reverted back to include checks for simplex space. Changed closure check to closure of 1 or 100

Author: jtlait

eis_toolkit/utilities/checks/compositional.py

@@ -1,29 +1,30 @@
-import numpy as np
+from numbers import Number
+
 import pandas as pd
 from beartype import beartype
-from beartype.typing import Optional
 
 from eis_toolkit.exceptions import InvalidCompositionException, NumericValueSignException
 from eis_toolkit.utilities.checks.dataframe import check_dataframe_contains_only_positive_numbers
 
 
 @beartype
-def check_in_simplex_sample_space(df: pd.DataFrame, expected_sum: Optional[np.float64] = None) -> None:
+def check_in_simplex_sample_space(df: pd.DataFrame, tolerance: Number = 0.0001) -> None:
     """
     Check that the compositions represented by the data rows belong to a simplex sample space.
 
+    Checks that data has not NaN values.
     Checks that each compositional data point belongs to the set of positive real numbers.
-    Checks that each composition is normalized to the same value.
+    Checks that input dataframe is closed to either 1 or 100.
 
     Args:
         df: The dataframe to check.
-        expected_sum: The expected sum of each row. If None, simply checks that the sum of each row is equal.
+        tolerance: Small tolerance value to allow floating-point imprecision.
 
     Returns:
-        True if values are valid and the sum of each row is the expected_sum.
+        None.
 
     Raises:
-        InvalidCompositionException: Data is not normalized to the expected value.
+        InvalidCompositionException: Data is not within the expected simplex sample space.
         NumericValueSignException: Data contains zeros or negative values.
     """
     if df.isnull().values.any():
@@ -32,9 +33,11 @@ def check_in_simplex_sample_space(df: pd.DataFrame, expected_sum: Optional[np.fl
     if not check_dataframe_contains_only_positive_numbers(df):
         raise NumericValueSignException("Data contains zeros or negative values.")
 
-    df_sum = np.sum(df, axis=1)
-    expected_sum = expected_sum if expected_sum is not None else df_sum.iloc[0]
-    if len(df_sum[df_sum.iloc[:] != expected_sum]) != 0:
-        raise InvalidCompositionException("Not each composition is normalized to the same value.")
+    row_sums = df.sum(axis=1)
+    closed_to_one = (row_sums - 1).abs() < tolerance
+    closed_to_hundred = (row_sums - 100).abs() < tolerance
+
+    if not closed_to_one.all() and not closed_to_hundred.all():
+        raise InvalidCompositionException(f"Input data is not closed to 1 or 100 within tolerance of {tolerance}.")
 
     return None

tests/transformations/coda/alr_test.py

@@ -9,34 +9,23 @@
 SAMPLE_DATAFRAME = pd.DataFrame(sample_array, columns=["a", "b", "c", "d"])
 
 
-def test_alr_transform_simple():
-    """Test ALR transformation core functionality."""
-    ones_df_4x4 = pd.DataFrame(np.ones((4, 4)), columns=["a", "b", "c", "d"])
-    zeros_df_4x4 = pd.DataFrame(np.zeros((4, 3)), columns=["V1", "V2", "V3"])
-    result = alr_transform(ones_df_4x4)
-    pd.testing.assert_frame_equal(result, zeros_df_4x4)
-
-
 def test_alr_transform():
     """Test ALR transformation core functionality."""
-    arr = np.array([[1, 4, 1, 1], [2, 1, 2, 2]])
+    arr = np.random.dirichlet(np.ones(4), size=4)
     df = pd.DataFrame(arr, columns=["a", "b", "c", "d"], dtype=np.float64)
 
     result = alr_transform(df, column="b", keep_denominator_column=True)
     expected = pd.DataFrame(
-        {
-            "V1": [np.log(0.25), np.log(2)],
-            "V2": [0, 0],
-            "V3": [np.log(0.25), np.log(2)],
-            "V4": [np.log(0.25), np.log(2)],
-        },
+        np.log(arr / arr[:, 1, None]),
+        columns=["V1", "V2", "V3", "V4"],
         dtype=np.float64,
     )
     pd.testing.assert_frame_equal(result, expected)
 
     result = alr_transform(df, column="b")
     expected = pd.DataFrame(
-        {"V1": [np.log(0.25), np.log(2)], "V2": [np.log(0.25), np.log(2)], "V3": [np.log(0.25), np.log(2)]},
+        np.log(np.delete(arr, 1, axis=1) / arr[:, 1, None]),
+        columns=["V1", "V2", "V3"],
         dtype=np.float64,
     )
     pd.testing.assert_frame_equal(result, expected)

tests/transformations/coda/clr_test.py

@@ -9,19 +9,16 @@
 SAMPLE_DATAFRAME = pd.DataFrame(sample_array, columns=["a", "b", "c", "d"])
 
 
-def test_clr_transform_simple():
-    """Test CLR transform core functionality."""
-    ones_df_4x4 = pd.DataFrame(np.ones((4, 4)), columns=["a", "b", "c", "d"])
-    zeros_df_4x4 = pd.DataFrame(np.zeros((4, 4)), columns=["V1", "V2", "V3", "V4"])
-    result = clr_transform(ones_df_4x4)
-    pd.testing.assert_frame_equal(result, zeros_df_4x4)
-
-
 def test_clr_transform():
     """Test CLR transform core functionality."""
-    result = clr_transform(SAMPLE_DATAFRAME)
+    arr = np.random.dirichlet(np.ones(4), size=4)
+    df = pd.DataFrame(arr, columns=["a", "b", "c", "d"], dtype=np.float64)
+    result = clr_transform(df)
+    geometric_means = np.prod(arr, axis=1) ** (1 / arr.shape[1])
     expected = pd.DataFrame(
-        {"V1": [1.38, 1.29], "V2": [-0.30, -0.08], "V3": [0.10, -0.15], "V4": [-1.18, -1.06]}, dtype=np.float64
+        np.log(arr / geometric_means[:, None]),
+        columns=["V1", "V2", "V3", "V4"],
+        dtype=np.float64,
     )
     pd.testing.assert_frame_equal(result, expected, atol=1e-2)
 

tests/utilities/compositional_test.py

@@ -77,7 +77,6 @@ def test_compositional_data_invalid():
 def test_check_for_simplex_sample_space():
     """Test whether or not a dataframe belongs to a simplex sample space is correctly identified."""
     unit_simplex_df = pd.DataFrame([[0.1, 0.2, 0.3, 0.4], [0.2, 0.3, 0.2, 0.3]])
-    simplex_df = pd.DataFrame([[1, 2, 3, 4], [2, 3, 2, 3]], columns=["a", "b", "c", "d"])
     non_simplex_positive_df = pd.DataFrame([1, 2, 3, 4], [5, 6, 7, 8])
     non_positive_df = pd.DataFrame([-1, 2, 3, 4], [1, 2, 3, 4])
 
@@ -87,13 +86,8 @@ def test_check_for_simplex_sample_space():
     with pytest.raises(NumericValueSignException):
         check_in_simplex_sample_space(non_positive_df)
 
-    with pytest.raises(InvalidCompositionException):
-        check_in_simplex_sample_space(simplex_df, np.float64(100))
-
     # Valid cases - assert no exception is raised
     try:
-        check_in_simplex_sample_space(simplex_df)
-        check_in_simplex_sample_space(simplex_df, np.float64(10))
-        check_in_simplex_sample_space(unit_simplex_df, np.float64(1.0))
+        check_in_simplex_sample_space(unit_simplex_df)
     except Exception as ex:
         assert False, f"{type(ex)}: {ex}"