Added processing of GPS tags for both JP4 and Tiff, changed Tiff tags (3c2b0b49) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/readers/ElphelJp4Reader.java

+15 −4

Original line number	Diff line number	Diff line
		@@ -45,6 +45,7 @@ import com.drew.metadata.Metadata;
		import com.drew.metadata.Tag;
		import com.drew.metadata.exif.ExifIFD0Directory;
		import com.drew.metadata.exif.ExifSubIFDDirectory;
		import com.drew.metadata.exif.GpsDirectory;

		import loci.common.ByteArrayHandle;
		import loci.common.Location;
		@@ -69,7 +70,7 @@ public class ElphelJp4Reader extends ImageIOReader{
		public static final String ELPHEL_PROPERTY_PREFIX = "ELPHEL_";
		public static final String CONTENT_FILENAME = "CONTENT_FILENAME";
		public static final boolean REORDER = true; // false;
		public static final String[][] REPLACEMENT_TAGS = // to/from!
		public static final String[][] REPLACEMENT_TAGS = // to/from! TODO: check/add for GPS?
		{{"SUBSEC_TIME_ORIGINAL", "Sub-Sec Time Original"},
		{"DATE_TIME_ORIGINAL", "Date/Time Original"},
		{"Instrument_Make", "Make"},
		@@ -92,6 +93,7 @@ public class ElphelJp4Reader extends ImageIOReader{
		private byte [] image_bytes = null;
		private ExifSubIFDDirectory directory;
		private ExifIFD0Directory directory_ifd0;
		private GpsDirectory directory_gps;
		private HashMap<String,String> REPLACEMENT_TAG_MAP = null; // per instance


		@@ -238,6 +240,7 @@ public class ElphelJp4Reader extends ImageIOReader{
		Metadata metadata = ImageMetadataReader.readMetadata(jpegFile);
		directory = metadata.getFirstDirectoryOfType(ExifSubIFDDirectory.class);
		directory_ifd0 = metadata.getFirstDirectoryOfType(ExifIFD0Directory.class);
		directory_gps = metadata.getFirstDirectoryOfType(GpsDirectory.class);
		}
		catch (Throwable e) {
		throw new ServiceException("Could not read EXIF data", e);
		@@ -271,6 +274,16 @@ public class ElphelJp4Reader extends ImageIOReader{
		}
		}
		}
		if (directory_gps != null) {
		for (Tag tag : directory_gps.getTags()) {
		String tag_name = tag.getTagName();
		if (REPLACEMENT_TAG_MAP.containsKey(tag_name)) {
		tags.put(REPLACEMENT_TAG_MAP.get(tag_name), tag.getDescription());
		} else {
		tags.put(tag.getTagName(), tag.getDescription());
		}
		}
		}
		// remove "sec" from exposure
		if (tags.containsKey(EXPOSURE_TIME)){
		tags.put(EXPOSURE_TIME, tags.get(EXPOSURE_TIME).split(" ")[0]);
		@@ -321,8 +334,6 @@ public class ElphelJp4Reader extends ImageIOReader{
		// LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
		}
		addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);


		}

src/main/java/com/elphel/imagej/readers/ElphelTiffReader.java

+167 −42

Original line number	Diff line number	Diff line
		@@ -32,15 +32,26 @@ import java.io.InputStream;
		import java.net.MalformedURLException;
		import java.net.URL;
		import java.net.URLConnection;
		import java.util.Date;
		import java.util.HashMap;
		import java.util.Hashtable;

		import org.apache.commons.compress.utils.IOUtils;
		import org.joda.time.DateTime;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import com.drew.imaging.ImageMetadataReader;
		import com.drew.metadata.Metadata;
		import com.drew.metadata.Tag;
		import com.drew.metadata.exif.ExifIFD0Directory;
		import com.drew.metadata.exif.ExifSubIFDDirectory;
		import com.drew.metadata.exif.GpsDirectory;

		import loci.common.ByteArrayHandle;
		import loci.common.Location;
		import loci.common.RandomAccessInputStream;
		import loci.common.services.ServiceException;
		import loci.formats.FormatException;
		import loci.formats.FormatTools;
		import loci.formats.in.MetadataLevel;
		@@ -49,6 +60,7 @@ 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;

		/*
		// non-IFD tags (for internal use)
		@@ -92,6 +104,22 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		public static final int TAG_SERIAL_NUMBER = 0xc62f;
		public static final int TAG_IMAGE_DESCRIPTION = 0x010e;

