HDF5 Esempio codice

Question

Utilizzo di HDF5DotNet, qualcuno può indicarmi il codice di esempio, che aprirà un file hdf5, estrarrà il contenuto di un set di dati e stamperà il contenuto sullo standard output?

Finora ho il seguente:

 H5.Open(); 
     var h5 = H5F.open("example.h5", H5F.OpenMode.ACC_RDONLY); 
     var dataset = H5D.open(h5, "/Timings/aaPCBTimes"); 
     var space = H5D.getSpace(dataset); 
     var size = H5S.getSimpleExtentDims(space); 

Poi si fa un po 'di confusione.

In realtà desidero eseguire alcune elaborazioni sui contenuti del set di dati, ma penso che una volta scaricato l'output standard, riesco a risolverlo da lì.

AGGIORNAMENTO: Ho risolto questo problema per risolvere il mio problema. Non sono riuscito a capire che un set di dati era un multi-array: pensavo che fosse più simile a un db table. Nel caso improbabile qualcuno è interessato,

double[,] dataArray = new double[size[0], 6]; 
var wrapArray = new H5Array<double>(dataArray); 
var dataType = H5D.getType(d); 
H5D.read(dataset, dataType, wrapArray); 
Console.WriteLine(dataArray[0, 0]); 

Answer 1

Prova questo:

using System; 
using HDF5DotNet; 

namespace CSharpExample1 
{ 
    class Program 
    { 
    // Function used with 
    static int myFunction(H5GroupId id, string objectName, Object param) 
    { 
     Console.WriteLine("The object name is {0}", objectName); 
     Console.WriteLine("The object parameter is {0}", param); 
     return 0; 
    } 

    static void Main(string[] args) 
    { 
     try 
     { 
      // We will write and read an int array of this length. 
      const int DATA_ARRAY_LENGTH = 12; 

      // Rank is the number of dimensions of the data array. 
      const int RANK = 1; 

      // Create an HDF5 file. 
      // The enumeration type H5F.CreateMode provides only the legal 
      // creation modes. Missing H5Fcreate parameters are provided 
      // with default values. 
      H5FileId fileId = H5F.create("myCSharp.h5", 
             H5F.CreateMode.ACC_TRUNC); 

      // Create a HDF5 group. 
      H5GroupId groupId = H5G.create(fileId, "/cSharpGroup", 0); 
      H5GroupId subGroup = H5G.create(groupId, "mySubGroup", 0); 

      // Demonstrate getObjectInfo 
      ObjectInfo info = H5G.getObjectInfo(fileId, "/cSharpGroup", true); 
      Console.WriteLine("cSharpGroup header size is {0}", info.headerSize); 
      Console.WriteLine("cSharpGroup nlinks is {0}", info.nHardLinks); 
      Console.WriteLine("cSharpGroup fileno is {0} {1}", 
       info.fileNumber[0], info.fileNumber[1]); 
      Console.WriteLine("cSharpGroup objno is {0} {1}", 
       info.objectNumber[0], info.objectNumber[1]); 
      Console.WriteLine("cSharpGroup type is {0}", info.objectType); 


      H5G.close(subGroup); 

      // Prepare to create a data space for writing a 1-dimensional 
      // signed integer array. 
      ulong[] dims = new ulong[RANK]; 
      dims[0] = DATA_ARRAY_LENGTH; 

      // Put descending ramp data in an array so that we can 
      // write it to the file. 
      int[] dset_data = new int[DATA_ARRAY_LENGTH]; 
      for (int i = 0; i < DATA_ARRAY_LENGTH; i++) 
       dset_data[i] = DATA_ARRAY_LENGTH - i; 

      // Create a data space to accommodate our 1-dimensional array. 
      // The resulting H5DataSpaceId will be used to create the 
      // data set. 
      H5DataSpaceId spaceId = H5S.create_simple(RANK, dims); 

