DOC - fix docstrings to allow latex doc build

Several docstrings lacked an intro line before the first section (often
the Parameters section).  This caused errors in the latex build of the
automated API docs.

Author: matthew-brett

nipy/labs/spatial_models/discrete_domain.py

@@ -291,7 +291,8 @@ class MeshDomain(object):
     """
 
     def __init__(self, coord, triangles):
-        """
+        """ Initialize mesh domain instance
+
         Parameters
         ----------
         coord: array of shape (n_vertices, 3),
@@ -305,7 +306,8 @@ def __init__(self, coord, triangles):
         # fixme: implement consistency checks
 
     def area(self):
-        """
+        """ Return array of areas for each node
+
         Returns
         -------
         area: array of shape self.V,
@@ -404,7 +406,8 @@ class DiscreteDomain(object):
     """
 
     def __init__(self, dim, coord, local_volume, id='', referential=''):
-        """
+        """ Initialize discrete domain instance
+
         Parameters
         ----------
         dim: int,
@@ -567,7 +570,8 @@ class StructuredDomain(DiscreteDomain):
 
     def __init__(self, dim, coord, local_volume, topology, did='',
                  referential=''):
-        """
+        """ Initialize structured domain instance
+
         Parameters
         ----------
         dim: int,
@@ -622,7 +626,8 @@ class NDGridDomain(StructuredDomain):
 
     def __init__(self, dim, ijk, shape, affine, local_volume, topology,
                 referential=''):
-        """
+        """ Initialize ndgrid domain instance
+
         Parameters
         ----------
         dim: int,

nipy/labs/spatial_models/mroi.py

@@ -5,7 +5,7 @@
 
 from nibabel import load, save, Nifti1Image
 
-import discrete_domain as ddom
+from . import discrete_domain as ddom
 
 ##############################################################################
 # class MultiROI
@@ -19,7 +19,8 @@ class MultiROI(object):
     """
 
     def __init__(self, domain, k, rid=''):
-        """
+        """ Initialize multi ROI instance
+
         Parameters
         ----------
         domain: ROI instance
@@ -75,7 +76,8 @@ class SubDomains(object):
     """
 
     def __init__(self, domain, label, id='', no_empty_label=True):
-        """
+        """ Initialize subdomains instance
+
         Parameters
         ----------
         domain: ROI instance
@@ -209,16 +211,16 @@ def select(self, valid, id='', auto=True, no_empty_label=True):
             return SD
 
     def make_feature(self, fid, data, override=True):
-        """Extract a set of ffeatures from a domain map
+        """Extract a set of features from a domain map
 
         Parameters
         ----------
-        fid: string,
-             feature identifier
+        fid: string
+            feature identifier
         data: array of shape(deomain.size) or (domain, size, dim),
-              domain map from which ROI features are axtracted
+            domain map from which ROI features are axtracted
         override: bool, optional,
-                  Allow feature overriding
+            Allow feature overriding
         """
         if data.shape[0] != self.domain.size:
             raise ValueError("Incorrect data provided")
@@ -333,7 +335,7 @@ def plot_feature(self, fid, ax=None):
 
         Parameters
         ----------
-        fid: string,
+        fid: string
              the feature identifier
         ax: axis handle, optional
         """
@@ -349,11 +351,14 @@ def plot_feature(self, fid, ax=None):
         return ax
 
     def set_roi_feature(self, fid, data):
-        """
+        """ Set feature defined by `fid` and `data` into ``self``
+
         Parameters
         ----------
-        fid: string, feature identifier
-        data: array of shape(self.k, p), with p>0
+        fid: string
+            feature identifier
+        data: array
+            shape(self.k, p), with p>0
         """
         if data.shape[0] != self.k:
             print data.shape[0], self.k, fid
@@ -368,15 +373,15 @@ def get_roi_feature(self, fid):
         return self.roi_features[fid]
 
     def to_image(self, path=None, descrip=None, write_type=np.int16, data=None):
-        """ Generates and possiblly writes a label image that represents self.
+        """ Generates and possibly writes a label image that represents self.
 
         Parameters
         ----------
         path: string, optional
               output image path
-        descrip: string, optional,
+        descrip: string, optional
                  descritpion associated with the output image
-        write_type: string, optional,
+        write_type: string, optional
                     type of the written data
         data: array os shape (self.k), optional,
               information to write into the image
@@ -461,6 +466,7 @@ def subdomain_from_position_and_image(nim, pos):
     """
     keeps the set of labels of the image corresponding to a certain index
     so that their position is closest to the prescribed one
+
     Parameters
     ----------
     mim: NiftiIImage instance, or string path toward such an image
@@ -482,11 +488,11 @@ def subdomain_from_balls(domain, positions, radii):
     Parameters
     ----------
     domain: StructuredDomain instance,
-            the description of a discrete domain
+        the description of a discrete domain
     positions: array of shape(k, dim):
-               the positions of the balls
+        the positions of the balls
     radii: array of shape(k):
-           the sphere radii
+        the sphere radii
     """
     # checks
     if np.size(positions) == positions.shape[0]:

nipy/labs/spatial_models/parcellation.py

@@ -33,7 +33,8 @@ class MultiSubjectParcellation(object):
 
     def __init__(self, domain, template_labels=None, individual_labels=None,
                  nb_parcel=None):
-        """
+        """ Initialize multi-subject parcellation
+
         Parameters
         ----------
         domain: discrete_domain.DiscreteDomain instance,
@@ -159,13 +160,15 @@ def make_feature(self, fid, data):
         return pfeature
 
     def set_feature(self, fid, data):
-        """
+        """ Set feature defined by `fid` and `data` into ``self``
+
         Parameters
         ----------
-        fid: string, the feature identifier
+        fid: string
+            the feature identifier
         data: array of shape (self.nb_parcel, self.nb_subj, dim) or
               (self.nb_parcel, self.nb_subj)
-              the data to be set as parcel- and subject-level information
+            the data to be set as parcel- and subject-level information
         """
         if len(data.shape) < 2:
             raise ValueError("Data array should at least have dimension 2")
@@ -176,7 +179,8 @@ def set_feature(self, fid, data):
             self.features.update({fid: data})
 
     def get_feature(self, fid):
-        """
+        """ Get feature defined by `fid`
+
         Parameters
         ----------
         fid: string, the feature identifier