Ejemplo n.º 1
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 public void Close()
 {
     if (m_fileId != null)
     {
         H5F.close(m_fileId);
     }
 }
Ejemplo n.º 2
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        public static void UpdateCampaignInfoSet()
        {
            long vdsFileId     = -1;
            long vdsMetaFileId = -1;
            long groupId       = -1;

            lock (_lock)
            {
                try
                {
                    if (File.Exists(_options.VdsFilePath))
                    {
                        vdsFileId     = H5F.open(_options.VdsFilePath, H5F.ACC_RDONLY);
                        vdsMetaFileId = H5F.open(_options.VdsMetaFilePath, H5F.ACC_RDONLY);

                        Program.CampaignInfoSet = GeneralHelper.GetCampaignInfoSet(vdsFileId, false);
                    }
                    else
                    {
                        Program.CampaignInfoSet = new List <CampaignInfo>();
                    }

                    Program.CampaignDescriptionSet = Program.CampaignInfoSet.ToDictionary(campaignInfo => campaignInfo.Name, campaignInfo =>
                    {
                        if (IOHelper.CheckLinkExists(vdsMetaFileId, campaignInfo.Name))
                        {
                            try
                            {
                                groupId = H5G.open(vdsMetaFileId, campaignInfo.Name);

                                if (H5A.exists(groupId, "description") > 0)
                                {
                                    return(IOHelper.ReadAttribute <string>(groupId, "description").First());
                                }
                            }
                            finally
                            {
                                if (H5I.is_valid(groupId) > 0)
                                {
                                    H5G.close(groupId);
                                }
                            }
                        }

                        return("no description available");
                    });
                }
                finally
                {
                    if (H5I.is_valid(vdsFileId) > 0)
                    {
                        H5F.close(vdsFileId);
                    }
                    if (H5I.is_valid(vdsMetaFileId) > 0)
                    {
                        H5F.close(vdsMetaFileId);
                    }
                }
            }
        }
 public void H5Freset_mdc_hit_rate_statsTest1()
 {
     Assert.IsTrue(
         H5F.reset_mdc_hit_rate_stats(m_v0_class_file) >= 0);
     Assert.IsTrue(
         H5F.reset_mdc_hit_rate_stats(m_v2_class_file) >= 0);
 }
Ejemplo n.º 4
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        public void H5FunmountTest2()
        {
            Assert.IsFalse(
                H5F.unmount(Utilities.RandomInvalidHandle(), "AA") >= 0);

            Assert.IsFalse(H5F.unmount(m_v0_class_file, "") >= 0);
        }
Ejemplo n.º 5
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 public void H5Fget_mdc_configTest2()
 {
     H5AC.cache_config_t conf = new H5AC.cache_config_t();
     Assert.IsFalse(
         H5F.get_mdc_config(Utilities.RandomInvalidHandle(),
                            ref conf) >= 0);
 }
Ejemplo n.º 6
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        public void Cleanup()
        {
            file_.Close();

            H5D.close(dataSet_);
            H5F.close(h5file_);
        }
Ejemplo n.º 7
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        public static double[][] ReadMesh(string fileName)
        {
            double[][] meshes    = new double[3][];
            string[]   meshNames = { "x", "y", "z" };

            H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);

            for (int i = 0; i < meshNames.Length; i++)
            {
                H5DataSetId  dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
                H5DataTypeId dtId = H5D.getType(dsId);

                if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
                {
                    Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
                }

                float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
                H5D.read(dsId, dtId, new H5Array <float>(mesh));

                meshes[i] = mesh.Select(x => (double)x * 1000.0).ToArray(); // m -> mm

                H5D.close(dsId);
                H5T.close(dtId);
            }

            H5F.close(fileId);

            return(meshes);
        }
Ejemplo n.º 8
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        public static T GetMetadata <T>(string filename, string path)
        {
            H5FileId zFile = null;

            if (!File.Exists(filename))
            {
                throw new Exception("File not found.");
            }

            try
            {
                zFile = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);

                return((T)HDFExtensions.ReadScalar <T>(zFile, path));
            }
            catch
            {
                throw new Exception("Path not found");
            }
            finally
            {
                if (zFile != null)
                {
                    H5F.close(zFile);
                }
            }
        }
Ejemplo n.º 9
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        /// <summary>
        /// Opens an existing file and loads up the group and dataset headers in the object.
        /// </summary>
        /// <param name="_filename"></param>
        public Hdf5File(string _filename)
        {
            if (!File.Exists(_filename))
            {
                throw new FileNotFoundException();
            }

