Add a function to check if TE values are in ms, otherwise update them (…

…ME-ICA#1151)

Co-authored-by: Dan Handwerker <[email protected]>

tedana/tests/test_utils.py

@@ -363,4 +363,13 @@ def test_millisec2sec():
     assert utils.millisec2sec(np.array([5000])) == np.array([5])
 
 
+def test_check_te_values():
+    """Ensure that check_te_values returns the correct values."""
+    assert utils.check_te_values([2, 3, 4]) == [2, 3, 4]
+    assert utils.check_te_values([0.15, 0.35, 0.55]) == [150, 350, 550]
+    # Check that the error is raised when TE values are in different units
+    with pytest.raises(ValueError):
+        utils.check_te_values([0.5, 1, 2.5])
+
+
 # TODO: "BREAK" AND UNIT TESTS

tedana/utils.py

@@ -634,3 +634,27 @@ def get_system_version_info():
         "Python": sys.version,
         "Python_Libraries": python_libraries,
     }
+
+
+def check_te_values(te_values):
+    """Check if all TE values are in ms by checking if they are higher than 1.
+
+    Parameters
+    ----------
+    te_values : list
+        TE values to check.
+
+    Returns
+    -------
+    list
+        TE values in milliseconds.
+    """
+    te_values = np.array(te_values)
+    if all(te_values > 1):
+        return te_values.tolist()
+    elif all((te_values > 0) & (te_values < 1)):
+        # Raise a warning and convert to ms by multiplying by 1000
+        LGR.warning("Assuming the provided TE values are in seconds. Converting to ms.")
+        return (te_values * 1000).tolist()
+    else:
+        raise ValueError("TE values must be positive and in milliseconds.")

tedana/workflows/tedana.py

@@ -572,6 +572,7 @@ def tedana_workflow(
 
     # ensure tes are in appropriate format
     tes = [float(te) for te in tes]
+    tes = utils.check_te_values(tes)
     n_echos = len(tes)
 
     # Coerce gscontrol to list