Skip to content

Commit

Permalink
clean up
Browse files Browse the repository at this point in the history
  • Loading branch information
Hailey Johnson committed Mar 15, 2024
1 parent 31b8087 commit 7689b84
Show file tree
Hide file tree
Showing 2 changed files with 73 additions and 31 deletions.
63 changes: 52 additions & 11 deletions cdm/core/src/main/java/ucar/nc2/dataset/VariableDS.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,8 @@ protected VariableDS(VariableDS vds, boolean isCopy) {
this.unsignedConversion = vds.unsignedConversion;
this.scaleOffset = vds.scaleOffset;
this.convertMissing = vds.convertMissing;
this.fillValue = vds.getFillValue();
this.hasFillValue = vds.hasFillValue();

// Add this so that old VariableDS units agrees with new VariableDS units.
String units = vds.getUnitsString();
Expand Down Expand Up @@ -556,8 +558,8 @@ public Array getMissingDataArray(int[] shape) {
}

Array array = Array.factoryConstant(getDataType(), shape, storage);
if (convertMissing != null && convertMissing.hasFillValue()) {
array.setObject(0, convertMissing.getFillValue());
if (hasFillValue) {
array.setObject(0, fillValue);
}
return array;
}
Expand Down Expand Up @@ -661,7 +663,7 @@ public boolean isMissing(double val) {
if (Double.isNaN(val)) {
return true;
}
return convertMissing != null && convertMissing.isMissing(val);
return convertMissing != null && convertMissing.isMissing(packVal(val));
}

@Override
Expand All @@ -671,32 +673,46 @@ public boolean hasValidData() {

@Override
public double getValidMin() {
return convertMissing != null ? convertMissing.getValidMin() : -Double.MAX_VALUE;
if (convertMissing == null) {
return -Double.MAX_VALUE;
}
if (scaleOffset == null) {
return convertMissing.getValidMin();
}
return scaleOffset.getScaleFactor() < 0 ? unpackVal(convertMissing.getValidMax())
: unpackVal(convertMissing.getValidMin());
}

@Override
public double getValidMax() {
return convertMissing != null ? convertMissing.getValidMax() : Double.MAX_VALUE;
if (convertMissing == null) {
return Double.MAX_VALUE;
}
if (scaleOffset == null) {
return convertMissing.getValidMax();
}
return scaleOffset.getScaleFactor() < 0 ? unpackVal(convertMissing.getValidMin())
: unpackVal(convertMissing.getValidMax());
}

@Override
public boolean isInvalidData(double val) {
return convertMissing != null && convertMissing.isInvalidData(val);
return convertMissing != null && convertMissing.isInvalidData(packVal(val));
}

@Override
public boolean hasFillValue() {
return convertMissing != null && convertMissing.hasFillValue();
return hasFillValue;
}

@Override
public double getFillValue() {
return convertMissing != null ? convertMissing.getFillValue() : Double.NaN;
return fillValue;
}

@Override
public boolean isFillValue(double val) {
return convertMissing != null && convertMissing.isFillValue(val);
return convertMissing != null && convertMissing.isFillValue(packVal(val));
}

@Override
Expand All @@ -706,12 +722,28 @@ public boolean hasMissingValue() {

@Override
public double[] getMissingValues() {
return convertMissing != null ? convertMissing.getMissingValues() : new double[] {0};
if (convertMissing == null) {
return new double[] {0};
}
double[] missingVals = convertMissing.getMissingValues();
double[] vals = new double[missingVals.length];
for (int i = 0; i < missingVals.length; i++) {
vals[i] = unpackVal(missingVals[i]);
}
return vals;
}

@Override
public boolean isMissingValue(double val) {
return convertMissing != null && convertMissing.isMissingValue(val);
return convertMissing != null && convertMissing.isMissingValue(packVal(val));
}

private double unpackVal(double val) {
return scaleOffset != null && !Double.isNaN(val) ? scaleOffset.convert(val) : val;
}

private double packVal(double val) {
return scaleOffset != null && !Double.isNaN(val) ? scaleOffset.applyScaleOffset(val) : val;
}

