diff --git a/cdm/misc/src/main/java/ucar/nc2/geotiff/GeotiffWriter.java b/cdm/misc/src/main/java/ucar/nc2/geotiff/GeotiffWriter.java
index 5ff54b7875..5c611a61ef 100644
--- a/cdm/misc/src/main/java/ucar/nc2/geotiff/GeotiffWriter.java
+++ b/cdm/misc/src/main/java/ucar/nc2/geotiff/GeotiffWriter.java
@@ -65,8 +65,9 @@ public void close() throws IOException {
/**
* Write GridDatatype data to the geotiff file.
*
- * This is for backwards-compatibility. Assumes dtype is FLOAT if greyScale is false, and assumes
- * dtype is BYTE if greyScale is true.
+ * Greyscale mode will auto-normalize the data from 1 to 255 and save as unsigned bytes, with 0's used
+ * for missing data. A color table can be applied if specified via `setColorTable()`.
+ * Non-greyscale mode will save the data as floats, encoding missing data as the data minimum minus one.
*
* @param dataset grid in contained in this dataset
* @param grid data is in this grid
@@ -75,21 +76,39 @@ public void close() throws IOException {
* @throws IOException on i/o error
*/
public void writeGrid(GridDataset dataset, GridDatatype grid, Array data, boolean greyScale) throws IOException {
- writeGrid(dataset, grid, data, greyScale, greyScale ? DataType.BYTE : DataType.FLOAT);
+ writeGrid(dataset, grid, data, greyScale, greyScale ? DataType.UBYTE : DataType.FLOAT);
}
/**
* Write GridDatatype data to the geotiff file.
*
+ * Greyscale mode will auto-normalize the data from 1 to 255 and save as unsigned bytes, with 0's used
+ * for missing data.
+ * Non-greyscale mode with a floating point dtype will save the data as floats, encoding missing data
+ * as the data's minimum minus one. Any other dtype will save the data coerced to the specified dtype.
+ *
+ * A color table can be applied if specified via `setColorTable()` and the dtype is UBYTE.
+ *
* @param dataset grid in contained in this dataset
* @param grid data is in this grid
* @param data 2D array in YX order
* @param greyScale if true, write greyScale image, else dataSample.
- * @param dtype DataType for the output.
+ * @param dtype DataType for the output. See other writeGrid() documentation for more details.
* @throws IOException on i/o error
+ * @throws IllegalArgumentException if above assumptions not valid
*/
public void writeGrid(GridDataset dataset, GridDatatype grid, Array data, boolean greyScale, DataType dtype)
- throws IOException {
+ throws IOException, IllegalArgumentException {
+ // This check has to be *before* resolving the dtype so that we are only
+ // checking explicitly specified data types.
+ if (greyScale && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When greyScale is true, dtype must be UBYTE");
+ }
+
+ if (colorTable != null && colorTable.length > 0 && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When using the color table, dtype must be UBYTE");
+ }
+
GridCoordSystem gcs = grid.getCoordinateSystem();
if (!gcs.isRegularSpatial()) {
@@ -136,8 +155,9 @@ public void writeGrid(GridDataset dataset, GridDatatype grid, Array data, boolea
* be equally spaced
*
*
- * This is for backwards-compatibility. Assumes dtype is FLOAT if greyScale is false, and assumes
- * dtype is BYTE if greyScale is true.
+ * Greyscale mode will auto-normalize the data from 1 to 255 and save as unsigned bytes, with 0's used
+ * for missing data. A color table can be applied if specified via `setColorTable()`.
+ * Non-greyscale mode will save the data as floats, encoding missing data as the data minimum minus one.
