# Leonard

# Meeting 2024-04-11

## Agenda

* Full data set paper
* Software paper
* mumott
* kappa
* deadlines

## Kappa
* read (--> PE)
* 2 Theoretical framework of SAXSTT
* 4 SAXSTT Algorithms
* still being written
* 5 Implementation of tensor tomography in Mumott

## Deadlines
* May 2, trial printing

## Full data set paper
* nothing to be done

## Software paper
* focus on section 3 and outlook

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# Meeting 2023-12-18

## Agenda
* Full dataset paper
* Software paper (Journal of Applied Crystallography, Acta Cryst A)
* Line integration merge request (from yesterday)
* mumott 2.0 release

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# Meeting 2023-09-20

## Agenda
* mumott 2.0
* "next paper" (full data set; beam time last week; local representation, regularization side aspect (TV+L1))
* new PhD student: end of October/beginning of November

## Mumott 2.0
* remove `SAXSProjectNumba` (already deprecated)
* pending Mads' input; remove `SAXSProjectorAstra`
* optimization with `ZonalHarmonics` → pipeline
* integrate `mumott-workflows/data_processing` into mumott (?)
* requires dedicated effort
* for WAXS need support for more complex handling of transmission
* could be done via a new utility class and ...
* an object of this class in `DataContainer`

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# Meeting 2023-05-29

## Agenda
* Ludvig
* mumott 1.0
* optimization

## Ludvig
* thesis defense
* invite @erhart to overleaf

## mumott 1.0
* created 1.1
* naming
* Frame --> Projection
* Functional -> Reconstruction (?)

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# Meeting 2023-03-21

r = sph.forward(coefficients=coeffs, indices=index)

\int f(coeff, probed_coordinates)

@property
def method.probed_coordinates(self) -> ProbedCoordinates:
    return func(self._geometry, method_information)


pc = ProbedCoordinates(...)
bs = SphericalHarmonics(pc)
bs.forward(...)  # use the precomputed

pc.vector = Method.probed_coordinates
bs.forward(...)  # recomputation triggered

# combine basis set and projector into method, which also knows about the data
proj = SAXSProjectorNumba(...)
bs = SphericalHarmonics(pc)
method = SAXS(dc, proj, bs)
res, grad = method.get_residual(gradient=True)

---------------

# Meeting 2023-03-21

## Agenda
* mumott

dc = DataContainer(...)

# option 1
dc.geometry['frame10.theta'] = 11.0
dc.geometry['phi'] = -50.0

# option 2
dc[10].theta = [0, 0, 1]
dc.phi = -50.0

# option 3
dc[10].theta = [0, 0, 1]
dc.geometry.phi = -50.0

# option 4
dc.geometry[10].theta = [0, 0, 1]
dc.geometry.phi = -50.0

# option 5
dc[10].theta = [0, 0, 1]
dc.geometry[10].theta = [0, 0, 1]

* aim for option 2
* internally one stack
* https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.transform.Slerp.html#scipy.spatial.transform.Slerp

----------------------

# Meeting 2023-03-10

## Agenda
* e-commons
* Ludvig
* mumott → alignment

## Todos
* https://gitlab.com/liebi-group/software/mumott/-/merge_requests/55
* generate class inheritance diagrams for `master` and `rot_mat`

----------------------

# Meeting 2023-02-24

## Agenda
* paper
* mumott
* e-commons
* Ludvig

## Paper
* supplementary information
* cover letter

## Mumott
* Mads' branch
* restructuring
* refactoring
* exposure of coordinate system
* testing MR
* https://gitlab.com/liebi-group/software/mumott/-/merge_requests/55
* alignment

## Next meeting
* toward paper 2

----------------------

# Meeting 2022-12-20

## Agenda
* mplpub
* figure updates
* [tutorial MR in mumott](https://gitlab.com/liebi-group/software/mumott/-/merge_requests/49)
* paper planning
* https://www.c3se.chalmers.se/working/

## mplpub
https://gitlab.com/materials-theory/common/mplpub/

## Figure updates
* use white space
* increase white space between a,b,c in Figure 2
* remove boxes

## Paper planning
### Primary
1. SIGTT paper
* target Nature Comp Sci
* shorten according to [information here](https://www.nature.com/natcomputsci/content)
* move full methods to the back
* write condensed summary of methods
1. Solving the missing wedge problem ... (full sampling paper)
* treat alignment parameters as hyperparameters of optimization problem
1. large beam
1. Multidirection/basis
* possibly include Ludvig L
* can be a "shorter" paper

* CS random sampling
* data split --> bagging
* total variation

### Secondary
1. Chameleon tongue/Multi-direction
2. WAXSTT

### Tertiary
1. Full Mueller matrix thing
2. Adrian Bone scaffold
3. Adrian Narwhal
4. Isabella's tendon
5. Isabella's embryonic bone

### Other "things"
* multi-direction method
* couple alignment to optimization/reconstruction
* regularization