diff options
| -rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 377 | ||||
| -rw-r--r-- | java/src/jni/h5aImp.c | 1104 | ||||
| -rw-r--r-- | java/src/jni/h5aImp.h | 151 | ||||
| -rw-r--r-- | java/src/jni/h5dImp.c | 78 | ||||
| -rw-r--r-- | java/src/jni/h5dImp.h | 11 | ||||
| -rw-r--r-- | release_docs/RELEASE.txt | 10 |
6 files changed, 1450 insertions, 281 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 51f1b4a..751528e 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 +1055,143 @@ 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_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 +1252,9 @@ 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 +1263,21 @@ 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 +1288,140 @@ 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 +1869,8 @@ 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 +1919,14 @@ 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 +1960,8 @@ 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 +1992,8 @@ 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 +2042,8 @@ 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 +2052,8 @@ 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 +2062,8 @@ 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); } @@ -1810,22 +2072,21 @@ 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); } public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; - public synchronized static native int H5Dread_reg_ref_data(long dataset_id, long mem_type_id, long mem_space_id, - long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; - public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) 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 +2190,14 @@ 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 +2231,8 @@ 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 +2295,8 @@ 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 +2305,8 @@ 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 +2315,8 @@ 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 +2325,8 @@ 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 +2335,8 @@ 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..e0ec4ca 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 +1163,206 @@ 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: H5Aget_space * Signature: (J)J */ diff --git a/java/src/jni/h5aImp.h b/java/src/jni/h5aImp.h index f3758eb..15cc83e 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 +177,48 @@ 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 diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c index 652c873..79a5d0a 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -1574,84 +1574,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref /* * Class: hdf_hdf5lib_H5 - * Method: H5Dread_reg_ref_data - * Signature: (JJJJJ[Ljava/lang/String;)I - */ -JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data - (JNIEnv *env, jclass clss, - jlong dataset_id, jlong mem_type_id, jlong mem_space_id, - jlong file_space_id, jlong xfer_plist_id, jobjectArray buf) -{ - herr_t status = -1; - h5str_t h5str; - size_t size; - hdset_reg_ref_t *ref_data; - jint i; - jint n; - jstring jstr; - - hid_t region_obj; - H5S_sel_type region_type; - - hid_t region = -1; - hid_t did = (hid_t) dataset_id; - hid_t tid = (hid_t) mem_type_id; - hid_t mem_sid = (hid_t) mem_space_id; - hid_t file_sid = (hid_t) file_space_id; - - n = ENVPTR->GetArrayLength(ENVPAR buf); - size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/ - ref_data = (hdset_reg_ref_t*)HDmalloc(size * (size_t)n); - - if (ref_data == NULL) { - h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to allocate buff for read"); - return -1; - } /* end if */ - - status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data); - - if (status < 0) { - HDfree(ref_data); - h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to read data"); - return -1; - } /* end if */ - - HDmemset(&h5str, 0, sizeof(h5str_t)); - h5str_new(&h5str, 1024); - for (i=0; i<n; i++) { - h5str.s[0] = '\0'; - - /* get name of the dataset the region reference points to using H5Rget_name */ - region_obj = H5Rdereference2(did, H5P_DEFAULT, H5R_DATASET_REGION, ref_data[i]); - if (region_obj >= 0) { - region = H5Rget_region(did, H5R_DATASET_REGION, ref_data[i]); - if (region >= 0) { - region_type = H5Sget_select_type(region); - if(region_type==H5S_SEL_POINTS) { - h5str_dump_region_points_data(&h5str, region, region_obj); - } /* end if */ - else { - h5str_dump_region_blocks_data(&h5str, region, region_obj); - } /* end else */ - - H5Sclose(region); - } /* end if */ - H5Dclose(region_obj); - } /* end if */ - jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); - - ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); - } /* end for */ - - h5str_free(&h5str); - HDfree(ref_data); - - return (jint)status; -} /* end Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data */ - -/* - * Class: hdf_hdf5lib_H5 * Method: _H5Dcreate2 * Signature: (JLjava/lang/String;JJJJJ)J */ diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h index 1fe71a8..f824452 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 @@ -267,15 +267,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref /* * Class: hdf_hdf5lib_H5 - * Method: H5Dread_reg_ref_data - * Signature: (JJJJJ[Ljava/lang/String;)I - */ -JNIEXPORT jint JNICALL -Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data - (JNIEnv*, jclass, jlong, jlong, jlong, jlong, jlong, jobjectArray); - -/* - * Class: hdf_hdf5lib_H5 * Method: _H5Dcreate2 * Signature: (JLjava/lang/String;JJJJJ)J */ diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 2196672..59f1944 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -150,7 +150,15 @@ New Features Java Library: ---------------- - - + - Duplicate the data read/write functions of Datasets for Attributes. + + Region references could not be displayed for attributes as they could + for datasets. Datasets had overloaded read and write functions for different + datatypes that were not available for attributes. After adding similar + functions, attribute region references work normally. + + (ADB - 2018/12/12, HDFVIEW-4) + Tools: ------ |