package test.object.misc; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.File; import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; import java.io.PrintWriter; import java.lang.reflect.Array; import java.lang.reflect.Method; import java.text.DecimalFormat; import java.util.Arrays; import java.util.BitSet; import java.util.HashMap; import java.util.List; import java.util.StringTokenizer; import java.util.Vector; import javax.swing.tree.DefaultMutableTreeNode; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.HDFNativeData; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.object.Attribute; import ncsa.hdf.object.CompoundDS; import ncsa.hdf.object.Dataset; import ncsa.hdf.object.Datatype; import ncsa.hdf.object.FileFormat; import ncsa.hdf.object.Group; import ncsa.hdf.object.HObject; import ncsa.hdf.object.h4.H4File; import ncsa.hdf.object.h4.H4SDS; import ncsa.hdf.object.h5.H5CompoundDS; import ncsa.hdf.object.h5.H5Datatype; import ncsa.hdf.object.h5.H5File; import ncsa.hdf.object.h5.H5Group; import ncsa.hdf.object.h5.H5ScalarDS; public class DebugHDF { public static void main(final String[] args) { try { int[] libversion = {0, 0, 0}; H5.H5get_libversion(libversion); System.out.println(libversion[0]+"."+libversion[1]+"."+libversion[2]); } catch (Exception ex) {ex.printStackTrace();} // try { create_debug_file();} catch(Exception ex) {} // try { createStrDataset( "G:\\temp\\H5DatasetCreate.h5"); } catch(Exception ex) {} // try { createDataset( "E:\\temp\\H5DatasetCreate.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { testchunkchche(); } catch (Exception ex) {ex.printStackTrace();} // try { TestHDFcompound(); } catch (Exception ex) {ex.printStackTrace();} // try { TestHDFdelete( "E:\\temp\\H5DatasetDelete.h5"); } catch(Exception ex) {ex.printStackTrace();}/ // try { TestHDFcomment( "E:\\temp\\H5DatasetComment.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestHDFgenotype( "E:\\temp\\genotypes_chr22_CEU.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestHDFvector( "E:\\temp\\TestVector.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { testSizeof(); } catch(Exception ex) {ex.printStackTrace();} // try { testSDgetchunkinfo("E:\\temp\\MOD021KM.A2006016.0942.hdf"); } catch(Exception ex) {ex.printStackTrace();} // try { testEnum("E:\\temp\\MOD021KM.A2006016.0942.hdf"); } catch(Exception ex) {ex.printStackTrace();} // try { testHDF5OpenClose(); } catch(Exception ex) {ex.printStackTrace();} // try { testHDF5Write("E:\\temp\\TestHDF5Write.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestHDF5Misc("E:\\hdf-files\\TestHDF5Misc.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestHDF5Get("E:\\hdf-files\\TestHDF5Get.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestHDF5Copy("d:\\hdf-files\\hdf5_test.h5", "/arrays/Vdata with mixed types"); } catch(Exception ex) {ex.printStackTrace();} // try { TestHDF5Copy("d:\\hdf-files\\hdf5_test.h5", "/arrays"); } catch(Exception ex) {ex.printStackTrace();} // try { TestHDF5Copy("d:\\hdf-files\\hdf5_test.h5", "/datatypes/H5T_NATIVE_INT"); } catch(Exception ex) {ex.printStackTrace();} // try { testGetObjID(); } catch(Exception ex) {ex.printStackTrace();} // try { testFillValue( "E:\\temp\\TestFillValue.h5"); } catch(Exception ex) {} // try { TestGetOneRow("E:\\hdf-files\\hdf5_test.h5", "/arrays/Vdata with mixed types", 0); } catch(Exception ex) {ex.printStackTrace();} // try { TestGetOneRow("E:\\hdf-files\\HDF5FileDAOTest.h5", "/Group0/1/Table0"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5OpenClose("TestH5Object.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { checkMemory(); } catch(Exception ex) {ex.printStackTrace();} // try { testCompressedStrings("G:\\temp\\test.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { testCreateLongPath("G:\\temp\\test_hdf5_5_group_levels.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5Bug847("d:\\hdf-files\\h5bug847.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5ReadChunk("d:\\hdf-files\\ExampleHDF5.hdf5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5Bug863("d:\\hdf-files\\bug863.h5"); } catch(final Exception ex) {ex.printStackTrace();} // try { checkMemory(); } catch(Exception ex) {ex.printStackTrace();} // try { testConvertFromUnsignedC();} catch(Exception ex) {ex.printStackTrace();} // try { TestH5ReadPerf("d:\\hdf-files\\ushort_8kx8k_fast_order.