diff options
author | Allen Byrne <50328838+byrnHDF@users.noreply.github.com> | 2021-03-10 13:41:14 (GMT) |
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committer | GitHub <noreply@github.com> | 2021-03-10 13:41:14 (GMT) |
commit | dd5b8a874757f23a1906d0a80ee77a112ad4a33d (patch) | |
tree | 93db0b67058adce2bf52c726a8745f6e2709ecd4 /java/src | |
parent | 2524ad19c0b375ead91b614baf85f556dfce2b41 (diff) | |
download | hdf5-dd5b8a874757f23a1906d0a80ee77a112ad4a33d.zip hdf5-dd5b8a874757f23a1906d0a80ee77a112ad4a33d.tar.gz hdf5-dd5b8a874757f23a1906d0a80ee77a112ad4a33d.tar.bz2 |
1 10 Fix java data export functions (#450)
* HDFFV-10865 - merge from dev, HDFArray perf fix.
* Remove duplicate setting
* Whitespace changes after clang format
* Undo version 11 clang format changes
* Merge CMake changes from develop
* test testing script merge from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge small changes from develop
* Minor non-space formatting changes
* #386 copyright corrections for java folder
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Merge updates
#358 patches from vtk
#361 fix header guard spelling
* format fix
* Fix missing underscore and make H5public.h closer to dev
* Merges from develop
#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup
* format alignment
* Add missing test ref file
* Merge #380 from develop
* Finish java merges from develop
* Fix java issues with tests and javadoc
* Correct use of attribute access plist
* Remove debug code
* Remove unused variable
* Change file access to read only for java tests
* Split clang format operations.
* More javadoc comments
* Remove pre-split setting
* format source
Diffstat (limited to 'java/src')
-rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 27 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/HDF5Constants.java | 9 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/HDF5GroupInfo.java | 21 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/HDFArray.java | 502 | ||||
-rw-r--r-- | java/src/hdf/hdf5lib/structs/H5A_info_t.java | 12 | ||||
-rw-r--r-- | java/src/jni/h5Constants.c | 8 | ||||
-rw-r--r-- | java/src/jni/h5dImp.c | 2 | ||||
-rw-r--r-- | java/src/jni/h5util.c | 202 | ||||
-rw-r--r-- | java/src/jni/h5util.h | 14 |
9 files changed, 457 insertions, 340 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 2d0ad76..db9350e 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -510,8 +510,8 @@ public class H5 implements java.io.Serializable { * * @param file_export_name * The file name to export data into. - * @param file_name - * The name of the HDF5 file containing the dataset. + * @param file_id + * The identifier of the HDF5 file containing the dataset. * @param object_path * The full path of the dataset to be exported. * @param binary_order @@ -523,7 +523,28 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native void H5export_dataset(String file_export_name, String file_name, + public synchronized static native void H5export_dataset(String file_export_name, long file_id, + String object_path, int binary_order) throws HDF5LibraryException; + + /** + * H5export_attribute is a utility function to save data in a file. + * + * @param file_export_name + * The file name to export data into. + * @param dataset_id + * The identifier of the dataset containing the attribute. + * @param object_path + * The attribute to be exported. + * @param binary_order + * 99 - export data as text. + * 1 - export data as binary Native Order. + * 2 - export data as binary Little Endian. + * 3 - export data as binary Big Endian. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native void H5export_attribute(String file_export_name, long dataset_id, String object_path, int binary_order) throws HDF5LibraryException; /** diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java index 5f72aee..ad9ed70 100644 --- a/java/src/hdf/hdf5lib/HDF5Constants.java +++ b/java/src/hdf/hdf5lib/HDF5Constants.java @@ -45,14 +45,23 @@ public class HDF5Constants { public static final int H5_SZIP_ALLOW_K13_OPTION_MASK = H5_SZIP_ALLOW_K13_OPTION_MASK(); /** Special parameters for szip compression */ public static final int H5_SZIP_CHIP_OPTION_MASK = H5_SZIP_CHIP_OPTION_MASK(); + /** indices on links, unknown index type */ public static final int H5_INDEX_UNKNOWN = H5_INDEX_UNKNOWN(); + /** indices on links, index on names */ public static final int H5_INDEX_NAME = H5_INDEX_NAME(); + /** indices on links, index on creation order */ public static final int H5_INDEX_CRT_ORDER = H5_INDEX_CRT_ORDER(); + /** indices on links, number of indices defined */ public static final int H5_INDEX_N = H5_INDEX_N(); + /** Common iteration orders, Unknown order */ public static final int H5_ITER_UNKNOWN = H5_ITER_UNKNOWN(); + /** Common iteration orders, Increasing order */ public static final int H5_ITER_INC = H5_ITER_INC(); + /** Common iteration orders, Decreasing order */ public static final int H5_ITER_DEC = H5_ITER_DEC(); + /** Common iteration orders, No particular order, whatever is fastest */ public static final int H5_ITER_NATIVE = H5_ITER_NATIVE(); + /** Common iteration orders, Number of iteration orders */ public static final int H5_ITER_N = H5_ITER_N(); public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION(); public static final int H5AC_MAX_TRACE_FILE_NAME_LEN = H5AC_MAX_TRACE_FILE_NAME_LEN(); diff --git a/java/src/hdf/hdf5lib/HDF5GroupInfo.java b/java/src/hdf/hdf5lib/HDF5GroupInfo.java index 44b41bb..4c31af7 100644 --- a/java/src/hdf/hdf5lib/HDF5GroupInfo.java +++ b/java/src/hdf/hdf5lib/HDF5GroupInfo.java @@ -41,6 +41,8 @@ public class HDF5GroupInfo { long mtime; int linklen; + /** Container for the information reported about an HDF5 Object + * from the H5Gget_obj_info() method */ public HDF5GroupInfo() { fileno = new long[2]; objno = new long[2]; @@ -88,27 +90,44 @@ public class HDF5GroupInfo { linklen = 0; } - /* accessors */ + /** fileno accessors + * @return the file number if successful + */ public long[] getFileno() { return fileno; } + /** accessors + * @return the object number if successful + */ public long[] getObjno() { return objno; } + /** accessors + * @return type of group if successful + */ public int getType() { return type; } + /** accessors + * @return the number of links in the group if successful + */ public int getNlink() { return nlink; } + /** accessors + * @return the modified time value if successful + */ public long getMtime() { return mtime; } + /** accessors + * @return a length of link name if successful + */ public int getLinklen() { return linklen; } diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java index 96291b3..bb9357e 100644 --- a/java/src/hdf/hdf5lib/HDFArray.java +++ b/java/src/hdf/hdf5lib/HDFArray.java @@ -20,19 +20,16 @@ import java.util.Arrays; /** * This is a class for handling multidimensional arrays for HDF. * <p> - * The purpose is to allow the storage and retrieval of arbitrary array types - * containing scientific data. + * The purpose is to allow the storage and retrieval of arbitrary array types containing scientific data. * <p> - * The methods support the conversion of an array to and from Java to a - * one-dimensional array of bytes suitable for I/O by the C library. + * The methods support the conversion of an array to and from Java to a one-dimensional array of bytes suitable for I/O + * by the C library. * <p> - * This class heavily uses the <a - * href="./hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a> class to - * convert between Java and C representations. + * This class heavily uses the <a href="./hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a> class to convert between + * Java and C representations. */ public class HDFArray { - private Object _theArray = null; private ArrayDescriptor _desc = null; private byte[] _barray = null; @@ -40,31 +37,27 @@ public class HDFArray { // public HDFArray() {} /** - * The input must be a Java Array (possibly multidimensional) of primitive - * numbers or sub-classes of Number. + * The input must be a Java Array (possibly multidimensional) of primitive numbers or sub-classes of Number. * <p> - * The input is analysed to determine the number of dimensions and size of - * each dimension, as well as the type of the elements. + * The input is analysed to determine the number of dimensions and size of each dimension, as well as the type of + * the elements. * <p> * The description is saved in private variables, and used to convert data. * * @param anArray - * The array object. - * + * The array object. * @exception hdf.hdf5lib.exceptions.HDF5Exception - * object is not an array. + * object is not an array. */ - public HDFArray(Object anArray) throws HDF5Exception { - + public HDFArray(Object anArray) throws HDF5Exception + { if (anArray == null) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: array is null?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: array is null?: "); } Class tc = anArray.getClass(); if (tc.isArray() == false) { /* exception: not an array */ - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: not an array?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: not an array?: "); throw (ex); } _theArray = anArray; @@ -72,8 +65,7 @@ public class HDFArray { /* extra error checking -- probably not needed */ if (_desc == null) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: internal error: array description failed?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: internal error: array description failed?: "); throw (ex); } } @@ -81,49 +73,48 @@ public class HDFArray { /** * Allocate a one-dimensional array of bytes sufficient to store the array. * - * @return A one-D array of bytes, filled with zeroes. The bytes are - * sufficient to hold the data of the Array passed to the - * constructor. + * @return A one-D array of bytes, filled with zeroes. The bytes are sufficient to hold the data of the Array passed + * to the constructor. * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * Allocation failed. + * Allocation failed. */ - public byte[] emptyBytes() throws HDF5JavaException { + public byte[] emptyBytes() + throws HDF5JavaException + { byte[] b = null; - if ((ArrayDescriptor.dims == 1) && (ArrayDescriptor.NT == 'B')) { + if ((ArrayDescriptor.dims == 1) + && (ArrayDescriptor.NT == 'B')) { b = (byte[]) _theArray; } else { b = new byte[ArrayDescriptor.totalSize]; } if (b == null) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: emptyBytes: allocation failed"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: emptyBytes: allocation failed"); throw (ex); } return (b); } /** - * Given a Java array of numbers, convert it to a one-dimensional array of - * bytes in correct native order. + * Given a Java array of numbers, convert it to a one-dimensional array of bytes in correct native order. * - * @return A one-D array of bytes, constructed from the Array passed to the - * constructor. + * @return A one-D array of bytes, constructed from the Array passed to the constructor. * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * the object not an array or other internal error. + * the object not an array or other internal error. */ - public byte[] byteify() throws HDF5JavaException { - + public byte[] byteify() + throws HDF5JavaException + { if (_barray != null) { return _barray; } if (_theArray == null) { /* exception: not an array */ - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify not an array?