*
* @param grid original grid
* @param data 2D array in YX order
@@ -148,12 +168,12 @@ public void writeGrid(GridDataset dataset, GridDatatype grid, Array data, boolea
* @param yInc increment y coord
* @param imageNumber used to write multiple images
* @throws IOException on i/o error
- * @throws IllegalArgumentException if above assumptions not valid *
+ * @throws IllegalArgumentException if above assumptions not valid
*/
void writeGrid(GridDatatype grid, Array data, boolean greyScale, double xStart, double yStart, double xInc,
double yInc, int imageNumber) throws IOException {
writeGrid(grid, data, greyScale, xStart, yStart, xInc, yInc, imageNumber,
- greyScale ? DataType.BYTE : DataType.FLOAT);
+ greyScale ? DataType.UBYTE : DataType.FLOAT);
}
/**
@@ -165,6 +185,13 @@ void writeGrid(GridDatatype grid, Array data, boolean greyScale, double xStart,
* be equally spaced
*
*
+ * Greyscale mode will auto-normalize the data from 1 to 255 and save as unsigned bytes, with 0's used
+ * for missing data.
+ * Non-greyscale mode with a floating point dtype will save the data as floats, encoding missing data
+ * as the data's minimum minus one. Any other dtype will save the data coerced to the specified dtype.
+ *
+ * A color table can be applied if specified via `setColorTable()` and the dtype is UBYTE.
+ *
* @param grid original grid
* @param data 2D array in YX order
* @param greyScale if true, normalize the data before writing, otherwise, only handle missing data.
@@ -175,31 +202,28 @@ void writeGrid(GridDatatype grid, Array data, boolean greyScale, double xStart,
* @param imageNumber used to write multiple images
* @param dtype if greyScale is false, then save the data in the given data type.
* Currently, this is a bit hobbled in order to avoid back-compatibility breaks.
- * If greyScale is true and this is not BYTE, then an exception is thrown.
+ * If dtype is DOUBLE, is is currenly downcasted to FLOAT.
+ * When dtype is floating point, missing data is encoded as the data's minimum minus one.
* If null, then use the datatype of the given array.
* @throws IOException on i/o error
- * @throws IllegalArgumentException if above assumptions not valid *
+ * @throws IllegalArgumentException if above assumptions not valid
*/
void writeGrid(GridDatatype grid, Array data, boolean greyScale, double xStart, double yStart, double xInc,
- double yInc, int imageNumber, DataType dtype) throws IOException {
-
- int nextStart;
- GridCoordSystem gcs = grid.getCoordinateSystem();
+ double yInc, int imageNumber, DataType dtype) throws IOException, IllegalArgumentException {
// This check has to be *before* resolving the dtype so that we are only
// checking explicitly specified data types.
- if (greyScale && dtype != DataType.BYTE) {
- throw new IllegalArgumentException("When greyScale is true, dtype must be BYTE or null");
+ if (greyScale && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When greyScale is true, dtype must be UBYTE");
}
- if (dtype == null) {
- dtype = data.getDataType();
- // Need to cap at single precision floats because that's what gets written for floating points
- if (dtype == DataType.DOUBLE) {
- dtype = DataType.FLOAT;
- }
+ if (colorTable != null && colorTable.length > 0 && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When using the color table, dtype must be UBYTE");
}
+ int nextStart;
+ GridCoordSystem gcs = grid.getCoordinateSystem();
+
// get rid of this when all projections are implemented
if (!gcs.isLatLon() && !(gcs.getProjection() instanceof LambertConformal)
&& !(gcs.getProjection() instanceof Stereographic) && !(gcs.getProjection() instanceof Mercator)
@@ -209,6 +233,14 @@ void writeGrid(GridDatatype grid, Array data, boolean greyScale, double xStart,
throw new IllegalArgumentException("Unsupported projection = " + gcs.getProjection().getClass().getName());
}
+ if (dtype == null) {
+ dtype = data.getDataType();
+ // Need to cap at single precision floats because that's what gets written for floating points
+ if (dtype == DataType.DOUBLE) {
+ dtype = DataType.FLOAT;
+ }
+ }
+
// write the data first
MAMath.MinMax dataMinMax = grid.getMinMaxSkipMissingData(data);
if (greyScale) {
@@ -235,6 +267,20 @@ private void writeMetadata(boolean greyScale, double xStart, double yStart, doub
int width, int imageNumber, int nextStart, MAMath.MinMax dataMinMax, Projection proj, DataType dtype)
throws IOException {
+ if (dtype == null) {
+ throw new IllegalArgumentException("dtype can't be null in writeMetadata()");
+ }
+
+ if (greyScale && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When greyScale is true, dtype must be UBYTE");
+ }
+
+ if (colorTable != null && colorTable.length > 0 && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When using the color table, the dtype must be UBYTE");
+ }
+
+ int elemSize = dtype.getSize();
+
geotiff.addTag(new IFDEntry(Tag.ImageWidth, FieldType.SHORT).setValue(width));
geotiff.addTag(new IFDEntry(Tag.ImageLength, FieldType.SHORT).setValue(height));
@@ -257,18 +303,6 @@ private void writeMetadata(boolean greyScale, double xStart, double yStart, doub
* geotiff.addTag( new IFDEntry(Tag.StripOffsets, FieldType.LONG).setValue(nextStart));
*/
- if (dtype == null) {
- throw new IllegalArgumentException("dtype can't be null in writeMetadata()");
- }
-
- // This check has to be *before* resolving the dtype so that we are only
- // checking explicitly specified data types.
