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Commit 6894dccd authored by Andrey Filippov's avatar Andrey Filippov
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Trying to get GPS data

parent db9a0992
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Showing with 1192 additions and 94 deletions
pom.xml
View file @ 6894dccd
......@@ -217,21 +217,20 @@
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.3.2</version><!--$NO-MVN-MAN-VER$-->
<version>1.3.2</version><!--$NO-MVN-MAN-VER$-->
<executions>
<execution>
<phase>package</phase>
<phase>package</phase>
<goals>
<goal>java</goal>
</goals>
</execution>
</executions>
<configuration>
<!-- <mainClass>Aberration_Calibration</mainClass> -->
<!-- <mainClass>Aberration_Calibration</mainClass> -->
<mainClass>Eyesis_Correction</mainClass>
</configuration>
</plugin>
......@@ -253,11 +252,35 @@
<format>Build {0,date,yyyy-MM-dd} {0,time,HH:MM:SS} on host {1}</format>
<items>
<item>timestamp</item>
<!-- <item>foxel-MRHM7AP</item> -->
</items>
</configuration>
</plugin>
</plugin>
<!-- Trying sources/javadocs -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.2</version>
<executions>
<execution>
<goals>
<goal>sources</goal>
<goal>resolve</goal>
</goals>
<configuration>
<classifier>javadoc</classifier>
</configuration>
</execution>
</executions>
</plugin>
<!-- End of Trying sources/javadocs -->
</plugins>
</pluginManagement>
</build>
......
src/main/java/com/elphel/imagej/correction/EyesisCorrections.java
View file @ 6894dccd
......@@ -2741,7 +2741,7 @@ public class EyesisCorrections {
} else {
if (debugLevel > 0) System.out.println("Saving RGBA result to "+path+".tiff");
try {
(new EyesisTiff()).saveTiffARGB32(
EyesisTiff.saveTiffARGB32(
imp,
path+".tiff", //path, // +".tiff",
false, // correctionsParameters.imageJTags,
......@@ -2777,7 +2777,7 @@ public class EyesisCorrections {
if ((imp.getStackSize() == 4) && imp.getStack().getSliceLabel(4).equals("alpha")){
try {
(new EyesisTiff()).saveTiff(
EyesisTiff.saveTiff(
imp,
path+".tiff",
mode, //
......
src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java
View file @ 6894dccd
......@@ -43,6 +43,7 @@ import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.WindowEvent;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
......@@ -70,9 +71,22 @@ import java.util.Properties;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import javax.imageio.ImageIO;
import javax.imageio.ImageTypeSpecifier;
import javax.imageio.ImageWriteParam;
import javax.imageio.ImageWriter;
import javax.imageio.metadata.IIOInvalidTreeException;
import javax.imageio.metadata.IIOMetadata;
import javax.imageio.metadata.IIOMetadataFormatImpl;
import javax.imageio.metadata.IIOMetadataNode;
import javax.imageio.plugins.tiff.ExifGPSTagSet;
import javax.imageio.plugins.tiff.TIFFDirectory;
import javax.imageio.plugins.tiff.TIFFTagSet;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileFilter;
import org.w3c.dom.Node;
import com.elphel.imagej.calibration.CalibrationFileManagement;
import com.elphel.imagej.calibration.CalibrationIllustration;
import com.elphel.imagej.calibration.CalibrationIllustrationParameters;
......@@ -95,6 +109,8 @@ import com.elphel.imagej.ims.EventLogger;
import com.elphel.imagej.ims.Imx5;
import com.elphel.imagej.jp4.JP46_Reader_camera;
import com.elphel.imagej.lwir.LwirReader;
import com.elphel.imagej.readers.ChangeImageResolution;
import com.elphel.imagej.readers.DumpImageMetadata;
import com.elphel.imagej.readers.EyesisTiff;
import com.elphel.imagej.tensorflow.TensorflowInferModel;
import com.elphel.imagej.tileprocessor.Clt1d;
......@@ -578,6 +594,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
if (ADVANCED_MODE) {
addButton("Tiff Writer", panel7);
addButton("Tiff Properties", panel7);
addButton("Add TIFF resolution", panel7);
}
plugInFrame.add(panel7);
......@@ -1662,7 +1679,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
/* ======================================================================== */
} else if (label.equals("Tiff Writer")) {
DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
EyesisTiff eyesisTiff = new EyesisTiff();
// EyesisTiff eyesisTiff = new EyesisTiff();
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel == null) {
IJ.showMessage("Error", "No images selected");
......@@ -1676,7 +1693,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
}
try {
try {
eyesisTiff.saveTiff(imp_sel, path, CORRECTION_PARAMETERS.equirectangularFormat,
EyesisTiff.saveTiff(imp_sel, path, CORRECTION_PARAMETERS.equirectangularFormat,
(CORRECTION_PARAMETERS.equirectangularFormat == 3) ? CORRECTION_PARAMETERS.outputRangeFP
: CORRECTION_PARAMETERS.outputRangeInt,
CORRECTION_PARAMETERS.imageJTags, DEBUG_LEVEL);
......@@ -1696,13 +1713,109 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
/* ======================================================================== */
} else if (label.equals("Tiff Properties")) {
DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
EyesisTiff eyesisTiff = new EyesisTiff();
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel == null) {
IJ.showMessage("Error", "No images selected");
return;
}
eyesisTiff.propertiesTiff(imp_sel);
String orig_path = imp_sel.getOriginalFileInfo().getFilePath();
try {
DumpImageMetadata.processFile(new File(orig_path));
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// EyesisTiff.propertiesTiff(imp_sel);
return;
/* ======================================================================== */
} else if (label.equals("Add TIFF resolution")) {
DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
ImagePlus imp_sel = WindowManager.getCurrentImage();
if (imp_sel == null) {
IJ.showMessage("Error", "No images selected");
return;
}
String orig_path = imp_sel.getOriginalFileInfo().getFilePath();
// Testing change image resolution
File inputFile = new File(orig_path);
IIOMetadata inMetadata = null;
try {
inMetadata = DumpImageMetadata.getFileMetadata(inputFile);
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
return;
}
double resolutionDPI = 600;
File outputFile = new File(orig_path+"_"+((int)resolutionDPI)+"-01.tiff");
BufferedImage image = null;
try {
image = ChangeImageResolution.readImage(inputFile); // wrong imageType 0 (should be 2)
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return;
}
IIOMetadataNode newMetadata = ChangeImageResolution.createResolutionMetadata(resolutionDPI);
// IIOMetadataNode addMetadata = ChangeImageResolution.createResolutionMetadata0(resolutionDPI);
// inMetaData.appendChild()
try {
inMetadata.mergeTree(IIOMetadataFormatImpl.standardMetadataFormatName, newMetadata);
} catch (IIOInvalidTreeException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
return;
}
Node metadata_as_tree = inMetadata.getAsTree("javax_imageio_tiff_image_1.0");
BufferedImage bufferedImageAlpha = new BufferedImage(
image.getWidth(),
image.getHeight(),
BufferedImage.TYPE_INT_ARGB
);
ImageWriter tiffWriter = ImageIO.getImageWritersByFormatName("tiff").next();
ImageWriteParam tiffWriteParam = tiffWriter.getDefaultWriteParam();
tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromRenderedImage(bufferedImageAlpha);
IIOMetadata imageMetadata = tiffWriter.getDefaultImageMetadata(imageType, tiffWriteParam);
TIFFDirectory directory = null;
try {
directory = TIFFDirectory.createFromMetadata(imageMetadata);
} catch (IIOInvalidTreeException e2) {
// TODO Auto-generated catch block
e2.printStackTrace();
}
/// TIFFTagSet tag_set = ExifGPSTagSet.getInstance();
/// directory.addTagSet(tag_set); // ExifGPSTagSet.getInstance());
//// imageMetadata = directory.getAsMetadata();
System.out.println("\n=== metadata_as_tree ===:");
DumpImageMetadata.displayMetadataNode(metadata_as_tree, 1);
System.out.println("\n=== imageMetadata as javax_imageio_tiff_image_1.0 ===:");
DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree("javax_imageio_tiff_image_1.0"), 1);
try {
// imageMetadata.mergeTree(IIOMetadataFormatImpl.standardMetadataFormatName, metadata_as_tree);
imageMetadata.mergeTree("javax_imageio_tiff_image_1.0", metadata_as_tree);
} catch (IIOInvalidTreeException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
return;
}
System.out.println("\n=== imageMetadata merged as javax_imageio_tiff_image_1.0 ===:");
DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree("javax_imageio_tiff_image_1.0"), 1);
// works with inMetadata. Will it with imageMetadata?
