Merge remote-tracking branch 'upstream/master' into enh/plotting_impr…

…ovements

Dockerfile

@@ -103,7 +103,7 @@ USER neuro
 # Update conda environment
 #-------------------------
 RUN /bin/bash -c "source activate neuro \
-      && pip install -q --no-cache-dir --upgrade pip \
+      && pip install --no-cache-dir --upgrade 'pip<19' \
       && pip install -q --no-cache-dir --upgrade -r /src/fitlins/requirements.txt" \
     && sync
 

fitlins/__about__.py

@@ -41,13 +41,13 @@
     'pandas>=0.19',
     'tables>=3.2.1',
     'nistats>=0.0.1b0',
-    'pybids>=0.6.5',
+    'pybids>=0.7',
     'jinja2',
 ]
 
 LINKS_REQUIRES = [
     'git+https://github.com/bids-standard/pybids.git@'
-    '36853b0bf222d3174ae7d9d1d9c7a7ecf5049cdd#egg=pybids',
+    'a4bbc811e67df8ffbc186cca4c3c61e0992af09f#egg=pybids',
 ]
 
 TESTS_REQUIRES = [

fitlins/cli/run.py

@@ -85,12 +85,15 @@ def get_parser():
     g_bids.add_argument('--derivative-label', action='store', type=str,
                         help='execution label to append to derivative directory name')
     g_bids.add_argument('--space', action='store',
-                        choices=['MNI152NLin2009cAsym'], default='MNI152NLin2009cAsym',
-                        help='registered space of input datasets')
+                        choices=['MNI152NLin2009cAsym', ''],
+                        default='MNI152NLin2009cAsym',
+                        help='registered space of input datasets. Empty value for no explicit space.')
     g_bids.add_argument('--include', action='store', default=None,
                         help='regex pattern to include files')
     g_bids.add_argument('--exclude', action='store', default=None,
                         help='regex pattern to exclude files')
+    g_bids.add_argument('--desc-label', action='store', default='preproc',
+                         help="use BOLD files with the provided description label")
 
     g_perfm = parser.add_argument_group('Options to handle performance')
     g_perfm.add_argument('--n-cpus', action='store', default=0, type=int,
@@ -110,6 +113,9 @@ def run_fitlins(argv=None):
     opts = get_parser().parse_args(argv)
     if opts.debug:
         logger.setLevel(logging.DEBUG)
+    if not opts.space:
+        # make it an explicit None
+        opts.space = None
 
     subject_list = None
     if opts.participant_label is not None:
@@ -141,7 +147,10 @@ def run_fitlins(argv=None):
 
     derivatives = True if not opts.derivatives else opts.derivatives
     # Need this when specifying args directly (i.e. neuroscout)
-    if len(derivatives) == 1:
+    # god bless neuroscout, but let's make it work for others!
+    if isinstance(derivatives, list) and len(derivatives) == 1:
+        # WRONG AND EVIL to those who have spaces in their paths... bad bad practice
+        # TODO - fix neuroscout
         derivatives = derivatives[0].split(" ")
 
     pipeline_name = 'fitlins'
@@ -155,7 +164,9 @@ def run_fitlins(argv=None):
     work_dir = mkdtemp() if opts.work_dir is None else opts.work_dir
 
     fitlins_wf = init_fitlins_wf(
-        opts.bids_dir, derivatives, deriv_dir, opts.space, model=model,
+        opts.bids_dir, derivatives, deriv_dir, opts.space,
+        desc=opts.desc_label,
+        model=model,
         participants=subject_list, base_dir=work_dir,
         include_pattern=opts.include, exclude_pattern=opts.exclude
         )

fitlins/interfaces/bids.py

@@ -198,13 +198,19 @@ def _load_level1(self, runtime, analysis):
             # ents is now pretty populous
             ents.pop('suffix', None)
             ents.pop('datatype', None)
-            if 'space' in ents:
-                # Guaranteed to be valid
-                space = ents.pop('space')
-            else:
-                # Picks first match
-                space = analysis.layout.get_spaces(suffix='bold',
-                                                   extensions=['.nii', '.nii.gz'])[0]
+            space = ents.pop('space', None)
+            if space is None:
+                spaces = analysis.layout.get_spaces(
+                    suffix='bold',
+                    extensions=['.nii', '.nii.gz'])
+                if spaces:
+                    spaces = sorted(spaces)
+                    space = spaces[0]
+                    if len(spaces) > 1:
+                        iflogger.warning(
+                            'No space was provided, but multiple spaces were detected: %s. '
+                            'Selecting the first (ordered lexicographically): %s'
+                            % (', '.join(spaces), space))
             preproc_files = analysis.layout.get(suffix='bold',
                                                 extensions=['.nii', '.nii.gz'],
                                                 space=space,

fitlins/workflows/base.py

@@ -9,8 +9,9 @@
 from ..interfaces.utils import MergeAll
 
 
-def init_fitlins_wf(bids_dir, derivatives, out_dir, space, exclude_pattern=None,
-                    include_pattern=None, model=None, participants=None,
+def init_fitlins_wf(bids_dir, derivatives, out_dir, space, desc=None,
+                    exclude_pattern=None, include_pattern=None,
+                    model=None, participants=None,
                     base_dir=None, name='fitlins_wf'):
     wf = pe.Workflow(name=name, base_dir=base_dir)
 
@@ -48,7 +49,9 @@ def init_fitlins_wf(bids_dir, derivatives, out_dir, space, exclude_pattern=None,
         BIDSSelect(
             bids_dir=bids_dir, derivatives=derivatives,
             selectors={
-                'type': 'preproc', 'suffix': 'bold', 'space': space}),
+                'suffix': 'bold',
+                'desc': desc,
+                'space': space}),
         name='getter')
 
     l1_model = pe.MapNode(

requirements.txt

@@ -5,4 +5,4 @@ nilearn>=0.4.0
 pandas>=0.19
 nipype>=1.1.6
 git+https://github.com/nistats/nistats.git@009ce3fddb3dd01e82bca3ad7d2cdbeece0138f2#egg=nistats
-git+https://github.com/bids-standard/pybids.git@36853b0bf222d3174ae7d9d1d9c7a7ecf5049cdd#egg=pybids
+git+https://github.com/bids-standard/pybids.git@a4bbc811e67df8ffbc186cca4c3c61e0992af09f#egg=pybids