change: improve performance on type conversions (especially reading compound data will profit)

SVN: 9628

source/c/COPYING

+Copyright Notice and Statement for NCSA Hierarchical Data Format (HDF)
+Java Software Library and Utilities
+
+NCSA Hierarchical Data Format (HDF) Software Library and Utilities 
+Copyright 1988-2004, the Board of Trustees of the University of Illinois.
+Copyright 2007-2009, Center for Information Sciences and Databases, ETH Zurich, Switzerland.  
+All rights reserved.
+
+Contributors to the library: National Center for Supercomputing 
+Applications (NCSA) at the University of Illinois, Lawrence 
+Livermore Nationall Laboratory (LLNL), Sandia National Laboratories (SNL), 
+Los Alamos National Laboratory (LANL). Fortner Software, Unidata 
+Program Center (netCDF), The Independent JPEG Group (JPEG), 
+Jean-loup Gailly and Mark Adler (gzip), and Digital Equipment 
+Corporation (DEC). Macintosh support contributed by Gregory L. Guerin.
+
+The package 'glguerin':
+Copyright 1998, 1999 by Gregory L. Guerin.
+Redistribute or reuse only as described below.
+These files are from the MacBinary Toolkit for Java:
+   <http://www.amug.org/~glguerin/sw/#macbinary>
+and are redistributed by NCSA with permission of the author.
+
+This work was supported in part by a Cooperative Agreement with 
+NASA under NASA grant NAG 5-2040 and NAG NCC5-599.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted for any purpose (including commercial purposes)
+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 materials provided with the distribution.
+
+3.  In addition, redistributions of modified forms of the source or binary
+    code must carry prominent notices stating that the original code was
+    changed and the date of the change.
+
+4.  All publications or advertising materials mentioning features or use of
+    this software must acknowledge that it was developed by the National
+    Center for Supercomputing Applications at the University of Illinois, and
+    credit the Contributors.
+
+5.  Neither the name of the University nor the names of the Contributors may
+    be used to endorse or promote products derived from this software without
+    specific prior written permission from the University or the Contributors.
+
+6.  THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY AND THE CONTRIBUTORS "AS IS"
+    WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no event
+    shall the University or the Contributors be liable for any damages
+    suffered by the users arising out of the use of this software, even if
+    advised of the possibility of such damage.
+
+--------------------------------------------------------------------------
+Portions of HDF5 were developed with support from the University of 
+California, Lawrence Livermore National Laboratory (UC LLNL).
+The following statement applies to those portions of the product
+and must be retained in any redistribution of source code, binaries,
+documentation, and/or accompanying materials:
+
+    This work was partially produced at the University of California,
+    Lawrence Livermore National Laboratory (UC LLNL) under contract no.
+    W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy 
+    (DOE) and The Regents of the University of California (University) 
+    for the operation of UC LLNL.
+
+    DISCLAIMER:
+    This work was prepared as an account of work sponsored by an agency 
+    of the United States Government.  Neither the United States 
+    Government nor the University of California nor any of their 
+    employees, makes any warranty, express or implied, or assumes any 
+    liability or responsibility for the accuracy, completeness, or 
+    usefulness of any information, apparatus, product, or process 
+    disclosed, or represents that its use would not infringe privately-
+    owned rights.  Reference herein to any specific commercial products, 
+    process, or service by trade name, trademark, manufacturer, or 
+    otherwise, does not necessarily constitute or imply its endorsement, 
+    recommendation, or favoring by the United States Government or the 
+    University of California.  The views and opinions of authors 
+    expressed herein do not necessarily state or reflect those of the 
+    United States Government or the University of California, and shall 
+    not be used for advertising or product endorsement purposes.
+--------------------------------------------------------------------------
+

source/c/compile_windows_i386.mak

@@ -231,7 +231,11 @@ LINK32_OBJS= \
 	"$(INTDIR)\h5tImp.obj" \
 	"$(INTDIR)\h5util.obj" \
 	"$(INTDIR)\h5zImp.obj" \
-	"$(INTDIR)\nativeData.obj"
+	"$(INTDIR)\copyByteDouble.obj" \
+	"$(INTDIR)\copyByteFloat.obj" \
+	"$(INTDIR)\copyByteInt.obj" \
+	"$(INTDIR)\copyByteLong.obj" \
+	"$(INTDIR)\copyByteShort.obj"
 