try {
ChangeImageResolution.writeImage(outputFile, image, imageMetadata); // inMetadata); // newMetadata);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return;
/* ======================================================================== */
} else if (label.equals("Configure PP")) {
......
src/main/java/com/elphel/imagej/ims/Did_ins.java
View file @ 6894dccd
package com.elphel.imagej.ims;
import java.time.LocalDate;
import java.time.LocalDateTime;
import java.util.Properties;
import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;
public abstract class Did_ins <T extends Did_ins <T>>{
final static LocalDateTime DT_01_06_1980 = LocalDateTime.of(1980,1,6,0,0);
final static int WEEK_SECONDS = 7 * 24 * 3600;
/** GPS number of weeks since January 6th, 1980 */
public int week; // uint32_t
......@@ -49,6 +52,20 @@ public abstract class Did_ins <T extends Did_ins <T>>{
return new int [] { week, (int)Math.round(timeOfWeek * 1000.0)};
}
public static LocalDateTime getLocalDateTime(int week, double tow) {
/** GPS number of weeks since January 6th, 1980 */
/** GPS time of week (since Sunday morning) in seconds */
int seconds = (int) Math.floor(tow);
int nanos = (int) Math.floor((tow-seconds)*1E9);
return DT_01_06_1980.plusWeeks(week).
plusSeconds(seconds).plusNanos(nanos);
}
public LocalDateTime getLocalDateTime() {
return getLocalDateTime(week, timeOfWeek);
}
public boolean isDidSane() {
if ((week < MIN_WEEK) || (week > MAX_WEEK)) {
System.out.println("isDidSane(): bad week = "+week+
......
src/main/java/com/elphel/imagej/readers/ChangeImageResolution.java 0 → 100644
View file @ 6894dccd
package com.elphel.imagej.readers;
//https://www.silverbaytech.com/2014/06/04/iiometadata-tutorial-part-3-writing-metadata/
/*
* Copyright (c) 2014 Kevin Hunter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
//package com.silverbaytech.blog.imageIoMetadata;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.util.Iterator;
import javax.imageio.IIOImage;
import javax.imageio.ImageIO;
import javax.imageio.ImageReader;
import javax.imageio.ImageTypeSpecifier;
import javax.imageio.ImageWriteParam;
import javax.imageio.ImageWriter;
import javax.imageio.metadata.IIOMetadata;
import javax.imageio.metadata.IIOMetadataFormatImpl;
import javax.imageio.metadata.IIOMetadataNode;
import javax.imageio.stream.ImageInputStream;
import javax.imageio.stream.ImageOutputStream;
public class ChangeImageResolution
{
private static String getFileExtension(File file)
{
String fileName = file.getName();
int lastDot = fileName.lastIndexOf('.');
return fileName.substring(lastDot + 1);
}
public static BufferedImage readImage(File file) throws IOException
{
ImageInputStream stream = null;
BufferedImage image = null;
try
{
stream = ImageIO.createImageInputStream(file);
Iterator<ImageReader> readers = ImageIO.getImageReaders(stream);
if (readers.hasNext())
{
ImageReader reader = readers.next();
reader.setInput(stream);
image = reader.read(0);
}
}
finally
{
if (stream != null)
{
stream.close();
}
}
return image;
}
//https://docs.oracle.com/en/java/javase/17/docs/api/java.desktop/javax/imageio/metadata/doc-files/standard_metadata.html
public static IIOMetadataNode createResolutionMetadata(double resolutionDPI)
{
String pixelSize = Double.toString(25.4 / resolutionDPI);
IIOMetadataNode horizontal = new IIOMetadataNode("HorizontalPixelSize");
horizontal.setAttribute("value", pixelSize);
IIOMetadataNode vertical = new IIOMetadataNode("VerticalPixelSize");
vertical.setAttribute("value", pixelSize);
IIOMetadataNode dimension = new IIOMetadataNode("Dimension");
dimension.appendChild(horizontal);
dimension.appendChild(vertical);
IIOMetadataNode root = new IIOMetadataNode(IIOMetadataFormatImpl.standardMetadataFormatName);
root.appendChild(dimension);
return root;
}
public static IIOMetadataNode createResolutionMetadata0(double resolutionDPI)
{
String pixelSize = Double.toString(25.4 / resolutionDPI);
IIOMetadataNode horizontal = new IIOMetadataNode("HorizontalPixelSize");
horizontal.setAttribute("value", pixelSize);
IIOMetadataNode vertical = new IIOMetadataNode("VerticalPixelSize");
vertical.setAttribute("value", pixelSize);
IIOMetadataNode dimension = new IIOMetadataNode("Dimension");
dimension.appendChild(horizontal);
dimension.appendChild(vertical);
return dimension;
// IIOMetadataNode root = new IIOMetadataNode(IIOMetadataFormatImpl.standardMetadataFormatName);
// root.appendChild(dimension);
// return root;
}
public static void writeImage(File outputFile, BufferedImage image, IIOMetadataNode newMetadata) throws IOException
{
String extension = getFileExtension(outputFile);
ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromBufferedImageType(image.getType());
ImageOutputStream stream = null;
try
{
Iterator<ImageWriter> writers = ImageIO.getImageWritersBySuffix(extension);
while(writers.hasNext())
{
ImageWriter writer = writers.next();
ImageWriteParam writeParam = writer.getDefaultWriteParam();
IIOMetadata imageMetadata = writer.getDefaultImageMetadata(imageType, writeParam);
if (!imageMetadata.isStandardMetadataFormatSupported())
{
continue;
}
if (imageMetadata.isReadOnly())
{
continue;
}
imageMetadata.mergeTree(IIOMetadataFormatImpl.standardMetadataFormatName, newMetadata);
IIOImage imageWithMetadata = new IIOImage(image, null, imageMetadata);
stream = ImageIO.createImageOutputStream(outputFile);
writer.setOutput(stream);
writer.write(null, imageWithMetadata, writeParam);
}
}
finally
{
if (stream != null)
{
stream.close();
}
}
}
public static void writeImage(File outputFile, BufferedImage image, IIOMetadata newMetadata) throws IOException
{
String extension = getFileExtension(outputFile);
ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromBufferedImageType(image.getType());
ImageOutputStream stream = null;
try
{
Iterator<ImageWriter> writers = ImageIO.getImageWritersBySuffix(extension);
while(writers.hasNext())
{
ImageWriter writer = writers.next();
ImageWriteParam writeParam = writer.getDefaultWriteParam();
/*
IIOMetadata imageMetadata = writer.getDefaultImageMetadata(imageType, writeParam);