- if (greyScale && dtype != DataType.BYTE) {
- throw new IllegalArgumentException("When greyScale is true, dtype must be BYTE");
- }
-
- int elemSize = dtype.getSize();
-
int[] soffset = new int[height];
int[] sbytecount = new int[height];
if (imageNumber == 1) {
@@ -301,15 +335,16 @@ private void writeMetadata(boolean greyScale, double xStart, double yStart, doub
geotiff.addTag(new IFDEntry(Tag.PhotometricInterpretation, FieldType.SHORT).setValue(1));
} else {
if (colorTable != null && colorTable.length > 0) {
+ // standard tags for Palette-color images ( see TIFF spec, section 5)
geotiff.addTag(new IFDEntry(Tag.PhotometricInterpretation, FieldType.SHORT).setValue(3));
geotiff.addTag(new IFDEntry(Tag.ColorMap, FieldType.SHORT, colorTable.length).setValue(colorTable));
} else {
- geotiff.addTag(new IFDEntry(Tag.PhotometricInterpretation, FieldType.SHORT).setValue(1)); // black is zero :
- // not used?
+ geotiff.addTag(new IFDEntry(Tag.PhotometricInterpretation, FieldType.SHORT).setValue(1)); // black is zero
}
- // standard tags for SampleFormat ( see TIFF spec, section 19)
+
geotiff.addTag(new IFDEntry(Tag.BitsPerSample, FieldType.SHORT).setValue(elemSize * 8));
+ // standard tags for SampleFormat ( see TIFF spec, section 19)
if (dtype.isIntegral()) {
geotiff.addTag(new IFDEntry(Tag.SampleFormat, FieldType.SHORT).setValue(dtype.isUnsigned() ? 1 : 2)); // UINT or
// INT
@@ -408,8 +443,8 @@ public int[] getColorTable() {
* be floored/ceilinged to the [0, 255] range. The color table is also assumed to be for pixel values
* between 0 and 255.
*
- * In order for the color table to be properly included in the geotiff, the "greyScale" mode must be false,
- * and the output data type must be byte or integer.
+ * In order for the color table to be properly included in the geotiff, the output data type must be unsigned bytes.
+ * This works even for greyscale mode.
*/
public void setColorTable(Map colorMap) {
setColorTable(colorMap, new Color(0, 0, 0));
@@ -424,8 +459,8 @@ public void setColorTable(Map colorMap) {
* For these RGB triplets, 0 is minimum intensity, 255 is maximum intensity. Values outside that range will
* be floored/ceilinged to the [0, 255] range. The color table is also assumed to be for pixel values
* between 0 and 255.
- * In order for the color table to be properly included in the geotiff, the "greyScale" mode must be false,
- * and the output data type must be byte or integer.
+ * In order for the color table to be properly included in the geotiff, the output data type must be unsigned bytes.
+ * This works even for greyscale mode.
*/
public void setColorTable(Map colorMap, Color defaultRGB) {
if (colorMap == null) {
@@ -433,9 +468,8 @@ public void setColorTable(Map colorMap, Color defaultRGB) {
return;
}
- // FIXME: This isn't quite right because this assumes that the data being written is
- // unsigned bytes, but the tiff spec says that it should be sized to the width of
- // the data type, but I would need to know the data type, which this writer doesn't know.
