Writing an HDF file with C, FORTRAN, Python, MATLAB and R

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Language

HDF4

PYTHON

import numpy
from pyhdf.SD import SD, SDC
 
# Open file for writing
fileName = "SDS.hdf"
filehdf  = SD(fileName, SDC.WRITE | SDC.CREATE)
 
# Init the data buffer to write : a vector of values from 0 to 24, separated by 1
data = numpy.arange(25)
# Make it a 2D array
data.shape = (5, 5)
 
# Create the dataset : set its name, data type et dimensions
sds_name = "SDStemplate"
sds = filehdf.create(sds_name, SDC.INT32, data.shape)
 
# Write the data to it
sds[:] = data
 
# Terminate access to the data set
sds.endaccess()
 
# Close the file
filehdf.end()

C

#include "mfhdf.h"
#define FILE_NAME "SDS.hdf"
#define SDS_NAME  "SDStemplate"
#define X_LENGTH  5
#define Y_LENGTH  5
 
main( )
{
    /************************* Variable declaration **************************/
    int32 sd_id, sds_id, sds_index;
    intn  status;
    int32 start[2], edges[2];
    int32 data[Y_LENGTH][X_LENGTH];
    int   i, j;
    /********************* End of variable declaration ***********************/
 
    /*
    * Data set data initialization.
    */
    for ( j = 0; j < Y_LENGTH; j++ ) {
        for ( i = 0; i < X_LENGTH; i++ )
            data[j][i] = ( i + j ) + 1;
    }
 
    /*
    * Open the file and initialize the SD interface.
    */
    sd_id = SDstart ( FILE_NAME, DFACC_WRITE );
    /*
     * Attach to the first data set.
    */
    sds_index = 0;
    sds_id = SDselect ( sd_id, sds_index );
    /*
    * Define the location and size of the data to be written to the data set.
    */
    start[0] = 0;
    start[1] = 0;
    edges[0] = Y_LENGTH;
    edges[1] = X_LENGTH;
 
    /*
    * Write the stored data to the data set. The third argument is set to NULL
    * to specify contiguous data elements. The last argument must
    * be explicitly cast to a generic pointer since SDwritedata is designed
    * to write generic data.
    */
    status = SDwritedata ( sds_id, start, NULL, edges, ( VOIDP ) data );
    /*
    * Terminate access to the data set.
    */
    status = SDendaccess ( sds_id );
    /*
    * Terminate access to the SD interface and close the file.
    */
    status = SDend ( sd_id );
}

FORTRAN

program  write_dataprogram  write_data
    implicit none
 
C
C     Parameter declaration.
C
    character * 7  FILE_NAME
    character * 11 SDS_NAME
    integer      X_LENGTH, Y_LENGTH, RANK
    parameter   ( FILE_NAME = "SDS.hdf",
    +             SDS_NAME  = "SDStemplate",
    +             X_LENGTH  = 5,
    +             Y_LENGTH  = 16,
    +             RANK      = 2 )
    integer       DFACC_WRITE, DFNT_INT32
    parameter   ( DFACC_WRITE = 2,
    +             DFNT_INT32  = 24 )
 
C
C     Function declaration.
C
    integer sfstart, sfselect, sfwdata, sfendacc, sfend
 
C**** Variable declaration *******************************************
C
    integer sd_id, sds_id, sds_index, status
    integer start ( 2 ), edges ( 2 ), stride ( 2 )
    integer i, j
    integer data( X_LENGTH, Y_LENGTH )
C
C**** End of variable declaration ************************************
C
 
C
C     Data set data initialization.
C
    do  20 j = 1, Y_LENGTH
        do  10 i = 1, X_LENGTH
            data ( i, j ) = i + j - 1
 10         continue
 20     continue
 