 "$(OUTDIR)\jhdf5.dll" : "$(OUTDIR)" $(DEF_FILE) $(LINK32_OBJS)
     $(LINK32) @<<
@@ -335,11 +339,32 @@ SOURCE=$(SRCDIR)\h5zImp.c
 	$(CPP) $(CPP_PROJ) $(SOURCE)
 
 
-SOURCE=$(SRCDIR)\nativeData.c
+SOURCE=$(SRCDIR)\copyByteDouble.c
 
-"$(INTDIR)\nativeData.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+"$(INTDIR)\copyByteDouble.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
 	$(CPP) $(CPP_PROJ) $(SOURCE)
 
+SOURCE=$(SRCDIR)\copyByteFloat.c
+
+"$(INTDIR)\copyByteFloat.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+SOURCE=$(SRCDIR)\copyByteInt.c
+
+"$(INTDIR)\copyByteInt.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+SOURCE=$(SRCDIR)\copyByteLong.c
+
+"$(INTDIR)\copyByteLong.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+SOURCE=$(SRCDIR)\copyByteShort.c
+
+"$(INTDIR)\copyByteShort.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+
 
 CLEAN :
 	-@erase "$(INTDIR)\exceptionImp.obj"
@@ -357,7 +382,11 @@ CLEAN :
 	-@erase "$(INTDIR)\h5tImp.obj"
 	-@erase "$(INTDIR)\h5zImp.obj"
 	-@erase "$(INTDIR)\h5util.obj"
-	-@erase "$(INTDIR)\nativeData.obj"
+	-@erase "$(INTDIR)\copyByteDouble.obj"
+	-@erase "$(INTDIR)\copyByteFloat.obj"
+	-@erase "$(INTDIR)\copyByteInt.obj"
+	-@erase "$(INTDIR)\copyByteLong.obj"
+	-@erase "$(INTDIR)\copyByteShort.obj"
 	-@erase "$(INTDIR)\vc80.idb"
 	-@erase "$(INTDIR)\jhdf5.exp"
 	-@erase "$(INTDIR)\jhdf5.lib"

source/c/compile_windows_x64.mak

@@ -231,7 +231,12 @@ LINK64_OBJS= \
 	"$(INTDIR)\h5tImp.obj" \
 	"$(INTDIR)\h5util.obj" \
 	"$(INTDIR)\h5zImp.obj" \
-	"$(INTDIR)\nativeData.obj"
+	"$(INTDIR)\copyByteDouble.obj" \
+	"$(INTDIR)\copyByteFloat.obj" \
+	"$(INTDIR)\copyByteInt.obj" \
+	"$(INTDIR)\copyByteLong.obj" \
+	"$(INTDIR)\copyByteShort.obj"
+
 
 "$(OUTDIR)\jhdf5.dll" : "$(OUTDIR)" $(DEF_FILE) $(LINK64_OBJS)
     $(LINK64) @<<
@@ -335,11 +340,32 @@ SOURCE=$(SRCDIR)\h5zImp.c
 	$(CPP) $(CPP_PROJ) $(SOURCE)
 
 
-SOURCE=$(SRCDIR)\nativeData.c
+SOURCE=$(SRCDIR)\copyByteDouble.c
+
+"$(INTDIR)\copyByteDouble.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+SOURCE=$(SRCDIR)\copyByteFloat.c
+
+"$(INTDIR)\copyByteFloat.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+SOURCE=$(SRCDIR)\copyByteInt.c
+
+"$(INTDIR)\copyByteInt.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+SOURCE=$(SRCDIR)\copyByteLong.c
 
-"$(INTDIR)\nativeData.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+"$(INTDIR)\copyByteLong.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
 	$(CPP) $(CPP_PROJ) $(SOURCE)
 
+SOURCE=$(SRCDIR)\copyByteShort.c
+
+"$(INTDIR)\copyByteShort.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
+	$(CPP) $(CPP_PROJ) $(SOURCE)
+
+
 
