BF: residual outputs reversed domain and range

matthew-brett · matthew-brett · commit 58e8916976d4 · 2012-06-05T12:21:51.000-07:00
The residual output reversed the coordmap domain and range. Until now
the tests didn't pick this up because we allowed through XYZ output
names that didn't match expected names for NIFTI. The nifti writer does
now check for these, and tranposes the image accordingly. Now the image
is being transposed, the test needs to look for the NIFTI transposed
shape.
diff --git a/nipy/modalities/fmri/fmristat/model.py b/nipy/modalities/fmri/fmristat/model.py
@@ -402,10 +402,9 @@ def output_resid(outfile, fmri_image, clobber=False):
         T[0,0] = (fmri_image.volume_start_times[1:] -
                   fmri_image.volume_start_times[:-1]).mean()
         # FIXME: NIFTI specific naming here
-        innames = ["l"] + list(g.function_range.coord_names)
-        outnames = ["t"] + list(g.function_domain.coord_names)
-        cmap = AffineTransform.from_params(innames,
-                                  outnames, T)
+        innames = ["t"] + list(g.function_domain.coord_names)
+        outnames = ["t"] + list(g.function_range.coord_names)
+        cmap = AffineTransform.from_params(innames, outnames, T)
         shape = (n,) + fmri_image[0].shape
     elif isinstance(fmri_image, Image):
         cmap = fmri_image.coordmap
diff --git a/nipy/modalities/fmri/fmristat/tests/test_model.py b/nipy/modalities/fmri/fmristat/tests/test_model.py
@@ -81,7 +81,7 @@ def test_run():
             f_data = f_img.get_data()
             assert_true(np.all((f_data>=0) & (f_data<30)))
             resid_img = load_image('resid_AR_out.nii')
-            assert_equal(resid_img.shape, funcim.shape[3:] + one_vol.shape)
+            assert_equal(resid_img.shape, funcim.shape)
             assert_array_almost_equal(np.mean(resid_img.get_data()), 0, 3)
             e_img = load_image('T_out_effect.nii')
             sd_img = load_image('T_out_sd.nii')