            Id = H5F.open(_filename, H5F.ACC_RDWR).ToId();

            if (Id.Value > 0)
            {
                FileId = Id;
                Path   = new Hdf5Path(".");

                Groups   = new Hdf5Groups(this);
                Datasets = new Hdf5Datasets(this);

                Attributes = new Hdf5Attributes(this);
                AttributeHelper.LoadAttributes(Attributes);

                GroupHelper.PopulateChildrenObjects(Id, this);
            }
            else
            {
                throw new Hdf5UnknownException();
            }
        }
Ejemplo n.º 10
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        //Load weights from hdf5 file. Weights must be saved as a vector per layer
        public static float[] loadH5(string path, string dsname)
        {
            //Get file id
            var h5fid = H5F.open(path, H5F.OpenMode.ACC_RDONLY);
            //Get dataset id
            var h5did = H5D.open(h5fid, dsname);
            //Dataset size
            var h5space = H5D.getSpace(h5did);
            var h5size  = H5S.getSimpleExtentDims(h5space);

            //Dataset size to array
            var S = h5size.ToArray();

            //Empty double array for the data
            double[] data = new double[S[0]];

            //Read the dataset

            var h5array = new H5Array <double>(data);
            var h5dtype = H5D.getType(h5did);

            H5D.read(h5did, h5dtype, h5array);

            //Convert to float
            float[] newarray = new float[data.Length];

            Parallel.For(0, data.Length, (k) =>
            {
                newarray[k] = (float)data[k];
            });

            return(newarray);
        }
Ejemplo n.º 11
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        public void H5Fget_filesizeTest2()
        {
            hsize_t size = 0;

            Assert.IsFalse(H5F.get_filesize(Utilities.RandomInvalidHandle(),
                                            ref size) >= 0);
        }
Ejemplo n.º 12
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        public override void CloseDocument()
        {
            if (fileId != null && fileId.Id > 0 && !_fileClosed)
            {
                foreach (var group in EpochGroupsIDs)
                {
                    try
                    {
                        H5G.close(group.GroupId);
                        H5G.close(group.SubGroupsId);
                        H5G.close(group.EpochsId);
                    }
                    catch (H5GcloseException ex)
                    {
                        log.DebugFormat("HDF5 group already closed: {0}", ex);
                    }
                }

                try
                {
                    H5F.close(fileId);
                }
                catch (H5FcloseException ex)
                {
                    log.DebugFormat("HDF5 file already closed: {0}", ex);
                }
                Interlocked.Decrement(ref _openHdf5FileCount);
                _fileClosed = true;
            }
        }
Ejemplo n.º 13
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 public Hdf5Operator(string filename)
 {
     _fname    = filename;
     _h5FileId = H5F.open(filename, H5F.ACC_RDONLY);
     GetAllFileAttributes();
     GetAllDatasetNames();
 }
Ejemplo n.º 14
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        public static double[, ,] ReadFieldData3D(string fileName)
        {
            H5FileId     fileId      = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
            H5DataSetId  fDataSetId  = H5D.open(fileId, "/FieldData/FD/f0");
            H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);

            if (!H5T.equal(fDataTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
            {
                Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
            }

            long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
            if (dims.Length != 3)
            {
                Console.WriteLine("Error: Invalid field data dimensions");
            }

            float[, ,] data = new float[dims[0], dims[1], dims[2]];
            H5D.read(fDataSetId, fDataTypeId, new H5Array <float>(data));

