Merge pull request #1519 from stweil/crlf

Fix line endings (CRLF -> LF)

6 files changed, 1527 insertions, 1529 deletions

diff --git a/src/bin/common/opj_apps_config.h.cmake.in b/src/bin/common/opj_apps_config.h.cmake.in
index 5e606907..a880205f 100644
--- a/src/bin/common/opj_apps_config.h.cmake.in
+++ b/src/bin/common/opj_apps_config.h.cmake.in
@@ -1,15 +1,13 @@
-#include "opj_config_private.h"

-

-/* create opj_apps_config.h for CMake */

-

-#cmakedefine OPJ_HAVE_LIBPNG @HAVE_LIBPNG@

-#cmakedefine OPJ_HAVE_PNG_H @HAVE_PNG_H@

-#cmakedefine OPJ_HAVE_LIBTIFF @HAVE_LIBTIFF@

-#cmakedefine OPJ_HAVE_TIFF_H @HAVE_TIFF_H@

-

-#cmakedefine OPJ_HAVE_LIBLCMS1

-#cmakedefine OPJ_HAVE_LIBLCMS2

-#cmakedefine OPJ_HAVE_LCMS1_H

-#cmakedefine OPJ_HAVE_LCMS2_H

-

-

+#include "opj_config_private.h"
+
+/* create opj_apps_config.h for CMake */
+
+#cmakedefine OPJ_HAVE_LIBPNG @HAVE_LIBPNG@
+#cmakedefine OPJ_HAVE_PNG_H @HAVE_PNG_H@
+#cmakedefine OPJ_HAVE_LIBTIFF @HAVE_LIBTIFF@
+#cmakedefine OPJ_HAVE_TIFF_H @HAVE_TIFF_H@
+
+#cmakedefine OPJ_HAVE_LIBLCMS1
+#cmakedefine OPJ_HAVE_LIBLCMS2
+#cmakedefine OPJ_HAVE_LCMS1_H
+#cmakedefine OPJ_HAVE_LCMS2_H
diff --git a/wrapping/java/openjp2/JavaOpenJPEGDecoder.c b/wrapping/java/openjp2/JavaOpenJPEGDecoder.c
index f91267fc..26743a39 100644
--- a/wrapping/java/openjp2/JavaOpenJPEGDecoder.c
+++ b/wrapping/java/openjp2/JavaOpenJPEGDecoder.c
@@ -1,885 +1,885 @@
-/*

- * Copyright (c) 2002-2014, Universite catholique de Louvain (UCL), Belgium

- * Copyright (c) 2002-2014, Professor Benoit Macq

- * Copyright (c) 2001-2003, David Janssens

- * Copyright (c) 2002-2003, Yannick Verschueren

+/*
+ * Copyright (c) 2002-2014, Universite catholique de Louvain (UCL), Belgium
+ * Copyright (c) 2002-2014, Professor Benoit Macq
+ * Copyright (c) 2001-2003, David Janssens
+ * Copyright (c) 2002-2003, Yannick Verschueren
  * Copyright (c) 2003-2007, Francois-Olivier Devaux 
- * Copyright (c) 2003-2014, Antonin Descampe

- * Copyright (c) 2005, Herve Drolon, FreeImage Team

- * Copyright (c) 2006-2007, Parvatha Elangovan

- * Copyright (c) 2007, Patrick Piscaglia (Telemis)

- * All rights reserved.

- *

- * Redistribution and use in source and binary forms, with or without

- * modification, are permitted provided that the following conditions

- * are met:

- * 1. Redistributions of source code must retain the above copyright

- *    notice, this list of conditions and the following disclaimer.

- * 2. Redistributions in binary form must reproduce the above copyright

- *    notice, this list of conditions and the following disclaimer in the

- *    documentation and/or other materials provided with the distribution.

- *

- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS `AS IS'

- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

- * ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE

- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR

- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF

- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS

- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN

- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)

- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

- * POSSIBILITY OF SUCH DAMAGE.

- */

-#include <stdio.h>

-#include <string.h>

-#include <stdlib.h>

-#include <jni.h>

-#include <math.h>

-

-#include "openjpeg.h"

-#include "opj_includes.h"

-#include "opj_getopt.h"

-#include "convert.h"

-#include "dirent.h"

-#include "org_openJpeg_OpenJPEGJavaDecoder.h"

-

-#ifndef _WIN32

-#define stricmp strcasecmp

-#define strnicmp strncasecmp

-#endif

-

-#include "format_defs.h"

-

-typedef struct callback_variables {

-	JNIEnv *env;

-	/** 'jclass' object used to call a Java method from the C */

-	jobject *jobj;

-	/** 'jclass' object used to call a Java method from the C */

-	jmethodID message_mid;

-	jmethodID error_mid;

-} callback_variables_t;

-

-typedef struct dircnt{

-	/** Buffer for holding images read from Directory*/

-	char *filename_buf;

-	/** Pointer to the buffer*/

-	char **filename;

-}dircnt_t;

-

-

-typedef struct img_folder{

-	/** The directory path of the folder containing input images*/

-	char *imgdirpath;

-	/** Output format*/

-	char *out_format;

-	/** Enable option*/

-	char set_imgdir;

-	/** Enable Cod Format for output*/

-	char set_out_format;

-

-}img_fol_t;

-

-

-void decode_help_display() {

-	fprintf(stdout,"HELP\n----\n\n");

-	fprintf(stdout,"- the -h option displays this help information on screen\n\n");

-

-/* UniPG>> */

-	fprintf(stdout,"List of parameters for the JPEG 2000 "

-#ifdef USE_JPWL

-		"+ JPWL "

-#endif /* USE_JPWL */

-		"decoder:\n");

-/* <<UniPG */

-	fprintf(stdout,"\n");

-	fprintf(stdout,"\n");

-	fprintf(stdout,"  -ImgDir \n");

-	fprintf(stdout,"	Image file Directory path \n");

-	fprintf(stdout,"  -OutFor \n");

-	fprintf(stdout,"    REQUIRED only if -ImgDir is used\n");

-	fprintf(stdout,"	  Need to specify only format without filename <BMP>  \n");

-	fprintf(stdout,"    Currently accepts PGM, PPM, PNM, PGX, BMP format\n");

-	fprintf(stdout,"  -i <compressed file>\n");

-	fprintf(stdout,"    REQUIRED only if an Input image directory not specified\n");

-	fprintf(stdout,"    Currently accepts J2K-files, JP2-files and JPT-files. The file type\n");

-	fprintf(stdout,"    is identified based on its suffix.\n");

-	fprintf(stdout,"  -o <decompressed file>\n");

-	fprintf(stdout,"    REQUIRED\n");

-	fprintf(stdout,"    Currently accepts PGM-files, PPM-files, PNM-files, PGX-files and\n");

-	fprintf(stdout,"    BMP-files. Binary data is written to the file (not ascii). If a PGX\n");

-	fprintf(stdout,"    filename is given, there will be as many output files as there are\n");

-	fprintf(stdout,"    components: an indice starting from 0 will then be appended to the\n");

-	fprintf(stdout,"    output filename, just before the \"pgx\" extension. If a PGM filename\n");

-	fprintf(stdout,"    is given and there are more than one component, only the first component\n");

-	fprintf(stdout,"    will be written to the file.\n");

-	fprintf(stdout,"  -r <reduce factor>\n");

-	fprintf(stdout,"    Set the number of highest resolution levels to be discarded. The\n");

-	fprintf(stdout,"    image resolution is effectively divided by 2 to the power of the\n");

-	fprintf(stdout,"    number of discarded levels. The reduce factor is limited by the\n");

-	fprintf(stdout,"    smallest total number of decomposition levels among tiles.\n");

-	fprintf(stdout,"  -l <number of quality layers to decode>\n");

-	fprintf(stdout,"    Set the maximum number of quality layers to decode. If there are\n");

-	fprintf(stdout,"    less quality layers than the specified number, all the quality layers\n");

-	fprintf(stdout,"    are decoded.\n");

-/* UniPG>> */

-#ifdef USE_JPWL

-	fprintf(stdout,"  -W <options>\n");

-	fprintf(stdout,"    Activates the JPWL correction capability, if the codestream complies.\n");

-	fprintf(stdout,"    Options can be a comma separated list of <param=val> tokens:\n");

-	fprintf(stdout,"    c, c=numcomps\n");

-	fprintf(stdout,"       numcomps is the number of expected components in the codestream\n");

-	fprintf(stdout,"       (search of first EPB rely upon this, default is %d)\n", JPWL_EXPECTED_COMPONENTS);

-#endif /* USE_JPWL */

-/* <<UniPG */

-	fprintf(stdout,"\n");

-}

-

-/* -------------------------------------------------------------------------- */

-

-int get_num_images(char *imgdirpath){

-	DIR *dir;

-	struct dirent* content;	

-	int num_images = 0;

-

-	/*Reading the input images from given input directory*/

-

-	dir= opendir(imgdirpath);

-	if(!dir){

-		fprintf(stderr,"Could not open Folder %s\n",imgdirpath);

-		return 0;

-	}

-	

-	while((content=readdir(dir))!=NULL){

-		if(strcmp(".",content->d_name)==0 || strcmp("..",content->d_name)==0 )

-			continue;

-		num_images++;

-	}

-	return num_images;

-}

-

-int load_images(dircnt_t *dirptr, char *imgdirpath){

-	DIR *dir;

-	struct dirent* content;	

-	int i = 0;

-

-	/*Reading the input images from given input directory*/

-

-	dir= opendir(imgdirpath);

-	if(!dir){

-		fprintf(stderr,"Could not open Folder %s\n",imgdirpath);

-		return 1;

-	}else	{

-		fprintf(stderr,"Folder opened successfully\n");

-	}

-	

-	while((content=readdir(dir))!=NULL){

-		if(strcmp(".",content->d_name)==0 || strcmp("..",content->d_name)==0 )

-			continue;

-

-		strcpy(dirptr->filename[i],content->d_name);

-		i++;

-	}

-	return 0;	

-}

-

-int get_file_format(char *filename) {

-	unsigned int i;

-	static const char *extension[] = {"pgx", "pnm", "pgm", "ppm", "bmp","tif", "raw", "tga", "j2k", "jp2", "jpt", "j2c" };

-	static const int format[] = { PGX_DFMT, PXM_DFMT, PXM_DFMT, PXM_DFMT, BMP_DFMT, TIF_DFMT, RAW_DFMT, TGA_DFMT, J2K_CFMT, JP2_CFMT, JPT_CFMT, J2K_CFMT };

-	char * ext = strrchr(filename, '.');

-	if (ext == NULL)

-		return -1;

-	ext++;

-	if(ext) {

-		for(i = 0; i < sizeof(format)/sizeof(*format); i++) {

-			if(strnicmp(ext, extension[i], 3) == 0) {

-				return format[i];

-			}

-		}

-	}

-

-	return -1;

-}

-

-

-/* -------------------------------------------------------------------------- */

-

-int parse_cmdline_decoder(int argc, char **argv, opj_dparameters_t *parameters,img_fol_t *img_fol) {

-	/* parse the command line */

-	int totlen;

-	opj_option_t long_option[]={

-		{"ImgDir",REQ_ARG, NULL ,'y'},

-		{"OutFor",REQ_ARG, NULL ,'O'},

-	};

-

-/* UniPG>> */

-	const char optlist[] = "i:o:r:l:hx:"

-

-#ifdef USE_JPWL

-					"W:"

-#endif /* USE_JPWL */

-					;

-	/*for (i=0; i<argc; i++) {

-		printf("[%s]",argv[i]);

-	}

-	printf("\n");*/

-

-/* <<UniPG */

-	totlen=sizeof(long_option);

-	img_fol->set_out_format = 0;

-	reset_options_reading();

-

-	while (1) {

-		int c = opj_getopt_long(argc, argv,optlist,long_option,totlen);

-		if (c == -1)

-			break;

-		switch (c) {

-			case 'i':			/* input file */

-			{

-				char *infile = opj_optarg;

-				parameters->decod_format = get_file_format(infile);

-				switch(parameters->decod_format) {

-					case J2K_CFMT:

-					case JP2_CFMT:

-					case JPT_CFMT:

-						break;

-					default:

-						fprintf(stderr, 

-							"!! Unrecognized format for infile : %s [accept only *.j2k, *.jp2, *.jpc or *.jpt] !!\n\n", 

-							infile);

-						return 1;

-				}

-				strncpy(parameters->infile, infile, sizeof(parameters->infile)-1);

-			}

-			break;

-				

-				/* ----------------------------------------------------- */

-

-			case 'o':			/* output file */

-			{

-				char *outfile = opj_optarg;

-				parameters->cod_format = get_file_format(outfile);

-				switch(parameters->cod_format) {

-					case PGX_DFMT:

-					case PXM_DFMT:

-					case BMP_DFMT:

-					case TIF_DFMT:

-					case RAW_DFMT:

-					case TGA_DFMT:

-						break;

-					default:

-						fprintf(stderr, "Unknown output format image %s [only *.pnm, *.pgm, *.ppm, *.pgx, *.bmp, *.tif, *.raw or *.tga]!! \n", outfile);

-						return 1;

-				}

-				strncpy(parameters->outfile, outfile, sizeof(parameters->outfile)-1);

-			}

-			break;

-			

-				/* ----------------------------------------------------- */

-

-			case 'O':			/* output format */

-			{

-				char outformat[50];

-				char *of = opj_optarg;

-				sprintf(outformat,".%s",of);

-				img_fol->set_out_format = 1;

-				parameters->cod_format = get_file_format(outformat);

-				switch(parameters->cod_format) {

-					case PGX_DFMT:

-						img_fol->out_format = "pgx";

-						break;

-					case PXM_DFMT:

-						img_fol->out_format = "ppm";

-						break;

-					case BMP_DFMT:

-						img_fol->out_format = "bmp";

-						break;

-					case TIF_DFMT:

-						img_fol->out_format = "tif";

-						break;

-					case RAW_DFMT:

-						img_fol->out_format = "raw";

-						break;

-					case TGA_DFMT:

-						img_fol->out_format = "raw";

-						break;

-					default:

-						fprintf(stderr, "Unknown output format image %s [only *.pnm, *.pgm, *.ppm, *.pgx, *.bmp, *.tif, *.raw or *.tga]!! \n", outformat);