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5ReadPerf("d:\\hdf-files\\ushort_8kx8k_fast_order.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5WriteFloats("g:\\temp\\t.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5Vlen("g:\\temp\\t.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5Array("g:\\temp\\t.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5DreadNIO("d:\\hdf-files\\ushort_8kx8k_fast_order.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestH5Compound2000Fields("g:\\temp\\h5comp2k.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestMemoryLeakOpenClose("D:\\hdf-files\\SAFNWC_MSG2_TPW__200807281015_CoMd.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { testTofwerkReaderBug1213("D:\\hdf-files\\bug1213_GCxGC_dummyData.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { testTofwerkReaderBug1213("D:\\hdf-files\\bug1213_GCxGC_dummyData_chunk100x200.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { testTofwerkReaderBug1213("G:\\Projects\\Java\\Release\\hdfview_release_test_files\\bug1213_GCxGC_dummyData_chunk10x20.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestMemoryLeak("D:\\hdf-files\\debug_memory_leak.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestBEAttr("G:\\temp\\TestBEAttr.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestVlenRead("d:\\hdf-files\\test_vlen.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { launchBrowser("http://www.armchairgeneral.com/tactics-101-021-intelligence-preparation-of-the-battlefield-in-urban-operations.htm"); } catch(Exception ex) {ex.printStackTrace();} // try { launchBrowser("G:\\Projects\\ERDC\\Data\\Hetereogenous_Objects\\Events_Intel-Report.pdf"); } catch(Exception ex) {ex.printStackTrace();} // try { launchBrowser("G:\\Projects\\ERDC\\Data\\Hetereogenous_Objects\\IPB_URL-Reference.txt"); } catch(Exception ex) {ex.printStackTrace();} // try { launchBrowser("G:\\Projects\\ERDC\\Data\\Hetereogenous_Objects\\Recon_Immersive-Video.avi"); } catch(Exception ex) {ex.printStackTrace();} // try { launchBrowser("G:\\Projects\\ERDC\\Data\\Hetereogenous_Objects\\Situation_Weather-XLS.xls"); } catch(Exception ex) {ex.printStackTrace();} // try { launchBrowser("G:\\Projects\\ERDC\\Data\\Hetereogenous_Objects\\Software_External-Link.txt"); } catch(Exception ex) {ex.printStackTrace();} // try { TestVlen("d:\\hdf-files\\test_vlen.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestPinning("G:\\Projects\\Rosetta\\debug\\test_pinning.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { createDataset("g:\\temp\\testDataset.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { TestVlen("d:\\hdf-files\\test_vlen.h5", FileFormat.WRITE); } catch(Exception ex) {ex.printStackTrace();} // try { TestVlen("d:\\hdf-files\\test_vlen_org.h5", FileFormat.READ); } catch(Exception ex) {ex.printStackTrace();} // try { TestVlen("g:\\temp\\test_vlen.h5", FileFormat.WRITE); } catch(Exception ex) {ex.printStackTrace();} // TestBit64(); // TestBitmask(); // TestBinaryWrite(1, 1); // TestBinaryWrite(9, 1); // TestBinaryWrite(15, 1); // TestBinaryWrite(127, 2); // TestBinaryWrite(2147483647, 2); // TestBinaryWrite(2147483647, 4); // TestBinaryWrite(9123456789123456789L, 8); // // try { TestBug1523("G:\\Projects\\HUGS\\data\\testfile02.h5.corrupt"); } catch(Exception ex) {ex.printStackTrace();} // try { TestBug1523("G:\\Projects\\HUGS\\data\\testfile02.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { createINF("G:\\temp\\inf.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { createNaN_INF("G:\\temp\\nan_inf.h5"); } catch(Exception ex) {ex.printStackTrace();} // try { testStrings("G:\\temp\\strs.h5"); } catch(Exception ex) {ex.printStackTrace();} // testVariableArity("null argument", null); // testVariableArity("no argument"); // testVariableArity("1 argument", 1); // testVariableArity("2 argument", 1,"string"); // testVariableArity("3 argument", 1,"string",2.59); // try { readDatatype(); } catch(Exception ex) {ex.printStackTrace();} // try { readTextFile("G:\\temp\\vlarsizes.txt"); } catch(Exception ex) {ex.printStackTrace();} // try {processa8apis(); } catch (Exception ex) {} // try {convertByte2Long(); } catch (Exception ex) {ex.printStackTrace();} // try {testH5IO("G:\\temp\\test.h5"); } catch (Exception ex) {ex.printStackTrace();} // try {testH5Core("G:\\temp\\test.h5"); } catch (Exception ex) {ex.printStackTrace();} // try {test1Dstrings("G:\\temp\\test.h5"); } catch (Exception ex) {ex.printStackTrace();} // try {testUpdateAttr("G:\\temp\\test.h5"); } catch (Exception ex) {ex.printStackTrace();} // try {testCreateVlenStr("G:\\temp\\test.h5"); } catch (Exception ex) {ex.printStackTrace();} // try {testH5TconvertStr(); } catch (Exception ex) {ex.printStackTrace();} // try {testH5DeleteDS("g:\\temp\\strs.h5"); } catch (Exception ex) {ex.printStackTrace();} // try {testExtendData("g:\\temp\\extended.h5", "dset", 1000, 1500); } catch (Exception ex) {ex.printStackTrace();} // try {createNestedcompound("g:\\temp\\nested_cmp.h5", "dset"); } catch (Exception ex) {ex.printStackTrace();} // try { testH5Vlen("G:\\temp\\str.h5") ; } catch (Exception ex) {ex.printStackTrace();} // try { testH5VlenObj("G:\\temp\\str2.h5") ; } catch (Exception ex) {ex.printStackTrace();} // try { testH5VlenAttr("G:\\temp\\vlen_str_attr.h5") ; } catch (Exception ex) {ex.printStackTrace();} // try {testRefData("g:\\temp\\refs.h5", "refs"); } catch (Exception ex) {ex.printStackTrace();} // try {testH5WriteDouble("g:\\temp\\double.h5"); } catch (Exception ex) {ex.printStackTrace();} // try {testGroupMemoryLeak("G:\\temp\\mem_leak.h5"); } catch (Exception ex) {ex.printStackTrace();} // try { testH5OflushCrash("G:\\temp\\H5Oflush_crash.h5"); } catch (Exception ex) {ex.printStackTrace();} // testPrintData(); //try { testObjReadData("g:\\temp\\dset.h5", "dset"); } catch (Exception ex) {ex.printStackTrace();} //try { testH5FileGet("g:\\temp\\dset.h5", "/dset/"); } catch (Exception ex) {ex.printStackTrace();} // try { // String fname = "g:\\temp\\dset.h5"; // new File(fname).delete(); // clean up existing file // // for (int i=0; i<10; i++) // testCreateDS(fname, "dset"+i); // // } catch (Exception ex) {ex.printStackTrace();} // try { testH5Write2D("g:\\temp\\dset.h5"); } catch (Exception ex) {ex.printStackTrace();} // try { testHDF4("g:\\temp\\test_hdf4.hdf"); } catch (Exception ex) {ex.printStackTrace();} //try { test3DHDF4("g:\\temp\\hdf3d.hdf", "3dint"); } catch (Exception ex) {ex.printStackTrace();} try { testH5DataType("G:\\temp\\H5Datatype.h5"); } catch (Exception ex) {ex.printStackTrace();} } public static void testRefData(String fname, String dname)throws Exception { int size = 10; long dims[] = {size}; long[] maxdims = {HDF5Constants.H5S_UNLIMITED}; byte[][] ref_buf = new byte[2][8]; float data[] = new float[size]; for (int i=0; i"Lon" tid_tmp = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, 8); H5.H5Tinsert(tid_tmp, "Lon", 0, HDF5Constants.H5T_NATIVE_DOUBLE); int tid_tmp_nested = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, 8); H5.H5Tinsert(tid_tmp_nested, "location", 0, tid_tmp); H5.H5Dwrite(did, tid_tmp_nested, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, lonData); H5.H5Tclose(tid_tmp_nested); H5.H5Tclose(tid_tmp); // write the second field of the nested compound, "location"->"Lat" tid_tmp = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, 8); H5.H5Tinsert(tid_tmp, "Lat", 0, HDF5Constants.H5T_NATIVE_DOUBLE); tid_tmp_nested = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, 8); H5.H5Tinsert(tid_tmp_nested, "location", 0, tid_tmp); H5.H5Dwrite(did, tid_tmp_nested, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, latData); H5.H5Tclose(tid_tmp_nested); H5.H5Tclose(tid_tmp); H5.H5Tclose(tid); H5.H5Tclose(tid_nested); H5.H5Sclose(sid); H5.H5Dclose(did); H5.H5Fclose(fid); } public static void testExtendData(String fname, String dname, int size, int newSize)throws Exception { long dims[] = {size}; long[] maxdims = {HDF5Constants.H5S_UNLIMITED}; long newDims[] = {newSize}; int extended = newSize - size; if (extended<=0) return; // nothing to extended float data[] = new float[size]; for (int i=0; i= 0) && (type_id >= 0) && (dataspace_id >= 0)) dataset_id = H5.H5Dcreate(file_id, dname, type_id, dataspace_id, HDF5Constants.H5P_DEFAULT); } catch (Exception e) { e.printStackTrace(); } // Write the data to the dataset. try { if ((dataset_id >= 0) && (type_id >= 0)) H5.H5DwriteString(dataset_id, type_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, strData); } catch (Exception e) { e.printStackTrace(); } // Write the data to the dataset. try { if ((dataset_id >= 0) && (type_id >= 0)) { String[] buf = new String[strData.length]; H5.H5Dread(dataset_id, H5.H5Dget_type(dataset_id), HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, buf); for (int i =0; i= 0) H5.H5Dclose(dataset_id); } catch (Exception e) { e.printStackTrace(); } // Terminate access to the data space. try { if (dataspace_id >= 0) H5.H5Sclose(dataspace_id); } catch (Exception e) { e.printStackTrace(); } // Terminate access to the file type. try { if (type_id >= 0) H5.H5Tclose(type_id); } catch (Exception e) { e.printStackTrace(); } // Close the file. try { if (file_id >= 0) H5.H5Fclose(file_id); } catch (Exception e) { e.printStackTrace(); } } private static void testUpdateAttr(String fname) throws Exception { int data[] = {1,2,3,4,5,6}; long[] dims = {data.length}; String dname = "/dset"; // create a new file and a new dataset H5File file = new H5File(fname, FileFormat.CREATE); Datatype dtype = file.createDatatype(Datatype.CLASS_INTEGER, 4, Datatype.NATIVE, Datatype.NATIVE); Dataset dataset = file.createScalarDS (dname, null, dtype, dims, null, null, 0, data); // create and write an attribute to the dataset long[] attrDims = {2}; int[] attrValue = {0, 10000}; Attribute attr = new Attribute("range", dtype, attrDims); attr.setValue(attrValue); // set the attribute value dataset.writeMetadata(attr); // close the file file.close(); // open the file with read and write access file = new H5File(fname, FileFormat.WRITE); // retrieve the dataset and attribute dataset = (Dataset)file.get(dname); attr = (Attribute)dataset.getMetadata().get(0); // change the attribute value if (attr!=null) { attrValue[0] = 100; attr.setValue(attrValue); dataset.writeMetadata(attr); } // close file resource file.close(); } public static void test1DExtendStrings(String fname) throws Exception { //row count of my dataset int rowCount = 5; //max string length int maxStringLength = 5; //buffer of test data to write String[] data = {"12345","12345","12345","12345","12345"}; byte[][] buffer = new byte[5][5]; for(int i=0; i0) { idx = line.indexOf(' '); idx2 = line.indexOf('('); newAPIs[nNew++] = line.substring(idx+1, idx2+1); } line = in_new18.readLine(); } idx = 0; for (int i=0; i0 || allAPIs[i].indexOf("*op_data")>0) isFunc = 1; line = isFunc+ "\t"+ isNew+ "\t"+ allAPIs[i].substring(0, idx) + "\t" +apiName; out.println(line); } in_new18.close(); in_all18.close(); out.close(); } public static void readTextFile(String fname) throws Exception { BufferedReader in = new BufferedReader(new FileReader(fname)); String line = in.readLine(); StringTokenizer st = new StringTokenizer(line, ",") ; int n = st.countTokens(); PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(fname+".out"))); while(st.hasMoreTokens()) { out.print(st.nextToken()); out.println(); } in.close(); out.close(); } public static void writeDatatype() throws Exception{ String fname = "g:\\temp\\t1.h5"; long[] dims0D = {1}; // retrieve an instance of H5File FileFormat fileFormat = FileFormat .getFileFormat(FileFormat.FILE_TYPE_HDF5); if (fileFormat == null) { System.err.println("Cannot find HDF5 FileFormat."); return; } // create a new file with a given file name. H5File testFile = (H5File) fileFormat.create(fname); if (testFile == null) { System.err.println("Failed to create file:" + fname); return; } // open the file and retrieve the root group testFile.open(); H5Group root = (H5Group) ((javax.swing.tree.DefaultMutableTreeNode) testFile .getRootNode()).getUserObject(); /** add an Attribute */ Datatype attrType = testFile.createDatatype( Datatype.CLASS_INTEGER, 4, Datatype.NATIVE, Datatype.NATIVE); Attribute attr = new Attribute("attribut int", attrType,dims0D); int[] attrValue = {15}; // attribute value attr.setValue(attrValue); // set the attribute value root.writeMetadata(attr); // close file resource testFile.close(); } private static void readDatatype() throws Exception { String fname = "g:\\temp\\t1.h5"; // retrieve an instance of H5File FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5); if (fileFormat == null) { System.err.println("Cannot find HDF5 FileFormat."); return; } // open the file with read and write access FileFormat testFile = fileFormat.open(fname, FileFormat.READ); if (testFile == null) { System.err.println("Failed to open file: "+fname); return; } // open the file and retrieve the file structure testFile.open(); Group root = (Group)((javax.swing.tree.DefaultMutableTreeNode)testFile.getRootNode()).getUserObject(); /** read Attribute */ Attribute attr = (Attribute)root.getMetadata().get(0); //System.out.println(attr); attr.getName(); // -> attribute int //System.out.println(attr.getName()); attr.getValue(); // -> [15] //System.out.println(attr.getValue()); attr.getType(); // -> null... // System.out.println(attr.getType()); } private static final void testVariableArity(String desc, Object... args) { System.out.print(desc+":\t"); if (args == null) { System.out.println("null args"); return; } if (args.length == 0) { System.out.println("no argument."); return; } for (int i=0; i=0; i--) { switch (hex[i]) { case 0: sb.append("0000"); break; case 1: sb.append("0001"); break; case 2: sb.append("0010"); break; case 3: sb.append("0011"); break; case 4: sb.append("0100"); break; case 5: sb.append("0101"); break; case 6: sb.append("0110"); break; case 7: sb.append("0111"); break; case 8: sb.append("1000"); break; case 9: sb.append("1001"); break; case 10: sb.append("1010"); break; case 11: sb.append("1011"); break; case 12: sb.append("1100"); break; case 13: sb.append("1101"); break; case 14: sb.append("1110"); break; case 15: sb.append("1111"); break; } } System.out.println(sb); return sb.toString(); } private static final void TestBitmask() { int bmask=0, value = 0; BitSet theMask = new BitSet(8); theMask.set(0); System.out.println(theMask.cardinality()); theMask.set(7); System.out.println(theMask.cardinality()); for (int i=0; i<8; i++) { if (theMask.get(i)) bmask += 1<ArrayElements().. * @param fname the file that contains datasets of int8, int16, int32, int64, * float, and double. * @throws Exception */ private static final void TestPinning(String fname) throws Exception { Object data; String dnames[] = {"bytes", "shorts", "ints", "longs", "floats", "doubles"}; Dataset dsets[] = new Dataset[dnames.length]; H5File h5file = new H5File(fname); // test_pinning.h5 try { h5file.open(); } catch (Exception ex) { ex.printStackTrace(); return; } for (int i=0; i 1 ? selectionCount[1] : 1)}; Object theData = H5Datatype.allocateArray(nativeDatatype, (int)lsize[0]); H5.H5Sselect_hyperslab(fsid, HDF5Constants.H5S_SELECT_SET, selectionStart, selectionStride, selectionCount, null ); H5.H5Dread( did, nativeDatatype, msid, fsid, HDF5Constants.H5P_DEFAULT, theData); H5.H5Tclose(tid); H5.H5Tclose(nativeDatatype); H5.H5Sclose(msid); H5.H5Sclose(fsid); ds.close(did); o = theData; } catch( Exception exc ) { throw new IOException(exc.toString()); } } return o; } private static void testBEAttr(String fname) throws Exception { long[] dims2D = {20, 10}; // retrieve an instance of H5File FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5); if (fileFormat == null) { System.err.println("Cannot find HDF5 FileFormat."); return; } // create a test file. H5File testFile = (H5File)fileFormat.create(fname); if (testFile == null) { System.err.println("Failed to create file:"+fname); return; } testFile.open(); Group root = (Group)((javax.swing.tree.DefaultMutableTreeNode)testFile.getRootNode()).getUserObject(); int[] dataIn = new int[20*10]; for (int i=0; i<20; i++) { for (int j=0; j<10; j++) { dataIn[i*10+j] = i*100+j; } } Datatype dtype = testFile.createDatatype( Datatype.CLASS_INTEGER, 4, Datatype.ORDER_BE, Datatype.NATIVE); Dataset dataset = testFile.createScalarDS ("2D 32-bit integer 20x10", root, dtype, dims2D, null, null, 0, dataIn); testFile.close(); // open the file with read and write access testFile = (H5File)fileFormat.open(fname, FileFormat.WRITE); if (testFile == null) { System.err.println("Failed to open file: "+fname); return; } // open the file and retrieve the file structure testFile.open(); root = (H5Group)((javax.swing.tree.DefaultMutableTreeNode)testFile.getRootNode()).getUserObject(); // retrieve athe dataset "2D 32-bit integer 20x10" dataset = (Dataset)root.getMemberList().get(0); // create 2D 32-bit (4 bytes) integer dataset of 20 by 10 long[] attrDims = {2}; // 1D of size two int[] attrValue = {0, 10000}; // attribute value // create a attribute of 1D integer of size two Attribute