/*
* 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
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* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
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package ucar.nc2.iosp.hdf5;
import junit.framework.TestCase;
import java.io.IOException;
import java.io.FileFilter;
import java.io.File;
import ucar.nc2.*;
import ucar.unidata.util.StringUtil;
/**
* Class Description.
*
* @author caron
*/
public class TestH5ReadAndCount extends TestCase {
static public String testDir = TestH5.testDir;
public TestH5ReadAndCount(String name) {
super(name);
}
public void testReadAndCount() throws IOException {
System.out.println(" dims vars gatts atts strFlds groups");
read(testDir + "support/astrarr.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "support/attstr.h5", 0, 0, 1, 0, 0, 1);
read(testDir + "support/bitop.h5", 0, 4, 0, 6, 0, 1);
read(testDir + "support/bool.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/cenum.h5", 0, 1, 0, 1, 1, 0);
read(testDir + "support/cstr.h5", 0, 1, 0, 1, 2, 0);
read(testDir + "support/cuslab.h5", 0, 1, 0, 1, 3, 0);
read(testDir + "support/dstr.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/dstrarr.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/DSwith_array_member.h5", 0, 1, 0, 1, 2, 0);
read(testDir + "support/enum.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/SDS_array_type.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/short.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/time.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/uvlstr.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/vlslab.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "support/vlstra.h5", 0, 0, 1, 0, 0, 0);
read(testDir + "support/zip.h5", 0, 1, 0, 1, 0, 1);
read(testDir + "samples/bitfield.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/enum.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/enumcmpnd.h5", 0, 1, 0, 1, 1, 0);
read(testDir + "samples/f32be.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/f32le.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/f64be.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/f64le.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i16be.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i16le.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i32be.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i32le.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i64be.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i64le.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i8be.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/i8le.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/il32be.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/il32le.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/opaque.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/strings.h5", 0, 1, 0, 1, 0, 0);
read(testDir + "samples/u16be.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/u16le.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/u32be.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/u32le.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/u64be.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/u64le.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/u8be.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/u8le.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/ul32be.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "samples/ul32le.h5", 0, 1, 0, 2, 0, 0);
read(testDir + "complex/compound_complex.h5", 0, 1, 0, 1, 7, 0);
read(testDir + "complex/compound_native.h5", 0, 1, 0, 1, 12, 0);
System.out.println(" dims vars gatts atts strFlds groups");
read(testDir + "msg/test.h5", 0, 57, 157, 204, 0, 60);
read(testDir + "wrf/wrf_bdy_par.h5", 0, 50, 44, 338, 3, 3);
read(testDir + "wrf/wrf_input_par.h5", 0, 110, 43, 758, 3, 3);
read(testDir + "wrf/wrf_out_par.h5", 0, 73, 43, 499, 3, 3);
read(testDir + "wrf/wrf_bdy_seq.h5", 0, 50, 44, 338, 3, 2);
read(testDir + "wrf/wrf_input_seq.h5", 0, 110, 43, 758, 3, 2);
read(testDir + "wrf/wrf_out_seq.h5", 0, 73, 43, 499, 3, 2);
read(testDir + "npoess/ExampleFiles/AVAFO_NPP_d2003125_t10109_e101038_b9_c2005829155458_devl_Tst.h5", 0, 7, 12, 51, 0, 4);
read(testDir + "npoess/ExampleFiles/GDNBF-VNCCO_NPP_d2003125_t101038_e10116_b9_c2005829162517_dev.h5", 0, 24, 16, 104, 0, 6);
read(testDir + "npoess/ExampleFiles/GIMFT-VIVIO_NPP_d2003125_t101038_e10116_b9_c2005829173243_dev.h5", 0, 20, 16, 98, 0, 6);
read(testDir + "npoess/ExampleFiles/GMOFT-VOCCO_NPP_d2003125_t101038_e10116_b9_c2005829163632_dev.h5", 0, 41, 16, 134, 0, 6);
