Mdt

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Added
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- Adds chunk indices look-a-head in the processing strategies. This allows the Processor to start pre-loading the next batch.

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Changed
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- Updates to the GUI.
- Updates to the maps visualizer.

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Added
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- Adds automatic changelog generation from the git log.
- Adds multivariate statistic to sampling output. Changes the KurtosisExtension to a KurtosisTensor single model.
- Adds catch for special case.
- Adds Tensor reorientation as a post processing. This reorients theta, phi and psi to match the sorted eigen vectors / eigen values.
- Adds compartment model sorting based on weights as a post-processing to composite models. Adds automatic sorting to Ball&Sticks and CHARMED models.
- Adds small boundary conditions to the Kurtosis model.
- Adds clickable point information to the map visualization GUI.
- Adds name collision resolution in the visualization GUI after dragging in images with the same name.
- Adds a library function for the kurtosis matrix multiplication.
- Added component construction to the __new__ of a component template. This allows the template to construct itself at object initialization.

Changed
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- Changes the way the logging is condensed during optimization.
- Updates to the GUI.
- Updates to the documentation. Also, the compartment models now no longer need their own files, they can be defined in any file in the compartment_models directory.
- Updates to the documentation, renamed the Kurtosis compartment to KurtosisExtension and made it require the Tensor in the Composite model.
- Updates to the documentation. Updates to the Kurtosis model. Sets boundary conditions correct and adds post-processing.
- Updates to the documentation style.

Fixed
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- Fixed bug in matplotlib renderer with the highlight voxel.
- Fixed the small GUI bug with the random maps naming.

Other
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- Removed calculated example files.
- Removed redundant logging.
- Small renaming updates.
- Adds some linear algebra methods to the utilities, Changed the way the psi component of the Tensor is used.
- More work on the post-sampling statistics.
- Removed redundant model.
- Moved more relaxometry compartments to the single python file. Slightly increased the number of voxels in sampling.
- Update to the cartesian to spherical function.
- First work on map sorting.
- Small bugfix in the MRI constants.
- Small function reshuffling, updates to comments.
- Small fix with the InitializationData in the fit model.
- Small bugfix to the GUI.
- Completely adds the Kurtosis model. Adds some small library functions as well for the Tensor and Kurtosis computations.

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Added
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- Adds ActiveAx cascade.

Other
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- Small release to add ActiveAx cascade model.
- Small update to docs.

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Changed
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- Updates to the documentation

Other
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- Small fix allowing b-value to be stored in protocol alongside Delta, delta and G.
- Removed the functionality of having the CL code in a separate file for the compartment models and the library models. Now everything is in the Python model definition.

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Added
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- Adds Kurtosis model.
- Adds the extra-axonal time dependent CHARMED from (De Santis 2016). Still needs to be tested though.
- Adds TimeDependentZeppelin for use in the extra-axonal time dependent CHARMED model. Also, the dependency_list in the compartments now also accepts other compartments as strings. Finally, the compartments now no longer need the prefix "cm" in their CL callable function"
- Adds the ActiveAx model.
- Adds the ActiveAx model, slight update to what the Neumann cylindrical function calculates.

Changed
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- Small update in the model fit GUI, separated the models from the cascades to make it more clear what these mean
- Adds three new models, ActiveAx, Time Dependent ActiveAx (see De Santis 2016), Kurtosis
- Simplified the processing strategies to make it more robust
- The visualization GUI can now load images from multiple folders
- The visualization GUI now also supports dragging nifti files into the viewer for loading and viewing.
- Updates to some of the relaxometry models, fixed the simulations to the latest MOT version.

Fixed
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- Fixed list/dict bug in viewer.
- Fixed the simulations module to work with the latest MOT version. Updates to some of the relaxometry models.

Other
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- Small documentation update.
- Update to Kurtosis.
- Merge branch 'master' of github.com:cbclab/MDT.
- Merged local copy, fixed small issue in the dragging of files in the visualization GUI.
- Some initial work on the AxCaliber model. We are not there yet.
- More simplifications to the models, adds reload function in the module loaders (for reloading the cache), add TemplateModifier that can rewrite the source code of a template.
- Merge branch 'master' of github.com:cbclab/MDT.
- In the model fit GUI, separated the models from the cascades to make it more clear what the cascades do.
- In the model fit GUI, separated the models from the cascades to make it more clear what the cascades do.
- Renamed the Silvia 2016 time dependent model from CHARMED to ActiveAx.
- Made ActiveAx diffusivity dependency more clear.
- Removed the GDRCylindersFixedRadii compartment model, it was not used anywhere. Simplified the NODDI tortuosity parameter dependency.
- Update to doc about the parameter renaming.
- The parameter definitions in the compartment model now support nicknaming to enable swapping a parameter without having to rename that parameter in the model equation or other code.
- Renamed the component_configs to component templates and moved some base classes to other folders. Also, all components constructed from templates now carry a back reference to that template as a class attribute.
- Small updates to the processing strategies.
- Prepared the processing strategies for possible multithreading.
- Small comment update in the processing strategy.
- Refactored the processing strategies such that paralellization may be possible in the future.