diff options
| -rw-r--r-- | java/examples/datatypes/H5Ex_T_Compound.java | 94 | ||||
| -rw-r--r-- | java/examples/datatypes/H5Ex_T_CompoundAttribute.java | 95 | ||||
| -rw-r--r-- | java/examples/datatypes/H5Ex_T_VLString.java | 8 | ||||
| -rw-r--r-- | java/src/jni/h5aImp.c | 20 | ||||
| -rw-r--r-- | java/src/jni/h5dImp.c | 30 | ||||
| -rw-r--r-- | java/src/jni/h5util.c | 901 | ||||
| -rw-r--r-- | java/src/jni/h5util.h | 8 | ||||
| -rw-r--r-- | java/test/TestH5A.java | 145 | ||||
| -rw-r--r-- | java/test/TestH5D.java | 519 | ||||
| -rw-r--r-- | java/test/testfiles/JUnit-TestH5A.txt | 3 | ||||
| -rw-r--r-- | java/test/testfiles/JUnit-TestH5D.txt | 5 |
11 files changed, 1407 insertions, 421 deletions
diff --git a/java/examples/datatypes/H5Ex_T_Compound.java b/java/examples/datatypes/H5Ex_T_Compound.java index a78d0e3..7a46bcf 100644 --- a/java/examples/datatypes/H5Ex_T_Compound.java +++ b/java/examples/datatypes/H5Ex_T_Compound.java @@ -23,6 +23,9 @@ package examples.datatypes; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.nio.charset.Charset; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; import hdf.hdf5lib.H5; import hdf.hdf5lib.HDF5Constants; @@ -87,6 +90,14 @@ public class H5Ex_T_Compound { this.pressure = pressure; } + Sensor(List data) + { + this.serial_no = (int)data.get(0); + this.location = (String)data.get(1); + this.temperature = (double)data.get(2); + this.pressure = (double)data.get(3); + } + Sensor(ByteBuffer databuf, int dbposition) { readBuffer(databuf, dbposition); } void writeBuffer(ByteBuffer databuf, int dbposition) @@ -115,6 +126,24 @@ public class H5Ex_T_Compound { this.pressure = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(3)); } + List get() + { + List data = new ArrayList<>(); + data.add(this.serial_no); + data.add(this.location); + data.add(this.temperature); + data.add(this.pressure); + return data; + } + + void put(List data) + { + this.serial_no = (int)data.get(0); + this.location = (String)data.get(1); + this.temperature = (double)data.get(2); + this.pressure = (double)data.get(3); + } + @Override public String toString() { @@ -127,21 +156,21 @@ public class H5Ex_T_Compound { private static void CreateDataset() { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - Sensor[] object_data = new Sensor[DIM0]; - byte[] dset_data = null; + long file_id = HDF5Constants.H5I_INVALID_HID; + long strtype_id = HDF5Constants.H5I_INVALID_HID; + long memtype_id = HDF5Constants.H5I_INVALID_HID; + long filetype_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + ArrayList[] object_data = new ArrayList[DIM0]; + byte[] dset_data = null; // Initialize data. - object_data[0] = new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57); - object_data[1] = new Sensor(1184, new String("Intake"), 55.12, 22.95); - object_data[2] = new Sensor(1027, new String("Intake manifold"), 103.55, 31.23); - object_data[3] = new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11); + object_data[0] = (ArrayList) new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57).get(); + object_data[1] = (ArrayList) new Sensor(1184, new String("Intake"), 55.12, 22.95).get(); + object_data[2] = (ArrayList) new Sensor(1027, new String("Intake manifold"), 103.55, 31.23).get(); + object_data[3] = (ArrayList) new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11).get(); // Create a new file using default properties. try { @@ -220,17 +249,10 @@ public class H5Ex_T_Compound { } // Write the compound data to the dataset. - // allocate memory for read buffer. - dset_data = new byte[(int)dims[0] * (int)Sensor_Datatype.getDataSize()]; - ByteBuffer outBuf = ByteBuffer.wrap(dset_data); - outBuf.order(ByteOrder.nativeOrder()); - for (int indx = 0; indx < (int)dims[0]; indx++) { - object_data[indx].writeBuffer(outBuf, indx * (int)Sensor_Datatype.getDataSize()); - } try { if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5Dwrite(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); + H5.H5DwriteVL(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, (Object[])object_data); } catch (Exception e) { e.printStackTrace(); @@ -292,14 +314,13 @@ public class H5Ex_T_Compound { private static void ReadDataset() { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - Sensor[] object_data2; - byte[] dset_data; + long file_id = HDF5Constants.H5I_INVALID_HID; + long strtype_id = HDF5Constants.H5I_INVALID_HID; + long memtype_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + Sensor[] object_data2 = new Sensor[(int)dims[0]]; // Open an existing file. try { @@ -362,21 +383,16 @@ public class H5Ex_T_Compound { e.printStackTrace(); } - // allocate memory for read buffer. - dset_data = new byte[(int)dims[0] * (int)Sensor_Datatype.getDataSize()]; - - object_data2 = new Sensor[(int)dims[0]]; + ArrayList[] object_data = new ArrayList[(int)dims[0]]; // Read data. try { if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5Dread(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); + H5.H5DreadVL(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, (Object[])object_data); - ByteBuffer inBuf = ByteBuffer.wrap(dset_data); - inBuf.order(ByteOrder.nativeOrder()); for (int indx = 0; indx < (int)dims[0]; indx++) { - object_data2[indx] = new Sensor(inBuf, indx * (int)Sensor_Datatype.getDataSize()); + object_data2[indx] = new Sensor(object_data[indx]); } } catch (Exception e) { diff --git a/java/examples/datatypes/H5Ex_T_CompoundAttribute.java b/java/examples/datatypes/H5Ex_T_CompoundAttribute.java index f331a1e..93e15fd 100644 --- a/java/examples/datatypes/H5Ex_T_CompoundAttribute.java +++ b/java/examples/datatypes/H5Ex_T_CompoundAttribute.java @@ -23,6 +23,9 @@ package examples.datatypes; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.nio.charset.Charset; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; import hdf.hdf5lib.H5; import hdf.hdf5lib.HDF5Constants; @@ -37,8 +40,6 @@ public class H5Ex_T_CompoundAttribute { protected static final int DOUBLESIZE = 8; protected final static int MAXSTRINGSIZE = 80; - // Using Java Externalization will add a two-byte object header in - // the stream, which needs to be called out in the datatypes. static class Sensor_Datatype { static int numberMembers = 4; static int[] memberDims = {1, 1, 1, 1}; @@ -90,6 +91,14 @@ public class H5Ex_T_CompoundAttribute { this.pressure = pressure; } + Sensor(List data) + { + this.serial_no = (int)data.get(0); + this.location = (String)data.get(1); + this.temperature = (double)data.get(2); + this.pressure = (double)data.get(3); + } + Sensor(ByteBuffer databuf, int dbposition) { readBuffer(databuf, dbposition); } void writeBuffer(ByteBuffer databuf, int dbposition) @@ -118,6 +127,24 @@ public class H5Ex_T_CompoundAttribute { this.pressure = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(3)); } + List get() + { + List data = new ArrayList<>(); + data.add(this.serial_no); + data.add(this.location); + data.add(this.temperature); + data.add(this.pressure); + return data; + } + + void put(List data) + { + this.serial_no = (int)data.get(0); + this.location = (String)data.get(1); + this.temperature = (double)data.get(2); + this.pressure = (double)data.get(3); + } + @Override public String toString() { @@ -130,22 +157,22 @@ public class H5Ex_T_CompoundAttribute { private static void CreateDataset() { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - Sensor[] object_data = new Sensor[DIM0]; - byte[] dset_data = null; + long file_id = HDF5Constants.H5I_INVALID_HID; + long strtype_id = HDF5Constants.H5I_INVALID_HID; + long memtype_id = HDF5Constants.H5I_INVALID_HID; + long filetype_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long attribute_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + ArrayList[] object_data = new ArrayList[DIM0]; + byte[] dset_data = null; // Initialize data. - object_data[0] = new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57); - object_data[1] = new Sensor(1184, new String("Intake"), 55.12, 22.95); - object_data[2] = new Sensor(1027, new String("Intake manifold"), 103.55, 31.23); - object_data[3] = new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11); + object_data[0] = (ArrayList) new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57).get(); + object_data[1] = (ArrayList) new Sensor(1184, new String("Intake"), 55.12, 22.95).get(); + object_data[2] = (ArrayList) new Sensor(1027, new String("Intake manifold"), 103.55, 31.23).get(); + object_data[3] = (ArrayList) new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11).get(); // Create a new file using default properties. try { @@ -238,15 +265,9 @@ public class H5Ex_T_CompoundAttribute { } // Write the compound data. - dset_data = new byte[(int)dims[0] * (int)Sensor_Datatype.getDataSize()]; - ByteBuffer outBuf = ByteBuffer.wrap(dset_data); - outBuf.order(ByteOrder.nativeOrder()); - for (int indx = 0; indx < (int)dims[0]; indx++) { - object_data[indx].writeBuffer(outBuf, indx * (int)Sensor_Datatype.getDataSize()); - } try { if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5Awrite(attribute_id, memtype_id, dset_data); + H5.H5AwriteVL(attribute_id, memtype_id, (Object[])object_data); } catch (Exception e) { e.printStackTrace(); @@ -316,15 +337,14 @@ public class H5Ex_T_CompoundAttribute { private static void ReadDataset() { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - Sensor[] object_data2; - byte[] dset_data; + long file_id = HDF5Constants.H5I_INVALID_HID; + long strtype_id = HDF5Constants.H5I_INVALID_HID; + long memtype_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long attribute_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + Sensor[] object_data2 = new Sensor[(int)dims[0]]; // Open an existing file. try { @@ -398,20 +418,15 @@ public class H5Ex_T_CompoundAttribute { e.printStackTrace(); } - // allocate memory for read buffer. - dset_data = new byte[(int)dims[0] * (int)Sensor_Datatype.getDataSize()]; - - object_data2 = new Sensor[(int)dims[0]]; + ArrayList[] object_data = new ArrayList[(int)dims[0]]; // Read data. try { if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5Aread(attribute_id, memtype_id, dset_data); + H5.H5AreadVL(attribute_id, memtype_id, (Object[])object_data); - ByteBuffer inBuf = ByteBuffer.wrap(dset_data); - inBuf.order(ByteOrder.nativeOrder()); for (int indx = 0; indx < (int)dims[0]; indx++) { - object_data2[indx] = new Sensor(inBuf, indx * (int)Sensor_Datatype.getDataSize()); + object_data2[indx] = new Sensor(object_data[indx]); } } catch (Exception e) { diff --git a/java/examples/datatypes/H5Ex_T_VLString.java b/java/examples/datatypes/H5Ex_T_VLString.java index 1d4c2c4..a9288a4 100644 --- a/java/examples/datatypes/H5Ex_T_VLString.java +++ b/java/examples/datatypes/H5Ex_T_VLString.java @@ -74,8 +74,8 @@ public class H5Ex_T_VLString { // Write the data to the dataset. try { if (dataset_id >= 0) - H5.H5Dwrite_VLStrings(dataset_id, type_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_data); + H5.H5DwriteVL(dataset_id, type_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_data); } catch (Exception e) { e.printStackTrace(); @@ -109,8 +109,8 @@ public class H5Ex_T_VLString { try { dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); type_id = H5.H5Dget_type(dataset_id); - H5.H5Dread_VLStrings(dataset_id, type_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_data); + H5.H5DreadVL(dataset_id, type_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_data); } catch (Exception e) { e.printStackTrace(); diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c index 71caf76..07ecdb8 100644 --- a/java/src/jni/h5aImp.c +++ b/java/src/jni/h5aImp.c @@ -1115,7 +1115,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem H5T_class_t type_class; jsize vl_array_len; htri_t vl_data_class; - herr_t status = FAIL; + herr_t status = FAIL; + htri_t is_variable = 0; UNUSED(clss); @@ -1124,10 +1125,11 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); - /* Get size of data array */ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0"); + if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (!(typeSize = H5Tget_size(mem_type_id))) H5_LIBRARY_ERROR(ENVONLY); @@ -1154,7 +1156,10 @@ done: if (sid >= 0) H5Sclose(sid); } - + if (is_variable) { + for (size_t i = 0; i < (size_t)vl_array_len; i++) + HDfree(((char **)readBuf)[i]); + } HDfree(readBuf); } @@ -1177,7 +1182,8 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me H5T_class_t type_class; jsize vl_array_len; htri_t vl_data_class; - herr_t status = FAIL; + herr_t status = FAIL; + htri_t is_variable = 0; UNUSED(clss); @@ -1192,6 +1198,8 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Awrite: write buffer length < 0"); } + if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (!(typeSize = H5Tget_size(mem_type_id))) H5_LIBRARY_ERROR(ENVONLY); @@ -1216,6 +1224,10 @@ done: H5Treclaim(attr_id, sid, H5P_DEFAULT, writeBuf); } + if (is_variable) { + for (size_t i = 0; i < (size_t)vl_array_len; i++) + HDfree(((char **)writeBuf)[i]); + } HDfree(writeBuf); } diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c index 56c5cc8..efddb96 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -1140,26 +1140,29 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong H5T_class_t type_class; jsize vl_array_len; htri_t vl_data_class; - herr_t status = FAIL; + herr_t status = FAIL; + htri_t is_variable = 0; UNUSED(clss); if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread: read buffer is NULL"); + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL"); if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Get size of data array */ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0"); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0"); } + if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (!(typeSize = H5Tget_size(mem_type_id))) H5_LIBRARY_ERROR(ENVONLY); if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread: failed to allocate raw VL read buffer"); + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer"); if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)readBuf)) < 0) @@ -1173,6 +1176,10 @@ done: if (readBuf) { if ((status >= 0) && vl_data_class) H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf); + if (is_variable) { + for (size_t i = 0; i < (size_t)vl_array_len; i++) + HDfree(((char **)readBuf)[i]); + } HDfree(readBuf); } @@ -1194,12 +1201,13 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong H5T_class_t type_class; jsize vl_array_len; // Only used by vl_data_class types htri_t vl_data_class; - herr_t status = FAIL; + herr_t status = FAIL; + htri_t is_variable = 0; UNUSED(clss); if (NULL == buf) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer is NULL"); + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL"); if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1207,14 +1215,16 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong /* Get size of data array */ if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) { CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); - H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer length < 0"); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer length < 0"); } + if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); if (!(typeSize = H5Tget_size(mem_type_id))) H5_LIBRARY_ERROR(ENVONLY); if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dwrite: failed to allocate raw VL write buffer"); + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer"); if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1229,6 +1239,10 @@ done: if (writeBuf) { if ((status >= 0) && vl_data_class) H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf); + if (is_variable) { + for (size_t i = 0; i < (size_t)vl_array_len; i++) + HDfree(((char **)writeBuf)[i]); + } HDfree(writeBuf); } diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index 4e62085..77fb244 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -77,6 +77,10 @@ static int render_bin_output_region_data_points(FILE *stream, hid_t region_sp hsize_t *ptdata); static int render_bin_output_region_points(FILE *stream, hid_t region_space, hid_t region_id, hid_t container); +jobject translate_atomic_rbuf(JNIEnv *env, jobject ret_buf, jlong mem_type_id, H5T_class_t type_class, + void *raw_buf); +void translate_atomic_wbuf(JNIEnv *env, jobject in_obj, jlong mem_type_id, H5T_class_t type_class, + void *raw_buf); /* Strings for output */ #define H5_TOOLS_GROUP "GROUP" @@ -4040,16 +4044,20 @@ done: H5Aclose(attr_id); } /* end Java_hdf_hdf5lib_H5_H5export_1attribute */ -herr_t -translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, jsize count, - jbyte *raw_buf) +jobject +translate_atomic_rbuf(JNIEnv *env, jobject ret_buf, jlong mem_type_id, H5T_class_t type_class, void *raw_buf) { - herr_t status = FAIL; - hid_t memb = H5I_INVALID_HID; - H5T_class_t vlClass; - size_t vlSize; - size_t i, x; - size_t typeSize; + jobject jobj = NULL; + hid_t memb = H5I_INVALID_HID; + int ret_buflen = -1; + jboolean found_jList = JNI_TRUE; + jobjectArray jList = NULL; + H5T_class_t vlClass; + size_t vlSize; + size_t i, x; + size_t typeSize; + // raw_buf is normally bytes except when used for variable length strings + char *char_buf = (char *)raw_buf; /* retrieve the java.util.ArrayList interface class */ jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList"); @@ -4079,6 +4087,485 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t if (!