diff options
author | Allen Byrne <byrn@hdfgroup.org> | 2018-06-26 14:35:07 (GMT) |
---|---|---|
committer | Allen Byrne <byrn@hdfgroup.org> | 2018-06-26 14:35:07 (GMT) |
commit | 7636342d959bfd3d023345bac76650932961d843 (patch) | |
tree | aca513b9b30c2551e5f2d946bc180097ed4733bf /java/src/jni | |
parent | f89bdb7753786994887fb882c459a898b1bade63 (diff) | |
download | hdf5-7636342d959bfd3d023345bac76650932961d843.zip hdf5-7636342d959bfd3d023345bac76650932961d843.tar.gz hdf5-7636342d959bfd3d023345bac76650932961d843.tar.bz2 |
Push updates from develop
Diffstat (limited to 'java/src/jni')
-rw-r--r-- | java/src/jni/h5Constants.c | 2 | ||||
-rw-r--r-- | java/src/jni/h5aImp.c | 322 | ||||
-rw-r--r-- | java/src/jni/h5aImp.h | 18 | ||||
-rw-r--r-- | java/src/jni/h5dImp.c | 206 | ||||
-rw-r--r-- | java/src/jni/h5util.c | 297 | ||||
-rw-r--r-- | java/src/jni/h5util.h | 21 |
6 files changed, 598 insertions, 268 deletions
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c index 0f4361f..c99745d 100644 --- a/java/src/jni/h5Constants.c +++ b/java/src/jni/h5Constants.c @@ -1231,6 +1231,8 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5T_1VARIABLE(JNIEnv *env, jclass cls) { return (int)H5T_VARIABLE; } JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5T_1VLEN(JNIEnv *env, jclass cls) { return H5T_VLEN; } +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5T_1VL_1T(JNIEnv *env, jclass cls) { return sizeof(hvl_t); } JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1CONT(JNIEnv *env, jclass cls) { return H5Z_CB_CONT; } diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c index 26ec4fc..13f5207 100644 --- a/java/src/jni/h5aImp.c +++ b/java/src/jni/h5aImp.c @@ -49,6 +49,10 @@ extern jobject visit_callback; /* Local Prototypes */ /********************/ +static herr_t H5AwriteVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf); +static herr_t H5AwriteVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf); +static herr_t H5AreadVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf); +static herr_t H5AreadVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf); static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *op_data); @@ -178,7 +182,6 @@ Java_hdf_hdf5lib_H5_H5Aread } /* end if */ else { status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); - if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT); h5libraryError(env); @@ -194,6 +197,323 @@ Java_hdf_hdf5lib_H5_H5Aread /* * Class: hdf_hdf5lib_H5 + * Method: H5AwriteVL + * Signature: (JJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5AwriteVL + (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) +{ + herr_t status = -1; + htri_t isStr = 0; + htri_t isVlenStr = 0; + htri_t isComplex = 0; + + if (buf == NULL) { + h5nullArgument(env, "H5AwriteVL: buf is NULL"); + } /* end if */ + else { + isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING); + if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { + unsigned i; + int nm = H5Tget_nmembers(mem_type_id); + for(i = 0; i <nm; i++) { + hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i); + isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) || + H5Tdetect_class((hid_t)nested_tid, H5T_VLEN); + H5Tclose(nested_tid); + } + } + else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) { + isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */ + } + if (isStr == 0 || isComplex>0 || isVlenStr) { + status = H5AwriteVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf); + } + else if (isStr > 0) { + status = H5AwriteVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf); + } + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */ + +herr_t +H5AwriteVL_str + (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) +{ + herr_t status = -1; + char **wdata; + jsize size; + jint