attr = new Attribute("data range", dtype, attrDims); attr.setValue(attrValue); // set the attribute value // attach the attribute to the dataset dataset.writeMetadata(attr); // read the attribute into memory List attrList = dataset.getMetadata(); attr = (Attribute)attrList.get(0); // print out attribute value System.out.println( attr.toString() ); System.out.println( attr.toString(" ") ); // close file resource testFile.close(); } private static void testMemoryLeak(String fname) throws Exception { /* a list of objects: char, compound, enum, float32, float64, image, * int16, int32, int64, int8, str, uchar, uint16, uint32, uint8 */ H5File testFile = null; Dataset dset = null; testFile = new H5File(fname, H5File.READ); dset = (Dataset)testFile.get("/char"); System.out.println(dset); testFile.close(); System.out.println("DONE!!!"); } private static void testTofwerkReaderBug1213 (final String filename) throws IOException { Object data = null; String gname = "/TimingData"; String dname = "/TimingData/BufTimes"; //String gname = "/PeakData"; //String dname = "/PeakData/PeakData"; // retrieve an instance of H5File FileFormat h5FileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5); H5File h5File = null; if (h5FileFormat == null) { throw new IOException("Cannot find HDF5 FileFormat."); } try { File file = new File(filename); System.out.println("Can Read?: " + file.canRead()); // open the file with read and write access h5File = (H5File) h5FileFormat.createInstance(file.getPath(), FileFormat.READ); h5File.open(); if (h5File == null) { throw new IOException("Failed to open file: "+file.getPath()); } // open the file and retrieve the file structure Group root = (Group)((javax.swing.tree.DefaultMutableTreeNode)h5File.getRootNode()).getUserObject(); java.util.List rootMembers = root.getMemberList(); java.util.List rootAttributes =root.getMetadata(); Group timingDataGroup = null; for(int i = 0; i < rootMembers.size(); i++) { Group curGrp = (Group)rootMembers.get(i); if (curGrp.getFullName().equals(gname)) { timingDataGroup = curGrp; break; } } java.util.List timingMembers = timingDataGroup.getMemberList(); Dataset dataset = null; for(int i = 0; i < timingMembers.size(); i++) { Dataset curSet = (Dataset)timingMembers.get(i); if (curSet.getFullName().equals(dname)) { dataset = curSet; break; } } dataset.init(); long[] start = dataset.getStartDims(); // the off set of the selection start[0] = 0; start[1] = 0; // crash here data = dataset.read(); h5File.close(); } catch (Exception e) { throw new IOException("Unhandled exception: " + e + ": " + e.getLocalizedMessage()); } System.out.println("Exiting successfully."); } private static void testMemoryLeakOpenClose(String fname) throws Exception { H5File testFile = null; while(true) { testFile = new H5File(fname, H5File.READ); testFile.open(); testFile.getRootNode(); try { Thread.sleep(100); } catch (Exception ex) {;} testFile.close(); } } private static void testH5Compound2000Fields(final String filename) throws Exception { int ncols = 12; FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5); H5File file = (H5File) fileFormat.create(filename); file.open(); Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) file.getRootNode()).getUserObject(); int[] memRanks = new int[ncols]; int[][] memDims = new int[ncols][1]; String name = "comp2k"; long[] dims = {32}; String[] memberNames = new String[ncols]; Datatype[] memberDatatypes = new Datatype[ncols]; int[] memberRanks = new int[ncols]; int[][] memberDims = new int[ncols][1]; for (int i = 0; i < ncols; i++) { memberNames[i] = "m"+i; memberDatatypes[i] = new H5Datatype(Datatype.CLASS_INTEGER, 1, -1, -1); memberRanks[i] = 1; memDims[i][0] = 1; } H5CompoundDS dset = null; try { dset = (H5CompoundDS)H5CompoundDS.create( name, root, dims, memberNames, memberDatatypes, memberRanks, memberDims); } catch (final Exception ex) { ex.printStackTrace(); } file.close(); } private static void testH5DreadNIO(final String filename) throws Exception { final String dname = "8kx8k"; final int NLOOPS = 20; final H5File file = new H5File(filename, H5File.READ); file.open(); H5ScalarDS dset = (H5ScalarDS)file.get(dname); dset.init(); int rank = dset.getRank(); long[] dims = dset.getDims(); long[] start = dset.getStartDims(); long[] count = dset.getSelectedDims(); for (int i=0; i *
