mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-25 04:09:44 +03:00
Scot Breitenfeld
39fa3e5538
Implements the two overloads specified in RFC-HDFG-2026-001
sec:modify-bindings -- one taking a String, one an int[] -- mirroring
the existing H5Pappend_filter overloads.
Both Java binding paths are covered, since the tree maintains two:
- JNI (java/src-jni): two private native methods dispatched from the
public overloads, plus the JNI implementations and declarations in
h5pDCPLImp.c/.h, following the H5Pappend_filter_str/_raw pattern
exactly.
- Panama/FFM (java/hdf): the H5Z_params_t struct is built directly in
an Arena and passed to the generated org.hdfgroup.javahdf5.hdf5_h
downcall, as the append string form already does. Unlike the append
case the cd_values form cannot delegate to H5Pmodify_filter, which
addresses an entry by filter ID and resolves to the first match
rather than by index, so it constructs the struct explicitly. The
generated binding is produced by jextract from the public headers,
so it picks up the new declaration automatically.
Adds testH5Pmodify_filter_by_idx_string and
testH5Pmodify_filter_by_idx_cdvalues to TestH5Z.java and updates the
JUnit golden file. Placement and the test count were derived from
@FixMethodOrder(MethodSorters.NAME_ASCENDING) rather than guessed, and
the file's surrounding format is unchanged.
Not compile-verified locally: this configuration has HDF5_BUILD_JAVA
OFF and the machine has a JRE but no JDK (no javac) and no jextract, so
nothing under java/ can be built here. The C library still builds clean
and the full C/Fortran suite is unchanged. What was checked statically:
the JNI symbol names against the mangling rule (underscores in the Java
method name become _1) and against the existing append pair; the
H5Z_params_t offsets (int type at 0, union at 8, cd_nelmts at 8,
cd_values at 16, 24 bytes total on 64-bit) and the enum values
(H5Z_PARAMS_CDVALUES 0, H5Z_PARAMS_STRING 1) against H5Zpublic.h; and
the H5Pget_filter call in the new test against the working call in
testH5Pappend_filter_cdvalues. Java CI should be treated as the real
gate.
446 lines
18 KiB
Java
446 lines
18 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the LICENSE file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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package test;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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import static org.junit.Assert.fail;
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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.HDF5Constants;
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import hdf.hdf5lib.exceptions.HDF5LibraryException;
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import org.junit.After;
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import org.junit.Before;
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import org.junit.FixMethodOrder;
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import org.junit.Rule;
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import org.junit.Test;
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import org.junit.rules.TestName;
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import org.junit.runners.MethodSorters;
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@FixMethodOrder(MethodSorters.NAME_ASCENDING)
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public class TestH5Z {
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@Rule
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public TestName testname = new TestName();
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@Before
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public void checkOpenIDs()
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{
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assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
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System.out.print(testname.getMethodName());
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}
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@After
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public void nextTestName()
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{
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System.out.println();
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}
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@Test
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public void testH5Zfilter_avail()
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{
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try {
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int filter_found;
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filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_FLETCHER32);
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assertTrue("H5.H5Zfilter_avail_FLETCHER32", filter_found > 0);
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filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_NBIT);
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assertTrue("H5.H5Zfilter_avail_NBIT", filter_found > 0);
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filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET);
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assertTrue("H5.H5Zfilter_avail_SCALEOFFSET", filter_found > 0);
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filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE);
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assertTrue("H5.H5Zfilter_avail_SHUFFLE", filter_found > 0);
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// Just make sure H5Zfilter_avail() doesn't fail with szip/zlib
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// since there is no way for us to determine if they should be present
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// or not.
