ENH: Add test subjects_dir config support, pass on tests

Author: larsoner

surfer/config.py

@@ -18,6 +18,7 @@
 
 [options]
 logging_level = INFO
+subjects_dir =
 """)
 
 config = ConfigParser.ConfigParser()

surfer/io.py

@@ -11,36 +11,8 @@
 import logging
 logger = logging.getLogger('surfer')
 
-
-def _get_subjects_dir(subjects_dir=None):
-    """Get the subjects directory from parameter or environment variable
-
-    Parameters
-    ----------
-    subjects_dir : str | None
-        The subjects directory.
-
-    Returns
-    -------
-    subjects_dir : str
-        The subjects directory. If the subjects_dir input parameter is not
-        None, its value will be returned, otherwise it will be obtained from
-        the SUBJECTS_DIR environment variable.
-    """
-
-    if subjects_dir is None:
-        if 'SUBJECTS_DIR' in os.environ:
-            subjects_dir = os.environ['SUBJECTS_DIR']
-        else:
-            raise ValueError('The subjects directory has to be specified '
-                             'using either the subjects_dir parameter or the '
-                             'SUBJECTS_DIR environment variable.')
-
-    if not os.path.exists(subjects_dir):
-        raise ValueError('The subjects directory %s does not exist.'
-                         % subjects_dir)
-
-    return subjects_dir
+from .config import config
+from .utils import _get_subjects_dir
 
 
 def read_scalar_data(filepath):
@@ -188,7 +160,7 @@ def read_stc(filepath):
 def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
                         projmeth="frac", projsum="avg", projarg=[0, 1, .1],
                         surf="white", smooth_fwhm=3, mask_label=None,
-                        target_subject=None, verbose=False):
+                        target_subject=None, verbose=None):
     """Sample MRI volume onto cortical manifold.
 
     Note: this requires Freesurfer to be installed with correct
@@ -220,8 +192,8 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
         Path to label file to constrain projection; otherwise uses cortex
     target_subject : string
         Subject to warp data to in surface space after projection
-    verbose : bool
-        If True, print the command used
+    verbose : bool, str, int, or None
+        If not None, override default verbose level (see surfer.verbose).
     """
     # Set the basic commands
     cmd_list = ["mri_vol2surf",
@@ -259,8 +231,7 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
     # Execute the command
     out_file = mktemp(prefix="pysurfer-v2s", suffix='.mgz')
     cmd_list.extend(["--o", out_file])
-    if verbose:
-        print " ".join(cmd_list)
+    logger.info(" ".join(cmd_list))
     p = Popen(cmd_list, stdout=PIPE, stderr=PIPE)
     stdout, stderr = p.communicate()
     out = p.returncode

surfer/tests/test_io.py

@@ -1,22 +1,19 @@
-import os
 from os.path import join as pjoin
 
 import numpy as np
-from numpy.testing import assert_array_almost_equal, assert_equal
+from numpy.testing import assert_array_almost_equal
 
-from .. import io
+from surfer import io
+from surfer.utils import requires_fsaverage
 
-if 'SUBJECTS_DIR' not in os.environ:
-    raise ValueError('Test suite relies on the definition of SUBJECTS_DIR')
-
-subj_dir = os.environ["SUBJECTS_DIR"]
+subj_dir = io._get_subjects_dir()
 subject_id = 'fsaverage'
-# subject_id = 'sample'
 data_path = pjoin(subj_dir, subject_id)
 
 
+@requires_fsaverage
 def test_surface():
-    """Test of Surface class"""
+    """Test IO for Surface class"""
     for subjects_dir in [None, subj_dir]:
         surface = io.Surface('fsaverage', 'lh', 'inflated',
                              subjects_dir=subjects_dir)

surfer/tests/test_viz.py

@@ -7,12 +7,10 @@
 
 from surfer import Brain
 from surfer import io
+from surfer.utils import requires_fsaverage
 from mayavi import mlab
 
-if 'SUBJECTS_DIR' not in os.environ:
-    raise ValueError('Test suite relies on the definition of SUBJECTS_DIR')
-
-subj_dir = os.environ["SUBJECTS_DIR"]
+subj_dir = io._get_subjects_dir()
 subject_id = 'fsaverage'
 std_args = [subject_id, 'lh', 'inflated']
 data_dir = pjoin(os.path.split(__file__)[0], '..', '..',
@@ -30,6 +28,7 @@ def has_freesurfer():
                                     'Requires FreeSurfer command line tools')
 
 
+@requires_fsaverage
 def test_offscreen():
     """Test offscreen rendering
     """
@@ -39,6 +38,7 @@ def test_offscreen():
     assert_array_equal(shot.shape, (800, 800, 3))
 
 
+@requires_fsaverage
 def test_image():
     """Test image saving
     """
@@ -52,6 +52,7 @@ def test_image():
     brain.close()
 
 
+@requires_fsaverage
 def test_brains():
     """Test plotting of Brain with different arguments
     """
@@ -67,13 +68,13 @@ def test_brains():
     subj_dirs = [None, subj_dir]
     for surf, hemi, curv, title, co, fig, sd \
             in zip(surfs, hemis, curvs, titles, config_opts, figs, subj_dirs):
-        print 'hello'
         brain = Brain(subject_id, hemi, surf, curv, title, co, fig, sd)
         brain.close()
     assert_raises(ValueError, Brain, subject_id, 'lh', 'inflated',
                   subjects_dir='')
 
 
+@requires_fsaverage
 def test_annot():
     """Test plotting of annot
     """
@@ -87,6 +88,7 @@ def test_annot():
     brain.close()
 