C
C     Open the file and initialize the SD interface.
C
    sd_id = sfstart( FILE_NAME, DFACC_WRITE )
C
C     Attach to the first data set.
C
    sds_index = 0
    sds_id = sfselect(sd_id, sds_index)
C
C     Define the location and size of the data to be written
C     to the data set. Note that setting values of the array stride to 1
C     specifies the contiguous writing of data.
C
    start  ( 1 ) = 0
    start  ( 2 ) = 0
    edges  ( 1 ) = X_LENGTH
    edges  ( 2 ) = Y_LENGTH
    stride ( 1 ) = 1
    stride ( 2 ) = 1
C
C     Write the stored data to the data set named in SDS_NAME.
C     Note that the routine sfwdata is used instead of sfwcdata
C     to write the numeric data.
C
    status = sfwdata ( sds_id, start, stride, edges, data )
C
C     Terminate access to the data set.
C
    status = sfendacc ( sds_id )
C
C     Terminate access to the SD interface and close the file.
C
    status = sfend ( sd_id )
    end

MATLAB

file_name = 'sds.hdf';
sds_name = 'a_sds';
 
% Open an existing hdf file or create it
sd_id = hdfsd( 'start',file_name , 'write');
if sd_id == -1
    sd_id = hdfsd( 'start', file_name, 'DFACC_CREATE');
end
 
 
% Create a dataset with its name, data type, rank and dimensions
data = [0 0 0; 1 1 1; 2 2 2; 3 3 3];
data_type = 'double';
rank = ndims(data);
dimsizes  = fliplr(size(data));
sds_id = hdfsd('create', sd_id, sds_name, data_type, rank, dimsizes);
 
 
% Write data to hdf file
sds_start = zeros(1,  ndims(data));
sds_stride = [] ;
sds_edges = fliplr(size(data));
status = hdfsd('writedata', sds_id, sds_start, sds_stride,  sds_edges, data) ;
 
 
% Close access to the sds
status = hdfsd('endaccess',sds_id);
 
 
% Close access to the hdf file
status = hdfsd('end',sd_id);


HDF5

MATLAB

filename = 'test.h5';
 
% Create the file
fid = H5F.create(filename);
% Create a group
gid = H5G.create(fid, 'group','H5P_DEFAULT');
% Create a dataset
fid = H5F.open(filename);
h5create(filename, '/group/sds1', [2 7],'Datatype', 'double','FillValue',5.5);
 
% Add attributes
h5writeatt(filename, '/group', 'Description', 'this is a group');
h5writeatt(filename, '/', 'Description', 'this is an example');
 
% Write data
h5write(filename,  '/group/sds1', [1 2 1 1 1 1 1 ;3  5 0 0 0 0 0]);
h5disp(filename);
 
% Close access
H5G.close(gid)
H5F.close(fid)

R

#To install the package rhdf5 , you need a current version (>2.15.0) of R
#After installing R you can run the following commands from the R command shell to install the bioconductor package rhdf5.
#source("http://bioconductor.org/biocLite.R")
#biocLite("rhdf5")
 
library(rhdf5)
 
filename="/home/Projets/R/myExample.h5"
groupname = "group"
 
 
# Create an h5 file
h5createFile(filename)
 
# Create a group in the h5 file
h5createGroup(filename, groupname)
 
# Create datasets in the h5 file
h5createDataset(filename, "group/toto", c(5,5))
h5createDataset(filename, "sds", c(4,2), storage.mode="integer")
 
# Write data in dataset named "group/tata" and "sds"
vec <- c(1,2,3,4,5,6) 
h5write(vec, filename, "group/tata")
# Or
fid <- H5Fopen(filename)
sdsid <- H5Dopen(fid, "sds")
H5Dwrite(sdsid, c(1,2,3,4,5,6,7,8))
H5Dclose(sdsid)
H5Fclose(fid)
 
# Create attributes
fid <- H5Fopen(filename)
sdsid <- H5Dopen(fid, "sds")
h5createAttribute(sdsid, "unit", 1,1)
h5createAttribute(fid, "Description", 1, 1,storage.mode="character", size = 22)
 
 
# Write attribute value
aid <- H5Aopen(sdsid, "unit")
H5Awrite(aid, 69)
H5Aclose(aid)
aid <- H5Aopen(fid, "Description")
H5Awrite(aid, "this is an example")
H5Aclose(aid)
 
# Close access
H5Dclose(sdsid)
H5Fclose(fid)

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