i; + + size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf); + + wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*)); + if (!wdata) { + h5JNIFatalError(env, "H5AwriteVL_str: 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); + } /* end if */ + } /* end if */ + + ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); + ENVPTR->DeleteLocalRef(ENVPAR obj); + } /* end if */ + } /* end for (i = 0; i < size; ++i) */ + + status = H5Awrite((hid_t)aid, (hid_t)tid, wdata); + + 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 (jint)status; +} + +herr_t +H5AwriteVL_asstr + (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) +{ + char **strs; + jstring jstr; + jint i; + jint n; + hid_t sid; + hsize_t dims[H5S_MAX_RANK]; + herr_t status = -1; + + n = ENVPTR->GetArrayLength(ENVPAR buf); + strs =(hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t)); + + if (strs == NULL) { + h5JNIFatalError(env, "H5AwriteVL_asstr: failed to allocate buff for read variable length strings"); + } /* end if */ + else { + status = H5Awrite(aid, tid, strs); + + if (status < 0) { + dims[0] = (hsize_t)n; + sid = H5Screate_simple(1, dims, NULL); + H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs); + H5Sclose(sid); + HDfree(strs); + h5JNIFatalError(env, "H5AwriteVL_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 H5AwriteVL_str */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5AreadVL + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5AreadVL + (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) +{ + herr_t status = -1; + htri_t isStr = 0; + htri_t isVlenStr = 0; + htri_t isComplex = 0; + + if (buf == NULL) { + h5nullArgument(env, "H5AreadVL: buf is NULL"); + } /* end if */ + else { + isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING); + if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { + unsigned i; + int nm = H5Tget_nmembers(mem_type_id); + for(i = 0; i <nm; i++) { + hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i); + isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) || + H5Tdetect_class((hid_t)nested_tid, H5T_VLEN); + H5Tclose(nested_tid); + } + } + else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) { + isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */ + } + if (isStr == 0 || isComplex>0 || isVlenStr) { + status = H5AreadVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf); + } + else if (isStr > 0) { + status = H5AreadVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf); + } + } /* end else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Aread_1VL */ + +herr_t +H5AreadVL_asstr + (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) +{ + jint i; + jint n; + hid_t sid; + jstring jstr; + h5str_t h5str; + hvl_t *rdata; + hsize_t dims[H5S_MAX_RANK]; + size_t size; + size_t max_len = 0; + herr_t status = -1; + + /* Get size of string array */ + n = ENVPTR->GetArrayLength(ENVPAR buf); + /* we will need to read n number of hvl_t structures */ + rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t)); + if (rdata == NULL) { + h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buff for read"); + } /* end if */ + else { + status = H5Aread(aid, tid, rdata); + + if (status < 0) { + dims[0] = (hsize_t)n; + sid = H5Screate_simple(1, dims, NULL); + H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); + H5Sclose(sid); + HDfree(rdata); + h5JNIFatalError(env, "H5AreadVL_asstr: failed to read data"); + } /* end if */ + else { + /* calculate the largest size of all the hvl_t structures read */ + max_len = 1; + for (i=0; i < n; i++) { + if ((rdata + i)->len > max_len) + max_len = (rdata + i)->len; + } + + /* create one malloc to hold largest element */ + size = H5Tget_size(tid) * max_len; + HDmemset(&h5str, 0, sizeof(h5str_t)); + h5str_new(&h5str, 4 * size); + + if (h5str.s == NULL) { + dims[0] = (hsize_t)n; + sid = H5Screate_simple(1, dims, NULL); + H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); + H5Sclose(sid); + HDfree(rdata); + h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buf"); + } /* end if */ + else { + H5T_class_t tclass = H5Tget_class(tid); + /* convert each element to char string */ + for (i=0; i < n; i++) { + h5str.s[0] = '\0'; + h5str_vlsprintf(&h5str, aid, tid, rdata+i, 0); + jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); + ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); + } /* end for */ + h5str_free(&h5str); + + dims[0] = (hsize_t)n; + sid = H5Screate_simple(1, dims, NULL); + H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); + H5Sclose(sid); + HDfree(rdata); + } /* end else */ + } /* end else */ + } /* end else */ + + return status; +} + +herr_t +H5AreadVL_str + (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) +{ + char **strs; + jstring jstr; + jint i; + jint n; + hid_t sid; + hsize_t dims[H5S_MAX_RANK]; + herr_t status = -1; + + n = ENVPTR->GetArrayLength(ENVPAR buf); + strs =(char**)HDcalloc((size_t)n, sizeof(char*)); + + if (strs == NULL) { + h5JNIFatalError(env, "H5AreadVL_str: failed to allocate buff for read variable length strings"); + } /* end if */ + else { + status = H5Aread(aid, tid, strs); + + if (status < 0) { + dims[0] = (hsize_t)n; + sid = H5Screate_simple(1, dims, NULL); + H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs); + H5Sclose(sid); + HDfree(strs); + h5JNIFatalError(env, "H5AreadVL_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 H5AreadVL_str */ + +/* + * Class: hdf_hdf5lib_H5 * Method: H5Aget_space * Signature: (J)J */ diff --git a/java/src/jni/h5aImp.h b/java/src/jni/h5aImp.h index 62769fd..f3758eb 100644 --- a/java/src/jni/h5aImp.h +++ b/java/src/jni/h5aImp.h @@ -69,6 +69,24 @@ Java_hdf_hdf5lib_H5_H5Aread /* * Class: hdf_hdf5lib_H5 + * Method: H5AwriteVL + * Signature: (JJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5AwriteVL + (JNIEnv *, jclass, jlong, jlong, jobjectArray); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5AreadVL + * Signature: (JJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5AreadVL + (JNIEnv *, jclass, jlong, jlong, jobjectArray); + +/* + * Class: hdf_hdf5lib_H5 * Method: H5Aget_space * Signature: (J)J */ diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c index 9784055..1d7b823 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -993,96 +993,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double /* * Class: hdf_hdf5lib_H5 - * Method: H5DreadVL - * Signature: (JJJJJ[Ljava/lang/String;)I - */ -JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5DreadVL - (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, "H5DreadVL: buf is NULL"); - } /* end if */ - else { - isVlenStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING); - - if (isVlenStr) - h5badArgument(env, "H5DreadVL: type is not variable length non-string"); - else - status = H5DreadVL_asstr(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 else */ - - return (jint)status; -} /* end Java_hdf_hdf5lib_H5_H5Dread_1VL */ - -herr_t -H5DreadVL_asstr - (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf) -{ - jint i; - jint n; - jstring jstr; - h5str_t h5str; - hvl_t *rdata; - size_t size; - size_t max_len = 0; - herr_t status = -1; - - n = ENVPTR->GetArrayLength(ENVPAR buf); - rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t)); - if (rdata == NULL) { - h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read"); - } /* end if */ - else { - status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata); - - if (status < 0) { - H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); - HDfree(rdata); - h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data"); - } /* end if */ - else { - max_len = 1; - for (i=0; i < n; i++) { - if ((rdata + i)->len > max_len) - max_len = (rdata + i)->len; - } - - size = H5Tget_size(tid) * max_len; - HDmemset(&h5str, 