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 df7a5102a51c591f9ac7a85be55f1b1bd375760b
Author: Martin Desruisseaux <martin.desruisse...@geomatys.com>
AuthorDate: Mon Apr 25 16:05:34 2022 +0200
Add partial support for color map file (*.clr).
In current implementation it can apply only to data type byte and unsigned
short.
In particular, color map on floating point values is not yet supported.
---
.../internal/coverage/j2d/ColorModelFactory.java | 7 +-
ide-project/NetBeans/build.xml | 2 +
.../sis/internal/storage/esri/RasterStore.java | 125 +++++++++++++++++++--
.../sis/internal/storage/esri/package-info.java | 13 +++
.../org/apache/sis/internal/storage/esri/BIP.hdr | 2 +
.../org/apache/sis/internal/storage/esri/BIP.stx | 7 ++
.../org/apache/sis/internal/storage/esri/grid.clr | 14 +++
7 files changed, 156 insertions(+), 14 deletions(-)
diff --git
a/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/j2d/ColorModelFactory.java
b/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/j2d/ColorModelFactory.java
index 99192128ee..f3a12df41c 100644
---
a/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/j2d/ColorModelFactory.java
+++
b/core/sis-feature/src/main/java/org/apache/sis/internal/coverage/j2d/ColorModelFactory.java
@@ -18,7 +18,6 @@ package org.apache.sis.internal.coverage.j2d;
import java.util.Map;
import java.util.Arrays;
-import java.util.Collection;
import java.util.Comparator;
import java.util.Optional;
import java.awt.Transparency;
@@ -317,9 +316,9 @@ public final class ColorModelFactory {
* @see Colorizer
*/
public static ColorModel createPiecewise(final int dataType, final int
numBands, final int visibleBand,
- final
Collection<Map.Entry<NumberRange<?>,Color[]>> colors)
+ final Map<NumberRange<?>,
Color[]> colors)
{
- return createPiecewise(dataType, numBands, visibleBand,
ColorsForRange.list(colors));
+ return createPiecewise(dataType, numBands, visibleBand,
ColorsForRange.list(colors.entrySet()));
}
/**
@@ -386,7 +385,7 @@ public final class ColorModelFactory {
/**
* Returns a color model interpolated for the given range of values. This
is a convenience method for
- * {@link #createPiecewise(int, int, int, Collection)} when the collection
contains only one element.
+ * {@link #createPiecewise(int, int, int, Map)} when the map contains only
one element.
*
* @param dataType the color model type.
* @param numBands the number of bands for the color model (usually
1).
diff --git a/ide-project/NetBeans/build.xml b/ide-project/NetBeans/build.xml
index 557ef9f261..bbb1786f11 100644
--- a/ide-project/NetBeans/build.xml
+++ b/ide-project/NetBeans/build.xml
@@ -304,6 +304,8 @@
<include name="**/*.txt"/>
<include name="**/*.asc"/>
<include name="**/*.hdr"/>
+ <include name="**/*.stx"/>
+ <include name="**/*.clr"/>
<include name="**/*.raw"/>
<include name="**/*.png"/>
<include name="**/*.pgw"/>
diff --git
a/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/RasterStore.java
b/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/RasterStore.java
index 6955c061b0..0e588da647 100644
---
a/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/RasterStore.java
+++
b/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/RasterStore.java
@@ -26,6 +26,7 @@ import java.io.FileNotFoundException;
import java.nio.file.NoSuchFileException;
import java.nio.file.Path;
import java.awt.image.ColorModel;
+import java.awt.image.DataBuffer;
import java.awt.image.SampleModel;
import java.awt.image.BufferedImage;
import java.awt.image.WritableRaster;
@@ -53,6 +54,7 @@ import org.apache.sis.internal.util.UnmodifiableArrayList;
import org.apache.sis.internal.util.Numerics;
import org.apache.sis.util.resources.Vocabulary;
import org.apache.sis.util.CharSequences;
+import org.apache.sis.util.ArraysExt;
import org.apache.sis.math.Statistics;
@@ -197,6 +199,89 @@ abstract class RasterStore extends PRJDataStore implements
GridCoverageResource
metadata = builder.buildAndFreeze();
}
+ /**
+ * Reads the {@code "*.clr"} auxiliary file. Syntax is as below, with one
line per color:
+ *
+ * <pre>value red green blue</pre>
+ *
+ * The specification said that lines that do not start with a number shall
be ignored as comment.
