Fix an inconsistency in the incoherent sum measurement and update the test

CDTools/tools/measurements.py

@@ -47,22 +47,22 @@ def incoherent_sum(wavefields, detector_slice=None, epsilon=1e-7, saturation=Non
     the wavefields. If a detector slice is given, the returned array
     will only include that slice from the simulated wavefronts.
 
-    The first index is the index of the diffraction pattern to measure,
-    the second index is the set of incoherently adding patterns, and
-    the next two indices index the wavefield. The final index is the complex
+    The first index is the set of incoherently adding patterns, and
+    the second index is the index of the diffraction pattern to measure.
+    The next two indices index the wavefield. The final index is the complex
     index.
     
     Args:
-        wavefields (torch.Tensor) : A JxLxMxNx2 stack of complex wavefields
+        wavefields (torch.Tensor) : An LxJxMxNx2 stack of complex wavefields
         detector_slice (slice) : Optional, a slice or tuple of slices defining a section of the simulation to return
         saturation (float) : Optional, a maximum saturation value to clamp the resulting intensities to
 
     Returns:
-        torch.Tensor : A real MxN array storing the incoherently summed intensities
+        torch.Tensor : A real JXMxN array storing the incoherently summed intensities
     """
     # This syntax just adds an axis to the slice to preserve the J direction
     if detector_slice is None:
-        output = t.sum(cmath.cabssq(wavefields),dim=-3) + epsilon
+        output = t.sum(cmath.cabssq(wavefields),dim=0) + epsilon
     else:
         if wavefields.dim() == 4:
             output =  t.sum(cmath.cabssq(wavefields[(np.s_[:],)+detector_slice]),dim=0) + epsilon

tests/tools/test_measurements.py

@@ -31,11 +31,11 @@ def test_intensity():
 def test_incoherent_sum():
     wavefields = t.rand((5,4,10,10,2))
     epsilon=1e-6
-    np_result = np.sum(np.abs(cmath.torch_to_complex(wavefields))**2,axis=1) + epsilon
+    np_result = np.sum(np.abs(cmath.torch_to_complex(wavefields))**2,axis=0) + epsilon
     assert t.allclose(measurements.incoherent_sum(wavefields,epsilon=epsilon),
                       t.tensor(np_result))
     # Test single field case
-    assert t.allclose(measurements.incoherent_sum(wavefields[0],epsilon=epsilon),
+    assert t.allclose(measurements.incoherent_sum(wavefields[:,0],epsilon=epsilon),
                       t.tensor(np_result[0]))
 
     
@@ -43,7 +43,7 @@ def test_incoherent_sum():
     assert t.allclose(measurements.incoherent_sum(wavefields,det_slice,epsilon=epsilon),
                       t.tensor(np_result[(np.s_[:],)+det_slice]))
     # Test single field case
-    assert t.allclose(measurements.incoherent_sum(wavefields[0],det_slice,epsilon=epsilon),
+    assert t.allclose(measurements.incoherent_sum(wavefields[:,0],det_slice,epsilon=epsilon),
                       t.tensor(np_result[0][det_slice]))