TEST: make specs

Author: effigies

nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py

@@ -102,8 +102,13 @@ def test_GLMFit_inputs():
         mrtm2=dict(
             argstr="--mrtm2 %s %s %f...",
         ),
+        nii=dict(
+            argstr="--nii",
+            xor=["nii", "nii_gz"],
+        ),
         nii_gz=dict(
             argstr="--nii.gz",
+            xor=["nii", "nii_gz"],
         ),
         no_contrast_ok=dict(
             argstr="--no-contrasts-ok",
@@ -220,6 +225,9 @@ def test_GLMFit_outputs():
         beta_file=dict(
             extensions=None,
         ),
+        bp_file=dict(
+            extensions=None,
+        ),
         dof_file=dict(
             extensions=None,
         ),
@@ -245,6 +253,9 @@ def test_GLMFit_outputs():
         gamma_file=dict(),
         gamma_var_file=dict(),
         glm_dir=dict(),
+        k2p_file=dict(
+            extensions=None,
+        ),
         mask_file=dict(
             extensions=None,
         ),

nipype/interfaces/freesurfer/tests/test_auto_GTMPVC.py

@@ -78,6 +78,9 @@ def test_GTMPVC_inputs():
         mgx=dict(
             argstr="--mgx %f",
         ),
+        no_pvc=dict(
+            argstr="--no-pvc",
+        ),
         no_reduce_fov=dict(
             argstr="--no-reduce-fov",
         ),
@@ -87,17 +90,20 @@ def test_GTMPVC_inputs():
         no_tfe=dict(
             argstr="--no-tfe",
         ),
-        opt=dict(
+        num_threads=dict(
             argstr="--threads %i",
         ),
+        opt=dict(
+            argstr="--opt %i",
+        ),
         opt_brain=dict(
             argstr="--opt-brain",
         ),
         opt_seg_merge=dict(
             argstr="--opt-seg-merge",
         ),
         opt_tol=dict(
-            argstr="--opt-tol %f %f %f",
+            argstr="--opt-tol %i %f %f",
         ),
         psf=dict(
             argstr="--psf %f",
@@ -128,12 +134,15 @@ def test_GTMPVC_inputs():
             argstr="--reg %s",
             extensions=None,
             mandatory=True,
+            xor=["reg_file", "regheader", "reg_identity"],
         ),
         reg_identity=dict(
-            argstr="--regheader",
+            argstr="--reg-identity",
+            xor=["reg_file", "regheader", "reg_identity"],
         ),
         regheader=dict(
             argstr="--regheader",
+            xor=["reg_file", "regheader", "reg_identity"],
         ),
         replace=dict(
             argstr="--replace %i %i",
@@ -157,7 +166,7 @@ def test_GTMPVC_inputs():
             argstr="--save_yhat_full_fov",
         ),
         save_yhat_with_noise=dict(
-            argstr="--ss %i %i",
+            argstr="--save-yhat-with-noise",
         ),
         scale_refval=dict(
             argstr="--scale-refval %f",
@@ -174,9 +183,6 @@ def test_GTMPVC_inputs():
             argstr="--ss %f %f %f",
         ),
         subjects_dir=dict(),
-        threads=dict(
-            argstr="--threads %i",
-        ),
         tt_reduce=dict(
             argstr="--tt-reduce",
         ),

nipype/interfaces/freesurfer/tests/test_auto_GTMSeg.py

@@ -44,7 +44,7 @@ def test_GTMSeg_inputs():
             extensions=None,
             usedefault=True,
         ),
-        output_usf=dict(
+        output_upsampling_factor=dict(
             argstr="--output-usf %i",
         ),
         subject_id=dict(
@@ -58,7 +58,7 @@ def test_GTMSeg_inputs():
         subsegwm=dict(
             argstr="--subsegwm",
         ),
-        usf=dict(
+        upsampling_factor=dict(
             argstr="--usf %i",
         ),
         wm_annot=dict(

nipype/interfaces/freesurfer/tests/test_auto_LoganRef.py

@@ -223,211 +223,52 @@ def test_LoganRef_inputs():
 
