[WIP] 0.7 release

bids/analysis/analysis.py

@@ -51,8 +51,7 @@ def _load_blocks(self, blocks):
             block = Block(self.layout, index=i, **block_args)
             self.blocks.append(block)
 
-    def setup(self, blocks=None, agg_func='mean', auto_contrasts=None,
-              **kwargs):
+    def setup(self, blocks=None, agg_func='mean', **kwargs):
         ''' Set up the sequence of blocks for analysis.
 
         Args:
@@ -69,8 +68,6 @@ def setup(self, blocks=None, agg_func='mean', auto_contrasts=None,
                 name of a function recognized by apply() in pandas, or a
                 Callable that takes a DataFrame as input and returns a Series
                 or a DataFrame. NOTE: CURRENTLY UNIMPLEMENTED.
-            auto_contrasts (bool): If True, a contrast is automatically
-                created for each column in the design matrix.
         '''
 
         # In the beginning, there was nothing
@@ -86,7 +83,7 @@ def setup(self, blocks=None, agg_func='mean', auto_contrasts=None,
             if blocks is not None and i not in blocks and b.name not in blocks:
                 continue
 
-            b.setup(input_nodes, auto_contrasts, **selectors)
+            b.setup(input_nodes, **selectors)
             input_nodes = b.output_nodes
 
 
@@ -108,14 +105,16 @@ class Block(object):
             generated when the model is fit.
         input_nodes (list): Optional list of AnalysisNodes to use as input to
             this Block (typically, the output from the preceding Block).
-        auto_contrasts (bool): If True, a contrast is automatically
-            created for each column in the design matrix. This parameter is
-            over-written by the setting in setup(). Default is True.
+        auto_contrasts (list, bool): Optional list of variable names to create
+            an indicator contrast for. Alternatively, if the boolean value True
+            is passed, a contrast is automatically generated for _all_
+            available variables. This parameter is over-written by the setting
+            in setup() if the latter is passed.
     '''
 
     def __init__(self, layout, level, index, name=None, transformations=None,
                 model=None, contrasts=None, input_nodes=None,
-                auto_contrasts=True):
+                auto_contrasts=False):
 
         self.layout = layout
         self.level = level
@@ -125,8 +124,8 @@ def __init__(self, layout, level, index, name=None, transformations=None,
         self.model = model or None
         self.contrasts = contrasts or []
         self.input_nodes = input_nodes or []
+        self.auto_contrasts = auto_contrasts or []
         self.output_nodes = []
-        self.auto_contrasts = auto_contrasts
 
     def _filter_objects(self, objects, kwargs):
         # Keeps only objects that match target entities, and also removes those
@@ -163,23 +162,18 @@ def _concatenate_input_nodes(self, nodes):
         entities = pd.concat(entities, axis=1).T
         return BIDSVariableCollection.from_df(data, entities, self.level)
 
-    def setup(self, input_nodes=None, auto_contrasts=None, **kwargs):
+    def setup(self, input_nodes=None, **kwargs):
         ''' Set up the Block and construct the design matrix.
 
         Args:
             input_nodes (list): Optional list of Node objects produced by
                 the preceding Block in the analysis. If None, uses any inputs
                 passed in at Block initialization.
-            auto_contrasts (bool): If True, a contrast is automatically
-                created for each column in the design matrix.
             kwargs: Optional keyword arguments to pass onto load_variables.
         '''
         self.output_nodes = []
         input_nodes = input_nodes or self.input_nodes or []
 
-        if auto_contrasts is not None:
-            self.auto_contrasts = auto_contrasts
-
         # TODO: remove the scan_length argument entirely once we switch tests
         # to use the synthetic dataset with image headers.
         if self.level != 'run':
@@ -192,6 +186,14 @@ def setup(self, input_nodes=None, auto_contrasts=None, **kwargs):
         objects, kwargs = self._filter_objects(objects, kwargs)
         groups = self._group_objects(objects)
 
+        # Set up and validate variable lists
+        model = self.model or {}
+        variables = model.get('variables', [])
+        hrf_variables = model.get('HRF_variables', [])
+        if not set(variables) >= set(hrf_variables):
+            raise ValueError("HRF_variables must be a subset ",
+                                "of variables in BIDS model.")
+
         for grp in groups:
             # Split into separate lists of Collections and Nodes
             input_nodes = [o for o in grp if isinstance(o, AnalysisNode)]
@@ -201,19 +203,11 @@ def setup(self, input_nodes=None, auto_contrasts=None, **kwargs):
                 node_coll = self._concatenate_input_nodes(input_nodes)
                 colls.append(node_coll)
 
