v2.0.0

v2.0.0
2023-09-14

🛠️Changed

• From multiprocessing to multithreading (huge speedup in models fit! 🚀)
  • models and lut modules in Cython
  • fit() methods in Cython
  • dir_to_lut_idx() method in Cython
• New NODDI maps names:
  • from ICVF to NDI
  • from OD to ODI
  • from FISO to FWF
• New output images name casing (e.g. from FIT_NDI.nii.gz to fit_NDI.nii.gz)
• Default Diffusion Tensor model fit method to compute the primary direction in each voxel from WLS to OLS
• Default number of threads used by BLAS libraries from -1 (all threads) to 1
• Parallel threads config name from parallel_jobs to n_threads
• Default study_path='.' and subject='.' in core.Evaluation()
• Default ndirs=500 in core.generate_kernels()
• Expire the deprecated ndirs parameter in core.setup()
• Replace tqdm with dicelib.ui.ProgressBar()
• Switched to proprietary license (see LICENSE file)

✨Added

• C++ interfaces for NNLS and LASSO solvers (provided by spams-cython)
• DTI_fit_method config to choose the Diffusion Tensor model fit method (from DIPY)
  • OLS (Ordinary Least Squares)
  • WLS (Weighted Least Squares)
• BLAS_n_threads config to set the number of threads used in the threadpool-backend of common BLAS implementations (e.g. OpenBLAS)
• doComputeRMSE config to compute the Root Mean Square Error image
• doSaveModulatedMaps to compute modulated maps for the NODDI model (Tissue-weighted mean), e.g. fit_NDI_modulated.nii.gz

🐛Fixed

• DeprecationWarning: dipy.reconst.shm.real_sym_sh_basis (with dipy>=1.4.0)