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desruisseaux pushed a commit to branch geoapi-4.0
in repository https://gitbox.apache.org/repos/asf/sis.git
The following commit(s) were added to refs/heads/geoapi-4.0 by this push:
new dabc81231b Try to be more robust to the GDAL convention in netcDF
file. This convention uses a "GeoTransform" attribute instead of coordinate
axes defined by variables. A difficulty is that this attribute is often 2D even
when the variables have more dimensions.
dabc81231b is described below
commit dabc81231bc6fa87d304ab663cb6a5f4231f8b10
Author: Martin Desruisseaux <[email protected]>
AuthorDate: Thu Jul 31 19:57:50 2025 +0200
Try to be more robust to the GDAL convention in netcDF file.
This convention uses a "GeoTransform" attribute instead of coordinate axes
defined by variables.
A difficulty is that this attribute is often 2D even when the variables
have more dimensions.
---
.../apache/sis/coverage/grid/SliceGeometry.java | 2 +-
.../iso/maintenance/DefaultScopeDescription.java | 5 +-
.../apache/sis/profile/japan/netcdf/GCOM_C.java | 4 +-
.../apache/sis/storage/netcdf/base/Convention.java | 30 ++---
.../sis/storage/netcdf/base/GridMapping.java | 135 ++++++++++++++++-----
.../apache/sis/gui/coverage/CoverageCanvas.java | 10 +-
6 files changed, 131 insertions(+), 55 deletions(-)
diff --git
a/endorsed/src/org.apache.sis.feature/main/org/apache/sis/coverage/grid/SliceGeometry.java
b/endorsed/src/org.apache.sis.feature/main/org/apache/sis/coverage/grid/SliceGeometry.java
index 82d3e37af5..d27bbd82c8 100644
---
a/endorsed/src/org.apache.sis.feature/main/org/apache/sis/coverage/grid/SliceGeometry.java
+++
b/endorsed/src/org.apache.sis.feature/main/org/apache/sis/coverage/grid/SliceGeometry.java
@@ -316,7 +316,7 @@ final class SliceGeometry implements
Function<RenderedImage, GridGeometry> {
}
numRow += derivative.getNumRow();
if (dimCRS < 0) {
- dimCRS = gridDimensions.length + (gridToCRS.getTargetDimensions()
- gridToCRS.getSourceDimensions());
+ dimCRS = gridDimensions.length;
}
/*
* Search for the greatest scale coefficient. For the greatest value,
take the row as the target
diff --git
a/endorsed/src/org.apache.sis.metadata/main/org/apache/sis/metadata/iso/maintenance/DefaultScopeDescription.java
b/endorsed/src/org.apache.sis.metadata/main/org/apache/sis/metadata/iso/maintenance/DefaultScopeDescription.java
index 22acce25bf..c3237e3320 100644
---
a/endorsed/src/org.apache.sis.metadata/main/org/apache/sis/metadata/iso/maintenance/DefaultScopeDescription.java
+++
b/endorsed/src/org.apache.sis.metadata/main/org/apache/sis/metadata/iso/maintenance/DefaultScopeDescription.java
@@ -157,7 +157,6 @@ public class DefaultScopeDescription extends ISOMetadata
implements ScopeDescrip
if (object != null) {
for (byte i=DATASET; i<=OTHER; i++) {
Collection<? extends CharSequence> props = null;
- Object value = null;
switch (i) {
case DATASET: value = object.getDataset();
break;
case FEATURES: props = object.getFeatures();
break;
@@ -171,8 +170,7 @@ public class DefaultScopeDescription extends ISOMetadata
implements ScopeDescrip
value = copySet(props, CharSequence.class);
}
if (value != null) {
- this.value = value;
- this.property = i;
+ property = i;
break;
}
}
@@ -219,6 +217,7 @@ public class DefaultScopeDescription extends ISOMetadata
implements ScopeDescrip
* or an unmodifiable empty set if another value is defined.
