Clip mtr map between -1 and 1

Gets rid of the silly values caused by noise

ukat/mapping/mtr.py

@@ -81,9 +81,9 @@ def __init__(self, pixel_array, affine, mask=None, moco=False):
         # The assumption is that MT_ON comes second in `pixel_array`
         self.mt_on = np.squeeze(self.pixel_array[..., 1] * self.mask)
         # Magnetisation Transfer Ratio calculation
-        self.mtr_map = np.squeeze(np.nan_to_num(((self.mt_off - self.mt_on) /
-                                                 self.mt_off),
-                                                posinf=0, neginf=0))
+        self.mtr_map = np.squeeze(((self.mt_off - self.mt_on) /self.mt_off))
+        self.mtr_map = np.clip(np.nan_to_num(self.mtr_map, posinf=0,
+                                             neginf=0), -1, 1)
 
     def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                  maps='all'):

ukat/mapping/tests/test_mtr.py

@@ -113,9 +113,9 @@ def test_real_data(self):
         images, affine = fetch.mtr_philips()
 
         # Gold standard statistics
-        gold_standard_mtr_real = [0.1845690591, 0.6237606679, -73.0, 1.0]
+        gold_standard_mtr_real = [0.214016,  0.289071, -1.0, 1.0]
         gold_standard_mtr_real_moco = [0.13357225589671437, 0.17257750673257655,
-                                       -1.7306390127939757, 1.0]
+                                       -1.0, 1.0]
         # The minimum should be 0, but the MT_ON and MT_OFF of real data
         # isn't perfectly aligned, which will result in outliers.
 
@@ -126,7 +126,7 @@ def test_real_data(self):
         mtrmap_stats = arraystats.ArrayStats(mapper.mtr_map).calculate()
         npt.assert_allclose([mtrmap_stats["mean"], mtrmap_stats["std"],
                             mtrmap_stats["min"], mtrmap_stats["max"]],
-                            gold_standard_mtr_real, rtol=0.01, atol=0)
+                            gold_standard_mtr_real, rtol=0.01, atol=1E-3)
 
         # Test with moco
         mask = images[..., 0] > 10000
@@ -136,7 +136,7 @@ def test_real_data(self):
                              mtrmap_moco_stats["std"],
                              mtrmap_moco_stats["min"],
                              mtrmap_moco_stats["max"]],
-                            gold_standard_mtr_real_moco, rtol=0.1, atol=5)
+                            gold_standard_mtr_real_moco, rtol=0.1, atol=1E-3)