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filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE);
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filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Zfilter_avail " + err);
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}
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}
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@Test
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public void testH5Zget_filter_info()
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{
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try {
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int filter_flag;
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filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_FLETCHER32);
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assertTrue("H5.H5Zget_filter_info_FLETCHER32_DECODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
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assertTrue("H5.H5Zget_filter_info_FLETCHER32_ENCODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
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filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_NBIT);
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assertTrue("H5.H5Zget_filter_info_NBIT_DECODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
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assertTrue("H5.H5Zget_filter_info_NBIT_ENCODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
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filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET);
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assertTrue("H5.H5Zget_filter_info_SCALEOFFSET_DECODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
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assertTrue("H5.H5Zget_filter_info_SCALEOFFSET_ENCODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
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filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE);
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assertTrue("H5.H5Zget_filter_info_DECODE_SHUFFLE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
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assertTrue("H5.H5Zget_filter_info_ENCODE_SHUFFLE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
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if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
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filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE);
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assertTrue("H5.H5Zget_filter_info_DEFLATE_DECODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
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assertTrue("H5.H5Zget_filter_info_DEFLATE_ENCODE_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
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}
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if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP)) {
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filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SZIP);
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// Decode should always be available, but we have no way of determining
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// if encode is so don't assert on that.
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assertTrue("H5.H5Zget_filter_info_DECODE_SZIP_ENABLED",
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(filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
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}
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Zget_filter_info " + err);
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}
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}
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@Test
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public void testH5Zget_filter_class_info()
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{
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try {
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hdf.hdf5lib.structs.H5Z_class_info_t info;
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// DEFLATE (if available)
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if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
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info = H5.H5Zget_filter_class_info(HDF5Constants.H5Z_FILTER_DEFLATE);
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assertTrue("H5Zget_filter_class_info: info must not be null", info != null);
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assertTrue("H5Zget_filter_class_info: DEFLATE id",
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info.id == HDF5Constants.H5Z_FILTER_DEFLATE);
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assertTrue("H5Zget_filter_class_info: DEFLATE decode flag",
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(info.config_flags & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) != 0);
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}
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// SHUFFLE
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info = H5.H5Zget_filter_class_info(HDF5Constants.H5Z_FILTER_SHUFFLE);
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assertTrue("H5Zget_filter_class_info: SHUFFLE info must not be null", info != null);
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assertTrue("H5Zget_filter_class_info: SHUFFLE id", info.id == HDF5Constants.H5Z_FILTER_SHUFFLE);
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assertTrue("H5Zget_filter_class_info: SHUFFLE decode flag",
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(info.config_flags & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) != 0);
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// FLETCHER32
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info = H5.H5Zget_filter_class_info(HDF5Constants.H5Z_FILTER_FLETCHER32);
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assertTrue("H5Zget_filter_class_info: FLETCHER32 info must not be null", info != null);
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assertTrue("H5Zget_filter_class_info: FLETCHER32 id",
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info.id == HDF5Constants.H5Z_FILTER_FLETCHER32);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Zget_filter_class_info " + err);
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}
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}
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@Test(expected = HDF5LibraryException.class)
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public void testH5Zget_filter_class_info_invalid() throws Throwable
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{
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H5.H5Zget_filter_class_info(32999);
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}
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@Test(expected = HDF5LibraryException.class)
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public void testH5Zunregister_predefined() throws Throwable
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{
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int filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE);
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assertTrue("H5.H5Zfilter_avail", filter_found > 0);
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H5.H5Zunregister(HDF5Constants.H5Z_FILTER_SHUFFLE);
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}
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@Test
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public void testH5Pappend_filter_string()
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{
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long dcpl_id = HDF5Constants.H5I_INVALID_HID;
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try {
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dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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assertTrue("H5Pcreate", dcpl_id >= 0);
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int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_SHUFFLE, 0, "");
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assertTrue("H5Pappend_filter (string, shuffle)", ret >= 0);
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int nfilters = H5.H5Pget_nfilters(dcpl_id);
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assertEquals("nfilters after H5Pappend_filter", 1, nfilters);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Pappend_filter_string: " + err);
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}
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finally {
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if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
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try {
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H5.H5Pclose(dcpl_id);
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}
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catch (Exception e) { /* ignore */
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}
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}
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}
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@Test
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public void testH5Pappend_filter_cdvalues()
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{
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long dcpl_id = HDF5Constants.H5I_INVALID_HID;
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try {
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dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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assertTrue("H5Pcreate", dcpl_id >= 0);
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int[] cd_values = new int[] {9};
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if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
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int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_DEFLATE, 0, cd_values);
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assertTrue("H5Pappend_filter (cd_values, deflate)", ret >= 0);
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int nfilters = H5.H5Pget_nfilters(dcpl_id);
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assertEquals("nfilters after H5Pappend_filter", 1, nfilters);
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// Verify the cd_values round-trip via H5Pget_filter.
