Conversion code for Merlin Medipix data

ePSIC-DLS / epsic_tools

Code for conversion and analysis of Merlin-Medipix data

GNU General Public License v3.0

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Conversion code for Merlin Medipix data #3

Closed M0hsend closed 5 years ago

M0hsend commented 5 years ago

Code to import Merlin Medipix (TEM / 4D-STEM) data using dask, reshaping using the exposure times appearing in the MIB header characters and saving output images and full / binned HDF5 files. The code is to be run on the DLS cluster - an example bash file is also provided.

M0hsend commented 5 years ago

TODO for this code:

Adding 4DSTEM loading from multiple MIB files, e.g. 1000 frames per file
Checking the effect of above on speed
Dask improvement, e.g. using dask.delayed by defining more functions?

TomSlater commented 5 years ago

The importing and reshaping functions look good to me. They work on my local PC in any case.

Should add to the TODO:

Write unit tests for all functions

TomSlater commented 5 years ago

Acquire minimum size datasets for the tests too!

chrisallen80 commented 5 years ago

Run on cluster for user data MG22549-6 no errors. Shall we merge now (so there is a stable and working version on ePSIC-DLS and start new pull requests for Mohsen's TODO list above and unit tests?

dnjohnstone commented 5 years ago

Hi @TomSlater would it be possible to merge this one up so that I can make a new PR adding docstrings etc please?

TomSlater commented 5 years ago

Merged now.

We have some test datasets now so I'll write up tests for functions (hopefully next week).