org.saddle.io

H5Store

object H5Store extends AnyRef

Implements (thread-safe) HDF5 I/O functionality for Series and Frames.

We serialize all reads and writes to the underlying library as recommended here:

http://www.hdfgroup.org/hdf-java-html/JNI/ -- "Following the JNI specification, the recommended procedure is to use Java synchronization to create a monitor to serialize access to the library."

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Type Members

  1. sealed trait H5Resource extends AnyRef

    Sealed trait representing resources that might be opened in an HDF5 file.

  2. case class H5StoreException(msg: String) extends RuntimeException with Product with Serializable

    For wrapping any HDF5 exception

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
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  2. final def !=(arg0: Any): Boolean

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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  5. final def ==(arg0: Any): Boolean

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  6. object H5A extends H5Resource with Product with Serializable

  7. object H5D extends H5Resource with Product with Serializable

  8. object H5F extends H5Resource with Product with Serializable

  9. object H5G extends H5Resource with Product with Serializable

  10. object H5P extends H5Resource with Product with Serializable

  11. object H5S extends H5Resource with Product with Serializable

  12. object H5T extends H5Resource with Product with Serializable

  13. final def asInstanceOf[T0]: T0

    Definition Classes
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  14. def assertException(condition: Boolean, errorMessage: String): Unit

  15. def clone(): AnyRef

    Attributes
    protected[lang]
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    @throws()

  16. def closeFile(fileid: Int): Unit

    Close an HDF5 file and return an integer handle.

    Close an HDF5 file and return an integer handle.

    fileid

    Integer handle of file

  17. def createFile(path: String): Int

    Create an HDF5 file and return an integer handle.

    Create an HDF5 file and return an integer handle.

    path

    Path of file

  18. final def eq(arg0: AnyRef): Boolean

    Definition Classes
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  19. def equals(arg0: Any): Boolean

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  20. def finalize(): Unit

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  21. final def getClass(): java.lang.Class[_]

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  22. def hashCode(): Int

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  23. final def isInstanceOf[T0]: Boolean

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  24. final def ne(arg0: AnyRef): Boolean

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  25. final def notify(): Unit

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  26. final def notifyAll(): Unit

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  27. def openFile(path: String, readOnly: Boolean = true): Int

    Open an HDF5 file and return an integer handle.

    Open an HDF5 file and return an integer handle.

    path

    Path of file

  28. def openResourceCount: Int

    Query for number of open resource handles held by HDF5 Library

  29. def readFrame[RX, CX, T](fileid: Int, group: String)(implicit arg0: ST[RX], arg1: ORD[RX], arg2: ST[CX], arg3: ORD[CX], arg4: ST[T]): Frame[RX, CX, T]

    Read a Frame from an HDF5 file.

    Read a Frame from an HDF5 file.

    RX

    Frame row index type

    CX

    Frame col index type

    T

    Frame values type

    fileid

    HDF5 file handle returned from openFile

    group

    Name of hdf5 group holding frame data

  30. def readFrame[RX, CX, T](path: String, group: String)(implicit arg0: ST[RX], arg1: ORD[RX], arg2: ST[CX], arg3: ORD[CX], arg4: ST[T]): Frame[RX, CX, T]

    Read a Frame from an HDF5 file.

    Read a Frame from an HDF5 file.

    RX

    Frame row index type

    CX

    Frame col index type

    T

    Frame values type

    path

    Path to file to read

    group

    Name of hdf5 group holding frame data

  31. def readFrameSlice[RX, CX, T](fileid: Int, group: String, rowFrom: RX, rowTo: RX, colFrom: CX, colTo: CX, rowInclusive: Boolean, colInclusive: Boolean)(implicit arg0: ST[RX], arg1: ORD[RX], arg2: ST[CX], arg3: ORD[CX], arg4: ST[T]): Frame[RX, CX, T]

    Read a Frame slice from an HDF5 file.

    Read a Frame slice from an HDF5 file. Note that the whole frame is still read into memory, so this isn't meant for working with huge data.

    RX

    Frame row index type

    CX

    Frame col index type

    T

    Frame values type

    fileid

    HDF5 file handle returned from openFile

    group

    Name of hdf5 group holding frame data

    rowFrom

    row to start slice

    rowTo

    row to end slice

    colFrom

    col to start slice

    colTo

    col to end slice

    rowInclusive

    whether to include or exclude rowTo label in slice

    colInclusive

    whether to include or exclude colTo label in slice

  32. def readFrameSlice[RX, CX, T](path: String, group: String, rowFrom: RX, rowTo: RX, colFrom: CX, colTo: CX, rowInclusive: Boolean, colInclusive: Boolean)(implicit arg0: ST[RX], arg1: ORD[RX], arg2: ST[CX], arg3: ORD[CX], arg4: ST[T]): Frame[RX, CX, T]

    Read a Frame slice from an HDF5 file.

    Read a Frame slice from an HDF5 file. Note that the whole frame is still read into memory, so this isn't meant for working with huge data.