(typeSize = H5Tget_size(mem_type_id))) H5_LIBRARY_ERROR(ENVONLY); + ret_buflen = ENVPTR->GetArrayLength(ENVONLY, ret_buf); + switch (type_class) { + case H5T_VLEN: { + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + /* Convert element to a list */ + hvl_t vl_elem; + + found_jList = JNI_TRUE; + jList = NULL; + + /* Get the number of sequence elements */ + HDmemcpy(&vl_elem, char_buf, sizeof(hvl_t)); + jsize nelmts = (jsize)vl_elem.len; + if (vl_elem.len != (size_t)nelmts) + H5_JNI_FATAL_ERROR(ENVONLY, "translate_atomic_rbuf: overflow of number of VL elements"); + + if (nelmts < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_rbuf: number of VL elements < 0"); + + /* The list we're going to return: */ + if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer"); + + translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)nelmts, vl_elem.p); + jobj = jList; + break; + } /* H5T_VLEN */ + case H5T_COMPOUND: { + int nmembs = H5Tget_nmembers(mem_type_id); + void *objBuf = NULL; + + /* The list we're going to return: */ + if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer"); + + /* Convert each element to a compound object */ + for (i = 0; i < (size_t)nmembs; i++) { + H5T_class_t memb_vlClass; + size_t memb_vlSize; + size_t memb_offset; + + if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if ((memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)i)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if ((memb_vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(memb_vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + translate_atomic_rbuf(ENVONLY, jList, memb, memb_vlClass, + char_buf + i * typeSize + memb_offset); + H5Tclose(memb); + } + jobj = jList; + break; + } /* H5T_COMPOUND */ + case H5T_ARRAY: { + void *objBuf = NULL; + size_t typeCount; + + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + typeCount = typeSize / vlSize; + + if (NULL == (objBuf = HDmalloc(typeSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate buffer"); + + /* Convert each element */ + /* Get the object element */ + HDmemcpy((char *)objBuf, char_buf, typeSize); + + /* The list we're going to return: */ + if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: failed to allocate list read buffer"); + + translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)typeCount, objBuf); + jobj = jList; + + if (objBuf) + HDfree(objBuf); + + break; + } /* H5T_ARRAY */ + case H5T_ENUM: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_INTEGER: { + /* Convert each element */ + switch (typeSize) { + case sizeof(jbyte): { + jbyte byteValue; + HDmemcpy(((char *)&byteValue), char_buf, typeSize); + + if (NULL == + (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jshort): { + jshort shortValue; + HDmemcpy(((char *)&shortValue), char_buf, typeSize); + + if (NULL == + (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, shortValue))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jint): { + jint intValue; + + HDmemcpy(((char *)&intValue), char_buf, typeSize); + + if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jlong): { + jlong longValue; + HDmemcpy(((char *)&longValue), char_buf, typeSize); + + if (NULL == + (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } /* H5T_INTEGER */ + case H5T_FLOAT: { + /* Convert each element to a list */ + switch (typeSize) { + case sizeof(jfloat): { + jfloat floatValue; + HDmemcpy(((char *)&floatValue), char_buf, typeSize); + + if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid, + (double)floatValue))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + case sizeof(jdouble): { + jdouble doubleValue; + HDmemcpy(((char *)&doubleValue), char_buf, typeSize); + + if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid, + doubleValue))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + } + } + break; + } /* H5T_FLOAT */ + case H5T_REFERENCE: { + /* Convert each element to a list */ + jboolean bb; + jbyte *barray = NULL; + + jsize byteArraySize = (jsize)typeSize; + if (typeSize != (size_t)byteArraySize) + H5_JNI_FATAL_ERROR(ENVONLY, "translate_atomic_rbuf: overflow of byteArraySize"); + + if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb, + "translate_atomic_rbuf reference: byte array not pinned"); + + HDmemcpy(barray, ((jbyte *)raw_buf), typeSize); + if (barray) + UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT); + + break; + } /* H5T_REFERENCE */ + case H5T_STRING: { + htri_t is_variable = 0; + + if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + /* Convert each element */ + if (is_variable) { + char **var_str_buf = (char **)raw_buf; + if (NULL == (jobj = ENVPTR->NewStringUTF(ENVONLY, *var_str_buf))) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: out of memory - unable to " + "construct string from UTF characters"); + } + } + else { + if (NULL == (jobj = ENVPTR->NewStringUTF(ENVONLY, char_buf))) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_rbuf: out of memory - unable to " + "construct string from UTF characters"); + } + } + + break; + } /* H5T_STRING */ + default: + H5_UNIMPLEMENTED(ENVONLY, "translate_atomic_rbuf: invalid class type"); + break; + } /* switch(type_class) */ + +done: + + return jobj; +} + +void +translate_atomic_wbuf(JNIEnv *env, jobject in_obj, jlong mem_type_id, H5T_class_t type_class, void *raw_buf) +{ + hid_t memb = H5I_INVALID_HID; + H5T_class_t vlClass; + size_t vlSize; + size_t i, x; + size_t typeSize; + // raw_buf is normally bytes except when used for variable length strings + char *char_buf = (char *)raw_buf; + + /* retrieve the java.util.ArrayList interface class */ + jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList"); + /* retrieve the toArray method */ + jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, arrCList, "toArray", "()[Ljava/lang/Object;"); + + /* Cache class types */ + jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); + jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); + jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); + jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); + jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); + jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); + + jmethodID byteValueMid = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B"); + jmethodID shortValueMid = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S"); + jmethodID intValueMid = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I"); + jmethodID longValueMid = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J"); + jmethodID floatValueMid = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F"); + jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D"); + + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + switch (type_class) { + case H5T_VLEN: { + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class((hid_t)memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + /* Convert element to a vlen element */ + hvl_t vl_elem; + + jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, in_obj); + + if (jnelmts < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_wbuf: number of VL elements < 0"); + + vl_elem.len = (size_t)jnelmts; + + if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_wbuf: failed to allocate vlen ptr buffer"); + + translate_wbuf(ENVONLY, (jobjectArray)in_obj, memb, vlClass, (jsize)jnelmts, vl_elem.p); + + HDmemcpy(char_buf, &vl_elem, sizeof(hvl_t)); + break; + } /* H5T_VLEN */ + case H5T_COMPOUND: { + void *objBuf = NULL; + + /* Convert each compound element */ + int nmembs = H5Tget_nmembers(mem_type_id); + + /* invoke the toArray method */ + if (mToArray == NULL) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, in_obj, mToArray); + jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array); + + if (jnelmts != nmembs) + H5_BAD_ARGUMENT_ERROR( + ENVONLY, "translate_atomic_wbuf: number of elements not equal to number of members"); + + /* Convert each compound object to an element */ + for (i = 0; i < (size_t)nmembs; i++) { + H5T_class_t memb_vlClass; + size_t memb_vlSize; + size_t memb_offset; + + if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if ((memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)i)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if ((memb_vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(memb_vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + jobject arr_obj = ENVPTR->GetObjectArrayElement(ENVONLY, array, i); + translate_atomic_wbuf(ENVONLY, arr_obj, memb, memb_vlClass, + char_buf + i * typeSize + memb_offset); + ENVPTR->DeleteLocalRef(ENVONLY, arr_obj); + H5Tclose(memb); + } + break; + } /* H5T_COMPOUND */ + case H5T_ARRAY: { + void *objBuf = NULL; + + if (!