mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-04-24 17:51:25 +08:00
Merge pull request #1120 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '4c1e89fba31abb357a05044c3f6a92450dfb753c': Fix attribute Read
This commit is contained in:
Allen Byrne
commit
4095b9260d
@ -1025,8 +1025,11 @@ class ArrayDescriptor {
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NTsize = 8;
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}
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else if (css.startsWith("Ljava.lang.String")) {
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NT = 'L';
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className = "java.lang.String";
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NTsize = 1;
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throw new HDF5JavaException(new String(
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"ArrayDesciptor: Error: String array not supported yet"));
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"ArrayDesciptor: Warning: String array not fully supported yet"));
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}
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else {
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/*
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@ -49,6 +49,10 @@ extern jobject visit_callback;
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/* Local Prototypes */
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/********************/
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static herr_t H5AwriteVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
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static herr_t H5AwriteVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
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static herr_t H5AreadVL_asstr (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
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static herr_t H5AreadVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectArray buf);
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static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *op_data);
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@ -178,7 +182,6 @@ Java_hdf_hdf5lib_H5_H5Aread
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} /* end if */
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else {
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status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP);
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if (status < 0) {
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ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
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h5libraryError(env);
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@ -192,6 +195,323 @@ Java_hdf_hdf5lib_H5_H5Aread
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return (jint)status;
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} /* end Java_hdf_hdf5lib_H5_H5Aread */
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/*
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* Class: hdf_hdf5lib_H5
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* Method: H5AwriteVL
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* Signature: (JJ[Ljava/lang/String;)I
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*/
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JNIEXPORT jint JNICALL
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Java_hdf_hdf5lib_H5_H5AwriteVL
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(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
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{
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herr_t status = -1;
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htri_t isStr = 0;
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htri_t isVlenStr = 0;
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htri_t isComplex = 0;
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if (buf == NULL) {
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h5nullArgument(env, "H5AwriteVL: buf is NULL");
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} /* end if */
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else {
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isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
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if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) {
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unsigned i;
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int nm = H5Tget_nmembers(mem_type_id);
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for(i = 0; i <nm; i++) {
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hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i);
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isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) ||
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H5Tdetect_class((hid_t)nested_tid, H5T_VLEN);
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H5Tclose(nested_tid);
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}
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}
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else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) {
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isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
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}
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if (isStr == 0 || isComplex>0 || isVlenStr) {
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status = H5AwriteVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
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}
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else if (isStr > 0) {
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status = H5AwriteVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
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}
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} /* end else */
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return (jint)status;
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} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */
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herr_t
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H5AwriteVL_str
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(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
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{
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herr_t status = -1;
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char **wdata;
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jsize size;
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jint i;
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size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
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wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
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if (!wdata) {
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h5JNIFatalError(env, "H5AwriteVL_str: cannot allocate buffer");
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} /* end if */
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else {
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HDmemset(wdata, 0, (size_t)size * sizeof(char*));
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for (i = 0; i < size; ++i) {
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jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) buf, i);
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if (obj != 0) {
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jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
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const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
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if (utf8) {
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wdata[i] = (char*)HDmalloc((size_t)length + 1);
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if (wdata[i]) {
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HDmemset(wdata[i], 0, ((size_t)length + 1));
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HDstrncpy(wdata[i], utf8, (size_t)length);
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} /* end if */
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} /* end if */
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ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
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ENVPTR->DeleteLocalRef(ENVPAR obj);
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} /* end if */
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} /* end for (i = 0; i < size; ++i) */
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status = H5Awrite((hid_t)aid, (hid_t)tid, wdata);
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for (i = 0; i < size; i++) {
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if(wdata[i]) {
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HDfree(wdata[i]);
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} /* end if */
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} /* end for */
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HDfree(wdata);
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if (status < 0)
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h5libraryError(env);
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} /* end else */
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return (jint)status;
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}
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herr_t
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H5AwriteVL_asstr
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(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
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{
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char **strs;
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jstring jstr;
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jint i;
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jint n;
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hid_t sid;
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hsize_t dims[H5S_MAX_RANK];
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herr_t status = -1;
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n = ENVPTR->GetArrayLength(ENVPAR buf);
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strs =(hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
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if (strs == NULL) {
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h5JNIFatalError(env, "H5AwriteVL_asstr: failed to allocate buff for read variable length strings");
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} /* end if */
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else {
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status = H5Awrite(aid, tid, strs);
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if (status < 0) {
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dims[0] = (hsize_t)n;
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sid = H5Screate_simple(1, dims, NULL);
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H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
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H5Sclose(sid);
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HDfree(strs);
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h5JNIFatalError(env, "H5AwriteVL_str: failed to read variable length strings");
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} /* end if */
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else {
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for (i=0; i < n; i++) {
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jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
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ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
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H5free_memory (strs[i]);
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} /* end for */
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/*
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for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings,
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H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect
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free space in time. Instead, use "H5free_memory(strs[i])" above to free individual strings
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after it is done.
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H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs);
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*/
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HDfree(strs);
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} /* end else */
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} /* end else */
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return status;
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} /* end H5AwriteVL_str */
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/*
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* Class: hdf_hdf5lib_H5
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* Method: H5AreadVL
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* Signature: (JJJJJ[Ljava/lang/String;)I
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*/
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JNIEXPORT jint JNICALL
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Java_hdf_hdf5lib_H5_H5AreadVL
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(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
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{
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herr_t status = -1;
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htri_t isStr = 0;
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htri_t isVlenStr = 0;
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htri_t isComplex = 0;
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if (buf == NULL) {
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h5nullArgument(env, "H5AreadVL: buf is NULL");
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} /* end if */
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else {
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isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
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if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) {
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unsigned i;
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int nm = H5Tget_nmembers(mem_type_id);
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for(i = 0; i <nm; i++) {
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hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i);
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isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) ||
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H5Tdetect_class((hid_t)nested_tid, H5T_VLEN);
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H5Tclose(nested_tid);
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}
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}
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else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) {
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isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
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}
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if (isStr == 0 || isComplex>0 || isVlenStr) {
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status = H5AreadVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
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}
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else if (isStr > 0) {
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status = H5AreadVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
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}
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} /* end else */
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return (jint)status;
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} /* end Java_hdf_hdf5lib_H5_H5Aread_1VL */
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herr_t
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H5AreadVL_asstr
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(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
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{
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jint i;
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jint n;
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hid_t sid;
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jstring jstr;
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h5str_t h5str;
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hvl_t *rdata;
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hsize_t dims[H5S_MAX_RANK];
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size_t size;
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size_t max_len = 0;
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herr_t status = -1;
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/* Get size of string array */
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n = ENVPTR->GetArrayLength(ENVPAR buf);
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/* we will need to read n number of hvl_t structures */
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rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
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if (rdata == NULL) {
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h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buff for read");
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} /* end if */
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else {
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status = H5Aread(aid, tid, rdata);
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if (status < 0) {
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dims[0] = (hsize_t)n;
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sid = H5Screate_simple(1, dims, NULL);
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H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
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H5Sclose(sid);
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HDfree(rdata);
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h5JNIFatalError(env, "H5AreadVL_asstr: failed to read data");
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} /* end if */
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else {
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/* calculate the largest size of all the hvl_t structures read */
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max_len = 1;
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for (i=0; i < n; i++) {
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if ((rdata + i)->len > max_len)
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max_len = (rdata + i)->len;
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}
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/* create one malloc to hold largest element */
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size = H5Tget_size(tid) * max_len;
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HDmemset(&h5str, 0, sizeof(h5str_t));
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h5str_new(&h5str, 4 * size);
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if (h5str.s == NULL) {
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dims[0] = (hsize_t)n;
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sid = H5Screate_simple(1, dims, NULL);
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H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
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H5Sclose(sid);
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HDfree(rdata);
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h5JNIFatalError(env, "H5AreadVL_asstr: failed to allocate buf");
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} /* end if */
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else {
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H5T_class_t tclass = H5Tget_class(tid);
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/* convert each element to char string */
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for (i=0; i < n; i++) {
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h5str.s[0] = '\0';
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h5str_vlsprintf(&h5str, aid, tid, rdata+i, 0);
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jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
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ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
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} /* end for */
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h5str_free(&h5str);
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dims[0] = (hsize_t)n;
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sid = H5Screate_simple(1, dims, NULL);
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H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata);
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H5Sclose(sid);
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HDfree(rdata);
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} /* end else */
|
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} /* end else */
|
||||
} /* end else */
|
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|
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return status;
|
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}
|
||||
|
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herr_t
|
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H5AreadVL_str
|
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(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
|
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{
|
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char **strs;
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jstring jstr;
|
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jint i;
|
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jint n;
|
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hid_t sid;
|
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hsize_t dims[H5S_MAX_RANK];
|
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herr_t status = -1;
|
||||
|
||||
n = ENVPTR->GetArrayLength(ENVPAR buf);
|
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strs =(char**)HDcalloc((size_t)n, sizeof(char*));
|
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|
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if (strs == NULL) {
|
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h5JNIFatalError(env, "H5AreadVL_str: failed to allocate buff for read variable length strings");
|
||||
} /* end if */
|
||||
else {
|
||||
status = H5Aread(aid, tid, strs);
|
||||
|
||||
if (status < 0) {
|
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dims[0] = (hsize_t)n;
|
||||
sid = H5Screate_simple(1, dims, NULL);
|
||||
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
|
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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);
|
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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
|
||||
|
||||
@ -67,6 +67,24 @@ JNIEXPORT jint JNICALL
|
||||
Java_hdf_hdf5lib_H5_H5Aread
|
||||
(JNIEnv *, jclass, jlong, jlong, jbyteArray);
|
||||
|
||||
/*
|
||||
* 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
|
||||
|
||||
@ -991,120 +991,6 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double
|
||||
return (jint)status;
|
||||
} /* end 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 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;
|
||||
}
|
||||
|
||||
/*
|
||||
* Class: hdf_hdf5lib_H5
|
||||
* Method: H5Dread_string
|
||||
@ -1242,6 +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
|
||||
|
||||
@ -2000,116 +2000,6 @@ h5tools_dump_simple_data
|
||||
* Functions designed to workaround issues with the Java-C interface
|
||||
*/
|
||||
|
||||
/*
|
||||
* 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
|
||||
|
||||
@ -46,24 +46,6 @@ 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);
|
||||
extern int h5str_dump_region_points_data(h5str_t *str, hid_t region, hid_t region_obj);
|
||||
|
||||
/*
|
||||
* 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
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user