From c4dc38c92728f0abdae87a04ec951f18d36f4eb9 Mon Sep 17 00:00:00 2001
From: singlesp <sps253@cornell.edu>
Date: Wed, 5 Feb 2025 12:48:48 -0500
Subject: [PATCH] pytest for variant numbering

---
 cubids/tests/test_variant_numbering.py | 112 +++++++++++++++++++++++++
 1 file changed, 112 insertions(+)
 create mode 100644 cubids/tests/test_variant_numbering.py

diff --git a/cubids/tests/test_variant_numbering.py b/cubids/tests/test_variant_numbering.py
new file mode 100644
index 00000000..9690ed4b
--- /dev/null
+++ b/cubids/tests/test_variant_numbering.py
@@ -0,0 +1,112 @@
+import pandas as pd
+import numpy as np
+import pytest
+from cubids.cubids import CuBIDS
+from cubids.utils import assign_variants
+
+@pytest.fixture
+def sample_summary_df():
+    """Create a sample summary DataFrame with multiple variant groups."""
+    return pd.DataFrame({
+        "EntitySet": [
+            "datatype-dwi_suffix-dwi",  # Dominant group
+            "datatype-dwi_suffix-dwi",  # EchoTime variant 1
+            "datatype-dwi_suffix-dwi",  # EchoTime variant 2
+            "datatype-dwi_suffix-dwi",  # RepetitionTime variant
+            "datatype-dwi_suffix-dwi",  # EchoTime + RepetitionTime variant
+            "datatype-dwi_suffix-dwi",  # Other variant
+        ],
+        "ParamGroup": [1, 2, 3, 4, 5, 6],
+        "EchoTime": ["0.05", "0.03", "0.07", "0.05", "0.03", "0.05"],
+        "RepetitionTime": ["2.5", "2.5", "2.5", "3.0", "3.0", "2.5"],
+        "FlipAngle": ["90", "90", "90", "90", "90", np.nan],
+    })
+
+def test_variant_numbering_basic(sample_summary_df):
+    """Test basic variant numbering functionality."""
+    rename_cols = ["EchoTime", "RepetitionTime", "FlipAngle"]
+    result = assign_variants(sample_summary_df, rename_cols)
+
+    # Check that dominant group (ParamGroup 1) has no rename
+    assert pd.isna(result.loc[0, "RenameEntitySet"])
+
+    # Check EchoTime variants are numbered
+    assert "VARIANTEchoTime1" in result.loc[1, "RenameEntitySet"]
+    assert "VARIANTEchoTime2" in result.loc[2, "RenameEntitySet"]
+
+    # Check RepetitionTime variant
+    assert "VARIANTRepetitionTime1" in result.loc[3, "RenameEntitySet"]
+
+    # Check combined variant
+    assert "VARIANTEchoTimeRepetitionTime1" in result.loc[4, "RenameEntitySet"]
+
+    # Check Other variant
+    assert "VARIANTOther1" in result.loc[5, "RenameEntitySet"]
+
+def test_variant_numbering_multiple_groups():
+    """Test variant numbering with multiple entity sets."""
+    df = pd.DataFrame({
+        "EntitySet": [
+            # First entity set
+            "datatype-dwi_direction-AP_suffix-dwi",
+            "datatype-dwi_direction-AP_suffix-dwi",
+            # Second entity set
+            "datatype-dwi_direction-PA_suffix-dwi",
+            "datatype-dwi_direction-PA_suffix-dwi",
+        ],
+        "ParamGroup": [1, 2, 1, 2],
+        "EchoTime": ["0.05", "0.03", "0.05", "0.03"],
+        "RepetitionTime": ["2.5", "2.5", "2.5", "2.5"],
+    })
+
+    result = assign_variants(df, ["EchoTime", "RepetitionTime"])
+
+    # Check that each entity set has its own variant numbering
+    variant_counts = result["RenameEntitySet"].str.count("VARIANTEchoTime1").fillna(0)
+    assert variant_counts.sum() == 2  # Should have two "VARIANTEchoTime1" instances
+
+def test_variant_numbering_acquisition_handling():
+    """Test variant numbering with existing acquisition entities."""
+    df = pd.DataFrame({
+        "EntitySet": [
+            "acquisition-base_datatype-dwi_suffix-dwi",
+            "acquisition-base_datatype-dwi_suffix-dwi",
+        ],
+        "ParamGroup": [1, 2],
+        "EchoTime": ["0.05", "0.03"],
+    })
+
+    result = assign_variants(df, ["EchoTime"])
+
+    # Check that acquisition entity is properly handled
+    assert "acquisition-baseVARIANTEchoTime1" in result.loc[1, "RenameEntitySet"]
+
+def test_variant_numbering_fieldmap():
+    """Test variant numbering with fieldmap-related variants."""
+    df = pd.DataFrame({
+        "EntitySet": ["datatype-dwi_suffix-dwi"] * 3,
+        "ParamGroup": [1, 2, 3],
+        "HasFieldmap": ["True", "False", "False"],
+        "UsedAsFieldmap": ["False", "True", "False"],
+    })
+
+    result = assign_variants(df, ["HasFieldmap", "UsedAsFieldmap"])
+
+    # Check fieldmap variant naming
+    assert "VARIANTNoFmap1" in result.loc[1, "RenameEntitySet"]
+    assert "VARIANTIsUsed1" in result.loc[1, "RenameEntitySet"]
+
+def test_variant_numbering_consistency():
+    """Test that variant numbering is consistent across multiple runs."""
+    df = pd.DataFrame({
+        "EntitySet": ["datatype-dwi_suffix-dwi"] * 4,
+        "ParamGroup": [1, 2, 3, 4],
+        "EchoTime": ["0.05", "0.03", "0.03", "0.07"],
+    })
+
+    # Run variant assignment twice
+    result1 = assign_variants(df, ["EchoTime"])
+    result2 = assign_variants(df, ["EchoTime"])
+
+    # Check results are identical
+    pd.testing.assert_frame_equal(result1, result2)
\ No newline at end of file