+ // TIFF spec allows for 4 or 8 bits per sample (making for 16 or 256 entries).
+ // Since we don't support saving data as 4 bits per sample, we'll force it to 256.
colorTable = new int[3 * 256];
for (int i = 0; i < 256; i++) {
// Scale it up to [0, 65535], which is needed by the ColorMap tag.
@@ -475,7 +509,7 @@ public static HashMap createColorMap(int[] flag_values, String[]
*
* @param data input data array (of any data type)
* @param isUnsigned coerce to unsigned bytes
- * @return integer data array
+ * @return byte data array
*/
static ArrayByte coerceByte(Array data, boolean isUnsigned) {
ArrayByte array = (ArrayByte) Array.factory(isUnsigned ? DataType.UBYTE : DataType.BYTE, data.getShape());
@@ -495,7 +529,7 @@ static ArrayByte coerceByte(Array data, boolean isUnsigned) {
*
* @param data input data array (of any data type)
* @param isUnsigned coerce to unsigned integers
- * @return integer data array
+ * @return short integer data array
*/
static ArrayShort coerceShort(Array data, boolean isUnsigned) {
ArrayShort array = (ArrayShort) Array.factory(isUnsigned ? DataType.USHORT : DataType.SHORT, data.getShape());
@@ -503,7 +537,7 @@ static ArrayShort coerceShort(Array data, boolean isUnsigned) {
IndexIterator resultIter = array.getIndexIterator();
while (dataIter.hasNext()) {
- resultIter.setIntNext(dataIter.getIntNext());
+ resultIter.setShortNext(dataIter.getShortNext());
}
return array;
@@ -516,7 +550,7 @@ static ArrayShort coerceShort(Array data, boolean isUnsigned) {
*
* @param data input data array (of any data type)
* @param isUnsigned coerce to unsigned integers
- * @return integer data array
+ * @return 32-bit integer data array
*/
static ArrayInt coerceInt(Array data, boolean isUnsigned) {
ArrayInt array = (ArrayInt) Array.factory(isUnsigned ? DataType.UINT : DataType.INT, data.getShape());
@@ -543,7 +577,7 @@ static ArrayFloat coerceFloat(Array data) {
IndexIterator resultIter = array.getIndexIterator();
while (dataIter.hasNext()) {
- resultIter.setIntNext(dataIter.getIntNext());
+ resultIter.setFloatNext(dataIter.getFloatNext());
}
return array;
@@ -574,7 +608,7 @@ private ArrayFloat replaceMissingValues(IsMissingEvaluator grid, Array data, MAM
}
/**
- * Replace missing values with 0; scale other values between 1 and 255, return a byte data array.
+ * Replace missing values with 0; scale other values between 1 and 255, return a ubyte data array.
*
* @param grid GridDatatype
* @param data input data array
@@ -820,22 +854,35 @@ private double geoShiftGetXstart(Array lon, double inc) {
/**
* Write GridCoverage data to the geotiff file.
*
+ * Greyscale mode will auto-normalize the data from 1 to 255 and save as unsigned bytes, with 0's used
+ * for missing data. A color table can be applied if specified via `setColorTable()`.
+ * Non-greyscale mode will save the data as floats, encoding missing data as the data minimum minus one.
+ *
* @param array GeoReferencedArray array in YX order
* @param greyScale if true, write greyScale image, else dataSample.
* @throws IOException on i/o error
*/
public void writeGrid(GeoReferencedArray array, boolean greyScale) throws IOException {
- writeGrid(array, greyScale, greyScale ? DataType.BYTE : DataType.FLOAT);
+ writeGrid(array, greyScale, greyScale ? DataType.UBYTE : DataType.FLOAT);
}
/**
* Write GridCoverage data to the geotiff file.
*
+ * Greyscale mode will auto-normalize the data from 1 to 255 and save as unsigned bytes, with 0's used
+ * for missing data.
+ * Non-greyscale mode with a floating point dtype will save the data as floats, encoding missing data
+ * as the data's minimum minus one. Any other dtype will save the data coerced to the specified dtype.
