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I had a similar need as you did, I solved the problem with boost filesystem library.

For file scanning with boost, it would look something like this:

int scanFiles( const path & directory, string filterFileType)
{   
    int fileCount=0;
    if( exists( directory ) )
    {
        directory_iterator end ;
        for( directory_iterator iter(directory) ; iter != end ; ++iter )
            if ( (is_regular_file( *iter ) && iter->path().extension().string() == filterFileType))
        {                               
            cout << iter->path().filename().string() << endl ; 
            fileCount++;
        }
    }   
    return fileCount;
}

While scanning you can return or update global Mat variable and use it to do your stuff.

But I don't think that OpenCV can scan through files natively.

I had a similar need as you did, I solved the problem with boost filesystem library.

For file scanning with boost, it would look something like this:

int scanFiles( const path & directory, string filterFileType)
{   
    int fileCount=0;
    if( exists( directory ) )
    {
        directory_iterator end ;
        for( directory_iterator iter(directory) ; iter != end ; ++iter )
            if ( (is_regular_file( *iter ) && iter->path().extension().string() == filterFileType))
        {                               
            cout << iter->path().filename().string() << endl ;  //this is the one of scanned file names
            fileCount++;
        }
    }   
    return fileCount;
}

While scanning you can return or update global Mat variable and use it to do your stuff.

But I don't think that OpenCV can scan through files natively.