 CLEAN :
 	-@erase "$(INTDIR)\exceptionImp.obj"
@@ -357,7 +383,11 @@ CLEAN :
 	-@erase "$(INTDIR)\h5tImp.obj"
 	-@erase "$(INTDIR)\h5zImp.obj"
 	-@erase "$(INTDIR)\h5util.obj"
-	-@erase "$(INTDIR)\nativeData.obj"
+	-@erase "$(INTDIR)\copyByteDouble.obj"
+	-@erase "$(INTDIR)\copyByteFloat.obj"
+	-@erase "$(INTDIR)\copyByteInt.obj"
+	-@erase "$(INTDIR)\copyByteLong.obj"
+	-@erase "$(INTDIR)\copyByteShort.obj"
 	-@erase "$(INTDIR)\vc80.idb"
 	-@erase "$(INTDIR)\jhdf5.exp"
 	-@erase "$(INTDIR)\jhdf5.lib"

source/c/copyByteDouble.c

+/****************************************************************************
+ * NCSA HDF                                                                 *
+ * National Computational Science Alliance                                  *
+ * University of Illinois at Urbana-Champaign                               *
+ * 605 E. Springfield, Champaign IL 61820                                   *
+ *                                                                          *
+ * Center for Information Sciences and Databases, ETH Zurich, Switzerland   *
+ *                                                                          *
+ * For conditions of distribution and use, see the accompanying             *
+ * COPYING file.                                                            *
+ *                                                                          *
+ ****************************************************************************/
+
+/*
+ *  This module contains the implementation of all the native methods
+ *  used for number conversion.  This is represented by the Java
+ *  class HDFNativeData.
+ *
+ *  These routines convert one dimensional arrays of bytes into
+ *  one-D arrays of other types (int, double, etc) and vice versa.
+ *
+ *  These routines are called from the Java parts of the Java-C
+ *  interface.
+ *
+ *  ***Important notes:
+ *
+ *     1.  These routines are designed to be portable--they use the
+ *         C compiler to do the required native data manipulation.
+ *     2.  These routines copy the data at least once -- a serious
+ *         but unavoidable performance hit.
+ */
+
+#define TARGET jdouble
+#define TARGET_ARRAY jdoubleArray
+#define METHODNAMETB "copyDoubleToByte"
+#define FUNCTIONNAMETB Java_ncsa_hdf_hdf5lib_HDFNativeData_copyDoubleToByte___3DI_3BII
+#define METHODNAMEBT "copyByteToDouble"
+#define FUNCTIONNAMEBT Java_ncsa_hdf_hdf5lib_HDFNativeData_copyByteToDouble___3BI_3DII
+#define COPY_FUNC GetDoubleArrayRegion
+
+#include "copyByteTarget.ctempl"

source/c/copyByteFloat.c

+/****************************************************************************
+ * NCSA HDF                                                                 *
+ * National Computational Science Alliance                                  *
+ * University of Illinois at Urbana-Champaign                               *
+ * 605 E. Springfield, Champaign IL 61820                                   *
+ *                                                                          *
+ * Center for Information Sciences and Databases, ETH Zurich, Switzerland   *
+ *                                                                          *
+ * For conditions of distribution and use, see the accompanying             *
+ * COPYING file.                                                            *
+ *                                                                          *
+ ****************************************************************************/
+
+/*
+ *  This module contains the implementation of all the native methods
+ *  used for number conversion.  This is represented by the Java
+ *  class HDFNativeData.
+ *
+ *  These routines convert one dimensional arrays of bytes into
+ *  one-D arrays of other types (int, float, etc) and vice versa.
+ *
+ *  These routines are called from the Java parts of the Java-C
+ *  interface.
+ *
+ *  ***Important notes:
+ *
+ *     1.  These routines are designed to be portable--they use the
+ *         C compiler to do the required native data manipulation.
+ *     2.  These routines copy the data at least once -- a serious
+ *         but unavoidable performance hit.
+ */
+
+#define TARGET jfloat
+#define TARGET_ARRAY jfloatArray
+#define METHODNAMETB "copyFloatToByte"
+#define FUNCTIONNAMETB Java_ncsa_hdf_hdf5lib_HDFNativeData_copyFloatToByte___3FI_3BII
+#define METHODNAMEBT "copyByteToFloat"
+#define FUNCTIONNAMEBT Java_ncsa_hdf_hdf5lib_HDFNativeData_copyByteToFloat___3BI_3FII
+#define COPY_FUNC GetFloatArrayRegion
+
+#include "copyByteTarget.ctempl"