      // Create a copy of a standard data type. We will use the 
      // resulting H5DataTypeId to create the data set. We could 
      // have used the HST.H5Type data directly in the call to 
      // H5D.create, but this demonstrates the use of H5T.copy 
      // and the use of a H5DataTypeId in H5D.create. 
      H5DataTypeId typeId = H5T.copy(H5T.H5Type.NATIVE_INT); 

      // Find the size of the type 
      uint typeSize = H5T.getSize(typeId); 
      Console.WriteLine("typeSize is {0}", typeSize); 

      // Set the order to big endian 
      H5T.setOrder(typeId, H5T.Order.BE); 

      // Set the order to little endian 
      H5T.setOrder(typeId, H5T.Order.LE); 

      // Create the data set. 
      H5DataSetId dataSetId = H5D.create(fileId, "/csharpExample", 
               typeId, spaceId); 

      // Write the integer data to the data set. 

      H5D.write(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), 
           new H5Array<int>(dset_data)); 

      // If we were writing a single value it might look like this. 
      // int singleValue = 100; 
      // H5D.writeScalar(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), 
      //  ref singleValue); 

      // Create an integer array to receive the read data. 
      int[] readDataBack = new int[DATA_ARRAY_LENGTH]; 

      // Read the integer data back from the data set 
      H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), 
       new H5Array<int>(readDataBack)); 

      // Echo the data 
      for(int i=0;i<DATA_ARRAY_LENGTH;i++) 
      { 
       Console.WriteLine(readDataBack[i]); 
      } 

      // Close all the open resources. 
      H5D.close(dataSetId); 

      // Reopen and close the data sets to show that we can. 
      dataSetId = H5D.open(fileId, "/csharpExample"); 
      H5D.close(dataSetId); 
      dataSetId = H5D.open(groupId, "/csharpExample"); 
      H5D.close(dataSetId); 

      H5S.close(spaceId); 
      H5T.close(typeId); 
      H5G.close(groupId); 

      //int x = 10; 
      //H5T.enumInsert<int>(typeId, "myString", ref x); 
      //H5G.close(groupId); 
      H5GIterateDelegate myDelegate; 
      myDelegate = myFunction; 
      int x = 9; 
      int index = H5G.iterate(fileId, "/cSharpGroup", 
       myDelegate, x, 0); 

      // Reopen the group id to show that we can. 
      groupId = H5G.open(fileId, "/cSharpGroup"); 
      H5G.close(groupId); 

      H5F.close(fileId); 

      // Reopen and reclose the file. 
      H5FileId openId = H5F.open("myCSharp.h5", 
             H5F.OpenMode.ACC_RDONLY); 
      H5F.close(openId); 
     } 
     // This catches all the HDF exception classes. Because each call 
     // generates unique exception, different exception can be handled 
     // separately. For example, to catch open errors we could have used 
     // catch (H5FopenException openException). 
     catch (HDFException e) 
     { 
      Console.WriteLine(e.Message); 
     } 

     Console.WriteLine("Processing complete!"); 
     Console.ReadLine(); 
    } 
} 
} 

Answer 2

Così, il vostro partenza è stata impressionante. Ho creato alcune estensioni che dovrebbero aiutarti. L'utilizzo di questo nel codice, si dovrebbe essere in grado di cose che rendono più senso in un linguaggio orientato agli oggetti, come ad esempio (nel tuo caso):

H5.Open(); 
var h5FileId= H5F.open("example.h5"); 
double[,] dataArray = h5FileId.Read2DArray<double>("/Timings/aaPCBTimes"); 
// or more generically... 
T[,] dataArray = h5FileId.Read2DArray<T>("/Timings/aaPCBTimes"); 

Qui ci sono le estensioni incompleti, Cercherò in aggiunta loro nel HDF5Net ...