0, sizeof(h5str_t)); - h5str_new(&h5str, 4 * size); - - if (h5str.s == NULL) { - H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); - HDfree(rdata); - h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buf"); - } /* end if */ - else { - for (i=0; i < n; i++) { - h5str.s[0] = '\0'; - h5str_sprintf(&h5str, did, tid, rdata+i, 0); - jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); - ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); - } /* end for */ - h5str_free(&h5str); - - H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); - HDfree(rdata); - } /* end else */ - } /* end else */ - } /* end else */ - - return status; -} - -/* - * Class: hdf_hdf5lib_H5 * Method: H5Dread_string * Signature: (JJJJJ[Ljava/lang/String;)I */ @@ -1218,6 +1128,120 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1string return (jint)status; } /* end Java_hdf_hdf5lib_H5_H5Dwrite_1string */ +/* + * Class: hdf_hdf5lib_H5 + * Method: H5DreadVL + * Signature: (JJJJJ[Ljava/lang/String;)I + */ +JNIEXPORT jint JNICALL +Java_hdf_hdf5lib_H5_H5DreadVL + (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 isStr = 0; + htri_t isVlenStr = 0; + htri_t isComplex = 0; + + if (buf == NULL) { + h5nullArgument(env, "H5DreadVL: buf is NULL"); + } /* end if */ + else { + isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING); + if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { + unsigned i; + int nm = H5Tget_nmembers(mem_type_id); + for(i = 0; i <nm; i++) { + hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i); + isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) || + H5Tdetect_class((hid_t)nested_tid, H5T_VLEN); + H5Tclose(nested_tid); + } + } + else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) { + isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */ + } + if (isStr == 0 || isComplex>0 || isVlenStr) { + status = H5DreadVL_asstr(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); + } + else if (isStr > 0) { + 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 else */ + + return (jint)status; +} /* end Java_hdf_hdf5lib_H5_H5Dread_1VL */ + +herr_t +H5DreadVL_asstr + (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf) +{ + jint i; + jint n; + jstring jstr; + h5str_t h5str; + hvl_t *rdata; + size_t size; + size_t max_len = 0; + herr_t status = -1; + + /* Get size of string array */ + n = ENVPTR->GetArrayLength(ENVPAR buf); + /* we will need to read n number of hvl_t structures */ + rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t)); + if (rdata == NULL) { + h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read"); + } /* end if */ + else { + status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata); + + if (status < 0) { + H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); + HDfree(rdata); + h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data"); + } /* end if */ + else { + /* calculate the largest size of all the hvl_t structures read */ + max_len = 1; + for (i=0; i < n; i++) { + if ((rdata + i)->len > max_len) + max_len = (rdata + i)->len; + } + + /* create one malloc to hold largest element */ + size = H5Tget_size(tid) * max_len; + HDmemset(&h5str, 0, sizeof(h5str_t)); + h5str_new(&h5str, 4 * size); + + if (h5str.s == NULL) { + H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); + HDfree(rdata); + h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buf"); + } /* end if */ + else { + H5T_class_t tclass = H5Tget_class(tid); + /* convert each element to char string */ + for (i=0; i < n; i++) { + h5str.s[0] = '\0'; + h5str_vlsprintf(&h5str, did, tid, rdata+i, 0); + jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); + ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); + } /* end for */ + h5str_free(&h5str); + + H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); + HDfree(rdata); + } /* end else */ + } /* end else */ + } /* end else */ + + return status; +} + /** * Read VLEN data into array of arrays. * Object[] buf contains VL arrays of data points @@ -1433,7 +1457,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref h5str_new(&h5str, 1024); for (i=0; i<n; i++) { h5str.s[0] = '\0'; - h5str_sprintf(&h5str, did, tid, ref_data[i], 0); + h5str_sprintf(&h5str, did, tid, ref_data[i], 0, 0); jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index 9a98202..385bfc7 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -21,6 +21,7 @@ extern "C" { #endif /* __cplusplus */ +#include <jni.h> #include <stdio.h> #include <string.h> #include <stdlib.h> @@ -152,6 +153,100 @@ h5str_append return HDstrcat(str->s, cstr); } /* end h5str_append */ +/** print value of a vlen data point into string. + Return Value: + On success, the total number of characters printed is returned. + On error, a negative number is returned. + */ +size_t +h5str_vlsprintf + (h5str_t *str, hid_t container, hid_t tid, hvl_t *ptr, int expand_data) +{ + unsigned char tmp_uchar = 0; + char tmp_char = 0; + unsigned short tmp_ushort = 0; + short tmp_short = 0; + unsigned int tmp_uint = 0; + int tmp_int = 0; + unsigned long tmp_ulong = 0; + long tmp_long = 0; + unsigned long long tmp_ullong = 0; + long long tmp_llong = 0; + float tmp_float = 0.0; + double tmp_double = 0.0; + long double tmp_ldouble = 0.0; + static char fmt_llong[8], fmt_ullong[8]; + + hid_t mtid = -1; + size_t offset; + size_t nll; + char *this_str; + size_t this_strlen; + int n; + H5T_class_t tclass = H5Tget_class(tid); + size_t size = H5Tget_size(tid); + H5T_sign_t nsign = H5Tget_sign(tid); + int bdata_print = 0; + + if (!str || !ptr) + return 0; + + /* Build default formats for long long types */ + if (!fmt_llong[0]) { + sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH); + sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH); + } /* end if */ + + this_str = NULL; + this_strlen = 0; + + switch (tclass) { + case H5T_COMPOUND: + { + unsigned i; + n = H5Tget_nmembers(tid); + h5str_append(str, " {"); + + for (i = 0; i < n; i++) { + offset = H5Tget_member_offset(tid, i); + mtid = H5Tget_member_type(tid, i); + h5str_sprintf(str, container, mtid, ((char *) (ptr->p)) + offset, ptr->len, expand_data); + if ((i + 1) < n) + h5str_append(str, ", "); + H5Tclose(mtid); + } + h5str_append(str, "} "); + } + break; + case H5T_ARRAY: + { + int rank = 0; + hsize_t i, dims[H5S_MAX_RANK], total_elmts; + h5str_append(str, "[ "); + + mtid = H5Tget_super(tid); + size = H5Tget_size(mtid); + rank = H5Tget_array_ndims(tid); + + H5Tget_array_dims2(tid, dims); + + total_elmts = 1; + for (i = 0; i < rank; i++) + total_elmts *= dims[i]; + + h5str_sprintf(str, container, mtid, ((char *) (ptr->p)), ptr->len, expand_data); + H5Tclose(mtid); + h5str_append(str, " ] "); + } + break; + default: + this_strlen = h5str_sprintf(str, container, tid, ((char *) (ptr->p)), ptr->len, expand_data); + break; + } /* end switch */ + + return this_strlen; +} /* end h5str_vlsprintf */ + /** print value of a data point into string. Return Value: On success, the total number of characters printed is returned. @@ -159,7 +254,7 @@ h5str_append */ size_t h5str_sprintf - (h5str_t *str, hid_t container, hid_t tid, void *ptr, int expand_data) + (h5str_t *str, hid_t container, hid_t tid, void *ptr, int ptr_len, int expand_data) { unsigned char tmp_uchar = 0; char tmp_char = 0; @@ -182,9 +277,8 @@ h5str_sprintf char *this_str; size_t this_strlen; int n; - hvl_t *vlptr; - char *cptr = (char*) ptr; - unsigned char *ucptr = (unsigned char*) ptr; + char *cptr = (char*) (ptr); + unsigned char *ucptr = (unsigned char*) (ptr); H5T_class_t tclass = H5Tget_class(tid); size_t size = H5Tget_size(tid); H5T_sign_t nsign = H5Tget_sign(tid); @@ -206,20 +300,20 @@ h5str_sprintf case H5T_FLOAT: if (sizeof(float) == size) { /* if (H5Tequal(tid, H5T_NATIVE_FLOAT)) */ - HDmemcpy(&tmp_float, ptr, sizeof(float)); + HDmemcpy(&tmp_float, cptr, sizeof(float)); this_str = (char*)HDmalloc(25); sprintf(this_str, "%g", tmp_float); } else if (sizeof(double) == size) { /* if (H5Tequal(tid, H5T_NATIVE_DOUBLE)) */ - HDmemcpy(&tmp_double, ptr, sizeof(double)); + HDmemcpy(&tmp_double, cptr, sizeof(double)); this_str = (char*)HDmalloc(25); sprintf(this_str, "%g", tmp_double); } #if H5_SIZEOF_LONG_DOUBLE !