Add csd plus

dmipy/core/modeling_framework.py

@@ -23,6 +23,7 @@
     MultiTissueConvexOptimizer)
 from ..optimizers_fod.csd_cvxpy import CsdCvxpyOptimizer
 from ..optimizers_fod.csd_tournier import CsdTournierOptimizer
+from ..optimizers_fod.csd_plus import CsdPlusOptimizer
 from ..utils.spherical_mean import (
     estimate_spherical_mean_multi_shell)
 from ..utils.utils import (
@@ -1919,11 +1920,13 @@ def fit(self, acquisition_scheme, data, mask=None, solver='csd',
         mask : (N-1)-dimensional integer/boolean array of size (N_x, N_y, ...),
             Optional mask of voxels to be included in the optimization.
         solver : string,
-            Can be 'csd', 'csd_tounier07' or 'csd_cvxpy', with the default
-            being 'csd'. Using 'csd' will make the algorithm automatically
-            use the 'tournier07' solver [1]_ if there are no volume fractions
-            to fit or they are fixed. Otherwise, the slower but more general
-            cvxpy solver [2]_ is used, which follows the formulation of [3]_.
+            Can be 'csd', 'csd_tounier07', 'csd_cvxpy' or 'csd_plus', with the
+            default being 'csd'. Using 'csd' will make the algorithm
+            automatically use the 'tournier07' solver [1]_ if there are no
+            volume fractionsto fit or they are fixed. Otherwise, the slower but
+            more general cvxpy solver [2]_ is used, which follows the
+            formulation of [3]_. Using 'csd_plus' will make the algorithm use
+            the global positivity constraints of [5]_.
         lambda_lb: positive float,
             Weight for Laplace-Beltrami regularization to impose smoothness
             into estimated FODs, follows [4]_.
@@ -1961,6 +1964,9 @@ def fit(self, acquisition_scheme, data, mask=None, solver='csd',
             analytical Q-ball imaging." Magnetic Resonance in Medicine: An
             Official Journal of the International Society for Magnetic
             Resonance in Medicine 58.3 (2007): 497-510.
+        .. [5] Dela Haije, Tom, Evren Özarslan, and Aasa Feragen. "Enforcing
+            necessary non-negativity constraints for common diffusion MRI models
+            using sum of squares programming." NeuroImage 209 (2020): 116405.
         """
         self._check_if_kernel_parameters_are_fixed()
         self._check_tissue_model_acquisition_scheme(acquisition_scheme)
@@ -2062,6 +2068,13 @@ def fit(self, acquisition_scheme, data, mask=None, solver='csd',
             if verbose:
                 print('Setup CVXPY FOD optimizer in {} seconds'.format(
                     time() - start))
+        elif solver == 'csd_plus':
+            fit_func = CsdPlusOptimizer(
+                acquisition_scheme, self, x0_, self.sh_order,
+                unity_constraint=self.unity_constraint)
+            if verbose:
+                print('Setup CSD-PLUS FOD optimizer in {} seconds'.format(
+                    time() - start))
         else:
             msg = "Unknown solver name {}".format(solver)
             raise ValueError(msg)

dmipy/data/sos_constraints/sh_constraint_0.csv

@@ -0,0 +1,6 @@
+1,3,3,0.28209479177387814
+2,0,0,1.
+2,1,1,1.
+2,2,2,1.
+2,3,3,-1.
+2,4,4,1.