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Searched refs:HDF5File (Results 1 – 25 of 40) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/hdf5/
H A DHDF5LibraryUnitTest.java39 final HDF5File reader = new HDF5File(TEST_PON); in testOpenReadOnly()
53 final HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testCreateHDF5File()
60 final HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testIsPresent()
78 final HDF5File file2 = new HDF5File(testFile, HDF5File.OpenMode.READ_ONLY); in testIsPresent()
90 final HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testCreateGroup()
102 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeDouble()
118 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeNaNDouble()
134 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeDoubleArray()
151 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testReMakeDoubleArray()
174 HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE); in testMakeDoubleMatrix()
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/packages/external/muq2/modules/Utilities/src/HDF5/
H A DHDF5File.cpp8 HDF5File::HDF5File(std::string const& filename_){ in HDF5File() function in HDF5File
17 HDF5File::~HDF5File() { in ~HDF5File()
25 bool HDF5File::DoesFileExist(const std::string& name) const { in DoesFileExist()
30 void HDF5File::Open(std::string const& filename_) { in Open()
58 void HDF5File::Close() { in Close()
76 void HDF5File::Copy(std::string const& dstName, std::shared_ptr<HDF5File> srcFile, std::string cons… in Copy()
167 void HDF5File::CreateGroup(std::string const& name) { in CreateGroup()
224 void HDF5File::FlushFile() { in FlushFile()
234 const std::shared_ptr<HDF5File> hdf5file;
259 void HDF5File::MergeFile(std::shared_ptr<HDF5File> const& otherFile) { in MergeFile()
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/dports/graphics/vigra/vigra-8acd73a/include/vigra/
H A Drandom_forest_hdf5_impex.hxx60 VIGRA_EXPORT void options_import_HDF5(HDF5File &, RandomForestOptions &,
66 VIGRA_EXPORT void dt_import_HDF5(HDF5File &, detail::DecisionTree &,
73 void rf_import_HDF5_to_map(HDF5File & h5context, X & param, in rf_import_HDF5_to_map()
119 void rf_export_map_to_HDF5(HDF5File & h5context, const X & param) in rf_export_map_to_HDF5()
154 inline std::string get_cwd(HDF5File & h5context) in get_cwd()
177 HDF5File & h5context, in rf_export_HDF5()
223 HDF5File h5context(filename , HDF5File::Open); in rf_export_HDF5()
250 HDF5File h5context(fileHandle, pathname); in rf_export_HDF5()
269 HDF5File & h5context, in rf_import_HDF5()
327 HDF5File h5context(filename, HDF5File::OpenReadOnly); in rf_import_HDF5()
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H A Dmulti_array_chunked_hdf5.hxx226 HDF5File::OpenMode mode = HDF5File::ReadOnly, in ChunkedArrayHDF5()
251 init(HDF5File::ReadOnly); in ChunkedArrayHDF5()
253 init(HDF5File::ReadWrite); in ChunkedArrayHDF5()
256 void init(HDF5File::OpenMode mode) in init()
260 if(mode == HDF5File::Replace) in init()
262 mode = HDF5File::New; in init()
264 else if(mode == HDF5File::Default) in init()
267 mode = HDF5File::ReadOnly; in init()
269 mode = HDF5File::New; in init()
272 if(mode == HDF5File::ReadOnly) in init()
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H A Dhdf5impex.hxx974 class HDF5File class
1047 HDF5File() in HDF5File() function in vigra::HDF5File
1055 explicit HDF5File(bool track_creation_times) in HDF5File() function in vigra::HDF5File
1126 HDF5File(HDF5File const & other) in HDF5File() function in vigra::HDF5File
1137 ~HDF5File() in ~HDF5File()
1150 HDF5File & operator=(HDF5File const & other) in operator =()
2761 HDF5File::createDataset(std::string datasetName, in createDataset()
2838 void HDF5File::write_(std::string &datasetName, in write_()
3118 void HDF5File::read_(std::string datasetName, in read_()
