anandbaburajan's Blog

GSoC: Week #10

anandbaburajan
Published: 08/03/2020

Hi there!

What did you do this week?

I completed ‘sync_offset’ for SER, fixed a few bugs, wrote tests for ‘reshaping’ all the formats and continued working on HDF5, FRMS6 and K2IS.

What is coming up next?

My next aim is to figure out how to integrate the reshape feature into the UDF interface and write tests for the same. This would be helpful to get the coordinates in the actual navigation space for UDFs. I’ll also continue working on offset for K2IS and HDF5. The FRMS6 format is almost done, I just need to figure out how to handle the dark frame correction when the signal dimensions are changed.

Did you get stuck anywhere?

No.

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GSoC: Week #9

anandbaburajan
Published: 07/27/2020

Hello!

What did you do this week?

I added ‘nav_shape’ and ‘sig_shape’ parameters for all the formats, implemented reshaping for formats using the general ‘get_tiles’, reworked on the API and the GUI forms.

What is coming up next?

My mentor suggested a much better way to implement ‘sync_offset’ into the HDF5 format, so I’ll work on that this week. I’ll also try to finish the offset feature for K2IS, FRMS6 and the SER format too, which uses its own I/O functions. There’s a small bug with the DM format which needs to be fixed. I’ll also write suitable tests for the reshaping feature for all the formats.

Did you get stuck anywhere?

No.

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GSoC: Week #8

anandbaburajan
Published: 07/19/2020

Hello!

What did you do this week?

I finally completed the sync offset feature, with and without a ROI, for the HDF5 format! I spent some time to understand the FRMS6 format, found a bug with the ROI selector in the GUI and opened an issue for the same. I also introduced a new member to our community and he’s interested to improve the UI which I’m really happy about!

What is coming up next?

I’ll finish the reshaping feature for most of the formats which use the common I/O implementation and I'll continue working on the offset feature for FRMS6.

Did you get stuck anywhere?

No, but I think I took quite some time to finish HDF5’s offset feature.

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GSoC: Week #7

anandbaburajan
Published: 07/13/2020

Hi!

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).

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GSoC: Week #6

anandbaburajan
Published: 07/06/2020

Hi!

What did you do this week?

I implemented the offset feature in ‘get_tiles_straight’ both with and without a region of interest for raw and ‘memory’ datasets, fixed the bug in ‘get_tiles_w_copy’ which marks the completion of the offset feature for rest of the formats except HDF5 and wrote tests for benchmarking. I spent rest of the time looking into possible ways of implementing the reshaping feature.

What is coming up next?

I’ll benchmark the offset feature for the different formats, try to improve it and finish it for HDF5. I’ll continue working towards the general reshaping feature and work on its integration with the UDF interface.

Did you get stuck anywhere?

I haven’t figured out how to deal with the K2IS format properly. I’m not sure if I should implement my feature into the existing sync flag, but I’m working on it. In raw files, setting a negative offset results in empty but colored frames in the GUI but not when used with the Python API in a Jupyter notebook.

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