if (!imageMetadata.isStandardMetadataFormatSupported())
{
continue;
}
if (imageMetadata.isReadOnly())
{
continue;
}
imageMetadata.mergeTree(IIOMetadataFormatImpl.standardMetadataFormatName, newMetadata);
*/
IIOImage imageWithMetadata = new IIOImage(image, null, newMetadata);
stream = ImageIO.createImageOutputStream(outputFile);
writer.setOutput(stream);
writer.write(null, imageWithMetadata, writeParam);
}
}
finally
{
if (stream != null)
{
stream.close();
}
}
}
public static void main(String[] args)
{
if (args.length != 3)
{
System.out
.println("Usage: ChangeImageResolution inputFile newResolutionDPI outputFile");
return;
}
try
{
File inputFile = new File(args[0]);
double resolutionDPI = Double.parseDouble(args[1]);
File outputFile = new File(args[2]);
BufferedImage image = readImage(inputFile);
IIOMetadataNode newMetadata = createResolutionMetadata(resolutionDPI);
writeImage(outputFile, image, newMetadata);
}
catch (Exception e)
{
e.printStackTrace();
}
}
}
src/main/java/com/elphel/imagej/readers/DumpImageMetadata.java 0 → 100644
View file @ 6894dccd
/*
https://www.silverbaytech.com/2014/05/29/iiometadata-tutorial-part-2-retrieving-image-metadata/
*/
package com.elphel.imagej.readers;
/*
* Copyright (c) 2014 Kevin Hunter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
//package com.silverbaytech.blog.imageIoMetadata;
import java.io.File;
import java.io.IOException;
import java.util.Iterator;
import javax.imageio.ImageIO;
import javax.imageio.ImageReader;
import javax.imageio.metadata.IIOMetadata;
import javax.imageio.stream.ImageInputStream;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
/**
* Dump the ImageIO metadata associated with one or more images.
*
* @author Kevin Hunter
*
*/
public class DumpImageMetadata
{
private static String getFileExtension(File file)
{
String fileName = file.getName();
int lastDot = fileName.lastIndexOf('.');
return fileName.substring(lastDot + 1);
}
private static void indent(int level)
{
for (int i = 0; i < level; i++)
{
System.out.print(" ");
}
}
private static void displayAttributes(NamedNodeMap attributes)
{
if (attributes != null)
{
int count = attributes.getLength();
for (int i = 0; i < count; i++)
{
Node attribute = attributes.item(i);
System.out.print(" ");
System.out.print(attribute.getNodeName());
System.out.print("='");
System.out.print(attribute.getNodeValue());
System.out.print("'");
}
}
}
public static void displayMetadataNode(Node node, int level)
{
indent(level);
System.out.print("<");
System.out.print(node.getNodeName());
NamedNodeMap attributes = node.getAttributes();
displayAttributes(attributes);
Node child = node.getFirstChild();
if (child == null)
{
String value = node.getNodeValue();
if (value == null || value.length() == 0)
{
System.out.println("/>");
}
else
{
System.out.print(">");
System.out.print(value);
System.out.print("<");
System.out.print(node.getNodeName());
System.out.println(">");
}
return;
}
System.out.println(">");
while (child != null)
{
displayMetadataNode(child, level + 1);
child = child.getNextSibling();
}
indent(level);
System.out.print("</");
System.out.print(node.getNodeName());
System.out.println(">");
}
private static void dumpMetadata(IIOMetadata metadata)
{
String[] names = metadata.getMetadataFormatNames();
int length = names.length;
for (int i = 0; i < length; i++)
{
indent(2);
System.out.println("Format name: " + names[i]);
displayMetadataNode(metadata.getAsTree(names[i]), 3);
}
}
private static void processFileWithReader(File file, ImageReader reader) throws IOException
{
ImageInputStream stream = null;
try
{
stream = ImageIO.createImageInputStream(file);
reader.setInput(stream, true);
IIOMetadata metadata = reader.getImageMetadata(0);
indent(1);
System.out.println("Image metadata");
dumpMetadata(metadata);
IIOMetadata smetadata = reader.getStreamMetadata();
if (smetadata != null)
{
indent(1);
System.out.println("Stream metadata");
dumpMetadata(smetadata);
}
}
finally
{
if (stream != null)
{
stream.close();
}
}
}
public static void processFile(File file) throws IOException
{
System.out.println("\nProcessing " + file.getName() + ":\n");
String extension = getFileExtension(file);
Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(extension);
while (readers.hasNext())
{
ImageReader reader = readers.next();
System.out.println("Reader: " + reader.getClass().getName());
processFileWithReader(file, reader);
}
}
public static IIOMetadata getFileMetadata(File file) throws IOException {
String extension = getFileExtension(file);
Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(extension);
IIOMetadata metadata = null;
if (readers.hasNext()) {
ImageReader reader = readers.next();
System.out.println("Reader: " + reader.getClass().getName());
// processFileWithReader(file, reader);
ImageInputStream stream = null;
try
{
stream = ImageIO.createImageInputStream(file);
reader.setInput(stream, true);
metadata = reader.getImageMetadata(0);
}
finally
{
if (stream != null)
{
stream.close();
}
}
}
return metadata;
}
public static void processDirectory(File directory) throws IOException
{
System.out.println("Processing all files in " + directory.getAbsolutePath());
File[] contents = directory.listFiles();
for (File file : contents)
{
if (file.isFile())
{
processFile(file);
}
}
}
public static void main(String[] args)
{
try
{
for (int i = 0; i < args.length; i++)
{
File fileOrDirectory = new File(args[i]);
if (fileOrDirectory.isFile())
{
processFile(fileOrDirectory);
}
else
{
processDirectory(fileOrDirectory);
}
}
System.out.println("\nDone");
}
catch (IOException e)
{
e.printStackTrace();
}
}
}
\ No newline at end of file
src/main/java/com/elphel/imagej/readers/ElphelTiffReader.java
View file @ 6894dccd
......@@ -59,9 +59,6 @@ import loci.formats.FormatTools;
import loci.formats.in.MetadataLevel;
import loci.formats.in.TiffReader;
import loci.formats.meta.MetadataStore;
import loci.formats.tiff.IFD;
import loci.formats.tiff.IFDList;
import loci.formats.tiff.TiffRational;
import ome.xml.model.primitives.Timestamp;
/*
......
