Merge branch 'fix/masked_registration' of https://github.com/chrisfil…

…o/nipy
nipy · Apr 27, 2012 · 2d62b47 · 2d62b47
2 parents 08651e1 + 454e3e4
commit 2d62b47
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Showing 2 changed files with 29 additions and 3 deletions.
diff --git a/nipy/algorithms/registration/histogram_registration.py b/nipy/algorithms/registration/histogram_registration.py
@@ -368,7 +368,8 @@ def clamp(x, bins=BINS, mask=None):
         y, bins = _clamp(x, y, bins)
     else:
         ym = y[mask]
-        ym, bins = _clamp(x, ym, bins)
+        xm = x[mask]
+        ym, bins = _clamp(xm, ym, bins)
         y[mask] = ym
     return y, bins
 

diff --git a/nipy/algorithms/registration/tests/test_histogram_registration.py b/nipy/algorithms/registration/tests/test_histogram_registration.py
@@ -12,6 +12,9 @@
 
 dummy_affine = np.eye(4)
 
+def make_data_bool(dx=100, dy=100, dz=50):
+    return (np.random.rand(dx, dy, dz)
+                   - np.random.rand()) > 0
 
 def make_data_uint8(dx=100, dy=100, dz=50):
     return (256 * (np.random.rand(dx, dy, dz)
@@ -28,8 +31,8 @@ def make_data_float64(dx=100, dy=100, dz=50):
                  - np.random.rand())).astype('float64')
 
 
-def _test_clamping(I, thI=0.0, clI=256):
-    R = HistogramRegistration(I, I, from_bins=clI)
+def _test_clamping(I, thI=0.0, clI=256, mask=None):
+    R = HistogramRegistration(I, I, from_bins=clI, from_mask=mask, to_mask=mask)
     R.subsample(spacing=[1, 1, 1])
     Ic = R._from_data
     Ic2 = R._to_data[1:-1, 1:-1, 1:-1]
@@ -55,6 +58,12 @@ def test_clamping_int16():
     _test_clamping(I)
 
 
+def test_masked_clamping_int16():
+    I = AffineImage(make_data_int16(), dummy_affine, 'ijk')
+    mask = AffineImage(make_data_bool(), dummy_affine, 'ijk')
+    _test_clamping(I, mask=mask)
+
+
 def test_clamping_int16_nonstd():
     I = AffineImage(make_data_int16(), dummy_affine, 'ijk')
     _test_clamping(I, 10, 165)
@@ -143,6 +152,22 @@ def test_histogram_registration():
     J = AffineImage(I.get_data().copy(), dummy_affine, 'ijk')
     R = HistogramRegistration(I, J)
     assert_raises(ValueError, R.subsample, spacing=[0, 1, 3])
+
+def test_histogram_masked_registration():
+    """ Test the histogram registration class.
+    """
+    I = AffineImage(make_data_int16(dx=100, dy=100, dz=50), dummy_affine, 'ijk')
+    J = AffineImage(make_data_int16(dx=100, dy=100, dz=50), dummy_affine, 'ijk')
+    mask = (np.zeros((100,100,50)) == 1)
+    mask[10:20,10:20,10:20] = True
+    mask_img = AffineImage(mask, dummy_affine, 'ijk')
+    R = HistogramRegistration(I, J, to_mask=mask_img, from_mask=mask_img)
+    sim1 = R.eval(Affine())
+    I = AffineImage(I.get_data()[mask].reshape(10,10,10), dummy_affine, 'ijk')
+    J = AffineImage(J.get_data()[mask].reshape(10,10,10), dummy_affine, 'ijk')
+    R = HistogramRegistration(I, J)
+    sim2 = R.eval(Affine())
+    assert_equal(sim1, sim2)
 
 
 if __name__ == "__main__":