This is an automated email from the ASF dual-hosted git repository.
desruisseaux pushed a commit to branch geoapi-4.0
in repository https://gitbox.apache.org/repos/asf/sis.git
commit 5b8c29b65aef1d3543a37d6158a0026a61170437
Author: Martin Desruisseaux <martin.desruisse...@geomatys.com>
AuthorDate: Tue Nov 30 00:18:46 2021 +0100
Allow netCDF reader to distinguish "discrete coverage" from "continuous
coverage".
In GCOM-C case, the "QA_flag" (data quality) variable is a discrete
coverage.
---
.../java/org/apache/sis/coverage/Category.java | 8 +++----
.../org/apache/sis/coverage/SampleDimension.java | 10 ++++----
.../apache/sis/internal/earth/netcdf/GCOM_C.java | 16 +++++++++----
.../apache/sis/internal/netcdf/RasterResource.java | 10 +++++---
.../org/apache/sis/internal/netcdf/Variable.java | 2 ++
.../apache/sis/internal/netcdf/VariableRole.java | 27 +++++++++++++++++++---
.../sis/internal/netcdf/impl/ChannelDecoder.java | 6 +++--
.../apache/sis/storage/netcdf/MetadataReader.java | 2 +-
8 files changed, 60 insertions(+), 21 deletions(-)
diff --git
a/core/sis-feature/src/main/java/org/apache/sis/coverage/Category.java
b/core/sis-feature/src/main/java/org/apache/sis/coverage/Category.java
index 8d21e70..019c4ea 100644
--- a/core/sis-feature/src/main/java/org/apache/sis/coverage/Category.java
+++ b/core/sis-feature/src/main/java/org/apache/sis/coverage/Category.java
@@ -227,14 +227,14 @@ public class Category implements Serializable {
ArgumentChecks.ensureNonNull("samples", samples);
if (units != null) {
ArgumentChecks.ensureNonNull("toUnits", toUnits);
- // The converse is not true: we allow 'units' to be null even if
'toUnits' is non-null.
+ // The converse is not true: we allow `units` to be null even if
`toUnits` is non-null.
}
this.name = Types.toInternationalString(name);
final double minimum = samples.getMinDouble(true);
final double maximum = samples.getMaxDouble(true);
final boolean isNaN = Double.isNaN(minimum);
/*
- * Following arguments check uses '!' in comparison in order to reject
NaN values in quantitative category.
+ * Following arguments check uses `!` in comparison in order to reject
NaN values in quantitative category.
* For qualitative category, NaN is accepted provided that it is the
same NaN for both ends of the range.
*/
if (!(minimum <= maximum)) {
@@ -301,7 +301,7 @@ public class Category implements Serializable {
name = original.name;
toConverse = Objects.requireNonNull(toSamples);
/*
- * Compute 'minimum' and 'maximum' (which must be real numbers) using
the conversion from samples
+ * Compute `minimum` and `maximum` (which must be real numbers) using
the conversion from samples
* to real values. To be strict, we should use some numerical
algorithm for finding a function's
* minimum and maximum. For linear and logarithmic functions, minimum
and maximum are always at
* the bounding input values, so we are using a very simple algorithm
for now.
@@ -449,7 +449,7 @@ public class Category implements Serializable {
public Optional<MathTransform1D> getTransferFunction() {
/*
* Note: if this method is invoked on "real values category", then we
need to return
- * the identity transform instead of 'toConverse'. This is done by
ConvertedCategory.
+ * the identity transform instead of `toConverse`. This is done by
ConvertedCategory.
*/
if (converse.isConvertedQualitative()) {
return Optional.empty();
diff --git
a/core/sis-feature/src/main/java/org/apache/sis/coverage/SampleDimension.java
b/core/sis-feature/src/main/java/org/apache/sis/coverage/SampleDimension.java
index ce4e432..819634f 100644
---
a/core/sis-feature/src/main/java/org/apache/sis/coverage/SampleDimension.java
+++
b/core/sis-feature/src/main/java/org/apache/sis/coverage/SampleDimension.java
@@ -1033,7 +1033,7 @@ public class SampleDimension implements Serializable {
* @param name the category name as a {@link String} or {@link
InternationalString} object.