  • byte[] int8 = {-1, -128, 127, 0}; *
  • short[] int16 = {-1, -32768, 32767, 0}; *
  • int[] int32 = {-1, -2147483648, 2147483647, 0}; * * Expected values *
      *
    • short[] uint8 = {255, 128, 127, 0}; *
    • int[] uint16 = {65535, 32768, 32767, 0}; *
    • long[] uint32 = {4294967295L, 2147483648L, 2147483647, 0}; *
    */ public final static void testConvertFromUnsignedC() { byte[] int8 = {-1, -128, 127, 0}; short[] int16 = {-1, -32768, 32767, 0}; int[] int32 = {-1, -2147483648, 2147483647, 0}; short[] uint8 = {255, 128, 127, 0}; int[] uint16 = {65535, 32768, 32767, 0}; long[] uint32 = {4294967295L, 2147483648L, 2147483647, 0}; short[] expected8 = (short[])Dataset.convertFromUnsignedC(int8, null); if (!(Arrays.equals(expected8, uint8))) { System.out.println("testConvertFromUnsignedC failed."); } int[] expected16 = (int[])Dataset.convertFromUnsignedC(int16, null); if (!(Arrays.equals(expected16, uint16))) { System.out.println("testConvertFromUnsignedC failed."); } long[] expected32 = (long[])Dataset.convertFromUnsignedC(int32, null); if (!(Arrays.equals(expected32, uint32))) { System.out.println("testConvertFromUnsignedC failed."); } } private static void testH5ReadChunk(final String filename) throws Exception { final String dnames[] = { "chunk1000x1000", "chunk100x1000", "chunk1x1000", "chunk50x50", "nochunk"}; final H5File file = new H5File(filename, H5File.READ); file.open(); for (int i=0; i1) { System.out.println("*** Possible memory leak!!!"); } file.close(); } } private static void testH5Bug847(final String filename) throws Exception { List list=null; final int TEST_INT_VALUE = 999999999; long[] count, start, dims; int rank, nmembers, nrows=1; H5File file; CompoundDS dset; String NAME_DATASET_COMPOUND = "/comp_dataset"; // create a test file create_test_file(filename); for (int rowIdx=0; rowIdx 0) { H5.H5Pset_deflate(plist, gzip); } } final int did = H5.H5Dcreate(file.getFID(), "/1D compound Strings", tid, sid, plist); try {H5.H5Pclose(plist);} catch (final Exception ex) {}; try {H5.H5Tclose(tid);} catch (final Exception ex) {}; try {H5.H5Sclose(sid);} catch (final Exception ex) {}; try {H5.H5Dclose(did);} catch (final Exception ex) {}; final H5CompoundDS dset = new H5CompoundDS(file, "1D compound Strings", "/", null); dset.init(); final long selected[] = dset.getSelectedDims(); selected[0] = dims[0]; dset.write(comp_data); // create 1D string compound dataset using hdf-java 2.4 file.createCompoundDS("/1D compound Strings2", null, dims, null, chunks, gzip, mnames, mdtypes, null, comp_data); // create 1D string scalar dataset using using hdf-java 2.3 or 2.4 file.createScalarDS("/1D scalar strings", null, strType, dims, null, chunks, gzip, strs); try { file.close(); } catch (final Exception ex) {} } private static void collectGarbage() { try { System.gc(); Thread.sleep(15); System.runFinalization(); Thread.sleep(15); } catch (final Exception ex){ ex.printStackTrace(); } } public static void checkMemory() throws Exception { final int _SIZE = 5000000; final Object[] array = new Object[_SIZE]; collectGarbage(); long totalMem = Runtime.getRuntime().totalMemory(); for (int i = 0; i < _SIZE; i++) { array[i] = new Object(); } long freeMem = Runtime.getRuntime().freeMemory(); long difference = ( totalMem - freeMem ) / _SIZE; System.out.println( difference + " \tbytes/object" ); collectGarbage(); totalMem = Runtime.getRuntime().totalMemory(); for (int i = 0; i < _SIZE; i++) { array[i] = new String(String.valueOf(i)); } freeMem = Runtime.getRuntime().freeMemory(); difference = ( totalMem - freeMem ) / _SIZE; System.out.println( difference + " \tbytes/String" ); } private static void testH5OpenClose(final String filename) throws Exception { int loop = 1000000; create_test_file(filename); final H5File file = new H5File(filename, H5File.READ); while (loop-- > 0) { file.open(); file.close(); } } private static void testGetOneRow (final String filename, final String objName) throws Exception { List data=null; // Get the source dataset final H5File file = new H5File(filename, H5File.READ); file.open(); final CompoundDS dset = (CompoundDS)file.get(objName); int rank = dset.getRank(); try { if (rank<=0) { dset.init(); } } catch (final Exception ex) {} rank = dset.getRank(); // 1) I read a table from