*/
private Set<CharSequence> getProperty(final byte code) {
+ @SuppressWarnings("LocalVariableHidesMemberVariable")
final Object value = this.value;
if (value != null) {
if (property == code) {
diff --git
a/endorsed/src/org.apache.sis.profile.japan/main/org/apache/sis/profile/japan/netcdf/GCOM_C.java
b/endorsed/src/org.apache.sis.profile.japan/main/org/apache/sis/profile/japan/netcdf/GCOM_C.java
index c538095ad7..746eb93493 100644
---
a/endorsed/src/org.apache.sis.profile.japan/main/org/apache/sis/profile/japan/netcdf/GCOM_C.java
+++
b/endorsed/src/org.apache.sis.profile.japan/main/org/apache/sis/profile/japan/netcdf/GCOM_C.java
@@ -345,7 +345,7 @@ public final class GCOM_C extends Convention {
*/
@Override
public Set<String> nameOfMappingNode(final Variable data) {
- final Set<String> names = new LinkedHashSet<>(4);
+ final var names = new LinkedHashSet<String>(4);
names.add(GEOMETRY_DATA);
names.addAll(super.nameOfMappingNode(data)); // Fallback if
geometry data does not exist.
return names;
@@ -390,7 +390,7 @@ public final class GCOM_C extends Convention {
} else {
return super.projection(node);
}
- final Map<String,Object> definition = new HashMap<>(4);
+ final var definition = new HashMap<String,Object>(4);
definition.put(CF.GRID_MAPPING_NAME, method);
definition.put(CONVERSION_NAME, name);
return definition;
diff --git
a/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/Convention.java
b/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/Convention.java
index 1ea0d3a379..a15188b97c 100644
---
a/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/Convention.java
+++
b/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/Convention.java
@@ -18,7 +18,6 @@ package org.apache.sis.storage.netcdf.base;
import java.util.Map;
import java.util.Set;
-import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.ServiceLoader;
@@ -487,12 +486,12 @@ public class Convention {
if (method == null) {
return null;
}
- final var definition = new HashMap<String,Object>();
+ final var definition = new LinkedHashMap<String,Object>();
definition.put(CF.GRID_MAPPING_NAME, method);
for (final String name : node.getAttributeNames()) try {
- final String ln = name.toLowerCase(Decoder.DATA_LOCALE);
+ final String nameLC = name.toLowerCase(Decoder.DATA_LOCALE);
Object value;
- switch (ln) {
+ switch (nameLC) {
case CF.GRID_MAPPING_NAME: continue; // Already stored.
case TOWGS84: {
/*
@@ -508,23 +507,24 @@ public class Convention {
break;
}
default: {
- if (ln.endsWith(NAME_SUFFIX)) {
+ if (nameLC.endsWith(NAME_SUFFIX)) {
value = node.getAttributeAsString(name);
if (value == null) continue;
- }
- /*
- * Assume that all map projection parameters in netCDF
files are numbers or array of numbers.
- * If values are array, then they are converted to an
array of {@code double[]} type.
- */
- value = node.getAttributeValue(name);
- if (value == null) continue;
- if (value instanceof Vector) {
- value = ((Vector) value).doubleValues();
+ } else {
+ /*
+ * Assume that all map projection parameters in netCDF
files are numbers or array of numbers.
+ * If values are array, then they are converted to an
array of {@code double[]} type.