            // Reorder
            double[, ,] fieldValues = new double[dims[2], dims[1], dims[0]];
            for (int i = 0; i < dims[0]; i++)
            {
                for (int j = 0; j < dims[1]; j++)
                {
                    for (int k = 0; k < dims[2]; k++)
                    {
                        fieldValues[k, j, i] = data[i, j, k];
                    }
                }
            }

            return(fieldValues);
        }
Ejemplo n.º 15
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 public void H5Fget_mdc_configTest1()
 {
     H5AC.cache_config_t conf = new H5AC.cache_config_t(
         H5AC.CURR_CACHE_CONFIG_VERSION);
     Assert.IsTrue(H5F.get_mdc_config(m_v0_class_file, ref conf) >= 0);
     Assert.IsTrue(H5F.get_mdc_config(m_v2_class_file, ref conf) >= 0);
 }
Ejemplo n.º 16
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        public static double ReadAttribute(string file, string dataSetOrGroup, string attribute)
        {
            double attr = Double.NaN;

            try
            {
                H5FileId      fileId     = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
                H5ObjectInfo  objectInfo = H5O.getInfoByName(fileId, dataSetOrGroup);
                H5GroupId     groupId    = null;
                H5DataSetId   dataSetId  = null;
                H5AttributeId attrId;

                if (objectInfo.objectType == H5ObjectType.GROUP)
                {
                    groupId = H5G.open(fileId, dataSetOrGroup);
                    attrId  = H5A.open(groupId, attribute);
                }
                else
                {
                    dataSetId = H5D.open(fileId, dataSetOrGroup);
                    attrId    = H5A.open(dataSetId, attribute);
                }
                H5DataTypeId attrTypeId = H5A.getType(attrId);

                double[] dAttrs = new double[] { };
                if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
                {
                    float[] fAttrs = new float[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
                    H5A.read(attrId, attrTypeId, new H5Array <float>(fAttrs));
                    dAttrs = (from f in fAttrs select(double) f).ToArray();
                }
                else if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_DOUBLE)))
                {
                    dAttrs = new double[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
                    H5A.read(attrId, attrTypeId, new H5Array <double>(dAttrs));
                }

                H5T.close(attrTypeId);
                H5A.close(attrId);
                if (groupId != null)
                {
                    H5G.close(groupId);
                }
                if (dataSetId != null)
                {
                    H5D.close(dataSetId);
                }
                H5F.close(fileId);

                return((double)dAttrs[0]);
            }

            catch (HDFException e)
            {
                Console.WriteLine("Error: Unhandled HDF5 exception");
                Console.WriteLine(e.Message);
            }

            return(attr);
        }
Ejemplo n.º 17
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        public static double[,] ReadFieldData2D(string file, string dataSet)
        {
            H5FileId     fileId      = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
            H5DataSetId  fDataSetId  = H5D.open(fileId, dataSet);
            H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);

            long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
            double[,] data = new double[dims[0], dims[1]];
            H5D.read(fDataSetId, fDataTypeId, new H5Array <double>(data));

            double[,] fieldValues = new double[dims[1], dims[0]];
            for (int i = 0; i < dims[1]; i++)
            {
                for (int j = 0; j < dims[0]; j++)
                {
                    fieldValues[i, j] = (double)data[j, i];
                }
            }

            H5T.close(fDataTypeId);
            H5D.close(fDataSetId);
            H5F.close(fileId);

            return(fieldValues);
        }
Ejemplo n.º 18
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 public void H5Fclear_elink_cacheTest1()
 {
     Assert.IsTrue(H5F.clear_elink_file_cache(m_v0_class_file) >= 0);
     Assert.IsTrue(H5F.clear_elink_file_cache(m_v2_class_file) >= 0);
     Assert.IsTrue(H5F.clear_elink_file_cache(m_v0_test_file) >= 0);
     Assert.IsTrue(H5F.clear_elink_file_cache(m_v2_test_file) >= 0);
 }
Ejemplo n.º 19
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        } // make_table

        static void test_getting_info()
        {
            try
            {
                Console.Write("Testing getting table/field information");

                // Open the file to check on the table.
                H5FileId fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);

                hssize_t nfields = 0, nrecords = 0;
                string[] field_names = { "c", "i", "l" };