+ * Any characters after the fourth number shall also be ignored and can be
used as comment.
+ *
+ * <h4>Limitations</h4>
+ * Current implementation requires the data type to be {@link
DataBuffer#TYPE_BYTE} or
+ * {@link DataBuffer#TYPE_SHORT}. A future version could create scaled
color model for
+ * floating point values as well.
+ *
+ * @param mapSize minimal size of index color model map. The actual
size may be larger.
+ * @param numBands number of bands in the sample model. Only one of them
will be visible.
+ * @return the color model, or {@code null} if the file does not contain
enough entries.
+ * @throws NoSuchFileException if the auxiliary file has not been found
(when opened from path).
+ * @throws FileNotFoundException if the auxiliary file has not been found
(when opened from URL).
+ * @throws IOException if another error occurred while opening the stream.
+ * @throws NumberFormatException if a number can not be parsed.
+ */
+ private ColorModel readColorMap(final int dataType, final int mapSize,
final int numBands)
+ throws DataStoreException, IOException
+ {
+ final int maxSize;
+ switch (dataType) {
+ case DataBuffer.TYPE_BYTE: maxSize = 0xFF; break;
+ case DataBuffer.TYPE_USHORT: maxSize = 0xFFFF; break;
+ default: return null; // Limitation
documented in above javadoc.
+ }
+ int count = 0;
+ long[] indexAndColors = ArraysExt.EMPTY_LONG; // Index in
highest 32 bits, ARGB in lowest 32 bits.
+ for (final CharSequence line :
CharSequences.splitOnEOL(readAuxiliaryFile(CLR))) {
+ final int end = CharSequences.skipTrailingWhitespaces(line, 0,
line.length());
+ final int start = CharSequences.skipLeadingWhitespaces(line, 0,
end);
+ if (start < end && Character.isDigit(Character.codePointAt(line,
start))) {
+ int column = 0;
+ long code = 0;
+ for (final CharSequence item :
CharSequences.split(line.subSequence(start, end), ' ')) {
+ if (item.length() != 0) {
+ int value = Integer.parseInt(item.toString());
+ if (column == 0) {
+ code = ((long) value) << Integer.SIZE;
+ } else {
+ value = Math.max(0, Math.min(255, value));
+ code |= value << ((3 - column) * Byte.SIZE);
+ }
+ if (++column >= 4) break;
+ }
+ }
+ if (count >= indexAndColors.length) {
+ indexAndColors = Arrays.copyOf(indexAndColors,
Math.max(count*2, 64));
+ }
+ indexAndColors[count++] = code | 0xFF000000L;
+ }
+ }
+ if (count <= 1) {
+ return null;
+ }
+ /*
+ * Sort the color entries in increasing index order. Because we put
the value in the highest bits,
+ * we can sort the `long` entries directly. If the file contains more
entries than what the color
+ * map can contains, the last entries are discarded.
+ */
+ Arrays.sort(indexAndColors, 0, count);
+ int[] ARGB = new int[Math.max(mapSize,
Math.toIntExact((indexAndColors[count-1] >>> Integer.SIZE) + 1))];
+ final int[] colors = new int[2];
+ for (int i=1; i<count; i++) {
+ final int lower = (int) (indexAndColors[i-1] >>> Integer.SIZE);
+ final int upper = (int) (indexAndColors[i ] >>> Integer.SIZE);
+ if (upper >= lower) {
+ colors[0] = (int) indexAndColors[i-1];
+ colors[1] = (int) indexAndColors[i ];
+ ColorModelFactory.expand(colors, ARGB, lower, upper + 1);
+ }
+ if (upper > maxSize) {
+ ARGB = Arrays.copyOf(ARGB, maxSize + 1);
+ break;
+ }
+ }
+ return ColorModelFactory.createIndexColorModel(numBands, VISIBLE_BAND,
ARGB, true, -1);
+ }
+
/**
* Reads the {@code "*.stx"} auxiliary file. Syntax is as below, with one
line per band.
