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 77cdb0047c6203bdf01102109ee055c18046b60e
Author: Martin Desruisseaux <martin.desruisse...@geomatys.com>
AuthorDate: Fri May 26 12:13:03 2023 +0200
When the GeoTIFF image is of floating point type, replace fill values by
NaN at reading time.
This is the same policy than with our netCDF reader.
---
.../org/apache/sis/coverage/SampleDimension.java | 7 +++++
.../sis/internal/coverage/SampleDimensions.java | 6 ++--
.../java/org/apache/sis/measure/NumberRange.java | 4 +--
.../sis/internal/geotiff/SchemaModifier.java | 2 +-
.../sis/storage/geotiff/CompressedSubset.java | 4 +--
.../org/apache/sis/storage/geotiff/DataCube.java | 18 ++++++++++++
.../org/apache/sis/storage/geotiff/DataSubset.java | 33 +++++++++++++++++++++-
.../sis/storage/geotiff/ImageFileDirectory.java | 13 +++++++--
8 files changed, 77 insertions(+), 10 deletions(-)
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 f0a24e8c9e..4ec24af099 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
@@ -1209,6 +1209,13 @@ public class SampleDimension implements Serializable {
toNaN.remove(c);
return c;
}
+
+ /** Removes all categories in the given range. */
+ @Override protected void removeRange(final int fromIndex,
final int toIndex) {
+ System.arraycopy(categories, toIndex, categories,
fromIndex, count - toIndex);
+ Arrays.fill(categories, toIndex, count, null);
+ count -= (toIndex - fromIndex);
+ }
};
}
diff --git
a/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/SampleDimensions.java
b/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/SampleDimensions.java
index 9952fb69c8..c7658d01a3 100644
---
a/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/SampleDimensions.java
+++
b/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/SampleDimensions.java
@@ -155,8 +155,9 @@ public final class SampleDimensions extends Static {
final SampleDimension band = bands[i];
if (band != null) {
final List<Category> categories = band.getCategories();
- final Number[] nodataValues = new Number[categories.size()];
- for (int j = 0; j < nodataValues.length; j++) {
+ final int count = categories.size();
+ final Number[] nodataValues = new Number[count + 1];
+ for (int j = 0; j < count; j++) {
final Category category = categories.get(j);
if (!category.isQuantitative()) {
final NumberRange<?> range = category.getSampleRange();
@@ -171,6 +172,7 @@ public final class SampleDimensions extends Static {
nodataValues[j] = value;
}
}
+ nodataValues[count] = band.getBackground().orElse(null);
sampleFilters[i] =
ImageProcessor.filterNodataValues(nodataValues);
}
}
diff --git
a/core/sis-utility/src/main/java/org/apache/sis/measure/NumberRange.java
b/core/sis-utility/src/main/java/org/apache/sis/measure/NumberRange.java
index 019eda568d..c4cc0a29a3 100644
--- a/core/sis-utility/src/main/java/org/apache/sis/measure/NumberRange.java
+++ b/core/sis-utility/src/main/java/org/apache/sis/measure/NumberRange.java
@@ -729,8 +729,8 @@ public class NumberRange<E extends Number & Comparable<?
super E>> extends Range
* This method converts {@code this} or the given argument to the widest
numeric type,
* then performs the same work than {@link #contains(Comparable)}.
*
- * @param value the value to check for inclusion in this range.
- * @return {@code true} if the given value is included in this range.
+ * @param value the value to check for inclusion in this range, or
{@code null}.
+ * @return {@code true} if the given value is non-null and included in
this range.
* @throws IllegalArgumentException if the given range cannot be converted
to a valid type
* through widening conversion.
*/
diff --git
a/storage/sis-geotiff/src/main/java/org/apache/sis/internal/geotiff/SchemaModifier.java
b/storage/sis-geotiff/src/main/java/org/apache/sis/internal/geotiff/SchemaModifier.java
index 40d751d177..0f0659c2a6 100644
---
a/storage/sis-geotiff/src/main/java/org/apache/sis/internal/geotiff/SchemaModifier.java
+++
b/storage/sis-geotiff/src/main/java/org/apache/sis/internal/geotiff/SchemaModifier.java
@@ -112,7 +112,7 @@ public interface SchemaModifier {
* @todo if we move this key in public API in the future, then it would be
a
* value in existing {@link org.apache.sis.storage.DataOptionKey}
class.
*/
- OptionKey<SchemaModifier> OPTION = new
InternalOptionKey<SchemaModifier>("SCHEMA_MODIFIER", SchemaModifier.class);
+ OptionKey<SchemaModifier> OPTION = new
InternalOptionKey<>("SCHEMA_MODIFIER", SchemaModifier.class);
/**
* The default instance which performs no modification.
diff --git
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/CompressedSubset.java
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/CompressedSubset.java
index 2639a4209f..fe926da63a 100644
---
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/CompressedSubset.java
+++
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/CompressedSubset.java
@@ -35,7 +35,7 @@ import static java.lang.Math.multiplyFull;
* Raster data obtained from a compressed GeoTIFF file in the domain requested
by user.