(memb = H5Tget_super(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + if ((vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + /* Convert each array element */ + /* invoke the toArray method */ + if (mToArray == NULL) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, in_obj, mToArray); + jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array); + + if (jnelmts < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_atomic_wbuf: number of array elements < 0"); + + if (NULL == (objBuf = HDmalloc((size_t)jnelmts * vlSize))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_atomic_wbuf: failed to allocate buffer"); + + translate_wbuf(ENVONLY, array, memb, vlClass, (jsize)jnelmts, objBuf); + + HDmemcpy(char_buf, (char *)objBuf, vlSize * jnelmts); + break; + } /* H5T_ARRAY */ + case H5T_ENUM: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_INTEGER: { + /* Convert each element */ + switch (typeSize) { + case sizeof(jbyte): { + jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, in_obj, byteValueMid); + HDmemcpy(char_buf, ((char *)&byteValue), typeSize); + } + case sizeof(jshort): { + jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, in_obj, shortValueMid); + HDmemcpy(char_buf, ((char *)&shortValue), typeSize); + break; + } + case sizeof(jint): { + jint intValue = ENVPTR->CallIntMethod(ENVONLY, in_obj, intValueMid); + HDmemcpy(char_buf, ((char *)&intValue), typeSize); + break; + } + case sizeof(jlong): { + jlong longValue = ENVPTR->CallLongMethod(ENVONLY, in_obj, longValueMid); + HDmemcpy(char_buf, ((char *)&longValue), typeSize); + break; + } + } + break; + } /* H5T_INTEGER */ + case H5T_FLOAT: { + /* Convert each element */ + switch (typeSize) { + case sizeof(jfloat): { + jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, in_obj, floatValueMid); + HDmemcpy(char_buf, ((char *)&floatValue), typeSize); + break; + } + case sizeof(jdouble): { + jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, in_obj, doubleValueMid); + HDmemcpy(char_buf, ((char *)&doubleValue), typeSize); + break; + } + } + break; + } /* H5T_FLOAT */ + case H5T_REFERENCE: { + /* Convert each array element */ + jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, in_obj, 0); + HDmemcpy(char_buf, ((char *)barray), typeSize); + ENVPTR->ReleaseByteArrayElements(ENVONLY, in_obj, barray, 0); + break; + } /* H5T_REFERENCE */ + case H5T_STRING: { + htri_t is_variable = 0; + + if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + /* Convert each pointer element */ + jsize length; + const char *utf8 = NULL; + + HDmemset(char_buf, 0, typeSize); + if (NULL != in_obj) { + PIN_JAVA_STRING(ENVONLY, in_obj, utf8, NULL, "translate_atomic_wbuf jobj not pinned"); + length = ENVPTR->GetStringUTFLength(ENVONLY, in_obj); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + if (is_variable) { + char *new_buf = (char *)HDcalloc((size_t)1, length + 1); + HDmemcpy(((char *)new_buf), utf8, length); + HDmemcpy(char_buf, &new_buf, typeSize); + } + else { + HDmemcpy(char_buf, utf8, length); + } + UNPIN_JAVA_STRING(ENVONLY, in_obj, utf8); + utf8 = NULL; + } + break; + } /* H5T_STRING */ + default: + H5_UNIMPLEMENTED(ENVONLY, "translate_atomic_wbuf: invalid class type"); + break; + } /* switch(type_class) */ + +done: + + return; +} + +void +translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, jsize count, + void *raw_buf) +{ + hid_t memb = H5I_INVALID_HID; + int ret_buflen = -1; + jboolean found_jList = JNI_TRUE; + jobjectArray jList = NULL; + jobject jobj = NULL; + H5T_class_t vlClass; + size_t vlSize; + size_t i, x; + size_t typeSize; + // raw_buf is normally bytes except when used for variable length strings + char *char_buf = (char *)raw_buf; + + /* retrieve the java.util.ArrayList interface class */ + jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList"); + jmethodID arrListMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "<init>", "(I)V"); + jmethodID arrAddMethod = ENVPTR->GetMethodID(ENVONLY, arrCList, "add", "(Ljava/lang/Object;)Z"); + + /* Cache class types */ + jclass cByte = ENVPTR->FindClass(ENVONLY, "java/lang/Byte"); + jclass cShort = ENVPTR->FindClass(ENVONLY, "java/lang/Short"); + jclass cInt = ENVPTR->FindClass(ENVONLY, "java/lang/Integer"); + jclass cLong = ENVPTR->FindClass(ENVONLY, "java/lang/Long"); + jclass cFloat = ENVPTR->FindClass(ENVONLY, "java/lang/Float"); + jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double"); + jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;"); + jmethodID shortValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;"); + jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;"); + jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;"); + jmethodID floatValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;"); + jmethodID doubleValueMid = + ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;"); + + if (!(typeSize = H5Tget_size(mem_type_id))) + H5_LIBRARY_ERROR(ENVONLY); + + ret_buflen = ENVPTR->GetArrayLength(ENVONLY, ret_buf); switch (type_class) { case H5T_VLEN: { if (!(memb = H5Tget_super(mem_type_id))) @@ -4090,13 +4577,13 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t /* Convert each element to a list */ for (i = 0; i < (size_t)count; i++) { - hvl_t vl_elem; - jboolean found_jList = JNI_TRUE; - int ret_buflen = -1; - jobjectArray jList = NULL; + hvl_t vl_elem; + + found_jList = JNI_TRUE; + jList = NULL; /* Get the number of sequence elements */ - HDmemcpy(&vl_elem, (char *)raw_buf + i * sizeof(hvl_t), sizeof(hvl_t)); + HDmemcpy(&vl_elem, char_buf + i * sizeof(hvl_t), sizeof(hvl_t)); jsize nelmts = (jsize)vl_elem.len; if (vl_elem.len != (size_t)nelmts) H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of number of VL elements"); @@ -4104,7 +4591,6 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t if (nelmts < 0) H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_rbuf: number of VL elements < 0"); - ret_buflen = ENVPTR->GetArrayLength(ENVONLY, ret_buf); /* The list we're going to return: */ if (i < ret_buflen) { jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i); @@ -4125,64 +4611,70 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t if (!addResult) H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: cannot add VL element"); } + else { + ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, i, (jobject)jList); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + } ENVPTR->DeleteLocalRef(ENVONLY, jList); } break; } /* H5T_VLEN */ case H5T_COMPOUND: { - int nmembs = H5Tget_nmembers(mem_type_id); - void *objBuf = NULL; - size_t offset; - - if (!(memb = H5Tget_super(mem_type_id))) - H5_LIBRARY_ERROR(ENVONLY); - if ((vlClass = H5Tget_class(memb)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (!(vlSize = H5Tget_size(memb))) - H5_LIBRARY_ERROR(ENVONLY); - - if (nmembs < 0) - goto done; - - /* Convert each element to a list */ - for (i = 0; i < (size_t)nmembs; i++) { - jboolean found_jList = JNI_TRUE; - jobjectArray jList = NULL; - int ret_buflen = -1; - - if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)i)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - offset = H5Tget_member_offset(mem_type_id, (unsigned int)i); - - if ((vlClass = H5Tget_class(memb)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - if (!(vlSize = H5Tget_size(memb))) - H5_LIBRARY_ERROR(ENVONLY); + void *objBuf = NULL; - /* Get the object element */ - HDmemcpy(&objBuf, (char *)raw_buf + offset, vlSize); + /* Convert each compound element to a list */ + for (i = 0; i < (size_t)count; i++) { + found_jList = JNI_TRUE; + jList = NULL; - ret_buflen = ENVPTR->GetArrayLength(ENVONLY, ret_buf); /* The list we're going to return: */ if (i < ret_buflen) { - if (NULL == - (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i))) - found_jList = JNI_FALSE; + jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)ret_buf, (jsize)i); } if (NULL == jList) { + found_jList = JNI_FALSE; if (NULL == (jList = (jobjectArray)ENVPTR->NewObject(ENVONLY, arrCList, arrListMethod, 0))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_rbuf: failed to allocate list read buffer"); } + int nmembs = H5Tget_nmembers(mem_type_id); + /* Convert each element to a list */ + for (x = 0; x < (size_t)nmembs; x++) { + H5T_class_t memb_vlClass; + size_t memb_vlSize; + size_t memb_offset; + + if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)x)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if ((memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)x)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)1, objBuf); - if (!found_jList) { - ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList); - ENVPTR->DeleteLocalRef(ENVONLY, jList); + if ((memb_vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(memb_vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + jobj = translate_atomic_rbuf(ENVONLY, jList, memb, memb_vlClass, + char_buf + i * typeSize + memb_offset); + if (jobj) { + if (found_jList == JNI_FALSE) + ENVPTR->CallBooleanMethod(ENVONLY, jList, arrAddMethod, (jobject)jobj); + else + ENVPTR->SetObjectArrayElement(ENVONLY, jList, i, (jobject)jobj); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + ENVPTR->DeleteLocalRef(ENVONLY, jobj); + } + + H5Tclose(memb); } + if (ret_buflen == 0) + ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList); + else + ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, i, jList); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + ENVPTR->DeleteLocalRef(ENVONLY, jList); } - H5Tclose(memb); break; } /* H5T_COMPOUND */ case H5T_ARRAY: { @@ -4195,7 +4687,6 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t H5_LIBRARY_ERROR(ENVONLY); if (!(vlSize = H5Tget_size(memb))) H5_LIBRARY_ERROR(ENVONLY); - if (!