agg, reallyFinalDtype, varElem); }); }
Example 10
Source File: NcMLReaderNew.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
private Optional<StructureDS.Builder> readStructureExisting(Group.Builder groupBuilder, @Nullable StructureDS.Builder<?> parentStructure, DataType dtype, Structure refStructure, Element varElem) { String name = varElem.getAttributeValue("name"); String nameInFile = Optional.ofNullable(varElem.getAttributeValue("orgName")).orElse(name); StructureDS.Builder<?> structBuilder; if (this.explicit) { // all metadata is in the ncml, do not copy if (dtype == DataType.STRUCTURE) { structBuilder = StructureDS.builder().setName(name).setOriginalVariable(refStructure); } else { structBuilder = SequenceDS.builder().setName(name).setOriginalVariable(refStructure); } } else { // modify existing if (parentStructure != null) { structBuilder = (StructureDS.Builder<?>) parentStructure.findMemberVariable(nameInFile) .orElseThrow(() -> new IllegalStateException("Cant find variable " + nameInFile)); } else { structBuilder = (StructureDS.Builder<?>) groupBuilder.findVariableLocal(nameInFile) .orElseThrow(() -> new IllegalStateException("Cant find variable " + nameInFile)); } } String dimNames = varElem.getAttributeValue("shape"); // list of dimension names if (dimNames != null) { List<Dimension> varDims = groupBuilder.makeDimensionsList(dimNames); structBuilder.addDimensions(varDims); // TODO check conformable } java.util.List<Element> attList = varElem.getChildren("attribute", ncNS); for (Element attElem : attList) { readAtt(structBuilder.getAttributeContainer(), refStructure, attElem); } java.util.List<Element> varList = varElem.getChildren("variable", ncNS); for (Element vElem : varList) { readMemberVariable(groupBuilder, structBuilder, refStructure, vElem); } // process remove command java.util.List<Element> removeList = varElem.getChildren("remove", ncNS); for (Element remElem : removeList) { cmdRemove(structBuilder, remElem.getAttributeValue("type"), remElem.getAttributeValue("name")); } // look for logical views // processLogicalViews(v, refGroup, varElem); return (this.explicit) ? Optional.of(structBuilder) : Optional.empty(); }
Example 11
Source File: NcMLReaderNew.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
private void readMemberVariable(Group.Builder groupBuilder, StructureDS.Builder<?> parentStructure, @Nullable Structure refParentStructure, Element varElem) { String name = varElem.getAttributeValue("name"); if (name == null) { errlog.format("NcML Variable name is required (%s)%n", varElem); return; } String nameInFile = Optional.ofNullable(varElem.getAttributeValue("orgName")).orElse(name); DataType dtype = null; String typeS = varElem.getAttributeValue("type"); if (typeS != null) { dtype = DataType.getType(typeS); } // see if it already exists Variable refv = (refParentStructure == null) ? null : refParentStructure.findVariable(nameInFile); if (refv == null) { // new if (dtype == null) { errlog.format("NcML Variable dtype is required for new (nested) variable (%s)%n", name); return; } if (dtype == DataType.STRUCTURE || dtype == DataType.SEQUENCE) { parentStructure.addMemberVariable(readStructureNew(groupBuilder, varElem)); } else { parentStructure.addMemberVariable(readVariableNew(groupBuilder, dtype, varElem)); } return; } // refv exists if (dtype == null) { dtype = refv.getDataType(); } if (dtype == DataType.STRUCTURE || dtype == DataType.SEQUENCE) { readStructureExisting(groupBuilder, parentStructure, dtype, (Structure) refv, varElem) .ifPresent(parentStructure::addMemberVariable); } else { readVariableExisting(groupBuilder, parentStructure, dtype, refv, varElem) .ifPresent(parentStructure::addMemberVariable); } }
Example 12
Source File: H5headerNew.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
private TypeInfo calcNCtype(MessageDatatype mdt) { int hdfType = mdt.type; int byteSize = mdt.byteSize; byte[] flags = mdt.flags; // boolean unsigned = mdt.unsigned; TypeInfo tinfo = new TypeInfo(hdfType, byteSize); if (hdfType == 0) { // int, long, short, byte tinfo.dataType = getNCtype(hdfType, byteSize, mdt.unsigned); tinfo.endian = ((flags[0] & 1) == 0) ? RandomAccessFile.LITTLE_ENDIAN : RandomAccessFile.BIG_ENDIAN; tinfo.unsigned = ((flags[0] & 8) == 0); } else if (hdfType == 1) { // floats, doubles tinfo.dataType = getNCtype(hdfType, byteSize, mdt.unsigned); tinfo.endian = ((flags[0] & 1) == 0) ? RandomAccessFile.LITTLE_ENDIAN : RandomAccessFile.BIG_ENDIAN; } else if (hdfType == 2) { // time tinfo.dataType = DataType.STRING; tinfo.endian = ((flags[0] & 1) == 0) ? RandomAccessFile.LITTLE_ENDIAN : RandomAccessFile.BIG_ENDIAN; } else if (hdfType == 3) { // fixed length strings map to CHAR. String is used for Vlen type = 1. tinfo.dataType = DataType.CHAR; tinfo.vpad = (flags[0] & 0xf); // when elem length = 1, there is a problem with dimensionality. // eg char cr(2); has a storage_size of [1,1]. } else if (hdfType == 4) { // bit field tinfo.dataType = getNCtype(hdfType, byteSize, mdt.unsigned); } else if (hdfType == 5) { // opaque tinfo.dataType = DataType.OPAQUE; } else if (hdfType == 6) { // structure tinfo.dataType = DataType.STRUCTURE; } else if (hdfType == 