Merge pull request #1683 from ShreyasFadnavis/csd-b0

test for new error in IVIM

dipy/data/fetcher.py

@@ -1092,7 +1092,7 @@ def read_ivim():
     fbval = pjoin(folder, 'ivim.bval')
     fbvec = pjoin(folder, 'ivim.bvec')
     bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
-    gtab = gradient_table(bvals, bvecs)
+    gtab = gradient_table(bvals, bvecs, b0_threshold=0)
     img = nib.load(fraw)
     return img, gtab
 

dipy/reconst/ivim.py

@@ -135,7 +135,7 @@ def __init__(self, gtab, split_b_D=400.0, split_b_S0=200., bounds=None,
                  x_scale=[1000., 0.1, 0.001, 0.0001],
                  options={'gtol': 1e-15, 'ftol': 1e-15,
                           'eps': 1e-15, 'maxiter': 1000}):
-        """
+        r"""
         Initialize an IVIM model.
 
         The IVIM model assumes that biological tissue includes a volume

dipy/reconst/tests/test_ivim.py

@@ -202,6 +202,23 @@ def test_with_higher_S0():
     assert_array_almost_equal(ivim_fit.model_params, params2)
 
 
+def test_b0_threshold_greater_than0():
+    """
+    Added test case for default b0_threshold set to 50.
+    Checks if error is thrown correctly.
+    """
+    bvals_b0t = np.array([50., 10., 20., 30., 40., 60., 80., 100.,
+                          120., 140., 160., 180., 200., 300., 400.,
+                          500., 600., 700., 800., 900., 1000.])
+    N = len(bvals_b0t)
+    bvecs = generate_bvecs(N)
+    gtab = gradient_table(bvals_b0t, bvecs.T)
+    with assert_raises(ValueError) as vae:
+        _ = IvimModel(gtab)
+        b0_s = "The IVIM model requires a measurement at b==0. As of "
+        assert b0_s in vae.exception
+
+
 def test_bounds_x0():
     """
     Test to check if setting bounds for signal where initial value is