(typeSize = H5Tget_size(mem_type_id))) H5_LIBRARY_ERROR(ENVONLY); @@ -4206,14 +4697,12 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t /* Convert each element to a list */ for (i = 0; i < (size_t)count; i++) { - jboolean found_jList = JNI_TRUE; - jobjectArray jList = NULL; - int ret_buflen = -1; + found_jList = JNI_TRUE; + jList = NULL; /* Get the object element */ - HDmemcpy((char *)objBuf, (char *)raw_buf + i * typeSize, typeSize); + HDmemcpy((char *)objBuf, char_buf + i * typeSize, typeSize); - ret_buflen = ENVPTR->GetArrayLength(ENVONLY, ret_buf); /* The list we're going to return: */ if (i < ret_buflen) { if (NULL == @@ -4228,10 +4717,12 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t } translate_rbuf(ENVONLY, jList, memb, vlClass, (jsize)typeCount, objBuf); - if (!found_jList) { + if (found_jList == JNI_FALSE) ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jList); - ENVPTR->DeleteLocalRef(ENVONLY, jList); - } + else + ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, i, jList); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + ENVPTR->DeleteLocalRef(ENVONLY, jList); } if (objBuf) @@ -4239,130 +4730,28 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t break; } /* H5T_ARRAY */ - case H5T_INTEGER: { - /* Convert each element to a list */ - for (i = 0; i < (size_t)count; i++) { - jobject jobj = NULL; - switch (typeSize) { - case sizeof(jbyte): { - jbyte byteValue; - for (x = 0; x < typeSize; x++) { - ((char *)&byteValue)[x] = ((char *)raw_buf)[i * typeSize + x]; - } - - if (NULL == - (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jshort): { - jshort shortValue; - for (x = 0; x < typeSize; x++) { - ((char *)&shortValue)[x] = ((char *)raw_buf)[i * typeSize + x]; - } - - if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid, - shortValue))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jint): { - jint intValue; - for (x = 0; x < typeSize; x++) { - ((char *)&intValue)[x] = ((char *)raw_buf)[i * typeSize + x]; - } - - if (NULL == - (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jlong): { - jlong longValue; - for (x = 0; x < typeSize; x++) { - ((char *)&longValue)[x] = ((char *)raw_buf)[i * typeSize + x]; - } - - if (NULL == - (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - } - if (jobj) { - ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jobj); - ENVPTR->DeleteLocalRef(ENVONLY, jobj); - } - else { - } - } - break; - } /* H5T_INTEGER */ - case H5T_FLOAT: { - /* Convert each element to a list */ - for (i = 0; i < (size_t)count; i++) { - jobject jobj = NULL; - switch (typeSize) { - case sizeof(jfloat): { - jfloat floatValue; - for (x = 0; x < typeSize; x++) { - ((char *)&floatValue)[x] = ((char *)raw_buf)[i * typeSize + x]; - } - - if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid, - (double)floatValue))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - case sizeof(jdouble): { - jdouble doubleValue; - for (x = 0; x < typeSize; x++) { - ((char *)&doubleValue)[x] = ((char *)raw_buf)[i * typeSize + x]; - } - - if (NULL == (jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid, - doubleValue))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } - } - if (jobj) { - ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jobj); - ENVPTR->DeleteLocalRef(ENVONLY, jobj); - } - } - break; - } /* H5T_FLOAT */ - case H5T_REFERENCE: { + case H5T_ENUM: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_INTEGER: + case H5T_FLOAT: + case H5T_REFERENCE: + case H5T_STRING: { /* Convert each element to a list */ for (i = 0; i < (size_t)count; i++) { - jboolean bb; - jbyte *barray = NULL; - jobject jobj = NULL; - - jsize byteArraySize = (jsize)typeSize; - if (typeSize != (size_t)byteArraySize) - H5_JNI_FATAL_ERROR(ENVONLY, "translate_rbuf: overflow of byteArraySize"); - - if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb, - "translate_rbuf reference: byte array not pinned"); - - for (x = 0; x < typeSize; x++) { - barray[x] = ((jbyte *)raw_buf)[i * typeSize + x]; - } - if (barray) - UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT); - + jobj = + translate_atomic_rbuf(ENVONLY, ret_buf, mem_type_id, type_class, char_buf + i * typeSize); if (jobj) { - ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, jobj); + if (ret_buflen == 0) + ENVPTR->CallBooleanMethod(ENVONLY, ret_buf, arrAddMethod, (jobject)jobj); + else + ENVPTR->SetObjectArrayElement(ENVONLY, ret_buf, i, (jobject)jobj); + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); ENVPTR->DeleteLocalRef(ENVONLY, jobj); } } break; - } /* H5T_REFERENCE */ + } default: H5_UNIMPLEMENTED(ENVONLY, "translate_rbuf: invalid class type"); break; @@ -4370,21 +4759,22 @@ translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t done: - return (jint)status; + return; } -herr_t +void translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t type_class, jsize count, - jbyte *raw_buf) + void *raw_buf) { - herr_t status = FAIL; - hid_t memb = H5I_INVALID_HID; - jobjectArray jList = NULL; - jobject jobj = NULL; + hid_t memb = H5I_INVALID_HID; + jobjectArray jList = NULL; + jobject jobj = NULL; H5T_class_t vlClass; size_t vlSize; size_t i, x; size_t typeSize; + // raw_buf is normally bytes except when used for variable length strings + char *char_buf = (char *)raw_buf; /* retrieve the java.util.ArrayList interface class */ jclass arrCList = ENVPTR->FindClass(ENVONLY, "java/util/ArrayList"); @@ -4441,16 +4831,59 @@ translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_wbuf: failed to allocate vlen ptr buffer"); - translate_wbuf(ENVONLY, (jobjectArray)array, memb, vlClass, (jsize)jnelmts, vl_elem.p); + translate_wbuf(ENVONLY, array, memb, vlClass, (jsize)jnelmts, vl_elem.p); - HDmemcpy((char *)raw_buf + i * sizeof(hvl_t), &vl_elem, sizeof(hvl_t)); + HDmemcpy(char_buf + i * sizeof(hvl_t), &vl_elem, sizeof(hvl_t)); ENVPTR->DeleteLocalRef(ENVONLY, jList); } /* end for (i = 0; i < count; i++) */ break; } /* H5T_VLEN */ case H5T_COMPOUND: { - H5_UNIMPLEMENTED(ENVONLY, "translate_wbuf: invalid H5T_COMPOUND type"); + void *objBuf = NULL; + + /* Convert each list to a compound element */ + for (i = 0; i < (size_t)count; i++) { + if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + int nmembs = H5Tget_nmembers(mem_type_id); + + /* invoke the toArray method */ + if (mToArray == NULL) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + jobjectArray array = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray); + jsize jnelmts = ENVPTR->GetArrayLength(ENVONLY, array); + + if (jnelmts != nmembs) + H5_BAD_ARGUMENT_ERROR( + ENVONLY, "translate_wbuf: number of elements not equal to number of members"); + + /* Convert each compound object to an element */ + for (x = 0; x < (size_t)nmembs; x++) { + H5T_class_t memb_vlClass; + size_t memb_vlSize; + size_t memb_offset; + + if ((memb = H5Tget_member_type(mem_type_id, (unsigned int)x)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if ((memb_offset = H5Tget_member_offset(mem_type_id, (unsigned int)x)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if ((memb_vlClass = H5Tget_class(memb)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (!(memb_vlSize = H5Tget_size(memb))) + H5_LIBRARY_ERROR(ENVONLY); + + jobject arr_obj = ENVPTR->GetObjectArrayElement(ENVONLY, array, x); + translate_atomic_wbuf(ENVONLY, arr_obj, memb, memb_vlClass, + char_buf + i * typeSize + memb_offset); + ENVPTR->DeleteLocalRef(ENVONLY, arr_obj); + H5Tclose(memb); + } + + ENVPTR->DeleteLocalRef(ENVONLY, jList); + } /* end for (i = 0; i < count; i++) */ break; } /* H5T_COMPOUND */ case H5T_ARRAY: { @@ -4477,91 +4910,25 @@ translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t if (jnelmts < 0) H5_BAD_ARGUMENT_ERROR(ENVONLY, "translate_wbuf: number of array elements < 0"); - if (NULL == (objBuf = HDmalloc((size_t)jnelmts * vlSize))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "translate_wbuf: failed to allocate buffer"); - - translate_wbuf(ENVONLY, (jobjectArray)array, memb, vlClass, (jsize)jnelmts, objBuf); - - HDmemcpy((char *)raw_buf + i * vlSize * jnelmts, (char *)objBuf, vlSize * jnelmts); + translate_wbuf(ENVONLY, array, memb, vlClass, (jsize)jnelmts, + char_buf + i * vlSize * jnelmts); // objBuf); ENVPTR->DeleteLocalRef(ENVONLY, jList); } /* end for (i = 0; i < count; i++) */ break; } /* H5T_ARRAY */ - case H5T_INTEGER: { - /* Convert each list to an array element */ - for (i = 0; i < (size_t)count; i++) { - if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - switch (typeSize) { - case sizeof(jbyte): { - jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid); - for (x = 0; x < typeSize; x++) { - ((char *)raw_buf)[i * typeSize + x] = ((char *)&byteValue)[x]; - } - break; - } - case sizeof(jshort): { - jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid); - for (x = 0; x < typeSize; x++) { - ((char *)raw_buf)[i * typeSize + x] = ((char *)&shortValue)[x]; - } - break; - } - case sizeof(jint): { - jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid); - for (x = 0; x < typeSize; x++) { - ((char *)raw_buf)[i * typeSize + x] = ((char *)&intValue)[x]; - } - break; - } - case sizeof(jlong): { - jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid); - for (x = 0; x < typeSize; x++) { - ((char *)raw_buf)[i * typeSize + x] = ((char *)&longValue)[x]; - } - break; - } - } - ENVPTR->DeleteLocalRef(ENVONLY, jobj); - } - break; - } /* H5T_INTEGER */ - case H5T_FLOAT: { - /* Convert each list to an array element */ - for (i = 0; i < (size_t)count; i++) { - if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i))) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - switch (typeSize) { - case sizeof(jfloat): { - jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid); - for (x = 0; x < typeSize; x++) { - ((char *)raw_buf)[i * typeSize + x] = ((char *)&floatValue)[x]; - } - break; - } - case sizeof(jdouble): { - jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid); - for (x = 0; x < typeSize; x++) { - ((char *)raw_buf)[i * typeSize + x] = ((char *)&doubleValue)[x]; - } - break; - } - } - ENVPTR->DeleteLocalRef(ENVONLY, jobj); - } - break; - } /* H5T_FLOAT */ - case H5T_REFERENCE: { + case H5T_ENUM: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_INTEGER: + case H5T_FLOAT: + case H5T_REFERENCE: + case H5T_STRING: { /* Convert each list to an array element */ for (i = 0; i < (size_t)count; i++) { if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)in_buf, (jsize)i))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0); - for (x = 0; x < typeSize; x++) { - ((char *)raw_buf)[i * typeSize + x] = ((char *)barray)[x]; - } - ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0); + translate_atomic_wbuf(ENVONLY, jobj, mem_type_id, type_class, char_buf + i * typeSize); ENVPTR->DeleteLocalRef(ENVONLY, jobj); } break; @@ -4573,7 +4940,7 @@ translate_wbuf(JNIEnv *env, jobjectArray in_buf, jlong mem_type_id, H5T_class_t done: - return (jint)status; + return; } #ifdef __cplusplus diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h index 27c9178..d8ecef9 100644 --- a/java/src/jni/h5util.h +++ b/java/src/jni/h5util.h @@ -51,10 +51,10 @@ extern int h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr, int b extern htri_t H5Tdetect_variable_str(hid_t tid); -extern herr_t translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, - jsize count, jbyte *raw_buf); -extern herr_t translate_wbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, - jsize count, jbyte *raw_buf); +extern void translate_rbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, + jsize count, void *raw_buf); +extern void translate_wbuf(JNIEnv *env, jobjectArray ret_buf, jlong mem_type_id, H5T_class_t type_class, + jsize count, void *raw_buf); /* * Symbols used to format the output of h5str_sprintf and diff --git a/java/test/TestH5A.java b/java/test/TestH5A.java index d17e16c..90fe24c 100644 --- a/java/test/TestH5A.java +++ b/java/test/TestH5A.java @@ -46,6 +46,7 @@ public class TestH5A { private static final int DIM_Y = 6; long H5fid = HDF5Constants.H5I_INVALID_HID; long H5dsid = HDF5Constants.H5I_INVALID_HID; + long H5atid = HDF5Constants.H5I_INVALID_HID; long H5did = HDF5Constants.H5I_INVALID_HID; long[] H5dims = {DIM_X, DIM_Y}; long type_id = HDF5Constants.H5I_INVALID_HID; @@ -136,8 +137,12 @@ public class TestH5A { } catch (Exception ex) { } - - _deleteFile(H5_FILE); + if (H5atid > 0) + try { + H5.H5Tclose(H5atid); + } + catch (Exception ex) { + } if (type_id > 0) try { @@ -163,6 +168,8 @@ public class TestH5A { } catch (Exception ex) { } + + _deleteFile(H5_FILE); System.out.println(); } @@ -1072,7 +1079,7 @@ public class TestH5A { HDF5Constants.H5P_DEFAULT); assertTrue("testH5Awrite_readVL: ", attr_id >= 0); - H5.H5Awrite_VLStrings(attr_id, atype_id, str_data); + H5.H5AwriteVL(attr_id, atype_id, str_data); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); @@ -1084,7 +1091,7 @@ public class TestH5A { strs[j] = ""; } try { - H5.H5Aread_VLStrings(attr_id, atype_id, strs); + H5.H5AreadVL(attr_id, atype_id, strs); } catch (Exception ex) { ex.printStackTrace(); @@ -1863,4 +1870,134 @@ public class TestH5A { } } } + + @Test + public void testH5AArray_string_buffer() throws Throwable + { + String att_str_name = "ArrayStringdata"; + long att_str_id = HDF5Constants.H5I_INVALID_HID; + long atype_str_id = HDF5Constants.H5I_INVALID_HID; + long aspace_id = HDF5Constants.H5I_INVALID_HID; + long[] strdims = {4}; + long[] dims = {6}; + long lsize = 1; + + String[] str_data0 = {"Parting", "is such", "sweet", "sorrow."}; + String[] str_data1 = {"Testing", "one", "two", "three."}; + String[] str_data2 = {"Dog,", "man's", "best", "friend."}; + String[] str_data3 = {"Diamonds", "are", "a", "girls!"}; + String[] str_data4 = {"S A", "T U R", "D A Y", "night"}; + String[] str_data5 = {"That's", "all", "folks", "!!!"}; + + ArrayList[] arr_str_data = new ArrayList[6]; + arr_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0)); + arr_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1)); + arr_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2)); + arr_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3)); + arr_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4)); + arr_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5)); + + try { + H5atid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); + } + catch (Throwable err) { + err.printStackTrace(); + fail("testH5AArray_string_buffer.H5.H5Tcopy: " + err); + } + assertTrue("testH5AArray_string_buffer.H5Tcopy: ", H5atid >= 0); + try { + H5.H5Tset_size(H5atid, HDF5Constants.H5T_VARIABLE); + assertTrue("testH5AArray_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5atid)); + } + catch (Throwable err) { + err.printStackTrace(); + fail("testH5DArray_string_buffer.H5Tset_size: " + err); + } + try { + atype_str_id = H5.H5Tarray_create(H5atid, 1, strdims); + assertTrue("testH5AArray_string_buffer.H5Tarray_create: ", atype_str_id >= 0); + } + catch (Exception err) { + if (atype_str_id > 0) + try { + H5.H5Tclose(atype_str_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5AArray_string_buffer: " + err); + } + + try { + aspace_id = H5.H5Screate_simple(1, dims, null); + assertTrue(aspace_id > 0); + att_str_id = H5.H5Acreate(H5did, att_str_name, atype_str_id, aspace_id, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + assertTrue("testH5AArray_string_buffer: ", att_str_id >= 0); + + H5.H5AwriteVL(att_str_id, atype_str_id, arr_str_data); + } + catch (Exception err) { + if (att_str_id > 0) + try { + H5.H5Dclose(att_str_id); + } + catch (Exception ex) { + } + if (atype_str_id > 0) + try { + H5.H5Tclose(atype_str_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5AArray_string_buffer: " + err); + } + finally { + if (aspace_id > 0) + try { + H5.H5Sclose(aspace_id); + } + catch (Exception ex) { + } + } + + H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); + + for (int j = 0; j < dims.length; j++) + lsize *= dims[j]; + + ArrayList[] arr_readbuf = new ArrayList[6]; + for (int j = 0; j < lsize; j++) + arr_readbuf[j] = new ArrayList<String>(); + + try { + H5.H5AreadVL(att_str_id, atype_str_id, arr_readbuf); + } + catch (Exception ex) { + ex.printStackTrace(); + } + finally { + if (att_str_id > 0) + try { + H5.H5Aclose(att_str_id); + } + catch (Exception ex) { + } + if (atype_str_id > 0) + try { + H5.H5Tclose(atype_str_id); + } + catch (Exception ex) { + } + } + assertTrue("testH5AArray_string_buffer:" + arr_readbuf[0].get(0), + arr_str_data[0].get(0).equals(arr_readbuf[0].get(0))); + assertTrue("testH5AArray_string_buffer:" + arr_readbuf[1].get(0), + arr_str_data[1].get(0).equals(arr_readbuf[1].get(0))); + assertTrue("testH5AArray_string_buffer:" + arr_readbuf[2].get(0), + arr_str_data[2].get(0).equals(arr_readbuf[2].get(0))); + assertTrue("testH5AArray_string_buffer:" + arr_readbuf[3].get(0), + arr_str_data[3].get(0).equals(arr_readbuf[3].get(0))); + } } diff --git a/java/test/TestH5D.java b/java/test/TestH5D.java index f204e38..eacaabf 100644 --- a/java/test/TestH5D.java +++ b/java/test/TestH5D.java @@ -158,7 +158,7 @@ public class TestH5D { assertTrue("TestH5D._createDataset.H5Dcreate: ", H5did >= 0); } - private final void _createVLDataset(long fid, long dsid, String name, long dapl) + private final void _createVLStrDataset(String name, long dapl) { try { H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); @@ -167,24 +167,24 @@ public class TestH5D { err.printStackTrace(); fail("H5.H5Tcopy: " + err); } - assertTrue("TestH5D._createVLDataset.H5Tcopy: ", H5dtid >= 0); + assertTrue("TestH5D._createVLStrDataset.H5Tcopy: ", H5dtid >= 0); try { H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE); - assertTrue("TestH5D._createVLDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid)); + assertTrue("TestH5D._createVLStrDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid)); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Tset_size: " + err); } try { - H5did = H5.H5Dcreate(fid, name, H5dtid, dsid, HDF5Constants.H5P_DEFAULT, + H5did = H5.H5Dcreate(H5fid, name, H5dtid, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } - assertTrue("TestH5D._createVLDataset.H5Dcreate: ", H5did >= 0); + assertTrue("TestH5D._createVLStrDataset.H5Dcreate: ", H5did >= 0); } private final void _closeH5file() throws HDF5LibraryException @@ -935,7 +935,7 @@ public class TestH5D { buf_data[(indx * DIM_Y) + jndx] == 126); } - @Test + @Ignore public void testH5Dvlen_get_buf_size() { String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.", @@ -946,12 +946,12 @@ public class TestH5D { for (int idx = 0; idx < str_data.length; idx++) str_data_bytes += str_data[idx].length() + 1; // Account for terminating null - _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + _createVLStrDataset("dset", HDF5Constants.H5P_DEFAULT); try { if ((H5did >= 0) && (H5dtid >= 0)) - H5.H5Dwrite_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_data); + H5.H5DwriteVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_data); } catch (Exception e) { e.printStackTrace(); @@ -966,25 +966,121 @@ public class TestH5D { } @Ignore - public void testH5Dvlen_read_default_buffer() throws Throwable + public void testH5Dvlen_string_buffer() throws Throwable { - String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.", - "Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!", - "S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!"