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/**
** -----------------------------------------------------------------------------**
** ElphelJp4Reader.java
**
** loci.format compatible reader for Elphel JP4 files
**
**
** Copyright (C) 2019 Elphel, Inc.
**
** -----------------------------------------------------------------------------**
**
** ElphelJp4Reader.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.io.IOException;
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 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.ImageIOReader;
import loci.formats.in.MetadataLevel;
//import loci.formats.services.EXIFService;
import ome.xml.meta.MetadataStore;
import ome.xml.model.primitives.Timestamp;
//ElphelTiffReader
public class ElphelJp4Reader extends ImageIOReader{
// -- Constants --
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 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!
{{"SUBSEC_TIME_ORIGINAL", "Sub-Sec Time Original"},
{"DATE_TIME_ORIGINAL", "Date/Time Original"},
{"Instrument_Make", "Make"},
{"Serial_Number", "Unknown tag (0xc62f)"},
{"Instrument_Model", "Model"}};
/** Logger for this class. */
private static final Logger LOGGER =
LoggerFactory.getLogger(ElphelTiffReader.class);
// -- Fields --
private URL url = null; // save here actual URL when reading file to memory
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 byte [] image_bytes = null;
private ExifSubIFDDirectory directory;
private ExifIFD0Directory directory_ifd0;
private HashMap<String,String> REPLACEMENT_TAG_MAP = null; // per instance
// -- Constructor --
/** Constructs a new Tiff reader. */
public ElphelJp4Reader() {
super("JP4", new String[] {"jp4"});
// mergeSubIFDs = true; // false;
// TODO: See if the selection is just between 2 readers (jp4 and tiff - just Elphel cameras),
// or these readers are combined with all other readers in readers.txt
suffixNecessary = true; // false
suffixSufficient = true; // false;
LOGGER.debug("ElphelTiffReader(), after super()");
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 --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (open) {
return super.isThisType(name, open);
}
return checkSuffix(name, getSuffixes());
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
/* https://docs.openmicroscopy.org/bio-formats/5.7.2/developers/reader-guide.html
* Check the first few bytes of a file to determine if the file can be read
* by this reader. You can assume that index 0 in the stream corresponds to
* the index 0 in the file. Return true if the file can be read; false if not
* (or if there is no way of checking).
*/
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException
{
final int blockLen = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
byte[] signature = new byte[blockLen];
stream.read(signature);
if (signature[0] != (byte) 0xff || signature[1] != (byte) 0xd8 ||
signature[2] != (byte) 0xff || (signature[3] & 0xf0) == 0)
{
return false;
}
return true;
}
@Override
public void setId(String id) throws FormatException, IOException { // same as for tiff?
image_bytes = null;
// buffered_data = null;
LOGGER.debug("setId("+id+"). before super" );
file_initialized = false;
mapped_externally = false;
if (Location.getIdMap().containsKey(id)) {
LOGGER.debug("id '"+id+"' is already mapped" );
content_fileName = id; // id; // maybe set to null to handle externally?
mapped_externally = true;
LOGGER.debug("Starting initFile() method, read file directly");
super.setId(id);
} else {
// If URL, then read to memory, if normal file - use direct access
url = null;
// String mime = null; // use to select jp4/tiff later? Or to check it is correct
content_fileName = null;
try {
url = new URL(id);
} catch (MalformedURLException e) {
LOGGER.warn("Bad URL: " + id);
}
if (url != null) {
LOGGER.debug("Starting initFile() method, read "+ id +" to memory first");
//https://www.rgagnon.com/javadetails/java-0487.html
URLConnection connection = url.openConnection();
String content_disposition = connection.getHeaderField("Content-Disposition");
// raw = "attachment; filename=abc.jpg"
if(content_disposition != null && content_disposition.indexOf("=") != -1) {
content_fileName = content_disposition.split("=")[1]; //getting value after '='
// trim quotes
content_fileName= content_fileName.substring(1, content_fileName.length()-1);
} else {
String mime = connection.getContentType();
int slash = mime.lastIndexOf("/");
String suffix = slash < 0 ? "" : mime.substring(slash+1);
content_fileName = "unknown." + suffix;
}
// currentId = fileName; //???