-            model = self.model or {}
-
-            variables = set(model.get('variables', []))
-            hrf_variables = set(model.get('HRF_variables', []))
-            if not variables >= hrf_variables:
-                raise ValueError("HRF_variables must be a subset ",
-                                 "of variables in BIDS model.")
-
             coll = merge_collections(colls) if len(colls) > 1 else colls[0]
 
             coll = apply_transformations(coll, self.transformations)
-            if model.get('variables'):
-                transform.select(coll, model['variables'])
+            if variables:
+                transform.select(coll, variables)
 
             node = AnalysisNode(self.level, coll, self.contrasts, input_nodes,
                                 self.auto_contrasts)
@@ -294,17 +288,21 @@ class AnalysisNode(object):
         collection (BIDSVariableCollection): The BIDSVariableCollection
             containing variables at this Node.
         contrasts (list): A list of contrasts defined in the originating Block.
-        auto_contrasts (bool): If True, a contrast is automatically
-            created for each column in the design matrix.
+        auto_contrasts (list): Optional list of variable names to create
+            an indicator contrast for. Alternatively, if the boolean value True
+            is passed, a contrast is automatically generated for _all_
+            available variables.
     '''
 
     def __init__(self, level, collection, contrasts, input_nodes=None,
-                 auto_contrasts=True):
+                 auto_contrasts=None):
         self.level = level
         self.collection = collection
         self._block_contrasts = contrasts
         self.input_nodes = input_nodes
-        self.auto_contrasts = auto_contrasts
+        if auto_contrasts == True:
+            auto_contrasts = collection.variables.keys()
+        self.auto_contrasts = auto_contrasts or []
         self._contrasts = None
 
     @property
@@ -403,8 +401,9 @@ def get_contrasts(self, names=None, entities=False):
 
         ### Add ability to set different types of identity contrasts
         if self.auto_contrasts:
-            for col_name in self.collection.variables.keys():
-                if col_name not in contrast_names:
+            for col_name in self.auto_contrasts:
+                if (col_name in self.collection.variables.keys()
+                    and col_name not in contrast_names):
                     contrasts.append({
                         'name': col_name,
                         'condition_list': [col_name],

bids/analysis/tests/test_analysis.py

@@ -9,20 +9,12 @@
 @pytest.fixture
 def analysis():
     layout_path = join(get_test_data_path(), 'ds005')
-    layout = BIDSLayout(layout_path, exclude='derivatives/')
+    layout = BIDSLayout(layout_path)
     json_file = join(layout_path, 'models', 'ds-005_type-test_model.json')
     analysis = Analysis(layout, json_file)
     analysis.setup(scan_length=480, subject=['01', '02'])
     return analysis
 
-@pytest.fixture
-def analysis_force_auto_contrasts():
-    layout_path = join(get_test_data_path(), 'ds005')
-    layout = BIDSLayout(layout_path, exclude='derivatives/')
-    json_file = join(layout_path, 'models', 'ds-005_type-test_model.json')
-    analysis = Analysis(layout, json_file)
-    analysis.setup(scan_length=480, subject=['01', '02'], auto_contrasts=True)
-    return analysis
 
 def test_design_matrix_info(analysis):
     result = analysis['run'].get_design_matrix(subject=['01', '02', '03'])
@@ -81,7 +73,7 @@ def test_post_first_level_sparse_design_matrix(analysis):
     result = analysis['session'].get_design_matrix(entities=False)
     assert len(result) == 2
     assert len(result[0]) == 3
-    assert result[0].sparse.shape == (3, 2)
+    assert result[0].sparse.shape == (6, 2)
     assert result[0].entities == {
         'subject': '01',
         'task': 'mixedgamblestask'}
@@ -95,7 +87,7 @@ def test_post_first_level_sparse_design_matrix(analysis):
     result = analysis['group'].get_design_matrix()
     assert len(result) == 1
     data = result[0].sparse
-    assert len(data) == 6
+    assert len(data) == 8
     assert data['subject'].nunique() == 2
 
     # # Make sure columns from different levels exist
@@ -114,10 +106,6 @@ def test_contrast_matrix_info(analysis):
         assert isinstance(contrasts[0], ContrastMatrixInfo)
         assert c._fields == ('data', 'index', 'entities')
 
-def test_force_auto_contrasts(analysis_force_auto_contrasts):
-    contrasts = analysis_force_auto_contrasts['run'].get_contrasts(subject='01')
-    assert contrasts[0][0].shape == (8, 9)
-
 
 # def test_get_contrasts(analysis):
 #     contrasts = analysis['run'].get_contrasts(subject='01')

bids/analysis/tests/test_transformations.py

@@ -11,7 +11,7 @@
 @pytest.fixture
 def collection():
     layout_path = join(get_test_data_path(), 'ds005')
-    layout = BIDSLayout(layout_path, exclude='derivatives/')
+    layout = BIDSLayout(layout_path)
     collection = layout.get_collections('run', types=['events'],
                                         scan_length=480, merge=True,
                                         sampling_rate=10)

bids/config.py

@@ -10,9 +10,7 @@
 
 _config_name = 'pybids_config.json'
 
-_default_settings = {
-    'loop_preproc': False
-}
+_default_settings = {}
 
 
 def set_option(key, value):

bids/layout/__init__.py

@@ -1,3 +1,3 @@
-from .bids_layout import BIDSLayout
-from .bids_validator import BIDSValidator
+from .layout import BIDSLayout
+from .validation import BIDSValidator
 __all__ = ["BIDSLayout", "BIDSValidator"]