}; - byte[] read_data = new byte[512]; + String dset_str_name = "VLStringdata"; + long dset_str_id = HDF5Constants.H5I_INVALID_HID; + long dtype_str_id = HDF5Constants.H5I_INVALID_HID; + long dspace_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {64}; + long lsize = 1; - _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + String[] str_data0 = {"Parting", "is such", "sweet", "sorrow."}; + String[] str_data1 = {"Testing", "one", "two", "three."}; + String[] str_data2 = {"Dog,", "man's", "best", "friend."}; + String[] str_data3 = {"Diamonds", "are", "a", "girls!"}; + String[] str_data4 = {"S A", "T U R", "D A Y", "night"}; + String[] str_data5 = {"That's", "all", "folks", "!!!"}; + + ArrayList[] vl_str_data = new ArrayList[6]; + vl_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0)); + vl_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1)); + vl_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2)); + vl_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3)); + vl_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4)); + vl_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5)); try { - H5.H5Dwrite_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_data); + H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); } - catch (Exception e) { - e.printStackTrace(); + catch (Throwable err) { + err.printStackTrace(); + fail("testH5Dvlen_string_buffer.H5.H5Tcopy: " + err); + } + assertTrue("testH5Dvlen_string_buffer.H5Tcopy: ", H5dtid >= 0); + try { + H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE); + assertTrue("testH5Dvlen_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid)); + } + catch (Throwable err) { + err.printStackTrace(); + fail("testH5Dvlen_string_buffer.H5Tset_size: " + err); + } + try { + dtype_str_id = H5.H5Tvlen_create(H5dtid); + assertTrue("testH5Dvlen_string_buffer.H5Tvlen_create: ", dtype_str_id >= 0); + } + catch (Exception err) { + if (dtype_str_id > 0) + try { + H5.H5Tclose(dtype_str_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5Dvlen_string_buffer: " + err); } - H5.H5Dread(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, - read_data); + try { + dspace_id = H5.H5Screate_simple(1, dims, null); + assertTrue(dspace_id > 0); + dset_str_id = + H5.H5Dcreate(H5fid, dset_str_name, dtype_str_id, dspace_id, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + assertTrue("testH5Dvlen_string_buffer: ", dset_str_id >= 0); + + H5.H5DwriteVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_str_data); + } + catch (Exception err) { + if (dset_str_id > 0) + try { + H5.H5Dclose(dset_str_id); + } + catch (Exception ex) { + } + if (dtype_str_id > 0) + try { + H5.H5Tclose(dtype_str_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5Dvlen_string_buffer: " + err); + } + finally { + if (dspace_id > 0) + try { + H5.H5Sclose(dspace_id); + } + catch (Exception ex) { + } + } + + H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); + + for (int j = 0; j < dims.length; j++) + lsize *= dims[j]; + + ArrayList[] vl_readbuf = new ArrayList[4]; + for (int j = 0; j < lsize; j++) + vl_readbuf[j] = new ArrayList<String>(); + + try { + H5.H5DreadVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, vl_readbuf); + } + catch (Exception ex) { + ex.printStackTrace(); + } + assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[0].get(0), + vl_str_data[0].get(0).equals(vl_readbuf[0].get(0))); + assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[1].get(0), + vl_str_data[1].get(0).equals(vl_readbuf[1].get(0))); + assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[2].get(0), + vl_str_data[2].get(0).equals(vl_readbuf[2].get(0))); + assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[3].get(0), + vl_str_data[3].get(0).equals(vl_readbuf[3].get(0))); } @Test @@ -995,20 +1091,21 @@ public class TestH5D { "S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!"}; String[] str_rdata = new String[DIM_X * DIM_Y]; - _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + _createVLStrDataset("dset", HDF5Constants.H5P_DEFAULT); try { if ((H5did >= 0) && (H5dtid >= 0)) - H5.H5Dwrite_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_wdata); + H5.H5DwriteVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_wdata); } catch (Exception e) { e.printStackTrace(); } + try { if ((H5did >= 0) && (H5dtid >= 0)) - H5.H5Dread_VLStrings(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_rdata); + H5.H5DreadVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_rdata); } catch (Exception e) { e.printStackTrace(); @@ -1158,46 +1255,46 @@ public class TestH5D { lsize *= dims[j]; // Read Integer data - ArrayList[] vl_readbuf = new ArrayList[4]; + ArrayList[] vl_int_readbuf = new ArrayList[4]; for (int j = 0; j < lsize; j++) - vl_readbuf[j] = new ArrayList<Integer>(); + vl_int_readbuf[j] = new ArrayList<Integer>(); try { H5.H5DreadVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_readbuf); + HDF5Constants.H5P_DEFAULT, vl_int_readbuf); } catch (Exception ex) { ex.printStackTrace(); } - assertTrue("testH5DVLwr:" + vl_readbuf[0].get(0), - vl_int_data[0].get(0).equals(vl_readbuf[0].get(0))); - assertTrue("testH5DVLwr:" + vl_readbuf[1].get(0), - vl_int_data[1].get(0).equals(vl_readbuf[1].get(0))); - assertTrue("testH5DVLwr:" + vl_readbuf[2].get(0), - vl_int_data[2].get(0).equals(vl_readbuf[2].get(0))); - assertTrue("testH5DVLwr:" + vl_readbuf[3].get(0), - vl_int_data[3].get(0).equals(vl_readbuf[3].get(0))); + assertTrue("testH5DVLwr:" + vl_int_readbuf[0].get(0), + vl_int_data[0].get(0).equals(vl_int_readbuf[0].get(0))); + assertTrue("testH5DVLwr:" + vl_int_readbuf[1].get(0), + vl_int_data[1].get(0).equals(vl_int_readbuf[1].get(0))); + assertTrue("testH5DVLwr:" + vl_int_readbuf[2].get(0), + vl_int_data[2].get(0).equals(vl_int_readbuf[2].get(0))); + assertTrue("testH5DVLwr:" + vl_int_readbuf[3].get(0), + vl_int_data[3].get(0).equals(vl_int_readbuf[3].get(0))); // Read Double data - vl_readbuf = new ArrayList[4]; + ArrayList[] vl_dbl_readbuf = new ArrayList[4]; for (int j = 0; j < lsize; j++) - vl_readbuf[j] = new ArrayList<Double>(); + vl_dbl_readbuf[j] = new ArrayList<Double>(); try { H5.H5DreadVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, vl_readbuf); + HDF5Constants.H5P_DEFAULT, vl_dbl_readbuf); } catch (Exception ex) { ex.printStackTrace(); } - assertTrue("testH5DVLwr:" + vl_readbuf[0].get(0), - vl_dbl_data[0].get(0).equals(vl_readbuf[0].get(0))); - assertTrue("testH5DVLwr:" + vl_readbuf[1].get(0), - vl_dbl_data[1].get(0).equals(vl_readbuf[1].get(0))); - assertTrue("testH5DVLwr:" + vl_readbuf[2].get(0), - vl_dbl_data[2].get(0).equals(vl_readbuf[2].get(0))); - assertTrue("testH5DVLwr:" + vl_readbuf[3].get(0), - vl_dbl_data[3].get(0).equals(vl_readbuf[3].get(0))); + assertTrue("testH5DVLwr:" + vl_dbl_readbuf[0].get(0), + vl_dbl_data[0].get(0).equals(vl_dbl_readbuf[0].get(0))); + assertTrue("testH5DVLwr:" + vl_dbl_readbuf[1].get(0), + vl_dbl_data[1].get(0).equals(vl_dbl_readbuf[1].get(0))); + assertTrue("testH5DVLwr:" + vl_dbl_readbuf[2].get(0), + vl_dbl_data[2].get(0).equals(vl_dbl_readbuf[2].get(0))); + assertTrue("testH5DVLwr:" + vl_dbl_readbuf[3].get(0), + vl_dbl_data[3].get(0).equals(vl_dbl_readbuf[3].get(0))); } catch (Throwable err) { err.printStackTrace(); @@ -1524,4 +1621,330 @@ public class TestH5D { } } } + + @Test + public void testH5DArray_string_buffer() throws Throwable + { + String dset_str_name = "ArrayStringdata"; + long dset_str_id = HDF5Constants.H5I_INVALID_HID; + long dtype_str_id = HDF5Constants.H5I_INVALID_HID; + long dspace_id = HDF5Constants.H5I_INVALID_HID; + long[] strdims = {4}; + long[] dims = {6}; + long lsize = 1; + + String[] str_data0 = {"Parting", "is such", "sweet", "sorrow."}; + String[] str_data1 = {"Testing", "one", "two", "three."}; + String[] str_data2 = {"Dog,", "man's", "best", "friend."}; + String[] str_data3 = {"Diamonds", "are", "a", "girls!"}; + String[] str_data4 = {"S A", "T U R", "D A Y", "night"}; + String[] str_data5 = {"That's", "all", "folks", "!!!"