    RX

    Frame row index type

    CX

    Frame col index type

    T

    Frame values type

    path

    Path to file to read

    group

    Name of hdf5 group holding frame data

    rowFrom

    row to start slice

    rowTo

    row to end slice

    colFrom

    col to start slice

    colTo

    col to end slice

    rowInclusive

    whether to include or exclude rowTo label in slice

    colInclusive

    whether to include or exclude colTo label in slice

  33. def readGroupNames(path: String, node: String = "/"): List[String]

    Read names of the groups at some level of the file hierarchy

    Read names of the groups at some level of the file hierarchy

    path

    Path of file

    node

    Node of the hierarchy tree

  34. def readGroupNamesFid(fileid: Int, node: String = "/"): List[String]

    Read names of the groups at some level of the file hierarchy, given an open file

    Read names of the groups at some level of the file hierarchy, given an open file

    fileid

    File handle from openFile

    node

    Node of the hierarchy tree

  35. def readSeries[X, T](fileid: Int, group: String)(implicit arg0: ST[X], arg1: ORD[X], arg2: ST[T]): Series[X, T]

    Read a Series from an already-open HDF5 file.

    Read a Series from an already-open HDF5 file.

    X

    Series index type

    T

    Series values type

    fileid

    HDF5 file handle returned from openFile

    group

    Name of hdf5 group holding series data

  36. def readSeries[X, T](path: String, group: String)(implicit arg0: ST[X], arg1: ORD[X], arg2: ST[T]): Series[X, T]

    Read a Series from an HDF5 file.

    Read a Series from an HDF5 file.

    X

    Series index type

    T

    Series values type

    path

    Path to file to read

    group

    Name of hdf5 group holding series data

  37. def readSeriesSlice[X, T](fileid: Int, group: String, from: X, to: X, inclusive: Boolean)(implicit arg0: ST[X], arg1: ORD[X], arg2: ST[T]): Series[X, T]

    Read a Series slice from an HDF5 file.

    Read a Series slice from an HDF5 file. Note that this still loads the entire series into memory, so this is NOT meant to work with very large data chunks.

    X

    Series index type

    T

    Series values type

    fileid

    HDF5 file handle returned from openFile

    group

    Name of hdf5 group holding series data

    from

    Starting index of slice

    to

    Ending index of slice

    inclusive

    Whether to include or exclude ending index label (default true)

  38. def readSeriesSlice[X, T](path: String, group: String, from: X, to: X, inclusive: Boolean)(implicit arg0: ST[X], arg1: ORD[X], arg2: ST[T]): Series[X, T]

    Read a Series slice from an HDF5 file.

    Read a Series slice from an HDF5 file. Note that this still loads the entire series into memory, so this is NOT meant to work with very large data chunks.

    X

    Series index type

    T

    Series values type

    path

    Path to file to read

    group

    Name of hdf5 group holding series data

    from

    Starting index of slice

    to

    Ending index of slice

    inclusive

    Whether to include or exclude ending index label (default true)

  39. final def synchronized[T0](arg0: ⇒ T0): T0

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  40. def toString(): String

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  41. final def wait(): Unit

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  42. final def wait(arg0: Long, arg1: Int): Unit

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  43. final def wait(arg0: Long): Unit

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  44. def writeFrame[R, C, T](fileid: Int, group: String, df: Frame[R, C, T])(implicit arg0: ST[R], arg1: ORD[R], arg2: ST[C], arg3: ORD[C], arg4: ST[T]): Unit

    Write a Frame to an HDF5 file.

    Write a Frame to an HDF5 file.

    R

    Frame row index type

    C

    Frame col index type

    T

    Framevalues type

    fileid

    HDF5 file handle returned from openFile

    group

    Name of hdf5 group to hold frame data

  45. def writeFrame[R, C, T](path: String, group: String, df: Frame[R, C, T])(implicit arg0: ST[R], arg1: ORD[R], arg2: ST[C], arg3: ORD[C], arg4: ST[T]): Unit

    Write a Frame to an HDF5 file.

    Write a Frame to an HDF5 file.

    R

    Frame row index type

    C

    Frame col index type

    T

    Framevalues type

    path

    Path to file to read

    group

    Name of hdf5 group to hold frame data

  46. def writeSeries[X, T](fileid: Int, group: String, s: Series[X, T])(implicit arg0: ST[X], arg1: ORD[X], arg2: ST[T]): Unit

    Write a Series to an already-open HDF5 file.

    Write a Series to an already-open HDF5 file.

    X

    Series index type

    T

    Series values type

    fileid

    HDF5 file handle returned from openFile

    group

    Name of hdf5 group to hold series data

  47. def writeSeries[X, T](path: String, group: String, s: Series[X, T])(implicit arg0: ST[X], arg1: ORD[X], arg2: ST[T]): Unit

    Write a Series to an HDF5 file.

    Write a Series to an HDF5 file.

    X

    Series index type

    T

    Series values type

    path

    Path to file to read

    group

    Name of hdf5 group to hold series data

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