+ */
+ value = node.getAttributeValue(name);
+ if (value == null) continue;
+ if (value instanceof Vector) {
+ value = ((Vector) value).doubleValues();
+ }
}
break;
}
}
- if (definition.putIfAbsent(name, value) != null) {
+ if (definition.putIfAbsent(nameLC, value) != null) {
node.error(Convention.class, "projection", null,
Errors.Keys.DuplicatedIdentifier_1, name);
}
} catch (NumberFormatException e) {
diff --git
a/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/GridMapping.java
b/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/GridMapping.java
index bc1f628017..9c8bc924ba 100644
---
a/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/GridMapping.java
+++
b/endorsed/src/org.apache.sis.storage.netcdf/main/org/apache/sis/storage/netcdf/base/GridMapping.java
@@ -59,17 +59,20 @@ import org.apache.sis.referencing.cs.AxesConvention;
import org.apache.sis.referencing.datum.BursaWolfParameters;
import org.apache.sis.referencing.datum.DefaultGeodeticDatum;
import org.apache.sis.referencing.operation.matrix.Matrix3;
+import org.apache.sis.referencing.operation.matrix.Matrices;
import org.apache.sis.referencing.operation.transform.MathTransforms;
import org.apache.sis.referencing.operation.transform.TransformSeparator;
import org.apache.sis.referencing.operation.provider.PseudoPlateCarree;
import org.apache.sis.referencing.privy.AxisDirections;
import org.apache.sis.referencing.privy.AffineTransform2D;
+import org.apache.sis.referencing.privy.ReferencingUtilities;
import org.apache.sis.storage.DataStoreContentException;
import org.apache.sis.storage.netcdf.internal.Resources;
import org.apache.sis.coverage.grid.GridGeometry;
import org.apache.sis.coverage.grid.GridExtent;
import org.apache.sis.coverage.grid.PixelInCell;
import org.apache.sis.system.Modules;
+import org.apache.sis.util.ComparisonMode;
import org.apache.sis.util.CharSequences;
import org.apache.sis.util.ArraysExt;
import org.apache.sis.util.Numbers;
@@ -89,8 +92,9 @@ import org.opengis.referencing.datum.DatumEnsemble;
/**
* Helper object for creating a {@link GridGeometry} instance defined by
attributes on a variable.
- * Those attributes are defined by CF-conventions, but some other non-CF
attributes are also in usage
- * (e.g. GDAL or ESRI conventions). This class uses a different approach than
{@link CRSBuilder},
+ * Those attributes are defined by <abbr>CF</abbr>-conventions, but some other
non-<abbr>CF</abbr>
+ * attributes are also recognized (e.g. <abbr>GDAL</abbr> and
<abbr>ESRI</abbr> conventions).
+ * This class uses a different approach than {@link CRSBuilder},
* which creates Coordinate Reference Systems by inspecting coordinate system
axes.
*
* @author Martin Desruisseaux (Geomatys)
@@ -98,6 +102,12 @@ import org.opengis.referencing.datum.DatumEnsemble;
* @see <a
href="http://cfconventions.org/cf-conventions/cf-conventions.html#grid-mappings-and-projections";>CF-conventions</a>
*/
final class GridMapping {
+ /**
+ * Names of some (not all) attributes where the <abbr>CRS</abbr> may be
encoded in <abbr>WKT</abbr> format.
+ * Values must be in lower-cases because {@link
Convention#projection(Node)} converts names to lower cases.
+ */
+ private static final String CRS_WKT = "crs_wkt", SPATIAL_REF =
"spatial_ref";
+
/**
* The variable on which projection parameters are defined as attributes.
* This is typically an empty variable referenced by the value of the
@@ -109,8 +119,8 @@ final class GridMapping {
/**
* The Coordinate Reference System inferred from grid mapping attribute
values, or {@code null} if none.
- * This CRS may have been constructed from Well Known Text or EPSG codes
declared in {@code "spatial_ref"},
- * {@code "ESRI_pe_string"} or {@code "EPSG_code"} attributes.
+ * This <abbr>CRS</abbr> may have been constructed from Well Known Text or
<abbr>EPSG</abbr> codes
+ * declared in {@value #SPATIAL_REF}, {@code "ESRI_pe_string"} or {@code
"EPSG_code"} attributes.
*
* <h4>Usage note</h4>
* This is built from different information than the one used by {@link
CRSBuilder},
@@ -121,8 +131,9 @@ final class GridMapping {
private CoordinateReferenceSystem crs;
/**
- * The <i>grid to CRS</i> transform, or {@code null} if none. This
information is usually not specified
- * except when using GDAL conventions. If {@code null}, then the transform
should be inferred by {@link Grid}.