}; + + ArrayList[] arr_str_data = new ArrayList[6]; + arr_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0)); + arr_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1)); + arr_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2)); + arr_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3)); + arr_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4)); + arr_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5)); + + try { + H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); + } + catch (Throwable err) { + err.printStackTrace(); + fail("testH5DArray_string_buffer.H5.H5Tcopy: " + err); + } + assertTrue("testH5DArray_string_buffer.H5Tcopy: ", H5dtid >= 0); + try { + H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE); + assertTrue("testH5DArray_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid)); + } + catch (Throwable err) { + err.printStackTrace(); + fail("testH5DArray_string_buffer.H5Tset_size: " + err); + } + try { + dtype_str_id = H5.H5Tarray_create(H5dtid, 1, strdims); + assertTrue("testH5DArray_string_buffer.H5Tarray_create: ", dtype_str_id >= 0); + } + catch (Exception err) { + if (dtype_str_id > 0) + try { + H5.H5Tclose(dtype_str_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5DArray_string_buffer: " + err); + } + + try { + dspace_id = H5.H5Screate_simple(1, dims, null); + assertTrue(dspace_id > 0); + dset_str_id = + H5.H5Dcreate(H5fid, dset_str_name, dtype_str_id, dspace_id, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + assertTrue("testH5DArray_string_buffer: ", dset_str_id >= 0); + + H5.H5DwriteVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, arr_str_data); + } + catch (Exception err) { + if (dset_str_id > 0) + try { + H5.H5Dclose(dset_str_id); + } + catch (Exception ex) { + } + if (dtype_str_id > 0) + try { + H5.H5Tclose(dtype_str_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5DArray_string_buffer: " + err); + } + finally { + if (dspace_id > 0) + try { + H5.H5Sclose(dspace_id); + } + catch (Exception ex) { + } + } + + H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); + + for (int j = 0; j < dims.length; j++) + lsize *= dims[j]; + + ArrayList[] arr_readbuf = new ArrayList[6]; + for (int j = 0; j < lsize; j++) + arr_readbuf[j] = new ArrayList<String>(); + + try { + H5.H5DreadVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, arr_readbuf); + } + catch (Exception ex) { + ex.printStackTrace(); + } + finally { + if (dset_str_id > 0) + try { + H5.H5Dclose(dset_str_id); + } + catch (Exception ex) { + } + if (dtype_str_id > 0) + try { + H5.H5Tclose(dtype_str_id); + } + catch (Exception ex) { + } + } + assertTrue("testH5DArray_string_buffer:" + arr_readbuf[0].get(0), + arr_str_data[0].get(0).equals(arr_readbuf[0].get(0))); + assertTrue("testH5DArray_string_buffer:" + arr_readbuf[1].get(0), + arr_str_data[1].get(0).equals(arr_readbuf[1].get(0))); + assertTrue("testH5DArray_string_buffer:" + arr_readbuf[2].get(0), + arr_str_data[2].get(0).equals(arr_readbuf[2].get(0))); + assertTrue("testH5DArray_string_buffer:" + arr_readbuf[3].get(0), + arr_str_data[3].get(0).equals(arr_readbuf[3].get(0))); + } + + @Test + public void testH5DArrayenum_rw() + { + String dset_enum_name = "ArrayEnumdata"; + long dset_enum_id = HDF5Constants.H5I_INVALID_HID; + long dtype_enum_id = HDF5Constants.H5I_INVALID_HID; + long dtype_arr_enum_id = HDF5Constants.H5I_INVALID_HID; + long dspace_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {4}; + long lsize = 1; + String enum_type = "Enum_type"; + byte[] enum_val = new byte[1]; + String enum_name = null; + + // Create a enumerate datatype + try { + dtype_enum_id = H5.H5Tcreate(HDF5Constants.H5T_ENUM, (long)1); + assertTrue("testH5DArrayenum_wr.H5Tarray_create: ", dtype_enum_id >= 0); + } + catch (Throwable err) { + if (dtype_enum_id > 0) + try { + H5.H5Tclose(dtype_enum_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5DArrayenum_rw:H5Tcreate " + err); + } + + try { + enum_val[0] = 10; + H5.H5Tenum_insert(dtype_enum_id, "RED", enum_val); + enum_val[0] = 11; + H5.H5Tenum_insert(dtype_enum_id, "GREEN", enum_val); + enum_val[0] = 12; + H5.H5Tenum_insert(dtype_enum_id, "BLUE", enum_val); + enum_val[0] = 13; + H5.H5Tenum_insert(dtype_enum_id, "ORANGE", enum_val); + enum_val[0] = 14; + H5.H5Tenum_insert(dtype_enum_id, "YELLOW", enum_val); + + // Query member number and member index by member name, for enumeration type. + assertTrue("Can't get member number", H5.H5Tget_nmembers(dtype_enum_id) == 5); + assertTrue("Can't get correct index number", + H5.H5Tget_member_index(dtype_enum_id, "ORANGE") == 3); + + // Commit enumeration datatype and close it */ + H5.H5Tcommit(H5fid, enum_type, dtype_enum_id, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + + H5.H5Tclose(dtype_enum_id); + + // Open the dataytpe for query + dtype_enum_id = H5.H5Topen(H5fid, enum_type, HDF5Constants.H5P_DEFAULT); + assertTrue("testH5DArrayenum_rw:H5Tcreate", dtype_enum_id >= 0); + + // Query member number and member index by member name, for enumeration type + assertTrue("Can't get member number", H5.H5Tget_nmembers(dtype_enum_id) == 5); + assertTrue("Can't get correct index number", + H5.H5Tget_member_index(dtype_enum_id, "ORANGE") == 3); + + // Query member value by member name, for enumeration type + H5.H5Tenum_valueof(dtype_enum_id, "ORANGE", enum_val); + assertTrue("Incorrect value for enum member", enum_val[0] == 13); + + // Query member value by member index, for enumeration type + H5.H5Tget_member_value(dtype_enum_id, 2, enum_val); + assertTrue("Incorrect value for enum member", enum_val[0] == 12); + + // Query member name by member value, for enumeration type + enum_val[0] = 14; + enum_name = H5.H5Tenum_nameof(dtype_enum_id, enum_val, 16); + assertTrue("Incorrect name for enum member", enum_name.compareTo("YELLOW") == 0); + + ArrayList[] arr_enum_data = new ArrayList[4]; + try { + // Write Integer data + arr_enum_data[0] = new ArrayList<Integer>(Arrays.asList(10, 11, 12, 13)); + arr_enum_data[1] = new ArrayList<Integer>(Arrays.asList(11, 12, 13, 14)); + arr_enum_data[2] = new ArrayList<Integer>(Arrays.asList(12, 13, 14, 10)); + arr_enum_data[3] = new ArrayList<Integer>(Arrays.asList(13, 14, 10, 11)); + Class dataClass = arr_enum_data.getClass(); + assertTrue("testH5DArrayenum_wr.getClass: " + dataClass, dataClass.isArray()); + + try { + dtype_arr_enum_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_U32LE, 1, dims); + assertTrue("testH5DArrayenum_wr.H5Tarray_create: ", dtype_arr_enum_id >= 0); + } + catch (Exception err) { + if (dtype_arr_enum_id > 0) + try { + H5.H5Tclose(dtype_arr_enum_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("H5.testH5DArrayenum_wr: " + err); + } + + dspace_id = H5.H5Screate_simple(1, dims, null); + assertTrue(dspace_id > 0); + dset_enum_id = H5.H5Dcreate(H5fid, dset_enum_name, dtype_arr_enum_id, dspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + assertTrue("testH5DVLwr: ", dset_enum_id >= 0); + + H5.H5DwriteVL(dset_enum_id, dtype_arr_enum_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, arr_enum_data); + } + catch (Throwable err) { + if (dset_enum_id > 0) + try { + H5.H5Dclose(dset_enum_id); + } + catch (Exception ex) { + } + if (dtype_enum_id > 0) + try { + H5.H5Tclose(dtype_enum_id); + } + catch (Exception ex) { + } + if (dtype_arr_enum_id > 0) + try { + H5.H5Tclose(dtype_arr_enum_id); + } + catch (Exception ex) { + } + err.printStackTrace(); + fail("testH5DArrayenum_rw:query " + err); + } + finally { + if (dspace_id > 0) + try { + H5.H5Sclose(dspace_id); + } + catch (Exception ex) { + } + } + + H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); + + for (int j = 0; j < dims.length; j++) + lsize *= dims[j]; + + // Read Integer data + ArrayList[] arr_readbuf = new ArrayList[4]; + for (int j = 0; j < lsize; j++) + arr_readbuf[j] = new ArrayList<Integer>(); + + try { + H5.H5DreadVL(dset_enum_id, dtype_arr_enum_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, arr_readbuf); + } + catch (Exception ex) { + ex.printStackTrace(); + } + assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[0].get(0), + arr_enum_data[0].get(0).equals(arr_readbuf[0].get(0))); + assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[1].get(0), + arr_enum_data[1].get(0).equals(arr_readbuf[1].get(0))); + assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[2].get(0), + arr_enum_data[2].get(0).equals(arr_readbuf[2].get(0))); + assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[3].get(0), + arr_enum_data[3].get(0).equals(arr_readbuf[3].get(0))); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.testH5DArrayenum_wr: " + err); + } + finally { + if (dset_enum_id > 0) + try { + H5.H5Dclose(dset_enum_id); + } + catch (Exception ex) { + } + if (dtype_enum_id > 0) + try { + H5.H5Tclose(dtype_enum_id); + } + catch (Exception ex) { + } + if (dtype_arr_enum_id > 0) + try { + H5.H5Tclose(dtype_arr_enum_id); + } + catch (Exception ex) { + } + } + } } diff --git a/java/test/testfiles/JUnit-TestH5A.txt b/java/test/testfiles/JUnit-TestH5A.txt index 49e5c97..f31c86c 100644 --- a/java/test/testfiles/JUnit-TestH5A.txt +++ b/java/test/testfiles/JUnit-TestH5A.txt @@ -29,9 +29,10 @@ JUnit version 4.11 .testH5Adelete_by_idx_null .testH5Adelete_by_idx_invalidobject .testH5Awrite_readVL +.testH5AArray_string_buffer .testH5Aget_info1 Time: XXXX -OK (31 tests) +OK (32 tests) diff --git a/java/test/testfiles/JUnit-TestH5D.txt b/java/test/testfiles/JUnit-TestH5D.txt index 19abd80..4c30621 100644 --- a/java/test/testfiles/JUnit-TestH5D.txt +++ b/java/test/testfiles/JUnit-TestH5D.txt @@ -1,4 +1,5 @@ JUnit version 4.11 +.testH5DArrayenum_rw .testH5DVLwrVL .testH5Dget_storage_size .testH5DArraywr @@ -14,8 +15,8 @@ JUnit version 4.11 .testH5Dget_storage_size_empty .testH5Diterate .testH5Dget_access_plist -.testH5Dvlen_get_buf_size .testH5Dget_space_closed +.testH5DArray_string_buffer .testH5Dget_space_status .testH5Dvlen_write_read .testH5Dget_space @@ -23,5 +24,5 @@ JUnit version 4.11 Time: XXXX -OK (21 tests) +OK (22 tests) |