-						return 1;

-						break;

-				}

-			}

-			break;

-

-				/* ----------------------------------------------------- */

-

-

-			case 'r':		/* reduce option */

-			{

-				sscanf(opj_optarg, "%d", &parameters->cp_reduce);

-			}

-			break;

-			

-				/* ----------------------------------------------------- */

-      

-

-			case 'l':		/* layering option */

-			{

-				sscanf(opj_optarg, "%d", &parameters->cp_layer);

-			}

-			break;

-			

-				/* ----------------------------------------------------- */

-

-			case 'h': 			/* display an help description */

-				decode_help_display();

-				return 1;				

-

-				/* ------------------------------------------------------ */

-

-			case 'y':			/* Image Directory path */

-				{

-					img_fol->imgdirpath = (char*)opj_malloc(strlen(opj_optarg) + 1);

-					strcpy(img_fol->imgdirpath,opj_optarg);

-					img_fol->set_imgdir=1;

-				}

-				break;

-				/* ----------------------------------------------------- */

-/* UniPG>> */

-#ifdef USE_JPWL

-			

-			case 'W': 			/* activate JPWL correction */

-			{

-				char *token = NULL;

-

-				token = strtok(opj_optarg, ",");

-				while(token != NULL) {

-

-					/* search expected number of components */

-					if (*token == 'c') {

-

-						static int compno;

-

-						compno = JPWL_EXPECTED_COMPONENTS; /* predefined no. of components */

-

-						if(sscanf(token, "c=%d", &compno) == 1) {

-							/* Specified */

-							if ((compno < 1) || (compno > 256)) {

-								fprintf(stderr, "ERROR -> invalid number of components c = %d\n", compno);

-								return 1;

-							}

-							parameters->jpwl_exp_comps = compno;

-

-						} else if (!strcmp(token, "c")) {

-							/* default */

-							parameters->jpwl_exp_comps = compno; /* auto for default size */

-

-						} else {

-							fprintf(stderr, "ERROR -> invalid components specified = %s\n", token);

-							return 1;

-						};

-					}

-

-					/* search maximum number of tiles */

-					if (*token == 't') {

-

-						static int tileno;

-

-						tileno = JPWL_MAXIMUM_TILES; /* maximum no. of tiles */

-

-						if(sscanf(token, "t=%d", &tileno) == 1) {

-							/* Specified */

-							if ((tileno < 1) || (tileno > JPWL_MAXIMUM_TILES)) {

-								fprintf(stderr, "ERROR -> invalid number of tiles t = %d\n", tileno);

-								return 1;

-							}

-							parameters->jpwl_max_tiles = tileno;

-

-						} else if (!strcmp(token, "t")) {

-							/* default */

-							parameters->jpwl_max_tiles = tileno; /* auto for default size */

-

-						} else {

-							fprintf(stderr, "ERROR -> invalid tiles specified = %s\n", token);

-							return 1;

-						};

-					}

-

-					/* next token or bust */

-					token = strtok(NULL, ",");

-				};

-				parameters->jpwl_correct = true;

-				fprintf(stdout, "JPWL correction capability activated\n");

-				fprintf(stdout, "- expecting %d components\n", parameters->jpwl_exp_comps);

-			}

-			break;	

-#endif /* USE_JPWL */

-/* <<UniPG */            

-

-				/* ----------------------------------------------------- */

-			

-			default:

-				fprintf(stderr,"WARNING -> this option is not valid \"-%c %s\"\n",c, opj_optarg);

-				break;

-		}

-	}

-

-	/* No check for possible errors before the -i and -o options are of course not mandatory*/

-

-	return 0;

-}

-

-/* -------------------------------------------------------------------------- */

-

-/**

-error callback returning the message to Java andexpecting a callback_variables_t client object

-*/

-void error_callback(const char *msg, void *client_data) {

-	callback_variables_t* vars = (callback_variables_t*) client_data;

-	JNIEnv *env = vars->env;

-	jstring jbuffer;

-

-	jbuffer = (*env)->NewStringUTF(env, msg);

-	(*env)->ExceptionClear(env);

-	(*env)->CallVoidMethod(env, *(vars->jobj), vars->error_mid, jbuffer);

-

-	if ((*env)->ExceptionOccurred(env)) {

-		fprintf(stderr,"C: Exception during call back method\n");

-		(*env)->ExceptionDescribe(env);

-		(*env)->ExceptionClear(env);

-	}

-	(*env)->DeleteLocalRef(env, jbuffer);

-}

-/**

-warning callback returning the message to Java andexpecting a callback_variables_t client object

-*/

-void warning_callback(const char *msg, void *client_data) {

-	callback_variables_t* vars = (callback_variables_t*) client_data;

-	JNIEnv *env = vars->env;

-	jstring jbuffer;

-

-	jbuffer = (*env)->NewStringUTF(env, msg);

-	(*env)->ExceptionClear(env);

-	(*env)->CallVoidMethod(env, *(vars->jobj), vars->message_mid, jbuffer);

-	

-	if ((*env)->ExceptionOccurred(env)) {

-		fprintf(stderr,"C: Exception during call back method\n");

-		(*env)->ExceptionDescribe(env);

-		(*env)->ExceptionClear(env);

-	}

-	(*env)->DeleteLocalRef(env, jbuffer);

-}

-/**

-information callback returning the message to Java andexpecting a callback_variables_t client object

-*/

-void info_callback(const char *msg, void *client_data) {

-	callback_variables_t* vars = (callback_variables_t*) client_data;

-	JNIEnv *env = vars->env;

-	jstring jbuffer;

-

-	jbuffer = (*env)->NewStringUTF(env, msg);

-	(*env)->ExceptionClear(env);

-	(*env)->CallVoidMethod(env, *(vars->jobj), vars->message_mid, jbuffer);

-

-	if ((*env)->ExceptionOccurred(env)) {

-		fprintf(stderr,"C: Exception during call back method\n");

-		(*env)->ExceptionDescribe(env);

-		(*env)->ExceptionClear(env);

-	}

-	(*env)->DeleteLocalRef(env, jbuffer);

-}

-

-

-/* --------------------------------------------------------------------------

-   --------------------   MAIN METHOD, CALLED BY JAVA -----------------------*/

-JNIEXPORT jint JNICALL Java_org_openJpeg_OpenJPEGJavaDecoder_internalDecodeJ2KtoImage(JNIEnv *env, jobject obj, jobjectArray javaParameters) {

-	int argc;		/* To simulate the command line parameters (taken from the javaParameters variable) and be able to re-use the */

-	char **argv;	/*  'parse_cmdline_decoder' method taken from the j2k_to_image project */

-	opj_dparameters_t parameters;	/* decompression parameters */

-	img_fol_t img_fol;

-	opj_event_mgr_t event_mgr;		/* event manager */

-	opj_image_t *image = NULL;

-	FILE *fsrc = NULL;

-	unsigned char *src = NULL;

-	int file_length;

-	int num_images;

-	int i,j,imageno;

-	opj_dinfo_t* dinfo = NULL;	/* handle to a decompressor */

-	opj_cio_t *cio = NULL;

-	int w,h;

-	long min_value, max_value;

-	short tempS; unsigned char tempUC, tempUC1, tempUC2;

-	/* ==> Access variables to the Java member variables*/

-	jsize		arraySize;

-	jclass		cls;

-	jobject		object;

-	jboolean	isCopy;

-	jfieldID	fid;

-	jbyteArray	jba;

-	jshortArray jsa;

-	jintArray	jia;

-	jbyte		*jbBody, *ptrBBody;

-	jshort		*jsBody, *ptrSBody;

-	jint		*jiBody, *ptrIBody;

-	callback_variables_t msgErrorCallback_vars;

-	/* <=== access variable to Java member variables */

-	int *ptr, *ptr1, *ptr2;				/* <== To transfer the decoded image to Java*/

-

-	/* configure the event callbacks */

-	memset(&event_mgr, 0, sizeof(opj_event_mgr_t));	

-	event_mgr.error_handler = error_callback;

-	event_mgr.warning_handler = warning_callback;

-	event_mgr.info_handler = info_callback;

-

-	/* JNI reference to the calling class*/

-	cls = (*env)->GetObjectClass(env, obj);

-

-	/* Pointers to be able to call a Java method for all the info and error messages*/

-	msgErrorCallback_vars.env = env;

-	msgErrorCallback_vars.jobj = &obj;

-	msgErrorCallback_vars.message_mid = (*env)->GetMethodID(env, cls, "logMessage", "(Ljava/lang/String;)V");

-	msgErrorCallback_vars.error_mid = (*env)->GetMethodID(env, cls, "logError", "(Ljava/lang/String;)V");

-

-	/* Get the String[] containing the parameters, and converts it into a char** to simulate command line arguments.*/

-	arraySize = (*env)->GetArrayLength(env, javaParameters);

-	argc = (int) arraySize +1;

-	argv = opj_malloc(argc*sizeof(char*));

-	argv[0] = "ProgramName.exe";	/* The program name: useless*/

-	j=0;

-	for (i=1; i<argc; i++) {

-		object = (*env)->GetObjectArrayElement(env, javaParameters, i-1);

-		argv[i] = (char*)(*env)->GetStringUTFChars(env, object, &isCopy);

-	}

-

-	/*printf("C: decoder params = ");

-	for (i=0; i<argc; i++) {

-		printf("[%s]",argv[i]);

-	}

-	printf("\n");*/

-

-	/* set decoding parameters to default values */

-	opj_set_default_decoder_parameters(&parameters);

-	parameters.decod_format = J2K_CFMT;

-

-	/* parse input and get user encoding parameters */

-	if(parse_cmdline_decoder(argc, argv, &parameters,&img_fol) == 1) {

-		/* Release the Java arguments array*/

-		for (i=1; i<argc; i++)

-			(*env)->ReleaseStringUTFChars(env, (*env)->GetObjectArrayElement(env, javaParameters, i-1), argv[i]);

-		return -1;

-	}

-	/* Release the Java arguments array*/

-	for (i=1; i<argc; i++)

-		(*env)->ReleaseStringUTFChars(env, (*env)->GetObjectArrayElement(env, javaParameters, i-1), argv[i]);

-

-	num_images=1;

-

-	/* Get additional information from the Java object variables*/

-	fid = (*env)->GetFieldID(env, cls,"skippedResolutions", "I");

-	parameters.cp_reduce = (short) (*env)->GetIntField(env, obj, fid);

-

-	/*Decoding image one by one*/

-	for(imageno = 0; imageno < num_images ; imageno++)

-	{

-		image = NULL;

-		fprintf(stderr,"\n");

-

-		/* read the input file and put it in memory into the 'src' object, if the -i option is given in JavaParameters.

-		   Implemented for debug purpose. */

-		/* -------------------------------------------------------------- */

-		if (parameters.infile && parameters.infile[0]!='\0') {

-			/*printf("C: opening [%s]\n", parameters.infile);*/

-			fsrc = fopen(parameters.infile, "rb");

-			if (!fsrc) {

-				fprintf(stderr, "ERROR -> failed to open %s for reading\n", parameters.infile);

-				return 1;

-			}

-			fseek(fsrc, 0, SEEK_END);

-			file_length = ftell(fsrc);

-			fseek(fsrc, 0, SEEK_SET);

-			src = (unsigned char *) opj_malloc(file_length);

-			fread(src, 1, file_length, fsrc);

-			fclose(fsrc);

-			/*printf("C: %d bytes read from file\n",file_length);*/

-		} else {

-			/* Preparing the transfer of the codestream from Java to C*/

-			/*printf("C: before transferring codestream\n");*/

-			fid = (*env)->GetFieldID(env, cls,"compressedStream", "[B");

-			jba = (*env)->GetObjectField(env, obj, fid);

-			file_length = (*env)->GetArrayLength(env, jba);

-			jbBody = (*env)->GetByteArrayElements(env, jba, &isCopy);

-			src = (unsigned char*)jbBody;

-		}

-

-		/* decode the code-stream */

-		/* ---------------------- */

-

-		switch(parameters.decod_format) {

-		case J2K_CFMT:

-		{

-			/* JPEG-2000 codestream */

-

-			/* get a decoder handle */

-			dinfo = opj_create_decompress(CODEC_J2K);

-

-			/* catch events using our callbacks and give a local context */

-			opj_set_event_mgr((opj_common_ptr)dinfo, &event_mgr, &msgErrorCallback_vars);

-

-			/* setup the decoder decoding parameters using user parameters */

-			opj_setup_decoder(dinfo, &parameters);

-

-			/* open a byte stream */

-			cio = opj_cio_open((opj_common_ptr)dinfo, src, file_length);

-

-			/* decode the stream and fill the image structure */

-			image = opj_decode(dinfo, cio);

-			if(!image) {

-				fprintf(stderr, "ERROR -> j2k_to_image: failed to decode image!\n");

-				opj_destroy_decompress(dinfo);

-				opj_cio_close(cio);

-				return 1;

-			}

-

-			/* close the byte stream */

-			opj_cio_close(cio);

-		}

-		break;

-

-		case JP2_CFMT:

-		{

-			/* JPEG 2000 compressed image data */

-

-			/* get a decoder handle */

-			dinfo = opj_create_decompress(CODEC_JP2);

-

-			/* catch events using our callbacks and give a local context */

-			opj_set_event_mgr((opj_common_ptr)dinfo, &event_mgr, &msgErrorCallback_vars);

-

-			/* setup the decoder decoding parameters using the current image and user parameters */

-			opj_setup_decoder(dinfo, &parameters);

-

-			/* open a byte stream */

-			cio = opj_cio_open((opj_common_ptr)dinfo, src, file_length);

-

-			/* decode the stream and fill the image structure */

-			image = opj_decode(dinfo, cio);

-			if(!image) {

-				fprintf(stderr, "ERROR -> j2k_to_image: failed to decode image!\n");

-				opj_destroy_decompress(dinfo);

-				opj_cio_close(cio);

-				return 1;

-			}

-

-			/* close the byte stream */

-			opj_cio_close(cio);

-

-		}

-		break;

-

-		case JPT_CFMT:

-		{

-			/* JPEG 2000, JPIP */

-

-			/* get a decoder handle */

-			dinfo = opj_create_decompress(CODEC_JPT);

-

-			/* catch events using our callbacks and give a local context */

-			opj_set_event_mgr((opj_common_ptr)dinfo, &event_mgr, &msgErrorCallback_vars);

-

-			/* setup the decoder decoding parameters using user parameters */

-			opj_setup_decoder(dinfo, &parameters);

-

-			/* open a byte stream */

-			cio = opj_cio_open((opj_common_ptr)dinfo, src, file_length);

-

-			/* decode the stream and fill the image structure */

-			image = opj_decode(dinfo, cio);

-			if(!image) {

-				fprintf(stderr, "ERROR -> j2k_to_image: failed to decode image!\n");

-				opj_destroy_decompress(dinfo);

-				opj_cio_close(cio);

-				return 1;

-			}

-

-			/* close the byte stream */

-			opj_cio_close(cio);

-		}

-		break;

-

-		default:

-			fprintf(stderr, "skipping file..\n");

-			continue;

-	}

-

-		/* free the memory containing the code-stream */

-		if (parameters.infile && parameters.infile[0]!='\0') {

-			opj_free(src);

-		} else {

-			(*env)->ReleaseByteArrayElements(env, jba, jbBody, 0);

-		}

-		src = NULL;

-

-		/* create output image.

