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imagej-elphel
Commit 3c2b0b49 authored by Andrey Filippov's avatar Andrey Filippov
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Added processing of GPS tags for both JP4 and Tiff, changed Tiff tags 

processing to match JP4 ones
parent e24b8d2f
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Showing with 182 additions and 46 deletions
src/main/java/com/elphel/imagej/readers/ElphelJp4Reader.java
View file @ 3c2b0b49
......@@ -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"},
......@@ -91,7 +92,8 @@ public class ElphelJp4Reader extends ImageIOReader{
private boolean file_initialized = false;
private byte [] image_bytes = null;
private ExifSubIFDDirectory directory;
private ExifIFD0Directory directory_ifd0;
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
View file @ 3c2b0b49
......@@ -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
{
......@@ -255,10 +295,130 @@ 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
public String[] getSeriesUsedFiles(boolean noPixels) {
......@@ -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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