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int[] cd_out = new int[1];
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int[] flags_out = new int[1];
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long[] cd_nelmts = new long[] {1};
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String[] name_out = new String[] {""};
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int filter_id =
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H5.H5Pget_filter(dcpl_id, 0, flags_out, cd_nelmts, cd_out, 256, name_out, new int[1]);
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assertEquals("filter id from H5Pget_filter", HDF5Constants.H5Z_FILTER_DEFLATE, filter_id);
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assertEquals("cd_nelmts", 1L, cd_nelmts[0]);
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assertEquals("cd_values[0] (deflate level)", 9, cd_out[0]);
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}
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Pappend_filter_cdvalues: " + err);
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}
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finally {
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if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
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try {
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H5.H5Pclose(dcpl_id);
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}
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catch (Exception e) { /* ignore */
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}
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}
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}
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@Test
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public void testH5Pmodify_filter_by_idx_string()
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{
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long dcpl_id = HDF5Constants.H5I_INVALID_HID;
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try {
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dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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assertTrue("H5Pcreate", dcpl_id >= 0);
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if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
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int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_DEFLATE, 0, "level=1");
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assertTrue("H5Pappend_filter (string, deflate)", ret >= 0);
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// Replace the configuration in place; position and ID are unchanged.
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ret = H5.H5Pmodify_filter_by_idx(dcpl_id, 0, 0, "level=9");
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assertTrue("H5Pmodify_filter_by_idx (string)", ret >= 0);
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int nfilters = H5.H5Pget_nfilters(dcpl_id);
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assertEquals("nfilters after H5Pmodify_filter_by_idx", 1, nfilters);
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// The entry keeps a stored string, which reports the new value.
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String[] params = new String[1];
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ret = H5.H5Pget_filter_params_by_idx(dcpl_id, 0, params);
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assertTrue("H5Pget_filter_params_by_idx", ret >= 0);
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assertNotNull("params[0] is non-null", params[0]);
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assertTrue("stored string reflects the modify: " + params[0],
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params[0].contains("level=9"));
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}
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Pmodify_filter_by_idx_string: " + err);
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}
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finally {
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if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
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try {
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H5.H5Pclose(dcpl_id);
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}
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catch (Exception e) { /* ignore */
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}
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}
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}
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@Test
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public void testH5Pmodify_filter_by_idx_cdvalues()
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{
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long dcpl_id = HDF5Constants.H5I_INVALID_HID;
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try {
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dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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assertTrue("H5Pcreate", dcpl_id >= 0);
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if (1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
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int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_DEFLATE, 0, "level=1");
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assertTrue("H5Pappend_filter (string, deflate)", ret >= 0);
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int[] cd_values = new int[] {6};
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ret = H5.H5Pmodify_filter_by_idx(dcpl_id, 0, 0, cd_values);
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assertTrue("H5Pmodify_filter_by_idx (cd_values)", ret >= 0);
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int nfilters = H5.H5Pget_nfilters(dcpl_id);
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assertEquals("nfilters after H5Pmodify_filter_by_idx", 1, nfilters);
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// cd_values were replaced.