*
* @author Martin Desruisseaux (Geomatys)
- * @version 1.1
+ * @version 1.4
* @since 1.1
*/
final class CompressedSubset extends DataSubset {
@@ -249,7 +249,7 @@ final class CompressedSubset extends DataSubset {
fillRemainingRows(bank.flip());
banks[b] = bank;
}
- return Raster.createWritableRaster(model, RasterFactory.wrap(dataType,
banks), location);
+ return createWritableRaster(RasterFactory.wrap(dataType, banks),
location);
}
/**
diff --git
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataCube.java
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataCube.java
index fc2a2679f4..e8b09a1f50 100644
---
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataCube.java
+++
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataCube.java
@@ -160,6 +160,24 @@ abstract class DataCube extends TiledGridResource
implements ResourceOnFileSyste
*/
abstract Predictor getPredictor();
+ /**
+ * Returns the fill value used in image of floating point type before
replacement by NaN.
+ * If no value is declared or if the image type is an integer type,
returns {@code null}.
+ * If non-null, this value will be replaced by {@link Float#NaN} at
reading time.
+ *
+ * <div class="note"><b>Rational:</b>
+ * the intend is to handle the image as if it was already converted to the
units of measurement.
+ * Our netCDF reader does the same thing, and we want a consistent
behavior of coverage readers.
+ * </div>
+ *
+ * If this method returns a non-null value, then {@link #getFillValue()}
should return NaN.
+ *
+ * @return value to be replaced by NaN at reading time, or {@code null} if
none.
+ *
+ * @see #getFillValue()
+ */
+ abstract Number getReplaceableFillValue();
+
/**
* Returns {@code true} if the image can be read with the {@link
DataSubset} base class,
* or {@code false} if the more sophisticated {@link CompressedSubset}
sub-class is needed.
diff --git
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataSubset.java
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataSubset.java
index 043a3df5d4..58192bc408 100644
---
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataSubset.java
+++
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/DataSubset.java
@@ -24,6 +24,8 @@ import java.io.IOException;
import java.awt.Point;
import java.awt.image.BandedSampleModel;
import java.awt.image.DataBuffer;
+import java.awt.image.DataBufferFloat;
+import java.awt.image.DataBufferDouble;
import java.awt.image.Raster;
import org.opengis.util.GenericName;
import org.apache.sis.image.DataType;
@@ -41,6 +43,7 @@ import org.apache.sis.internal.storage.io.ChannelDataInput;
import org.apache.sis.internal.geotiff.Resources;
import org.apache.sis.util.resources.Errors;
import org.apache.sis.util.Localized;
+import org.apache.sis.util.ArraysExt;
import org.apache.sis.math.Vector;
import static java.lang.Math.addExact;
@@ -523,7 +526,7 @@ class DataSubset extends TiledGridCoverage implements
Localized {
banks[b] = bank;
}
final DataBuffer buffer = RasterFactory.wrap(type, banks);
- return Raster.createWritableRaster(model, buffer, location);
+ return createWritableRaster(buffer, location);
}
/**
@@ -544,4 +547,32 @@ class DataSubset extends TiledGridCoverage implements
Localized {
}
}
}
+
+ /**
+ * Creates the raster with the given data buffer, which contains the
pixels that have been read.
+ *
+ * @param buffer the sample values which have been read from the
GeoTIFF tile.
+ * @param location pixel coordinates in the upper-left corner of the
tile to return.
+ * @return raster with the given sample values.
+ */
+ final Raster createWritableRaster(final DataBuffer buffer, final Point
location) {
+ final Number fill = source.getReplaceableFillValue();
+ if (fill != null) {
+ switch (buffer.getDataType()) {
+ case DataBuffer.TYPE_FLOAT: {
+ for (float[] bank : ((DataBufferFloat)
buffer).getBankData()) {
+ ArraysExt.replace(bank, fill.floatValue(), Float.NaN);
+ }
+ break;
+ }
+ case DataBuffer.TYPE_DOUBLE: {
+ for (double[] bank : ((DataBufferDouble)
buffer).getBankData()) {
+ ArraysExt.replace(bank, fill.doubleValue(),
Double.NaN);
+ }
+ break;
+ }
+ }
+ }
+ return Raster.createWritableRaster(model, buffer, location);
+ }
}
diff --git
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/ImageFileDirectory.java
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/ImageFileDirectory.java
index be107010df..0d255f0953 100644
---
a/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/ImageFileDirectory.java
+++
b/storage/sis-geotiff/src/main/java/org/apache/sis/storage/geotiff/ImageFileDirectory.java
@@ -1691,6 +1691,15 @@ final class ImageFileDirectory extends DataCube {
return colorModel;
}
+ /**
+ * Returns the fill value to be replaced by NaN at reading time.
+ * This is possible only for images of floating point type.
+ */
+ @Override
+ Number getReplaceableFillValue() {
+ return (sampleFormat == FLOAT) ? noData : null;
+ }
+
/**
* Returns the value to use for filling empty spaces in the raster, or
{@code null} if none,
* not different than zero or not valid for the target data type.
@@ -1698,11 +1707,11 @@ final class ImageFileDirectory extends DataCube {
*/
@Override
protected Number getFillValue() {
- return getFillValue(false);
+ return (sampleFormat != FLOAT) ? getFillValue(false) : Double.NaN;
}
/**
- * Returns the value to use for filling empty spaces in the raster, or
{@code null} if none,
+ * Returns the value to use for filling empty spaces in the raster, or
{@code null} if none.
* The exclusion of zero value is optional, controlled by the {@code
acceptZero} argument.
*
* @param acceptZero whether to return a number for the zero value.