src/main/java/com/elphel/imagej/readers/ElphelTiffWriter.java 0 → 100644
View file @ 6894dccd
/**
**
** ElphelTiffWriter - Write Tiff files w/o loci
**
** Copyright (C) 2023 Elphel, Inc.
**
** -----------------------------------------------------------------------------**
**
** ElphelTiffWriter.java is free software: you can redistribute it and/or modify
** it under the terms of the GNU General Public License as published by
** the Free Software Foundation, either version 3 of the License, or
** (at your option) any later version.
**
** This program is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
** GNU General Public License for more details.
**
** You should have received a copy of the GNU General Public License
** along with this program. If not, see <http://www.gnu.org/licenses/>.
** -----------------------------------------------------------------------------**
**
*/
package com.elphel.imagej.readers;
import java.awt.image.BufferedImage;
import java.awt.image.ColorModel;
import java.awt.image.DataBufferInt;
import java.awt.image.Raster;
import java.awt.image.SampleModel;
import java.io.File;
import java.io.IOException;
import java.time.LocalDateTime;
import javax.imageio.IIOImage;
import javax.imageio.ImageIO;
import javax.imageio.ImageTypeSpecifier;
import javax.imageio.ImageWriteParam;
import javax.imageio.ImageWriter;
import javax.imageio.metadata.IIOInvalidTreeException;
import javax.imageio.metadata.IIOMetadata;
import javax.imageio.metadata.IIOMetadataFormatImpl;
import javax.imageio.metadata.IIOMetadataNode;
import javax.imageio.stream.FileImageOutputStream;
import javax.imageio.plugins.tiff.TIFFDirectory;
import javax.imageio.plugins.tiff.TIFFTagSet;
import javax.imageio.plugins.tiff.ExifGPSTagSet;
import javax.imageio.plugins.tiff.ExifParentTIFFTagSet;
import javax.imageio.plugins.tiff.TIFFField;
import org.w3c.dom.Node;
import com.elphel.imagej.ims.Did_ins;
import ij.ImagePlus;
public class ElphelTiffWriter {
public static String TIFF_METADATA_FORMAT = "javax_imageio_tiff_image_1.0";
public static String TIFF_FIELD_TAG = "TIFFField";
public static String TIFF_ASCIIS_TAG = "TIFFAsciis";
public static String TIFF_ASCII_TAG = "TIFFAscii";
public static String TIFF_RATIONALS_TAG = "TIFFRationals";
public static String TIFF_RATIONAL_TAG = "TIFFRational";
public static String TIFF_FIELD_VALUE_ATTRIBUTE = "value";
public static void saveTiffARGB32(
ImagePlus imp,
String path,
boolean imageJTags,
int debugLevel
) {
// ImageWriter tiffWriter;
// ImageWriteParam tiffWriteParam;
IIOMetadata tiffStreamMetadata;
IIOMetadata primaryIFD;
BufferedImage bufferedImage = (BufferedImage) imp.getImage(); // properties=null
BufferedImage thumbnail;
File outputFile = new File(path);
System.out.println("saveTiffARGB32(): will write to "+outputFile);
System.out.println("ElphelTiffWriter.saveTiffARGB32");
// Write only the primary IFD and image data.
// Specify uncompressed output.
ImageWriter tiffWriter = ImageIO.getImageWritersByFormatName("tiff").next();
ImageWriteParam tiffWriteParam = tiffWriter.getDefaultWriteParam();
// tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
// tiffWriteParam.setSourceSubsampling(param.getSourceXSubsampling(), param.getSourceYSubsampling(), param.getSubsamplingXOffset(), param.getSubsamplingYOffset());
// tiffWriteParam.setSourceRegion(param.getSourceRegion());
// tiffWriteParam.setSourceBands(param.getSourceBands());
/*
* https://docs.oracle.com/javase%2F9%2Fdocs%2Fapi%2F%2F/javax/imageio/metadata/doc-files/tiff_metadata.html
Setting up the image metadata to write to a TIFF stream may be simplified by using
the TIFFDirectory class which represents a TIFF IFD. A field in a TIFF IFD is represented
by an instance of TIFFField. For each field to be written a TIFFField may be added to
the TIFFDirectory and the latter converted to an IIOMetadata object by invoking
TIFFDirectory.getAsMetadata. The IIOMetadata object so obtained may then be passed to
the TIFF writer.
ImageTypeSpecifier
ImageTypeSpecifier(ColorModel colorModel, SampleModel sampleModel)
Constructs an ImageTypeSpecifier directly from a ColorModel and a SampleModel.
static long computeImageSize(RenderedImage image) {
long bits = 0;
final int bands = image.getSampleModel().getNumBands();
for (int i = 0; i < bands; i++) {
bits += image.getSampleModel().getSampleSize(i);
}
return (long) Math.ceil(bits / 8) * image.getWidth() * image.getHeight();
}
void setRGB(int startX, int startY, int w, int h, int[] rgbArray, int offset, int scansize)
Sets an array of integer pixels in the default RGB color model (TYPE_INT_ARGB) and default sRGB color space, into a portion of the image data.
