Final bits of tidying and documentation/comments

Author: alexdaniel654

ukat/mapping/t1.py

@@ -132,6 +132,9 @@ class T1:
     r2 : np.ndarray
         The R-Squared value of the fit, values close to 1 indicate a good
         fit, lower values indicate a poorer fit
+    deformation_field : np.ndarray
+        The deformation field generated by the model-driven registration
+        process.
     shape : tuple
         The shape of the T1 map
     n_ti : int
@@ -266,7 +269,6 @@ def __init__(self, pixel_array, inversion_list, affine, tss=0, tss_axis=-2,
             assert (tss_axis < self.dimensions), \
                 'tss_axis must be less than the number of spatial dimensions'
             if (self.tss_axis != 2) & (self.mdr is True):
-                print(self.tss_axis)
                 raise ValueError('Temporal slice spacing only supported '
                                  'along the z direction when using '
                                  'model-driven registration.')
@@ -278,8 +280,10 @@ def __init__(self, pixel_array, inversion_list, affine, tss=0, tss_axis=-2,
                               'using parameters=3.')
 
         if mdr:
+            # The mdreg package can handle register each slice of an M2D
+            # image separately provided the inversion times of each slice
+            # are the same.
             if self.tss == 0:
-                print('Fitting with no TSS')
                 pixel_array, deform, _, _ = mdreg.fit(
                     self.pixel_array,
                     force_2d=True,
@@ -309,6 +313,10 @@ def __init__(self, pixel_array, inversion_list, affine, tss=0, tss_axis=-2,
                 pixel_array = np.zeros(self.pixel_array.shape)
                 deform = np.zeros((*self.pixel_array.shape[:3], 2,
                                    self.pixel_array.shape[3]))
+
+                # The following for loop is a workaround to allow a
+                # different inversion list for each slice of data. Most of
+                # the code comes from the mdreg.fit() function.
                 for slice in range(self.shape[-1]):
                     print('-----------------')
                     print('Fitting slice ' + str(slice).zfill(3))
@@ -344,7 +352,6 @@ def __init__(self, pixel_array, inversion_list, affine, tss=0, tss_axis=-2,
             # Changing the dimensions of the deformation field to a more
             # intuitive order.
             self.deformation_field = np.swapaxes(deform, -2, -1)
-
             self.pixel_array = pixel_array
 
         # Fit Data
@@ -680,6 +687,9 @@ def magnitude_correct(pixel_array):
 
 # Private wrapper for use by mdreg
 def _t1_fit(pixel_array, inversion_list=None, affine=None, **kwargs):
+    """
+    Private wrapper for use by mdreg
+    """
     map = T1(pixel_array, inversion_list, affine, **kwargs)
     if map.parameters == 2:
         pars = np.stack((map.t1_map, map.m0_map), axis=-1)