ENH: Set w2_thresh to positive values for clarity, update doc to indicate 3*eps

Author: effigies

nibabel/nifti1.py

@@ -688,7 +688,7 @@ class Nifti1Header(SpmAnalyzeHeader):
     single_magic = b'n+1'
 
     # Quaternion threshold near 0, based on float32 precision
-    quaternion_threshold = -np.finfo(np.float32).eps * 3
+    quaternion_threshold = np.finfo(np.float32).eps * 3
 
     def __init__(self, binaryblock=None, endianness=None, check=True, extensions=()):
         """Initialize header from binary data block and extensions"""

nibabel/quaternions.py

@@ -44,8 +44,8 @@ def fillpositive(xyz, w2_thresh=None):
     w2_thresh : None or float, optional
        threshold to determine if w squared is non-zero.
        If None (default) then w2_thresh set equal to
-       ``-np.finfo(xyz.dtype).eps``, if possible, otherwise
-       ``-np.finfo(np.float64).eps``
+       3 * ``np.finfo(xyz.dtype).eps``, if possible, otherwise
+       3 * ``np.finfo(np.float64).eps``
 
     Returns
     -------
@@ -89,9 +89,9 @@ def fillpositive(xyz, w2_thresh=None):
     # If necessary, guess precision of input
     if w2_thresh is None:
         try:  # trap errors for non-array, integer array
-            w2_thresh = -np.finfo(xyz.dtype).eps * 3
+            w2_thresh = np.finfo(xyz.dtype).eps * 3
         except (AttributeError, ValueError):
-            w2_thresh = -FLOAT_EPS * 3
+            w2_thresh = FLOAT_EPS * 3
     # Use maximum precision
     xyz = np.asarray(xyz, dtype=MAX_FLOAT)
     # Calculate w

nibabel/tests/test_quaternions.py

@@ -108,7 +108,7 @@ def test_fillpositive_simulated_error(dtype):
     # as xyz with small error, and we want to recover the w of 0
 
     # Permit 1 epsilon per value (default, but make explicit here)
-    w2_thresh = 3 * -np.finfo(dtype).eps
+    w2_thresh = 3 * np.finfo(dtype).eps
 
     pos_error = neg_error = False
     for _ in range(50):