/*
* Copyright 1998-2009 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
* Access and use of this software shall impose the following obligations
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
* supporting documentation. Further, UCAR requests that the user credit
* UCAR/Unidata in any publications that result from the use of this
* software or in any product that includes this software. The names UCAR
* and/or Unidata, however, may not be used in any advertising or publicity
* to endorse or promote any products or commercial entity unless specific
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* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
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*
* THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
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* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package ucar.nc2.iosp.hdf5;
import org.junit.experimental.categories.Category;
import ucar.ma2.Array;
import ucar.ma2.Index;
import ucar.nc2.NCdumpW;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Variable;
import ucar.nc2.dataset.NetcdfDataset;
import ucar.unidata.util.test.category.NeedsCdmUnitTest;
import ucar.unidata.util.test.TestDir;
import java.io.File;
import java.io.FileFilter;
import java.io.IOException;
/**
* TestSuite that runs all the sample testsNew
*
*/
@Category(NeedsCdmUnitTest.class)
public class TestH5 {
public static boolean dumpFile = false;
public static String testDir = TestDir.cdmUnitTestDir + "formats/hdf5/";
public static NetcdfFile open( String filename) {
try {
System.out.println("**** Open "+filename);
NetcdfFile ncfile = NetcdfFile.open(filename);
if (TestH5.dumpFile) System.out.println("open "+ncfile);
return ncfile;
} catch (java.io.IOException e) {
System.out.println(" fail = "+e);
e.printStackTrace();
assert(false);
return null;
}
}
public static NetcdfFile openH5( String filename) {
try {
System.out.println("**** Open "+ testDir+filename);
NetcdfFile ncfile = NetcdfFile.open( testDir+filename);
if (TestH5.dumpFile) System.out.println("open H5 "+ncfile);
return ncfile;
} catch (java.io.IOException e) {
System.out.println(" fail = "+e);
e.printStackTrace();
assert(false);
return null;
}
}
public static NetcdfDataset openH5dataset( String filename) {
try {
System.out.println("**** Open "+ testDir+filename);
NetcdfDataset ncfile = NetcdfDataset.openDataset( testDir+filename);
if (TestH5.dumpFile) System.out.println("open H5 "+ncfile);
return ncfile;
} catch (java.io.IOException e) {
System.out.println(" fail = "+e);
e.printStackTrace();
assert(false);
return null;
}
}
public static class H5FileFilter implements FileFilter {
public boolean accept(File file) {
String name = file.getPath();
return (name.endsWith(".h5") || name.endsWith(".H5") || name.endsWith(".he5") || name.endsWith(".nc"));
}
}
//////////////////////////////////////////////////////////////////////////
// file that is offset 2048 bytes - NPP!
@org.junit.Test
public void testSuperblockIsOffset() throws IOException {
try (NetcdfFile ncfile = TestH5.openH5("superblockIsOffsetNPP.h5")) {
Variable v = ncfile.findVariable("BeamTime");
System.out.printf("%s%n", v);
Array data = v.read();
System.out.printf("%s%n", NCdumpW.toString(data, "offset data", null));
Index ii = data.getIndex();
assert (data.getLong(ii.set(11, 93)) == 1718796166693743L);
}
}
// file that is offset 512 bytes - MatLab, using compact layout (!)
@org.junit.Test
public void testOffsetCompactLayout() throws IOException {
try (NetcdfFile ncfile = TestH5.openH5("matlab_cols.mat")) {
Variable v = ncfile.findVariable("b");
System.out.printf("%s%n", v);
Array data = v.read();
System.out.printf("%s%n", NCdumpW.toString(data, "offset data", null));
Index ii = data.getIndex();
assert (data.getDouble(ii.set(3, 2)) == 12.0);
}
}
// groups have a cycle using hard link
/*
$ h5dump h5ex_g_traverse.h5
HDF5 "h5ex_g_traverse.h5" {
GROUP "/" {
GROUP "group1" {
DATASET "dset1" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 1, 1 ) / ( 1, 1 ) }
DATA {
(0,0): 0
}
}
GROUP "group3" {
DATASET "dset2" {
HARDLINK "/group1/dset1"
}
GROUP "group4" {
GROUP "group1" {
GROUP "group5" {
HARDLINK "/group1"
}
}
GROUP "group2" {
}
}
}
}
GROUP "group2" {
HARDLINK "/group1/group3"
}
}
*/
@org.junit.Test
public void testGroupHardLinks() throws IOException {
try (NetcdfFile ncfile = TestH5.openH5("groupHasCycle.h5")) {
System.out.printf("%s%n", ncfile);
}
}
}