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License: Other
Tomography Reconstructon Pipeline
License: Other
line 213 in utils - need to remove squeeze from result (wrt SWTP single frame sinogram centre of mass/alignment correction). It needs the extra dimension in the result even though only 1 (i.e. single slice)
There is an import error here, looks like it should be a simple fix
Should be able to state that either all datasets should be used in a plugin or a plugin should be applied to all datasets without specifying them individually
Would be nice to be able to say after pip installing savu
import savu
savu.full_test()
and it run all the tests properly
Some example data from Steve would be good here
To sub-sample the data
the astra import statement seems to hang when running in mpi
want to return new centre of rotation value not just the frame from sinogram alignment
There seems to be an issue when generating the initial size of the hdf5 file associated with the paganin step, not sure whether this is not passing the right information though, or why this is happening.
Should make it possible to make savu run in windows, and also make the Travis build quicker.
So point out something like setting the PYTHONPATH and then using python tomo_recon.py ...
There are links to local data in the test, causing it to fail, Disabled for now.
Currently it is failing as the system has changed, Mark needs to understand more about how to use the experiment
Should allow you to load, save, add and remove items, and modify parameters.
There are quite a few things which could do with a refactor.
the dark and flatfield plugin seems to work incorrectly over MPI. if I were to guess the first part of the flatfield is applied to all sections of the projections, there is a tell tale issue with the top left of each part which is the timestamp on the images.
So grepping about we are definatly getting some threads wrong. there are also some odd timing issues. A little annoying as its a transitory problem, which makes me think more barriers is needed
There are a series of processes, which need to be updated to the new Plugin runner test style
After using pandas, a text log will be fine to process.
create a new CGLS plugin which uses the multithreaded code options.
should extent AllCpusPlugin and make use of
self.availble_cpus
i.e in savu.plugins there should probably be
savu.plugins.filters
savu.plugins.reconstruction
and any others which are required.
In GpuPlugin the run_process(...) function looks in "processes" for "GPU". This is currently fixed to be "CPU0" so it doesn't run the plugin (I hope that's a little clearer...). I don't know what your plans are for developing this?
So this only runs in one thread on CPU0, but tells the process how many threads it can use.
Should just e a case of testing the downsample plugin with the new setup process.
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