*/
// Raster raster = bufferedImage.getData(); // use pixels from IJ
BufferedImage bufferedImageAlpha = new BufferedImage(
bufferedImage.getWidth(),
bufferedImage.getHeight(),
BufferedImage.TYPE_INT_ARGB
);
int [] ipixels = (int[])imp.getProcessor().getPixels();
final int[] bia_as_arr = ( (DataBufferInt) bufferedImageAlpha.getRaster().getDataBuffer() ).getData();
System.arraycopy(ipixels, 0, bia_as_arr, 0, bia_as_arr.length);
/*
bufferedImageAlpha.setRGB( // slow
0, // int startX,
0, // int startY,
bufferedImage.getWidth(), // int w,
bufferedImage.getHeight(), // int h,
ipixels, // int[] rgbArray,
0, // int offset,
bufferedImage.getWidth()); // int scansize);
*/
// bufferedImageAlpha.setData(raster);
//BufferedImage.TYPE_INT_ARGB
// ColorModel colorModel = ColorModel.getRGBdefault();
// SampleModel samleModel = bufferedImage.getSampleModel();
// ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromRenderedImage(bufferedImage);
ImageTypeSpecifier imageType = ImageTypeSpecifier.createFromRenderedImage(bufferedImageAlpha);
IIOMetadata imageMetadata = tiffWriter.getDefaultImageMetadata(imageType, tiffWriteParam);
// just for testing:
double [] lla = { 49.9476514222895,28.5547846609957,323.750316821841};
LocalDateTime dt = Did_ins.getLocalDateTime(2286, 491072.634526699);
double pix_in_meters = 0.01;
/*
ExifGPSTagSet exif_tag_set = ExifGPSTagSet.getInstance();
TIFFTagSet [] tag_sets = {ExifGPSTagSet.getInstance()} ;
ExifParentTIFFTagSet eptts = ExifParentTIFFTagSet.getInstance();
TIFFDirectory gps_directory = new TIFFDirectory(
tag_sets, eptts.getTag(
ExifParentTIFFTagSet.TAG_GPS_INFO_IFD_POINTER));
TIFFTagSet tag_set = ExifGPSTagSet.getInstance();
TIFFField gps_ifd = null;
// int df = TIFFField.TIFF_IFD_POINTER; // 13
gps_ifd = new TIFFField(
eptts.getTag(
ExifParentTIFFTagSet.TAG_GPS_INFO_IFD_POINTER), // 'ExifIFDPointer', // TIFFTag tag,
13, // TIFFField.TIFF_IFD_POINTER, // int type,
(long) 0, // long offset,
(TIFFDirectory) gps_directory); // TIFFDirectory dir)
directory.addTIFFField(gps_ifd);
directory.addTagSet(tag_set); // ExifGPSTagSet.getInstance());
*/
/* */
TIFFDirectory directory = null;
try {
directory = TIFFDirectory.createFromMetadata(imageMetadata);
} catch (IIOInvalidTreeException e2) {
// TODO Auto-generated catch block
e2.printStackTrace();
}
TIFFTagSet tag_set = ExifGPSTagSet.getInstance();
TIFFTagSet eptts = ExifParentTIFFTagSet.getInstance();
directory.addTagSet(tag_set); // ExifGPSTagSet.getInstance());
directory.addTagSet(eptts); // ExifParentTIFFTagSet.getInstance());
//ExifGPSTagSet
imageMetadata = directory.getAsMetadata();
/* */
Node root_gps = imageMetadata.getAsTree(TIFF_METADATA_FORMAT);//?
System.out.println("\n=== root_gps ===:");
DumpImageMetadata.displayMetadataNode(root_gps, 1);
Node ifd = root_gps.getFirstChild();
IIOMetadataNode gpsRootNode = new IIOMetadataNode("TIFFIFD");
gpsRootNode.setAttribute("parentTagNumber", "34853");
gpsRootNode.setAttribute("parentTagName", "GPSInfoIFDPointer");
gpsRootNode.setAttribute("tagSets", "javax.imageio.plugins.tiff.ExifGPSTagSet");
IIOMetadataNode childNode = new IIOMetadataNode(TIFF_FIELD_TAG);
childNode.setAttribute("number", "1");
childNode.setAttribute("name", "GPSLatitudeRef");
IIOMetadataNode asciiNode = new IIOMetadataNode(TIFF_ASCIIS_TAG);
IIOMetadataNode childAsciiNode = new IIOMetadataNode(TIFF_ASCII_TAG);
childAsciiNode.setAttribute(TIFF_FIELD_VALUE_ATTRIBUTE, "N");
asciiNode.appendChild(childAsciiNode);
childNode.appendChild(asciiNode);
gpsRootNode.appendChild(childNode);
ifd.appendChild(gpsRootNode);
System.out.println("\n=== ifd ===:");
DumpImageMetadata.displayMetadataNode(ifd, 1);
/*
IIOMetadataNode childNode = new IIOMetadataNode(FileConstants.TIFF_FIELD_TAG);
childNode.setAttribute(FileConstants.TIFF_FIELD_NUMBER_ATTRIBUTE, "1");
childNode.setAttribute(FileConstants.TIFF_FIELD_NAME_ATTRIBUTE, "GPSLatitudeRef");
IIOMetadataNode asciiNode = new IIOMetadataNode("TIFFAsciis");
IIOMetadataNode childAsciiNode = new IIOMetadataNode("TIFFAscii");
childAsciiNode.setAttribute(FileConstants.TIFF_FIELD_VALUE_ATTRIBUTE, "N");
asciiNode.appendChild(childAsciiNode);
childNode.appendChild(asciiNode);
gpsRootNode.appendChild(childNode);
ifd.appendChild(gpsRootNode);
//Update metadata with new tree
metadata.setFromTree(FileConstants.TIFF_METADATA_FORMAT, root);
ImageOutputStream outstr = ImageIO.createImageOutputStream(writeTarget);
writer.setOutput(outstr);
//Write the image
IIOImage img = new IIOImage(renderedImage, Collections.<BufferedImage> emptyList(), metadata);
writer.write(img);
outstr.close();
public static String TIFF_METADATA_FORMAT = "javax_imageio_tiff_image_1.0";
public static String TIFF_FIELD_TAG = "TIFFField";
public static String TIFF_ASCIIS_TAG = "TIFFAsciis";
public static String TIFF_ASCII_TAG = "TIFFAscii";
public static String TIFF_RATIONALS_TAG = "TIFFRationals";
public static String TIFF_RATIONAL_TAG = "TIFFRational";
public static String TIFF_FIELD_VALUE_ATTRIBUTE = "value";
*/
IIOMetadataNode dimension = createResolutionMetadata(pix_in_meters);
// imageMetadata.appendChild(dimension);
//// IIOMetadataNode root_dimension = new IIOMetadataNode(TIFF_METADATA_FORMAT); // IIOMetadataFormatImpl.standardMetadataFormatName);
// root_dimension.appendChild(dimension);
//// root_dimension.appendChild(root_gps);
System.out.println("\n=== root_gps ===:"); // should have 2 tagSets, but has only baseline
/*
<javax_imageio_tiff_image_1.0>
<TIFFIFD tagSets='javax.imageio.plugins.tiff.BaselineTIFFTagSet,javax.imageio.plugins.tiff.GeoTIFFTagSet'>
*/
DumpImageMetadata.displayMetadataNode(root_gps, 1);
System.out.println("\n=== imageMetadata - before merge ===:");
DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree(TIFF_METADATA_FORMAT), 1);
// lost GPS data after merge
try {
imageMetadata.mergeTree(TIFF_METADATA_FORMAT, root_gps); // dimension); // Root must have "TIFFIFD" child
// imageMetadata.setFromTree(TIFF_METADATA_FORMAT, root_dimension); // dimension);