source/c/copyByteInt.c

+/****************************************************************************
+ * NCSA HDF                                                                 *
+ * National Computational Science Alliance                                  *
+ * University of Illinois at Urbana-Champaign                               *
+ * 605 E. Springfield, Champaign IL 61820                                   *
+ *                                                                          *
+ * Center for Information Sciences and Databases, ETH Zurich, Switzerland   *
+ *                                                                          *
+ * For conditions of distribution and use, see the accompanying             *
+ * COPYING file.                                                            *
+ *                                                                          *
+ ****************************************************************************/
+
+/*
+ *  This module contains the implementation of all the native methods
+ *  used for number conversion.  This is represented by the Java
+ *  class HDFNativeData.
+ *
+ *  These routines convert one dimensional arrays of bytes into
+ *  one-D arrays of other types (int, float, etc) and vice versa.
+ *
+ *  These routines are called from the Java parts of the Java-C
+ *  interface.
+ *
+ *  ***Important notes:
+ *
+ *     1.  These routines are designed to be portable--they use the
+ *         C compiler to do the required native data manipulation.
+ *     2.  These routines copy the data at least once -- a serious
+ *         but unavoidable performance hit.
+ */
+
+#define TARGET jint
+#define TARGET_ARRAY jintArray
+#define METHODNAMETB "copyIntToByte"
+#define FUNCTIONNAMETB Java_ncsa_hdf_hdf5lib_HDFNativeData_copyIntToByte___3II_3BII
+#define METHODNAMEBT "copyByteToInt"
+#define FUNCTIONNAMEBT Java_ncsa_hdf_hdf5lib_HDFNativeData_copyByteToInt___3BI_3III
+#define COPY_FUNC GetIntArrayRegion
+
+#include "copyByteTarget.ctempl"

source/c/copyByteLong.c

+/****************************************************************************
+ * NCSA HDF                                                                 *
+ * National Computational Science Alliance                                  *
+ * University of Illinois at Urbana-Champaign                               *
+ * 605 E. Springfield, Champaign IL 61820                                   *
+ *                                                                          *
+ * Center for Information Sciences and Databases, ETH Zurich, Switzerland   *
+ *                                                                          *
+ * For conditions of distribution and use, see the accompanying             *
+ * COPYING file.                                                            *
+ *                                                                          *
+ ****************************************************************************/
+
+/*
+ *  This module contains the implementation of all the native methods
+ *  used for number conversion.  This is represented by the Java
+ *  class HDFNativeData.
+ *
+ *  These routines convert one dimensional arrays of bytes into
+ *  one-D arrays of other types (int, float, etc) and vice versa.
+ *
+ *  These routines are called from the Java parts of the Java-C
+ *  interface.
+ *
+ *  ***Important notes:
+ *
+ *     1.  These routines are designed to be portable--they use the
+ *         C compiler to do the required native data manipulation.
+ *     2.  These routines copy the data at least once -- a serious
+ *         but unavoidable performance hit.
+ */
+
+#define TARGET jlong
+#define TARGET_ARRAY jlongArray
+#define METHODNAMETB "copyLongToByte"
+#define FUNCTIONNAMETB Java_ncsa_hdf_hdf5lib_HDFNativeData_copyLongToByte___3JI_3BII
+#define METHODNAMEBT "copyByteToLong"
+#define FUNCTIONNAMEBT Java_ncsa_hdf_hdf5lib_HDFNativeData_copyByteToLong___3BI_3JII
+#define COPY_FUNC GetLongArrayRegion
+
+#include "copyByteTarget.ctempl"

source/c/copyByteShort.c

+/****************************************************************************
+ * NCSA HDF                                                                 *
+ * National Computational Science Alliance                                  *
+ * University of Illinois at Urbana-Champaign                               *
+ * 605 E. Springfield, Champaign IL 61820                                   *
+ *                                                                          *
+ * Center for Information Sciences and Databases, ETH Zurich, Switzerland   *
+ *                                                                          *
+ * For conditions of distribution and use, see the accompanying             *
+ * COPYING file.                                                            *
+ *                                                                          *
+ ****************************************************************************/
+
+/*
+ *  This module contains the implementation of all the native methods
+ *  used for number conversion.  This is represented by the Java
+ *  class HDFNativeData.
+ *
+ *  These routines convert one dimensional arrays of bytes into
+ *  one-D arrays of other types (int, float, etc) and vice versa.
+ *
+ *  These routines are called from the Java parts of the Java-C
+ *  interface.
+ *
+ *  ***Important notes:
+ *
+ *     1.  These routines are designed to be portable--they use the
+ *         C compiler to do the required native data manipulation.
+ *     2.  These routines copy the data at least once -- a serious
+ *         but unavoidable performance hit.
+ */
+
+#define TARGET jshort
+#define TARGET_ARRAY jshortArray
+#define METHODNAMETB "copyShortToByte"
+#define FUNCTIONNAMETB Java_ncsa_hdf_hdf5lib_HDFNativeData_copyShortToByte___3SI_3BII
+#define METHODNAMEBT "copyByteToShort"
+#define FUNCTIONNAMEBT Java_ncsa_hdf_hdf5lib_HDFNativeData_copyByteToShort___3BI_3SII
+#define COPY_FUNC GetShortArrayRegion
+
+#include "copyByteTarget.ctempl"

