added optional package cvxpy

AthenaEPI · Mar 14, 2018 · 170e1e8 · 170e1e8
1 parent 04c8003
commit 170e1e8
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/dmipy/core/modeling_framework.py b/dmipy/core/modeling_framework.py
@@ -22,7 +22,7 @@
     FittedMultiCompartmentSphericalHarmonicsModel)
 from ..optimizers.brute2fine import (
     GlobalBruteOptimizer, Brute2FineOptimizer)
-from ..optimizers_fod.cvxpy_fod import MultiCompartmentCSDOptimizer
+from ..optimizers_fod.cvxpy_fod import GeneralPurposeCSDOptimizer
 from ..optimizers.mix import MixOptimizer
 from dipy.utils.optpkg import optional_package
 pathos, have_pathos, _ = optional_package("pathos")
@@ -1600,7 +1600,7 @@ def fit(self, acquisition_scheme, data, mask=None,
 
         start = time()
         if solver == 'cvxpy':
-            fit_func = MultiCompartmentCSDOptimizer(
+            fit_func = GeneralPurposeCSDOptimizer(
                 acquisition_scheme, self, self.sh_order, unity_constraint)
         start = time()
         for idx, pos in enumerate(zip(*mask_pos)):

diff --git a/dmipy/core/tests/test_csd_equivalence_parametric_distributions.py b/dmipy/core/tests/test_csd_equivalence_parametric_distributions.py
@@ -3,13 +3,17 @@
 from dmipy.core import modeling_framework
 from dmipy.data.saved_acquisition_schemes import wu_minn_hcp_acquisition_scheme
 from dipy.data import get_sphere
+import numpy as np
 from numpy.testing import (
     assert_array_almost_equal, assert_almost_equal, assert_raises)
+from dipy.utils.optpkg import optional_package
+cvxpy, have_cvxpy, _ = optional_package("cvxpy")
 
 scheme = wu_minn_hcp_acquisition_scheme()
 sphere = get_sphere('symmetric724')
 
 
+@np.testing.dec.skipif(not have_cvxpy)
 def test_equivalence_csd_and_parametric_fod(
         odi=0.15, mu=[0., 0.], lambda_par=1.7e-9):
     stick = cylinder_models.C1Stick()
@@ -37,6 +41,7 @@ def test_equivalence_csd_and_parametric_fod(
     assert_array_almost_equal(data, fitted_signal[0], 4)
 
 
+@np.testing.dec.skipif(not have_cvxpy)
 def test_multi_compartment_fod_with_parametric_model(
         odi=0.15, mu=[0., 0.], lambda_iso=3e-9, lambda_par=1.7e-9,
         vf_intra=0.7):
@@ -70,6 +75,7 @@ def test_multi_compartment_fod_with_parametric_model(
     assert_array_almost_equal(data, predicted_signal[0], 4)
 
 
+@np.testing.dec.skipif(not have_cvxpy)
 def test_spherical_harmonics_model_raises(
         odi=0.15, mu=[0., 0.], lambda_par=1.7e-9):
     stick = cylinder_models.C1Stick()

diff --git a/dmipy/optimizers_fod/cvxpy_fod.py b/dmipy/optimizers_fod/cvxpy_fod.py
@@ -1,15 +1,16 @@
 import numpy as np
-import cvxpy
 from dipy.data import get_sphere, HemiSphere
 from dipy.reconst.shm import real_sym_sh_mrtrix
+from dipy.utils.optpkg import optional_package
+cvxpy, have_cvxpy, _ = optional_package("cvxpy")
 
 
 __all__ = [
-    'MultiCompartmentCSDOptimizer'
+    'GeneralPurposeCSDOptimizer'
 ]
 
 
-class MultiCompartmentCSDOptimizer:
+class GeneralPurposeCSDOptimizer:
     """
     General purpose optimizer for multi-compartment constrained spherical
     deconvolution (MC-CSD) to estimate Fiber Orientation Distributions (FODs).