                // Get the table info.
                TableInfo table = H5TB.getTableInfo(fileId, TABLE_NAME);

                if (table.nFields != N_FIELDS)
                {
                    Console.WriteLine("\ntest_getting_info: incorrect number of fields: read {0} - should be {1}",
                                      nfields, N_FIELDS);
                    nerrors++;
                }
                if (table.nRecords != N_RECORDS)
                {
                    Console.WriteLine("\ntest_getting_info: incorrect number of fields: read {0} - should be {1}",
                                      nrecords, N_RECORDS);
                    nerrors++;
                }

                // Get field info.
                int []         sizes      = new int[N_FIELDS];
                int []         offsets    = new int[N_FIELDS];
                TableFieldInfo tablefield = H5TB.getFieldInfo(fileId, TABLE_NAME);

                int ii;
                for (ii = 0; ii < N_FIELDS; ii++)
                {
                    if (tablefield.fieldName[ii] != field_names[ii])
                    {
                        Console.WriteLine("\ntest_getting_info: field #{0} has incorrect name: read {0} - should be {1}",
                                          ii, field_names[ii], tablefield.fieldName[ii]);
                        nerrors++;
                    }
                }

                H5F.close(fileId);

                Console.WriteLine("\t\t\tPASSED");
            }
            catch (HDFException anyHDF5E)
            {
                Console.WriteLine(anyHDF5E.Message);
                nerrors++;
            }
            catch (System.Exception sysE)
            {
                Console.WriteLine(sysE.TargetSite);
                Console.WriteLine(sysE.Message);
                nerrors++;
            }
        } // test_getting_info
Ejemplo n.º 20
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        public void H5Fget_intentTest1()
        {
            uint intent = 4711;

            Assert.IsTrue(H5F.get_intent(m_v0_class_file, ref intent) >= 0);
            Assert.IsTrue(H5F.get_intent(m_v2_class_file, ref intent) >= 0);
        }
Ejemplo n.º 21
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        private static void ConvertHdf4To5(Hdf4FileAttrs hdf4FileAttrs, string f5name,
                                           Action <string, int, int> messageAction)
        {
            try
            {
                // Create a new file using H5F_ACC_TRUNC access,
                // default file creation properties, and default file
                // access properties.
                H5FileId fileId = H5F.create(f5name, H5F.CreateMode.ACC_TRUNC);

                int nxf5 = hdf4FileAttrs.Hdf4FileAttr.XDim;
                int nyf5 = hdf4FileAttrs.Hdf4FileAttr.YDim;
                int rank = 2;

                //测试读取的科学数据集及其属性
                int sdscount = hdf4FileAttrs.Hdf4FileAttr.DataFields.Count;
                for (int k = 0; k < sdscount; k++)
                {
                    ConvertHdf4To5BySds(hdf4FileAttrs, messageAction, k, nyf5, nxf5, rank, fileId);
                }

                HDFAttributeDef[] attributeDef5s = hdf4FileAttrs.GetHDFAttributeDefs();
                foreach (HDFAttributeDef attributeDef5 in attributeDef5s)
                {
                    WriteHdfAttributes.WriteHdfAttribute(fileId, attributeDef5);
                }

                H5F.close(fileId);
            }
            catch (Exception ex)
            {
                throw new Exception("拼接Hdf4时出错,具体信息:" + ex.Message, ex);
            }
        }
Ejemplo n.º 22
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 private static H5FileId GetFileId()
 {
     return
         (File.Exists(Global.GetOutputPath(Global.Configuration.HDF5Path))
                                 ? H5F.open(Global.GetOutputPath(Global.Configuration.HDF5Path), H5F.OpenMode.ACC_RDWR)
                                 : H5F.create(Global.GetOutputPath(Global.Configuration.HDF5Path), H5F.CreateMode.ACC_EXCL));
 }
Ejemplo n.º 23
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        /// <summary>
        /// Opens a Hdf-5 file
        /// </summary>
        /// <param name="filename"></param>
        /// <param name="readOnly"></param>
        /// <returns></returns>
        public static long OpenFile(string filename, bool readOnly = false)
        {
            uint access = (readOnly) ? H5F.ACC_RDONLY : H5F.ACC_RDWR;
            var  fileId = H5F.open(filename, access);

