[TST] Expand parameters tested in integration tests (#502)

* Add args to integration tests.

* Fix import error.

* Fix 5-echo test.

* Move rerun into another directory.

* Fix outputs.

* Fix...

* Dummy commit.

tedana/tests/data/cornell_three_echo_outputs.txt

@@ -40,9 +40,6 @@ figures/comp_032.png
 figures/comp_033.png
 figures/comp_034.png
 figures/comp_035.png
-figures/comp_036.png
-figures/comp_037.png
-figures/comp_038.png
 dn_ts_OC.nii.gz
 feats_OC2.nii.gz
 figures

tedana/tests/data/nih_five_echo_outputs_verbose.txt

@@ -1,14 +1,19 @@
+T1gs.nii.gz
 adaptive_mask.nii.gz
 betas_OC.nii.gz
 betas_hik_OC.nii.gz
+betas_hik_OC_T1c.nii.gz
 dn_ts_OC.nii.gz
+dn_ts_OC_T1c.nii.gz
 dn_ts_e1.nii.gz
 dn_ts_e2.nii.gz
 dn_ts_e3.nii.gz
 dn_ts_e4.nii.gz
 dn_ts_e5.nii.gz
 feats_OC2.nii.gz
+glsig.1D
 hik_ts_OC.nii.gz
+hik_ts_OC_T1c.nii.gz
 hik_ts_e1.nii.gz
 hik_ts_e2.nii.gz
 hik_ts_e3.nii.gz
@@ -27,6 +32,7 @@ meica_R2_pred.nii.gz
 meica_S0_pred.nii.gz
 meica_betas_catd.nii.gz
 meica_metric_weights.nii.gz
+meica_mix_T1c.1D
 mepca_R2_pred.nii.gz
 mepca_S0_pred.nii.gz
 mepca_betas_catd.nii.gz
@@ -37,10 +43,13 @@ pca_mixing.tsv
 report.txt
 s0v.nii.gz
 s0vG.nii.gz
+sphis_hik.nii.gz
 t2sv.nii.gz
 t2svG.nii.gz
 ts_OC.nii.gz
 ts_OC_whitened.nii.gz
+tsoc_nogs.nii.gz
+tsoc_orig.nii.gz
 figures
 figures/Component_Overview.png
 figures/Kappa_vs_Rho_Scatter.png
@@ -108,4 +117,3 @@ figures/comp_059.png
 figures/comp_060.png
 figures/comp_061.png
 figures/comp_062.png
-figures/comp_063.png

tedana/tests/test_integration.py

@@ -91,7 +91,10 @@ def test_integration_five_echo(skip_integration):
         tes=[15.4, 29.7, 44.0, 58.3, 72.6],
         out_dir=out_dir,
         tedpca='mdl',
-        debug=True, verbose=True)
+        gscontrol=['gsr', 't1c'],
+        png_cmap='bone',
+        debug=True,
+        verbose=True)
 
     # Just a check on the component table pending a unit test of load_comptable
     comptable = os.path.join(out_dir, 'ica_decomposition.json')
@@ -140,6 +143,7 @@ def test_integration_three_echo(skip_integration):
     if skip_integration:
         pytest.skip('Skipping three-echo integration test')
     out_dir = '/tmp/data/three-echo/TED.three-echo'
+    out_dir2 = '/tmp/data/three-echo/TED.three-echo-rerun'
     if os.path.exists(out_dir):
         shutil.rmtree(out_dir)
 
@@ -151,7 +155,16 @@ def test_integration_three_echo(skip_integration):
         tes=[14.5, 38.5, 62.5],
         out_dir=out_dir,
         low_mem=True,
-        tedpca='kundu')
+        tedpca='kundu-stabilize')
+
+    # test rerunning the workflow
+    tedana_workflow(
+        data='/tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz',
+        tes=[14.5, 38.5, 62.5],
+        out_dir=out_dir2,
+        mixm=os.path.join(out_dir, 'ica_mixing.tsv'),
+        ctab=os.path.join(out_dir, 'ica_decomposition.json'),
+        no_png=True)
 
     # compare the generated output files
     fn = resource_filename('tedana',