3404 HDF5File file(info.getFilePath(), HDF5File::OpenReadOnly); in doxygen_overloaded_function()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/hdf5/
H A Dhdf5file.c27 typedef struct HDF5File HDF5File; typedef
28 #define KFILE_IMPL HDF5File
43 struct HDF5File struct
62 rc_t CC HDF5FileDestroy ( HDF5File *self ) in HDF5FileDestroy() argument
91 rc_t CC HDF5FileRandomAccess ( const HDF5File *self ) in HDF5FileRandomAccess()
116 rc_t CC HDF5FileSetSize ( HDF5File *self, uint64_t size ) in HDF5FileSetSize()
294 rc_t CC HDF5FileWrite ( HDF5File *self, uint64_t pos, in HDF5FileWrite()
307 uint32_t CC HDF5FileType ( const HDF5File *self ) in HDF5FileType()
339 HDF5File *f; in HDF5FileMake()
369 HDF5File * hdf5_self; in MakeHDF5ArrayFile()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/hdf5/
H A Dhdf5file.c27 typedef struct HDF5File HDF5File; typedef
28 #define KFILE_IMPL HDF5File
43 struct HDF5File struct
62 rc_t CC HDF5FileDestroy ( HDF5File *self ) in HDF5FileDestroy() argument
91 rc_t CC HDF5FileRandomAccess ( const HDF5File *self ) in HDF5FileRandomAccess()
116 rc_t CC HDF5FileSetSize ( HDF5File *self, uint64_t size ) in HDF5FileSetSize()
294 rc_t CC HDF5FileWrite ( HDF5File *self, uint64_t pos, in HDF5FileWrite()
307 uint32_t CC HDF5FileType ( const HDF5File *self ) in HDF5FileType()
339 HDF5File *f; in HDF5FileMake()
369 HDF5File * hdf5_self; in MakeHDF5ArrayFile()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/utils/
H A DHDF5UtilsUnitTest.java7 import org.broadinstitute.hdf5.HDF5File;
43 try (final HDF5File hdf5File = new HDF5File(tempOutputHD5, HDF5File.OpenMode.CREATE)) { in testCreateLargeMatrix()
47 …try (final HDF5File hdf5FileForReading = new HDF5File(tempOutputHD5, HDF5File.OpenMode.READ_ONLY))… in testCreateLargeMatrix()
/dports/graphics/vigra/vigra-8acd73a/vigranumpy/src/core/
H A Dmulti_array_chunked.cxx691 if(mode == HDF5File::Default) in construct_ChunkedArrayHDF5()
694 mode = HDF5File::New; in construct_ChunkedArrayHDF5()
695 else if(HDF5File(filename, HDF5File::ReadOnly).existsDataset(datasetName)) in construct_ChunkedArrayHDF5()
696 mode = HDF5File::ReadOnly; in construct_ChunkedArrayHDF5()
698 mode = HDF5File::Replace; in construct_ChunkedArrayHDF5()
701 if(mode == HDF5File::Replace) in construct_ChunkedArrayHDF5()
703 mode = HDF5File::New; in construct_ChunkedArrayHDF5()
707 filemode = HDF5File::New; in construct_ChunkedArrayHDF5()
709 HDF5File file(filename, filemode); in construct_ChunkedArrayHDF5()
727 HDF5File file(handle); in construct_ChunkedArrayHDF5id()
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H A Drandom_forest_3.cxx158 HDF5File h5ctx(filename); in pythonImportFromHDF5()
168 HDF5File h5ctx(filename, HDF5File::ReadWrite ); in pythonExportHDF5()
/dports/audio/csound/csound-6.15.0/Opcodes/hdf5/
H A DHDF5IO.h76 typedef struct HDF5File struct
82 } HDF5File; argument
85 HDF5File *HDF5IO_newHDF5File(CSOUND *csound, AUXCH *hdf5FileMemory,
88 void HDF5IO_deleteHDF5File(CSOUND *csound, HDF5File *hdf5File);
96 HDF5File *hdf5File;
126 HDF5File *hdf5File;
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/
H A DHDF5SimpleCountCollection.java10 import org.broadinstitute.hdf5.HDF5File;
55 private final HDF5File file;
66 HDF5SimpleCountCollection(final HDF5File file) { in HDF5SimpleCountCollection()
113 try (final HDF5File file = new HDF5File(outFile, HDF5File.OpenMode.CREATE)) { in write()
H A DSimpleCountCollection.java4 import org.broadinstitute.hdf5.HDF5File;
98 ? readHDF5(new HDF5File(file)) in readAndSubset()
115 private static SimpleCountCollection readHDF5(final HDF5File file) { in readHDF5()
/dports/graphics/vigra/vigra-8acd73a/src/impex/
H A Dhdf5_rf_impex.cxx70 void options_import_HDF5(HDF5File & h5context, in options_import_HDF5()
79 void options_export_HDF5(HDF5File & h5context, RandomForestOptions const & opt, in options_export_HDF5()
87 void dt_import_HDF5(HDF5File & h5context, detail::DecisionTree & tree, in dt_import_HDF5()
