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Diffstat (limited to 'java/src/jni/h5dImp.c')
| -rw-r--r-- | java/src/jni/h5dImp.c | 1758 |
1 files changed, 1758 insertions, 0 deletions
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c new file mode 100644 index 0000000..f70cb5e --- /dev/null +++ b/java/src/jni/h5dImp.c @@ -0,0 +1,1758 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * For details of the HDF libraries, see the HDF Documentation at: + * http://hdfdfgroup.org/HDF5/doc/ + * + */ + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +#include <jni.h> +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include "hdf5.h" +#include "h5util.h" +#include "h5dImp.h" + +extern JavaVM *jvm; +extern jobject visit_callback; + +#ifdef __cplusplus + #ifdef _WINDOWS + #include <direct.h> + #endif + #define CBENVPTR (cbenv) + #define CBENVPAR + #define JVMPTR (jvm) + #define JVMPAR + #define JVMPAR2 +#else + #define CBENVPTR (*cbenv) + #define CBENVPAR cbenv, + #define JVMPTR (*jvm) + #define JVMPAR jvm + #define JVMPAR2 jvm, +#endif + +/********************/ +/* Local Prototypes */ +/********************/ + +static herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); +static herr_t H5DreadVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); +static herr_t H5DwriteVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); +static herr_t H5DwriteVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); + +/********************/ +/* Local Macros */ +/********************/ + +#define PIN_BYTE_ARRAY() { \ + if (isCriticalPinning) \ + buffP = (jbyte*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ + else \ + buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); \ +} + +#define UNPIN_BYTE_ARRAY(mode) { \ + if (isCriticalPinning) \ + ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ + else \ + ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, mode); \ +} + +#define PIN_SHORT_ARRAY() { \ + if (isCriticalPinning) \ + buffP = (jshort*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ + else \ + buffP = ENVPTR->GetShortArrayElements(ENVPAR buf, &isCopy); \ +} + +#define UNPIN_SHORT_ARRAY(mode) { \ + if (isCriticalPinning) \ + ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ + else \ + ENVPTR->ReleaseShortArrayElements(ENVPAR buf, buffP, mode); \ +} + +#define PIN_INT_ARRAY() { \ + if (isCriticalPinning) \ + buffP = (jint*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ + else \ + buffP = ENVPTR->GetIntArrayElements(ENVPAR buf, &isCopy); \ +} + +#define UNPIN_INT_ARRAY(mode) { \ + if (isCriticalPinning) \ + ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ + else \ + ENVPTR->ReleaseIntArrayElements(ENVPAR buf, buffP, mode); \ +} + +#define PIN_LONG_ARRAY() { \ + if (isCriticalPinning) \ + buffP = (jlong*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ + else \ + buffP = ENVPTR->GetLongArrayElements(ENVPAR buf,&isCopy); \ +} + +#define UNPIN_LONG_ARRAY(mode) { \ + if (isCriticalPinning) \ + ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ + else \ + ENVPTR->ReleaseLongArrayElements(ENVPAR buf, buffP, mode); \ +} + +#define PIN_FLOAT_ARRAY() { \ + if (isCriticalPinning) \ + buffP = (jfloat*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ + else \ + buffP = ENVPTR->GetFloatArrayElements(ENVPAR buf, &isCopy); \ +} + +#define UNPIN_FLOAT_ARRAY(mode) { \ + if (isCriticalPinning) \ + ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ + else \ + ENVPTR->ReleaseFloatArrayElements(ENVPAR buf, buffP, mode); \ +} + +#define PIN_DOUBLE_ARRAY() { \ + if (isCriticalPinning) \ + buffP = (jdouble*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ + else \ + buffP = ENVPTR->GetDoubleArrayElements(ENVPAR buf, &isCopy); \ +} + +#define UNPIN_DOUBLE_ARRAY(mode) { \ + if (isCriticalPinning) \ + ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ + else \ + ENVPTR->ReleaseDoubleArrayElements(ENVPAR buf, buffP, mode); \ +} + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dcreate + * Signature: (JLjava/lang/String;JJJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dcreate(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong type_id, + jlong space_id, jlong create_plist_id) +{ + hid_t dset_id = -1; + const char *fileName; + + PIN_JAVA_STRING(name, fileName, -1); + + dset_id = H5Dcreate2((hid_t)loc_id, fileName, (hid_t)type_id, (hid_t)space_id, H5P_DEFAULT, (hid_t)create_plist_id, H5P_DEFAULT); + + UNPIN_JAVA_STRING(name, fileName); + + if (dset_id < 0) + h5libraryError(env); + + return (jlong)dset_id; +} /* end Java_hdf_hdf5lib_H5__1H5Dcreate */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dopen + * Signature: (JLjava/lang/String;)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dopen(JNIEnv *env, jclass clss, jlong loc_id, jstring name) +{ + hid_t dset_id = -1; + const char *fileName; + + PIN_JAVA_STRING(name, fileName, -1); + + dset_id = H5Dopen2((hid_t)loc_id, fileName, H5P_DEFAULT); + + UNPIN_JAVA_STRING(name, fileName); + if (dset_id < 0) + h5libraryError(env); + + return (jlong)dset_id; +} /* end Java_hdf_hdf5lib_H5__1H5Dopen */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dget_space + * Signature: (J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dget_1space(JNIEnv *env, jclass clss, jlong dataset_id) +{ + hid_t retVal = -1; + + retVal = H5Dget_space((hid_t)dataset_id); + if (retVal < 0) + h5libraryError(env); + + return (jlong)retVal; +} /* end Java_hdf_hdf5lib_H5__1H5Dget_1space */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dget_type + * Signature: (J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dget_1type(JNIEnv *env, jclass clss, jlong dataset_id) +{ + hid_t retVal = -1; + + retVal = H5Dget_type((hid_t)dataset_id); + if (retVal < 0) + h5libraryError(env); + + return (jlong)retVal; +} /* end Java_hdf_hdf5lib_H5__1H5Dget_1type */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dget_create_plist + * Signature: (J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dget_1create_1plist(JNIEnv *env, jclass clss, jlong dataset_id) +{ + hid_t retVal = -1; + + retVal = H5Dget_create_plist((hid_t)dataset_id); + if (retVal < 0) + h5libraryError(env); + + return (jlong)retVal; +} /* end Java_hdf_hdf5lib_H5__1H5Dget_1create_1plist */ + +static htri_t +H5Tdetect_variable_str(hid_t tid) { + htri_t ret_val = 0; + + if (H5Tget_class(tid) == H5T_COMPOUND) { + unsigned i; + unsigned nm = (unsigned)H5Tget_nmembers(tid); + for(i = 0; i < nm; i++) { + htri_t status = 0; + hid_t mtid = 0; + if((mtid = H5Tget_member_type(tid, i)) < 0) + return -1; /* exit immediately on error */ + if((status = H5Tdetect_variable_str(mtid)) < 0) + return status; /* exit immediately on error */ + ret_val |= status; + H5Tclose (mtid); + } /* end for */ + } /* end if */ + else + ret_val = H5Tis_variable_str(tid); + + return ret_val; +} /* end H5Tdetect_variable_str */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread + * Signature: (JJJJJ[BZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning) +{ + herr_t status; + jbyte *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dread: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dread: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dread: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread: buf does not support variable length type"); + } /* end else if */ + else { + PIN_BYTE_ARRAY(); + + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dread: buf not pinned"); + } /* end if */ + else { + status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + if (status < 0) { + UNPIN_BYTE_ARRAY(JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + UNPIN_BYTE_ARRAY(0); /* update java buffer for return */ + } /* end else */ + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite + * Signature: (JJJJJ[BZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning) +{ + herr_t status; + jbyte *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dwrite: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dwrite: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dwrite: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite: buf does not support variable length type"); + } /* end else if */ + else { + PIN_BYTE_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dwrite: buf not pinned"); + } /* end if */ + else { + status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + UNPIN_BYTE_ARRAY(JNI_ABORT); /* no need to update buffer */ + + if (status < 0) + h5libraryError(env); + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dclose + * Signature: (J)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5__1H5Dclose(JNIEnv *env, jclass clss, jlong dataset_id) +{ + herr_t retVal = -1; + + retVal = H5Dclose((hid_t)dataset_id); + + if (retVal < 0) + h5libraryError(env); + + return (jint)retVal; +} /* end Java_hdf_hdf5lib_H5__1H5Dclose */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dget_storage_size + * Signature: (J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Dget_1storage_1size(JNIEnv *env, jclass clss, jlong dataset_id) +{ + hsize_t retVal = (hsize_t)-1; + + if (dataset_id < 0) { + h5badArgument(env, "H5Dget_storage_size: not a dataset"); + } /* end if */ + else { + retVal = H5Dget_storage_size((hid_t)dataset_id); + } /* end else */ + + return (jlong)retVal; +} /* end Java_hdf_hdf5lib_H5_H5Dget_1storage_1size */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dvlen_reclaim + * Signature: (JJJ[B)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim(JNIEnv *env, jclass clss, jlong type_id, jlong space_id, + jlong xfer_plist_id, jbyteArray buf) +{ + herr_t status = -1; + jbyte *byteP; + jboolean isCopy; + + if (buf == NULL) { + h5nullArgument(env, "H5Dvlen_reclaim: buf is NULL"); + } /* end if */ + else { + byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); + if (byteP == NULL) { + h5JNIFatalError(env, "H5Dvlen_reclaim: buf not pinned"); + } /* end if */ + else { + status = H5Dvlen_reclaim((hid_t)type_id, (hid_t)space_id, (hid_t)xfer_plist_id, byteP); + + ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT); + + if (status < 0) + h5libraryError(env); + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim */ + +/* + //////////////////////////////////////////////////////////////////// + // // + // New APIs for read data from library // + // Using