		// added 08/03/2021
		public static final String MAKER_NOTE = "Makernote";
		public static final String SUB_SEC_TIME_ORIGINAL = "SUBSEC_TIME_ORIGINAL"; // "Sub-Sec Time Original";
		public static final String EXPOSURE_TIME = "Exposure Time";
		public static final String DATE_TIME_ORIGINAL = "DATE_TIME_ORIGINAL"; // "Date/Time Original";
		public static final boolean REORDER = true; // false;
		public static final String[][] REPLACEMENT_TAGS = // to/from! TODO: check/add for GPS?
		{{"SUBSEC_TIME_ORIGINAL", "Sub-Sec Time Original"},
		{"DATE_TIME_ORIGINAL", "Date/Time Original"},
		{"Instrument_Make", "Make"},
		{"Serial_Number", "Unknown tag (0xc62f)"},
		{"Instrument_Model", "Model"}};





		/** Merge SubIFDs into the main IFD list. */
		// protected transient boolean mergeSubIFDs = true; // false;
		@@ -113,12 +141,18 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		private String content_fileName = null; // from Content-disposition
		private boolean mapped_externally = false; // file is read/mapped externally, do not close it here
		private boolean file_initialized = false;

		// private String companionFile;
		// private String description;
		// private String calibrationUnit;
		// private Double physicalSizeZ;
		// private Double timeIncrement;
		// private Integer xOrigin, yOrigin;
		private ExifSubIFDDirectory directory;
		private ExifIFD0Directory directory_ifd0;
		private GpsDirectory directory_gps;
		private HashMap<String,String> REPLACEMENT_TAG_MAP = null; // per instance


		// -- Constructor --

		@@ -132,6 +166,12 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		suffixSufficient = true; // false;
		/// mergeSubIFDs = true; // false;
		LOGGER.debug("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
		if (REPLACEMENT_TAG_MAP == null) {
		REPLACEMENT_TAG_MAP = new HashMap<String,String>();
		for (String [] line: REPLACEMENT_TAGS) {
		REPLACEMENT_TAG_MAP.put(line[1], line[0]);
		}
		}
		}

		// -- IFormatReader API methods --
		@@ -245,8 +285,8 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		file_initialized = true;
		}

		@Override
		protected void initFile(java.lang.String id)
		// @Override
		protected void initFileOld(java.lang.String id)
		throws FormatException,
		java.io.IOException
		{
		@@ -255,9 +295,129 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		LOGGER.debug("Starting initFile() method");
		super.initFile(id);
		LOGGER.debug("Ending initFile() method");
		}

		/* @see loci.formats.FormatReader#initFile(String) */
		// copied from ElphelJp4Reader
		@Override
		protected void initFile(String id) throws FormatException, IOException {
		LOGGER.debug("initFile("+id+"), currentId="+currentId+", before super" );
		try {
		super.initFile(id); // fails class_not_found
		}
		catch (IllegalArgumentException e) {
		throw new FormatException(e);
		}
		LOGGER.debug("initFile("+id+"), currentId="+currentId+", after super" );
		// Below needs to be modified - EXIFService does not work with mapFile
		MetadataStore store = makeFilterMetadata();
		LOGGER.debug("Parsing TIFF EXIF data");
		HashMap<String, String> tags = null;
		try {
		// Reimplementing ExifServiceImpl as original does not have ExifIFD0Directory
		try (RandomAccessInputStream jpegFile = new RandomAccessInputStream(id)) {
		try {
		Metadata metadata = ImageMetadataReader.readMetadata(jpegFile);
		directory = metadata.getFirstDirectoryOfType(ExifSubIFDDirectory.class);
		directory_ifd0 = metadata.getFirstDirectoryOfType(ExifIFD0Directory.class);
		directory_gps = metadata.getFirstDirectoryOfType(GpsDirectory.class);
		}
		catch (Throwable e) {
		throw new ServiceException("Could not read EXIF data", e);
		}
		}
		Date date = directory.getDate(ExifSubIFDDirectory.TAG_DATETIME_ORIGINAL);

		if (date != null) {
		Timestamp timestamp = new Timestamp(new DateTime(date));
		store.setImageAcquisitionDate(timestamp, 0);
		}

		tags = new HashMap<String, String>();
		if (directory != null) {
		for (Tag tag : directory.getTags()) {
		String tag_name = tag.getTagName();
		if (REPLACEMENT_TAG_MAP.containsKey(tag_name)) {
		tags.put(REPLACEMENT_TAG_MAP.get(tag_name), tag.getDescription());
		} else {
		tags.put(tag.getTagName(), tag.getDescription());
		}
		}
		}
		if (directory_ifd0 != null) {
		for (Tag tag : directory_ifd0.getTags()) {
		String tag_name = tag.getTagName();
		if (REPLACEMENT_TAG_MAP.containsKey(tag_name)) {
		tags.put(REPLACEMENT_TAG_MAP.get(tag_name), tag.getDescription());
		} else {
		tags.put(tag.getTagName(), tag.getDescription());
		}
		}
		}
		if (directory_gps != null) {
		for (Tag tag : directory_gps.getTags()) {
		String tag_name = tag.getTagName();
		if (REPLACEMENT_TAG_MAP.containsKey(tag_name)) {
		tags.put(REPLACEMENT_TAG_MAP.get(tag_name), tag.getDescription());
		} else {
		tags.put(tag.getTagName(), tag.getDescription());
		}
		}
		}
		// remove "sec" from exposure
		if (tags.containsKey(EXPOSURE_TIME)){
		tags.put(EXPOSURE_TIME, tags.get(EXPOSURE_TIME).split(" ")[0]);
		}