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify not an array?: "); throw (ex); } @@ -140,73 +131,53 @@ public class HDFArray { byte[] therow; if (ArrayDescriptor.NT == 'I') { - therow = HDFNativeData.intToByte(0, - ArrayDescriptor.dimlen[1], (int[]) _theArray); + therow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[1], (int[]) _theArray); } else if (ArrayDescriptor.NT == 'S') { - therow = HDFNativeData.shortToByte(0, - ArrayDescriptor.dimlen[1], (short[]) _theArray); + therow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[1], (short[]) _theArray); } else if (ArrayDescriptor.NT == 'F') { - therow = HDFNativeData.floatToByte(0, - ArrayDescriptor.dimlen[1], (float[]) _theArray); + therow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[1], (float[]) _theArray); } else if (ArrayDescriptor.NT == 'J') { - therow = HDFNativeData.longToByte(0, - ArrayDescriptor.dimlen[1], (long[]) _theArray); + therow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[1], (long[]) _theArray); } else if (ArrayDescriptor.NT == 'D') { - therow = HDFNativeData - .doubleToByte(0, ArrayDescriptor.dimlen[1], - (double[]) _theArray); + therow = HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[1], (double[]) _theArray); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { therow = ByteObjToByte((Byte[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Integer")) { + else if (ArrayDescriptor.className.equals("java.lang.Integer")) { therow = IntegerToByte((Integer[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Short")) { + else if (ArrayDescriptor.className.equals("java.lang.Short")) { therow = ShortToByte((Short[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Float")) { + else if (ArrayDescriptor.className.equals("java.lang.Float")) { therow = FloatObjToByte((Float[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Double")) { + else if (ArrayDescriptor.className.equals("java.lang.Double")) { therow = DoubleObjToByte((Double[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Long")) { + else if (ArrayDescriptor.className.equals("java.lang.Long")) { therow = LongObjToByte((Long[]) _theArray); } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unknown type of Object?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown type of Object?"); throw (ex); } } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unknown type of data?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown type of data?"); throw (ex); } - System - .arraycopy( - therow, - 0, - _barray, - 0, - (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize)); + System.arraycopy(therow, 0, _barray, 0, (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize)); return _barray; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); throw (ex); } } @@ -216,8 +187,7 @@ public class HDFArray { _barray = new byte[ArrayDescriptor.totalSize]; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); throw (ex); } @@ -240,8 +210,7 @@ public class HDFArray { else { /* check range of index */ if (index > (ArrayDescriptor.dimlen[i] - 1)) { - throw new java.lang.IndexOutOfBoundsException( - "HDFArray: byteify index OOB?"); + throw new java.lang.IndexOutOfBoundsException("HDFArray: byteify index OOB?"); } oo = java.lang.reflect.Array.get(oo, index); ArrayDescriptor.currentindex[i] = index; @@ -253,144 +222,107 @@ public class HDFArray { byte arow[]; try { if (ArrayDescriptor.NT == 'J') { - arow = HDFNativeData - .longToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); - arow = HDFNativeData - .longToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'I') { - arow = HDFNativeData - .intToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (int[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (int[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'S') { - arow = HDFNativeData - .shortToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'B') { arow = (byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]; } else if (ArrayDescriptor.NT == 'F') { /* 32 bit float */ - arow = HDFNativeData - .floatToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'D') { /* 64 bit float */ - arow = HDFNativeData - .doubleToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { arow = ByteObjToByte((Byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Integer")) { + else if (ArrayDescriptor.className.equals("java.lang.Integer")) { arow = IntegerToByte((Integer[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Short")) { + else if (ArrayDescriptor.className.equals("java.lang.Short")) { arow = ShortToByte((Short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Float")) { + else if (ArrayDescriptor.className.equals("java.lang.Float")) { arow = FloatObjToByte((Float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Double")) { + else if (ArrayDescriptor.className.equals("java.lang.Double")) { arow = DoubleObjToByte((Double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Long")) { arow = LongObjToByte((Long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify Object type not implemented?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify Object type not implemented?"); throw (ex); } } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify unknown type not implemented?