NIOFileHandle: don't read from the file to fill a trash buffer

[popiel]

The writeSetup method in NIOFileHandle ensures that the buffer used for speeding up reads is aligned sanely with any write that we're going to do, so that we can also use it as a write-through cache. In the process, it may resize the buffer and read into it from the file on disk. However, the write method taking a ByteBuffer immediately throws away that read buffer, so resizing it and filling it is simply a waste of time.

This work was motivated by the desire to speed up image format conversions for image files in excess of 50GB. In conjunction with additional changes in bioformats and ome-codecs, I have achieved a geometric to linear time asymptotic improvement, plus another ~30% speed improvement of just the linear time cost. The patch for ome-codecs has already been submitted, and the patches for bioformats will be forthcoming in the next few days.

[dgault]

Thanks for opening this @popiel, the logic certainly seems to make sense in that the write with ByteBuffer is throwing away the buffer after so there is no need for the setup in this instance. I will continue testing and profiling the improvements but on initial tests it is providing a good performance boost.

[sbesson]

Thanks @popiel. Merging for inclusion in upcoming milestone of Bio-Formats 6. As mentioned by David above we will carry on profiling the writing of files across various Bio-Formats tools.