=0 else if (sizeof(long double) == size) { /* if (H5Tequal(tid, H5T_NATIVE_LDOUBLE)) */ - HDmemcpy(&tmp_ldouble, ptr, sizeof(long double)); + HDmemcpy(&tmp_ldouble, cptr, sizeof(long double)); this_str = (char*)HDmalloc(27); sprintf(this_str, "%Lf", tmp_ldouble); } @@ -256,13 +350,13 @@ h5str_sprintf if (sizeof(char) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_UCHAR)) */ - HDmemcpy(&tmp_uchar, ptr, sizeof(unsigned char)); + HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char)); this_str = (char*)HDmalloc(7); sprintf(this_str, "%u", tmp_uchar); } else { /* if (H5Tequal(tid, H5T_NATIVE_SCHAR)) */ - HDmemcpy(&tmp_char, ptr, sizeof(char)); + HDmemcpy(&tmp_char, cptr, sizeof(char)); this_str = (char*)HDmalloc(7); sprintf(this_str, "%hhd", tmp_char); } @@ -270,13 +364,13 @@ h5str_sprintf else if (sizeof(int) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_UINT)) */ - HDmemcpy(&tmp_uint, ptr, sizeof(unsigned int)); + HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int)); this_str = (char*)HDmalloc(14); sprintf(this_str, "%u", tmp_uint); } else { /* if (H5Tequal(tid, H5T_NATIVE_INT)) */ - HDmemcpy(&tmp_int, ptr, sizeof(int)); + HDmemcpy(&tmp_int, cptr, sizeof(int)); this_str = (char*)HDmalloc(14); sprintf(this_str, "%d", tmp_int); } @@ -284,13 +378,13 @@ h5str_sprintf else if (sizeof(short) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_USHORT)) */ - HDmemcpy(&tmp_ushort, ptr, sizeof(unsigned short)); + HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short)); this_str = (char*)HDmalloc(9); sprintf(this_str, "%u", tmp_ushort); } else { /* if (H5Tequal(tid, H5T_NATIVE_SHORT)) */ - HDmemcpy(&tmp_short, ptr, sizeof(short)); + HDmemcpy(&tmp_short, cptr, sizeof(short)); this_str = (char*)HDmalloc(9); sprintf(this_str, "%d", tmp_short); } @@ -298,13 +392,13 @@ h5str_sprintf else if (sizeof(long) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_ULONG)) */ - HDmemcpy(&tmp_ulong, ptr, sizeof(unsigned long)); + HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long)); this_str = (char*)HDmalloc(23); sprintf(this_str, "%lu", tmp_ulong); } else { /* if (H5Tequal(tid, H5T_NATIVE_LONG)) */ - HDmemcpy(&tmp_long, ptr, sizeof(long)); + HDmemcpy(&tmp_long, cptr, sizeof(long)); this_str = (char*)HDmalloc(23); sprintf(this_str, "%ld", tmp_long); } @@ -312,13 +406,13 @@ h5str_sprintf else if (sizeof(long long) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_ULLONG)) */ - HDmemcpy(&tmp_ullong, ptr, sizeof(unsigned long long)); + HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long)); this_str = (char*)HDmalloc(25); sprintf(this_str, fmt_ullong, tmp_ullong); } else { /* if (H5Tequal(tid, H5T_NATIVE_LLONG)) */ - HDmemcpy(&tmp_llong, ptr, sizeof(long long)); + HDmemcpy(&tmp_llong, cptr, sizeof(long long)); this_str = (char*)HDmalloc(25); sprintf(this_str, fmt_llong, tmp_llong); } @@ -333,8 +427,8 @@ h5str_sprintf for (i = 0; i < n; i++) { offset = H5Tget_member_offset(tid, i); mtid = H5Tget_member_type(tid, i); - h5str_sprintf(str, container, mtid, cptr + offset, expand_data); - if (i < n - 1) + h5str_sprintf(str, container, mtid, cptr + offset, ptr_len, expand_data); + if ((i + 1) < n) h5str_append(str, ", "); H5Tclose(mtid); } @@ -344,7 +438,7 @@ h5str_sprintf case H5T_ENUM: { char enum_name[1024]; - if (H5Tenum_nameof(tid, ptr, enum_name, sizeof enum_name) >= 0) { + if (H5Tenum_nameof(tid, cptr, enum_name, sizeof