Mdt

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Changed
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- Updated the map view config syntax for the voxel highlights (now called annotations).
- Updates following MOT in DKI measures.
- Changed the config layout of the maps visualizer with regards to the colorbar settings.

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Changed
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- Changed the parameter proposal and transform function of the PHI parameter.

Fixed
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- Fixes issue 4, the MDT gui crashed on startup with Qt version 5.9.1.

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Added
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- Adds colormap order in the GUI when a map is interpreted as colormap.
- Adds relaxometry models.
- Adds sampling output selection to the sampler.
- Adds another post-processing switch to the sampling post-processing.
- Adds nibabel and numpy array decoration to store path info alongside the niftis when loaded with mdt.load_nifti().
- Adds Hessian and covariance computation as post-processing to the models.

Changed
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- Updates to the batch profiles.
- Updates to CHARMED boundary conditions.

Other
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- Removed the sampling statistics calculation from the post-processing, it did not work out theoretically.
- Adds an utility function for computing the correlations from the covariances.
- Small update to the scientific scrollers in the gui. Interchanged the position of max and min in the gui.
- Renamed evaluation_model to likelihood_function in the composite models. This covers the usage better.

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Added
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- Adds support for multiple output files in the mdt-math-img CLI function.
- Adds post sampling log messages
- Adds caching to deferred loading collections.

Changed
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- Changed the signature of write_nifti and moved the header argument to the optional keyword arguments.
- Updates to the documentation of the configuration.
- Small improvements in the post-sampling processing.
- the function ``write_nifti`` now creates the directories if they do not exist yet.

Fixed
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- Fixed non working documentation build on read the docs. Removed the ``sphinxarg.ext`` since it is not supported yet on read the docs.

Other
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- Small path updates to the batch profiles.
- MDT now also saves the log likelihood and log priors after sampling.
- Made the sampler sample from the complete log likelihood. This allows storing the likelihood and prior values and use them later for maximum posterior and maximum likelihood calculations.
- Simplified model compartment expressions due to improvements in MOT.

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Changed
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- Changes the default sampling settings of the phi parameter. Since it is supposed to wrap around 2*pi, we can not use the circular gaussian approximation if we are constraining it between 0 and pi, instead we use a simple gaussian proposal and a truncated gaussian sampling estimate.
- Updates to the processing strategies. Adds an interface for MRIModels to work with the processing strategies.

Other
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- Following the changes in MOT, we can now let a compartment model and a library function evaluate itself given some input data.

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Added
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- Adds some of the new config switches in the maps visualizer to the graphical interface.
- Adds the possibility of interpreting vector maps as RGB maps. Useful for displaying Tensor FA orientation maps.
- Added overridden method to the problem data.
- Adds support for fitting when the protocol is empty.
- Added parameter name logging to MDT instead of in MOT.

Changed
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- Updated the processing strategy with a better mask file placement (technical thing).
- Updates to the sampling post-processing.
- Updates to the documentation.
- Updated the InputDataMRI interface to contain a few more properties.
- Updated the changelog generation slightly.
- Updated the ExpT1DecIR model, adds a cascade. Updated the way cascades are updated as such that it allows for multiple copies of the same model in a cascade.
- Updates to the GUI.
- Updates the parser to the latest version of Grako.

Fixed
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- Fixed naming issues when loading new maps in the map viewer.
- Fixes the image squeezing in the viewer when adding a colorbar.
- Fixed the issue with the get_free_param_names removal.

Other
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- Version bump.
- Small refactoring in the processing strategy.
- Renamed the S0-TIGre model to S0_TI_GRE.
- Reverted some changes on the S0-T1-GRE model.
- Renamed InputDataMRI to MRIInputData and InputDataDMRI to SimpleMRIInputData.
- Renamed 'problem_data' to 'input_data', 'DMRIProblemData' to 'InputDataDMRI' and all other possible renamings. This also deprecates the function since it has been renamed to .
- Following changes in MOT.