* @param minimum the minimum value (inclusive) in the given units.
* @param maximum the maximum value (inclusive) in the given units.
- * @param units the units of measurement.
+ * @param units the units of measurement, or {@code null} if
unknown or not applicable.
* @return {@code this}, for method call chaining.
* @throws IllegalArgumentException if a value is NaN or if {@code
minimum} is greater than {@code maximum}.
*/
@@ -1051,7 +1051,7 @@ public class SampleDimension implements Serializable {
* @param name the category name as a {@link String} or {@link
InternationalString} object.
* @param minimum the minimum value (inclusive) in the given units.
* @param maximum the maximum value (inclusive) in the given units.
- * @param units the units of measurement.
+ * @param units the units of measurement, or {@code null} if
unknown or not applicable.
* @return {@code this}, for method call chaining.
* @throws IllegalArgumentException if a value is NaN or if {@code
minimum} is greater than {@code maximum}.
*/
@@ -1075,7 +1075,8 @@ public class SampleDimension implements Serializable {
* @param upper the upper sample value, exclusive.
* @param scale the scale value which is multiplied to sample
values for the category. Must be different than zero.
* @param offset the offset value to add to sample values for this
category.
- * @param units the units of measurement of values after conversion
by the scale factor and offset.
+ * @param units the units of measurement of values after conversion
by the scale factor and offset,
+ * or {@code null} if unknown or not applicable.
* @return {@code this}, for method call chaining.
* @throws IllegalArgumentException if {@code lower} is not smaller
than {@code upper},
* or if {@code scale} or {@code offset} are not real numbers,
or if {@code scale} is zero.
@@ -1100,7 +1101,8 @@ public class SampleDimension implements Serializable {
* @param samples the minimum and maximum sample values in the
category. Element class is usually
* {@link Integer}, but {@link Float} and {@link
Double} types are accepted as well.
* @param toUnits the transfer function from sample values to real
values in the specified units.
- * @param units the units of measurement of values after
conversion by the transfer function.
+ * @param units the units of measurement of values after
conversion by the transfer function,
+ * or {@code null} if unknown or not applicable.
* @return {@code this}, for method call chaining.
* @throws ClassCastException if the range element class is not a
{@link Number} subclass.
* @throws IllegalArgumentException if the range is invalid.
diff --git
a/profiles/sis-japan-profile/src/main/java/org/apache/sis/internal/earth/netcdf/GCOM_C.java
b/profiles/sis-japan-profile/src/main/java/org/apache/sis/internal/earth/netcdf/GCOM_C.java
index ad4aebb..9df14da 100644
---
a/profiles/sis-japan-profile/src/main/java/org/apache/sis/internal/earth/netcdf/GCOM_C.java
+++
b/profiles/sis-japan-profile/src/main/java/org/apache/sis/internal/earth/netcdf/GCOM_C.java
@@ -113,7 +113,7 @@ import ucar.nc2.constants.CF;
*
* @author Alexis Manin (Geomatys)
* @author Martin Desruisseaux (Geomatys)
- * @version 1.1
+ * @version 1.2
*
* @see <a href="http://global.jaxa.jp/projects/sat/gcom_c/";>SHIKISAI (GCOM-C)
on JAXA</a>
* @see <a
href="https://en.wikipedia.org/wiki/Global_Change_Observation_Mission";>GCOM on
Wikipedia</a>
@@ -128,6 +128,11 @@ public final class GCOM_C extends Convention {
private static final Pattern SENTINEL_VALUE =
Pattern.compile(".*\\bGCOM-C\\b.*");
/**
+ * Name of the variable storing data quality flags.
+ */
+ private static final String QA_FLAG = "QA_flag";
+
+ /**
* Mapping from ACDD or CF-Convention attribute names to names of
attributes used by GCOM-C.
