What did you do this week?
I reworked on the positive offset feature for HDF5 to improve it based on what I have learned from the other formats. HDF5’s I/O implementation is different from the other formats as it uses the h5py library and the dataset’s navigation dimensions can’t be flattened before reading. So it got a bit complicated to reshape the slices with an offset and therefore my implementation often requires reading twice from the dataset. I also fixed an integer overflow bug, refactored and benchmarked ‘get_tiles_straight’ and ‘get_tiles_w_copy’.
What is coming up next?
This week’s focus would be to finish my prototype for the general reshaping feature as I only have a simple prototype to handle HDF5 files with a flattened scan dimensions yet. I’ll also complete HDF5’s negative offset feature with and without a ROI this week. I’ll work on the FRMS6 format too this week if possible.
Did you get stuck anywhere?
No. The ‘empty’ but ‘colored’ frames issue in the GUI which I mentioned earlier is occurring with HDF5 too along with some other formats. So I think the visualisation code needs some changes to handle missing data (zeros or NaNs).