H5Dread(..., Object buf) requires function calls // + // theArray.emptyBytes() and theArray.arrayify(buf), which // + // triples the actual memory needed by the data set. // + // Using the following APIs solves the problem. // + // // + //////////////////////////////////////////////////////////////////// +*/ +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_short + * Signature: (JJJJJ[SZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1short(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jshortArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jshort *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dread_short: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dread: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_short: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dread_short: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_short: buf does not support variable length type"); + } /* end else if */ + else { + PIN_SHORT_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dread_short: buf not pinned"); + } /* end if */ + else { + status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + if (status < 0) { + UNPIN_SHORT_ARRAY(JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + UNPIN_SHORT_ARRAY(0); + } /* end else */ + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1short */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite_short + * Signature: (JJJJJ[SZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite_1short(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jshortArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jshort *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL ) { + h5nullArgument(env, "H5Dwrite_short: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dwrite_short: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_short: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dwrite_short: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_short: buf does not support variable length type"); + } /* end else if */ + else { + PIN_SHORT_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dwrite_short: buf not pinned"); + } /* end if */ + else { + status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + UNPIN_SHORT_ARRAY(JNI_ABORT); + + if (status < 0) + h5libraryError(env); + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1short */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_int + * Signature: (JJJJJ[IZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jintArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jint *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dread_int: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dread_int: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_int: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dread_int: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_int: buf does not support variable length type"); + } /* end else if */ + else { + PIN_INT_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dread_int: buf not pinned"); + } /* end if */ + else { + status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + if (status < 0) { + UNPIN_INT_ARRAY(JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + UNPIN_INT_ARRAY(0); + } /* end else */ + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1int */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite_int + * Signature: (JJJJJ[IZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite_1int(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jintArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jint *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dwrite_int: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dwrite_int: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_int: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dwrite_int: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_int: buf does not support variable length type"); + } /* end else if */ + else { + PIN_INT_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dwrite_int: buf not pinned"); + } /* end if */ + else { + status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + UNPIN_INT_ARRAY(JNI_ABORT); + + if (status < 0) + h5libraryError(env); + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1int */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_long + * Signature: (JJJJJ[JZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1long(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jlongArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jlong *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dread_long: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dread_long: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_long: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dread_long: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_long: buf does not support variable length type"); + } /* end else if */ + else { + PIN_LONG_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dread_long: buf not pinned"); + } /* end if */ + else { + status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + if (status < 