* This map does not include attributes for geographic extent because the
"Lower_left_latitude",
* "Lower_left_longitude", "Lower_right_latitude", <i>etc.</i> attributes
are difficult to use.
@@ -238,7 +243,7 @@ public final class GCOM_C extends Convention {
*/
@Override
public VariableRole roleOf(final Variable variable) {
- VariableRole role = super.roleOf(variable);
+ final VariableRole role = super.roleOf(variable);
if (role == VariableRole.COVERAGE) {
/*
* Exclude (for now) some variables associated to longitude and
latitude: Obs_time, Sensor_zenith, Solar_zenith.
@@ -246,7 +251,10 @@ public final class GCOM_C extends Convention {
*/
final String group = variable.getGroupName();
if (GEOMETRY_DATA.equalsIgnoreCase(group)) {
- role = VariableRole.OTHER;
+ return VariableRole.OTHER;
+ }
+ if (QA_FLAG.equals(variable.getName())) {
+ return VariableRole.DISCRETE_COVERAGE;
}
}
return role;
@@ -272,7 +280,7 @@ public final class GCOM_C extends Convention {
public String nameOfDimension(final Variable dataOrAxis, final int index) {
String name = super.nameOfDimension(dataOrAxis, index);
if (name == null) {
- if ("QA_flag".equals(dataOrAxis.getName())) {
+ if (QA_FLAG.equals(dataOrAxis.getName())) {
/*
* The "QA_flag" variable is missing "Dim0" and "Dim1"
attribute in GCOM-C version 1.00.
* However not all GCOM-C files use a localization grid. We
use the presence of spatial
diff --git
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/RasterResource.java
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/RasterResource.java
index 7fa5889..7001f2e 100644
---
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/RasterResource.java
+++
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/RasterResource.java
@@ -210,7 +210,7 @@ public final class RasterResource extends
AbstractGridResource implements Resour
final Map<GenericName,List<RasterResource>> byName = new HashMap<>();
// For detecting name collisions.
for (int i=0; i<variables.length; i++) {
final Variable variable = variables[i];
- if (variable == null || variable.getRole() !=
VariableRole.COVERAGE) {
+ if (!VariableRole.isCoverage(variable)) {
continue; //
Skip variables that are not grid coverages.
}
final GridGeometry grid = variable.getGridGeometry();
@@ -268,7 +268,7 @@ public final class RasterResource extends
AbstractGridResource implements Resour
int suffixLength = name.length() - suffixStart;
for (int j=i; ++j < variables.length;) {
final Variable candidate = variables[j];
- if (candidate == null || candidate.getRole() !=
VariableRole.COVERAGE) {
+ if (!VariableRole.isCoverage(candidate)) {
variables[j] = null;
// For avoiding to revisit that variable again.
continue;
}
@@ -504,7 +504,11 @@ public final class RasterResource extends
AbstractGridResource implements Resour
} else {
String name = band.getDescription();
if (name == null) name = band.getName();
- builder.addQuantitative(name, range, mt, band.getUnit());
+ if (band.getRole() == VariableRole.DISCRETE_COVERAGE) {
+ builder.addQualitative(name, range);
+ } else {
+ builder.addQuantitative(name, range, mt, band.getUnit());
+ }
}
} catch (TransformException e) {
/*
diff --git
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/Variable.java
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/Variable.java
index e71bfa5..55b301a 100644
---
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/Variable.java
+++
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/Variable.java
@@ -933,6 +933,8 @@ public abstract class Variable extends Node {
/**
* Builds the function converting values from their packed formats in the
variable to "real" values.
+ * This method is invoked in contexts where a transfer function is assumed
to exist. Consequently it
+ * shall never return {@code null}, but may return the identity function.
