MATLAB: Do I receive an ‘Out of Memory’ error using FREAD function when the file is smaller than the largest contiguous memory block

fopenfreadMATLABmemoryofoutuint16

I have a large binary file of uint16 data named fname. It smaller than the largest free memory block. When I execute the following commands:

fid=fopen('fname');
F=fread(fid,'uint16')

I receive the following result:

 ??? Error using ===> fread.
 Out of memory. Type HELP MEMORY for your options

Best Answer

Here, the 'uint16' refers to how to interpret the data in the file and not how to represent it in MATLAB. Thus, class(F) will return double, so the FILESIZE * sizeof(double)/sizeof(uint16) will be larger than the memory block and out of memory error is expected.

To work around this issue, use the 'uint16=>uint16' option to FREAD to make MATLAB interpret the data as uint16 and also store it in MATLAB as uint16. This can be done using either of the following commands

1. F = fread(fid,'uint16=>uint16');
2. F = fread(fid,'*uint16');

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MATLAB: Do I get an OutOfMemory error when using FREAD and FPRINTF with large amounts of text (ASCII) data

The data type "char" is represented internally in MATLAB as Unicode, which means that 2 Byte of memory are needed per character in order to represent the data. To work around this issue, you will either need to have a largest contiguous free block that is at least twice the size of the data that you are loading, or you could read the data as an unsigned char, as follows:

fId = fopen('largefile.txt', 'rt');
y = fread(fId, 'uchar=>uchar')';
fclose(fId);

The function FPRINTF in MATLAB is vectorized, unlike the FPRINTF function in the C programming language. Because of this, there is some extra overhead in parsing the MATLAB data and preparing it before it can be passed to the low-level C-FPRINTF function. This overhead may or may not be reflected in the output of FEATURE MEMSTATS. So in the end, more memory is needed to write a file using FPRINTF than the amount of memory that is used by the data passed to it.

MATLAB is a higher programming language, because of this; it needs to convert the data to a low-level format first, before passing it to a low-level function.

MATLAB: How to specify the output type of an fread(fid…)

Try this little experiment (based on the first example in the doc)

%%

fid = fopen('nine.bin','w');
fwrite(fid,[1:9]);
fclose(fid);
%%
fid = fopen('nine.bin','r');
num = fread( fid, [1,9], 'uint8=>uint8' );
fclose(fid);

and

>> whos num
  Name      Size            Bytes  Class    Attributes
  num       1x9                 9  uint8

Best Answer

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MATLAB: Do I get an OutOfMemory error when using FREAD and FPRINTF with large amounts of text (ASCII) data

MATLAB: How to specify the output type of an fread(fid…)

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