Merge pull request #2478 from jhlegarreta/DealAppropriatelyWithUserWa…

…rnings

ENH: Deal appropriately with user warnings

dipy/core/gradients.py

@@ -297,9 +297,9 @@ def gradient_table_from_bvals_bvecs(bvals, bvecs, b0_threshold=50, atol=1e-2,
 
     # checking for the correctness of bvals
     if b0_threshold < bvals.min():
-        warn("b0_threshold (value: {0}) is too low, increase your \
-             b0_threshold. It should be higher than the lowest b0 value \
-             ({1}).".format(b0_threshold, bvals.min()))
+        warn("b0_threshold (value: {0}) is too low, increase your "
+             "b0_threshold. It should be higher than the lowest b0 value "
+             "({1}).".format(b0_threshold, bvals.min()))
 
     bvecs = np.where(np.isnan(bvecs), 0, bvecs)
     bvecs_close_to_1 = abs(vector_norm(bvecs) - 1) <= atol

dipy/reconst/shm.py

@@ -462,7 +462,7 @@ def real_sh_descoteaux(sh_order, theta, phi,
     return real_sh, m, n
 
 
-@deprecate_with_version('dipy.reconst.shm.real_sym_sh_mrtix is deprecated, '
+@deprecate_with_version('dipy.reconst.shm.real_sym_sh_mrtrix is deprecated, '
                         'Please use dipy.reconst.shm.real_sh_tournier instead',
                         since='1.3', until='2.0')
 def real_sym_sh_mrtrix(sh_order, theta, phi):

dipy/reconst/tests/test_ivim.py

@@ -74,7 +74,8 @@ def setup_module():
                             120., 140., 160., 180., 200., 300., 400.,
                             500., 600., 700., 800., 900., 1000.])
 
-    gtab_no_b0 = gradient_table(bvals_no_b0, bvecs.T, b0_threshold=0)
+    with pytest.warns(UserWarning):
+        gtab_no_b0 = gradient_table(bvals_no_b0, bvecs.T, b0_threshold=0)
 
     bvals_with_multiple_b0 = np.array([0., 0., 0., 0., 40., 60., 80., 100.,
                                        120., 140., 160., 180., 200., 300.,

dipy/reconst/tests/test_mcsd.py

@@ -193,14 +193,20 @@ def test_multi_shell_fiber_response():
 def test_mask_for_response_msmt():
     gtab, data, masks_gt, _ = get_test_data()
 
-    wm_mask, gm_mask, csf_mask = mask_for_response_msmt(gtab, data,
-                                                        roi_center=None,
-                                                        roi_radii=(1, 1, 0),
-                                                        wm_fa_thr=0.7,
-                                                        gm_fa_thr=0.3,
-                                                        csf_fa_thr=0.15,
-                                                        gm_md_thr=0.001,
-                                                        csf_md_thr=0.0032)
+    with warnings.catch_warnings(record=True) as w:
+        wm_mask, gm_mask, csf_mask = mask_for_response_msmt(gtab, data,
+                                                            roi_center=None,
+                                                            roi_radii=(1, 1, 0),
+                                                            wm_fa_thr=0.7,
+                                                            gm_fa_thr=0.3,
+                                                            csf_fa_thr=0.15,
+                                                            gm_md_thr=0.001,
+                                                            csf_md_thr=0.0032)
+
+    npt.assert_equal(len(w), 1)
+    npt.assert_(issubclass(w[0].category, UserWarning))
+    npt.assert_("""Some b-values are higher than 1200.""" in
+                str(w[0].message))
 
     # Verifies that masks are not empty:
     masks_sum = int(np.sum(wm_mask) + np.sum(gm_mask) + np.sum(csf_mask))
@@ -214,14 +220,20 @@ def test_mask_for_response_msmt():
 def test_mask_for_response_msmt_nvoxels():
     gtab, data, _, _ = get_test_data()
 
-    wm_mask, gm_mask, csf_mask = mask_for_response_msmt(gtab, data,
-                                                        roi_center=None,
-                                                        roi_radii=(1, 1, 0),
-                                                        wm_fa_thr=0.7,
-                                                        gm_fa_thr=0.3,
-                                                        csf_fa_thr=0.15,
-                                                        gm_md_thr=0.001,
-                                                        csf_md_thr=0.0032)
+    with warnings.catch_warnings(record=True) as w:
+        wm_mask, gm_mask, csf_mask = mask_for_response_msmt(gtab, data,
+                                                            roi_center=None,
+                                                            roi_radii=(1, 1, 0),
+                                                            wm_fa_thr=0.7,
+                                                            gm_fa_thr=0.3,
+                                                            csf_fa_thr=0.15,
+                                                            gm_md_thr=0.001,
+                                                            csf_md_thr=0.0032)
+
+    npt.assert_equal(len(w), 1)
+    npt.assert_(issubclass(w[0].category, UserWarning))
+    npt.assert_("""Some b-values are higher than 1200.""" in
+                str(w[0].message))
 
     wm_nvoxels = np.sum(wm_mask)
     gm_nvoxels = np.sum(gm_mask)

dipy/reconst/tests/test_shm.py

@@ -3,6 +3,7 @@
 import warnings
 import numpy as np
 import numpy.linalg as npl
+import numpy.testing as npt
 
 from dipy.testing import assert_true
 from numpy.testing import (assert_array_equal, assert_array_almost_equal,
@@ -117,7 +118,22 @@ def test_gen_dirac():
 
 def test_real_sym_sh_mrtrix():
     coef, expected, sphere = mrtrix_spherical_functions()
-    basis, m, n = real_sym_sh_mrtrix(8, sphere.theta, sphere.phi)
+
+    with warnings.catch_warnings(record=True) as w:
+        warnings.simplefilter("always")
+        basis, m, n = real_sym_sh_mrtrix(8, sphere.theta, sphere.phi)
+
+    npt.assert_equal(len(w), 2)
+    npt.assert_(issubclass(w[0].category, DeprecationWarning))
+    npt.assert_(
+        "dipy.reconst.shm.real_sym_sh_mrtrix is deprecated, Please use "
+        "dipy.reconst.shm.real_sh_tournier instead" in str(w[0].message))
+    npt.assert_(issubclass(w[1].category, PendingDeprecationWarning))
+    npt.assert_(
+        "The legacy tournier07 basis is outdated and will be deprecated "
+        "in a future release of DIPY. Consider using the new tournier07 "
+        "basis." in str(w[1].message))
+
     func = np.dot(coef, basis.T)
     assert_array_almost_equal(func, expected, 4)