// LOGGER.debug("Mime type = "+mime);
// https://stackoverflow.com/questions/2793150/how-to-use-java-net-urlconnection-to-fire-and-handle-http-requests
//https://stackoverflow.com/questions/2295221/java-net-url-read-stream-to-byte
InputStream is = url.openStream (); //
byte[] inBytes = IOUtils.toByteArray(is);
if (is != null) is.close();
LOGGER.debug("Bytes read: "+ inBytes.length);
Location.mapFile(content_fileName, new ByteArrayHandle(inBytes));
// HashMap<String,Object> dbg_loc = Location.getIdMap();
super.setId(content_fileName);
} else { // read file normally
content_fileName = id;
LOGGER.debug("read file directly");
super.setId(id);
}
}
//getReader
// super.setId(id);
LOGGER.debug("setId("+id+"). after super" );
file_initialized = true;
}
/* @see loci.formats.FormatReader#initFile(String) */
@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 JPEG 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);
}
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());
}
}
}
// 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)){
String [] s = tags.get(EXPOSURE_TIME).split("/");
exposure = 1.0 * Integer.parseInt(s[0]) / Integer.parseInt(s[1].split(" ")[0]);
}
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;
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#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
// HashMap<String,Object> dbg_loc = Location.getIdMap();
String saveCurrentId = currentId;
currentId = null;
LOGGER.debug("close("+fileOnly+") before super");
super.close(fileOnly); // curerent_id == null only during actual close?
LOGGER.debug("close("+fileOnly+") after super");
currentId = saveCurrentId;
// if ((content_fileName != null) && file_initialized){
if (!mapped_externally && file_initialized){ // will try to unmap non-mapped file, OK
Location.mapFile(content_fileName, null);
file_initialized = false;
}
// dbg_loc = Location.getIdMap();
if (!fileOnly) {
// companionFile = null;
// description = null;
// calibrationUnit = null;
// physicalSizeZ = null;
// timeIncrement = null;
// xOrigin = null;
// yOrigin = null;
}
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*
* openBytes(int, byte[], int, int, int, int) Returns a byte array containing
* the pixel data for a specified subimage from the given file. The dimensions
* of the subimage (upper left X coordinate, upper left Y coordinate, width,
* and height) are specified in the final four int parameters.
* This should throw a FormatException if the image number is invalid (less than
* 0 or >= the number of images). The ordering of the array returned by openBytes
* should correspond to the values returned by isLittleEndian and isInterleaved.
* Also, the length of the byte array should be
* [image_width * image height * bytes_per_pixel]. Extra bytes will generally
* be truncated. It is recommended that the first line of this method be
* FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h) - this ensures
* that all of the parameters are valid.
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
LOGGER.debug("openBytes() - before super()");
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
if (image_bytes == null) {
jp4Decode(no);
}
int width = getSizeX();
int y1 = y + h;
int dest=0;
for (int line = y; line < y1; line++) {
System.arraycopy(image_bytes,
line*width+x,
buf,
dest,
w);
dest += w;
}
LOGGER.debug("openBytes() - after super()");
return buf;
}
public void jp4Decode(int no) throws FormatException, IOException {
int width = getSizeX();
int height = getSizeY();
image_bytes = new byte[width*height];
byte [] ib = new byte [width*height];
byte [][] macroblock=new byte[16][16];
super.openBytes(no, ib, 0, 0, width, height);
if (REORDER) {
int yb,y,xb,x,offset,nb,xbyr,ybyr; //,i;
for (yb=0;yb<(height>>4); yb++) for (xb=0;xb<(width>>4); xb++) { /* iterating macroblocks */
for (nb=0; nb<4;nb++) {
xbyr=nb & 1;
ybyr=(nb>>1) & 1;
for (y=0;y<8;y++) {
offset=((yb<<4)+y)*width+ (nb<<3) +((xb>=(width>>5))?(((xb<<5)-width)+(width<<3)):(xb<<5));
for (x=0;x<8;x++) {
macroblock[(y<<1) | ybyr][(x<<1) | xbyr]=ib[offset+x];
}
}
}
for (y=0;y<16;y++) {
System.arraycopy(macroblock[y],
0,
image_bytes,
((yb<<4)+y)*width + (xb<<4),
16);
}
}
} else {
image_bytes = ib; // temporary
}
LOGGER.debug("jp4Decode()");
}
}