-			If the -o parameter is given in the JavaParameters, write the decoded version into a file.

-			Implemented for debug purpose. */

-		/* ---------------------------------- */

-		switch (parameters.cod_format) {

-		case PXM_DFMT:			/* PNM PGM PPM */

-			if (imagetopnm(image, parameters.outfile)) {

-				fprintf(stdout,"Outfile %s not generated\n",parameters.outfile);

-			}

-			else {

-				fprintf(stdout,"Generated Outfile %s\n",parameters.outfile);

-			}

-			break;

-

-		case PGX_DFMT:			/* PGX */

-			if(imagetopgx(image, parameters.outfile)){

-				fprintf(stdout,"Outfile %s not generated\n",parameters.outfile);

-			}

-			else {

-				fprintf(stdout,"Generated Outfile %s\n",parameters.outfile);

-			}

-			break;

-

-		case BMP_DFMT:			/* BMP */

-			if(imagetobmp(image, parameters.outfile)){

-				fprintf(stdout,"Outfile %s not generated\n",parameters.outfile);

-			}

-			else {

-				fprintf(stdout,"Generated Outfile %s\n",parameters.outfile);

-			}

-			break;

-

-		}

-

-		/* ========= Return the image to the Java structure ===============*/

-#ifdef CHECK_THRESHOLDS

-		printf("C: checking thresholds\n");

-#endif

-		/* First compute the real with and height, in function of the resolutions decoded.*/

-		/*wr = (image->comps[0].w + (1 << image->comps[0].factor) -1) >> image->comps[0].factor;*/

-		/*hr = (image->comps[0].h + (1 << image->comps[0].factor) -1) >> image->comps[0].factor;*/

-		w = image->comps[0].w;

-		h = image->comps[0].h;

-

-		if (image->numcomps==3) {	/* 3 components color image*/

-			ptr = image->comps[0].data;

-			ptr1 = image->comps[1].data;

-			ptr2 = image->comps[2].data;

-#ifdef CHECK_THRESHOLDS 

-			if (image->comps[0].sgnd) {

-				min_value = -128;

-				max_value = 127;

-			} else {

-				min_value = 0;

-				max_value = 255;

-			}

-#endif			

-			/* Get the pointer to the Java structure where the data must be copied*/

-			fid = (*env)->GetFieldID(env, cls,"image24", "[I");

-			jia = (*env)->GetObjectField(env, obj, fid);

-			jiBody = (*env)->GetIntArrayElements(env, jia, 0);

-			ptrIBody = jiBody;

-			printf("C: transferring image24: %d int to Java pointer=%d\n",image->numcomps*w*h, ptrIBody);

-

-			for (i=0; i<w*h; i++) {

-				tempUC = (unsigned char)(ptr[i]);

-				tempUC1 = (unsigned char)(ptr1[i]);

-				tempUC2 = (unsigned char)(ptr2[i]);

-#ifdef CHECK_THRESHOLDS

-				if (tempUC < min_value)

-					tempUC=min_value;

-				else if (tempUC > max_value)

-					tempUC=max_value;

-				if (tempUC1 < min_value)

-					tempUC1=min_value;

-				else if (tempUC1 > max_value)

-					tempUC1=max_value;

-				if (tempUC2 < min_value)

-					tempUC2=min_value;

-				else if (tempUC2 > max_value)

-					tempUC2=max_value;

-#endif

-				*(ptrIBody++)  = (int) ( (tempUC2<<16) + (tempUC1<<8) + tempUC );

-			}

-			(*env)->ReleaseIntArrayElements(env, jia, jiBody, 0);

-

-		} else {	/* 1 component 8 or 16 bpp image*/

-			ptr = image->comps[0].data;

-			printf("C: before transferring a %d bpp image to java (length = %d)\n",image->comps[0].prec ,w*h);

-			if (image->comps[0].prec<=8) {

-				fid = (*env)->GetFieldID(env, cls,"image8", "[B");

-				jba = (*env)->GetObjectField(env, obj, fid);

-				jbBody = (*env)->GetByteArrayElements(env, jba, 0);

-				ptrBBody = jbBody;

-#ifdef CHECK_THRESHOLDS 

-				if (image->comps[0].sgnd) {

-					min_value = -128;

-					max_value = 127;

-				} else {

-					min_value = 0;

-					max_value = 255;

-				}

-#endif								

-				/*printf("C: transferring %d shorts to Java image8 pointer = %d\n", wr*hr,ptrSBody);*/

-				for (i=0; i<w*h; i++) {

-					tempUC = (unsigned char) (ptr[i]);

-#ifdef CHECK_THRESHOLDS

-					if (tempUC<min_value)

-						tempUC = min_value;

-					else if (tempUC > max_value)

-						tempUC = max_value;

-#endif

-					*(ptrBBody++) = tempUC;

-				}

-				(*env)->ReleaseByteArrayElements(env, jba, jbBody, 0);

-				printf("C: image8 transferred to Java\n");

-			} else {

-				fid = (*env)->GetFieldID(env, cls,"image16", "[S");

-				jsa = (*env)->GetObjectField(env, obj, fid);

-				jsBody = (*env)->GetShortArrayElements(env, jsa, 0);

-				ptrSBody = jsBody;

-#ifdef CHECK_THRESHOLDS 

-				if (image->comps[0].sgnd) {

-					min_value = -32768;

-					max_value = 32767;

-				} else {

-					min_value = 0;

-					max_value = 65535;

-				}

-				printf("C: minValue = %d, maxValue = %d\n", min_value, max_value);

-#endif				

-				printf("C: transferring %d shorts to Java image16 pointer = %d\n", w*h,ptrSBody);

-				for (i=0; i<w*h; i++) {

-					tempS = (short) (ptr[i]);

-#ifdef CHECK_THRESHOLDS

-					if (tempS<min_value) {

-						printf("C: value %d truncated to %d\n", tempS, min_value);

-						tempS = min_value;

-					} else if (tempS > max_value) {

-						printf("C: value %d truncated to %d\n", tempS, max_value);

-						tempS = max_value;

-					}

-#endif

-					*(ptrSBody++) = tempS;

-				}

-				(*env)->ReleaseShortArrayElements(env, jsa, jsBody, 0);

-				printf("C: image16 completely filled\n");

-			}

-		}	

-

-

-		/* free remaining structures */

-		if(dinfo) {

-			opj_destroy_decompress(dinfo);

-		}

-		/* free image data structure */

-		opj_image_destroy(image);