		for (String tagName : tags.keySet()) {
		addGlobalMeta(tagName, tags.get(tagName));
		} //{Makernote=105455 131072 127570 300581 171508736 171508736 171508736 171508736 169869312 124780556 1118544 0 0 327779 648 1296, Sub-Sec Time Original=560439, Exposure Time=11167/500000 sec, Date/Time Original=2019:05:13 04:30:26}

		}
		catch (ServiceException e) {
		LOGGER.debug("Could not parse EXIF data", e);
		}
		long [] maker_note = null;
		double exposure = Double.NaN;
		String date_time = null;
		if (tags.containsKey(MAKER_NOTE)){
		String [] smn = tags.get(MAKER_NOTE).split(" ");
		maker_note = new long[smn.length];
		for (int i = 0; i < maker_note.length; i++) {
		maker_note[i] = Integer.parseInt(smn[i]);
		}
		}
		if (tags.containsKey(EXPOSURE_TIME)){
		if (tags.get(EXPOSURE_TIME).contains("/")) {
		String [] s = tags.get(EXPOSURE_TIME).split("/");
		exposure = 1.0 * Integer.parseInt(s[0]) / Integer.parseInt(s[1].split(" ")[0]);
		} else {
		exposure = Double.parseDouble(tags.get(EXPOSURE_TIME));
		}
		}
		if (tags.containsKey(DATE_TIME_ORIGINAL)){
		date_time = tags.get(DATE_TIME_ORIGINAL);
		if (tags.containsKey(SUB_SEC_TIME_ORIGINAL)){
		date_time += "."+tags.get(SUB_SEC_TIME_ORIGINAL);
		}
		}
		// int bytes_per_pixel = 1;
		int bpp = getBitsPerPixel();
		int bytes_per_pixel = (bpp + 7) / 9;
		Hashtable<String, String> property_table = ElphelMeta.getMeta(
		null, maker_note, exposure, date_time, bytes_per_pixel, true );
		LOGGER.debug("Created elphelMeta table, size="+property_table.size());
		for (String key:property_table.keySet()) {
		addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
		}
		MetadataLevel level = getMetadataOptions().getMetadataLevel();
		if (level != MetadataLevel.MINIMUM) {
		// Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
		// LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
		}
		addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
		}


		/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
		@Override
		@@ -297,6 +457,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		// -- Internal BaseTiffReader API methods --

		/* @see BaseTiffReader#initStandardMetadata() */
		/* Removed 08/03/2021 to match IP4
		@Override
		protected void initStandardMetadata() throws FormatException, IOException {
		LOGGER.debug("initStandardMetadata() - before super()");
		@@ -364,46 +525,10 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		// check for ImageJ-style TIFF comment
		boolean ij = checkCommentImageJ(comment);
		// if (ij) parseCommentImageJ(comment);
		/*
		// check for MetaMorph-style TIFF comment
		boolean metamorph = checkCommentMetamorph(comment);
		if (metamorph && level != MetadataLevel.MINIMUM) {
		parseCommentMetamorph(comment);
		}
		put("MetaMorph", metamorph ? "yes" : "no");

		// check for other INI-style comment
		if (!ij && !metamorph && level != MetadataLevel.MINIMUM) {
		parseCommentGeneric(comment);
		}
		*/
		// check for another file with the same name
		/*
		if (isGroupFiles()) {
		Location currentFile = new Location(currentId).getAbsoluteFile();
		String currentName = currentFile.getName();
		Location directory = currentFile.getParentFile();
		String[] files = directory.list(true);
		if (files != null) {
		for (String file : files) {
		String name = file;
		if (name.indexOf(".") != -1) {
		name = name.substring(0, name.indexOf("."));
		}

		if (currentName.startsWith(name) &&
		checkSuffix(name, COMPANION_SUFFIXES))
		{
		companionFile = new Location(directory, file).getAbsolutePath();
		break;
		}
		}
		}
		}
		*/
		}

		/* @see BaseTiffReader#initMetadataStore() */
		/* Removed 08/03/2021 to match IP4
		@Override
		protected void initMetadataStore() throws FormatException {
		super.initMetadataStore();
		@@ -413,7 +538,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
		// }
		populateMetadataStoreImageJ(store);
		}

		*/
		/**
		* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
		*/

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