enum_name) >= 0) { h5str_append(str, enum_name); } else { @@ -363,7 +457,7 @@ h5str_sprintf } break; case H5T_REFERENCE: - if (h5str_is_zero(ptr, size)) { + if (h5str_is_zero(cptr, size)) { h5str_append(str, "NULL"); } else { @@ -379,9 +473,9 @@ h5str_sprintf H5S_sel_type region_type; /* get name of the dataset the region reference points to using H5Rget_name */ - region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, ptr); + region_obj = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, cptr); if (region_obj >= 0) { - region = H5Rget_region(container, H5R_DATASET_REGION, ptr); + region = H5Rget_region(container, H5R_DATASET_REGION, cptr); if (region >= 0) { if(expand_data) { region_type = H5Sget_select_type(region); @@ -393,7 +487,7 @@ h5str_sprintf } } else { - if(H5Rget_name(region_obj, H5R_DATASET_REGION, ptr, (char*)ref_name, 1024) >= 0) { + if(H5Rget_name(region_obj, H5R_DATASET_REGION, cptr, (char*)ref_name, 1024) >= 0) { h5str_append(str, ref_name); } @@ -424,7 +518,7 @@ h5str_sprintf hid_t obj; this_str = (char*)HDmalloc(64); - obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, ptr); + obj = H5Rdereference2(container, H5P_DEFAULT, H5R_OBJECT, cptr); H5Oget_info2(obj, &oi, H5O_INFO_ALL); /* Print object data and close object */ @@ -450,31 +544,30 @@ h5str_sprintf total_elmts *= dims[i]; for (i = 0; i < total_elmts; i++) { - h5str_sprintf(str, container, mtid, cptr + i * size, expand_data); - if (i < total_elmts - 1) + h5str_sprintf(str, container, mtid, cptr + i * size, ptr_len, expand_data); + if ((i + 1) < total_elmts) h5str_append(str, ", "); } H5Tclose(mtid); - h5str_append(str, "] "); + h5str_append(str, " ] "); } break; case H5T_VLEN: - { - unsigned int i; - mtid = H5Tget_super(tid); - size = H5Tget_size(mtid); - - vlptr = (hvl_t *) cptr; - - nll = vlptr->len; - for (i = 0; i < (int)nll; i++) { - h5str_sprintf(str, container, mtid, ((char *) (vlptr->p)) + i * size, expand_data); - if (i < (int)nll - 1) - h5str_append(str, ", "); + { + unsigned int i; + mtid = H5Tget_super(tid); + size = H5Tget_size(mtid); + + h5str_append(str, "{"); + for (i = 0; i < (int)ptr_len; i++) { + h5str_sprintf(str, container, mtid, cptr + i * size, ptr_len, expand_data); + if ((i + 1) < (int)ptr_len) + h5str_append(str, ", "); + } + H5Tclose(mtid); + h5str_append(str, "}"); } - H5Tclose(mtid); - } - break; + break; default: { @@ -563,7 +656,7 @@ h5str_print_region_data_blocks if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) { if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) { for (numindex = 0; numindex < numelem; numindex++) { - h5str_sprintf(str, region_id, type_id, ((char*)region_buf + numindex * type_size), 1); + h5str_sprintf(str, region_id, type_id, ((char*)region_buf + numindex * type_size), 0, 1); if (numindex + 1 < numelem) h5str_append(str, ", "); @@ -763,7 +856,7 @@ h5str_print_region_data_points for (jndx = 0; jndx < npoints; jndx++) { if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) { - h5str_sprintf(str, region_id, type_id, ((char*)region_buf + jndx * type_size), 1); + h5str_sprintf(str, region_id, type_id, ((char*)region_buf + jndx * type_size), 0, 1); if (jndx + 1 < npoints) h5str_append(str, ", "); @@ -1883,7 +1976,7 @@ h5tools_dump_simple_data /* Render the data element*/ h5str_new(&buffer, 32 * size); - bytes_in = h5str_sprintf(&buffer, container, type, memref, 1); + bytes_in = h5str_sprintf(&buffer, container, type, memref, 0, 1); if(i > 0) { HDfprintf(stream, ", "); if (line_count >= H5TOOLS_TEXT_BLOCK) { @@ -1909,116 +2002,6 @@ h5tools_dump_simple_data /* * Class: hdf_hdf5lib_H5 - * Method: H5AwriteVL - * Signature: (JJ[Ljava/lang/String;)I - */ -JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5AwriteVL - (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) -{ - herr_t status = -1; - char **wdata; - jsize size; - jint i; - - size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf); - - wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*)); - if (!wdata) { - h5JNIFatalError(env, "H5AwriteVL: 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); - } /* end if */ - } /* end if */ - - ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); - ENVPTR->DeleteLocalRef(ENVPAR obj); - } /* end if */ - } /* end for (i = 0; i < size; ++i) */ - - status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, wdata); - - 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 (jint)status; -} /* end Java_hdf_hdf5lib_H5_H5AwriteVL */ - -/* - * Class: hdf_hdf5lib_H5 - * Method: H5AreadVL - * Signature: (JJ[Ljava/lang/String;)I - */ -JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5AreadVL - (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) -{ - herr_t status = -1; - jstring jstr; - char **strs; - int i, n; - hid_t sid; - hsize_t dims[H5S_MAX_RANK]; - - n = ENVPTR->GetArrayLength(ENVPAR buf); - - strs =(char **)HDmalloc((size_t)n * sizeof(char *)); - if (strs == NULL) { - h5JNIFatalError( env, "H5AreadVL: failed to allocate buff for read variable length strings"); - } /* end if */ - else { - status = H5Aread(attr_id, mem_type_id, strs); - if (status < 0) { - dims[0] = (hsize_t)n; - sid = H5Screate_simple(1, dims, NULL); - H5Dvlen_reclaim(mem_type_id, sid, H5P_DEFAULT, strs); - H5Sclose(sid); - HDfree(strs); - h5JNIFatalError(env, "H5AreadVL: 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); - HDfree (strs[i]); - } /* end for */ - - /* - for repeatedly reading an attribute 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 "free(strs[i])" to free individual strings - after it is done. - H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs); - */ - - HDfree(strs); - } /* end else */ - } /* end else */ - return status; -} /* end Java_hdf_hdf5lib_H5_H5AreadVL */ - -/* - * Class: hdf_hdf5lib_H5 * Method: H5AreadComplex * Signature: (JJ[Ljava/lang/String;)I */ @@ -2059,7 +2042,7 @@ Java_hdf_hdf5lib_H5_H5AreadComplex else { for (i = 0; i < n; i++) { h5str.s[0] = '\0'; - h5str_sprintf(&h5str, attr_id, mem_type_id, rdata + ((size_t)i * size), 0); + h5str_sprintf(&h5str, attr_id, mem_type_id, rdata + ((size_t)i * size), 0, 0); jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); } /* end for */ diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h index 434a107..c6b41d2 100644 --- a/java/src/jni/h5util.h +++ b/java/src/jni/h5util.h @@ -39,7 +39,8 @@ extern void h5str_new (h5str_t *str, size_t len); extern void h5str_free (h5str_t *str); extern void h5str_resize (h5str_t *str, size_t new_len); extern char* h5str_append (h5str_t *str, const char* cstr); -extern size_t h5str_sprintf(h5str_t *str, hid_t container, hid_t tid, void *buf, int expand_data); +extern size_t h5str_vlsprintf(h5str_t *str, hid_t container, hid_t tid, hvl_t *buf, int expand_data); +extern size_t h5str_sprintf(h5str_t *str, hid_t container, hid_t tid, void *buf, int ptrlen, int expand_data); extern void h5str_array_free(char **strs, size_t len); extern int h5str_dump_simple_dset(FILE *stream, hid_t dset, int binary_order); extern int h5str_dump_region_blocks_data(h5str_t *str, hid_t region, hid_t region_obj); @@ -47,24 +48,6 @@ extern int h5str_dump_region_points_data(h5str_t *str, hid_t region, hid_t r /* * Class: hdf_hdf5lib_H5 - * Method: H5AwriteVL - * Signature: (JJ[Ljava/lang/String;)I - */ -JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5AwriteVL - (JNIEnv *, jclass, jlong, jlong, jobjectArray); - -/* - * Class: hdf_hdf5lib_H5 - * Method: H5AreadVL - * Signature: (JJ[Ljava/lang/String;)I - */ -JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5AreadVL - (JNIEnv *, jclass, jlong, jlong, jobjectArray); - -/* - * Class: hdf_hdf5lib_H5 * Method: H5AreadComplex * Signature: (JJ[Ljava/lang/String;)I */ |