+ * The <i>grid to CRS</i> transform, or {@code null} if none.
+ * This information is usually not specified except when using
<abbr>GDAL</abbr> conventions.
+ * If {@code null}, then the transform should be inferred by {@link Grid}.
*/
private MathTransform gridToCRS;
@@ -185,8 +196,8 @@ final class GridMapping {
/**
* Parses the map projection parameters defined as attribute associated to
the given variable.
- * This method tries to parse CF-compliant attributes first. If none are
found, non-standard
- * extensions (for example GDAL usage) are tried next.
+ * This method tries to parse <abbr>CF</abbr>-compliant attributes,
potentially mixed with
+ * non-standard extensions (for example <abbr>GDAL</abbr>).
*/
private static GridMapping parse(final Node mapping) {
final var gm = new GridMapping(mapping);
@@ -228,7 +239,21 @@ final class GridMapping {
if (value instanceof Number || value instanceof double[]
|| value instanceof float[]) {
it.remove();
parameters.parameter(name).setValue(value);
- } else if (value instanceof String &&
!name.endsWith(Convention.NAME_SUFFIX)) {
+ } else if (value instanceof String) {
+ final var text = (String) value;
+ if (name.endsWith(Convention.NAME_SUFFIX)) {
+ continue;
+ }
+ switch (name) {
+ case CRS_WKT:
+ case SPATIAL_REF: continue; // Will be parsed
after this loop.
+ case "geotransform": { // "GeoTransform"
made lower-case.
+ if (parseGeoTransform(null, text)) {
+ it.remove();
+ }
+ continue;
+ }
+ }
/*
* In principle we should ignore non-numeric
parameters. But in practice, some badly encoded
* netCDF files store parameters as strings instead of
numbers. If the parameter name is
@@ -243,15 +268,22 @@ final class GridMapping {
final Class<?> type =
parameter.getDescriptor().getValueClass();
if (Numbers.isNumber(type)) {
it.remove();
- parameter.setValue(Double.parseDouble((String)
value));
+ parameter.setValue(Double.parseDouble(text));
} else if (Numbers.isNumber(type.getComponentType())) {
it.remove();
- parameter.setValue(parseDoubles((String) value),
null);
+ parameter.setValue(parseDoubles(text), null);
}
}
- } catch (IllegalArgumentException ex) { //
Includes NumberFormatException.
- warning(mapping, ex, null,
Resources.Keys.CanNotSetProjectionParameter_5,
- mapping.decoder.getFilename(), mapping.getName(),
name, value, ex.getLocalizedMessage());
+ } catch (IllegalArgumentException ex) { // Includes
NumberFormatException.
+ warning(mapping,
+ ex,
+ null, // Default to `Resources` bundle.
+ Resources.Keys.CanNotSetProjectionParameter_5,
+ mapping.decoder.getFilename(),
+ mapping.getName(),
+ name,
+ value,
+ ex.getLocalizedMessage());
}
}
/*
@@ -282,8 +314,8 @@ final class GridMapping {
* obvious (except for CompoundCRS).
*/
final var done = new ArrayList<String>(2);
- setOrVerifyWKT(definition, "crs_wkt", done);
- setOrVerifyWKT(definition, "spatial_ref", done);
+ setOrVerifyWKT(definition, CRS_WKT, done);
+ setOrVerifyWKT(definition, SPATIAL_REF, done);
/*
* Report all projection parameters that have not been used. If
the map is not rendered
* at expected location, it may be because we have ignored some
important parameters.
@@ -297,7 +329,11 @@ final class GridMapping {
* Build the "grid to CRS" if present. This is not defined by
CF-convention,
* but may be present in some non-CF conventions.