+ *
+ * A color table can be applied if specified via `setColorTable()` and the dtype is UBYTE.
+ *
* @param array GeoReferencedArray array in YX order
* @param greyScale if true, write greyScale image, else dataSample.
* @param dtype if greyScale is false, then save the data in the given data type.
* Currently, this is a bit hobbled in order to avoid back-compatibility breaks.
- * If greyScale is true and this is not BYTE, then an exception is thrown.
+ * If greyScale is true and this is not UBYTE, then an exception is thrown.
+ * If dtype is DOUBLE, it downcasted to FLOAT instead.
+ * If using the colorTable and this is not UBYTE, then an exception is thrown.
* If null, then use the datatype of the given array.
* @throws IOException on i/o error
* @throws IllegalArgumentException if data isn't regular or if contradicting the greyScale argument.
@@ -843,6 +890,16 @@ public void writeGrid(GeoReferencedArray array, boolean greyScale) throws IOExce
public void writeGrid(GeoReferencedArray array, boolean greyScale, DataType dtype)
throws IOException, IllegalArgumentException {
+ // This check has to be *before* resolving the dtype so that we are only
+ // checking explicitly specified data types.
+ if (greyScale && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When greyScale is true, dtype must be UBYTE");
+ }
+
+ if (colorTable != null && colorTable.length > 0 && dtype != DataType.UBYTE) {
+ throw new IllegalArgumentException("When using the colorTable, the dtype must be UBYTE");
+ }
+
CoverageCoordSys gcs = array.getCoordSysForData();
if (!gcs.isRegularSpatial())
throw new IllegalArgumentException("Must have 1D x and y axes for " + array.getCoverageName());
@@ -866,12 +923,6 @@ public void writeGrid(GeoReferencedArray array, boolean greyScale, DataType dtyp
yStart = yaxis.getCoordEdgeLast() * scaler;
}
- // This check has to be *before* resolving the dtype so that we are only
- // checking explicitly specified data types.
- if (greyScale && dtype != DataType.BYTE) {
- throw new IllegalArgumentException("When greyScale is true, dtype must be BYTE or null");
- }
-
if (dtype == null) {
dtype = data.getDataType();
// Need to cap at single precision floats because that's what gets written for floating points
diff --git a/cdm/misc/src/test/java/ucar/nc2/geotiff/TestGeoTiffPalette.java b/cdm/misc/src/test/java/ucar/nc2/geotiff/TestGeoTiffPalette.java
index 1203bfa1d6..5492e139d8 100644
--- a/cdm/misc/src/test/java/ucar/nc2/geotiff/TestGeoTiffPalette.java
+++ b/cdm/misc/src/test/java/ucar/nc2/geotiff/TestGeoTiffPalette.java
@@ -106,6 +106,30 @@ public void testSetColorTable() {
Assert.assertNull(resultTable);
}
+ @Test
+ public void testInputChecks() {
+ // Check that exceptions are raised if attempting to write out a grid with a color table, but not for
+ // an appropriate dtype.
+
+ GeotiffWriter writer = new GeotiffWriter("should_not_be_made.tif");
+ HashMap colorMap =
+ GeotiffWriter.createColorMap(new int[] {1, 2, 3, 4}, new String[] {"#00AAff", "#151412", "#DE01aB", "#100ABB"});
+ int[] colorTable;
+ writer.setColorTable(colorMap, Color.black);
+ Exception badargs;
+ badargs = Assert.assertThrows(IllegalArgumentException.class, () -> {
+ writer.writeGrid(null, false, DataType.BYTE);
+ });
+ badargs = Assert.assertThrows(IllegalArgumentException.class, () -> {
+ writer.writeGrid(null, null, null, false, DataType.UINT);
+ });
+ badargs = Assert.assertThrows(IllegalArgumentException.class, () -> {
+ writer.writeGrid(null, null, false, 0, 0, 0, 0, 0, DataType.SHORT);
+ });
+ badargs = Assert.assertThrows(IllegalArgumentException.class, () -> {
+ writer.writeGrid(null, null, false, 0, 0, 0, 0, 0, DataType.FLOAT);
+ });
+ }
@Test
public void testWritePalette() throws IOException {