Skip to content

I
imagej-elphel
Commit 3c2b0b49 authored by Andrey Filippov's avatar Andrey Filippov
Browse files
Options

Added processing of GPS tags for both JP4 and Tiff, changed Tiff tags 

processing to match JP4 ones
parent e24b8d2f
Show whitespace changes
Inline Side-by-side
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"},
......@@ -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
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)
*/
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment