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authorAllen Byrne <byrn@hdfgroup.org>2018-12-10 22:52:34 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2018-12-10 22:52:34 (GMT)
commit7ffba76bc372cec11739b2afa578138129876e7e (patch)
treec147a2e6217e7c349d031010a17d63c56279c7e4
parent6f52793adcd5a14aa63731e3c33c9737b5a04d16 (diff)
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HDFVIEW-4 add datatype read to H5A like H5D
-rw-r--r--java/src/hdf/hdf5lib/H5.java377
-rw-r--r--java/src/jni/h5aImp.c1183
-rw-r--r--java/src/jni/h5aImp.h160
-rw-r--r--java/src/jni/h5dImp.h2
-rw-r--r--java/test/testfiles/JUnit-TestH5Edefault.txt26
5 files changed, 1548 insertions, 200 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index f9f9b65..8b40e2c 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -852,7 +852,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public static long H5Aget_space(long attr_id) throws HDF5LibraryException {
+ public static long H5Aget_space(long attr_id) throws HDF5LibraryException
+ {
long id = _H5Aget_space(attr_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aget_space add {}", id);
@@ -888,7 +889,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public static long H5Aget_type(long attr_id) throws HDF5LibraryException {
+ public static long H5Aget_type(long attr_id) throws HDF5LibraryException
+ {
long id = _H5Aget_type(attr_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aget_type add {}", id);
@@ -918,8 +920,9 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - Name is null.
**/
- public static long H5Aopen(long obj_id, String attr_name, long aapl_id) throws HDF5LibraryException,
- NullPointerException {
+ public static long H5Aopen(long obj_id, String attr_name, long aapl_id)
+ throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen(obj_id, attr_name, aapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen add {}", id);
@@ -959,7 +962,8 @@ public class H5 implements java.io.Serializable {
* - Name is null.
**/
public static long H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long aapl_id,
- long lapl_id) throws HDF5LibraryException, NullPointerException {
+ long lapl_id) throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen_by_idx add {}", id);
@@ -994,7 +998,8 @@ public class H5 implements java.io.Serializable {
* - obj_name is null.
**/
public static long H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, long lapl_id)
- throws HDF5LibraryException, NullPointerException {
+ throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen_by_name add {}", id);
@@ -1015,8 +1020,10 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of an attribute to read.
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
- * @param buf
- * IN: Buffer for data to be read.
+ * @param obj
+ * Buffer to store data read from the file.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
@@ -1025,9 +1032,19 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - data buffer is null.
**/
- public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] buf)
+ public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ return H5Aread(attr_id, mem_type_id, obj, true);
+ }
+
/**
* H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with
* mem_type_id. The entire attribute is read into data object from the file.
@@ -1038,31 +1055,146 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Object for data to be read.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
+ * @exception HDF5Exception
+ * - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data buffer is null. See public synchronized static native int H5Aread( )
**/
- public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception,
- NullPointerException {
- HDFArray theArray = new HDFArray(obj);
- byte[] buf = theArray.emptyBytes();
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ int status = -1;
+ boolean is1D = false;
- // This will raise an exception if there is an error
- int status = H5Aread(attr_id, mem_type_id, buf);
+ Class dataClass = obj.getClass();
+ if (!dataClass.isArray()) {
+ throw (new HDF5JavaException("H5Aread: data is not an array"));
+ }
- // No exception: status really ought to be OK
- if (status >= 0) {
- obj = theArray.arrayify(buf);
+ String cname = dataClass.getName();
+ is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
+ char dname = cname.charAt(cname.lastIndexOf("[") + 1);
+ log.trace("H5Aread: cname={} is1D={} dname={}", cname, is1D, dname);
+
+ if (is1D && (dname == 'B')) {
+ log.trace("H5Aread_dname_B");
+ status = H5Aread(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'S')) {
+ log.trace("H5Aread_dname_S");
+ status = H5Aread_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'I')) {
+ log.trace("H5Aread_dname_I");
+ status = H5Aread_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'J')) {
+ log.trace("H5Aread_dname_J");
+ status = H5Aread_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'F')) {
+ log.trace("H5Aread_dname_F");
+ status = H5Aread_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'D')) {
+ log.trace("H5Aread_dname_D");
+ status = H5Aread_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
+ }
+ else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && (is1D && (dataClass.getComponentType() == String.class))) || H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+ log.trace("H5Aread_reg_ref");
+ status = H5Aread_reg_ref(attr_id, mem_type_id, (String[]) obj);
+ }
+ else if (is1D && (dataClass.getComponentType() == String.class)) {
+ log.trace("H5Aread_string type");
+ status = H5Aread_string(attr_id, mem_type_id, (String[]) obj);
+ }
+ else {
+ // Create a data buffer to hold the data into a Java Array
+ HDFArray theArray = new HDFArray(obj);
+ byte[] buf = theArray.emptyBytes();
+ log.trace("H5Aread_else");
+
+ // This will raise an exception if there is an error
+ status = H5Aread(attr_id, mem_type_id, buf, isCriticalPinning);
+
+ // No exception: status really ought to be OK
+ if (status >= 0) {
+ obj = theArray.arrayify(buf);
+ }
+
+ // clean up these: assign 'null' as hint to gc()
+ buf = null;
+ theArray = null;
}
return status;
}
- public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, String[] buf)
+ public synchronized static native int H5Aread_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_double(long attr_id, long mem_type_id, double[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_double(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_float(long attr_id, long mem_type_id, float[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_float(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_int(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_long(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_reg_ref_data(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_short(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf)
@@ -1123,7 +1255,9 @@ public class H5 implements java.io.Serializable {
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
* @param buf
- * IN: Data to be written.
+ * IN: Buffer with data to be written to the file.
+ * @param isCriticalPinning
+ * IN: request lock on data reference.
*
* @return a non-negative value if successful
*
@@ -1132,9 +1266,21 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - data is null.
**/
- public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
+ public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite(attr_id, mem_type_id, obj, true);
+ }
+
/**
* H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with
* mem_type_id. The entire attribute is written from data object to the file.
@@ -1145,28 +1291,140 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Data object to be written.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
+ * @exception HDF5Exception
+ * - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
- * - data object is null. See public synchronized static native int H5Awrite(int attr_id, int
- * mem_type_id, byte[] buf);
+ * - data object is null
**/
- public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj)
- throws HDF5Exception, NullPointerException
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
{
- HDFArray theArray = new HDFArray(obj);
- byte[] buf = theArray.byteify();
+ int status = -1;
+ boolean is1D = false;
- int retVal = H5Awrite(attr_id, mem_type_id, buf);
- buf = null;
- theArray = null;
- return retVal;
+ Class dataClass = obj.getClass();
+ if (!dataClass.isArray()) {
+ throw (new HDF5JavaException("H5Dwrite: data is not an array"));
+ }
+
+ String cname = dataClass.getName();
+ is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
+ char dname = cname.charAt(cname.lastIndexOf("[") + 1);
+
+ if (is1D && (dname == 'B')) {
+ status = H5Awrite(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'S')) {
+ status = H5Awrite_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'I')) {
+ status = H5Awrite_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'J')) {
+ status = H5Awrite_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'F')) {
+ status = H5Awrite_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'D')) {
+ status = H5Awrite_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dataClass.getComponentType() == String.class)) {
+ log.trace("H5Dwrite_string type");
+ status = H5Awrite_string(attr_id, mem_type_id, (String[]) obj);
+ }
+ else {
+ HDFArray theArray = new HDFArray(obj);
+ byte[] buf = theArray.byteify();
+
+ status = H5Awrite(attr_id, mem_type_id, buf);
+ buf = null;
+ theArray = null;
+ }
+
+ return status;
+ }
+
+ public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_double(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_float(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_int(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_long(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_short(attr_id, mem_type_id, buf, true);
}
- public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, String[] buf)
+ public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ /**
+ * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from
+ * the application memory buffer buf into the file.
+ *
+ * ---- contributed by Rosetta Biosoftware
+ *
+ * @param attr_id
+ * Identifier of the attribute read from.
+ * @param mem_type_id
+ * Identifier of the memory datatype.
+ * @param buf
+ * Buffer with data to be written to the file.
+ *
+ * @return a non-negative value if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+
+ public synchronized static native int H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
/**
@@ -1614,8 +1872,8 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException,
- NullPointerException {
+ public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Dopen2(loc_id, name, dapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dopen add {}", id);
@@ -1664,12 +1922,14 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true);
}
@@ -1703,7 +1963,8 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException,
- NullPointerException {
+ NullPointerException
+ {
int status = -1;
boolean is1D = false;
@@ -1734,7 +1995,8 @@ public class H5 implements java.io.Serializable {
}
else if (is1D && (dname == 'J')) {
log.trace("H5Dread_dname_J");
- status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj);
+ status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj,
+ isCriticalPinning);
}
else if (is1D && (dname == 'F')) {
log.trace("H5Dread_dname_F");
@@ -1783,7 +2045,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1792,7 +2055,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1801,7 +2065,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1810,7 +2075,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1825,7 +2091,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1929,12 +2196,14 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true);
}
@@ -1968,7 +2237,8 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException,
- NullPointerException {
+ NullPointerException
+ {
int status = -1;
boolean is1D = false;
@@ -2031,7 +2301,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2040,7 +2311,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2049,7 +2321,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2058,7 +2331,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2067,7 +2341,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index aba2240..68f203e 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -60,6 +60,94 @@ static herr_t H5AreadVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectAr
static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *cb_data);
+/********************/
+/* 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
@@ -129,36 +217,129 @@ Java_hdf_hdf5lib_H5__1H5Aopen_1idx
return (jlong)attr_id;
} /* end Java_hdf_hdf5lib_H5__1H5Aopen_1idx */
+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: H5Aread
+ * Signature: (JJ[BZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jbyte *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument( env,"H5Aread: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread: 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, "H5Aread: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_BYTE_ARRAY();
+
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_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_H5Aread */
+
/*
* Class: hdf_hdf5lib_H5
* Method: H5Awrite
- * Signature: (JJ[B)I
+ * Signature: (JJ[BZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Awrite
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf)
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf, jboolean isCriticalPinning)
{
herr_t status = -1;
- jbyte *byteP;
+ jbyte *buffP;
jboolean isCopy;
+ htri_t data_class;
if (buf == NULL) {
h5nullArgument( env,"H5Awrite: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite: buf does not support variable length type");
+ } /* end else if */
else {
- byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
- if (byteP == NULL) {
- h5JNIFatalError(env,"H5Awrite: buf is not pinned");
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Awrite: H5Tdetect_variable_str() failed");
} /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite: buf does not support variable length type");
+ } /* end else if */
else {
- status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP);
+ PIN_BYTE_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- /* free the buffer without copying back */
- ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
+ UNPIN_BYTE_ARRAY(JNI_ABORT); /* no need to update buffer */
- if (status < 0)
- h5libraryError(env);
- }
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
} /* end else */
return (jint)status;
@@ -166,190 +347,653 @@ Java_hdf_hdf5lib_H5_H5Awrite
/*
* Class: hdf_hdf5lib_H5
- * Method: H5Aread
- * Signature: (JJ[B)I
+ * Method: H5Aread_short
+ * Signature: (JJ[SZ)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Aread
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf)
+Java_hdf_hdf5lib_H5_H5Aread_1short
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jshortArray buf, jboolean isCriticalPinning)
{
herr_t status = -1;
- jbyte *byteP;
+ jshort *buffP;
jboolean isCopy;
+ htri_t data_class;
if (buf == NULL) {
- h5nullArgument( env,"H5Aread: buf is NULL");
+ h5nullArgument(env, "H5Aread_short: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_short: buf does not support variable length type");
+ } /* end else if */
else {
- byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
- if (byteP == NULL) {
- h5JNIFatalError( env,"H5Aread: buf is not pinned");
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_short: H5Tdetect_variable_str() failed");
} /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_short: buf does not support variable length type");
+ } /* end else 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);
+ PIN_SHORT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_short: buf not pinned");
} /* end if */
- else {
- ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, 0);
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_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_H5Aread */
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1short */
/*
* Class: hdf_hdf5lib_H5
- * Method: H5AwriteVL
- * Signature: (JJ[Ljava/lang/String;)I
+ * Method: H5Awrite_short
+ * Signature: (JJ[SZ)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AwriteVL
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
+Java_hdf_hdf5lib_H5_H5Awrite_1short
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jshortArray buf, jboolean isCriticalPinning)
{
- herr_t status = -1;
- htri_t isStr = 0;
- htri_t isVlenStr = 0;
- htri_t isComplex = 0;
+ herr_t status = -1;
+ jshort *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL ) {
+ h5nullArgument(env, "H5Awrite_short: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_short: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_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, "H5Awrite_short: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_short: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_SHORT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_short: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_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_H5Awrite_1short */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1int
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jintArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jint *buffP;
+ jboolean isCopy;
+ htri_t data_class;
if (buf == NULL) {
- h5nullArgument(env, "H5AwriteVL: buf is NULL");
+ h5nullArgument(env, "H5Aread_int: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread_int: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_int: buf does not support variable length type");
+ } /* end else 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);
- }
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_int: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_int: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_INT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_int: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_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_H5Awrite_1VL */
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1int */
-herr_t
-H5AwriteVL_str
- (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1int
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jintArray buf, jboolean isCriticalPinning)
{
- herr_t status = -1;
- char **wdata;
- jsize size;
- jint i;
+ herr_t status = -1;
+ jint *buffP;
+ jboolean isCopy;
+ htri_t data_class;
- size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_int: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_int: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_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, "H5Awrite_int: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_int: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_INT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_int: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
- if (!wdata) {
- h5JNIFatalError(env, "H5AwriteVL_str: cannot allocate buffer");
+ UNPIN_INT_ARRAY(JNI_ABORT);
+
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1int */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1long
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jlongArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jlong *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Aread_long: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread_long: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_long: buf does not support variable length type");
+ } /* end else 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);
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_long: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_long: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_LONG_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_long: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- 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 */
+ 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 */
- ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
- ENVPTR->DeleteLocalRef(ENVPAR obj);
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1long */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1long
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jlongArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jlong *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_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, "H5Awrite_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, "H5Awrite_long: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_long: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_LONG_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_long: buf not pinned");
} /* end if */
- } /* end for (i = 0; i < size; ++i) */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- status = H5Awrite((hid_t)aid, (hid_t)tid, wdata);
+ UNPIN_LONG_ARRAY(JNI_ABORT);
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
- for (i = 0; i < size; i++) {
- if(wdata[i]) {
- HDfree(wdata[i]);
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1long */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1float
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jfloatArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jfloat *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Aread_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, "H5Aread_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, "H5Aread_float: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_float: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_FLOAT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_float: buf not pinned");
} /* end if */
- } /* end for */
- HDfree(wdata);
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- if (status < 0)
- h5libraryError(env);
+ 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_H5Aread_1float */
-herr_t
-H5AwriteVL_asstr
- (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1float
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jfloatArray buf, jboolean isCriticalPinning)
{
- char **strs;
- jstring jstr;
- jint i;
- jint n;
- hid_t sid;
- hsize_t dims[H5S_MAX_RANK];
- herr_t status = -1;
+ herr_t status = -1;
+ jfloat *buffP;
+ jboolean isCopy;
+ htri_t data_class;
- n = ENVPTR->GetArrayLength(ENVPAR buf);
- strs =(hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_float: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_float: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_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, "H5Awrite_float: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_float: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_FLOAT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_float: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- if (strs == NULL) {
- h5JNIFatalError(env, "H5AwriteVL_asstr: failed to allocate buff for read variable length strings");
+ UNPIN_FLOAT_ARRAY(JNI_ABORT);
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1float */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1double
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jdoubleArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jdouble *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Aread_double: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread_double: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_double: buf does not support variable length type");
+ } /* end else if */
else {
- status = H5Awrite(aid, tid, strs);
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_double: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_double: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_DOUBLE_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_double: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- 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");
+ 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_H5Aread_1double */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1double
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jdoubleArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jdouble *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_double: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_double: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_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, "H5Awrite_double: H5Tdetect_variable_str() failed");
} /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_double: buf does not support variable length type");
+ } /* end else if */
else {
- for (i=0; i < n; i++) {
- jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
- ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
- H5free_memory (strs[i]);
+ PIN_DOUBLE_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_double: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_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_H5Awrite_1double */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_string
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1string
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_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, "H5Aread_string: buf is NULL");
+ } /* end if */
+ else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) {
+ h5nullArgument(env, "H5Aread_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, "H5Aread_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, "H5Aread_string: memory allocation failed.");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_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_H5Aread_1string */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_string
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1string
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray j_buf)
+{
+ herr_t status = -1;
+ char *c_buf;
+ jsize str_len;
+ jsize i;
+ jsize n;
+
+ if (j_buf == NULL) {
+ h5nullArgument(env, "H5Awrite_string: buf is NULL");
+ } /* end if */
+ else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) {
+ h5nullArgument(env, "H5Awrite_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, "H5Awrite_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) {
+ HDstrncpy(&c_buf[i * str_len], utf8, str_len);
+ } /* end if */
+
+ ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
+ ENVPTR->DeleteLocalRef(ENVPAR obj);
+ } /* end if */
} /* 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);
- */
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, c_buf);
- HDfree(strs);
+ if (c_buf)
+ HDfree(c_buf);
+ c_buf = NULL;
+
+ if (status < 0) {
+ h5libraryError(env);
+ } /* end if */
} /* end else */
} /* end else */
- return status;
-} /* end H5AwriteVL_str */
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1string */
/*
* Class: hdf_hdf5lib_H5
* Method: H5AreadVL
- * Signature: (JJJJJ[Ljava/lang/String;)I
+ * Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AreadVL
@@ -519,6 +1163,285 @@ H5AreadVL_str
/*
* 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: H5Aread_reg_ref
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_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 aid = (hid_t) attr_id;
+ hid_t tid = (hid_t) mem_type_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, "H5Aread_reg_ref: failed to allocate buff for read");
+ return -1;
+ } /* end if */
+
+ status = H5Aread(aid, tid, ref_data);
+
+ if (status < 0) {
+ HDfree(ref_data);
+ h5JNIFatalError(env, "H5Aread_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, aid, tid, ref_data[i], 0, 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_H5Aread_1reg_1ref */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_reg_ref_data
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref_1data
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
+{
+ herr_t status = -1;
+
+ h5unimplemented(env, "H5Aread_reg_ref_data: not implemented");
+ status = -1;
+
+#ifdef notdef
+ 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 aid = (hid_t) attr_id;
+ hid_t tid = (hid_t) mem_type_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, "H5Aread_reg_ref_data: failed to allocate buff for read");
+ return -1;
+ } /* end if */
+
+ status = H5Aread(aid, tid, ref_data);
+
+ if (status < 0) {
+ HDfree(ref_data);
+ h5JNIFatalError(env, "H5Aread_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);
+#endif
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref_1data */
+
+/*
+ * 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 f3758eb..753a03d 100644
--- a/java/src/jni/h5aImp.h
+++ b/java/src/jni/h5aImp.h
@@ -51,21 +51,120 @@ Java_hdf_hdf5lib_H5__1H5Aopen_1idx
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5Aread
+ * Signature: (JJ[B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread
+ (JNIEnv *, jclass, jlong, jlong, jbyteArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Awrite
* Signature: (JJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Awrite
- (JNIEnv *, jclass, jlong, jlong, jbyteArray);
+ (JNIEnv *, jclass, jlong, jlong, jbyteArray, jboolean);
/*
* Class: hdf_hdf5lib_H5
- * Method: H5Aread
- * Signature: (JJ[B)I
+ * Method: H5Aread_short
+ * Signature: (JJ[SZ)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Aread
- (JNIEnv *, jclass, jlong, jlong, jbyteArray);
+Java_hdf_hdf5lib_H5_H5Aread_1short
+ (JNIEnv*, jclass, jlong, jlong, jshortArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_short
+ * Signature: (JJ[SZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1short
+ (JNIEnv*, jclass, jlong, jlong, jshortArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1int
+ (JNIEnv*, jclass, jlong, jlong, jintArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1int
+ (JNIEnv*, jclass, jlong, jlong, jintArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1long
+ (JNIEnv*, jclass, jlong, jlong, jlongArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1long
+ (JNIEnv*, jclass, jlong, jlong, jlongArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1float
+ (JNIEnv*, jclass, jlong, jlong, jfloatArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1float
+ (JNIEnv*, jclass, jlong, jlong, jfloatArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1double
+ (JNIEnv*, jclass, jlong, jlong, jdoubleArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1double
+ (JNIEnv*, jclass, jlong, jlong, jdoubleArray, jboolean);
+
+/*
+ * 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
@@ -78,12 +177,57 @@ Java_hdf_hdf5lib_H5_H5AwriteVL
/*
* Class: hdf_hdf5lib_H5
- * Method: H5AreadVL
+ * Method: H5Aread_string
* Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AreadVL
- (JNIEnv *, jclass, jlong, jlong, jobjectArray);
+Java_hdf_hdf5lib_H5_H5Aread_1string
+ (JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_string
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1string
+(JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_VLStrings
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1VLStrings
+(JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_VLStrings
+ * Signature: (JJ[B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings
+ (JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_reg_ref
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref
+(JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_reg_ref_data
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref_1data
+ (JNIEnv*, jclass, jlong, jlong, jobjectArray);
/*
* Class: hdf_hdf5lib_H5
diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h
index 1fe71a8..9dffef4 100644
--- a/java/src/jni/h5dImp.h
+++ b/java/src/jni/h5dImp.h
@@ -250,7 +250,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1VLStrings
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_VLStrings
- * Signature: (JJJJJ[BZ)I
+ * Signature: (JJJJJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings
diff --git a/java/test/testfiles/JUnit-TestH5Edefault.txt b/java/test/testfiles/JUnit-TestH5Edefault.txt
index 71d1431..48c6254 100644
--- a/java/test/testfiles/JUnit-TestH5Edefault.txt
+++ b/java/test/testfiles/JUnit-TestH5Edefault.txt
@@ -38,17 +38,20 @@ HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
minor: Unable to open file
#001: (file name) line (number) in H5VL_file_open(): open failed
major: Virtual Object Layer
- minor: Unable to initialize object
- #002: (file name) line (number) in H5VL_native_file_open(): unable to open file
+ minor: Can't open object
+ #002: (file name) line (number) in H5VL__file_open(): open failed
+ major: Virtual Object Layer
+ minor: Can't open object
+ #003: (file name) line (number) in H5VL__native_file_open(): unable to open file
major: File accessibility
minor: Unable to open file
- #003: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
+ #004: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
major: File accessibility
minor: Unable to open file
- #004: (file name) line (number) in H5FD_open(): open failed
+ #005: (file name) line (number) in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
- #005: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
+ #006: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
major: File accessibility
minor: Unable to open file
HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
@@ -57,16 +60,19 @@ HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
minor: Unable to open file
#001: (file name) line (number) in H5VL_file_open(): open failed
major: Virtual Object Layer
- minor: Unable to initialize object
- #002: (file name) line (number) in H5VL_native_file_open(): unable to open file
+ minor: Can't open object
+ #002: (file name) line (number) in H5VL__file_open(): open failed
+ major: Virtual Object Layer
+ minor: Can't open object
+ #003: (file name) line (number) in H5VL__native_file_open(): unable to open file
major: File accessibility
minor: Unable to open file
- #003: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
+ #004: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
major: File accessibility
minor: Unable to open file
- #004: (file name) line (number) in H5FD_open(): open failed
+ #005: (file name) line (number) in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
- #005: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
+ #006: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
major: File accessibility
minor: Unable to open file