Merge pull request #2867 from TheChymera/order

FIX: Sort conditions in bids_gen_info to ensure consistent order

Author: effigies

nipype/algorithms/modelgen.py

@@ -13,10 +13,12 @@
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
+
+str_basetype = str
 from builtins import range, str, bytes, int
 
 from copy import deepcopy
-import os, math, csv
+import csv, math, os
 
 from nibabel import load
 import numpy as np
@@ -145,7 +147,7 @@ def scale_timings(timelist, input_units, output_units, time_repetition):
     return timelist
 
 def bids_gen_info(bids_event_files,
-                  condition_column='trial_type',
+                  condition_column='',
                   amplitude_column=None,
                   time_repetition=False,
                   ):
@@ -173,9 +175,13 @@ def bids_gen_info(bids_event_files,
     info = []
     for bids_event_file in bids_event_files:
         with open(bids_event_file) as f:
-            f_events = csv.DictReader(f, skipinitialspace=True, delimiter='\t')
+            f_events = csv.DictReader(f, skipinitialspace=True, delimiter=str_basetype('\t'))
             events = [{k: v for k, v in row.items()} for row in f_events]
-        conditions = list(set([i[condition_column] for i in events]))
+        if not condition_column:
+            condition_column = '_trial_type'
+            for i in events:
+                i.update({condition_column: 'ev0'})
+        conditions = sorted(set([i[condition_column] for i in events]))
         runinfo = Bunch(conditions=[], onsets=[], durations=[], amplitudes=[])
         for condition in conditions:
             selected_events = [i for i in events if i[condition_column]==condition]
@@ -185,10 +191,7 @@ def bids_gen_info(bids_event_files,
                 decimals = math.ceil(-math.log10(time_repetition))
                 onsets = [np.round(i, decimals) for i in onsets]
                 durations = [np.round(i ,decimals) for i in durations]
-            if condition:
-                runinfo.conditions.append(condition)
-            else:
-                runinfo.conditions.append('e0')
+            runinfo.conditions.append(condition)
             runinfo.onsets.append(onsets)
             runinfo.durations.append(durations)
             try:

nipype/algorithms/tests/test_modelgen.py

@@ -11,9 +11,19 @@
 
 import pytest
 import numpy.testing as npt
+from nipype.testing import example_data
 from nipype.interfaces.base import Bunch, TraitError
-from nipype.algorithms.modelgen import (SpecifyModel, SpecifySparseModel,
-                                        SpecifySPMModel)
+from nipype.algorithms.modelgen import (bids_gen_info, SpecifyModel,
+                                        SpecifySparseModel, SpecifySPMModel)
+
+
+def test_bids_gen_info():
+    fname = example_data('events.tsv')
+    res = bids_gen_info([fname])
+    assert res[0].onsets == [[183.75, 313.75, 483.75, 633.75, 783.75, 933.75, 1083.75, 1233.75]]
+    assert res[0].durations == [[20.0, 20.0, 20.0, 20.0, 20.0, 20.0, 20.0, 20.0]]
+    assert res[0].amplitudes ==[[1, 1, 1, 1, 1, 1, 1, 1]]
+    assert res[0].conditions == ['ev0']
 
 
 def test_modelgen1(tmpdir):

nipype/testing/data/events.tsv

@@ -0,0 +1,9 @@
+onset	duration	frequency	pulse_width	amplitude
+183.75	20.0	20.0	0.005	1.0
+313.75	20.0	20.0	0.005	1.0
+483.75	20.0	20.0	0.005	1.0
+633.75	20.0	20.0	0.005	1.0
+783.75	20.0	20.0	0.005	1.0
+933.75	20.0	20.0	0.005	1.0
+1083.75	20.0	20.0	0.005	1.0
+1233.75	20.0	20.0	0.005	1.0