-

-	}

-	return 1; /* OK */

-}

-/*end main*/

-

+ * Copyright (c) 2003-2014, Antonin Descampe
+ * Copyright (c) 2005, Herve Drolon, FreeImage Team
+ * Copyright (c) 2006-2007, Parvatha Elangovan
+ * Copyright (c) 2007, Patrick Piscaglia (Telemis)
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS `AS IS'
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <jni.h>
+#include <math.h>
+
+#include "openjpeg.h"
+#include "opj_includes.h"
+#include "opj_getopt.h"
+#include "convert.h"
+#include "dirent.h"
+#include "org_openJpeg_OpenJPEGJavaDecoder.h"
+
+#ifndef _WIN32
+#define stricmp strcasecmp
+#define strnicmp strncasecmp
+#endif
+
+#include "format_defs.h"
+
+typedef struct callback_variables {
+	JNIEnv *env;
+	/** 'jclass' object used to call a Java method from the C */
+	jobject *jobj;
+	/** 'jclass' object used to call a Java method from the C */
+	jmethodID message_mid;
+	jmethodID error_mid;
+} callback_variables_t;
+
+typedef struct dircnt{
+	/** Buffer for holding images read from Directory*/
+	char *filename_buf;
+	/** Pointer to the buffer*/
+	char **filename;
+}dircnt_t;
+
+
+typedef struct img_folder{
+	/** The directory path of the folder containing input images*/
+	char *imgdirpath;
+	/** Output format*/
+	char *out_format;
+	/** Enable option*/
+	char set_imgdir;
+	/** Enable Cod Format for output*/
+	char set_out_format;
+
+}img_fol_t;
+
+
+void decode_help_display() {
+	fprintf(stdout,"HELP\n----\n\n");
+	fprintf(stdout,"- the -h option displays this help information on screen\n\n");
+
+/* UniPG>> */
+	fprintf(stdout,"List of parameters for the JPEG 2000 "
+#ifdef USE_JPWL
+		"+ JPWL "
+#endif /* USE_JPWL */
+		"decoder:\n");
+/* <<UniPG */
+	fprintf(stdout,"\n");
+	fprintf(stdout,"\n");
+	fprintf(stdout,"  -ImgDir \n");
+	fprintf(stdout,"	Image file Directory path \n");
+	fprintf(stdout,"  -OutFor \n");
+	fprintf(stdout,"    REQUIRED only if -ImgDir is used\n");
+	fprintf(stdout,"	  Need to specify only format without filename <BMP>  \n");
+	fprintf(stdout,"    Currently accepts PGM, PPM, PNM, PGX, BMP format\n");
+	fprintf(stdout,"  -i <compressed file>\n");
+	fprintf(stdout,"    REQUIRED only if an Input image directory not specified\n");
+	fprintf(stdout,"    Currently accepts J2K-files, JP2-files and JPT-files. The file type\n");
+	fprintf(stdout,"    is identified based on its suffix.\n");
+	fprintf(stdout,"  -o <decompressed file>\n");
+	fprintf(stdout,"    REQUIRED\n");
+	fprintf(stdout,"    Currently accepts PGM-files, PPM-files, PNM-files, PGX-files and\n");
+	fprintf(stdout,"    BMP-files. Binary data is written to the file (not ascii). If a PGX\n");
+	fprintf(stdout,"    filename is given, there will be as many output files as there are\n");
+	fprintf(stdout,"    components: an indice starting from 0 will then be appended to the\n");
+	fprintf(stdout,"    output filename, just before the \"pgx\" extension. If a PGM filename\n");
+	fprintf(stdout,"    is given and there are more than one component, only the first component\n");
+	fprintf(stdout,"    will be written to the file.\n");
+	fprintf(stdout,"  -r <reduce factor>\n");
+	fprintf(stdout,"    Set the number of highest resolution levels to be discarded. The\n");
+	fprintf(stdout,"    image resolution is effectively divided by 2 to the power of the\n");
+	fprintf(stdout,"    number of discarded levels. The reduce factor is limited by the\n");
+	fprintf(stdout,"    smallest total number of decomposition levels among tiles.\n");
+	fprintf(stdout,"  -l <number of quality layers to decode>\n");
+	fprintf(stdout,"    Set the maximum number of quality layers to decode. If there are\n");
+	fprintf(stdout,"    less quality layers than the specified number, all the quality layers\n");
+	fprintf(stdout,"    are decoded.\n");
+/* UniPG>> */
+#ifdef USE_JPWL
+	fprintf(stdout,"  -W <options>\n");
+	fprintf(stdout,"    Activates the JPWL correction capability, if the codestream complies.\n");
+	fprintf(stdout,"    Options can be a comma separated list of <param=val> tokens:\n");
+	fprintf(stdout,"    c, c=numcomps\n");
+	fprintf(stdout,"       numcomps is the number of expected components in the codestream\n");
+	fprintf(stdout,"       (search of first EPB rely upon this, default is %d)\n", JPWL_EXPECTED_COMPONENTS);
+#endif /* USE_JPWL */
+/* <<UniPG */
+	fprintf(stdout,"\n");
+}
+
+/* -------------------------------------------------------------------------- */
+
+int get_num_images(char *imgdirpath){
+	DIR *dir;
+	struct dirent* content;	
+	int num_images = 0;
+
+	/*Reading the input images from given input directory*/
+
+	dir= opendir(imgdirpath);
+	if(!dir){
+		fprintf(stderr,"Could not open Folder %s\n",imgdirpath);
+		return 0;
+	}
+	
+	while((content=readdir(dir))!=NULL){
+		if(strcmp(".",content->d_name)==0 || strcmp("..",content->d_name)==0 )
+			continue;
+		num_images++;
+	}
+	return num_images;
+}
+
+int load_images(dircnt_t *dirptr, char *imgdirpath){
+	DIR *dir;
+	struct dirent* content;	
+	int i = 0;
+
+	/*Reading the input images from given input directory*/
+
+	dir= opendir(imgdirpath);
+	if(!dir){
+		fprintf(stderr,"Could not open Folder %s\n",imgdirpath);
+		return 1;
+	}else	{
+		fprintf(stderr,"Folder opened successfully\n");
+	}
+	
+	while((content=readdir(dir))!=NULL){
+		if(strcmp(".",content->d_name)==0 || strcmp("..",content->d_name)==0 )
+			continue;
+
+		strcpy(dirptr->filename[i],content->d_name);
+		i++;
+	}
+	return 0;	
+}
+
+int get_file_format(char *filename) {
+	unsigned int i;
+	static const char *extension[] = {"pgx", "pnm", "pgm", "ppm", "bmp","tif", "raw", "tga", "j2k", "jp2", "jpt", "j2c" };
+	static const int format[] = { PGX_DFMT, PXM_DFMT, PXM_DFMT, PXM_DFMT, BMP_DFMT, TIF_DFMT, RAW_DFMT, TGA_DFMT, J2K_CFMT, JP2_CFMT, JPT_CFMT, J2K_CFMT };
+	char * ext = strrchr(filename, '.');
+	if (ext == NULL)
+		return -1;
+	ext++;
+	if(ext) {
+		for(i = 0; i < sizeof(format)/sizeof(*format); i++) {
+			if(strnicmp(ext, extension[i], 3) == 0) {
+				return format[i];
+			}
+		}
+	}
+
+	return -1;
+}
+
+
+/* -------------------------------------------------------------------------- */
+
+int parse_cmdline_decoder(int argc, char **argv, opj_dparameters_t *parameters,img_fol_t *img_fol) {
+	/* parse the command line */
+	int totlen;
+	opj_option_t long_option[]={
+		{"ImgDir",REQ_ARG, NULL ,'y'},
+		{"OutFor",REQ_ARG, NULL ,'O'},
+	};
+
+/* UniPG>> */
+	const char optlist[] = "i:o:r:l:hx:"
+
+#ifdef USE_JPWL
+					"W:"
+#endif /* USE_JPWL */
+					;
+	/*for (i=0; i<argc; i++) {
+		printf("[%s]",argv[i]);
+	}
+	printf("\n");*/
+
+/* <<UniPG */
+	totlen=sizeof(long_option);
+	img_fol->set_out_format = 0;
+	reset_options_reading();
+
+	while (1) {
+		int c = opj_getopt_long(argc, argv,optlist,long_option,totlen);
+		if (c == -1)
+			break;
+		switch (c) {
+			case 'i':			/* input file */
+			{
+				char *infile = opj_optarg;
+				parameters->decod_format = get_file_format(infile);
+				switch(parameters->decod_format) {
+					case J2K_CFMT:
+					case JP2_CFMT:
+					case JPT_CFMT:
+						break;
+					default:
+						fprintf(stderr, 
+							"!! Unrecognized format for infile : %s [accept only *.j2k, *.jp2, *.jpc or *.jpt] !!\n\n", 
+							infile);
+						return 1;
+				}
+				strncpy(parameters->infile, infile, sizeof(parameters->infile)-1);
+			}
+			break;
+				
+				/* ----------------------------------------------------- */
+
+			case 'o':			/* output file */
+			{
+				char *outfile = opj_optarg;
+				parameters->cod_format = get_file_format(outfile);
+				switch(parameters->cod_format) {
+					case PGX_DFMT:
+					case PXM_DFMT:
+					case BMP_DFMT:
+					case TIF_DFMT:
+					case RAW_DFMT:
+					case TGA_DFMT:
+						break;
+					default:
+						fprintf(stderr, "Unknown output format image %s [only *.pnm, *.pgm, *.ppm, *.pgx, *.bmp, *.tif, *.raw or *.tga]!! \n", outfile);
+						return 1;
+				}
+				strncpy(parameters->outfile, outfile, sizeof(parameters->outfile)-1);
+			}
+			break;
+			
+				/* ----------------------------------------------------- */
+
+			case 'O':			/* output format */
+			{
+				char outformat[50];
+				char *of = opj_optarg;
+				sprintf(outformat,".%s",of);
+				img_fol->set_out_format = 1;
+				parameters->cod_format = get_file_format(outformat);
+				switch(parameters->cod_format) {
+					case PGX_DFMT:
+						img_fol->out_format = "pgx";
+						break;
+					case PXM_DFMT:
+						img_fol->out_format = "ppm";
+						break;
+					case BMP_DFMT:
+						img_fol->out_format = "bmp";
+						break;
+					case TIF_DFMT:
+						img_fol->out_format = "tif";
+						break;
+					case RAW_DFMT:
+						img_fol->out_format = "raw";
+						break;
+					case TGA_DFMT:
+						img_fol->out_format = "raw";
+						break;
+					default:
+						fprintf(stderr, "Unknown output format image %s [only *.pnm, *.pgm, *.ppm, *.pgx, *.bmp, *.tif, *.raw or *.tga]!! \n", outformat);
+						return 1;
+						break;
+				}
+			}
+			break;
+
+				/* ----------------------------------------------------- */
+
+
+			case 'r':		/* reduce option */
+			{
+				sscanf(opj_optarg, "%d", &parameters->cp_reduce);
+			}
+			break;
+			
+				/* ----------------------------------------------------- */
+      
+
+			case 'l':		/* layering option */
+			{
+				sscanf(opj_optarg, "%d", &parameters->cp_layer);
+			}
+			break;
+			
+				/* ----------------------------------------------------- */
+
+			case 'h': 			/* display an help description */
+				decode_help_display();
+				return 1;				
+
+				/* ------------------------------------------------------ */
+
+			case 'y':			/* Image Directory path */
+				{
+					img_fol->imgdirpath = (char*)opj_malloc(strlen(opj_optarg) + 1);
+					strcpy(img_fol->imgdirpath,opj_optarg);
+					img_fol->set_imgdir=1;
+				}
+				break;
+				/* ----------------------------------------------------- */
+/* UniPG>> */
+#ifdef USE_JPWL
+			
+			case 'W': 			/* activate JPWL correction */
+			{
+				char *token = NULL;
+
+				token = strtok(opj_optarg, ",");
+				while(token != NULL) {
+
+					/* search expected number of components */
+					if (*token == 'c') {
+
+						static int compno;
+
+						compno = JPWL_EXPECTED_COMPONENTS; /* predefined no. of components */
+
+						if(sscanf(token, "c=%d", &compno) == 1) {
+							/* Specified */
+							if ((compno < 1) || (compno > 256)) {
+								fprintf(stderr, "ERROR -> invalid number of components c = %d\n", compno);
+								return 1;
+							}
+							parameters->jpwl_exp_comps = compno;
+
+						} else if (!strcmp(token, "c")) {
+							/* default */
+							parameters->jpwl_exp_comps = compno; /* auto for default size */
+
+						} else {
+							fprintf(stderr, "ERROR -> invalid components specified = %s\n", token);
+							return 1;
+						};
+					}
+
+					/* search maximum number of tiles */
+					if (*token == 't') {
+
+						static int tileno;
+
+						tileno = JPWL_MAXIMUM_TILES; /* maximum no. of tiles */
+
+						if(sscanf(token, "t=%d", &tileno) == 1) {
+							/* Specified */
+							if ((tileno < 1) || (tileno > JPWL_MAXIMUM_TILES)) {
+								fprintf(stderr, "ERROR -> invalid number of tiles t = %d\n", tileno);
+								return 1;
+							}
+							parameters->jpwl_max_tiles = tileno;
+
+						} else if (!strcmp(token, "t")) {
+							/* default */
+							parameters->jpwl_max_tiles = tileno; /* auto for default size */
+
+						} else {
+							fprintf(stderr, "ERROR -> invalid tiles specified = %s\n", token);
+							return 1;
+						};
+					}
+
+					/* next token or bust */
+					token = strtok(NULL, ",");
+				};
+				parameters->jpwl_correct = true;
+				fprintf(stdout, "JPWL correction capability activated\n");
+				fprintf(stdout, "- expecting %d components\n", parameters->jpwl_exp_comps);
+			}
+			break;	
+#endif /* USE_JPWL */
+/* <<UniPG */            
+
+				/* ----------------------------------------------------- */
+			
+			default:
+				fprintf(stderr,"WARNING -> this option is not valid \"-%c %s\"\n",c, opj_optarg);
+				break;
+		}
+	}
+
+	/* No check for possible errors before the -i and -o options are of course not mandatory*/
+
+	return 0;
+}
+
+/* -------------------------------------------------------------------------- */
+
+/**
+error callback returning the message to Java andexpecting a callback_variables_t client object
+*/
+void error_callback(const char *msg, void *client_data) {
+	callback_variables_t* vars = (callback_variables_t*) client_data;
+	JNIEnv *env = vars->env;
+	jstring jbuffer;
+
+	jbuffer = (*env)->NewStringUTF(env, msg);
+	(*env)->ExceptionClear(env);
+	(*env)->CallVoidMethod(env, *(vars->jobj), vars->error_mid, jbuffer);
+
+	if ((*env)->ExceptionOccurred(env)) {
+		fprintf(stderr,"C: Exception during call back method\n");
+		(*env)->ExceptionDescribe(env);
+		(*env)->ExceptionClear(env);
+	}
+	(*env)->DeleteLocalRef(env, jbuffer);
+}
+/**
+warning callback returning the message to Java andexpecting a callback_variables_t client object
+*/
+void warning_callback(const char *msg, void *client_data) {
+	callback_variables_t* vars = (callback_variables_t*) client_data;
+	JNIEnv *env = vars->env;
+	jstring jbuffer;
+
+	jbuffer = (*env)->NewStringUTF(env, msg);
+	(*env)->ExceptionClear(env);
+	(*env)->CallVoidMethod(env, *(vars->jobj), vars->message_mid, jbuffer);
+	
+	if ((*env)->ExceptionOccurred(env)) {
+		fprintf(stderr,"C: Exception during call back method\n");
+		(*env)->ExceptionDescribe(env);
+		(*env)->ExceptionClear(env);
+	}
+	(*env)->DeleteLocalRef(env, jbuffer);
+}
+/**
+information callback returning the message to Java andexpecting a callback_variables_t client object
+*/
+void info_callback(const char *msg, void *client_data) {
+	callback_variables_t* vars = (callback_variables_t*) client_data;
