hdf5 (MATLAB Functions)

HDF5 data type classes

Syntax

```
hdf5*(...)
```

Description

MATLAB provides a set of classes to represent HDF5 data types. MATLAB defines a general HDF5 data type class, with subclasses for individual HDF5 data types. The following figure illustrates these classes and subclasses. For more information about a specific class, see the sections that follow. To learn more about the HDF5 data types in general, see the NCSA HDF Web page at http://hdf.ncsa.uiuc.edu. For information about using these classes, see Remarks.

h5array

The HDF5 h5array class associates a name with an array. The following are the data members of the h5array class.

Data Members

Data
Multidimensional array

Name
Text string specifying the name of the object

Data Members
`Data`	Multidimensional array
`Name`	Text string specifying the name of the object

The following are the methods of the h5array class. This table shows the function calling syntax. You can also access methods using subscripted reference (dot notation). For an example of the syntax, see HDF5 Enumerated Object Example.

Methods
Description
Syntax

hdf5.h5array
Constructs object of class h5array.
arr = hdf5.h5array;
arr = hdf5.h5array(data)

where arr is an h5array object and data can be numeric, a cell array, or an HDF5 data type.

setData
Sets the value of the object's Data member.
setData(arr, data)

where arr is an h5array object and data can be numeric, a cell array, or an HDF5 data type.

setName
Sets the value of the object's Name member.
setName(arr, name)

where arr is an h5array object and name is a string or cell array.

Methods	Description	Syntax
`hdf5.h5array`	Constructs object of class `h5array`.	`arr = hdf5.h5array;` `arr = hdf5.h5array(data)` where `arr` is an `h5array` object and `data` can be numeric, a cell array, or an HDF5 data type.
`setData`	Sets the value of the object's `Data` member.	`setData(arr, data)` where `arr` is an `h5array` object and `data` can be numeric, a cell array, or an HDF5 data type.
`setName`	Sets the value of the object's `Name` member.	`setName(arr, name)` where `arr` is an `h5array` object and `name` is a string or cell array.

h5compound

The HDF5 h5compound class associates a name with a structure, where you can define the field names in the structure and their values. The following are the data members of the h5compound class.

Data Members

Data
Multidimensional array.

MemberNames
Text string specifying the names of fields in the structure

Name
Text string specifying the name of the object

Data Members
`Data`	Multidimensional array.
`MemberNames`	Text string specifying the names of fields in the structure
`Name`	Text string specifying the name of the object

The following are the methods of the h5compound class.

Methods
Description
Syntax

hdf5.h5compound
Constructs object of class h5compound.
C = hdf5.h5compound;
C = hdf5.h5compound(mName1,mName2,...)

where C is an h5compound object and mName1 and mName2 are text strings that specify field names. The constructor creates a corresponding data field for every member name.

addMember
Creates a new field in the structure.
addMember(C, mName)

where mName is a text string that specifies the name of the field. This method automatically creates a corresponding data field for the new member name.

setMember
Sets the value of the Data element associated with a particular field.
setData(C, mName, mData)

where C is an h5compound object, mName is the name of a field in the object, and mdata is the value you want to assign to the field. mData can be numeric or an HDF5 data type.

setMemberNames
Specifies the names of fields in the structure.
setData(C, mName1, mName2,...)

where C is an h5compound object and mName1 and mName2 are text strings that specify field names. The constructor creates a corresponding data field for every member name.

setName
Sets the value of the object's Name member.
setName(C, name)

where arr is an h5compound object and name is a string or cell array.

Methods	Description	Syntax
`hdf5.h5compound`	Constructs object of class `h5compound`.	`C = hdf5.h5compound;` `C = hdf5.h5compound(mName1,mName2,...)` where `C` is an `h5compound` object and `mName1` and `mName2` are text strings that specify field names. The constructor creates a corresponding data field for every member name.
`addMember`	Creates a new field in the structure.	`addMember(C, mName)` where `mName` is a text string that specifies the name of the field. This method automatically creates a corresponding data field for the new member name.
`setMember`	Sets the value of the `Data` element associated with a particular field.	`setData(C, mName, mData)` where `C` is an `h5compound` object, `mName` is the name of a field in the object, and `mdata` is the value you want to assign to the field. `mData` can be numeric or an HDF5 data type.
`setMemberNames`	Specifies the names of fields in the structure.	`setData(C, mName1, mName2,...)` where `C` is an `h5compound` object and `mName1` and `mName2` are text strings that specify field names. The constructor creates a corresponding data field for every member name.
`setName`	Sets the value of the object's `Name` member.	`setName(C, name)` where `arr` is an `h5compound` object and `name` is a string or cell array.

h5enum

The HDF5 h5enum class defines an enumerated types, where you can specify the enumerations (text strings) and the values the represent. The following are the data members of the h5enum class.

Data Members

Data
Multidimensional array

EnumNames
Text string specifying the enumerations, that is, the text strings that represent values.

