[DOC] Improve logging of component table-based manual classification (#…

…852)

* Update tedana.py

* Test manual classification using comptable.

* Change clfs in five-echo manual clf test.

* Fix the test.

* Update test_integration.py

tedana/tests/test_integration.py

@@ -72,14 +72,20 @@ def download_test_data(osf, outpath):
 
 
 def test_integration_five_echo(skip_integration):
-    """Integration test of the full tedana workflow using five-echo test data"""
+    """Integration test of the full tedana workflow using five-echo test data."""
 
     if skip_integration:
         pytest.skip("Skipping five-echo integration test")
+
     out_dir = "/tmp/data/five-echo/TED.five-echo"
+    out_dir_manual = "/tmp/data/five-echo/TED.five-echo-manual"
+
     if os.path.exists(out_dir):
         shutil.rmtree(out_dir)
 
+    if os.path.exists(out_dir_manual):
+        shutil.rmtree(out_dir_manual)
+
     # download data and run the test
     download_test_data("https://osf.io/9c42e/download", os.path.dirname(out_dir))
     prepend = "/tmp/data/five-echo/p06.SBJ01_S09_Task11_e"
@@ -103,8 +109,7 @@ def test_integration_five_echo(skip_integration):
     assert isinstance(df, pd.DataFrame)
 
     # Test re-running, but use the CLI
-    out_dir2 = "/tmp/data/five-echo/TED.five-echo-manual"
-    acc_comps = df.loc[df["classification"] == "accepted"].index.values
+    acc_comps = df.loc[df["classification"] == "ignored"].index.values
     acc_comps = [str(c) for c in acc_comps]
     mixing = os.path.join(out_dir, "desc-ICA_mixing.tsv")
     t2smap = os.path.join(out_dir, "T2starmap.nii.gz")
@@ -115,7 +120,7 @@ def test_integration_five_echo(skip_integration):
         + [str(te) for te in echo_times]
         + [
             "--out-dir",
-            out_dir2,
+            out_dir_manual,
             "--debug",
             "--verbose",
             "--manacc",
@@ -140,10 +145,16 @@ def test_integration_four_echo(skip_integration):
 
     if skip_integration:
         pytest.skip("Skipping four-echo integration test")
+
     out_dir = "/tmp/data/four-echo/TED.four-echo"
+    out_dir_manual = "/tmp/data/four-echo/TED.four-echo-manual"
+
     if os.path.exists(out_dir):
         shutil.rmtree(out_dir)
 
+    if os.path.exists(out_dir_manual):
+        shutil.rmtree(out_dir_manual)
+
     # download data and run the test
     download_test_data("https://osf.io/gnj73/download", os.path.dirname(out_dir))
     prepend = "/tmp/data/four-echo/"
@@ -161,8 +172,30 @@ def test_integration_four_echo(skip_integration):
         verbose=True,
     )
 
+    # Test re-running with the component table
+    mixing_matrix = os.path.join(out_dir, "desc-ICA_mixing.tsv")
+    comptable = os.path.join(out_dir, "desc-tedana_metrics.tsv")
+    temporary_comptable = os.path.join(out_dir, "temporary_metrics.tsv")
+    comptable_df = pd.read_table(comptable)
+    comptable_df.loc[comptable_df["classification"] == "ignored", "classification"] = "accepted"
+    comptable_df.to_csv(temporary_comptable, sep="\t", index=False)
+    tedana_cli.tedana_workflow(
+        data=datalist,
+        tes=[11.8, 28.04, 44.28, 60.52],
+        out_dir=out_dir_manual,
+        tedpca="kundu-stabilize",
+        gscontrol=["gsr", "mir"],
+        png_cmap="bone",
+        mixm=mixing_matrix,
+        ctab=temporary_comptable,
+        debug=True,
+        verbose=False,
+    )
+    os.remove(temporary_comptable)
+
     # compare the generated output files
     fn = resource_filename("tedana", "tests/data/fiu_four_echo_outputs.txt")
+
     check_integration_outputs(fn, out_dir)
 
 
@@ -171,11 +204,16 @@ 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"
+    out_dir_manual = "/tmp/data/three-echo/TED.three-echo-rerun"
+
     if os.path.exists(out_dir):
         shutil.rmtree(out_dir)
 
+    if os.path.exists(out_dir_manual):
+        shutil.rmtree(out_dir_manual)
+
     # download data and run the test
     download_test_data("https://osf.io/rqhfc/download", os.path.dirname(out_dir))
     tedana_cli.tedana_workflow(
@@ -195,7 +233,7 @@ def test_integration_three_echo(skip_integration):
         "38.5",
         "62.5",
         "--out-dir",
-        out_dir2,
+        out_dir_manual,
         "--debug",
         "--verbose",
         "--ctab",

tedana/workflows/tedana.py

@@ -736,6 +736,7 @@ def tedana_workflow(
             )
             comptable, metric_metadata = selection.kundu_selection_v2(comptable, n_echos, n_vols)
         else:
+            LGR.info("Using supplied component table for classification")
             comptable = pd.read_table(ctab)
             # Change rationale value of rows with NaN to empty strings
             comptable.loc[comptable.rationale.isna(), "rationale"] = ""