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify unknown type not implemented?"); throw (ex); } - System - .arraycopy( - arow, - 0, - _barray, - n, - (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize)); + System.arraycopy(arow, 0, _barray, n, + (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize)); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); throw (ex); } } /* assert: the whole array is completed--currentindex should == len - 1 */ - /* error checks */ - if (n < ArrayDescriptor.totalSize) { - throw new java.lang.InternalError(new String( - "HDFArray::byteify: Panic didn't complete all input data: n= " - + n + " size = " + ArrayDescriptor.totalSize)); + throw new java.lang.InternalError(new String("HDFArray::byteify: Panic didn't complete all input data: n= " + + n + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i < ArrayDescriptor.dims; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { throw new java.lang.InternalError(new String( - "Panic didn't complete all data: currentindex[" + i - + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " - + (ArrayDescriptor.dimlen[i] - 1) + " ?)")); + "Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] + + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + " ?)")); } } return _barray; } /** - * Given a one-dimensional array of bytes representing numbers, convert it - * to a java array of the shape and size passed to the constructor. + * Given a one-dimensional array of bytes representing numbers, convert it to a java array of the shape and size + * passed to the constructor. * * @param bytes - * The bytes to construct the Array. - * @return An Array (possibly multidimensional) of primitive or number - * objects. - * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * the object not an array or other internal error. + * The bytes to construct the Array. + * @return + * An Array (possibly multidimensional) of primitive or number objects. + * @exception + * hdf.hdf5lib.exceptions.HDF5JavaException the object not an array or other internal error. */ - public Object arrayify(byte[] bytes) throws HDF5JavaException { - + public Object arrayify(byte[] bytes) throws HDF5JavaException + { if (_theArray == null) { /* exception: not an array */ - HDF5JavaException ex = new HDF5JavaException( - "arrayify: not an array?: "); + HDF5JavaException ex = new HDF5JavaException("arrayify: not an array?: "); throw (ex); } if (java.lang.reflect.Array.getLength(bytes) != ArrayDescriptor.totalSize) { /* exception: array not right size */ - HDF5JavaException ex = new HDF5JavaException( - "arrayify: array is wrong size?: "); + HDF5JavaException ex = new HDF5JavaException("arrayify: array is wrong size?: "); throw (ex); } _barray = bytes; /* hope that the bytes are correct.... */ @@ -401,95 +333,76 @@ public class HDFArray { try { if (ArrayDescriptor.NT == 'I') { int[] x = HDFNativeData.byteToInt(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'S') { short[] x = HDFNativeData.byteToShort(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'F') { float x[] = HDFNativeData.byteToFloat(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'J') { long x[] = HDFNativeData.byteToLong(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'D') { double x[] = HDFNativeData.byteToDouble(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'B') { - System.arraycopy(_barray, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(_barray, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { Byte I[] = ByteToByteObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Integer")) { + else if (ArrayDescriptor.className.equals("java.lang.Integer")) { Integer I[] = ByteToInteger(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Short")) { + else if (ArrayDescriptor.className.equals("java.lang.Short")) { Short I[] = ByteToShort(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Float")) { + else if (ArrayDescriptor.className.equals("java.lang.Float")) { Float I[] = ByteToFloatObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Double")) { + else if (ArrayDescriptor.className.equals("java.lang.Double")) { Double I[] = ByteToDoubleObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.className.equals("java.lang.Long")) { Long I[] = ByteToLongObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else { - HDF5JavaException ex = new HDF5JavaException( - "arrayify: Object type not implemented yet..."); + HDF5JavaException ex = new HDF5JavaException("arrayify: Object type not implemented yet..."); throw (ex); } } else { - HDF5JavaException ex = new HDF5JavaException( - "arrayify: unknown type not implemented yet..."); + HDF5JavaException ex = new HDF5JavaException("arrayify: unknown type not implemented yet..."); throw (ex); } } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: arrayify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: arrayify array too big?"); throw (ex); } } @@ -501,6 +414,7 @@ public class HDFArray { int index = 0; int i; Object flattenedArray = null; + switch (ArrayDescriptor.NT) { case 'J': flattenedArray = (Object) HDFNativeData.byteToLong(_barray); @@ -521,36 +435,27 @@ public class HDFArray { flattenedArray = (Object) _barray; break; case 'L': - switch (ArrayDescriptor.className) { - case "java.lang.Byte": - flattenedArray = (Object) ByteToByteObj(_barray); - break; - case "java.lang.Short": - flattenedArray = (Object) ByteToShort(_barray); - break; - case "java.lang.Integer": - flattenedArray = (Object) ByteToInteger(_barray); - break; - case "java.lang.Long": - flattenedArray = (Object) ByteToLongObj(_barray); - break; - case "java.lang.Float": - flattenedArray = (Object) ByteToFloatObj(_barray); - break; - case "java.lang.Double": - flattenedArray = (Object) ByteToDoubleObj(_barray); - break; - default: - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unsupported Object type: " - + ArrayDescriptor.NT); - throw (ex); - } // end of switch statement for arrays of boxed objects - default: - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unknown or unsupported type: " - + ArrayDescriptor.NT); - throw (ex); + { + if (ArrayDescriptor.className.equals("java.lang.Byte")) + flattenedArray = (Object) ByteToByteObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Short")) + flattenedArray = (Object) ByteToShort(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Integer")) + flattenedArray = (Object) ByteToInteger(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Long")) + flattenedArray = (Object) ByteToLongObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Float")) + flattenedArray = (Object) ByteToFloatObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Double")) + flattenedArray = (Object) ByteToDoubleObj(_barray); + else { + HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); + throw (ex); + } + } // end of statement for arrays of boxed objects + default: + HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown or unsupported type: " + ArrayDescriptor.NT); + throw (ex); } // end of switch statement for arrays of primitives while (n < ArrayDescriptor.totalSize) { @@ -579,7 +484,6 @@ public class HDFArray { /* array-ify */ try { - Object arow = null; int mm = m + ArrayDescriptor.dimlen[ArrayDescriptor.dims]; switch (ArrayDescriptor.NT) { @@ -602,75 +506,64 @@ public class HDFArray { arow = (Object) Arrays.copyOfRange((double[]) flattenedArray, m, mm); break; case 'L': - switch (ArrayDescriptor.className) { - case "java.lang.Byte": - arow = (Object) Arrays.copyOfRange((Byte[])flattenedArray, m, mm); - break; - case "java.lang.Short": - arow = (Object) Arrays.copyOfRange((Short[])flattenedArray, m, mm); - break; - case "java.lang.Integer": - arow = (Object) Arrays.copyOfRange((Integer[])flattenedArray, m, mm); - break; - case "java.lang.Long": - arow = (Object) Arrays.copyOfRange((Long[])flattenedArray, m, mm); - break; - case "java.lang.Float": - arow = (Object) Arrays.copyOfRange((Float[])flattenedArray, m, mm); - break; - case "java.lang.Double": - arow = (Object) Arrays.copyOfRange((Double[])flattenedArray, m, mm); - break; - } // end of switch statement for arrays of boxed numerics + { + if (ArrayDescriptor.className.equals("java.lang.Byte")) + arow = (Object) Arrays.copyOfRange((Byte[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Short")) + arow = (Object) Arrays.copyOfRange((Short[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Integer")) + arow = (Object) Arrays.copyOfRange((Integer[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Long")) + arow = (Object) Arrays.copyOfRange((Long[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Float")) + arow = (Object) Arrays.copyOfRange((Float[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Double")) + arow = (Object) Arrays.copyOfRange((Double[]) flattenedArray, m, mm); + else { + HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); + throw (ex); + } + } // end of statement for arrays of boxed numerics } // end of switch statement for arrays of primitives - java.lang.reflect.Array.set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - arow); + java.lang.reflect.Array.set(ArrayDescriptor.objs[ArrayDescriptor.dims - 2], + (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; m = mm; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: arrayify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: arrayify array too big?"); throw (ex); } - } /* assert: the whole array is completed--currentindex should == len - 1 */ - /* error checks */ - if (n < ArrayDescriptor.totalSize) { - throw new java.lang.InternalError(new String( - "HDFArray::arrayify Panic didn't complete all input data: n= " - + n + " size = " + ArrayDescriptor.totalSize)); + throw new java.lang.InternalError(new String("HDFArray::arrayify Panic didn't complete all input data: n= " + + n + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i <= ArrayDescriptor.dims - 2; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { - throw new java.lang.InternalError(new String( - "HDFArray::arrayify Panic didn't complete all data: currentindex[" - + i + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " - + (ArrayDescriptor.dimlen[i] - 1) + "?")); + throw new java.lang.InternalError( + new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + + "?")); } } - if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) { - throw new java.lang.InternalError(new String( - "HDFArray::arrayify Panic didn't complete all data: currentindex[" - + i + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " + (ArrayDescriptor.dimlen[i]) - + "?")); + if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims + - 1]) { + throw new java.lang.InternalError( + new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i]) + "?")); } - return _theArray; } - private byte[] IntegerToByte(Integer in[]) { + private byte[] IntegerToByte(Integer in[]) + { int nelems = java.lang.reflect.Array.getLength(in); int[] out = new int[nelems]; @@ -680,7 +573,8 @@ public class HDFArray { return HDFNativeData.intToByte(0, nelems, out); } - private Integer[] ByteToInteger(byte[] bin) { + private Integer[] ByteToInteger(byte[] bin) + { int in[] = HDFNativeData.byteToInt(bin); int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; @@ -691,7 +585,8 @@ public class HDFArray { return out; } - private Integer[] ByteToInteger(int start, int len, byte[] bin) { + private Integer[] ByteToInteger(int start, int len, byte[] bin) + { int in[] = HDFNativeData.byteToInt(start, len, bin); int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; @@ -702,7 +597,8 @@ public class HDFArray { return out; } - private byte[] ShortToByte(Short in[]) { + private byte[] ShortToByte(Short in[]) + { int nelems = java.lang.reflect.Array.getLength(in); short[] out = new short[nelems]; @@ -712,7 +608,8 @@ public class HDFArray { return HDFNativeData.shortToByte(0, nelems, out); } - private Short[] ByteToShort(byte[] bin) { + private Short[] ByteToShort(byte[] bin) + { short in[] = HDFNativeData.byteToShort(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Short[] out = new Short[nelems]; @@ -723,7 +620,8 @@ public class HDFArray { return out; } - private Short[] ByteToShort(int start, int len, byte[] bin) { + private Short[] ByteToShort(int start, int len, byte[] bin) + { short in[] = (short[]) HDFNativeData.byteToShort(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Short[] out = new Short[nelems]; @@ -734,7 +632,8 @@ public class HDFArray { return out; } - private byte[] ByteObjToByte(Byte in[]) { + private byte[] ByteObjToByte(Byte in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); byte[] out = new byte[nelems]; @@ -744,7 +643,8 @@ public class HDFArray { return out; } - private Byte[] ByteToByteObj(byte[] bin) { + private Byte[] ByteToByteObj(byte[] bin) + { int nelems = java.lang.reflect.Array.getLength((Object) bin); Byte[] out = new Byte[nelems]; @@ -754,7 +654,8 @@ public class HDFArray { return out; } - private Byte[] ByteToByteObj(int start, int len, byte[] bin) { + private Byte[] ByteToByteObj(int start, int len, byte[] bin) + { Byte[] out = new Byte[len]; for (int i = 0; i < len; i++) { @@ -763,7 +664,8 @@ public class HDFArray { return out; } - private byte[] FloatObjToByte(Float in[]) { + private byte[] FloatObjToByte(Float in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); float[] out = new float[nelems]; @@ -773,7 +675,8 @@ public class HDFArray { return HDFNativeData.floatToByte(0, nelems, out); } - private Float[] ByteToFloatObj(byte[] bin) { + private Float[] ByteToFloatObj(byte[] bin) + { float in[] = (float[]) HDFNativeData.byteToFloat(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Float[] out = new Float[nelems]; @@ -784,7 +687,8 @@ public class HDFArray { return out; } - private Float[] ByteToFloatObj(int start, int len, byte[] bin) { + private Float[] ByteToFloatObj(int start, int len, byte[] bin) + { float in[] = (float[]) HDFNativeData.byteToFloat(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Float[] out = new Float[nelems]; @@ -795,7 +699,8 @@ public class HDFArray { return out; } - private byte[] DoubleObjToByte(Double in[]) { + private byte[] DoubleObjToByte(Double in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); double[] out = new double[nelems]; @@ -805,7 +710,8 @@ public class HDFArray { return HDFNativeData.doubleToByte(0, nelems, out); } - private Double[] ByteToDoubleObj(byte[] bin) { + private Double[] ByteToDoubleObj(byte[] bin) + { double in[] = (double[]) HDFNativeData.byteToDouble(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Double[] out = new Double[nelems]; @@ -816,7 +722,8 @@ public class HDFArray { return out; } - private Double[] ByteToDoubleObj(int start, int len, byte[] bin) { + private Double[] ByteToDoubleObj(int start, int len, byte[] bin) + { double in[] = (double[]) HDFNativeData.byteToDouble(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Double[] out = new Double[nelems]; @@ -827,7 +734,8 @@ public class HDFArray { return out; } - private byte[] LongObjToByte(Long in[]) { + private byte[] LongObjToByte(Long in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); long[] out = new long[nelems]; @@ -837,7 +745,8 @@ public class HDFArray { return HDFNativeData.longToByte(0, nelems, out); } - private Long[] ByteToLongObj(byte[] bin) { + private Long[] ByteToLongObj(byte[] bin) + { long in[] = (long[]) HDFNativeData.byteToLong(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Long[] out = new Long[nelems]; @@ -848,7 +757,8 @@ public class HDFArray { return out; } - private Long[] ByteToLongObj(int start, int len, byte[] bin) { + private Long[] ByteToLongObj(int start, int len, byte[] bin) + { long in[] = (long[]) HDFNativeData.byteToLong(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Long[] out = new Long[nelems]; @@ -861,13 +771,11 @@ public class HDFArray { } /** - * This private class is used by HDFArray to discover the shape and type of an - * arbitrary array. + * This private class is used by HDFArray to discover the shape and type of an arbitrary array. * <p> * We use java.lang.reflection here. */ class ArrayDescriptor { - static String theType = ""; static Class theClass = null; static int[] dimlen = null; @@ -882,13 +790,12 @@ class ArrayDescriptor { static int dims = 0; static String className; - public ArrayDescriptor(Object anArray) throws HDF5Exception { - + public ArrayDescriptor(Object anArray) throws HDF5Exception + { Class tc = anArray.getClass(); if (tc.isArray() == false) { /* exception: not an array */ - HDF5Exception ex = new HDF5JavaException( - "ArrayDescriptor: not an array?: "); + HDF5Exception ex = new HDF5JavaException("ArrayDescriptor: not an array?: "); throw (ex); } @@ -960,16 +867,14 @@ class ArrayDescriptor { NT = 'L'; className = "java.lang.String"; NTsize = 1; - throw new HDF5JavaException(new String( - "ArrayDesciptor: Warning: String array not fully supported yet")); + throw new HDF5JavaException(new String("ArrayDesciptor: Warning: String array not fully supported yet")); } else { /* * exception: not a numeric type */ - throw new HDF5JavaException(new String( - "ArrayDesciptor: Error: array is not numeric (type is " - + css + ") ?")); + throw new HDF5JavaException( + new String("ArrayDesciptor: Error: array is not numeric (type is " + css + ") ?")); } /* fill in the table */ @@ -1013,7 +918,8 @@ class ArrayDescriptor { /** * Debug dump */ - public void dumpInfo() { + public void dumpInfo() + { System.out.println("Type: " + theType); System.out.println("Class: " + theClass); System.out.println("NT: " + NT + " NTsize: " + NTsize); @@ -1023,10 +929,8 @@ class ArrayDescriptor { for (i = 0; i <= dims; i++) { Class tc = objs[i].getClass(); String ss = tc.toString(); - System.out.println(i + ": start " + dimstart[i] + ": len " - + dimlen[i] + " current " + currentindex[i] - + " bytetoindex " + bytetoindex[i] + " object " + objs[i] - + " otype " + ss); + System.out.println(i + ": start " + dimstart[i] + ": len " + dimlen[i] + " current " + currentindex[i] + + " bytetoindex " + bytetoindex[i] + " object " + objs[i] + " otype " + ss); } } } diff --git a/java/src/hdf/hdf5lib/structs/H5A_info_t.java b/java/src/hdf/hdf5lib/structs/H5A_info_t.java index 4bc1b0d..f2c10f0 100644 --- a/java/src/hdf/hdf5lib/structs/H5A_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5A_info_t.java @@ -20,10 +20,14 @@ import java.io.Serializable; */ public class H5A_info_t implements Serializable{ private static final long serialVersionUID = 2791443594041667613L; - public boolean corder_valid; // Indicate if creation order is valid - public long corder; // Creation order of attribute - public int cset; // Character set of attribute name - public long data_size; // Size of raw data + /** Indicate if creation order is valid */ + public boolean corder_valid; + /** Creation order of attribute */ + public long corder; + /** Character set of attribute name */ + public int cset; + /** Size of raw data */ + public long data_size; H5A_info_t(boolean corder_valid, long corder, int cset, long data_size) { this.corder_valid = corder_valid; diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c index 590f51a..c3307a8 100644 --- a/java/src/jni/h5Constants.c +++ b/java/src/jni/h5Constants.c @@ -1362,7 +1362,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1DIRECT(JNIEnv *env, jclass cls) #ifdef H5_HAVE_DIRECT return H5FD_DIRECT; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jlong JNICALL @@ -1376,7 +1376,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1HDFS(JNIEnv *env, jclass cls) #ifdef H5_HAVE_LIBHDFS return H5FD_HDFS; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jlong JNICALL @@ -1405,7 +1405,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1ROS3(JNIEnv *env, jclass cls) #ifdef H5_HAVE_ROS3_VFD return H5FD_ROS3; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jlong JNICALL @@ -1419,7 +1419,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1WINDOWS(JNIEnv *env, jclass cls) #ifdef H5_HAVE_WINDOWS return H5FD_DIRECT; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jint JNICALL diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c index 24d0714..24263a5 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -1657,7 +1657,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref(JNIEnv *env, jclass clss, jlong dataset_id for (i = 0; i < n; i++) { h5str.s[0] = '\0'; - if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, &ref_data[i], 0)) + if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, (void *)&ref_data[i], 0)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s))) diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index c4021ec..e21b1ad 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -52,6 +52,8 @@ void * edata; /* Local Prototypes */ /********************/ +int h5str_region_dataset(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_buf, int expand_data); + static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj, int expand_data); static int h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj, @@ -644,7 +646,6 @@ h5str_region_dataset(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_b H5S_sel_type region_type = H5S_SEL_ERROR; hid_t region_obj = H5I_INVALID_HID; hid_t region_sid = H5I_INVALID_HID; - char ref_name[1024]; int ret_value = FAIL; @@ -654,14 +655,6 @@ h5str_region_dataset(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_b if ((region_sid = H5Rget_region(container, H5R_DATASET_REGION, ref_buf)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (expand_data) { - if (H5Rget_name(region_obj, H5R_DATASET_REGION, ref_buf, (char *)ref_name, 1024) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (!h5str_append(out_str, ref_name)) - H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); - } - if ((region_type = H5Sget_select_type(region_sid)) > H5S_SEL_ERROR) { if (H5S_SEL_POINTS == region_type) { if (h5str_dump_region_points(ENVONLY, out_str, region_sid, region_obj, expand_data) < 0) @@ -2691,6 +2684,125 @@ done: return ret_value; } /* end h5str_dump_simple_dset */ +int +h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order) +{ + hid_t f_space = H5I_INVALID_HID; /* file data space */ + hsize_t alloc_size; + int ndims; /* rank of dataspace */ + unsigned i; /* counters */ + hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/ + hsize_t p_nelmts; /* total selected elmts */ + + unsigned char *sm_buf = NULL; /* buffer for raw data */ + hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ + + int ret_value = 0; + + /* VL data special information */ + unsigned int vl_data = 0; /* contains VL datatypes */ + hid_t p_type = H5I_INVALID_HID; + hid_t f_type = H5I_INVALID_HID; + + if (attr_id < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_dump_simple_mem: attr ID < 0"); + + if ((f_type = H5Aget_type(attr_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + switch (binary_order) { + case 1: { + if ((p_type = h5str_get_native_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + break; + } + + case 2: { + if ((p_type = h5str_get_little_endian_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + break; + } + + case 3: { + if ((p_type = h5str_get_big_endian_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + break; + } + + default: { + if ((p_type = H5Tcopy(f_type)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + break; + } + } + + if (H5I_INVALID_HID == (f_space = H5Aget_space(attr_id))) + H5_LIBRARY_ERROR(ENVONLY); + + if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) { + if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + /* Calculate the number of elements we're going to print */ + p_nelmts = 1; + + if (ndims > 0) { + for (i = 0; i < (size_t)ndims; i++) + p_nelmts *= total_size[i]; + } /* end if */ + + if (p_nelmts > 0) { + /* Check if we have VL data in the dataset's datatype */ + if (h5str_detect_vlen(p_type) != 0) + vl_data = 1; + + alloc_size = p_nelmts * H5Tget_size(p_type); + if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)alloc_size))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf"); + + /* Read the data */ + if (H5Aread(attr_id, p_type, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (binary_order == 99) { + if (h5str_dump_simple_data(ENVONLY, stream, attr_id, p_type, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + else { + if (h5str_render_bin_output(stream, attr_id, p_type, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + + /* Reclaim any VL memory, if necessary */ + if (vl_data) { + if (H5Dvlen_reclaim(p_type, f_space, H5P_DEFAULT, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } + } + } + + ret_value = SUCCEED; + +done: + if (sm_buf) + HDfree(sm_buf); + if (f_space >= 0) + H5Sclose(f_space); + if (p_type >= 0) + H5Tclose(p_type); + if (f_type >= 0) + H5Tclose(f_type); + + return ret_value; +} + htri_t H5Tdetect_variable_str(hid_t tid) { @@ -3323,18 +3435,16 @@ done: /* * Class: hdf_hdf5lib_H5 * Method: H5export_dataset - * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V */ JNIEXPORT void JNICALL -Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_export_name, jstring file_name, +Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_export_name, jlong file_id, jstring object_path, jint binary_order) { const char *file_export = NULL; const char *object_name = NULL; - const char *fileName = NULL; jboolean isCopy; herr_t ret_val = FAIL; - hid_t file_id = H5I_INVALID_HID; hid_t dataset_id = H5I_INVALID_HID; FILE * stream = NULL; @@ -3343,17 +3453,9 @@ Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_exp if (NULL == file_export_name) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL"); - if (NULL == file_name) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_name is NULL"); - if (NULL == object_path) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL"); - PIN_JAVA_STRING(ENVONLY, file_name, fileName, NULL, "H5export_dataset: file name not pinned"); - - if ((file_id = H5Fopen(fileName, (unsigned)H5F_ACC_RDWR, (hid_t)H5P_DEFAULT)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - PIN_JAVA_STRING(ENVONLY, object_path, object_name, &isCopy, "H5export_dataset: object_path not pinned"); if ((dataset_id = H5Dopen2(file_id, object_name, H5P_DEFAULT)) < 0) @@ -3380,14 +3482,64 @@ done: UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export); if (object_name) UNPIN_JAVA_STRING(ENVONLY, object_path, object_name); - if (fileName) - UNPIN_JAVA_STRING(ENVONLY, file_name, fileName); if (dataset_id >= 0) H5Dclose(dataset_id); - if (file_id >= 0) - H5Fclose(file_id); } /* end Java_hdf_hdf5lib_H5_H5export_1dataset */ +/* + * Class: hdf_hdf5lib_H5 + * Method: H5export_attribute + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *env, jclass clss, jstring file_export_name, jlong dset_id, + jstring object_path, jint binary_order) +{ + const char *file_export = NULL; + const char *object_name = NULL; + jboolean isCopy; + herr_t ret_val = FAIL; + hid_t attr_id = H5I_INVALID_HID; + FILE * stream = NULL; + + UNUSED(clss); + + if (NULL == file_export_name) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL"); + + if (NULL == object_path) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL"); + + PIN_JAVA_STRING(ENVONLY, object_path, object_name, &isCopy, "H5export_dataset: object_path not pinned"); + + if ((attr_id = H5Aopen(dset_id, object_name, H5P_DEFAULT)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + PIN_JAVA_STRING(ENVONLY, file_export_name, file_export, NULL, + "H5export_dataset: file_export name not pinned"); + + if (NULL == (stream = HDfopen(file_export, "w+"))) + H5_JNI_FATAL_ERROR(ENVONLY, "HDfopen failed"); + + if ((ret_val = h5str_dump_simple_mem(ENVONLY, stream, attr_id, binary_order)) < 0) + H5_ASSERTION_ERROR(ENVONLY, "h5str_dump_simple_dset failed"); + + if (stream) { + HDfclose(stream); + stream = NULL; + } + +done: + if (stream) + HDfclose(stream); + if (file_export) + UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export); + if (object_name) + UNPIN_JAVA_STRING(ENVONLY, object_path, object_name); + if (attr_id >= 0) + H5Aclose(attr_id); +} /* end Java_hdf_hdf5lib_H5_H5export_1attribute */ + #ifdef __cplusplus } #endif diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h index 19415b4..64913a7 100644 --- a/java/src/jni/h5util.h +++ b/java/src/jni/h5util.h @@ -45,6 +45,7 @@ extern size_t h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_ int expand_data); extern void h5str_array_free(char **strs, size_t len); extern int h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order); +extern int h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr, int binary_order); extern htri_t H5Tdetect_variable_str(hid_t tid); @@ -103,9 +104,16 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max(JNIEnv *, jcla /* * Class: hdf_hdf5lib_H5 * Method: H5export_dataset - * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V */ -JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *, jclass, jstring, jstring, jstring, - jint); +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *, jclass, jstring, jlong, jstring, jint); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5export_attribute + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *, jclass, jstring, jlong, jstring, + jint); #endif /* H5UTIL_H__ */ |