EnumValues
The values associated with enumerations

Name
Text string specifying the name of the object

Data Members
`Data`	Multidimensional array
`EnumNames`	Text string specifying the enumerations, that is, the text strings that represent values.
`EnumValues`	The values associated with enumerations
`Name`	Text string specifying the name of the object

The following are the methods of the h5enum class.

Methods
Description
Syntax

hdf5.h5enum
Constructs object of class h5enum.
E = hdf5.h5enum;
E = hdf5.h5enum(eNames, eVals)

where E is an h5enum object, eNames is a cell array of strings, and eVals is vector of integers. eNames and eVals must have the same number of elements.

defineEnum
Defines the set of enumerations with the integer values they represent.
detineEnum(E, eNames, eVals)

where E is an h5enum object, eNames is a cell array of strings, and eVals is vector of integers. eNames and eVals must have the same number of elements.

getString
Returns data as enumeration's values, not integer values
enumdata = getString(E)

where enumdata is a cell array of strings and E is an h5enum object.

setData
Sets the value of the object's Data member.
setData(E, eData)

where E is an h5enum object and eData is a vector of integers.

setEnumNames
Specifies the enumerations.
setEnumNames(E, eNames)

where E is an h5enum object and eNames is a cell array of strings.

setEnumValues
Specifies the value associated with each enumeration.
setEnumValues(E, eVals)

where E is an h5enum object and eVals is a vector of integers.

setName
Sets the value of the object's Name member.
setName(E, name)

where E is an h5enum object and name is a string or cell array.

Methods	Description	Syntax
`hdf5.h5enum`	Constructs object of class `h5enum`.	`E = hdf5.h5enum;` `E = hdf5.h5enum(eNames, eVals)` where `E` is an `h5enum` object, `eNames` is a cell array of strings, and `eVals` is vector of integers. `eNames` and `eVals` must have the same number of elements.
`defineEnum`	Defines the set of enumerations with the integer values they represent.	`detineEnum(E, eNames, eVals)` where `E` is an `h5enum` object, `eNames` is a cell array of strings, and `eVals` is vector of integers. `eNames` and `eVals` must have the same number of elements.
`getString`	Returns data as enumeration's values, not integer values	`enumdata = getString(E)` where `enumdata` is a cell array of strings and `E` is an `h5enum` object.
`setData`	Sets the value of the object's `Data` member.	`setData(E, eData)` where `E` is an `h5enum` object and `eData` is a vector of integers.
`setEnumNames`	Specifies the enumerations.	`setEnumNames(E, eNames)` where `E` is an `h5enum` object and `eNames` is a cell array of strings.
`setEnumValues`	Specifies the value associated with each enumeration.	`setEnumValues(E, eVals)` where `E` is an `h5enum` object and `eVals` is a vector of integers.
`setName`	Sets the value of the object's `Name` member.	`setName(E, name)` where `E` is an `h5enum` object and `name` is a string or cell array.

h5string

The HDF5 h5string class associates a name with an text string and provides optional padding behavior. The following are the data members of the h5string class.

Data Members

Data
Text string

Length
Scalar value

Name
Text string specifying the name of the object

Padding
Type of padding to use: 'spacepad', 'nullterm', or 'nullpad'

Data Members
`Data`	Text string
`Length`	Scalar value
`Name`	Text string specifying the name of the object
`Padding`	Type of padding to use: `'spacepad'`, '`nullterm'`, or `'nullpad'`

The following are the methods of the h5string class.

Methods
Description
Syntax

hdf5.h5string
Constructs object of class h5string.
str = hdf5.h5string;
str = hdf5.h5string(data)
str = hdf5.h5string(data, padType)

where str is an h5string object, data is a text string, and padType is a text string specifying one of the supported pad types.

setData
Sets the value of the object's Data member.
setData(str, data)

where str is an h5string object and data is a text string.

setLength
Sets the value of the object's Length member.
setLength(str, lenVal)

where str is an h5string object and lenVal is a scalar.

setName
Sets the value of the object's Name member.
setName(str, name)

where str is an h5string object and name is a string or cell array.

setPadding
Specifies the value of the object's Padding member.
setData(str, padType)

where str is an h5string object and padType is a text string specifying one of the supported pad types.

Methods	Description	Syntax
`hdf5.h5string`	Constructs object of class `h5string`.	`str = hdf5.h5string;` `str = hdf5.h5string(data)` `str = hdf5.h5string(data, padType)` where `str` is an `h5string` object, `data` is a text string, and `padType` is a text string specifying one of the supported pad types.
`setData`	Sets the value of the object's `Data` member.	`setData(str, data)` where `str` is an `h5string` object and `data` is a text string.
`setLength`	Sets the value of the object's `Length` member.	`setLength(str, lenVal)` where `str` is an `h5string` object and `lenVal` is a scalar.
`setName`	Sets the value of the object's `Name` member.	`setName(str, name)` where `str` is an `h5string` object and `name` is a string or cell array.
`setPadding`	Specifies the value of the object's `Padding` member.	`setData(str, padType)` where `str` is an `h5string` object and `padType` is a text string specifying one of the supported pad types.

h5vlen

The HDF5 h5vlen class associates a name with an array. The following are the data members of the h5vlen class.