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int[] cd_out = new int[1];
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int[] flags_out = new int[1];
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long[] cd_nelmts = new long[] {1};
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String[] name_out = new String[] {""};
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int filter_id =
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H5.H5Pget_filter(dcpl_id, 0, flags_out, cd_nelmts, cd_out, 256, name_out, new int[1]);
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assertEquals("filter id unchanged by modify", HDF5Constants.H5Z_FILTER_DEFLATE, filter_id);
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assertEquals("cd_values[0] after modify", 6, cd_out[0]);
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}
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Pmodify_filter_by_idx_cdvalues: " + err);
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}
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finally {
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if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
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try {
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H5.H5Pclose(dcpl_id);
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}
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catch (Exception e) { /* ignore */
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}
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}
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}
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@Test
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public void testH5Pget_filter_params_by_idx()
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{
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long dcpl_id = HDF5Constants.H5I_INVALID_HID;
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try {
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dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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assertTrue("H5Pcreate", dcpl_id >= 0);
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int ret = H5.H5Pappend_filter(dcpl_id, HDF5Constants.H5Z_FILTER_SHUFFLE, 0, "");
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assertTrue("H5Pappend_filter shuffle", ret >= 0);
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String[] params = new String[1];
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int retval = H5.H5Pget_filter_params_by_idx(dcpl_id, 0, params);
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assertTrue("H5Pget_filter_params_by_idx returned non-negative", retval >= 0);
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assertNotNull("params[0] is non-null", params[0]);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Pget_filter_params_by_idx: " + err);
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}
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finally {
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if (dcpl_id != HDF5Constants.H5I_INVALID_HID)
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try {
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H5.H5Pclose(dcpl_id);
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}
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catch (Exception e) { /* ignore */
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}
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}
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}
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@Test
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public void testH5Zconfig_get_param_int()
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{
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try {
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String cfg = "level = 6";
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long[] val = new long[1];
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int ret = H5.H5Zconfig_get_param(cfg, "level", val);
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assertTrue("H5Zconfig_get_param (int) returned non-negative", ret >= 0);
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assertEquals("H5Zconfig_get_param (int) value", 6L, val[0]);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("testH5Zconfig_get_param_int: " + err);
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Zconfig_get_param_double()
|
|
{
|
|
try {
|
|
String cfg = "scale = 1.5";
|
|
double[] val = new double[1];
|
|
int ret = H5.H5Zconfig_get_param(cfg, "scale", val);
|
|
assertTrue("H5Zconfig_get_param (double) returned non-negative", ret >= 0);
|
|
assertEquals("H5Zconfig_get_param (double) value", 1.5, val[0], 1e-10);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Zconfig_get_param_double: " + err);
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Zconfig_get_param_bool()
|
|
{
|
|
try {
|
|
String cfg = "lossless = true";
|
|
boolean[] val = new boolean[1];
|
|
int ret = H5.H5Zconfig_get_param(cfg, "lossless", val);
|
|
assertTrue("H5Zconfig_get_param (bool) returned non-negative", ret >= 0);
|
|
assertTrue("H5Zconfig_get_param (bool) value", val[0]);
|
|
|
|
String cfg2 = "lossless = false";
|
|
int ret2 = H5.H5Zconfig_get_param(cfg2, "lossless", val);
|
|
assertTrue("H5Zconfig_get_param (bool, false) returned non-negative", ret2 >= 0);
|
|
assertFalse("H5Zconfig_get_param (bool) value (false)", val[0]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Zconfig_get_param_bool: " + err);
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Zconfig_get_param_str()
|
|
{
|
|
try {
|
|
String cfg = "mode = \"fast\"";
|
|
String[] val = new String[1];
|
|
int ret = H5.H5Zconfig_get_param(cfg, "mode", val);
|
|
assertTrue("H5Zconfig_get_param (str) returned non-negative", ret >= 0);
|
|
assertEquals("H5Zconfig_get_param (str) value", "fast", val[0]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Zconfig_get_param_str: " + err);
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Zconfig_get_param_missing_key()
|
|
{
|
|
try {
|
|
String cfg = "level = 5";
|
|
long[] val = new long[1];
|
|
int ret = H5.H5Zconfig_get_param(cfg, "missing_key", val);
|
|
assertTrue("H5Zconfig_get_param with missing key returns 0 (not found)", ret == 0);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Zconfig_get_param_missing_key: " + err);
|
|
}
|
|
}
|
|
}
|