+	JNIEnv *env = vars->env;
+	jstring jbuffer;
+
+	jbuffer = (*env)->NewStringUTF(env, msg);
+	(*env)->ExceptionClear(env);
+	(*env)->CallVoidMethod(env, *(vars->jobj), vars->message_mid, jbuffer);
+
+	if ((*env)->ExceptionOccurred(env)) {
+		fprintf(stderr,"C: Exception during call back method\n");
+		(*env)->ExceptionDescribe(env);
+		(*env)->ExceptionClear(env);
+	}
+	(*env)->DeleteLocalRef(env, jbuffer);
+}
+
+
+/* --------------------------------------------------------------------------
+   --------------------   MAIN METHOD, CALLED BY JAVA -----------------------*/
+JNIEXPORT jint JNICALL Java_org_openJpeg_OpenJPEGJavaDecoder_internalDecodeJ2KtoImage(JNIEnv *env, jobject obj, jobjectArray javaParameters) {
+	int argc;		/* To simulate the command line parameters (taken from the javaParameters variable) and be able to re-use the */
+	char **argv;	/*  'parse_cmdline_decoder' method taken from the j2k_to_image project */
+	opj_dparameters_t parameters;	/* decompression parameters */
+	img_fol_t img_fol;
+	opj_event_mgr_t event_mgr;		/* event manager */
+	opj_image_t *image = NULL;
+	FILE *fsrc = NULL;
+	unsigned char *src = NULL;
+	int file_length;
+	int num_images;
+	int i,j,imageno;
+	opj_dinfo_t* dinfo = NULL;	/* handle to a decompressor */
+	opj_cio_t *cio = NULL;
+	int w,h;
+	long min_value, max_value;
+	short tempS; unsigned char tempUC, tempUC1, tempUC2;
+	/* ==> Access variables to the Java member variables*/
+	jsize		arraySize;
+	jclass		cls;
+	jobject		object;
+	jboolean	isCopy;
+	jfieldID	fid;
+	jbyteArray	jba;
+	jshortArray jsa;
+	jintArray	jia;
+	jbyte		*jbBody, *ptrBBody;
+	jshort		*jsBody, *ptrSBody;
+	jint		*jiBody, *ptrIBody;
+	callback_variables_t msgErrorCallback_vars;
+	/* <=== access variable to Java member variables */
+	int *ptr, *ptr1, *ptr2;				/* <== To transfer the decoded image to Java*/
+
+	/* configure the event callbacks */
+	memset(&event_mgr, 0, sizeof(opj_event_mgr_t));	
+	event_mgr.error_handler = error_callback;
+	event_mgr.warning_handler = warning_callback;
+	event_mgr.info_handler = info_callback;
+
+	/* JNI reference to the calling class*/
+	cls = (*env)->GetObjectClass(env, obj);
+
+	/* Pointers to be able to call a Java method for all the info and error messages*/
+	msgErrorCallback_vars.env = env;
+	msgErrorCallback_vars.jobj = &obj;
+	msgErrorCallback_vars.message_mid = (*env)->GetMethodID(env, cls, "logMessage", "(Ljava/lang/String;)V");
+	msgErrorCallback_vars.error_mid = (*env)->GetMethodID(env, cls, "logError", "(Ljava/lang/String;)V");
+
+	/* Get the String[] containing the parameters, and converts it into a char** to simulate command line arguments.*/
+	arraySize = (*env)->GetArrayLength(env, javaParameters);
+	argc = (int) arraySize +1;
+	argv = opj_malloc(argc*sizeof(char*));
+	argv[0] = "ProgramName.exe";	/* The program name: useless*/
+	j=0;
+	for (i=1; i<argc; i++) {
+		object = (*env)->GetObjectArrayElement(env, javaParameters, i-1);
+		argv[i] = (char*)(*env)->GetStringUTFChars(env, object, &isCopy);
+	}
+
+	/*printf("C: decoder params = ");
+	for (i=0; i<argc; i++) {
+		printf("[%s]",argv[i]);
+	}
+	printf("\n");*/
+
+	/* set decoding parameters to default values */
+	opj_set_default_decoder_parameters(&parameters);
+	parameters.decod_format = J2K_CFMT;
+
+	/* parse input and get user encoding parameters */
+	if(parse_cmdline_decoder(argc, argv, &parameters,&img_fol) == 1) {
+		/* Release the Java arguments array*/
+		for (i=1; i<argc; i++)
+			(*env)->ReleaseStringUTFChars(env, (*env)->GetObjectArrayElement(env, javaParameters, i-1), argv[i]);
+		return -1;
+	}
+	/* Release the Java arguments array*/
+	for (i=1; i<argc; i++)
+		(*env)->ReleaseStringUTFChars(env, (*env)->GetObjectArrayElement(env, javaParameters, i-1), argv[i]);
+
+	num_images=1;
+
+	/* Get additional information from the Java object variables*/
+	fid = (*env)->GetFieldID(env, cls,"skippedResolutions", "I");
+	parameters.cp_reduce = (short) (*env)->GetIntField(env, obj, fid);
+
+	/*Decoding image one by one*/
+	for(imageno = 0; imageno < num_images ; imageno++)
+	{
+		image = NULL;
+		fprintf(stderr,"\n");
+
+		/* read the input file and put it in memory into the 'src' object, if the -i option is given in JavaParameters.
+		   Implemented for debug purpose. */
+		/* -------------------------------------------------------------- */
+		if (parameters.infile && parameters.infile[0]!='\0') {
+			/*printf("C: opening [%s]\n", parameters.infile);*/
+			fsrc = fopen(parameters.infile, "rb");
+			if (!fsrc) {
+				fprintf(stderr, "ERROR -> failed to open %s for reading\n", parameters.infile);
+				return 1;
+			}
+			fseek(fsrc, 0, SEEK_END);
+			file_length = ftell(fsrc);
+			fseek(fsrc, 0, SEEK_SET);
+			src = (unsigned char *) opj_malloc(file_length);
+			fread(src, 1, file_length, fsrc);
+			fclose(fsrc);
+			/*printf("C: %d bytes read from file\n",file_length);*/
+		} else {
+			/* Preparing the transfer of the codestream from Java to C*/
+			/*printf("C: before transferring codestream\n");*/
+			fid = (*env)->GetFieldID(env, cls,"compressedStream", "[B");
+			jba = (*env)->GetObjectField(env, obj, fid);
+			file_length = (*env)->GetArrayLength(env, jba);
+			jbBody = (*env)->GetByteArrayElements(env, jba, &isCopy);
+			src = (unsigned char*)jbBody;
+		}
+
+		/* decode the code-stream */
+		/* ---------------------- */
+
+		switch(parameters.decod_format) {
+		case J2K_CFMT:
+		{
+			/* JPEG-2000 codestream */
+
+			/* get a decoder handle */
+			dinfo = opj_create_decompress(CODEC_J2K);
+
+			/* catch events using our callbacks and give a local context */
+			opj_set_event_mgr((opj_common_ptr)dinfo, &event_mgr, &msgErrorCallback_vars);
+
+			/* setup the decoder decoding parameters using user parameters */
+			opj_setup_decoder(dinfo, &parameters);
+
+			/* open a byte stream */
+			cio = opj_cio_open((opj_common_ptr)dinfo, src, file_length);
+
+			/* decode the stream and fill the image structure */
+			image = opj_decode(dinfo, cio);
+			if(!image) {
+				fprintf(stderr, "ERROR -> j2k_to_image: failed to decode image!\n");
+				opj_destroy_decompress(dinfo);
+				opj_cio_close(cio);
+				return 1;
+			}
+
+			/* close the byte stream */
+			opj_cio_close(cio);
+		}
+		break;
+
+		case JP2_CFMT:
+		{
+			/* JPEG 2000 compressed image data */
+
+			/* get a decoder handle */
+			dinfo = opj_create_decompress(CODEC_JP2);
+
+			/* catch events using our callbacks and give a local context */
+			opj_set_event_mgr((opj_common_ptr)dinfo, &event_mgr, &msgErrorCallback_vars);
+
+			/* setup the decoder decoding parameters using the current image and user parameters */
+			opj_setup_decoder(dinfo, &parameters);
+
+			/* open a byte stream */
+			cio = opj_cio_open((opj_common_ptr)dinfo, src, file_length);
+
+			/* decode the stream and fill the image structure */
+			image = opj_decode(dinfo, cio);
+			if(!image) {
+				fprintf(stderr, "ERROR -> j2k_to_image: failed to decode image!\n");
+				opj_destroy_decompress(dinfo);
+				opj_cio_close(cio);
+				return 1;
+			}
+
+			/* close the byte stream */
+			opj_cio_close(cio);
+
+		}
+		break;
+
+		case JPT_CFMT:
+		{
+			/* JPEG 2000, JPIP */
+
+			/* get a decoder handle */
+			dinfo = opj_create_decompress(CODEC_JPT);
+
+			/* catch events using our callbacks and give a local context */
+			opj_set_event_mgr((opj_common_ptr)dinfo, &event_mgr, &msgErrorCallback_vars);
+
+			/* setup the decoder decoding parameters using user parameters */
+			opj_setup_decoder(dinfo, &parameters);
+
+			/* open a byte stream */
+			cio = opj_cio_open((opj_common_ptr)dinfo, src, file_length);
+
+			/* decode the stream and fill the image structure */
+			image = opj_decode(dinfo, cio);
+			if(!image) {
+				fprintf(stderr, "ERROR -> j2k_to_image: failed to decode image!\n");
+				opj_destroy_decompress(dinfo);
+				opj_cio_close(cio);
+				return 1;
+			}
+
+			/* close the byte stream */
+			opj_cio_close(cio);
+		}
+		break;
+
+		default:
+			fprintf(stderr, "skipping file..\n");
+			continue;
+	}
+
+		/* free the memory containing the code-stream */
+		if (parameters.infile && parameters.infile[0]!='\0') {
+			opj_free(src);
+		} else {
+			(*env)->ReleaseByteArrayElements(env, jba, jbBody, 0);
+		}
+		src = NULL;
+
+		/* create output image.
+			If the -o parameter is given in the JavaParameters, write the decoded version into a file.
+			Implemented for debug purpose. */
+		/* ---------------------------------- */
+		switch (parameters.cod_format) {
+		case PXM_DFMT:			/* PNM PGM PPM */
+			if (imagetopnm(image, parameters.outfile)) {
+				fprintf(stdout,"Outfile %s not generated\n",parameters.outfile);
+			}
+			else {
+				fprintf(stdout,"Generated Outfile %s\n",parameters.outfile);
+			}
+			break;
+
+		case PGX_DFMT:			/* PGX */
+			if(imagetopgx(image, parameters.outfile)){
+				fprintf(stdout,"Outfile %s not generated\n",parameters.outfile);
+			}
+			else {
+				fprintf(stdout,"Generated Outfile %s\n",parameters.outfile);
+			}
+			break;
+
+		case BMP_DFMT:			/* BMP */
+			if(imagetobmp(image, parameters.outfile)){
+				fprintf(stdout,"Outfile %s not generated\n",parameters.outfile);
+			}
+			else {
+				fprintf(stdout,"Generated Outfile %s\n",parameters.outfile);
+			}
+			break;
+
+		}
+
+		/* ========= Return the image to the Java structure ===============*/
+#ifdef CHECK_THRESHOLDS
+		printf("C: checking thresholds\n");
+#endif
+		/* First compute the real with and height, in function of the resolutions decoded.*/
+		/*wr = (image->comps[0].w + (1 << image->comps[0].factor) -1) >> image->comps[0].factor;*/
+		/*hr = (image->comps[0].h + (1 << image->comps[0].factor) -1) >> image->comps[0].factor;*/
+		w = image->comps[0].w;
+		h = image->comps[0].h;
+
+		if (image->numcomps==3) {	/* 3 components color image*/
+			ptr = image->comps[0].data;
+			ptr1 = image->comps[1].data;
+			ptr2 = image->comps[2].data;
+#ifdef CHECK_THRESHOLDS 
+			if (image->comps[0].sgnd) {
+				min_value = -128;
+				max_value = 127;
+			} else {
+				min_value = 0;
+				max_value = 255;
+			}
+#endif			
+			/* Get the pointer to the Java structure where the data must be copied*/
+			fid = (*env)->GetFieldID(env, cls,"image24", "[I");
+			jia = (*env)->GetObjectField(env, obj, fid);
+			jiBody = (*env)->GetIntArrayElements(env, jia, 0);
+			ptrIBody = jiBody;
+			printf("C: transferring image24: %d int to Java pointer=%d\n",image->numcomps*w*h, ptrIBody);
+
+			for (i=0; i<w*h; i++) {
+				tempUC = (unsigned char)(ptr[i]);
+				tempUC1 = (unsigned char)(ptr1[i]);
+				tempUC2 = (unsigned char)(ptr2[i]);
+#ifdef CHECK_THRESHOLDS
+				if (tempUC < min_value)
+					tempUC=min_value;
+				else if (tempUC > max_value)
+					tempUC=max_value;
+				if (tempUC1 < min_value)
+					tempUC1=min_value;
+				else if (tempUC1 > max_value)
+					tempUC1=max_value;
+				if (tempUC2 < min_value)
+					tempUC2=min_value;
+				else if (tempUC2 > max_value)
+					tempUC2=max_value;
+#endif
+				*(ptrIBody++)  = (int) ( (tempUC2<<16) + (tempUC1<<8) + tempUC );
+			}
+			(*env)->ReleaseIntArrayElements(env, jia, jiBody, 0);
+
+		} else {	/* 1 component 8 or 16 bpp image*/
+			ptr = image->comps[0].data;
+			printf("C: before transferring a %d bpp image to java (length = %d)\n",image->comps[0].prec ,w*h);
+			if (image->comps[0].prec<=8) {
+				fid = (*env)->GetFieldID(env, cls,"image8", "[B");
+				jba = (*env)->GetObjectField(env, obj, fid);
+				jbBody = (*env)->GetByteArrayElements(env, jba, 0);
+				ptrBBody = jbBody;
+#ifdef CHECK_THRESHOLDS 
+				if (image->comps[0].sgnd) {
+					min_value = -128;
+					max_value = 127;
+				} else {
+					min_value = 0;
+					max_value = 255;
+				}
+#endif								
+				/*printf("C: transferring %d shorts to Java image8 pointer = %d\n", wr*hr,ptrSBody);*/
+				for (i=0; i<w*h; i++) {
+					tempUC = (unsigned char) (ptr[i]);
+#ifdef CHECK_THRESHOLDS
+					if (tempUC<min_value)
+						tempUC = min_value;
+					else if (tempUC > max_value)
+						tempUC = max_value;
+#endif
+					*(ptrBBody++) = tempUC;
+				}
+				(*env)->ReleaseByteArrayElements(env, jba, jbBody, 0);
+				printf("C: image8 transferred to Java\n");
+			} else {
+				fid = (*env)->GetFieldID(env, cls,"image16", "[S");
+				jsa = (*env)->GetObjectField(env, obj, fid);
+				jsBody = (*env)->GetShortArrayElements(env, jsa, 0);
+				ptrSBody = jsBody;
+#ifdef CHECK_THRESHOLDS 
+				if (image->comps[0].sgnd) {
+					min_value = -32768;
+					max_value = 32767;
+				} else {
+					min_value = 0;
+					max_value = 65535;
+				}
+				printf("C: minValue = %d, maxValue = %d\n", min_value, max_value);
+#endif				
+				printf("C: transferring %d shorts to Java image16 pointer = %d\n", w*h,ptrSBody);
+				for (i=0; i<w*h; i++) {
+					tempS = (short) (ptr[i]);
+#ifdef CHECK_THRESHOLDS
+					if (tempS<min_value) {
+						printf("C: value %d truncated to %d\n", tempS, min_value);
+						tempS = min_value;
+					} else if (tempS > max_value) {
+						printf("C: value %d truncated to %d\n", tempS, max_value);
+						tempS = max_value;
+					}
+#endif
+					*(ptrSBody++) = tempS;
+				}
+				(*env)->ReleaseShortArrayElements(env, jsa, jsBody, 0);
+				printf("C: image16 completely filled\n");
+			}
+		}	
+
+
+		/* free remaining structures */
+		if(dinfo) {
+			opj_destroy_decompress(dinfo);
+		}
+		/* free image data structure */
+		opj_image_destroy(image);
+
+	}
+	return 1; /* OK */
+}
+/*end main*/
+
diff --git a/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaDecoder.java b/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaDecoder.java
index 97008e3b..f1042000 100644
--- a/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaDecoder.java
+++ b/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaDecoder.java
@@ -1,250 +1,250 @@
-/*