 def test_LoganRef_outputs():
     output_map = dict(
-        allow_ill_cond=dict(
-            argstr="--illcond",
-        ),
-        allow_repeated_subjects=dict(
-            argstr="--allowsubjrep",
-        ),
-        args=dict(
-            argstr="%s",
-        ),
-        bp=dict(
+        beta_file=dict(
             extensions=None,
         ),
-        calc_AR1=dict(
-            argstr="--tar1",
-        ),
-        check_opts=dict(
-            argstr="--checkopts",
-        ),
-        compute_log_y=dict(
-            argstr="--logy",
-        ),
-        contrast=dict(
-            argstr="--C %s...",
-        ),
-        cortex=dict(
-            argstr="--cortex",
-            xor=["label_file"],
-        ),
-        debug=dict(
-            argstr="--debug",
-        ),
-        design=dict(
-            argstr="--X %s",
+        bp_file=dict(
             extensions=None,
-            xor=("fsgd", "design", "one_sample"),
-        ),
-        diag=dict(
-            argstr="--diag %d",
         ),
-        diag_cluster=dict(
-            argstr="--diag-cluster",
-        ),
-        environ=dict(
-            nohash=True,
-            usedefault=True,
-        ),
-        fixed_fx_dof=dict(
-            argstr="--ffxdof %d",
-            xor=["fixed_fx_dof_file"],
-        ),
-        fixed_fx_dof_file=dict(
-            argstr="--ffxdofdat %d",
+        dof_file=dict(
             extensions=None,
-            xor=["fixed_fx_dof"],
         ),
-        fixed_fx_var=dict(
-            argstr="--yffxvar %s",
+        error_file=dict(
             extensions=None,
         ),
-        force_perm=dict(
-            argstr="--perm-force",
-        ),
-        fsgd=dict(
-            argstr="--fsgd %s %s",
-            xor=("fsgd", "design", "one_sample"),
-        ),
-        fwhm=dict(
-            argstr="--fwhm %f",
+        error_stddev_file=dict(
+            extensions=None,
         ),
-        glm_dir=dict(
-            argstr="--glmdir %s",
-            genfile=True,
+        error_var_file=dict(
+            extensions=None,
         ),
-        hemi=dict(),
-        in_file=dict(
-            argstr="--y %s",
-            copyfile=False,
+        estimate_file=dict(
             extensions=None,
-            mandatory=True,
         ),
-        invert_mask=dict(
-            argstr="--mask-inv",
+        frame_eigenvectors=dict(
+            extensions=None,
         ),
-        label_file=dict(
-            argstr="--label %s",
+        ftest_file=dict(),
+        fwhm_file=dict(
             extensions=None,
-            xor=["cortex"],
         ),
-        logan=dict(
-            argstr="--logan %s %s %f...",
+        gamma_file=dict(),
+        gamma_var_file=dict(),
+        glm_dir=dict(),
+        k2p_file=dict(
+            extensions=None,
         ),
         mask_file=dict(
-            argstr="--mask %s",
             extensions=None,
         ),
-        mrtm1=dict(
-            argstr="--mrtm1 %s %s...",
-        ),
-        mrtm2=dict(
-            argstr="--mrtm2 %s %s %f...",
-        ),
-        nii_gz=dict(
-            argstr="--nii.gz",
-        ),
-        no_contrast_ok=dict(
-            argstr="--no-contrasts-ok",
-        ),
-        no_est_fwhm=dict(
-            argstr="--no-est-fwhm",
-        ),
-        no_mask_smooth=dict(
-            argstr="--no-mask-smooth",
-        ),
-        no_prune=dict(
-            argstr="--no-prune",
-            xor=["prunethresh"],
-        ),
-        one_sample=dict(
-            argstr="--osgm",
-            xor=("one_sample", "fsgd", "design", "contrast"),
-        ),
-        pca=dict(
-            argstr="--pca",
-        ),
-        per_voxel_reg=dict(
-            argstr="--pvr %s...",
-        ),
-        profile=dict(
-            argstr="--profile %d",
-        ),
-        prune=dict(
-            argstr="--prune",
-        ),
-        prune_thresh=dict(
-            argstr="--prune_thr %f",
-            xor=["noprune"],
-        ),
-        resynth_test=dict(
-            argstr="--resynthtest %d",
-        ),
-        save_cond=dict(
-            argstr="--save-cond",
-        ),
-        save_estimate=dict(
-            argstr="--yhat-save",
-        ),
-        save_res_corr_mtx=dict(
-            argstr="--eres-scm",
-        ),
-        save_residual=dict(
-            argstr="--eres-save",
-        ),
-        seed=dict(
-            argstr="--seed %d",
-        ),
-        self_reg=dict(
-            argstr="--selfreg %d %d %d",
-        ),
-        sim_done_file=dict(
-            argstr="--sim-done %s",
+        sig_file=dict(),
+        singular_values=dict(
             extensions=None,
         ),
-        sim_sign=dict(
-            argstr="--sim-sign %s",
-        ),
-        simulation=dict(
-            argstr="--sim %s %d %f %s",
-        ),
-        subject_id=dict(),
-        subjects_dir=dict(),
-        surf=dict(
-            argstr="--surf %s %s %s",
-            requires=["subject_id", "hemi"],
-        ),
-        surf_geo=dict(
-            usedefault=True,
-        ),
-        synth=dict(
-            argstr="--synth",
-        ),
-        uniform=dict(
-            argstr="--uniform %f %f",
-        ),
-        var_fwhm=dict(
-            argstr="--var-fwhm %f",
-        ),
-        vox_dump=dict(
-            argstr="--voxdump %d %d %d",
-        ),
-        weight_file=dict(
+        spatial_eigenvectors=dict(
             extensions=None,
-            xor=["weighted_ls"],
         ),
-        weight_inv=dict(
-            argstr="--w-inv",
-            xor=["weighted_ls"],
-        ),
-        weight_sqrt=dict(
-            argstr="--w-sqrt",
-            xor=["weighted_ls"],
-        ),
-        weighted_ls=dict(
-            argstr="--wls %s",
+        svd_stats_file=dict(
             extensions=None,
-            xor=("weight_file", "weight_inv", "weight_sqrt"),
         ),
     )
     outputs = LoganRef.output_spec()