7) { // reference tinfo.endian = RandomAccessFile.LITTLE_ENDIAN; tinfo.dataType = DataType.LONG; // file offset of the referenced object // LOOK - should get the object, and change type to whatever it is (?) } else if (hdfType == 8) { // enums if (tinfo.byteSize == 1) tinfo.dataType = DataType.ENUM1; else if (tinfo.byteSize == 2) tinfo.dataType = DataType.ENUM2; else if (tinfo.byteSize == 4) tinfo.dataType = DataType.ENUM4; else { log.warn("Illegal byte suze for enum type = {}", tinfo.byteSize); throw new IllegalStateException("Illegal byte suze for enum type = " + tinfo.byteSize); } // enumMap = mdt.map; } else if (hdfType == 9) { // variable length array tinfo.isVString = mdt.isVString; tinfo.isVlen = mdt.isVlen; if (mdt.isVString) { tinfo.vpad = ((flags[0] >> 4) & 0xf); tinfo.dataType = DataType.STRING; } else { tinfo.dataType = getNCtype(mdt.getBaseType(), mdt.getBaseSize(), mdt.base.unsigned); tinfo.endian = mdt.base.endian; tinfo.unsigned = mdt.base.unsigned; } } else if (hdfType == 10) { // array : used for structure members tinfo.endian = (mdt.getFlags()[0] & 1) == 0 ? RandomAccessFile.LITTLE_ENDIAN : RandomAccessFile.BIG_ENDIAN; if (mdt.isVString()) { tinfo.dataType = DataType.STRING; } else { int basetype = mdt.getBaseType(); tinfo.dataType = getNCtype(basetype, mdt.getBaseSize(), mdt.unsigned); } } else if (warnings) { log.debug("WARNING not handling hdf dataType = " + hdfType + " size= " + byteSize); } if (mdt.base != null) { tinfo.base = calcNCtype(mdt.base); } return tinfo; }
Example 13
Source File: H5headerNew.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
DataType getNCtype(int hdfType, int size, boolean unsigned) { if ((hdfType == 0) || (hdfType == 4)) { // integer, bit field DataType.Signedness signedness = unsigned ? DataType.Signedness.UNSIGNED : DataType.Signedness.SIGNED; if (size == 1) return DataType.BYTE.withSignedness(signedness); else if (size == 2) return DataType.SHORT.withSignedness(signedness); else if (size == 4) return DataType.INT.withSignedness(signedness); else if (size == 8) return DataType.LONG.withSignedness(signedness); else if (warnings) { log.debug("WARNING HDF5 file " + raf.getLocation() + " not handling hdf integer type (" + hdfType + ") with size= " + size); log.warn( "HDF5 file " + raf.getLocation() + " not handling hdf integer type (" + hdfType + ") with size= " + size); return null; } } else if (hdfType == 1) { if (size == 4) return DataType.FLOAT; else if (size == 8) return DataType.DOUBLE; else if (warnings) { log.debug("WARNING HDF5 file " + raf.getLocation() + " not handling hdf float type with size= " + size); log.warn("HDF5 file " + raf.getLocation() + " not handling hdf float type with size= " + size); return null; } } else if (hdfType == 3) { // fixed length strings. String is used for Vlen type = 1 return DataType.CHAR; } else if (hdfType == 6) { return DataType.STRUCTURE; } else if (hdfType == 7) { // reference return DataType.ULONG; } else if (hdfType == 9) { return null; // dunno } else if (warnings) { log.debug("WARNING not handling hdf type = " + hdfType + " size= " + size); log.warn("HDF5 file " + raf.getLocation() + " not handling hdf type = " + hdfType + " size= " + size); } return null; }
Example 14
Source File: NetcdfCopier.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 4 votes |
private Variable.Builder copyVariable(Group.Builder parent, Variable oldVar) throws IOException { Variable.Builder vb; DataType newType = oldVar.getDataType(); String dimNames = Dimensions.makeDimensionsString(oldVar.getDimensions()); if (newType == DataType.STRUCTURE) { Structure oldStruct = (Structure) oldVar; Structure.Builder sb = Structure.builder().setName(oldVar.getShortName()); for (Variable nested : oldStruct.getVariables()) { sb.addMemberVariable(copyVariable(parent, nested)); } vb = sb; } else { vb = Variable.builder().setName(oldVar.getShortName()).setDataType(newType); if (!extended && newType == DataType.STRING) { // find maximum length Array data = oldVar.read(); IndexIterator ii = data.getIndexIterator(); int max_len = 0; while (ii.hasNext()) { String s = (String) ii.getObjectNext(); max_len = Math.max(max_len, s.length()); } // add last dimension String strlenDimName = oldVar.getShortName() + "_strlen"; parent.addDimension(Dimension.builder(strlenDimName, max_len).setIsShared(false).build()); newType = DataType.CHAR; vb.setDataType(DataType.CHAR); dimNames += " " + strlenDimName; } } vb.setParentGroupBuilder(parent).setDimensionsByName(dimNames); if (newType.isEnum()) { EnumTypedef en = oldVar.getEnumTypedef(); vb.setEnumTypeName(en.getShortName()); } // attributes for (Attribute att : oldVar.attributes()) { vb.addAttribute(convertAttribute(att)); if (debug) { System.out.println("add varAtt= " + att); } } return vb; }
Example 15
Source File: Evaluator.java From netcdf-java with BSD 3-Clause "New" or "Revised" License | 2 votes |
/** * Does this dataset have a record structure? netcdf-3 specific * * @param ds in this dataset * @return true if record structure exists */ public static boolean hasNetcdf3RecordStructure(NetcdfDataset ds) { Variable v = ds.findVariable("record"); return (v != null) && (v.getDataType() == DataType.STRUCTURE); }