104 void dt_export_HDF5(HDF5File & h5context, in dt_export_HDF5()
/dports/graphics/vigra/vigra-8acd73a/test/hdf5impex/
H A Dtest.cxx407 HDF5File file (file_name, HDF5File::New); in testHDF5FileDataAccess()
420 HDF5File file_copy(file); in testHDF5FileDataAccess()
427 HDF5File file_copy2; in testHDF5FileDataAccess()
689 HDF5File file (file_name, HDF5File::New); in testHDF5FileAttributes()
888 HDF5File file (file_name, HDF5File::New); in testHDF5FileBlockAccess()
968 HDF5File file (file_name, HDF5File::New); in testHDF5FileChunks()
1049 HDF5File file (file_name, HDF5File::New); in testHDF5FileCompression()
1122 HDF5File file (file_name, HDF5File::New); in testHDF5FileBrowsing()
1182 HDF5File file; in testHDF5FileTutorial()
1249 HDF5File file_open ("tutorial_HDF5File.h5", HDF5File::Open); in testHDF5FileTutorial()
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/packages/external/muq2/MUQ/Utilities/HDF5/
H A DAttributes.h23 Attribute(std::shared_ptr<HDF5File> file_, in Attribute()
75 std::shared_ptr<HDF5File> file;
89 AttributeList(std::shared_ptr<HDF5File> file_, in AttributeList()
99 std::shared_ptr<HDF5File> file;
H A DH5Object.h25 H5Object AddChildren(std::shared_ptr<HDF5File> file,
55 …friend H5Object muq::Utilities::AddChildren(std::shared_ptr<HDF5File> file, std::string const& pat…
61 H5Object(std::shared_ptr<HDF5File> file_, in H5Object()
205 std::shared_ptr<HDF5File> file;
H A DHDF5File.h23 class HDF5File : public std::enable_shared_from_this<HDF5File> {
33 HDF5File(std::string const& filename_);
36 virtual ~HDF5File();
56 …void Copy(std::string const& destName, std::shared_ptr<HDF5File> srcFile, std::string const& srcNa…
613 void MergeFile(std::shared_ptr<HDF5File> const& otherFile);
H A DBlockDataset.h26 std::shared_ptr<HDF5File> file_, in BlockDataset()
94 std::shared_ptr<HDF5File> file;
/dports/biology/py-loompy/loompy-3.0.6/loompy/
H A Dutils.py4 from h5py import File as HDF5File unknown
18 def get_loom_spec_version(f: HDF5File) -> str: argument
26 def compare_loom_spec_version(f: HDF5File, v: str) -> int: argument
/dports/graphics/vigra/vigra-8acd73a/test/random_forest_3/
H A Dtest.cxx222 HDF5File hfile("data/rf.h5", HDF5File::ReadOnly); in test_import()
251 HDF5File infile("data/rf.h5", HDF5File::ReadOnly); in test_export()
255 HDF5File outfile("data/rf_out.h5", HDF5File::New); in test_export()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/utils/
H A DHDF5Utils.java5 import org.broadinstitute.hdf5.HDF5File;
60 public static List<SimpleInterval> readIntervals(final HDF5File file, in readIntervals()
78 public static <T extends SimpleInterval> void writeIntervals(final HDF5File file, in writeIntervals()
99 public static double[][] readChunkedDoubleMatrix(final HDF5File file, in readChunkedDoubleMatrix()
146 public static void writeChunkedDoubleMatrix(final HDF5File file, in writeChunkedDoubleMatrix()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/denoising/
H A DHDF5SVDReadCountPanelOfNormals.java16 import org.broadinstitute.hdf5.HDF5File;
120 private final HDF5File file;
131 private HDF5SVDReadCountPanelOfNormals(final HDF5File file) { in HDF5SVDReadCountPanelOfNormals()
224 public static HDF5SVDReadCountPanelOfNormals read(final HDF5File file) { in read()
256 try (final HDF5File file = new HDF5File(outFile, HDF5File.OpenMode.CREATE)) { in create()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/
H A DDenoiseReadCounts.java7 import org.broadinstitute.hdf5.HDF5File;
184 …try (final HDF5File hdf5PanelOfNormalsFile = new HDF5File(inputPanelOfNormalsFile)) { //HDF5File … in doWork()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/formats/collections/
H A DHDF5SimpleCountCollectionUnitTest.java5 import org.broadinstitute.hdf5.HDF5File;
32 … final HDF5SimpleCountCollection rcc = new HDF5SimpleCountCollection(new HDF5File(outputFile)); in basicTest()

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