 
+@requires_fsaverage
 def test_contour():
     """Test plotting of contour overlay
     """
@@ -101,6 +103,7 @@ def test_contour():
     brain.close()
 
 
+@requires_fsaverage
 @requires_fs
 def test_data():
     """Test plotting of data
@@ -114,6 +117,7 @@ def test_data():
     brain.close()
 
 
+@requires_fsaverage
 def test_foci():
     """Test plotting of foci
     """
@@ -134,6 +138,7 @@ def test_foci():
     brain.close()
 
 
+@requires_fsaverage
 def test_label():
     """Test plotting of label
     """
@@ -156,6 +161,7 @@ def test_label():
     brain.close()
 
 
+@requires_fsaverage
 def test_meg_inverse():
     """Test plotting of MEG inverse solution
     """
@@ -178,6 +184,7 @@ def test_meg_inverse():
     brain.close()
 
 
+@requires_fsaverage
 def test_morphometry():
     """Test plotting of morphometry
     """
@@ -189,6 +196,7 @@ def test_morphometry():
     brain.close()
 
 
+@requires_fsaverage
 def test_overlay():
     """Test plotting of overlay
     """
@@ -221,6 +229,7 @@ def test_overlay():
     brain.close()
 
 
+@requires_fsaverage
 def test_probabilistic_labels():
     """Test plotting of probabilistic labels
     """
@@ -246,6 +255,7 @@ def test_probabilistic_labels():
     brain.close()
 
 
+@requires_fsaverage
 def test_text():
     """Test plotting of text
     """
@@ -255,6 +265,7 @@ def test_text():
     brain.close()
 
 
+@requires_fsaverage
 def test_animate():
     """Test animation
     """
@@ -269,6 +280,7 @@ def test_animate():
     brain.close()
 
 
+@requires_fsaverage
 def test_views():
     """Test showing different views
     """

surfer/utils.py

@@ -1,14 +1,14 @@
 import logging
 import warnings
 import sys
+import os
 from os import path as op
 import inspect
 from functools import wraps
 
 import numpy as np
 from scipy import sparse
 from scipy.spatial.distance import cdist
-from .io import Surface
 from .config import config
 
 logger = logging.getLogger('surfer')
@@ -215,11 +215,11 @@ def mesh_edges(faces):
     nfaces = len(faces)
     a, b, c = faces.T
     edges = sparse.coo_matrix((np.ones(nfaces), (a, b)),
-                                            shape=(npoints, npoints))
+                              shape=(npoints, npoints))
     edges = edges + sparse.coo_matrix((np.ones(nfaces), (b, c)),
-                                            shape=(npoints, npoints))
+                                      shape=(npoints, npoints))
     edges = edges + sparse.coo_matrix((np.ones(nfaces), (c, a)),
-                                            shape=(npoints, npoints))
+                                      shape=(npoints, npoints))
     edges = edges + edges.T
     edges = edges.tocoo()
     return edges
@@ -268,7 +268,7 @@ def smoothing_matrix(vertices, adj_mat, smoothing_steps=20, verbose=None):
         data1 = e_use * np.ones(len(idx_use))
         idx_use = np.where(data1)[0]
         scale_mat = sparse.dia_matrix((1 / data1[idx_use], 0),
-                                  shape=(len(idx_use), len(idx_use)))
+                                      shape=(len(idx_use), len(idx_use)))
 
         smooth_mat = scale_mat * e_use[idx_use, :] * smooth_mat
 
@@ -283,7 +283,7 @@ def smoothing_matrix(vertices, adj_mat, smoothing_steps=20, verbose=None):
                                    (idx_use[smooth_mat.row],
                                    smooth_mat.col)),
                                    shape=(n_vertices,
-                                         len(vertices)))
+                                          len(vertices)))
 
     return smooth_mat
 
@@ -336,3 +336,50 @@ def coord_to_label(subject_id, coord, label, hemi='lh', n_steps=30,
     for i in idx:
         x, y, z = geo.coords[i]
         f.write('%d  %f  %f  %f 0.000000\n' % (i, x, y, z))
+
+
+def _get_subjects_dir(subjects_dir=None):
+    """Get the subjects directory from parameter or environment variable
+
+    Parameters
+    ----------
+    subjects_dir : str | None
+        The subjects directory.
+
+    Returns
+    -------
+    subjects_dir : str
+        The subjects directory. If the subjects_dir input parameter is not
+        None, its value will be returned, otherwise it will be obtained from
+        the SUBJECTS_DIR environment variable. If that does not exist,
+        it will be obtained from the configuration file.
+    """
+    if subjects_dir is None:
+        if 'SUBJECTS_DIR' in os.environ:
+            subjects_dir = os.environ['SUBJECTS_DIR']
+        else:
+            subjects_dir = config.get('options', 'subjects_dir')
+            if subjects_dir == '':
+                raise ValueError('The subjects directory has to be specified '
+                                 'using the subjects_dir parameter, the '
+                                 'SUBJECTS_DIR environment variable, or the '
+                                 '"subjects_dir" entry in the config file')
+
+    if not os.path.exists(subjects_dir):
+        raise ValueError('The subjects directory %s does not exist.'
+                         % subjects_dir)
+
+    return subjects_dir
+
+
+def has_fsaverage(subjects_dir=None):
+    """Determine whether the user has a usable fsaverage"""
+    fs_dir = op.join(_get_subjects_dir(subjects_dir), 'fsaverage')
+    if not op.isdir(fs_dir):
+        return False
+    if not op.isdir(op.join(fs_dir, 'surf')):
+        return False
+    return True
+
+requires_fsaverage = np.testing.dec.skipif(not has_fsaverage(),
+                                           'Requires fsaverage subject data')