public static class HdfExtensions 
{ 
    // thank you http://stackoverflow.com/questions/4133377/splitting-a-string-number-every-nth-character-number 
    public static IEnumerable<String> SplitInParts(this String s, Int32 partLength) 
    { 
     if (s == null) 
      throw new ArgumentNullException("s"); 
     if (partLength <= 0) 
      throw new ArgumentException("Part length has to be positive.", "partLength"); 

     for (var i = 0; i < s.Length; i += partLength) 
      yield return s.Substring(i, Math.Min(partLength, s.Length - i)); 
    } 

    public static T[] Read1DArray<T>(this H5FileId fileId, string dataSetName) 
    { 
     var dataset = H5D.open(fileId, dataSetName); 
     var space = H5D.getSpace(dataset); 
     var dims = H5S.getSimpleExtentDims(space); 
     var dataType = H5D.getType(dataset); 
     if (typeof(T) == typeof(string)) 
     { 
      int stringLength = H5T.getSize(dataType); 
      byte[] buffer = new byte[dims[0] * stringLength]; 
      H5D.read(dataset, dataType, new H5Array<byte>(buffer)); 
      string stuff = System.Text.ASCIIEncoding.ASCII.GetString(buffer); 
      return stuff.SplitInParts(stringLength).Select(ss => (T)(object)ss).ToArray(); 
     } 
     T[] dataArray = new T[dims[0]]; 
     var wrapArray = new H5Array<T>(dataArray); 
     H5D.read(dataset, dataType, wrapArray); 
     return dataArray; 
    } 

    public static T[,] Read2DArray<T>(this H5FileId fileId, string dataSetName) 
    { 
     var dataset = H5D.open(fileId, dataSetName); 
     var space = H5D.getSpace(dataset); 
     var dims = H5S.getSimpleExtentDims(space); 
     var dataType = H5D.getType(dataset); 
     if (typeof(T) == typeof(string)) 
     { 
      // this will also need a string hack... 
     } 
     T[,] dataArray = new T[dims[0], dims[1]]; 
     var wrapArray = new H5Array<T>(dataArray); 
     H5D.read(dataset, dataType, wrapArray); 
     return dataArray; 
    } 
} 

Answer 3

Ecco un esempio di lavoro:

using System.Collections.Generic; 
using System; 
using System.Linq; 
using System.Text; 
using System.Threading.Tasks; 
using HDF5DotNet; 
namespace HDF5Test 
{ 
    public class HDFTester 
    { 
     static int myFunction(H5GroupId id, string objectName, Object param) 
     { 
      Console.WriteLine("The object name is {0}", objectName); 
      Console.WriteLine("The object parameter is {0}", param); 
      return 0; 
     } 

     public static void runTest() 
     { 
      try 
      { 
       // We will write and read an int array of this length. 
       const int DATA_ARRAY_LENGTH = 12; 

       // Rank is the number of dimensions of the data array. 
       const int RANK = 1; 

       // Create an HDF5 file. 
       // The enumeration type H5F.CreateMode provides only the legal 
       // creation modes. Missing H5Fcreate parameters are provided 
       // with default values. 
       H5FileId fileId = H5F.create("myCSharp.h5", 
        H5F.CreateMode.ACC_TRUNC); 

       // Create a HDF5 group. 
       H5GroupId groupId = H5G.create(fileId, "/cSharpGroup"); 
       H5GroupId subGroup = H5G.create(groupId, "mySubGroup"); 

       // Demonstrate getObjectInfo 
       ObjectInfo info = H5G.getObjectInfo(fileId, "/cSharpGroup", true); 
       Console.WriteLine("cSharpGroup header size is {0}", info.headerSize); 
       Console.WriteLine("cSharpGroup nlinks is {0}", info.nHardLinks); 
       Console.WriteLine("cSharpGroup fileno is {0} {1}", 
        info.fileNumber[0], info.fileNumber[1]); 
       Console.WriteLine("cSharpGroup objno is {0} {1}", 
        info.objectNumber[0], info.objectNumber[1]); 
       Console.WriteLine("cSharpGroup type is {0}", info.objectType); 


