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Save and Load Parts of Variables in MAT-Files

You can save and load parts of variables directly in MAT-files without loading them into memory using the matfile function. The primary advantage of using the matfile function over the load or save functions is that you can process parts of very large data sets that are otherwise too large to fit in memory. When working with these large variables, read and write as much data into memory as possible at a time. Otherwise, repeated file access can negatively impact the performance of your code.

Save and Load Using the matfile Function

This example shows how to load, modify, and save part of a variable in an existing MAT-file using the matfile function.

Create a Version 7.3 MAT-file with two variables, A and B.

A = rand(5);
B = magic(10);
save example.mat A B -v7.3;
clear A B

Construct a MatFile object from the MAT-file, example.mat. The matfile function creates a MatFile object that corresponds to the MAT-file and contains the properties of the MatFile object. By default, matfile only permits loading from existing MAT-files.

exampleObject = matfile('example.mat');

To enable saving, call matfile with the Writable parameter.

exampleObject = matfile('example.mat','Writable',true);

Alternatively, construct the object and set Properties.Writable in separate steps.

exampleObject = matfile('example.mat');
exampleObject.Properties.Writable = true;

Load the first row of B from example.mat into variable firstRowB and modify the data. When you index into objects associated with Version 7.3 MAT-files, MATLAB® loads only the part of the variable that you specify.

firstRowB = exampleObject.B(1,:); 
firstRowB = 2 * firstRowB;

Update the values in the first row of variable B in example.mat using the values stored in firstRowB.

exampleObject.B(1,:) = firstRowB;

For very large files, the best practice is to read and write as much data into memory as possible at a time. Otherwise, repeated file access negatively impacts the performance of your code. For example, suppose that your file contains many rows and columns, and that loading a single row requires most of the available memory. Rather than updating one element at a time, update each row.

[nrowsB,ncolsB] = size(exampleObject,'B');
for row = 1:nrowsB
  exampleObject.B(row,:) = row * exampleObject.B(row,:);

If memory is not a concern, you can update the entire contents of a variable at a time.

exampleObject.B = 10 * exampleObject.B;

Alternatively, update a variable by calling the save function with the -append option. The -append option requests that the save function replace only the specified variable, B, and leave other variables in the file intact. This method always requires that you load and save the entire variable.

B(1,:) = 2 * B(1,:);

Add a variable to the file using the object.

exampleObject.C = magic(8);

You also can add the variable by calling the save function with the -append option.

C = magic(8);
clear C

Load Parts of Variables Dynamically

This example shows how to access parts of variables from a MAT-file dynamically. This technique is useful when working with MAT-files whose variables names are not all known.

Construct a MatFile object that corresponds to the sample file topography.mat. Use the who function to store the variable names from the file in the cell array varlist.

exampleObject = matfile("topography.mat");
varlist = who(exampleObject)
varlist = 3x1 cell
    {'topo'    }

The second and third variables, topomap1 and topomap2, are both three-column matrices containing colormap data. Load the colormap data from the third column of each of these two variables into a field of a structure S. For each field, specify a field name that is the original variable name prepended by "colormap_". Then access the data in each variable as properties of exampleObject. Because varName is a variable, enclose it in parentheses.

for index = 2:3
    varName = varlist{index};
    S.("colormap_"+varName) = exampleObject.(varName)(:,3);

View the contents of the structure. The structure has two fields, colormap_topomap1 and colormap_topomap2, and each contains a column vector.

S = struct with fields:
    colormap_topomap1: [64x1 double]
    colormap_topomap2: [128x1 double]

Avoid Inadvertently Loading Entire Variables

When you do not know the size of a large variable in a MAT-file and want to load only parts of that variable at a time, avoid using the end keyword. Using the end keyword temporarily loads the entire contents of the variable in question into memory. For very large variables, loading takes a long time or generates Out of Memory errors. Instead, call the size method for MatFile objects.

For example, this code temporarily loads the entire contents of B in memory:

lastColB = exampleObject.B(:,end);

Use this code instead to improve performance:

[nrows,ncols] = size(exampleObject,'B');
lastColB = exampleObject.B(:,ncols);

Similarly, any time you refer to a variable with syntax of the form matObj.varName, such as exampleObject.B, MATLAB® temporarily loads the entire variable into memory. Therefore, make sure to call the size method for MatFile objects with syntax such as:

[nrows,ncols] = size(exampleObject,'B');

rather than passing the entire contents of exampleObject.B to the size function,

[nrows,ncols] = size(exampleObject.B);

The difference in syntax is subtle, but significant.

Partial Loading and Saving Requires Version 7.3 MAT-Files

Any load or save operation that uses a MatFile object associated with a Version 7 or earlier MAT-file temporarily loads the entire variable into memory.

Use the matfile function to create files in Version 7.3 format. For example, this code

newfile = matfile('newfile.mat');

creates a MAT-file that supports partial loading and saving.

However, by default, the save function creates Version 7 MAT-files. Convert existing MAT-files to Version 7.3 by calling the save function with the -v7.3 option, such as:


To change your preferences to save new files in Version 7.3 format, access the Environment section on the Home tab, and click Preferences. Select MATLAB > General > MAT-Files. This preference is not available in MATLAB Online™.

See Also

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