* Value between {…} are optional and can be skipped with a # sign in
place of the number.
@@ -207,17 +292,16 @@ abstract class RasterStore extends PRJDataStore
implements GridCoverageResource
*
* @todo Stretch values are not yet stored.
*
- * @param numBands length of the array to return.
* @return statistics for each band. Some elements may be null if not
specified in the file.
* @throws NoSuchFileException if the auxiliary file has not been found
(when opened from path).
* @throws FileNotFoundException if the auxiliary file has not been found
(when opened from URL).
* @throws IOException if another error occurred while opening the stream.
* @throws NumberFormatException if a number can not be parsed.
*/
- private Statistics[] readStatistics(final String name, final SampleModel
sm, final int numBands)
+ private Statistics[] readStatistics(final String name, final SampleModel
sm)
throws DataStoreException, IOException
{
- final Statistics[] stats = new Statistics[numBands];
+ final Statistics[] stats = new Statistics[sm.getNumBands()];
for (final CharSequence line :
CharSequences.splitOnEOL(readAuxiliaryFile(STX))) {
final int end = CharSequences.skipTrailingWhitespaces(line, 0,
line.length());
final int start = CharSequences.skipLeadingWhitespaces(line, 0,
end);
@@ -246,7 +330,7 @@ abstract class RasterStore extends PRJDataStore implements
GridCoverageResource
}
if (band >= 1 && band <= stats.length) {
final int count = Math.multiplyExact(sm.getWidth(),
sm.getHeight());
- stats[band - 1] = new Statistics(name, 0, count, minimum,
maximum, mean, stdev, true);
+ stats[band - 1] = new Statistics(name, 0, count, minimum,
maximum, mean, stdev, false);
}
}
}
@@ -270,11 +354,9 @@ abstract class RasterStore extends PRJDataStore implements
GridCoverageResource
* overwrite them because we need the minimum/maximum values for
building the sample dimensions.
*/
try {
- stats = readStatistics(name, sm, bands.length);
- } catch (NoSuchFileException | FileNotFoundException e) {
- listeners.warning(Level.FINE,
Resources.format(Resources.Keys.CanNotReadAuxiliaryFile_1, STX), e);
+ stats = readStatistics(name, sm);
} catch (IOException | NumberFormatException e) {
- throw new
DataStoreReferencingException(Resources.format(Resources.Keys.CanNotReadAuxiliaryFile_1,
STX), e);
+ canNotReadAuxiliaryFile(STX, e);
}
/*
* Build the sample dimensions and the color model.
@@ -334,18 +416,41 @@ abstract class RasterStore extends PRJDataStore
implements GridCoverageResource
/*
* Create the color model using the statistics of the band that we
choose to make visible,
* or using a RGB color model if the number of bands or the data
type is compatible.
+ * The color file is optional and will be used if present.
*/
if (band == VISIBLE_BAND) {
if (isRGB) {
colorModel = ColorModelFactory.createRGB(sm);
} else {
- colorModel = ColorModelFactory.createGrayScale(dataType,
bands.length, band, minimum, maximum);
+ try {
+ colorModel = readColorMap(dataType, (int) (maximum +
1), bands.length);
+ } catch (IOException | NumberFormatException e) {
+ canNotReadAuxiliaryFile(CLR, e);
+ }
+ if (colorModel == null) {
+ colorModel =
ColorModelFactory.createGrayScale(dataType, bands.length, band, minimum,
maximum);
+ }
}
}
}
sampleDimensions = UnmodifiableArrayList.wrap(bands);
}
+ /**
+ * Sends a warning about a failure to read an optional auxiliary file.
+ * This is used for errors that affect only the rendering, not the
georeferencing.
+ *
+ * @param suffix suffix of the auxiliary file.
+ * @param exception error that occurred while reading the auxiliary file.
