Merge pull request dipy#3254 from deka27/keyword-direction

NF: Applying Decorators in Module (Direction)

dipy/direction/bootstrap_direction_getter.pyx

@@ -101,8 +101,8 @@ cdef class BootDirectionGetter(DirectionGetter):
             Angular threshold for excluding ODF peaks.
 
         """
-        return cls(data, model, max_angle, sphere, max_attempts, sh_order,
-                   b_tol, **kwargs)
+        return cls(data, model, max_angle, sphere=sphere, max_attempts=max_attempts, sh_order=sh_order,
+                   b_tol=b_tol, **kwargs)
 
 
     cpdef cnp.ndarray[cnp.float_t, ndim=2] initial_direction(self,

dipy/direction/closest_peak_direction_getter.pyx

@@ -163,11 +163,11 @@ cdef class PmfGenDirectionGetter(BasePmfDirectionGetter):
             raise ValueError(msg)
 
         pmf_gen = SimplePmfGen(np.asarray(pmf,dtype=float), sphere)
-        return cls(pmf_gen, max_angle, sphere, pmf_threshold, **kwargs)
+        return cls(pmf_gen, max_angle, sphere, pmf_threshold=pmf_threshold, **kwargs)
 
     @classmethod
     def from_shcoeff(cls, shcoeff, max_angle, sphere=default_sphere,
-                     pmf_threshold=0.1, basis_type=None, legacy=True,
+                    pmf_threshold=0.1, basis_type=None, legacy=True,
                      sh_to_pmf=False, **kwargs):
         """Probabilistic direction getter from a distribution of directions
         on the sphere
@@ -219,7 +219,7 @@ cdef class PmfGenDirectionGetter(BasePmfDirectionGetter):
         else:
             pmf_gen = SHCoeffPmfGen(np.asarray(shcoeff,dtype=float), sphere,
                                     basis_type, legacy=legacy)
-        return cls(pmf_gen, max_angle, sphere, pmf_threshold, **kwargs)
+        return cls(pmf_gen, max_angle, sphere, pmf_threshold=pmf_threshold, **kwargs)
 
 
 cdef class ClosestPeakDirectionGetter(PmfGenDirectionGetter):

dipy/direction/peaks.py

@@ -18,12 +18,15 @@
     search_descending,
 )
 from dipy.reconst.shm import sh_to_sf_matrix
+from dipy.testing.decorators import warning_for_keywords
 from dipy.utils.deprecator import deprecated_params
 from dipy.utils.multiproc import determine_num_processes
 
 
+@warning_for_keywords()
 def peak_directions_nl(
     sphere_eval,
+    *,
     relative_peak_threshold=0.25,
     min_separation_angle=25,
     sphere=default_sphere,
@@ -95,8 +98,14 @@ def _helper(x):
     return directions, values
 
 
+@warning_for_keywords()
 def peak_directions(
-    odf, sphere, relative_peak_threshold=0.5, min_separation_angle=25, is_symmetric=True
+    odf,
+    sphere,
+    *,
+    relative_peak_threshold=0.5,
+    min_separation_angle=25,
+    is_symmetric=True,
 ):
     """Get the directions of odf peaks.
 
@@ -420,29 +429,31 @@ def _peaks_from_model_parallel_sub(args):
         sphere,
         relative_peak_threshold,
         min_separation_angle,
-        mask,
-        return_odf,
-        return_sh,
-        gfa_thr,
-        normalize_peaks,
-        sh_order,
-        sh_basis_type,
-        legacy,
-        npeaks,
-        B,
-        invB,
+        mask=mask,
+        return_odf=return_odf,
+        return_sh=return_sh,
+        gfa_thr=gfa_thr,
+        normalize_peaks=normalize_peaks,
+        sh_order_max=sh_order,
+        sh_basis_type=sh_basis_type,
+        legacy=legacy,
+        npeaks=npeaks,
+        B=B,
+        invB=invB,
         parallel=False,
         num_processes=None,
     )
 
 
 @deprecated_params("sh_order", new_name="sh_order_max", since="1.9", until="2.0")
+@warning_for_keywords()
 def peaks_from_model(
     model,
     data,
     sphere,
     relative_peak_threshold,
     min_separation_angle,
+    *,
     mask=None,
     return_odf=False,
     return_sh=True,
@@ -601,7 +612,10 @@ def peaks_from_model(
 