an H5 file; and use the 'select subset' code // to get only one row's worth of data before calling 'getData() final long[] count = dset.getSelectedDims(); final long[] start = dset.getStartDims(); final long[] dims = dset.getDims(); for (int i=0; i:"); printHObject(group); } private static void printHObject (final HObject hObject) throws Exception { if (hObject instanceof Group) { printHObject((Group)hObject); } if (hObject instanceof CompoundDS) { printHObject((CompoundDS)hObject); } if (hObject instanceof Dataset) { printHObject((Dataset)hObject); } } private static void printHObject (final Group group) throws Exception { final List list = group.getMemberList(); if (list == null) { return; } final int n = list.size(); for (int i=0; i= 0) { objects [i] = object; } else { object = null; // Discard the warm up object runGC (); heap1 = usedMemory (); // Take a before heap snapshot } } runGC (); final long heap2 = usedMemory (); // Take an after heap snapshot: final int size = Math.round (((float)(heap2 - heap1))/count); System.out.println ("'before' heap: " + heap1 + ", 'after' heap: " + heap2); System.out.println ("heap delta: " + (heap2 - heap1) + ", {" + objects [0].getClass () + "} size = " + size + " bytes"); for (int i = 0; i < count; ++ i) { objects [i] = null; } objects = null; } private static void runGC () throws Exception { // It helps to call Runtime.gc() // using several method calls: for (int r = 0; r < 4; ++ r) { _runGC (); } } private static void _runGC () throws Exception { long usedMem1 = usedMemory (), usedMem2 = Long.MAX_VALUE; final Runtime s_runtime = Runtime.getRuntime (); for (int i = 0; (usedMem1 < usedMem2) && (i < 500); ++ i) { s_runtime.runFinalization (); s_runtime.gc (); Thread.yield (); usedMem2 = usedMem1; usedMem1 = usedMemory (); } } private static long usedMemory () { final Runtime s_runtime = Runtime.getRuntime (); return s_runtime.totalMemory () - s_runtime.freeMemory (); } private static void testHDFvector( final String fileName ) throws Exception { // retrieve an instance of H5File final FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5); if (fileFormat == null) { System.err.println("Cannot find HDF5 FileFormat."); return; } // create a new file with a given file name. final H5File tFile = (H5File)fileFormat.create(fileName); if (tFile == null) { System.err.println("Failed to create file:"+fileName); return; } final FileFormat testFile = fileFormat.open(fileName,FileFormat.WRITE); if(testFile == null){ System.err.println("Failed to open file " + fileName); return; } testFile.open(); final Group root = (Group)((javax.swing.tree.DefaultMutableTreeNode)testFile.getRootNode()).getUserObject(); Vector v = new Vector(); v.addElement(new Float(1.2)); v.addElement(new Float(2.3)); v.addElement(new Float(4.5)); putData(testFile, root, "Vector Dataset",v,true, null); v = getData(root, "Vector Dataset"); System.out.println("first time getData " + v); //adding five more elements tothe vector v.addElement(new Float(4)); v.addElement(new Float(5)); v.addElement(new Float(6)); v.addElement(new Float(7)); final long[] extended_dims = {7}; putData(testFile, root, "Vector Dataset",v,false, extended_dims); System.out.println("After adding four more elements to the vector"); v = getData(root, "Vector Dataset"); System.out.println("Second time getData " + v); testFile.close(); } public static void putData(final FileFormat testFile, final Group root, final String name, final Vector value, final boolean flag, final long[] extended_dims)throws Exception { final int size = value.size(); final long[] dims = {size}; final int dataLen = 0; // set the data values final float[] dataFl = new float[size]; for (int i=0; i"+n); myfile.close(); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } private static void test3DHDF4(String filename, String dsetname) throws Exception { H4File file = new H4File(filename, H5File.READ); if (file==null){ System.err.println("Cannot find HDF4 file: "+filename); return; } file.open(); Group g = (Group) ((DefaultMutableTreeNode)file.getRootNode()).getUserObject(); H4SDS sds = (H4SDS) g.getMemberList().get(0); if (sds==null){ System.err.println("Cannot find HDF4 SDS: "+dsetname); return; } // only read 2D Object data=sds.read(); int n = Array.getLength(data); for (int i=0; i