0) { + UNPIN_LONG_ARRAY(JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + UNPIN_LONG_ARRAY(0); + } /* end else */ + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1long */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite_long + * Signature: (JJJJJ[JZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite_1long(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jlongArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jlong *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dwrite_long: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dwrite_long: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_long: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dwrite_long: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_long: buf does not support variable length type"); + } /* end else if */ + else { + PIN_LONG_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dwrite_long: buf not pinned"); + } /* end if */ + else { + status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + UNPIN_LONG_ARRAY(JNI_ABORT); + if (status < 0) + h5libraryError(env); + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1long */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_float + * Signature: (JJJJJ[FZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1float(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jfloatArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jfloat *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dread_float: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dread_float: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_float: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dread_float: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_float: buf does not support variable length type"); + } /* end else if */ + else { + PIN_FLOAT_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dread_float: buf not pinned"); + } /* end if */ + else { + status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + if (status < 0) { + UNPIN_FLOAT_ARRAY(JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + UNPIN_FLOAT_ARRAY(0); + } /* end else */ + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1float */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite_float + * Signature: (JJJJJ[FZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite_1float(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jfloatArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jfloat *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dwrite_float: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dwrite_float: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_float: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dwrite_float: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_float: buf does not support variable length type"); + } /* end else if */ + else { + PIN_FLOAT_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dwrite_float: buf not pinned"); + } /* end if */ + else { + status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + UNPIN_FLOAT_ARRAY(JNI_ABORT); + if (status < 0) + h5libraryError(env); + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1float */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_double + * Signature: (JJJJJ[DZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1double(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jdoubleArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jdouble *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dread_double: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dread_double: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_double: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dread_double: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dread_double: buf does not support variable length type"); + } /* end else if */ + else { + PIN_DOUBLE_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dread_double: buf not pinned"); + } /* end if */ + else { + status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + if (status < 0) { + UNPIN_DOUBLE_ARRAY(JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + UNPIN_DOUBLE_ARRAY(0); + } /* end else */ + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1double */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite_double + * Signature: (JJJJJ[DZ)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite_1double(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jdoubleArray buf, jboolean isCriticalPinning) +{ + herr_t status = -1; + jdouble *buffP; + jboolean isCopy; + htri_t data_class; + + if (buf == NULL) { + h5nullArgument(env, "H5Dwrite_double: buf is NULL"); + } /* end if */ + else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) { + h5JNIFatalError(env, "H5Dwrite_double: H5Tdetect_class() failed"); + } /* end else if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_double: buf does not support variable length type"); + } /* end else if */ + else { + /* recursive detect any vlen string in type (compound, array ...) */ + if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) { + h5JNIFatalError(env, "H5Dwrite_double: H5Tdetect_variable_str() failed"); + } /* end