         # Get peaks of odf
         direction, pk, ind = peak_directions(
-            odf, sphere, relative_peak_threshold, min_separation_angle
+            odf,
+            sphere,
+            relative_peak_threshold=relative_peak_threshold,
+            min_separation_angle=min_separation_angle,
         )
 
         # Calculate peak metrics
@@ -713,7 +727,11 @@ def peaks_from_positions(
     for i, s in enumerate(vox_positions):
         odf = trilinear_interpolate4d(odfs, s)
         peaks, _, _ = peak_directions(
-            odf, sphere, relative_peak_threshold, min_separation_angle, is_symmetric
+            odf,
+            sphere,
+            relative_peak_threshold=relative_peak_threshold,
+            min_separation_angle=min_separation_angle,
+            is_symmetric=is_symmetric,
         )
         nbr_peaks = min(npeaks, peaks.shape[0])
         peaks_arr[i, :nbr_peaks, :] = peaks[:nbr_peaks, :]

dipy/direction/probabilistic_direction_getter.pyx

@@ -27,7 +27,6 @@ cdef class ProbabilisticDirectionGetter(PmfGenDirectionGetter):
     directions more than ``max_angle`` degrees from the incoming direction are
     set to 0 and the result is normalized.
     """
-
     def __init__(self, pmf_gen, max_angle, sphere, pmf_threshold=.1, **kwargs):
         """Direction getter from a pmf generator.
 
@@ -57,7 +56,7 @@ cdef class ProbabilisticDirectionGetter(PmfGenDirectionGetter):
 
         """
         PmfGenDirectionGetter.__init__(self, pmf_gen, max_angle, sphere,
-                                       pmf_threshold, **kwargs)
+                                       pmf_threshold=pmf_threshold, **kwargs)
         # The vertices need to be in a contiguous array
         self.vertices = self.sphere.vertices.copy()
 
@@ -128,10 +127,9 @@ cdef class DeterministicMaximumDirectionGetter(ProbabilisticDirectionGetter):
     """Return direction of a sphere with the highest probability mass
     function (pmf).
     """
-
     def __init__(self, pmf_gen, max_angle, sphere, pmf_threshold=.1, **kwargs):
         ProbabilisticDirectionGetter.__init__(self, pmf_gen, max_angle, sphere,
-                                              pmf_threshold, **kwargs)
+                                              pmf_threshold=pmf_threshold, **kwargs)
 
     cdef int get_direction_c(self, double[::1] point, double[::1] direction):
         """Find direction with the highest pmf to updates ``direction`` array

dipy/direction/ptt_direction_getter.pyx

@@ -126,7 +126,7 @@ cdef class PTTDirectionGetter(ProbabilisticDirectionGetter):
         self.rejection_sampling_nbr_sample = 10 # Adaptively set in Trekker.
 
         ProbabilisticDirectionGetter.__init__(self, pmf_gen, max_angle, sphere,
-                                       pmf_threshold, **kwargs)
+                                       pmf_threshold=pmf_threshold, **kwargs)
 
 
     cdef void initialize_candidate(self, double[:] init_dir):

dipy/direction/tests/test_bootstrap_direction_getter.py

@@ -219,7 +219,13 @@ def test_bdg_residual(rng):
         )
         csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order_max=6)
     npt.assert_raises(
-        ValueError, BootDirectionGetter, data, csd_model, 60, hsph_updated, 6
+        ValueError,
+        BootDirectionGetter,
+        data,
+        csd_model,
+        60,
+        sphere=hsph_updated,
+        max_attempts=6,
     )
 
 
@@ -291,8 +297,22 @@ def test_boot_pmf():
             category=PendingDeprecationWarning,
         )
         npt.assert_raises(
-            ValueError, BootDirectionGetter, data, tensor_model, 60, hsph_updated, 6, 20
+            ValueError,
+            BootDirectionGetter,
+            data,
+            tensor_model,
+            60,
+            sphere=hsph_updated,
+            max_attempts=6,
+            b_tol=20,
         )
         npt.assert_raises(
-            ValueError, BootDirectionGetter, data, tensor_model, 60, hsph_updated, 6, -1
+            ValueError,
+            BootDirectionGetter,
+            data,
+            tensor_model,
+            60,
+            sphere=hsph_updated,
+            max_attempts=6,
+            b_tol=-1,
         )