- * Copyright (c) 2002-2014, Universite catholique de Louvain (UCL), Belgium

- * Copyright (c) 2002-2014, Professor Benoit Macq

- * Copyright (c) 2002-2007, Patrick Piscaglia, Telemis s.a.

- * All rights reserved.

- *

- * Redistribution and use in source and binary forms, with or without

- * modification, are permitted provided that the following conditions

- * are met:

- * 1. Redistributions of source code must retain the above copyright

- *    notice, this list of conditions and the following disclaimer.

- * 2. Redistributions in binary form must reproduce the above copyright

- *    notice, this list of conditions and the following disclaimer in the

- *    documentation and/or other materials provided with the distribution.

- *

- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS `AS IS'

- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

- * ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE

- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR

- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF

- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS

- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN

- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)

- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

- * POSSIBILITY OF SUCH DAMAGE.

- */ 

-package org.openJpeg;

-

-import java.util.Vector;

-

-/** This class decodes one J2K codestream into an image (width + height + depth + pixels[], 

- * using the OpenJPEG.org library.

- * To be able to log messages, the called must register a IJavaJ2KDecoderLogger object.

- */

-public class OpenJPEGJavaDecoder {

-

-	public interface IJavaJ2KDecoderLogger {

-		public void logDecoderMessage(String message);

-		public void logDecoderError(String message);

-	}

-	

-    private static boolean isInitialized = false;

-    

-	// ===== decompression parameters =============>

-	// These value may be changed for each image

-    private String[] decoder_arguments = null;

-	/** number of resolutions decompositions */

-	private int nbResolutions = -1;

-	/** the quality layers */

-	private int[] layers = null;

-

-	/** Contains the 8 bpp version of the image. May NOT be filled together with image16 or image24.<P>

-	 * We store in Java the 8 or 16 bpp version of the image while the decoder uses a 32 bpp version, because <UL>

-	 * <LI> the storage capacity required is smaller

-	 * <LI> the transfer Java <-- C will be faster

-	 * <LI> the conversion byte/short ==> int will be done faster by the C

-	 * </UL>*/

-	private byte[] image8 = null;

-	/** Contains the 16 bpp version of the image. May NOT be filled together with image8 or image24*/

-	private short[] image16 = null;

-	/** Contains the 24 bpp version of the image. May NOT be filled together with image8 or image16 */

-	private int[] image24 = null;

-	/** Holds the J2K compressed bytecode to decode */

-    private byte compressedStream[] = null;

-    /** Holds the compressed version of the index file, to be used by the decoder */

-    private byte compressedIndex[] = null;

-    /** Width and Height of the image */

-    private int width = -1;

-    private int height = -1;

-    private int depth = -1;

-    /** This parameter is never used in Java but is read by the C library to know the number of resolutions to skip when decoding, 

-     * i.e. if there are 5 resolutions and skipped=1 ==> decode until resolution 4.  */

-    private int skippedResolutions = 0;

-    

-    private Vector<IJavaJ2KDecoderLogger> loggers = new Vector();

-

-

-    public OpenJPEGJavaDecoder(String openJPEGlibraryFullPathAndName, IJavaJ2KDecoderLogger messagesAndErrorsLogger) throws ExceptionInInitializerError

-    {

-    	this(openJPEGlibraryFullPathAndName);

-    	loggers.addElement(messagesAndErrorsLogger);

-    }

-

-    public OpenJPEGJavaDecoder(String openJPEGlibraryFullPathAndName) throws ExceptionInInitializerError

-    {

-    	if (!isInitialized) {

-    		try {

-    			System.load(openJPEGlibraryFullPathAndName);

-    			isInitialized = true;

-    		} catch (Throwable t) {

-    			throw new ExceptionInInitializerError("OpenJPEG Java Decoder: probably impossible to find the C library");

-    		}

-    	}

-    }

-    

-    public void addLogger(IJavaJ2KDecoderLogger messagesAndErrorsLogger) {

-    	loggers.addElement(messagesAndErrorsLogger);

-    }

-    

-    public void removeLogger(IJavaJ2KDecoderLogger messagesAndErrorsLogger) {

-    	loggers.removeElement(messagesAndErrorsLogger);

-    }

-    

-    public int  decodeJ2KtoImage() {

-		if ((image16 == null || (image16 != null && image16.length != width*height)) && (depth==-1 || depth==16)) {

-			image16 = new short[width*height];

-			logMessage("OpenJPEGJavaDecoder.decompressImage: image16 length = " + image16.length + " (" + width + " x " + height + ") ");

-		}

-		if ((image8 == null || (image8 != null && image8.length != width*height)) && (depth==-1 || depth==8)) {

-			image8 = new byte[width*height];

-			logMessage("OpenJPEGJavaDecoder.decompressImage: image8 length = " + image8.length + " (" + width + " x " + height + ") ");

-		}

-		if ((image24 == null || (image24 != null && image24.length != width*height)) && (depth==-1 || depth==24)) {

-			image24 = new int[width*height];

-			logMessage("OpenJPEGJavaDecoder.decompressImage: image24 length = " + image24.length + " (" + width + " x " + height + ") ");

-		}

-		

-		String[] arguments = new String[0 + (decoder_arguments != null ? decoder_arguments.length : 0)];

-		int offset = 0;

-		if (decoder_arguments != null) {

-			for (int i=0; i<decoder_arguments.length; i++) {

-				arguments[i+offset] = decoder_arguments[i];

-			}

-		}

-

-		return internalDecodeJ2KtoImage(arguments);

-    }

-    

-    /** 

-     * Decode the j2k stream given in the codestream byte[] and fills the image8, image16 or image24 array, according to the bit depth.

-     */

-    private native int internalDecodeJ2KtoImage(String[] parameters);

-

-    /** Image depth in bpp */

-	public int getDepth() {

-		return depth;

-	}

-

-    /** Image depth in bpp */

-	public void setDepth(int depth) {

-		this.depth = depth;

-	}

-

-	/** Image height in pixels */

-	public int getHeight() {

-		return height;

-	}

-

-	/** Image height in pixels */

-	public void setHeight(int height) {

-		this.height = height;

-	}

-

-	/** Number of resolutions contained in the image */

-	public int getNbResolutions() {

-		return nbResolutions;

-	}

-

-	/** Number of resolutions contained in the image */

-	public void setNbResolutions(int nbResolutions) {

-		this.nbResolutions = nbResolutions;

-	}

-

-	/** Width of the image in pixels */

-	public int getWidth() {

-		return width;

-	}

-

-	/** Width of the image in pixels */

-	public void setWidth(int width) {

-		this.width = width;

-	}

-

-	/** Contains the decompressed version of the image, if the depth in is [9,16] bpp.

-	 * Returns NULL otherwise.

-	 */

-	public short[] getImage16() {

-		return image16;

-	}

-

-	/** Contains the decompressed version of the image, if the depth in is [17,24] bpp and the image is in color.

-	 * Returns NULL otherwise.

-	 */

-	public int[] getImage24() {

-		return image24;

-	}

-

-	/** Contains the decompressed version of the image, if the depth in is [1,8] bpp.

-	 * Returns NULL otherwise.

-	 */

-	public byte[] getImage8() {

-		return image8;

-	}

-

-	/** Sets the compressed version of the index file for this image.

-	 * This index file is used by the decompressor

-	 */

-	public void setCompressedIndex(byte[] compressedIndex) {

-		this.compressedIndex = compressedIndex;

-	}

-

-	/** Sets the codestream to be decoded */

-	public void setCompressedStream(byte[] compressedStream) {

-		this.compressedStream = compressedStream;

-	}

-

-	/** @return the compressed code stream length, or -1 if not defined */

-	public long getCodestreamLength() {

-		if (compressedStream == null)

-			return -1;

-		else return compressedStream.length;

-	}

-	

-	/** This method is called either directly or by the C methods */

-	public void logMessage(String message) {

-		for (IJavaJ2KDecoderLogger logger:loggers)

-			logger.logDecoderMessage(message);

-	}

-	

-	/** This method is called either directly or by the C methods */

-	public void logError(String error) {

-		for (IJavaJ2KDecoderLogger logger:loggers)

-			logger.logDecoderError(error);

-	}

-

-	public void reset() {

-		nbResolutions = -1;

-		layers = null;

-		image8 = null;

-		image16 = null;

-		image24 = null;

-		compressedStream = null;

-	    compressedIndex = null;

-	    width = -1;

-	    height = -1;

-	    depth = -1;

-	}

-

-	public void setSkippedResolutions(int numberOfSkippedResolutions) {

-		skippedResolutions = numberOfSkippedResolutions;

-	}

-

-	/** Contains all the decoding arguments other than the input/output file */

-	public void setDecoderArguments(String[] argumentsForTheDecoder) {

-		decoder_arguments = argumentsForTheDecoder;

-	}

-

-

-}

+/*
+ * Copyright (c) 2002-2014, Universite catholique de Louvain (UCL), Belgium
+ * Copyright (c) 2002-2014, Professor Benoit Macq
+ * Copyright (c) 2002-2007, Patrick Piscaglia, Telemis s.a.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS `AS IS'
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */ 
+package org.openJpeg;
+
+import java.util.Vector;
+
+/** This class decodes one J2K codestream into an image (width + height + depth + pixels[], 
+ * using the OpenJPEG.org library.
+ * To be able to log messages, the called must register a IJavaJ2KDecoderLogger object.
+ */
+public class OpenJPEGJavaDecoder {
+
+	public interface IJavaJ2KDecoderLogger {
+		public void logDecoderMessage(String message);
+		public void logDecoderError(String message);
+	}
+	
+    private static boolean isInitialized = false;
+    
+	// ===== decompression parameters =============>
+	// These value may be changed for each image
+    private String[] decoder_arguments = null;
+	/** number of resolutions decompositions */
+	private int nbResolutions = -1;
+	/** the quality layers */
+	private int[] layers = null;
+
+	/** Contains the 8 bpp version of the image. May NOT be filled together with image16 or image24.<P>
+	 * We store in Java the 8 or 16 bpp version of the image while the decoder uses a 32 bpp version, because <UL>
+	 * <LI> the storage capacity required is smaller
+	 * <LI> the transfer Java <-- C will be faster
+	 * <LI> the conversion byte/short ==> int will be done faster by the C
+	 * </UL>*/
+	private byte[] image8 = null;
+	/** Contains the 16 bpp version of the image. May NOT be filled together with image8 or image24*/
+	private short[] image16 = null;
+	/** Contains the 24 bpp version of the image. May NOT be filled together with image8 or image16 */
+	private int[] image24 = null;
+	/** Holds the J2K compressed bytecode to decode */
+    private byte compressedStream[] = null;
+    /** Holds the compressed version of the index file, to be used by the decoder */
+    private byte compressedIndex[] = null;
+    /** Width and Height of the image */
+    private int width = -1;
+    private int height = -1;
+    private int depth = -1;
+    /** This parameter is never used in Java but is read by the C library to know the number of resolutions to skip when decoding, 
+     * i.e. if there are 5 resolutions and skipped=1 ==> decode until resolution 4.  */
+    private int skippedResolutions = 0;
+    
+    private Vector<IJavaJ2KDecoderLogger> loggers = new Vector();
+
+
+    public OpenJPEGJavaDecoder(String openJPEGlibraryFullPathAndName, IJavaJ2KDecoderLogger messagesAndErrorsLogger) throws ExceptionInInitializerError
+    {
+    	this(openJPEGlibraryFullPathAndName);
+    	loggers.addElement(messagesAndErrorsLogger);
+    }
+
+    public OpenJPEGJavaDecoder(String openJPEGlibraryFullPathAndName) throws ExceptionInInitializerError
+    {
+    	if (!isInitialized) {
+    		try {
+    			System.load(openJPEGlibraryFullPathAndName);
+    			isInitialized = true;
+    		} catch (Throwable t) {
+    			throw new ExceptionInInitializerError("OpenJPEG Java Decoder: probably impossible to find the C library");
+    		}
+    	}
+    }
+    
+    public void addLogger(IJavaJ2KDecoderLogger messagesAndErrorsLogger) {
+    	loggers.addElement(messagesAndErrorsLogger);
+    }
+    
+    public void removeLogger(IJavaJ2KDecoderLogger messagesAndErrorsLogger) {
+    	loggers.removeElement(messagesAndErrorsLogger);
+    }
+    
+    public int  decodeJ2KtoImage() {
+		if ((image16 == null || (image16 != null && image16.length != width*height)) && (depth==-1 || depth==16)) {
+			image16 = new short[width*height];
+			logMessage("OpenJPEGJavaDecoder.decompressImage: image16 length = " + image16.length + " (" + width + " x " + height + ") ");
+		}
+		if ((image8 == null || (image8 != null && image8.length != width*height)) && (depth==-1 || depth==8)) {
+			image8 = new byte[width*height];
+			logMessage("OpenJPEGJavaDecoder.decompressImage: image8 length = " + image8.length + " (" + width + " x " + height + ") ");
+		}
+		if ((image24 == null || (image24 != null && image24.length != width*height)) && (depth==-1 || depth==24)) {
+			image24 = new int[width*height];
+			logMessage("OpenJPEGJavaDecoder.decompressImage: image24 length = " + image24.length + " (" + width + " x " + height + ") ");
+		}
+		
+		String[] arguments = new String[0 + (decoder_arguments != null ? decoder_arguments.length : 0)];
+		int offset = 0;
+		if (decoder_arguments != null) {
+			for (int i=0; i<decoder_arguments.length; i++) {
+				arguments[i+offset] = decoder_arguments[i];
+			}
+		}
+
+		return internalDecodeJ2KtoImage(arguments);
+    }
+    
+    /** 
+     * Decode the j2k stream given in the codestream byte[] and fills the image8, image16 or image24 array, according to the bit depth.
+     */
+    private native int internalDecodeJ2KtoImage(String[] parameters);
+
+    /** Image depth in bpp */
+	public int getDepth() {
+		return depth;
+	}
+
+    /** Image depth in bpp */
+	public void setDepth(int depth) {
+		this.depth = depth;
+	}
+
+	/** Image height in pixels */
+	public int getHeight() {
+		return height;
+	}
+
+	/** Image height in pixels */
+	public void setHeight(int height) {
+		this.height = height;
+	}
+
+	/** Number of resolutions contained in the image */
+	public int getNbResolutions() {
+		return nbResolutions;
+	}
+
+	/** Number of resolutions contained in the image */
+	public void setNbResolutions(int nbResolutions) {
+		this.nbResolutions = nbResolutions;
+	}
+
+	/** Width of the image in pixels */
+	public int getWidth() {
+		return width;
+	}
+
+	/** Width of the image in pixels */
+	public void setWidth(int width) {
+		this.width = width;
+	}
+
+	/** Contains the decompressed version of the image, if the depth in is [9,16] bpp.
+	 * Returns NULL otherwise.
+	 */
+	public short[] getImage16() {
+		return image16;
+	}
+
+	/** Contains the decompressed version of the image, if the depth in is [17,24] bpp and the image is in color.
+	 * Returns NULL otherwise.
+	 */
+	public int[] getImage24() {
+		return image24;
+	}
+
+	/** Contains the decompressed version of the image, if the depth in is [1,8] bpp.
+	 * Returns NULL otherwise.
+	 */
+	public byte[] getImage8() {
+		return image8;
+	}
+
+	/** Sets the compressed version of the index file for this image.
+	 * This index file is used by the decompressor
+	 */
+	public void setCompressedIndex(byte[] compressedIndex) {
+		this.compressedIndex = compressedIndex;
+	}
+
+	/** Sets the codestream to be decoded */
+	public void setCompressedStream(byte[] compressedStream) {
+		this.compressedStream = compressedStream;
+	}
+
+	/** @return the compressed code stream length, or -1 if not defined */
+	public long getCodestreamLength() {
+		if (compressedStream == null)
+			return -1;
+		else return compressedStream.length;
+	}
+	
+	/** This method is called either directly or by the C methods */
+	public void logMessage(String message) {
+		for (IJavaJ2KDecoderLogger logger:loggers)
+			logger.logDecoderMessage(message);
+	}
+	
+	/** This method is called either directly or by the C methods */
+	public void logError(String error) {
+		for (IJavaJ2KDecoderLogger logger:loggers)
+			logger.logDecoderError(error);
+	}
+
+	public void reset() {
+		nbResolutions = -1;
+		layers = null;
+		image8 = null;
+		image16 = null;
+		image24 = null;
+		compressedStream = null;
+	    compressedIndex = null;
+	    width = -1;
+	    height = -1;
+	    depth = -1;
+	}
+
+	public void setSkippedResolutions(int numberOfSkippedResolutions) {
+		skippedResolutions = numberOfSkippedResolutions;
+	}
+
+	/** Contains all the decoding arguments other than the input/output file */
+	public void setDecoderArguments(String[] argumentsForTheDecoder) {
+		decoder_arguments = argumentsForTheDecoder;
+	}
+
+
+}
diff --git a/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaEncoder.java b/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaEncoder.java
index 931105c1..8df669aa 100644
--- a/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaEncoder.java
+++ b/wrapping/java/openjp2/java-sources/org/openJpeg/OpenJPEGJavaEncoder.java
@@ -1,338 +1,338 @@
-/*

- * Copyright (c) 2002-2014, Universite catholique de Louvain (UCL), Belgium

- * Copyright (c) 2002-2014, Professor Benoit Macq

- * Copyright (c) 2002-2007, Patrick Piscaglia, Telemis s.a.