if */ + else if(data_class == 1) { + h5badArgument(env, "H5Dwrite_double: buf does not support variable length type"); + } /* end else if */ + else { + PIN_DOUBLE_ARRAY(); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dwrite_double: buf not pinned"); + } /* end if */ + else { + status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); + + UNPIN_DOUBLE_ARRAY(JNI_ABORT); + if (status < 0) + h5libraryError(env); + } /* end else */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1double */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_string + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1string(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jobjectArray j_buf) +{ + herr_t status = -1; + char *c_buf; + char *cstr; + size_t str_len; + jsize i; + jsize n; + size_t pos; + jstring jstr; + + c_buf = cstr = NULL; + if (j_buf == NULL) { + h5nullArgument(env, "H5Dread_string: buf is NULL"); + } /* end if */ + else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) { + h5nullArgument(env, "H5Dread_string: buf length <= 0"); + } /* end else if */ + else if ((str_len = H5Tget_size((hid_t)mem_type_id)) <=0) { + h5libraryError(env); + } /* end else if */ + else { + if ((cstr = (char*)HDmalloc(str_len + 1)) == NULL) { + h5JNIFatalError(env, "H5Dread_string: memory allocation failed."); + } /* end if */ + else { + if ((c_buf = (char*)HDmalloc((size_t)n * str_len)) == NULL) { + if (cstr) + HDfree(cstr); + cstr = NULL; + h5JNIFatalError(env, "H5Dread_string: memory allocation failed."); + } /* end if */ + else { + status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, c_buf); + + if (status < 0) { + if (cstr) + HDfree(cstr); + cstr = NULL; + if (c_buf) + HDfree(c_buf); + c_buf = NULL; + h5libraryError(env); + } /* end if */ + else { + pos = 0; + for (i = 0; i < n; i++) { + HDmemcpy(cstr, c_buf+pos, str_len); + cstr[str_len] = '\0'; + jstr = ENVPTR->NewStringUTF(ENVPAR cstr); + ENVPTR->SetObjectArrayElement(ENVPAR j_buf, i, jstr); + pos += str_len; + } /* end for */ + } /* end else */ + + if (c_buf) + HDfree(c_buf); + } /* end else cbuf allocation*/ + + if (cstr) + HDfree(cstr); + } /* end else cstr allocation*/ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1string */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite_string + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite_1string(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jobjectArray j_buf) +{ + herr_t status = -1; + char *c_buf; + jsize str_len; + jsize i; + jsize n; + + if (j_buf == NULL) { + h5nullArgument(env, "H5Dwrite_string: buf is NULL"); + } /* end if */ + else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) { + h5nullArgument(env, "H5Dwrite_string: buf length <= 0"); + } /* end else if */ + else if ((str_len = (jsize)H5Tget_size((hid_t)mem_type_id)) <=0) { + h5libraryError(env); + } /* end else if */ + else { + if ((c_buf = (char*)HDmalloc((size_t)n * (size_t)str_len)) == NULL) { + h5JNIFatalError(env, "H5Dwrite_string: memory allocation failed."); + } /* end if */ + else { + for (i = 0; i < n; i++) { + jstring obj = (jstring)ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray)j_buf, i); + if (obj != 0) { + jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj); + const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0); + + if (utf8) { + strncpy(&c_buf[i * str_len], utf8, str_len); + } /* end if */ + + ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); + ENVPTR->DeleteLocalRef(ENVPAR obj); + } /* end if */ + } /* end for */ + + status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, + (hid_t)file_space_id, (hid_t)xfer_plist_id, c_buf); + + if (c_buf) + HDfree(c_buf); + c_buf = NULL; + + if (status < 0) { + h5libraryError(env); + } /* end if */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1string */ + +/** + * Read VLEN data into array of arrays. + * Object[] buf contains VL arrays of data points + * Currently only deal with variable length of atomic data types + */ +/* old version */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_VLStrings + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) +{ + herr_t status = -1; + htri_t isVlenStr=0; + + if (buf == NULL) { + h5nullArgument(env, "H5Dread_VLStrings: buf is NULL"); + } /* end if */ + else { + isVlenStr = H5Tis_variable_str((hid_t)mem_type_id); + + if (isVlenStr) { + status = H5DreadVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id, + (hid_t)mem_space_id, (hid_t)file_space_id, + (hid_t)xfer_plist_id, buf); + } /* end if */ + else + h5badArgument(env, "H5Dread_VLStrings: type is not variable length String"); + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */ + +herr_t +H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t + file_sid, hid_t xfer_plist_id, jobjectArray buf) +{ + char **strs; + jstring jstr; + jint i; + jint n; + herr_t status = -1; + + n = ENVPTR->GetArrayLength(ENVPAR buf); + strs =(char**)HDcalloc((size_t)n, sizeof(char*)); + + if (strs == NULL) { + h5JNIFatalError(env, "H5DreadVL_str: failed to allocate buff for read variable length strings"); + } /* end if */ + else { + status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, strs); + + if (status < 0) { + H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs); + HDfree(strs); + h5JNIFatalError(env, "H5DreadVL_str: failed to read variable length strings"); + } /* end if */ + else { + for (i=0; i < n; i++) { + jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]); + ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); + H5free_memory (strs[i]); + } /* end for */ + + /* + for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings, + H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect + free space in time. Instead, use "H5free_memory(strs[i])" above to free individual strings + after it is done. + H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs); + */ + + HDfree(strs); + } /* end else */ + } /* end else */ + + return status; +} /* end H5DreadVL_str */ + + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dwrite_VLStrings + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) +{ + herr_t status = -1; + htri_t isVlenStr=0; + + if (buf == NULL) { + h5nullArgument(env, "H5Dwrite_VLStrings: buf is NULL"); + } /* end if */ + else { + isVlenStr = H5Tis_variable_str((hid_t)mem_type_id); + + if (isVlenStr) { + status = H5DwriteVL_str(env, (hid_t)dataset_id, (hid_t)mem_type_id, + (hid_t)mem_space_id, (hid_t)file_space_id, + (hid_t)xfer_plist_id, buf); + } /* end if */ + else + h5badArgument(env, "H5Dwrite_VLStrings: type is not variable length String"); + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings */ + +herr_t +H5DwriteVL_str(JNIEnv *env, hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, + hid_t file_space_id, hid_t xfer_plist_id, jobjectArray buf) +{ + herr_t status = -1; + char **wdata; + jsize size; + jsize i; + + size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf); + wdata = (char**)HDmalloc((size_t)size * sizeof (char*)); + + if (!wdata) { + h5JNIFatalError(env, "H5DwriteVL_string: cannot allocate buffer"); + } /* end if */ + else { + HDmemset(wdata, 0, (size_t)size * sizeof(char*)); + for (i = 0; i < size; ++i) { + jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray)buf, i); + if (obj != 0) { + jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj); + const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0); + + if (utf8) { + wdata[i] = (char*)HDmalloc((size_t)length + 1); + if (wdata[i]) { + HDmemset(wdata[i], 0, (size_t)length + 1); + HDstrncpy(wdata[i], utf8, (size_t)length + 1); + } /* end if */ + } /* end if */ + + ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); + ENVPTR->DeleteLocalRef(ENVPAR obj); + } /* end if */ + } /* end for (i = 0; i < size; ++i) */ + + status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, wdata); + + /* now free memory*/ + for (i = 0; i < size; i++) { + if(wdata[i]) { + HDfree(wdata[i]); + } /* end if */ + } /* end for */ + HDfree(wdata); + + if (status < 0) + h5libraryError(env); + } /* end else */ + + return status; +} /* end H5DwriteVL_str */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_reg_ref + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref (JNIEnv *env, jclass clss, + jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) +{ + herr_t status = -1; + h5str_t h5str; + size_t size; + hdset_reg_ref_t *ref_data; + jint i; + jint n; + jstring jstr; + + hid_t region = -1; + hid_t did = (hid_t) dataset_id; + hid_t tid = (hid_t) mem_type_id; + hid_t mem_sid = (hid_t) mem_space_id; + hid_t file_sid = (hid_t) file_space_id; + + n = ENVPTR->GetArrayLength(ENVPAR buf); + size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/ + ref_data = (hdset_reg_ref_t*)HDmalloc(size * (size_t)n); + + if (ref_data == NULL) { + h5JNIFatalError(env, "H5Dread_reg_ref: failed to allocate buff for read"); + return -1; + } /* end if */ + + status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data); + + if (status < 0) { + HDfree(ref_data); + h5JNIFatalError(env, "H5Dread_reg_ref: failed to read data"); + return -1; + } /* end if */ + + HDmemset(&h5str, 0, sizeof(h5str_t)); + h5str_new(&h5str, 1024); + for (i=0; i<n; i++) { + h5str.s[0] = '\0'; + h5str_sprintf(&h5str, did, tid, ref_data[i], 0); + jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); + + ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); + } /* end for */ + + h5str_free(&h5str); + HDfree(ref_data); + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dread_reg_ref_data + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data (JNIEnv *env, jclass clss, + jlong dataset_id, jlong mem_type_id, jlong mem_space_id, + jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) +{ + herr_t status = -1; + h5str_t h5str; + size_t size; + hdset_reg_ref_t *ref_data; + jint i; + jint n; + jstring jstr; + + hid_t region_obj; + H5S_sel_type region_type; + + hid_t region = -1; + hid_t did = (hid_t) dataset_id; + hid_t tid = (hid_t) mem_type_id; + hid_t mem_sid = (hid_t) mem_space_id; + hid_t file_sid = (hid_t) file_space_id; + + n = ENVPTR->GetArrayLength(ENVPAR buf); + size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/ + ref_data = (hdset_reg_ref_t*)HDmalloc(size * (size_t)n); + + if (ref_data == NULL) { + h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to