Data Members

Data
Multidimensional array

Name
Text string specifying the name of the object

Data Members
`Data`	Multidimensional array
`Name`	Text string specifying the name of the object

The following are the methods of the h5vlen class.

Methods
Description
Syntax

hdf5.h5vlen
Constructs object of class h5vlen.
V = hdf5.h5vlen;
V = hdf5.h5vlen(data)

where V is h5vlen object and data can be a scalar, vector, text string, cell array, or an HDF5 data type.

setData
Sets the value of the object's Data member.
setData(V, data)

where V is h5vlen object and data can be a scalar, vector, text string, cell array, or an HDF5 data type.

setName
Sets the value of the object's Name member.
setName(V, name)

where name is a string or cell array.

Methods	Description	Syntax
`hdf5.h5vlen`	Constructs object of class `h5vlen`.	`V = hdf5.h5vlen;` `V = hdf5.h5vlen(data)` where `V` is `h5vlen` object and `data` can be a scalar, vector, text string, cell array, or an HDF5 data type.
`setData`	Sets the value of the object's `Data` member.	`setData(V, data)` where `V` is `h5vlen` object and `data` can be a scalar, vector, text string, cell array, or an HDF5 data type.
`setName`	Sets the value of the object's `Name` member.	`setName(V, name)` where `name` is a string or cell array.

Remarks

The hdf5read function uses the HDF5 data type classes when the data it is reading from the HDF5 file cannot be represented in the workspace using a native MATLAB data type. For example, if an HDF5 file contains a data set made up of an enumerated data type which cannot be represented in MATLAB, hdf5read uses the HDF5 h5enum class to represent the data. An h5enum object has data members that store the enumerations (text strings), their corresponding values, and the enumerated data.

You might also need to use these HDF5 data type classes when using the hdf5write function to write data from the MATLAB workspace to an HDF5 file. By default, hdf5write can convert most MATLAB data to appropriate HDF5 data types. However, if this default data type mapping is not suitable, you can create HDF5 data types directly.

Examples

HDF5 Array Object Example

Create an array in the MATLAB workspace.

```
data = magic(5);
```

Create an HDF5 h5array object, passing the MATLAB array as the only argument to the constructor.

dset = hdf5.h5array(data)

hdf5.h5array:
 
    Name: ''
    Data: [5x5 double]

Assign a name to the object.

dset.setName('my numeric array data set')

HDF5 Compound Object Example

Create several variables in the MATLAB workspace.

data = magic(5);
str = 'a text string';

Create an HDF5 h5compound object, specifying member names. The method creates corresponding Data fields for each member name.

dset2 = hdf5.h5compound('temp1','temp2','temp3')

Adding member "temp1"
Adding member "temp2"
Adding member "temp3"

hdf5.h5compound:
 
           Name: ''
           Data: {[]  []  []}
    MemberNames: {'temp1'  'temp2'  'temp3'}

Set the values of the members.

setMember(dset2,'temp1',89)
setMember(dset2,'temp2',95)
setMember(dset2,'temp3',108)

dset2

hdf5.h5compound:
 
           Name: ''
           Data: {[89]  [95]  [108]}
    MemberNames: {'temp1'  'temp2'  'temp3'}

HDF5 Enumerated Object Example

Create an HDF5 h5enum object.

```
enum_obj = hdf5.h5enum;
```

Define the enumerations and their corresponding values. The values must be integers.

enum_obj.defineEnum({'RED' 'GREEN' 'BLUE'}, uint8([1 2 3]));

enum_obj now contains the definition of the enumeration that associates the names RED, GREEN, and BLUE with the numbers 1, 2, and 3.

Add enumerated data to the object.

enum_obj.setData(uint8([2 1 3 3 2 3 2 1]));

Use the h5enum getString method to read the data as enumerated values, rather than integers.

vals = enum_obj.getString

vals = 

  Columns 1 through 7

    'GREEN'    'RED'    'BLUE'    'BLUE'    'GREEN'    'BLUE'    'GREEN'

  Column 8

    'RED'

HDF5 h5string Object Example

Create an HDF5 string object.

hdf5.h5vlen({0 [0 1] [0 2] [0:10]})

hdf5.h5vlen:
 
    Name: ''
    Data: [0 0 1 0 2 0 1 2 3 4 5 6 7 8 9 10]

HDF5 h5string Object Example

Create an HDF5 h5vlen object.

hdf5.h5vlen({0 [0 1] [0 2] [0:10]})

hdf5.h5vlen:
 
    Name: ''
    Data: [0 0 1 0 2 0 1 2 3 4 5 6 7 8 9 10]

See Also

hdf5read, hdf5write

hdf hdf5info