*/
- gridToCRS = mapping.decoder.convention().gridToCRS(mapping,
baseToCRS);
+ if (gridToCRS == null) {
+ gridToCRS = mapping.decoder.convention().gridToCRS(mapping,
baseToCRS);
+ } else {
+ gridToCRS = MathTransforms.concatenate(gridToCRS, baseToCRS);
+ }
return true;
} catch (ClassCastException | IllegalArgumentException |
FactoryException | TransformException e) {
warningInMapping(mapping, e, Resources.Keys.CanNotCreateCRS_3,
null);
@@ -400,7 +436,10 @@ final class GridMapping {
*/
if (isSpecified) {
final Map<String,?> properties = properties(definition,
Convention.GEOGRAPHIC_CRS_NAME, main, datum);
- return decoder.getCRSFactory().createGeographicCRS(properties,
datum, ensemble,
+ return decoder.getCRSFactory().createGeographicCRS(
+ properties,
+ datum,
+ ensemble,
defaultDefinitions.geographic().getCoordinateSystem());
} else {
return defaultDefinitions.geographic();
@@ -471,9 +510,13 @@ final class GridMapping {
}
if (crs == null) {
crs = check;
- } else if (!Utilities.equalsIgnoreMetadata(crs, check)) {
- warning(mapping, null, null, Resources.Keys.InconsistentCRS_2,
- mapping.decoder.getFilename(), mapping.getName());
+ } else if (!Utilities.deepEquals(crs, check,
ComparisonMode.ALLOW_VARIANT)) {
+ warning(mapping, // Node
+ null, // Exception
+ null, // Resources
+ Resources.Keys.InconsistentCRS_2,
+ mapping.decoder.getFilename(),
+ mapping.getName());
}
}
}
@@ -492,8 +535,14 @@ final class GridMapping {
* @return whether this method found grid geometry attributes.
*/
private boolean parseGeoTransform() {
- final String wkt = mapping.getAttributeAsString("spatial_ref");
- final String gtr = mapping.getAttributeAsString("GeoTransform");
+ return parseGeoTransform(mapping.getAttributeAsString(SPATIAL_REF),
+ mapping.getAttributeAsString("GeoTransform"));
+ }
+
+ /**
+ * Implementation of {@link #parseGeoTransform()} with given attribute
values.
+ */
+ private boolean parseGeoTransform(final String wkt, final String gtr) {
short message = Resources.Keys.CanNotCreateCRS_3;
boolean done = false;
try {
@@ -617,19 +666,41 @@ final class GridMapping {
}
/**
- * Creates a new grid geometry with the extent of the given variable and a
potentially null CRS.
+ * Creates a new grid geometry with the extent of the given variable and a
potentially null <abbr>CRS</abbr>.
* This method should be invoked only as a fallback when no existing
{@link GridGeometry} can be used.
* The CRS and "grid to CRS" transform are null, unless some partial
information was found for example
* as WKT string.
*/
final GridGeometry createGridCRS(final Variable variable) {
final List<Dimension> dimensions = variable.getGridDimensions();
- final long[] upper = new long[dimensions.size()];
- for (int i=0; i<upper.length; i++) {
- final int d = (upper.length - 1) - i; // Convert CRS
dimension to netCDF dimension.
+ final int srcDim = dimensions.size();
+ final long[] upper = new long[srcDim];
+ for (int i=0; i<srcDim; i++) {
+ final int d = (srcDim - 1) - i; // Convert CRS dimension
to netCDF dimension.
upper[i] = dimensions.get(d).length();
}
- return new GridGeometry(new GridExtent(null, null, upper, false),
PixelInCell.CELL_CENTER, gridToCRS, crs);
+ MathTransform implicitG2C = gridToCRS;
+ CoordinateReferenceSystem implicitCRS = crs;
+ if (implicitG2C != null) {
+ implicitG2C = MathTransforms.concatenate(
+ changeOfDimension(srcDim,
implicitG2C.getSourceDimensions()),
+ implicitG2C,
+ changeOfDimension(implicitG2C.getTargetDimensions(),
+
ReferencingUtilities.getDimension(implicitCRS)));
+ }
+ final var extent = new GridExtent(null, null, upper, false);
+ return new GridGeometry(extent, PixelInCell.CELL_CENTER, implicitG2C,
implicitCRS);
+ }
+
+ /**
+ * Returns a transform for changing the number of dimensions of a math
transform.