       H5G.close(subGroup); 

       // Prepare to create a data space for writing a 1-dimensional 
       // signed integer array. 
       long[] dims = new long[RANK]; 
       dims[0] = DATA_ARRAY_LENGTH; 

       // Put descending ramp data in an array so that we can 
       // write it to the file. 
       int[] dset_data = new int[DATA_ARRAY_LENGTH]; 
       for (int i = 0; i < DATA_ARRAY_LENGTH; i++) 
        dset_data[i] = DATA_ARRAY_LENGTH - i; 

       // Create a data space to accommodate our 1-dimensional array. 
       // The resulting H5DataSpaceId will be used to create the 
       // data set. 
       H5DataSpaceId spaceId = H5S.create_simple(RANK, dims); 

       // Create a copy of a standard data type. We will use the 
       // resulting H5DataTypeId to create the data set. We could 
       // have used the HST.H5Type data directly in the call to 
       // H5D.create, but this demonstrates the use of H5T.copy 
       // and the use of a H5DataTypeId in H5D.create. 
       H5DataTypeId typeId = H5T.copy(H5T.H5Type.NATIVE_INT); 

       // Find the size of the type 
       int typeSize = H5T.getSize(typeId); 
       Console.WriteLine("typeSize is {0}", typeSize); 

       // Set the order to big endian 
       H5T.setOrder(typeId, H5T.Order.BE); 

       // Set the order to little endian 
       H5T.setOrder(typeId, H5T.Order.LE); 

       // Create the data set. 
       H5DataSetId dataSetId = H5D.create(fileId, "/csharpExample", 
        typeId, spaceId); 

       // Write the integer data to the data set. 

       H5D.write(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), 
        new H5Array<int>(dset_data)); 

       // If we were writing a single value it might look like this. 
       // int singleValue = 100; 
       // H5D.writeScalar(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), 
       //  ref singleValue); 

       // Create an integer array to receive the read data. 
       int[] readDataBack = new int[DATA_ARRAY_LENGTH]; 

       // Read the integer data back from the data set 
       H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), 
        new H5Array<int>(readDataBack)); 

       // Echo the data 
       for (int i = 0; i < DATA_ARRAY_LENGTH; i++) 
       { 
        Console.WriteLine(readDataBack[i]); 
       } 

       // Close all the open resources. 
       H5D.close(dataSetId); 

       // Reopen and close the data sets to show that we can. 
       dataSetId = H5D.open(fileId, "/csharpExample"); 
       H5D.close(dataSetId); 
       dataSetId = H5D.open(groupId, "/csharpExample"); 
       H5D.close(dataSetId); 

       H5S.close(spaceId); 
       H5T.close(typeId); 
       H5G.close(groupId); 

       //int x = 10; 
       //H5T.enumInsert<int>(typeId, "myString", ref x); 
       //H5G.close(groupId); 
       H5GIterateCallback myDelegate; 
       myDelegate = myFunction; 
       int x = 9; 
       int start = 0; 
       int index = H5G.iterate(fileId, "/cSharpGroup",myDelegate, x, ref start); 

       // Reopen the group id to show that we can. 
       groupId = H5G.open(fileId, "/cSharpGroup"); 
       H5G.close(groupId); 

       H5F.close(fileId); 

       // Reopen and reclose the file. 
       H5FileId openId = H5F.open("myCSharp.h5", 
        H5F.OpenMode.ACC_RDONLY); 
       H5F.close(openId); 
      } 
       // This catches all the HDF exception classes. Because each call 
       // generates unique exception, different exception can be handled 
       // separately. For example, to catch open errors we could have used 
       // catch (H5FopenException openException). 
      catch (HDFException e) 
      { 
       Console.WriteLine(e.Message); 
      } 

      Console.WriteLine("Processing complete!"); 
      Console.ReadLine(); 

     } 
    } 
}