read(testDir + "npoess/ExampleFiles/GMOFT-VSSTO_NPP_d2003125_t101038_e10116_b9_c2005829165313_dev.h5", 0, 25, 16, 109, 0, 6);
read(testDir + "npoess/ExampleFiles/RVIRS_NPP_d2003125_t101038_e10116_b9_c200582917556_devl_Tst.h5", 0, 3, 8, 26, 0, 4);
read(testDir + "npoess/ExampleFiles/SVI01-GIMFG_NPP_d2003125_t101038_e10116_b9_c2005829153351_dev.h5", 0, 29, 15, 116, 0, 6);
read(testDir + "npoess/ExampleFiles/SVM04-GMOFG_NPP_d2003125_t101038_e10116_b9_c2005829171444_dev.h5", 0, 29, 15, 116, 0, 6);
read(testDir + "npoess/ExampleFiles/VI1BO_NPP_d2003125_t101038_e10116_b9_c2005829155954_devl_Tst.h5", 0, 6, 12, 43, 0, 4);
read(testDir + "npoess/ExampleFiles/VI2BO_NPP_d2003125_t101038_e10116_b9_c2005829165919_devl_Tst.h5", 0, 6, 12, 43, 0, 4);
read(testDir + "npoess/ExampleFiles/VLSTO-GMOFT_NPP_d2003125_t102618_e102646_b9_c2005830184722_de.h5", 0, 23, 16, 106, 0, 6);
read(testDir + "IASI/IASI_xxx_1C_M02_20070704193256Z_20070704211159Z_N_O_20070704211805Z.h5", 0, 28, 0, 790, 674, 10);
read(testDir + "IASI/IASI.h5", 0, 28, 0, 777, 661, 10);
read(testDir + "aura/OMI-Aura_L3-OMTO3e_2005m1214_v002-2006m0929t143855.he5", 2, 4, 20, 28, 0, 7);
read(testDir + "aura/MLS-Aura_L2GP-BrO_v01-52-c01_2007d029.he5", 5, 27, 7, 162, 0, 11); // */
// EOS Grids
System.out.println(" dims vars gatts atts strFlds groups");
read(testDir + "aura/MLS-Aura_L3DM-O3_v02-00-c01_2005d026.he5", 33, 83, 40, 512, 0, 30);
read(testDir + "aura/TES-Aura_L3-CH4-M2007m07_F01_04.he5", 3, 15, 27, 80, 0, 7);
read(testDir + "aura/TES-Aura_L3-CH4-M2007m08_F01_04.he5", 3, 15, 27, 80, 0, 7);
// EOS Swaths
read(testDir + "aura/OMI-Aura_L2-OMTO3_2007m0624t1616-o15646_v002-2007m0625t152428.he5", 5, 44, 21, 342, 0, 8);
read(testDir + "HIRDLS/HIR2ARSP_c3_na.he5", 4, 6, 8, 6, 0, 9);
read(testDir + "HIRDLS/HIRDLS1_v4.0.2a-aIrix-c2_2003d106.he5", 9, 77, 2, 158, 0, 8);
read(testDir + "HIRDLS/HIRDLS2-AFGL_b027_na.he5", 3, 72, 12, 357, 0, 9);
read(testDir + "HIRDLS/HIRDLS2-Aura73p_b029_2000d275.he5", 3, 102, 12, 523, 0, 9);
read(testDir + "HIRDLS/HIRPROF-AFGL_b038_na.he5", 4, 214, 11, 1072, 0, 8);
read(testDir + "HIRDLS/HIRPROF-Aura73p_b038_2000d275.he5", 4, 214, 11, 1072, 0, 8);
read(testDir + "HIRDLS/HIRPROF_v582v2.he5", 3, 71, 11, 356, 0, 9);
read(testDir + "HIRDLS/HIRRAD-Wells-10scans.he5", 5, 38, 10, 45, 0, 9);
}
private void read(String filename, int ndims, int nvars, int ngatts, int natts, int nstructFields, int ngroups) throws IOException {
NetcdfFile ncfile = NetcdfFile.open(filename);
Counter c = new Counter();
c.count(ncfile.getRootGroup());
if (false) {
filename = filename.substring(testDir.length() + 1);
filename = StringUtil.replace(filename, '\\', "/");
System.out.println("read(testDir+\"" + filename + "\"," + c.ndims + "," + c.nvars + "," + c.ngatts + "," + c.natts + "," + c.nstructFields
+ "," + c.ngroups + ");");
ncfile.close();
return;
}
print(ndims, c.ndims);
print(nvars, c.nvars);
print(ngatts, c.ngatts);
print(natts, c.natts);
print(nstructFields, c.nstructFields);
print(ngroups, c.ngroups);
System.out.println(" " + filename);
ncfile.close();
}
private class Counter {
int ndims, nvars, natts, ngatts, nstructFields, ngroups;
private void count(Group g) {
ndims += g.getDimensions().size();
nvars += g.getVariables().size();
ngatts += g.getAttributes().size();
ngroups += g.getGroups().size();
for (Variable v : g.getVariables()) {
natts += v.getAttributes().size();
if (v instanceof Structure) {
nstructFields += ((Structure) v).getVariables().size();
}
}
for (Group ng : g.getGroups())
count(ng);
}
}
private void print(int want, int have) {
System.out.format("%5d", have);
System.out.print((want != have) ? "*" : " ");
}
public void readAll() throws IOException {
readAllDir(testDir, new FileFilter() {
public boolean accept(File pathname) {
return pathname.getName().endsWith(".h5") || pathname.getName().endsWith(".he5");
}
});
}
public void readAllDir(String dirName, FileFilter ff) throws IOException {
System.out.println("---------------Reading directory " + dirName);
File allDir = new File(dirName);
File[] allFiles = allDir.listFiles();
if (null == allFiles) {
System.out.println("---------------INVALID " + dirName);
return;
}
for (File f : allFiles) {
String name = f.getAbsolutePath();
if (f.isDirectory())
continue;
if ((ff == null) || ff.accept(f))
read(name, 0, 0, 0, 0, 0, 0);
}
for (File f : allFiles) {
if (f.isDirectory())
readAllDir(f.getAbsolutePath(), ff);
}
}
public void problem() throws IOException {
//H5header.setDebugFlags(new ucar.nc2.util.DebugFlagsImpl("H4header/chunked"));
NetcdfFile ncfile = NetcdfFile.open(testDir + "eos/aura/MLS-Aura_L3DM-O3_v02-00-c01_2005d026.he5");
//Variable v = ncfile.findVariable("HDFEOS/GRIDS/OMI Column Amount O3/Data Fields/Reflectivity331");
//assert v != null;
//v.read();
}
}