h5read

Read data from HDF5 dataset

Syntax

data = h5read(filename,ds)

data = h5read(filename,ds,start,count)

data = h5read(filename,ds,start,count,stride)

Description

data = h5read(filename,ds) reads all the data from the dataset ds contained in the HDF5 file filename.

data = h5read(filename,ds,start,count) reads a subset of data from the dataset beginning at the location specified in start. The count argument specifies the number of elements to read along each dimension.

data = h5read(filename,ds,start,count,stride) returns a subset of data with the interval between the indices of each dimension of the dataset specified by stride.

Examples

Read Entire HDF5 Dataset

Get the metadata for a dataset from the HDF5 file and then read the dataset.

Display the metadata for a dataset /g4/lat from the HDF5 file example.h5.

h5disp('example.h5','/g4/lat')

HDF5 example.h5 
Dataset 'lat' 
    Size:  19
    MaxSize:  19
    Datatype:   H5T_IEEE_F64LE (double)
    ChunkSize:  []
    Filters:  none
    FillValue:  0.000000
    Attributes:
        'units':  'degrees_north'
        'CLASS':  'DIMENSION_SCALE'
        'NAME':  'lat'

Read the dataset.

data = h5read('example.h5','/g4/lat')

data = 19×1

   -90
   -80
   -70
   -60
   -50
   -40
   -30
   -20
   -10
     0
      ⋮

Read Subset of HDF5 Dataset

Get the metadata for a dataset from the HDF5 file and then read a subset of the dataset.

Display the metadata for a dataset /g4/world from the HDF5 file example.h5.

h5disp('example.h5','/g4/world')

HDF5 example.h5 
Dataset 'world' 
    Size:  36x19
    MaxSize:  36x19
    Datatype:   H5T_IEEE_F64LE (double)
    ChunkSize:  []
    Filters:  none
    FillValue:  0.000000

Starting from the beginning of data, read a 5-by-3 subset of the data from the dataset.

start = [1 1];
count = [5 3];
data = h5read('example.h5','/g4/world',start,count)

data = 5×3

     0     0     0
     0     0     0
     0     0     0
     0     0     0
     0     0     0

Read HDF5 Dataset with Specified Spacing Between Indices

Read data from a dataset, where the data is sampled at a specified spacing between the dataset indices along each dimension.

First, display the metadata for a dataset /g4/lon from the HDF5 file example.h5. The variable in the dataset has one dimension with 36 elements.

h5disp('example.h5','/g4/lon')  

HDF5 example.h5 
Dataset 'lon' 
    Size:  36
    MaxSize:  36
    Datatype:   H5T_IEEE_F64LE (double)
    ChunkSize:  []
    Filters:  none
    FillValue:  0.000000
    Attributes:
        'units':  'degrees_east'
        'CLASS':  'DIMENSION_SCALE'
        'NAME':  'lon'

Start reading from the location in startLoc and read variable data at intervals specified in stride. A value of 1 in stride accesses adjacent values in the corresponding dimension, whereas a value of 2 accesses every other value in the corresponding dimension, and so on.

startLoc = 1; 
count  = 18; 
stride = 2; 
subsetData  = h5read('example.h5','/g4/lon',startLoc,count,stride);

Examine the output variable subsetData.

whos subsetData

  Name             Size            Bytes  Class     Attributes

  subsetData      18x1               144  double              

Input Arguments

filename — File name

character vector | string scalar

File name, specified as a character vector or string scalar containing the name of an existing HDF5 file.

Depending on the location of your file, filename can take on one of these forms.

Location	Form
Current folder	Specify the name of the file in filename. Example: 'myFile.h5'
Other folders	If the file is not in the current folder or in a folder on the MATLAB® path, then specify the full or relative path name in filename. Example: 'C:\myFolder\myFile.h5' Example: 'myFolder\myFile.h5'
Remote Location	If the file is stored at a remote location, then filename must contain the full path of the file specified as a uniform resource locator (URL) of the form: scheme_name://path_to_file/my_file.ext Based on your remote location, scheme_name can be one of the values in this table. Remote Location scheme_name Amazon S3™ s3 Windows Azure® Blob Storage wasb, wasbs HDFS™ hdfs For more information, see Work with Remote Data. Example: 's3://bucketname/path_to_file/myFile.h5'

ds — Dataset name

character vector | string scalar

Dataset name, specified as a character vector or string scalar containing the name of the dataset in the HDF5 file. An HDF5 dataset is a multidimensional array of data elements, together with supporting metadata.

start — Starting location

vector of ones (default) | numeric vector

Starting location, specified as a numeric vector of positive integers. For an N-dimensional dataset, start is a vector of length N containing 1-based indices. The elements of start correspond, in order, to the variable dimensions.

If you do not specify start, then the h5read function starts reading the dataset from the first index along each dimension.

count — Number of elements

vector of Inf's (default) | numeric vector

Number of elements to read, specified as a numeric vector of positive integers. For an N-dimensional dataset, count is a vector of length N, specifying the number of elements to read along each dimension. The elements of count correspond, in order, to the variable dimensions. If any element of count is Inf, then h5read reads until the end of the corresponding dimension.

If you do not specify count, then the h5read function reads data until the end of each dimension.

stride — Spacing between indices

vector of ones (default) | numeric vector

Space between the indices along each dimension of the dataset, specified as a numeric vector of integers. For an N-dimensional variable in the dataset, stride is a vector of length N. The elements of the stride vector correspond, in order, to the variable dimensions. A value of 1 accesses adjacent values of the variable in the corresponding dimension. Whereas, a value of 2 accesses every other value of the variable in the corresponding dimension, and so on.

If you do not specify stride, then the h5read function reads the data with a default spacing of 1 along each dimension.