Merge pull request #3166 from AnnaD15/AnnaD15-patch-1

[FIX] FSL model.py make multiple F-tests

Author: effigies

.zenodo.json

@@ -765,6 +765,11 @@
       "name": "Mihai, Paul Glad",
       "orcid": "0000-0001-5715-6442"
     },
+    {
+      "affiliation": "Department of Psychology, University of Bielefeld, Bielefeld, Germany.",
+      "name": "Doll, Anna",
+      "orcid": "0000-0002-0799-0831"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Gorgolewski, Krzysztof J.",

nipype/interfaces/fsl/model.py

@@ -1574,8 +1574,7 @@ def _run_interface(self, runtime):
                     for tcon in con[2]:
                         convals[tconmap[self.inputs.contrasts.index(tcon)]] = 1
                     fcon_txt.append(" ".join(["%d" % val for val in convals]))
-                    fcon_txt = "\n".join(fcon_txt)
-            fcon_txt += "\n"
+            fcon_txt = "\n".join(fcon_txt) + "\n"
         # write group file
         grp_txt = ["/NumWaves       1", "/NumPoints      %d" % npoints, "", "/Matrix"]
         for i in range(npoints):

nipype/interfaces/fsl/tests/test_model.py

@@ -6,26 +6,28 @@
 import pytest
 import nipype.interfaces.fsl.model as fsl
 from nipype.interfaces.fsl import no_fsl
+from pathlib import Path
+from ....pipeline import engine as pe 
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_MultipleRegressDesign(tmpdir):
-    tmpdir.chdir()
-    foo = fsl.MultipleRegressDesign()
-    foo.inputs.regressors = dict(
+    designer = pe.Node(fsl.MultipleRegressDesign(), name='designer', base_dir=str(tmpdir))
+    designer.inputs.regressors = dict(
         voice_stenght=[1, 1, 1], age=[0.2, 0.4, 0.5], BMI=[1, -1, 2]
     )
     con1 = ["voice_and_age", "T", ["age", "voice_stenght"], [0.5, 0.5]]
     con2 = ["just_BMI", "T", ["BMI"], [1]]
-    foo.inputs.contrasts = [con1, con2, ["con3", "F", [con1, con2]]]
-    res = foo.run()
+    designer.inputs.contrasts = [con1, con2, ["con3", "F", [con1, con2]], ["con4", "F", [con2]]]
+    res = designer.run()
+    outputs = res.outputs.get_traitsfree()
 
-    for ii in ["mat", "con", "fts", "grp"]:
-        assert (
-            getattr(res.outputs, "design_" + ii) == tmpdir.join("design." + ii).strpath
-        )
+    for ftype in ["mat", "con", "fts", "grp"]:
+        assert Path(outputs["design_" + ftype]).exists()
 
-    design_mat_expected_content = """/NumWaves       3
+    expected_content = {}
+
+    expected_content["design_mat"] = """/NumWaves       3
 /NumPoints      3
 /PPheights      3.000000e+00 5.000000e-01 1.000000e+00
 
@@ -35,7 +37,7 @@ def test_MultipleRegressDesign(tmpdir):
 2.000000e+00 5.000000e-01 1.000000e+00
 """
 
-    design_con_expected_content = """/ContrastName1   voice_and_age
+    expected_content["design_con"] = """/ContrastName1   voice_and_age
 /ContrastName2   just_BMI
 /NumWaves       3
 /NumContrasts   2
@@ -47,22 +49,22 @@ def test_MultipleRegressDesign(tmpdir):
 1.000000e+00 0.000000e+00 0.000000e+00
 """
 
-    design_fts_expected_content = """/NumWaves       2
-/NumContrasts   1
+    expected_content["design_fts"] = """/NumWaves       2
+/NumContrasts   2
 
 /Matrix
 1 1
+0 1
 """
 
-    design_grp_expected_content = """/NumWaves       1
+    expected_content["design_grp"] = """/NumWaves       1
 /NumPoints      3
 
 /Matrix
 1
 1
 1
 """
-    for ii in ["mat", "con", "fts", "grp"]:
-        assert tmpdir.join("design." + ii).read() == eval(
-            "design_" + ii + "_expected_content"
-        )
+    for ftype in ["mat", "con", "fts", "grp"]:
+        outfile = "design_" + ftype
+        assert Path(outputs[outfile]).read_text() == expected_content[outfile]