+ * For convenience, a target number of dimensions of 0 means no change.
+ */
+ private static MathTransform changeOfDimension(final int srcDim, final int
tgtDim) {
+ if (tgtDim == srcDim || tgtDim == 0) {
+ return MathTransforms.identity(srcDim);
+ }
+ return MathTransforms.linear(Matrices.createDimensionSelect(srcDim,
ArraysExt.range(0, tgtDim)));
}
/**
@@ -674,7 +745,7 @@ final class GridMapping {
if (firstAffectedCoordinate < 0) {
firstAffectedCoordinate = 0;
if (isWKT && crs != null) {
- explicitCRS = crs; // If
specified by WKT, use the CRS verbatim.
+ explicitCRS = crs; // If specified by
WKT, use the CRS verbatim.
}
}
}
@@ -691,13 +762,13 @@ final class GridMapping {
}
isSameGrid = implicitCRS.equals(explicitCRS);
if (isSameGrid) {
- explicitCRS = implicitCRS;
// Keep existing instance if appropriate.
+ explicitCRS = implicitCRS; // Keep existing
instance if appropriate.
}
}
}
/*
* Perform the same substitution as above, but in the "grid to CRS"
transform. Note that the "grid to CRS"
- * is usually not specified, so the block performing substitution will
rarely be executed. If executed, then
+ * is usually not specified, so the block performing substitution will
rarely be executed. If executed,
* then we need to perform selection in target dimensions (not source
dimensions) because the first affected
* coordinate computed above is in CRS dimension, which is the target
of "grid to CRS" transform.
*/
@@ -725,7 +796,7 @@ final class GridMapping {
components = ArraysExt.resize(components, count);
explicitG2C = MathTransforms.compound(components);
if (implicitG2C.equals(explicitG2C)) {
- explicitG2C = implicitG2C;
// Keep using existing instance if appropriate.
+ explicitG2C = implicitG2C; // Keep using existing
instance if appropriate.
} else {
isSameGrid = false;
}
diff --git
a/optional/src/org.apache.sis.gui/main/org/apache/sis/gui/coverage/CoverageCanvas.java
b/optional/src/org.apache.sis.gui/main/org/apache/sis/gui/coverage/CoverageCanvas.java
index 965841c4a6..a60d484aee 100644
---
a/optional/src/org.apache.sis.gui/main/org/apache/sis/gui/coverage/CoverageCanvas.java
+++
b/optional/src/org.apache.sis.gui/main/org/apache/sis/gui/coverage/CoverageCanvas.java
@@ -77,6 +77,7 @@ import org.apache.sis.gui.internal.GUIUtilities;
import org.apache.sis.gui.internal.LogHandler;
import org.apache.sis.util.ArraysExt;
import org.apache.sis.util.Debug;
+import org.apache.sis.util.Exceptions;
import org.apache.sis.util.logging.Logging;
import org.apache.sis.util.privy.CollectionsExt;
import org.apache.sis.io.TableAppender;
@@ -656,8 +657,13 @@ public class CoverageCanvas extends MapCanvasAWT {
*/
@Override protected void succeeded() {
runAfterRendering(() -> {
- setNewSource(getValue(), ranges, zoom);
- requestRepaint(); // Cause `Worker`
class to be executed.
+ try {
+ setNewSource(getValue(), ranges, zoom);
+ requestRepaint(); // Cause
`Worker` class to be executed.
+ } catch (RuntimeException ex) { // Mostly for
`BackingStoreException`.
+ clear();
+ ExceptionReporter.canNotUseResource(fixedPane,
Exceptions.unwrap(ex));
+ }
});
}