} catch (IIOInvalidTreeException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
return;
}
System.out.println("\n=== imageMetadata - after merge ===:");
DumpImageMetadata.displayMetadataNode(imageMetadata.getAsTree(TIFF_METADATA_FORMAT), 1);
System.out.println();
FileImageOutputStream outputStream;
try {
outputStream = new FileImageOutputStream(outputFile);
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
return;
}
tiffWriter.setOutput(outputStream);
// IIOImage image_with_metadata = new IIOImage(bufferedImage, null, primaryIFD);
// IIOImage image_with_metadata = new IIOImage(bufferedImage, null, null);
IIOImage image_with_metadata = new IIOImage(bufferedImageAlpha, null, imageMetadata);
System.out.println();
try {
tiffWriter.write(
null, // tiffStreamMetadata,
image_with_metadata,
tiffWriteParam);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
System.out.println();
}
private static IIOMetadataNode createResolutionMetadata(double resolutionPixelInMeters) {
// String pixelSize = Double.toString(25.4 / resolutionDPI);
String pixelSize = Double.toString(1000*resolutionPixelInMeters); // millimeters
IIOMetadataNode horizontal = new IIOMetadataNode("HorizontalPixelSize");
horizontal.setAttribute("value", pixelSize);
IIOMetadataNode vertical = new IIOMetadataNode("VerticalPixelSize");
vertical.setAttribute("value", pixelSize);
IIOMetadataNode dimension = new IIOMetadataNode("Dimension");
dimension.appendChild(horizontal);
dimension.appendChild(vertical);
return dimension;
// IIOMetadataNode root = new IIOMetadataNode(IIOMetadataFormatImpl.standardMetadataFormatName);
// root.appendChild(dimension);
// return root;
}
private static IIOMetadataNode createGpsMetadata(double [] lla, LocalDateTime dt) {
IIOMetadataNode gpsRootNode = new IIOMetadataNode("TIFFIFD");
// gpsRootNode.setAttribute(FileConstants.TIFF_FIELD_NUMBER_ATTRIBUTE, "34853");
return gpsRootNode;
}
/*
*
FileImageOutputStream outputStream = new FileImageOutputStream(outputFile);
writer.setOutput(outputStream);
IIOImage image = new IIOImage(outputImage, null, null);
writer.write(null, image, imageWriteParam);
writer.dispose();
*
*
*
image BufferedImage (id=191)
accelerationPriority 0.5
colorModel DirectColorModel (id=192)
imageType 1
osis null
properties null
raster IntegerInterleavedRaster (id=196)
surfaceManager null
*/
/*
public static void saveTiffARGB32(
ImagePlus imp,
String path,
boolean imageJTags,
int debugLevel
) throws IOException, FormatException, ServiceException, DependencyException{
int IFDImageFullWidth= 0x8214; // not defined in loci.formats.tiff.IFD
int IFDImageFullLength=0x8215; // not defined in loci.formats.tiff.IFD
// public static final int META_DATA_BYTE_COUNTS = 50838; // private tag registered with Adobe
// public static final int META_DATA = 50839; // private tag registered with Adobe
int IFDImageJByteCounts= 0xc696; // was array {12( if no slices, roi, etc.), bytes in info}
int IFDImageJInfo= 0xc697; // ImageJ info, starting with magic IJIJinfo,
byte [] ImageJInfoMagic={73,74,73,74,105,110,102,111,0,0,0,1};
int pixelsDenominator=1000;
String description=(imp.getProperty("description")!=null)?((String) imp.getProperty("description")):"Elphel Eyesis4pi";
int [] iPixels= (int []) imp.getProcessor().getPixels();
byte [] bytes=new byte[iPixels.length*4];
int pIndex=0;
for (int i=0;i<iPixels.length;i++){
bytes[pIndex++]=(byte) ((iPixels[i]>>16)& 0xff); // R
bytes[pIndex++]=(byte) ((iPixels[i]>> 8)& 0xff); // G
bytes[pIndex++]=(byte) ((iPixels[i]>> 0)& 0xff); // B
bytes[pIndex++]=(byte) ((iPixels[i]>>24)& 0xff); // alpha
}
IFD ifd=new IFD();
ifd.put(IFD.LITTLE_ENDIAN, false);
// ifd.put(new Integer(IFD.LITTLE_ENDIAN), new Boolean(true));
ifd.put(IFD.IMAGE_WIDTH, imp.getWidth());
ifd.put(IFD.IMAGE_LENGTH, imp.getHeight());
ifd.put(IFD.SAMPLES_PER_PIXEL, 4);
ifd.putIFDValue(IFD.SOFTWARE, "Elphel Eyesis");
ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, description);
// copy some other data?
ifd.putIFDValue(IFD.COMPRESSION, 1); //TiffCompression.UNCOMPRESSED);
ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION,2); // RGB
ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // extra 2 bytes (over 3) meaning Unassociated alpha data
// ifd.putIFDValue(IFD.EXTRA_SAMPLES,1); // extra 1 byte (over 3) meaning Associated alpha data
ifd.putIFDValue(IFD.SAMPLE_FORMAT,1); //
// int [] bpsArray={8,8,8,8};
// ifd.putIFDValue(IFD.BITS_PER_SAMPLE, bpsArray); // will be done automatically
if (imp.getProperty("XPosition")!=null) {
ifd.putIFDValue(IFD.X_POSITION,
new TiffRational((int) Math.round(pixelsDenominator*Double.parseDouble((String) imp.getProperty("XPosition"))) , pixelsDenominator));
}
if (imp.getProperty("YPosition")!=null) {
ifd.putIFDValue(IFD.Y_POSITION,
new TiffRational((int) Math.round(pixelsDenominator*Double.parseDouble((String) imp.getProperty("YPosition"))) , pixelsDenominator));
}
if (imp.getProperty("ImageFullWidth")!=null){
ifd.putIFDValue(IFDImageFullWidth, (long) Integer.parseInt((String) imp.getProperty("ImageFullWidth")));
}
if (imp.getProperty("ImageFullLength")!=null){
ifd.putIFDValue(IFDImageFullLength, (long) Integer.parseInt((String) imp.getProperty("ImageFullLength")));
}
//TODO: Seems to match ImageJ Info, but it is not recognized :-(
if (imageJTags && (imp.getProperty("Info")!=null) && (imp.getProperty("Info") instanceof String)){
int skipFirstBytes=2;
String info=(String) imp.getProperty("Info");
byte [] bInfoBody=info.getBytes("UTF-16");
int [] bInfo = new int [ImageJInfoMagic.length+bInfoBody.length-skipFirstBytes];
int index=0;
for (int i=0;i<ImageJInfoMagic.length;i++) bInfo[index++]=ImageJInfoMagic[i];
for (int i=skipFirstBytes;i<bInfoBody.length; i++) bInfo[index++]=bInfoBody[i]; // first 2 bytes {-2, -1} ???
long [] imageJcounts={12, bInfoBody.length-skipFirstBytes};
ifd.putIFDValue(IFDImageJByteCounts, imageJcounts);
ifd.putIFDValue(IFDImageJInfo, bInfo);
}
(new File(path)).delete(); // Otherwise TiffSaver appends!