source/c/copyByteTarget.ctempl

+/****************************************************************************
+ * NCSA HDF                                                                 *
+ * National Computational Science Alliance                                  *
+ * University of Illinois at Urbana-Champaign                               *
+ * 605 E. Springfield, Champaign IL 61820                                   *
+ *                                                                          *
+ * Center for Information Sciences and Databases, ETH Zurich, Switzerland   *
+ *                                                                          *
+ * For conditions of distribution and use, see the accompanying             *
+ * COPYING file.                                                            *
+ *                                                                          *
+ ****************************************************************************/
+
+/*
+ *  This module contains the implementation of all the native methods
+ *  used for number conversion.  This is represented by the Java
+ *  class HDFNativeData.
+ *
+ *  These routines convert one dimensional arrays of bytes into
+ *  one-D arrays of other types (int, float, etc) and vice versa.
+ *
+ *  These routines are called from the Java parts of the Java-C
+ *  interface.
+ *
+ *  ***Important notes:
+ *
+ *     1.  These routines are designed to be portable--they use the
+ *         C compiler to do the required native data manipulation.
+ *     2.  These routines copy the data at least once -- a serious
+ *         but unavoidable performance hit.
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#include "hdf5.h"
+#include <jni.h>
+
+extern jboolean h5JNIFatalError( JNIEnv *env, char *functName);
+extern jboolean h5nullArgument( JNIEnv *env, char *functName);
+extern jboolean h5badArgument( JNIEnv *env, char *functName);
+
+#define INDATA_IS_NULL_ERR_TB METHODNAMETB ": inData is NULL"
+#define OUTDATA_IS_NULL_ERR_TB METHODNAMETB ": outData is NULL"
+#define OOB_IN_ERR_TB METHODNAMETB ": inStart or len is out of bounds"
+#define OOB_OUT_ERR_TB METHODNAMETB ": outStart or len is out of bounds"
+#define PINNING_OUT_ERR_TB METHODNAMETB ": pinning outArray failed"
+
+#define INDATA_IS_NULL_ERR_BT METHODNAMEBT ": inData is NULL"
+#define OUTDATA_IS_NULL_ERR_BT METHODNAMEBT ": outData is NULL"
+#define OOB_IN_ERR_BT METHODNAMEBT ": inStart or len is out of bounds"
+#define OOB_OUT_ERR_BT METHODNAMEBT ": outStart or len is out of bounds"
+#define PINNING_OUT_ERR_BT METHODNAMEBT ": pinning outArray failed"
+
+/*
+ *   public static native void copy<TARGET_CAPT>oByte(<TARGET>[] inData, int inStart, 
+ *                                byte[] outData, int outStart, int len);
+ */
+JNIEXPORT void JNICALL FUNCTIONNAMETB
+(JNIEnv *env,
+  jclass clss,
+  TARGET_ARRAY inData, /* IN: array of TARGET */
+  jint inStart,
+  jbyteArray outData, /* OUT: array of byte */
+  jint outStart,
+  jint len
+)  
+{
+    jsize inSize, outSize;
+    jint lenInBytes;
+    jbyte *outArray;
+    jboolean isCopy;
+
+    if (inData == NULL) {
+        h5nullArgument(env, INDATA_IS_NULL_ERR_BT);
+        return;
+    }
+
+    if (outData == NULL) {
+        h5nullArgument(env, OUTDATA_IS_NULL_ERR_TB);
+        return;
+    }
+
+    lenInBytes = len * sizeof(TARGET);
+
+#ifdef __cplusplus