            return(fileId);
        }
Ejemplo n.º 24
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        public Dictionary <string, string> TryReadDataTable(string datasetName)
        {
            Dictionary <string, string> result = null;
            var subDsDic = ds.GetSubDatasets();

            if (subDsDic.Count > 0)
            {
                H5ID h5FileId  = H5F.open(fileName, H5F.ACC_RDONLY);
                H5ID datasetId = H5D.open(h5FileId, datasetName);
                H5ID typeId    = H5D.get_type(datasetId);
                H5ID spaceId   = H5D.get_space(datasetId);
                if (H5T.get_class(typeId) == H5T.class_t.COMPOUND)
                {
                    int      numCount = H5T.get_nmembers(typeId);
                    var      size     = H5T.get_size(typeId);
                    byte[]   buffer   = new byte[size.ToInt32()];
                    GCHandle hnd      = GCHandle.Alloc(buffer, GCHandleType.Pinned);
                    int      ndims    = H5S.get_simple_extent_ndims(spaceId);
                    if (ndims == 1)
                    {
                        result = new Dictionary <string, string>();
                        H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());

                        for (uint i = 0; i < numCount; i++)
                        {
                            string name   = Marshal.PtrToStringAnsi(H5T.get_member_name(typeId, i));
                            int    offset = H5T.get_member_offset(typeId, i).ToInt32();

                            H5ID        subTypeId = H5T.get_member_type(typeId, i);
                            H5T.class_t typeClass = H5T.get_member_class(typeId, i);
                            string      value     = ReadBuffer(buffer, offset, typeClass, subTypeId);
                            result.Add(name, value);
                            H5T.close(subTypeId);
                        }
                    }

                    hnd.Free();
                }

                if (spaceId != 0)
                {
                    H5S.close(spaceId);
                }
                if (typeId != 0)
                {
                    H5T.close(typeId);
                }
                if (datasetId != 0)
                {
                    H5D.close(datasetId);
                }
                if (h5FileId != 0)
                {
                    H5F.close(h5FileId);
                }
            }

            return(result);
        }
Ejemplo n.º 25
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        public File(string filename, H5F.OpenMode mode = H5F.OpenMode.ACC_RDONLY)
        {
            _filename = filename;
            _mode = mode;

            EnsureH5Lib();
            OpenFile();
        }
Ejemplo n.º 26
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 public void H5Fset_mdc_configTest2()
 {
     H5AC.cache_config_t conf = new H5AC.cache_config_t(
         H5AC.CURR_CACHE_CONFIG_VERSION);
     Assert.IsFalse(
         H5F.set_mdc_config(Utilities.RandomInvalidHandle(),
                            ref conf) >= 0);
 }
Ejemplo n.º 27
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 public static void ClassCleanup()
 {
     // close the global test files
     Assert.IsTrue(H5F.close(m_v0_class_file) >= 0);
     Assert.IsTrue(H5F.close(m_v2_class_file) >= 0);
     File.Delete(m_v0_class_file_name);
     File.Delete(m_v2_class_file_name);
 }
Ejemplo n.º 28
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 public bool OpenHDF(FileName file, H5F.OpenMode mode = H5F.OpenMode.ACC_RDONLY)
 {
     try
      {
     file_id = H5F.open(file.FullPath, mode);
     last_exception = null;
     if (file_id.Id >= 0)
        return true;
     else
        return false;
      }
      catch (Exception ex)
      {
     last_exception = ex;
     return false;
      }
 }
Ejemplo n.º 29
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 public bool CreateHDF(FileName file, H5F.CreateMode mode = H5F.CreateMode.ACC_TRUNC)
 {
     try
      {
     file_id = H5F.create(file.FullPath, mode);
     last_exception = null;
     if (file_id.Id >= 0)
        return true;
     else
        return false;
      }
      catch (Exception ex)
      {
     last_exception = ex;
     return false;
      }
 }