allocate buff for read"); + return -1; + } /* end if */ + + status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data); + + if (status < 0) { + HDfree(ref_data); + h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to read data"); + return -1; + } /* end if */ + + HDmemset(&h5str, 0, sizeof(h5str_t)); + h5str_new(&h5str, 1024); + for (i=0; i<n; i++) { + h5str.s[0] = '\0'; + + /* get name of the dataset the region reference points to using H5Rget_name */ + region_obj = H5Rdereference2(did, H5P_DEFAULT, H5R_DATASET_REGION, ref_data[i]); + if (region_obj >= 0) { + region = H5Rget_region(did, H5R_DATASET_REGION, ref_data[i]); + if (region >= 0) { + region_type = H5Sget_select_type(region); + if(region_type==H5S_SEL_POINTS) { + h5str_dump_region_points_data(&h5str, region, region_obj); + } /* end if */ + else { + h5str_dump_region_blocks_data(&h5str, region, region_obj); + } /* end else */ + + H5Sclose(region); + } /* end if */ + H5Dclose(region_obj); + } /* end if */ + jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); + + ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); + } /* end for */ + + h5str_free(&h5str); + HDfree(ref_data); + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dcreate2 + * Signature: (JLjava/lang/String;JJJJJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dcreate2(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong type_id, + jlong space_id, jlong link_plist_id, jlong create_plist_id, jlong access_plist_id) +{ + hid_t dset_id = -1; + const char *fileName; + + PIN_JAVA_STRING(name, fileName, -1); + + dset_id = H5Dcreate2((hid_t)loc_id, fileName, (hid_t)type_id, (hid_t)space_id, (hid_t)link_plist_id, (hid_t)create_plist_id, (hid_t)access_plist_id); + + UNPIN_JAVA_STRING(name, fileName); + if (dset_id < 0) + h5libraryError(env); + + return (jlong)dset_id; +} /* end Java_hdf_hdf5lib_H5__1H5Dcreate2 */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dopen2 + * Signature: (JLjava/lang/String;J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dopen2(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong access_plist) +{ + hid_t dset_id; + const char *fileName; + + PIN_JAVA_STRING(name, fileName, -1); + + dset_id = H5Dopen2((hid_t)loc_id, fileName, (hid_t)access_plist); + + UNPIN_JAVA_STRING(name, fileName); + if (dset_id < 0) + h5libraryError(env); + + return (jlong)dset_id; +} /* end Java_hdf_hdf5lib_H5__1H5Dopen2 */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: _H5Dcreate_anon + * Signature: (JJJJJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5__1H5Dcreate_1anon(JNIEnv *env, jclass clss, jlong loc_id, jlong type_id, jlong space_id, jlong dcpl_id, jlong dapl_id) +{ + hid_t dset_id = -1; + + dset_id = H5Dcreate_anon((hid_t)loc_id, (hid_t)type_id, (hid_t)space_id, (hid_t)dcpl_id, (hid_t)dapl_id); + if (dset_id < 0) + h5libraryError(env); + + return (jlong)dset_id; +} /* end Java_hdf_hdf5lib_H5__1H5Dcreate_1anon */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dget_space_status + * Signature: (J)I; + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Dget_1space_1status(JNIEnv *env, jclass clss, jlong loc_id) +{ + H5D_space_status_t space_status = H5D_SPACE_STATUS_ERROR; + + if (H5Dget_space_status((hid_t)loc_id, &space_status) < 0) + h5libraryError(env); + + return (jint)space_status; +} /* end Java_hdf_hdf5lib_H5_H5Dget_1space_1status */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dget_access_plist + * Signature: (J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Dget_1access_1plist(JNIEnv *env, jclass clss, jlong loc_id) +{ + hid_t retVal = -1; + + retVal = H5Dget_access_plist((hid_t)loc_id); + if (retVal < 0) + h5libraryError(env); + + return (jlong)retVal; +} /* end Java_hdf_hdf5lib_H5_H5Dget_1access_1plist */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dget_offset + * Signature: (J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Dget_1offset(JNIEnv *env, jclass clss, jlong loc_id) +{ + haddr_t offset = HADDR_UNDEF; + + offset = H5Dget_offset((hid_t)loc_id); + if (offset == HADDR_UNDEF) + h5libraryError(env); + + return (jlong)offset; +} /* end Java_hdf_hdf5lib_H5_H5Dget_1offset */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dvlen_get_buf_size + * Signature: (JJJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size(JNIEnv *env, jclass clss, jlong dataset_id, jlong type_id, jlong space_id) +{ + hsize_t sz = 0; + + if (H5Dvlen_get_buf_size((hid_t)dataset_id, (hid_t)type_id, (hid_t)space_id, &sz) < 0) + h5libraryError(env); + + return (jlong)sz; +} /* end Java_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size_1long */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dfill + * Signature: ([BJ[BJJ)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Dfill(JNIEnv *env, jclass clss, jbyteArray fill, jlong fill_type_id, jbyteArray buf, jlong buf_type_id, jlong space_id) +{ + herr_t status; + jbyte *fillP; + jbyte *buffP; + jboolean isCopy1; + jboolean isCopy2; + + + if (buf == NULL) { + h5nullArgument(env, "H5Dfill: buf is NULL"); + return; + } /* end if */ + buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy2); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Dfill: buf not pinned"); + return; + } /* end if */ + + if(fill) { + fillP = ENVPTR->GetByteArrayElements(ENVPAR fill, &isCopy1); + if (fillP == NULL) { + ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT); + h5JNIFatalError( env, "H5Dfill: fill not pinned"); + return; + } /* end if */ + } /* end if */ + else + fillP = NULL; + + status = H5Dfill((const void*)fillP, (hid_t)fill_type_id, (void*)buffP, (hid_t)buf_type_id, (hid_t)space_id); + if(fillP) { + /* free the buffer without copying back */ + /* end if */ ENVPTR->ReleaseByteArrayElements(ENVPAR fill, fillP, JNI_ABORT); + } + if (status < 0) { + ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + if (isCopy2 == JNI_TRUE) { + ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, 0); + } /* end if */ + } /* end else */ +} /* end Java_hdf_hdf5lib_H5_H5Dfill */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Dset_extent + * Signature: (J[J)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Dset_1extent(JNIEnv *env, jclass clss, jlong loc_id, jlongArray buf) +{ + herr_t status; + hsize_t *dims; + jlong *buffP; + jsize rank; + jboolean isCopy; + int i = 0; + + if (buf == NULL) { + h5nullArgument(env, "H5Dset_extent: buf is NULL"); + return; + } /* end if */ + + rank = ENVPTR->GetArrayLength(ENVPAR buf); + if (rank <= 0) { + h5JNIFatalError(env, "H5Dset_extent: rank <=0"); + } /* end if */ + else { + buffP = ENVPTR->GetLongArrayElements(ENVPAR buf, &isCopy); + if (buffP == NULL) { + h5JNIFatalError( env, "H5Dset_extent: buf not pinned"); + } /* end if */ + else { + dims = (hsize_t*)HDmalloc((size_t)rank * sizeof(hsize_t)); + for (i = 0; i< rank; i++) + dims[i] = (hsize_t)buffP[i]; + + status = H5Dset_extent((hid_t)loc_id, (hsize_t*)dims); + + HDfree (dims); + + /* free the buffer without copying back */ + ENVPTR->ReleaseLongArrayElements(ENVPAR buf, buffP, JNI_ABORT); + + if (status < 0) { + h5libraryError(env); + } /* end if */ + } /* end else */ + } /* end else */ +} /* end Java_hdf_hdf5lib_H5_H5Dset_1extent */ + +static herr_t +H5D_iterate_cb(void* elem, hid_t elem_id, unsigned ndim, const hsize_t *point, void *op_data) { + JNIEnv *cbenv; + jint status; + jclass cls; + jmethodID mid; + jbyteArray elemArray; + jlongArray pointArray; + jsize size; + + if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) { + JVMPTR->DetachCurrentThread(JVMPAR); + return -1; + } /* end if */ + cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback); + if (cls == 0) { + JVMPTR->DetachCurrentThread(JVMPAR); + return -1; + } /* end if */ + mid = CBENVPTR->GetMethodID(CBENVPAR cls, "callback", "([BJI[JLhdf/hdf5lib/callbacks/H5D_iterate_t;)I"); + if (mid == 0) { + JVMPTR->DetachCurrentThread(JVMPAR); + return -1; + } /* end if */ + + if (elem == NULL) { + JVMPTR->DetachCurrentThread(JVMPAR); + return -1; + } /* end if */ + if (point == NULL) { + JVMPTR->DetachCurrentThread(JVMPAR); + return -1; + } /* end if */ + + size = (jsize)H5Tget_size(elem_id); + elemArray = CBENVPTR->NewByteArray(CBENVPAR size); + if (elemArray == NULL) { + JVMPTR->DetachCurrentThread(JVMPAR); + return -1; + } /* end if */ + CBENVPTR->SetByteArrayRegion(CBENVPAR elemArray, 0, size, (jbyte *)elem); + + pointArray = CBENVPTR->NewLongArray(CBENVPAR 2); + if (pointArray == NULL) { + JVMPTR->DetachCurrentThread(JVMPAR); + return -1; + } /* end if */ + CBENVPTR->SetLongArrayRegion(CBENVPAR pointArray, 0, 2, (const jlong *)point); + + status = CBENVPTR->CallIntMethod(CBENVPAR visit_callback, mid, (void*)elemArray, elem_id, ndim, pointArray, op_data); + + CBENVPTR->GetByteArrayRegion(CBENVPAR elemArray, 0, size, (jbyte *)elem); + + JVMPTR->DetachCurrentThread(JVMPAR); + + return status; +} /* end H5D_iterate_cb */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Diterate + * Signature: ([BJJLjava/lang/Object;Ljava/lang/Object;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5Diterate(JNIEnv *env, jclass clss, jbyteArray buf, jlong buf_type, jlong space, + jobject callback_op, jobject op_data) +{ + herr_t status = -1; + jboolean isCopy; + jbyte *buffP; + + ENVPTR->GetJavaVM(ENVPAR &jvm); + visit_callback = callback_op; + + if (op_data == NULL) { + h5nullArgument(env, "H5Diterate: op_data is NULL"); + return -1; + } /* end if */ + if (callback_op == NULL) { + h5nullArgument(env, "H5Diterate: callback_op is NULL"); + return -1; + } /* end if */ + + if (buf == NULL) { + h5nullArgument(env, "H5Diterate: buf is NULL"); + return -1; + } /* end if */ + buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); + if (buffP == NULL) { + h5JNIFatalError(env, "H5Diterate: buf not pinned"); + } /* end if */ + else { + status = H5Diterate((void*)buffP, (hid_t)buf_type, (hid_t)space, (H5D_operator_t)H5D_iterate_cb, (void*)op_data); + + if (status < 0) { + ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT); + h5libraryError(env); + } /* end if */ + else { + if (isCopy == JNI_TRUE) { + ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, 0); + } /* end if */ + } /* end else */ + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Diterate */ + + +#ifdef __cplusplus +} /* end extern "C" */ +#endif /* __cplusplus */ |