- * All rights reserved.

- *

- * Redistribution and use in source and binary forms, with or without

- * modification, are permitted provided that the following conditions

- * are met:

- * 1. Redistributions of source code must retain the above copyright

- *    notice, this list of conditions and the following disclaimer.

- * 2. Redistributions in binary form must reproduce the above copyright

- *    notice, this list of conditions and the following disclaimer in the

- *    documentation and/or other materials provided with the distribution.

- *

- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS `AS IS'

- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

- * ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE

- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR

- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF

- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS

- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN

- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)

- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

- * POSSIBILITY OF SUCH DAMAGE.

- */  

-package org.openJpeg;

-

-import java.io.File;

-import java.util.Vector;

-

-/** This class encodes one image into the J2K format, 

- * using the OpenJPEG.org library.

- * To be able to log messages, the called must register a IJavaJ2KEncoderLogger object.

- */

-public class OpenJPEGJavaEncoder {

-

-	public interface IJavaJ2KEncoderLogger {

-		public void logEncoderMessage(String message);

-		public void logEncoderError(String message);

-	}

-	

-    private static boolean isInitialized = false;

-    

-	// ===== Compression parameters =============>

-	// These value may be changed for each image

-    private String[] encoder_arguments = null;

-	/** number of resolutions decompositions */

-	private int nbResolutions = -1;

-	/** the quality layers, expressed as compression rate */

-	private float[] ratioLayers = null;

-	/** the quality layers, expressed as PSNR values. This variable, if defined, has priority over the ratioLayers variable */

-	private float[] psnrLayers = null;

-	

-	/** Contains the 8 bpp version of the image. May NOT be filled together with image16 or image24.<P>

-	 * We store the 8 or 16 bpp version of the original image while the encoder uses a 32 bpp version, because <UL>

-	 * <LI> the storage capacity required is smaller

-	 * <LI> the transfer Java --> C will be faster

-	 * <LI> the conversion byte/short ==> int will be done faster by the C

-	 * </UL>*/

-	private byte[] image8 = null;

-	/** Contains the 16 bpp version of the image. May NOT be filled together with image8 or image24*/

-	private short[] image16 = null;

-	/** Contains the 24 bpp version of the image. May NOT be filled together with image8 or image16 */

-	private int[] image24 = null;

-	/** Holds the result of the compression, i.e. the J2K compressed bytecode */

-    private byte compressedStream[] = null;

-    /** Holds the compressed stream length, which may be smaller than compressedStream.length if this byte[] is pre-allocated */

-    private long compressedStreamLength = -1;

-    /** Holds the compressed version of the index file, returned by the encoder */

-    private byte compressedIndex[] = null;

-    /** Width and Height of the image */

-    private int width = -1;

-    private int height = -1;

-    private int depth = -1;

-    /** Tile size. We suppose the same size for the horizontal and vertical tiles.

-     * If size == -1 ==> no tiling */

-    private int tileSize = -1;

-    // <===== Compression parameters =============

-    

-    private Vector<IJavaJ2KEncoderLogger> loggers = new Vector();

-

-    public OpenJPEGJavaEncoder(String openJPEGlibraryFullPathAndName, IJavaJ2KEncoderLogger messagesAndErrorsLogger) throws ExceptionInInitializerError

-    {

-    	this(openJPEGlibraryFullPathAndName);

-    	loggers.addElement(messagesAndErrorsLogger);

-    }

-

-    public OpenJPEGJavaEncoder(String openJPEGlibraryFullPathAndName) throws ExceptionInInitializerError

-    {

-    	if (!isInitialized) {

-    		try {

-    			String absolutePath = (new File(openJPEGlibraryFullPathAndName)).getCanonicalPath();

-    			System.load(absolutePath);

-    			isInitialized = true;

-    		} catch (Throwable t) {

-    			t.printStackTrace();

-    			throw new ExceptionInInitializerError("OpenJPEG Java Encoder: probably impossible to find the C library");

-    		}

-    	}

-    }

-    

-    public void addLogger(IJavaJ2KEncoderLogger messagesAndErrorsLogger) {

-    	loggers.addElement(messagesAndErrorsLogger);

-    }

-    

-    public void removeLogger(IJavaJ2KEncoderLogger messagesAndErrorsLogger) {

-    	loggers.removeElement(messagesAndErrorsLogger);

-    }

-    

-    /** This method compresses the given image.<P>

-     * It returns the compressed J2K codestream into the compressedStream byte[].<P>

-     * It also returns the compression index as a compressed form, into the compressedIndex byte[].<P>

-     * One of the image8, image16 or image24 arrays must be correctly initialized and filled.<P>

-     * The width, height and depth variables must be correctly filled.<P>

-     * The nbResolutions, nbLayers and if needed the float[] psnrLayers or ratioLayers must also be filled before calling this method.

-     */

-    public void encodeImageToJ2K() {

-		// Need to allocate / reallocate the compressed stream buffer ? (size = max possible size = original image size)

-		if (compressedStream== null || (compressedStream.length != width*height*depth/8)) {

-			logMessage("OpenJPEGJavaEncoder.encodeImageToJ2K: (re-)allocating " + (width*height*depth/8) + " bytes for the compressedStream");

-			compressedStream = new byte[width*height*depth/8];

-		}

-		// Arguments = 

-		// - number of resolutions "-n 5" : 2

-		// - size of tile "-t 512,512" : 2

-		// 

-		// Image width, height, depth and pixels are directly fetched by C from the Java class

-		int nbArgs = 2 + (tileSize == -1 ? 0 : 2) + (encoder_arguments != null ? encoder_arguments.length : 0);

-		if (psnrLayers != null && psnrLayers.length>0 && psnrLayers[0] != 0)

-			// If psnrLayers is defined and doesn't just express "lossless"

-			nbArgs += 2;

-		else if (ratioLayers != null && ratioLayers.length>0 && ratioLayers[0]!=0.0)

-			nbArgs += 2;

-		String[] arguments = new String[nbArgs];

-		int offset = 0;

-		arguments[offset] = "-n"; arguments[offset+1] = "" + nbResolutions; offset += 2;

-		if (tileSize!= -1) {

-			arguments[offset++] = "-t"; 

-			arguments[offset++] = "" + tileSize + "," + tileSize;

-		}

-		// If PSNR layers are defined, use them to encode the images

-		if (psnrLayers != null && psnrLayers.length>0 && psnrLayers[0]!=-1) {

-			arguments[offset++] = "-q";

-			String s = "";

-			for (int i=0; i<psnrLayers.length; i++)

-				s += psnrLayers[i] + ",";

-			arguments[offset++] = s.substring(0, s.length()-1);

-		} else if (ratioLayers != null && ratioLayers.length>0 && ratioLayers[0]!=0.0) {

-			// Specify quality ratioLayers, as compression ratios

-			arguments[offset++] = "-r";

-			String s = "";

-			for (int i=0; i<ratioLayers.length; i++)

-				s += ratioLayers[i] + ",";

-			arguments[offset++] = s.substring(0, s.length()-1);

-		}

-		if (encoder_arguments != null) {

-			for (int i=0; i<encoder_arguments.length; i++) {

-				arguments[i+offset] = encoder_arguments[i];

-			}

-		}

-		logMessage("Encoder additional arguments = " + arrayToString(arguments));

-		long startTime = (new java.util.Date()).getTime();

-		compressedStreamLength = internalEncodeImageToJ2K(arguments);

-		logMessage("compression time = " + ((new java.util.Date()).getTime() - startTime) + " msec");

-    }

-    

-    /** 

-     * Fills the compressedStream byte[] and the compressedIndex byte[]

-     * @return the codestream length.

-     */

-    private native long internalEncodeImageToJ2K(String[] parameters);

-

-    /** Image depth in bpp */

-	public int getDepth() {

-		return depth;

-	}

-

-    /** Image depth in bpp */

-	public void setDepth(int depth) {

-		this.depth = depth;

-	}

-

-	/** Image height in pixels  */

-	public int getHeight() {

-		return height;

-	}

-

-	/** Image height in pixels  */

-	public void setHeight(int height) {

-		this.height = height;

-	}

-

-	/** This method must be called in depth in [9,16].

-	 * @param an array of shorts, containing width*height values

-	 */

-	public void setImage16(short[] image16) {

-		this.image16 = image16;

-	}

-

-	/** This method must be called in depth in [17,24] for RGB images.

-	 * @param an array of int, containing width*height values

-	 */

-	public void setImage24(int[] image24) {

-		this.image24 = image24;

-	}

-

-	/** This method must be called in depth in [1,8].

-	 * @param an array of bytes, containing width*height values

-	 */

-	public void setImage8(byte[] image8) {

-		this.image8 = image8;

-	}

-

-	/** Return the ratioLayers, i.e. the compression ratio for each quality layer.

-	 * If the last value is 0.0, last layer is lossless compressed.

-	 */

-	public float[] getRatioLayers() {

-		return ratioLayers;

-	}

-

-	/**

-	 * sets the quality layers.

-	 * At least one level.

-	 * Each level is expressed as a compression ratio (float).

-	 * If the last value is 0.0, the last layer will be losslessly compressed

-	 */

-	public void setRatioLayers(float[] layers) {

-		this.ratioLayers = layers;

-	}

-

-	/** Return the PSNR Layers, i.e. the target PSNR for each quality layer.

-	 * If the last value is -1, last layer is lossless compressed.

-	 */

-	public float[] getPsnrLayers() {

-		return psnrLayers;

-	}

-

-	/**

-	 * sets the quality layers.

-	 * At least one level.

-	 * Each level is expressed as a target PSNR (float).

-	 * If the last value is -1, the last layer will be losslessly compressed

-	 */

-	public void setPsnrLayers(float[] layers) {

-		this.psnrLayers = layers;

-	}

-

-	/** Set the number of resolutions that must be created */

-	public void setNbResolutions(int nbResolutions) {

-		this.nbResolutions = nbResolutions;

-	}

-

-	public int getWidth() {

-		return width;

-	}

-

-	/** Width of the image, in pixels */

-	public void setWidth(int width) {

-		this.width = width;

-	}

-

-	/** Return the compressed index file.

-	 * Syntax: TODO PP:

-	 */

-	public byte[] getCompressedIndex() {

-		return compressedIndex;

-	}

-	

-	public void setCompressedIndex(byte[] index) {

-		compressedIndex = index;

-	}

-

-	public byte[] getCompressedStream() {

-		return compressedStream;

-	}

-

-	public void reset() {

-		nbResolutions = -1;

-		ratioLayers = null;

-		psnrLayers = null;

-		image8 = null;

-		image16 = null;

-		image24 = null;

-		compressedStream = null;

-	    compressedIndex = null;

-	    width = -1;

-	    height = -1;

-	    depth = -1;

-	}

-

-	public short[] getImage16() {

-		return image16;

-	}

-

-	public int[] getImage24() {

-		return image24;

-	}

-

-	public byte[] getImage8() {

-		return image8;

-	}

-	

-	/** Sets the size of the tiles. We assume square tiles */

-	public void setTileSize(int tileSize) {

-		this.tileSize = tileSize;

-	}

-	

-	/** Contains all the encoding arguments other than the input/output file, compression ratio, tile size */

-	public void setEncoderArguments(String[] argumentsForTheEncoder) {

-		encoder_arguments = argumentsForTheEncoder;

-	}

-

-	public void logMessage(String message) {

-		for (IJavaJ2KEncoderLogger logger:loggers)

-			logger.logEncoderMessage(message);

-	}

-	

-	public void logError(String error) {

-		for (IJavaJ2KEncoderLogger logger:loggers)

-			logger.logEncoderError(error);

-	}

-

-	public long getCompressedStreamLength() {

-		return compressedStreamLength;

-	}

-	

-	private String arrayToString(String[] array) {

-		if (array == null)

-			return "NULL";

-		StringBuffer sb = new StringBuffer();

-		for (int i=0; i<array.length; i++)

-			sb.append(array[i]).append(" ");

-		sb.delete(sb.length()-1, sb.length());

-		return sb.toString();