TiffSaver tiffSaver = new TiffSaver(path);
tiffSaver.setWritingSequentially(true);
tiffSaver.setLittleEndian(false);
tiffSaver.writeHeader();
// tiffSaver.writeIFD(ifd,0); //* SHould not write here, some fields are calculated during writeImage, that writes IFD too
System.out.println("bytes.length="+bytes.length);
tiffSaver.writeImage(bytes,
ifd,
0, //int no,
0, //int pixelType:INT8, INT16, INT32, UINT8, UINT16, UINT32, FLOAT, BIT, DOUBLE, COMPLEX, DOUBLECOMPLEX; - used to find bpp
true); // boolean last)
}
*/
}
src/main/java/com/elphel/imagej/readers/EyesisTiff.java
View file @ 6894dccd
......@@ -57,6 +57,9 @@ import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import com.elphel.imagej.correction.Eyesis_Correction;
import com.elphel.imagej.tileprocessor.QuadCLTCPU;
//import org.apache.log4j.Logger;
import ij.IJ;
......@@ -305,13 +308,42 @@ the type of pixel data in this file getPixelType()
) throws IOException, FormatException, ServiceException, DependencyException{
if (imp.getType()==ImagePlus.COLOR_RGB) { // 4*8 bit - type = 0
if (debugLevel>1) System.out.println("Saving 8-bit TIFF with alpha-channel: "+path); // is it possible to just add alpha to high bytes?
saveTiffARGB32(imp, path, imageJTags, debugLevel);
ElphelTiffWriter.saveTiffARGB32(imp, path, imageJTags, debugLevel);
// saveTiffARGB32(imp, path, imageJTags, debugLevel);
return;
} else if (imp.getStackSize()==4) {
if (debugLevel>1) System.out.println("Saving 32-bit float TIFF with alpha-channel: "+path);
saveTiffARGB(imp, path, mode, scale, imageJTags,debugLevel);
return;
} else if (imp.getType()==ImagePlus.GRAY32) {
int lwir_palette = 0;
double [] minmax = null;
String title = imp.getTitle();
float [] fpixels = (float[]) imp.getProcessor().getPixels();
double [] dpixels = new double [fpixels.length];
for (int i = 0; i < fpixels.length; i++) {
dpixels[i] = fpixels[i];
}
ImagePlus imp_rgb = QuadCLTCPU.linearStackToColorLWIR(
Eyesis_Correction.CLT_PARAMETERS, // clt_parameters, // CLTParameters clt_parameters,
lwir_palette, // int lwir_palette, // <0 - do not convert
minmax, // minmax, // double [] minmax,
title, // String name,
"-rgba", // String suffix, // such as disparity=...
true, // boolean toRGB,
new double[][] {dpixels}, // faded_textures[nslice], // double [][] texture_data,
imp.getWidth(), // int width, // int tilesX,
imp.getHeight(), // int height, // int tilesY,
debugLevel); // int debugLevel )
// File test_dump = new File("/home/elphel/Documents/DoD/Ukraine/photos/test/1694531940_120446-02-gps.tiff");
// DumpImageMetadata.processFile(test_dump);
if (debugLevel>1) System.out.println("Saving 8-bit RGBA TIFF with alpha-channel: "+path); // is it possible to just add alpha to high bytes?
ElphelTiffWriter.saveTiffARGB32(imp_rgb, path, imageJTags, debugLevel);
// saveTiffARGB32(imp_rgb, path, imageJTags, debugLevel);
return;
}
IJ.showMessage("Not yet implemented for this image type");
}
......@@ -523,8 +555,8 @@ the type of pixel data in this file getPixelType()
// copy some other data?
ifd.putIFDValue(IFD.COMPRESSION, 1); //TiffCompression.UNCOMPRESSED);
ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION,2); // RGB
// ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // extra bytes (over 3) meaning Unassociated alpha data
ifd.putIFDValue(IFD.EXTRA_SAMPLES,1); // extra bytes (over 3) meaning Unassociated alpha data
ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // extra 2 bytes (over 3) meaning Unassociated alpha data
// ifd.putIFDValue(IFD.EXTRA_SAMPLES,1); // extra 1 byte (over 3) meaning Associated alpha data
ifd.putIFDValue(IFD.SAMPLE_FORMAT,1); //
// int [] bpsArray={8,8,8,8};
// ifd.putIFDValue(IFD.BITS_PER_SAMPLE, bpsArray); // will be done automatically
......@@ -571,7 +603,6 @@ the type of pixel data in this file getPixelType()
public static void propertiesTiff(ImagePlus imp){
FileInfo fi = imp.getOriginalFileInfo();
if ((fi==null) ||(fi.directory==null) || (fi.fileFormat!=FileInfo.TIFF)) {
......@@ -628,7 +659,15 @@ the type of pixel data in this file getPixelType()
sb.append("}");
byte [] bstring=new byte [Array.getLength(value)];
for (int i=0;i<bstring.length;i++) bstring[i]= (byte) Integer.parseInt(Array.get(value, i).toString());
for (int i=0;i<bstring.length;i++) {
try {
bstring[i]= (byte) Integer.parseInt(Array.get(value, i).toString());
} catch (java.lang.NumberFormatException e) {
// TODO Auto-generated catch block
// e.printStackTrace();
bstring[i]=(byte) 0x3f;
}
}
// String astring=new String((byte []) value);
String astring="";
try {
......
src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java
View file @ 6894dccd
......@@ -9161,80 +9161,90 @@ public class QuadCLTCPU {
// convert to ImageStack of 3 slices
// String [] sliceNames = is_mono? new String[]{"mono"}: new String[]{"red", "blue", "green"};
int main_color_index = is_mono? 0 : 2;
double [][] rbg_in = is_mono?