*/
final TransferFunction getTransferFunction() {
return decoder.convention().transferFunction(this);
diff --git
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/VariableRole.java
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/VariableRole.java
index 2c37ac8..97a092d 100644
---
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/VariableRole.java
+++
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/VariableRole.java
@@ -21,7 +21,7 @@ package org.apache.sis.internal.netcdf;
* Specifies whether a variable is used as a coordinate system axis, a
coverage or other purpose.
*
* @author Martin Desruisseaux (Geomatys)
- * @version 1.1
+ * @version 1.2
* @since 1.0
* @module
*/
@@ -32,11 +32,18 @@ public enum VariableRole {
AXIS,
/**
- * The variable is a grid coverage.
+ * The variable is a continuous grid coverage.
+ * Interpolation between cells is allowed.
*/
COVERAGE,
/**
+ * The variable is a discrete grid coverage, for example data quality
masks.
+ * Interpolation between cells is not allowed.
+ */
+ DISCRETE_COVERAGE,
+
+ /**
* The variable is a property of a feature.
*/
FEATURE,
@@ -50,5 +57,19 @@ public enum VariableRole {
/**
* Unidentified kind of variable.
*/
- OTHER
+ OTHER;
+
+ /**
+ * Returns {@code true} if the role of the given variable is {@link
#COVERAGE} or {@link #DISCRETE_COVERAGE}.
+ *
+ * @param candidate the variable for which to check the role, or {@code
null}.
+ * @return whether the given variable is non-null and its role is a
continuous or discrete coverage.
+ */
+ public static boolean isCoverage(final Variable candidate) {
+ if (candidate != null) {
+ final VariableRole role = candidate.getRole();
+ return (role == COVERAGE || role == DISCRETE_COVERAGE);
+ }
+ return false;
+ }
}
diff --git
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/impl/ChannelDecoder.java
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/impl/ChannelDecoder.java
index 6452e53..e0d9792 100644
---
a/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/impl/ChannelDecoder.java
+++
b/storage/sis-netcdf/src/main/java/org/apache/sis/internal/netcdf/impl/ChannelDecoder.java
@@ -74,7 +74,7 @@ import org.apache.sis.math.Vector;
*
* @author Johann Sorel (Geomatys)
* @author Martin Desruisseaux (Geomatys)
- * @version 1.1
+ * @version 1.2
*
* @see <a
href="http://portal.opengeospatial.org/files/?artifact_id=43734";>NetCDF Classic
and 64-bit Offset Format (1.0)</a>
*
@@ -974,7 +974,9 @@ public final class ChannelDecoder extends Decoder {
final Map<DimensionInfo, List<VariableInfo>> dimToAxes = new
IdentityHashMap<>();
for (final VariableInfo variable : variables) {
switch (variable.getRole()) {
- case COVERAGE: {
+ case COVERAGE:
+ case DISCRETE_COVERAGE:
+ {
// If Convention.roleOf(…) overwrote the value
computed by VariableInfo,
// remember the new value for avoiding to ask again in
next loops.
variable.isCoordinateSystemAxis = false;
diff --git
a/storage/sis-netcdf/src/main/java/org/apache/sis/storage/netcdf/MetadataReader.java
b/storage/sis-netcdf/src/main/java/org/apache/sis/storage/netcdf/MetadataReader.java
index 7bd6ae3..be567fd 100644
---
a/storage/sis-netcdf/src/main/java/org/apache/sis/storage/netcdf/MetadataReader.java
+++
b/storage/sis-netcdf/src/main/java/org/apache/sis/storage/netcdf/MetadataReader.java
@@ -882,7 +882,7 @@ split: while ((start =
CharSequences.skipLeadingWhitespaces(value, start, lengt
private void addContentInfo() {
final Map<List<String>, List<Variable>> contents = new HashMap<>(4);
for (final Variable variable : decoder.getVariables()) {
- if (variable.getRole() == VariableRole.COVERAGE) {
+ if (VariableRole.isCoverage(variable)) {
final List<org.apache.sis.internal.netcdf.Dimension>
dimensions = variable.getGridDimensions();
final String[] names = new String[dimensions.size()];
for (int i=0; i<names.length; i++) {
