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Many fixes and improvements to geotiff colortable handling
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* Make it possible to use colortable regardless of greyscale mode, so long as it is UBYTE
* Fix some of the coercion code
* Added more tests
* Improved documentation and input checking
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@WeatherGod @tdrwenski
WeatherGod authored and tdrwenski committed Jul 1, 2024
1 parent 39bf09e commit f90f9e7
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Showing 2 changed files with 134 additions and 59 deletions.
169 changes: 110 additions & 59 deletions cdm/misc/src/main/java/ucar/nc2/geotiff/GeotiffWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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()) {
Expand Down Expand Up @@ -136,8 +155,9 @@ public void writeGrid(GridDataset dataset, GridDatatype grid, Array data, boolea
* <li>be equally spaced
* </ol>
*
* 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
Expand All @@ -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);
}

/**
Expand All @@ -165,6 +185,13 @@ void writeGrid(GridDatatype grid, Array data, boolean greyScale, double xStart,
* <li>be equally spaced
* </ol>
*
* 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.
Expand All @@ -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)
Expand All @@ -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) {
Expand All @@ -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));

Expand All @@ -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) {
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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<Integer, Color> colorMap) {
setColorTable(colorMap, new Color(0, 0, 0));
Expand All @@ -424,18 +459,17 @@ public void setColorTable(Map<Integer, Color> 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<Integer, Color> colorMap, Color defaultRGB) {
if (colorMap == null) {
colorTable = null;
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.
Expand Down Expand Up @@ -475,7 +509,7 @@ public static HashMap<Integer, Color> 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());
Expand All @@ -495,15 +529,15 @@ 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());
IndexIterator dataIter = data.getIndexIterator();
IndexIterator resultIter = array.getIndexIterator();

while (dataIter.hasNext()) {
resultIter.setIntNext(dataIter.getIntNext());
resultIter.setShortNext(dataIter.getShortNext());
}

return array;
Expand All @@ -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());
Expand All @@ -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;
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -820,29 +854,52 @@ 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.
*/
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());
Expand All @@ -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
Expand Down
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