+ */
+ private void canNotReadAuxiliaryFile(final String suffix, final Exception
exception) {
+ Level level = Level.WARNING;
+ if (exception instanceof NoSuchFileException || exception instanceof
FileNotFoundException) {
+ level = Level.FINE;
+ }
+ listeners.warning(level,
Resources.format(Resources.Keys.CanNotReadAuxiliaryFile_1, suffix), exception);
+ }
+
/**
* Default names of bands when the color model is RGB or RGBA.
*/
@@ -380,7 +485,7 @@ abstract class RasterStore extends PRJDataStore implements
GridCoverageResource
ColorModel cm = colorModel;
if (!range.isIdentity()) {
bands = Arrays.asList(range.select(sampleDimensions));
- cm = range.select(colorModel).orElse(null);
+ cm = range.select(cm).orElse(null);
if (cm == null) {
final SampleDimension band = bands.get(VISIBLE_BAND);
cm = ColorModelFactory.createGrayScale(data.getSampleModel(),
VISIBLE_BAND, band.getSampleRange().orElse(null));
diff --git
a/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/package-info.java
b/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/package-info.java
index e03933fae7..1746e7c191 100644
---
a/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/package-info.java
+++
b/storage/sis-storage/src/main/java/org/apache/sis/internal/storage/esri/package-info.java
@@ -32,6 +32,19 @@
* ({@code XDIM}, {@code YDIM}, color file, statistics file,
<i>etc.</i>).</li>
* </ul>
*
+ * <h2>Limitations</h2>
+ * Statistics file ({@code *.stx}) contains {@code band}, {@code minimum},
{@code maximum}, {@code mean},
+ * {@code std_deviation}, {@code linear_stretch_min} and {@code
linear_stretch_max} values.
+ * But in current Apache SIS implementation, the last two values ({@code
linear_stretch_*}) are ignored.
+ *
+ * <p>Color map file ({@code *.clr}) is read only when the raster does not
have 3 or 4 bands
+ * (in which case the raster is considered RGB) and when the data type is byte
or unsigned short.
+ * In all other cases, notably in the case of floating point values, the color
map is ignored.</p>
+ *
+ * <p>Current implementation of ASCII Grid store loads, caches and returns the
full image
+ * no matter the subregion or subsampling specified to the {@code read(…)}
method.
+ * Sub-setting parameters are ignored.</p>
+ *
* @author Martin Desruisseaux (Geomatys)
* @version 1.2
*
diff --git
a/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/BIP.hdr
b/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/BIP.hdr
index 197bf27453..550b24582e 100644
---
a/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/BIP.hdr
+++
b/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/BIP.hdr
@@ -1,4 +1,6 @@
Header file for the `BIP.raw` test raster.
+The BIP test also contains a `BIP.stx` file
+for testing the loading of statistics data.
NROWS 9
NCOLS 9
diff --git
a/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/BIP.stx
b/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/BIP.stx
new file mode 100644
index 0000000000..8585d48ce5
--- /dev/null
+++
b/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/BIP.stx
@@ -0,0 +1,7 @@
+Pseudo-statistics about the `BIP.raw` file content.
+Format is (where <…> are mandatory and {…} optional):
+
+ <band> <minimum> <maximum> {mean} {std_deviation} {linear_stretch_min}
{linear_stretch_max}
+
+1 2 250 100 10
+Above values are not real statistics.
diff --git
a/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/grid.clr
b/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/grid.clr
new file mode 100644
index 0000000000..8626f5ff73
--- /dev/null
+++
b/storage/sis-storage/src/test/resources/org/apache/sis/internal/storage/esri/grid.clr
@@ -0,0 +1,14 @@
+Color map for `grid.asc` file. This auxiliary file is
+actually is actually for BIP/BIL/BSQ raster formats,
+but Apache SIS applies it to ASCII Grid file as well.
+
+-10 0 0 255 (blue)
+ 0 0 255 255 (cyan)
+ 10 0 255 0 (green)
+ 20 255 255 0 (yellow)
+ 30 255 165 0 (orange)
+ 40 160 32 240 (purple)
+
+Note: in current Apache SIS implementation this file is ignored
+because ASCII grid data are floating points and color maps are
+restricted to integer types.