-	}

-}

+/*
+ * Copyright (c) 2002-2014, Universite catholique de Louvain (UCL), Belgium
+ * Copyright (c) 2002-2014, Professor Benoit Macq
+ * Copyright (c) 2002-2007, Patrick Piscaglia, Telemis s.a.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS `AS IS'
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */  
+package org.openJpeg;
+
+import java.io.File;
+import java.util.Vector;
+
+/** This class encodes one image into the J2K format, 
+ * using the OpenJPEG.org library.
+ * To be able to log messages, the called must register a IJavaJ2KEncoderLogger object.
+ */
+public class OpenJPEGJavaEncoder {
+
+	public interface IJavaJ2KEncoderLogger {
+		public void logEncoderMessage(String message);
+		public void logEncoderError(String message);
+	}
+	
+    private static boolean isInitialized = false;
+    
+	// ===== Compression parameters =============>
+	// These value may be changed for each image
+    private String[] encoder_arguments = null;
+	/** number of resolutions decompositions */
+	private int nbResolutions = -1;
+	/** the quality layers, expressed as compression rate */
+	private float[] ratioLayers = null;
+	/** the quality layers, expressed as PSNR values. This variable, if defined, has priority over the ratioLayers variable */
+	private float[] psnrLayers = null;
+	
+	/** Contains the 8 bpp version of the image. May NOT be filled together with image16 or image24.<P>
+	 * We store the 8 or 16 bpp version of the original image while the encoder uses a 32 bpp version, because <UL>
+	 * <LI> the storage capacity required is smaller
+	 * <LI> the transfer Java --> C will be faster
+	 * <LI> the conversion byte/short ==> int will be done faster by the C
+	 * </UL>*/
+	private byte[] image8 = null;
+	/** Contains the 16 bpp version of the image. May NOT be filled together with image8 or image24*/
+	private short[] image16 = null;
+	/** Contains the 24 bpp version of the image. May NOT be filled together with image8 or image16 */
+	private int[] image24 = null;
+	/** Holds the result of the compression, i.e. the J2K compressed bytecode */
+    private byte compressedStream[] = null;
+    /** Holds the compressed stream length, which may be smaller than compressedStream.length if this byte[] is pre-allocated */
+    private long compressedStreamLength = -1;
+    /** Holds the compressed version of the index file, returned by the encoder */
+    private byte compressedIndex[] = null;
+    /** Width and Height of the image */
+    private int width = -1;
+    private int height = -1;
+    private int depth = -1;
+    /** Tile size. We suppose the same size for the horizontal and vertical tiles.
+     * If size == -1 ==> no tiling */
+    private int tileSize = -1;
+    // <===== Compression parameters =============
+    
+    private Vector<IJavaJ2KEncoderLogger> loggers = new Vector();
+
+    public OpenJPEGJavaEncoder(String openJPEGlibraryFullPathAndName, IJavaJ2KEncoderLogger messagesAndErrorsLogger) throws ExceptionInInitializerError
+    {
+    	this(openJPEGlibraryFullPathAndName);
+    	loggers.addElement(messagesAndErrorsLogger);
+    }
+
+    public OpenJPEGJavaEncoder(String openJPEGlibraryFullPathAndName) throws ExceptionInInitializerError
+    {
+    	if (!isInitialized) {
+    		try {
+    			String absolutePath = (new File(openJPEGlibraryFullPathAndName)).getCanonicalPath();
+    			System.load(absolutePath);
+    			isInitialized = true;
+    		} catch (Throwable t) {
+    			t.printStackTrace();
+    			throw new ExceptionInInitializerError("OpenJPEG Java Encoder: probably impossible to find the C library");
+    		}
+    	}
+    }
+    
+    public void addLogger(IJavaJ2KEncoderLogger messagesAndErrorsLogger) {
+    	loggers.addElement(messagesAndErrorsLogger);
+    }
+    
+    public void removeLogger(IJavaJ2KEncoderLogger messagesAndErrorsLogger) {
+    	loggers.removeElement(messagesAndErrorsLogger);
+    }
+    
+    /** This method compresses the given image.<P>
+     * It returns the compressed J2K codestream into the compressedStream byte[].<P>
+     * It also returns the compression index as a compressed form, into the compressedIndex byte[].<P>
+     * One of the image8, image16 or image24 arrays must be correctly initialized and filled.<P>
+     * The width, height and depth variables must be correctly filled.<P>
+     * The nbResolutions, nbLayers and if needed the float[] psnrLayers or ratioLayers must also be filled before calling this method.
+     */
+    public void encodeImageToJ2K() {
+		// Need to allocate / reallocate the compressed stream buffer ? (size = max possible size = original image size)
+		if (compressedStream== null || (compressedStream.length != width*height*depth/8)) {
+			logMessage("OpenJPEGJavaEncoder.encodeImageToJ2K: (re-)allocating " + (width*height*depth/8) + " bytes for the compressedStream");
+			compressedStream = new byte[width*height*depth/8];
+		}
+		// Arguments = 
+		// - number of resolutions "-n 5" : 2
+		// - size of tile "-t 512,512" : 2
+		// 
+		// Image width, height, depth and pixels are directly fetched by C from the Java class
+		int nbArgs = 2 + (tileSize == -1 ? 0 : 2) + (encoder_arguments != null ? encoder_arguments.length : 0);
+		if (psnrLayers != null && psnrLayers.length>0 && psnrLayers[0] != 0)
+			// If psnrLayers is defined and doesn't just express "lossless"
+			nbArgs += 2;
+		else if (ratioLayers != null && ratioLayers.length>0 && ratioLayers[0]!=0.0)
+			nbArgs += 2;
+		String[] arguments = new String[nbArgs];
+		int offset = 0;
+		arguments[offset] = "-n"; arguments[offset+1] = "" + nbResolutions; offset += 2;
+		if (tileSize!= -1) {
+			arguments[offset++] = "-t"; 
+			arguments[offset++] = "" + tileSize + "," + tileSize;
+		}
+		// If PSNR layers are defined, use them to encode the images
+		if (psnrLayers != null && psnrLayers.length>0 && psnrLayers[0]!=-1) {
+			arguments[offset++] = "-q";
+			String s = "";
+			for (int i=0; i<psnrLayers.length; i++)
+				s += psnrLayers[i] + ",";
+			arguments[offset++] = s.substring(0, s.length()-1);
+		} else if (ratioLayers != null && ratioLayers.length>0 && ratioLayers[0]!=0.0) {
+			// Specify quality ratioLayers, as compression ratios
+			arguments[offset++] = "-r";
+			String s = "";
+			for (int i=0; i<ratioLayers.length; i++)
+				s += ratioLayers[i] + ",";
+			arguments[offset++] = s.substring(0, s.length()-1);
+		}
+		if (encoder_arguments != null) {
+			for (int i=0; i<encoder_arguments.length; i++) {
+				arguments[i+offset] = encoder_arguments[i];
+			}
+		}
+		logMessage("Encoder additional arguments = " + arrayToString(arguments));
+		long startTime = (new java.util.Date()).getTime();
+		compressedStreamLength = internalEncodeImageToJ2K(arguments);
+		logMessage("compression time = " + ((new java.util.Date()).getTime() - startTime) + " msec");
+    }
+    
+    /** 
+     * Fills the compressedStream byte[] and the compressedIndex byte[]
+     * @return the codestream length.
+     */
+    private native long internalEncodeImageToJ2K(String[] parameters);
+
+    /** Image depth in bpp */
+	public int getDepth() {
+		return depth;
+	}
+
+    /** Image depth in bpp */
+	public void setDepth(int depth) {
+		this.depth = depth;
+	}
+
+	/** Image height in pixels  */
+	public int getHeight() {
+		return height;
+	}
+
+	/** Image height in pixels  */
+	public void setHeight(int height) {
+		this.height = height;
+	}
+
+	/** This method must be called in depth in [9,16].
+	 * @param an array of shorts, containing width*height values
+	 */
+	public void setImage16(short[] image16) {
+		this.image16 = image16;
+	}
+
+	/** This method must be called in depth in [17,24] for RGB images.
+	 * @param an array of int, containing width*height values
+	 */
+	public void setImage24(int[] image24) {
+		this.image24 = image24;
+	}
+
+	/** This method must be called in depth in [1,8].
+	 * @param an array of bytes, containing width*height values
+	 */
+	public void setImage8(byte[] image8) {
+		this.image8 = image8;
+	}
+
+	/** Return the ratioLayers, i.e. the compression ratio for each quality layer.
+	 * If the last value is 0.0, last layer is lossless compressed.
+	 */
+	public float[] getRatioLayers() {
+		return ratioLayers;
+	}
+
+	/**
+	 * sets the quality layers.
+	 * At least one level.
+	 * Each level is expressed as a compression ratio (float).
+	 * If the last value is 0.0, the last layer will be losslessly compressed
+	 */
+	public void setRatioLayers(float[] layers) {
+		this.ratioLayers = layers;
+	}
+
+	/** Return the PSNR Layers, i.e. the target PSNR for each quality layer.
+	 * If the last value is -1, last layer is lossless compressed.
+	 */
+	public float[] getPsnrLayers() {
+		return psnrLayers;
+	}
+
+	/**
+	 * sets the quality layers.
+	 * At least one level.
+	 * Each level is expressed as a target PSNR (float).
+	 * If the last value is -1, the last layer will be losslessly compressed
+	 */
+	public void setPsnrLayers(float[] layers) {
+		this.psnrLayers = layers;
+	}
+
+	/** Set the number of resolutions that must be created */
+	public void setNbResolutions(int nbResolutions) {
+		this.nbResolutions = nbResolutions;
+	}
+
+	public int getWidth() {
+		return width;
+	}
+
+	/** Width of the image, in pixels */
+	public void setWidth(int width) {
+		this.width = width;
+	}
+
+	/** Return the compressed index file.
+	 * Syntax: TODO PP:
+	 */
+	public byte[] getCompressedIndex() {
+		return compressedIndex;
+	}
+	
+	public void setCompressedIndex(byte[] index) {
+		compressedIndex = index;
+	}
+
+	public byte[] getCompressedStream() {
+		return compressedStream;
+	}
+
+	public void reset() {
+		nbResolutions = -1;
+		ratioLayers = null;
+		psnrLayers = null;
+		image8 = null;
+		image16 = null;
+		image24 = null;
+		compressedStream = null;
+	    compressedIndex = null;
+	    width = -1;
+	    height = -1;
+	    depth = -1;
+	}
+
+	public short[] getImage16() {
+		return image16;
+	}
+
+	public int[] getImage24() {
+		return image24;
+	}
+
+	public byte[] getImage8() {
+		return image8;
+	}
+	
+	/** Sets the size of the tiles. We assume square tiles */
+	public void setTileSize(int tileSize) {
+		this.tileSize = tileSize;
+	}
+	
+	/** Contains all the encoding arguments other than the input/output file, compression ratio, tile size */
+	public void setEncoderArguments(String[] argumentsForTheEncoder) {
+		encoder_arguments = argumentsForTheEncoder;
+	}
+
+	public void logMessage(String message) {
+		for (IJavaJ2KEncoderLogger logger:loggers)
+			logger.logEncoderMessage(message);
+	}
+	
+	public void logError(String error) {
+		for (IJavaJ2KEncoderLogger logger:loggers)
+			logger.logEncoderError(error);
+	}
+
+	public long getCompressedStreamLength() {
+		return compressedStreamLength;
+	}
+	
+	private String arrayToString(String[] array) {
+		if (array == null)
+			return "NULL";
+		StringBuffer sb = new StringBuffer();
+		for (int i=0; i<array.length; i++)
+			sb.append(array[i]).append(" ");
+		sb.delete(sb.length()-1, sb.length());
+		return sb.toString();
+	}
+}
diff --git a/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaDecoder.h b/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaDecoder.h
index 0e8de2e7..914d25d3 100644
--- a/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaDecoder.h
+++ b/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaDecoder.h
@@ -1,21 +1,21 @@
-/* DO NOT EDIT THIS FILE - it is machine generated */

-#include <jni.h>

-/* Header for class org_openJpeg_OpenJPEGJavaDecoder */

-

-#ifndef _Included_org_openJpeg_OpenJPEGJavaDecoder

-#define _Included_org_openJpeg_OpenJPEGJavaDecoder

-#ifdef __cplusplus

-extern "C" {

-#endif

-/*

- * Class:     org_openJpeg_OpenJPEGJavaDecoder

- * Method:    internalDecodeJ2KtoImage

- * Signature: ([Ljava/lang/String;)I

- */

-JNIEXPORT jint JNICALL Java_org_openJpeg_OpenJPEGJavaDecoder_internalDecodeJ2KtoImage

-  (JNIEnv *, jobject, jobjectArray);

-

-#ifdef __cplusplus

-}

-#endif

-#endif

+/* DO NOT EDIT THIS FILE - it is machine generated */
+#include <jni.h>
+/* Header for class org_openJpeg_OpenJPEGJavaDecoder */
+
+#ifndef _Included_org_openJpeg_OpenJPEGJavaDecoder
+#define _Included_org_openJpeg_OpenJPEGJavaDecoder
+#ifdef __cplusplus
+extern "C" {
+#endif
+/*
+ * Class:     org_openJpeg_OpenJPEGJavaDecoder
+ * Method:    internalDecodeJ2KtoImage
+ * Signature: ([Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL Java_org_openJpeg_OpenJPEGJavaDecoder_internalDecodeJ2KtoImage
+  (JNIEnv *, jobject, jobjectArray);
+
+#ifdef __cplusplus
+}
+#endif
+#endif
diff --git a/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaEncoder.h b/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaEncoder.h
index 22b3d958..5a0dc570 100644
--- a/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaEncoder.h
+++ b/wrapping/java/openjp2/org_openJpeg_OpenJPEGJavaEncoder.h
@@ -1,21 +1,21 @@
-/* DO NOT EDIT THIS FILE - it is machine generated */

-#include <jni.h>

-/* Header for class org_openJpeg_OpenJPEGJavaEncoder */

-

-#ifndef _Included_org_openJpeg_OpenJPEGJavaEncoder

-#define _Included_org_openJpeg_OpenJPEGJavaEncoder

-#ifdef __cplusplus

-extern "C" {

-#endif

-/*

- * Class:     org_openJpeg_OpenJPEGJavaEncoder

- * Method:    internalEncodeImageToJ2K

- * Signature: ([Ljava/lang/String;)J

- */

-JNIEXPORT jlong JNICALL Java_org_openJpeg_OpenJPEGJavaEncoder_internalEncodeImageToJ2K

-  (JNIEnv *, jobject, jobjectArray);

-

-#ifdef __cplusplus

-}

-#endif

-#endif

+/* DO NOT EDIT THIS FILE - it is machine generated */
+#include <jni.h>
+/* Header for class org_openJpeg_OpenJPEGJavaEncoder */
+
+#ifndef _Included_org_openJpeg_OpenJPEGJavaEncoder
+#define _Included_org_openJpeg_OpenJPEGJavaEncoder
+#ifdef __cplusplus
+extern "C" {
+#endif
+/*
+ * Class:     org_openJpeg_OpenJPEGJavaEncoder
+ * Method:    internalEncodeImageToJ2K
+ * Signature: ([Ljava/lang/String;)J
+ */
+JNIEXPORT jlong JNICALL Java_org_openJpeg_OpenJPEGJavaEncoder_internalEncodeImageToJ2K
+  (JNIEnv *, jobject, jobjectArray);
+
+#ifdef __cplusplus
+}
+#endif
+#endif