/** @deprecated Use NetcdfDataset.builder() */
Expand Down Expand Up @@ -831,6 +863,8 @@ public Array convert(Array in, boolean convertUnsigned, boolean applyScaleOffset
protected DataType orgDataType; // keep separate for the case where there is no orgVar.
protected String orgName; // in case Variable was renamed, and we need to keep track of the original name
String orgFileTypeId; // the original fileTypeId.
private boolean hasFillValue = false;
private double fillValue = Double.MAX_VALUE;

protected VariableDS(Builder<?> builder, Group parentGroup) {
super(builder, parentGroup);
Expand All @@ -857,6 +891,13 @@ protected VariableDS(Builder<?> builder, Group parentGroup) {
this.scaleOffset = builder.scaleOffset;

createEnhancements();
if (convertMissing != null) {
fillValue = unpackVal(convertMissing.getFillValue());
hasFillValue = true;
} else {
fillValue = ConvertMissing.getFillValueOrDefault(this);
hasFillValue = !Double.isNaN(fillValue);
}

// We have to complete this after the NetcdfDataset is built.
this.coordSysNames = builder.coordSysNames;
Expand Down
41 changes: 21 additions & 20 deletions cdm/core/src/main/java/ucar/nc2/filter/ConvertMissing.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,26 +62,8 @@ public static ConvertMissing createFromVariable(VariableDS var) {
}

/// fill_value
boolean hasFillValue = var.hasFillValue();
double fillValue = var.getFillValue();
// need fill value info before convertMissing
Attribute fillValueAtt = var.findAttribute(CDM.FILL_VALUE);
if (fillValueAtt != null && !fillValueAtt.isString()) {
DataType fillType = FilterHelpers.getAttributeDataType(fillValueAtt, var.getSignedness());
fillValue = var.convertUnsigned(fillValueAtt.getNumericValue(), fillType).doubleValue();
hasFillValue = true;
} else {
// No _FillValue attribute found. Instead, if file is NetCDF and variable is numeric, use the default fill value.
String ncfileId = var.getNetcdfFile() == null ? null : var.getNetcdfFile().getFileTypeId();
if (DataFormatType.NETCDF.getDescription().equals(ncfileId)
|| DataFormatType.NETCDF4.getDescription().equals(ncfileId)) {
DataType fillType = var.getDataType();
if (fillType.isNumeric()) {
fillValue = var.convertUnsigned(N3iosp.getFillValueDefault(fillType), fillType).doubleValue();
hasFillValue = true;
}
}
}
double fillValue = getFillValueOrDefault(var);
boolean hasFillValue = !Double.isNaN(fillValue);

/// missing_value
double[] missingValue = null;
Expand Down Expand Up @@ -267,4 +249,23 @@ public Array convertMissing(Array in) {

return out;
}

public static double getFillValueOrDefault(VariableDS var) {
// need fill value info before convertMissing
Attribute fillValueAtt = var.findAttribute(CDM.FILL_VALUE);
if (fillValueAtt != null && !fillValueAtt.isString()) {
DataType fillType = FilterHelpers.getAttributeDataType(fillValueAtt, var.getSignedness());
return var.convertUnsigned(fillValueAtt.getNumericValue(), fillType).doubleValue();
}
// No _FillValue attribute found. Instead, if file is NetCDF and variable is numeric, use the default fill value.
String ncfileId = var.getNetcdfFile() == null ? null : var.getNetcdfFile().getFileTypeId();
if (DataFormatType.NETCDF.getDescription().equals(ncfileId)
|| DataFormatType.NETCDF4.getDescription().equals(ncfileId)) {
DataType fillType = var.getDataType();
if (fillType.isNumeric()) {
return var.convertUnsigned(N3iosp.getFillValueDefault(fillType), fillType).doubleValue();
}
}
return Double.NaN;
}
}

0 comments on commit 7689b84

Please sign in to comment.