+    inSize = env->GetArrayLength(inData);
+#else
+    inSize = (*env)->GetArrayLength(env, inData);
+#endif
+    if ((inStart < 0) || (inStart + len > inSize)) {
+        h5badArgument(env, OOB_IN_ERR_TB);
+        return;
+    }
+
+#ifdef __cplusplus
+    outSize = env->GetArrayLength(outData);
+#else
+    outSize = (*env)->GetArrayLength(env, outData);
+#endif
+    if ((outStart < 0) || (outStart + lenInBytes > outSize)) {
+        h5badArgument(env, OOB_OUT_ERR_TB);
+        return;
+    }
+
+#ifdef __cplusplus
+    outArray = env->GetPrimitiveArrayCritical(outData, &isCopy);
+#else
+    outArray = (*env)->GetPrimitiveArrayCritical(env, outData, &isCopy);
+#endif
+    if (outArray == NULL) {
+        h5JNIFatalError(env, PINNING_OUT_ERR_TB);
+        return;
+    }
+
+#ifdef __cplusplus
+    env->COPY_FUNC(inData, inStart, len, (TARGET*) (outArray + outStart));
+#else
+    (*env)->COPY_FUNC(env, inData, inStart, len, (TARGET*) (outArray + outStart));
+#endif
+
+#ifdef __cplusplus
+    env->ReleasePrimitiveArrayCritical(outData, outArray, 0);
+#else
+    (*env)->ReleasePrimitiveArrayCritical(env, outData,outArray, 0);
+#endif
+
+    return;
+}
+
+/*
+ *   public static native void copyByteTo<TARGET_CAP>(byte[] inData, int inStart, 
+ *                                TARGET[] outData, int outStart, int len);
+ */
+JNIEXPORT void JNICALL FUNCTIONNAMEBT
+(JNIEnv *env,
+  jclass clss,
+  jbyteArray inData, /* IN: array of byte */
+  jint inStart,
+  TARGET_ARRAY outData, /* OUT: array of TAGET */
+  jint outStart,
+  jint len
+  )  
+{
+    jsize inSize, outSize;
+    jint lenInBytes;
+    TARGET *outArray;
+    jboolean isCopy;
+
+    if (inData == NULL) {
+        h5nullArgument(env, INDATA_IS_NULL_ERR_BT);
+        return;
+    }
+
+    if (outData == NULL) {
+        h5nullArgument(env, OUTDATA_IS_NULL_ERR_BT);
+        return;
+    }
+
+    lenInBytes = len * sizeof(TARGET);
+
+#ifdef __cplusplus
+    inSize = env->GetArrayLength(inData);
+#else
+    inSize = (*env)->GetArrayLength(env, inData);
+#endif
+    if ((inStart < 0) || (inStart + lenInBytes > inSize)) {
+        h5badArgument(env, OOB_IN_ERR_BT);
+        return;
+    }
+
+#ifdef __cplusplus
+    outSize = env->GetArrayLength(outData);
+#else
+    outSize = (*env)->GetArrayLength(env, outData);
+#endif
+    if ((outStart < 0) || (outStart + len > outSize)) {
+        h5badArgument(env, OOB_OUT_ERR_BT);
+        return;
+    }
+
+#ifdef __cplusplus
+    outArray = env->GetPrimitiveArrayCritical(outData, &isCopy);
+#else
+    outArray = (*env)->GetPrimitiveArrayCritical(env, outData, &isCopy);
+#endif
+    if (outArray == NULL) {
+        h5JNIFatalError(env, PINNING_OUT_ERR_BT);
+        return;
+    }
+
+#ifdef __cplusplus
+    env->GetByteArrayRegion(inData, inStart, lenInBytes, outArray + outStart);
+#else
+    (*env)->GetByteArrayRegion(env, inData, inStart, lenInBytes, (jbyte*) (outArray + outStart));
+#endif
+
+#ifdef __cplusplus
+    env->ReleasePrimitiveArrayCritical(outData, outArray, 0);
+#else
+    (*env)->ReleasePrimitiveArrayCritical(env, outData, outArray, 0);
+#endif
+
+    return;
+}
+
+#ifdef __cplusplus
+}
+#endif

source/c/h5dImp.c

@@ -262,9 +262,9 @@ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread
         return -1;
     }
 #ifdef __cplusplus
-    byteP = env->GetByteArrayElements(buf,&isCopy);
+    byteP = env->GetPrimitiveArrayCritical(buf,&isCopy);