new double [][] {texture_data[0]} :
new double[][] {texture_data[0],texture_data[1],texture_data[2]};
double [] alpha_pixels = null; // (0..1.0)
if (texture_data.length > rbg_in.length) {
alpha_pixels = texture_data[rbg_in.length];
}
if (!toRGB) { // Double [][] uses
ImagePlus imp;
if (alpha_pixels != null) {
String [] titles = {"Y","alpha"};
ImageStack stack = ShowDoubleFloatArrays.makeStack(
new double[][] {rbg_in[0],alpha_pixels}, // iclt_data,
width, // (tilesX + 0) * clt_parameters.transform_size,
height, // (tilesY + 0) * clt_parameters.transform_size,
titles, // or use null to get chn-nn slice names
true); // replace NaN with 0.0
imp = new ImagePlus(name+suffix, stack);
imp.getProcessor().resetMinAndMax();
} else {
ImageProcessor ip= new FloatProcessor(width,height);
ip.setPixels(rbg_in[0]);
ip.resetMinAndMax();
imp = new ImagePlus(name+suffix, ip);
}
return imp;
}
String [] rgb_titles = {"red","green","blue"};
String [] rgba_titles = {"red","green","blue","alpha"};
String [] titles = (alpha_pixels == null) ? rgb_titles : rgba_titles;
int num_slices = (alpha_pixels == null) ? 3 : 4;
double mn = minmax[0]; // colorProcParameters.lwir_low;
double mx = minmax[1]; // colorProcParameters.lwir_high;
ThermalColor tc = new ThermalColor(
lwir_palette, // colorProcParameters.lwir_palette,
mn,
mx,
255.0);
double [][] rgba = new double [num_slices][];
for (int i = 0; i < 3; i++) rgba[i] = new double [texture_data[main_color_index].length];
for (int i = 0; i < rbg_in[main_color_index].length; i++) {
if (i==160000) {
System.out.println ("i="+i);
}
double [] rgb = tc.getRGB(texture_data[main_color_index][i]);
rgba[0][i] = rgb[0]; // red
rgba[1][i] = rgb[1]; // green
rgba[2][i] = rgb[2]; // blue
}
if (alpha_pixels != null) {
rgba[3] = alpha_pixels; // 0..1
}
ImageStack stack = ShowDoubleFloatArrays.makeStack(
rgba, // iclt_data,
width, // (tilesX + 0) * clt_parameters.transform_size,
height, // (tilesY + 0) * clt_parameters.transform_size,
titles, // or use null to get chn-nn slice names
true); // replace NaN with 0.0
ImagePlus imp_rgba = EyesisCorrections.convertRGBAFloatToRGBA32(
stack, // ImageStack stackFloat, //r,g,b,a
// name+"ARGB"+suffix, // String title,
name+suffix, // String title,
0.0, // double r_min,
255.0, // double r_max,
0.0, // double g_min,
255.0, // double g_max,
0.0, // double b_min,
255.0, // double b_max,
0.0, // double alpha_min,
1.0); // double alpha_max)
return imp_rgba;
double [][] rbg_in = is_mono? new double [][] {texture_data[0]} : new double[][] {texture_data[0],texture_data[1],texture_data[2]};
double [] alpha_pixels = null; // (0..1.0)
if (texture_data.length > rbg_in.length) {
alpha_pixels = texture_data[rbg_in.length];
} else {
alpha_pixels = new double[texture_data[0].length];
for (int i = 0; i < alpha_pixels.length; i++) {
alpha_pixels[i] = Double.isNaN(rbg_in[0][i]) ? 0.0 : 1.0;
}
}
if (!toRGB) { // Double [][] uses
ImagePlus imp;
if (alpha_pixels != null) {
String [] titles = {"Y","alpha"};
ImageStack stack = ShowDoubleFloatArrays.makeStack(
new double[][] {rbg_in[0],alpha_pixels}, // iclt_data,
width, // (tilesX + 0) * clt_parameters.transform_size,
height, // (tilesY + 0) * clt_parameters.transform_size,
titles, // or use null to get chn-nn slice names
true); // replace NaN with 0.0
imp = new ImagePlus(name+suffix, stack);
imp.getProcessor().resetMinAndMax();
} else {
ImageProcessor ip= new FloatProcessor(width,height);
ip.setPixels(rbg_in[0]);
ip.resetMinAndMax();
imp = new ImagePlus(name+suffix, ip);
}
return imp;
}
String [] rgb_titles = {"red","green","blue"};
String [] rgba_titles = {"red","green","blue","alpha"};
String [] titles = (alpha_pixels == null) ? rgb_titles : rgba_titles;
int num_slices = (alpha_pixels == null) ? 3 : 4;
if (minmax == null) {
minmax = new double [] {Double.NaN, Double.NaN};
for (int i = 0; i < rbg_in[0].length; i++) if (!Double.isNaN(rbg_in[0][i])){
if (!(rbg_in[0][i] >= minmax[0])) minmax[0] = rbg_in[0][i];
if (!(rbg_in[0][i] <= minmax[1])) minmax[1] = rbg_in[0][i];
}
}
double mn = minmax[0]; // colorProcParameters.lwir_low;
double mx = minmax[1]; // colorProcParameters.lwir_high;
ThermalColor tc = new ThermalColor(
lwir_palette, // colorProcParameters.lwir_palette,
mn,
mx,
255.0);
double [][] rgba = new double [num_slices][];
for (int i = 0; i < 3; i++) rgba[i] = new double [texture_data[main_color_index].length];
for (int i = 0; i < rbg_in[main_color_index].length; i++) {
if (i==160000) {
System.out.println ("i="+i);
}
double [] rgb = tc.getRGB(texture_data[main_color_index][i]);
rgba[0][i] = rgb[0]; // red
rgba[1][i] = rgb[1]; // green
rgba[2][i] = rgb[2]; // blue
}
if (alpha_pixels != null) {
rgba[3] = alpha_pixels; // 0..1
}
ImageStack stack = ShowDoubleFloatArrays.makeStack(
rgba, // iclt_data,
width, // (tilesX + 0) * clt_parameters.transform_size,
height, // (tilesY + 0) * clt_parameters.transform_size,
titles, // or use null to get chn-nn slice names
true); // replace NaN with 0.0
ImagePlus imp_rgba = EyesisCorrections.convertRGBAFloatToRGBA32(
stack, // ImageStack stackFloat, //r,g,b,a
// name+"ARGB"+suffix, // String title,
name+suffix, // String title,
0.0, // double r_min,
255.0, // double r_max,
0.0, // double g_min,
255.0, // double g_max,
0.0, // double b_min,
255.0, // double b_max,
0.0, // double alpha_min,
1.0); // double alpha_max)
return imp_rgba;
}
......@@ -16328,7 +16338,8 @@ public class QuadCLTCPU {
width, // int width, // int tilesX,
height, // int height, // int tilesY,
debugLevel); // int debugLevel )
String preview_path = model_dir + Prefs.getFileSeparator() + title+".jpeg";
int jpeg_q = correctionsParameters.JPEG_quality;
String preview_path = model_dir + Prefs.getFileSeparator() + title+((jpeg_q==0)? ".tiff":".jpeg");
if (new File(preview_path).exists() && !correctionsParameters.thumb_overwrite) {
System.out.println("file "+preview_path+" exists, skipping preview generation");
return false;
......@@ -16341,7 +16352,7 @@ public class QuadCLTCPU {
model_dir,
false,
false,
correctionsParameters.JPEG_quality, // jpegQuality); // jpegQuality){// <0 - keep current, 0 - force Tiff, >0 use for JPEG
jpeg_q, // jpegQuality); // jpegQuality){// <0 - keep current, 0 - force Tiff, >0 use for JPEG
(debugLevel > -2) ? debugLevel : 1); // int debugLevel (print what it saves)
return true;
}
......
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