XmippH5File Class Reference

#include <xmipp_hdf5.h>

Inheritance diagram for XmippH5File:

Collaboration diagram for XmippH5File:

Public Member Functions
void	showTree (std::ostream &out=std::cout)
void	openFile (const H5std_string &name, unsigned int flags, const H5::FileAccPropList &access_plist=H5::FileAccPropList::DEFAULT)
int	getDataset (const char *dsname, Matrix1D< double > &data, bool reportError=true) const
bool	checkDataset (const char *dsname) const

Detailed Description

Definition at line 69 of file xmipp_hdf5.h.

Member Function Documentation

checkDataset()

bool XmippH5File::checkDataset

(

const char *

dsname

)

const

Return true if the dataset dsname exists in the file

Parameters

dsname

Dataset name to check

Returns

true if dataset exists, false otherwise.

Definition at line 121 of file xmipp_hdf5.cpp.

{
    H5::DataSet dataset;
    // Open the dataset
    try
    {
        dataset = openDataSet(dsname);
    }
    catch (H5::Exception &h5e)
    {
        return false;
    }
    dataset.close();
    return true;
}

getDataset()

int XmippH5File::getDataset	(	const char *	dsname,
		Matrix1D< double > &	data,
		bool	reportError = true
	)		const

Return the values in the dataset dsname and return them in a Matrix1D double data

Parameters

dsname	Dataset name
data	Vector data
reportError	If true throw an exception in case of failure, otherwise it returns a negative number

Definition at line 137 of file xmipp_hdf5.cpp.

{
    H5::DataSet dataset;
    // Open the dataset
    try
    {
        dataset = openDataSet(dsname);
    }
    catch (H5::Exception &h5e)
    {
        if ( reportError )
            REPORT_ERROR(ERR_ARG_MISSING,formatString("getDataset: %s dataset " \
                         "does not exist in file %s.", dsname, this->getFileName().c_str()));
        //        std::cerr << "getDataset Error: " << h5e.getCDetailMsg() << std::endl;
        return -1;
    }

    //Get dataspace of the dataset.
    H5::DataSpace filespace = dataset.getSpace();

    // Check the number of dimensions in the dataspace is one.
    if (filespace.getSimpleExtentNdims()!= 1 )
        REPORT_ERROR(ERR_ARG_INCORRECT, formatString("getDataset: Dataset %s has "\
                     "more than 1 dimension", dsname));

    // Get the size of the dimension in the dataspace
    hsize_t dim[1];
    filespace.getSimpleExtentDims(dim);


    hsize_t offset[1]; // Hyperslab offset in the file
    //    hsize_t  count[1]; // Size of the hyperslab in the file

    // Define the offset and count of the hyperslab to be read.
    offset[0] = 0;
    //    count[0]  = dim[0];

    filespace.selectHyperslab( H5S_SELECT_SET, dim, offset );

    // Allocate space for data and define the memspace
    data.resizeNoCopy((int)*dim);

    H5::DataSpace memspace(1, dim);

    // Read data from hyperslab in the file into the hyperslab in memory
    dataset.read(MATRIX1D_ARRAY(data), H5::PredType::NATIVE_DOUBLE, memspace, filespace);

    filespace.close();
    memspace.close();
    dataset.close();

    return 0;
}

openFile()

void XmippH5File::openFile	(	const H5std_string &	name,
		unsigned int	flags,
		const H5::FileAccPropList &	access_plist = H5::FileAccPropList::DEFAULT
	)

Open HDF5 file

Parameters

name	File name
flags	tandard hdf5 flags
access_plist	Standard hdf5 plist

Definition at line 112 of file xmipp_hdf5.cpp.

{
    if ( isHdf5(name.c_str()) )
        H5::H5File::openFile(name.c_str(), flags, access_plist);
    else
        REPORT_ERROR(ERR_IMG_UNKNOWN, formatString("XmippH5File: Format of %s is not HDF5.",name.c_str()));
}

showTree()

void XmippH5File::showTree

(

std::ostream &

out = std::cout

)

Show the groups and dataset and print them in the output stream out.

Parameters

out	Output stream

Definition at line 191 of file xmipp_hdf5.cpp.

{
    H5TreeInfo h5Info;

    h5Info.out = &out;
    h5Info.rootname = "";

    this->iterateElems("/", NULL, showObjectInfo, &h5Info);
}

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The documentation for this class was generated from the following files:

• xmippCore/core/xmipp_hdf5.h
• xmippCore/core/xmipp_hdf5.cpp