use permutations on background variables too

Author: tommyod

src/semeio/fmudesign/create_design.py

@@ -121,7 +121,12 @@ def generate(self, inputdict: Mapping[str, Any]) -> None:
 
         # If background values used - read or generate
         if "background" in inputdict:
-            self.add_background(inputdict["background"], max_reals, rng)
+            self.add_background(
+                inputdict["background"],
+                max_reals,
+                rng,
+                correlation_iterations=inputdict.get("correlation_iterations", 0),
+            )
 
         sensitivity: SensitivityType
 
@@ -348,6 +353,7 @@ def add_background(
         back_dict: Mapping[str, Any] | None,
         max_values: int,
         rng: np.random.Generator,
+        correlation_iterations: int = 0,
     ) -> None:
         """Adding background as specified in dictionary.
         Either from external file or from distributions in background
@@ -357,13 +363,21 @@ def add_background(
             back_dict (OrderedDict): how to generate background values
             max_values (int): number of background values to generate
             rng (numpy.random.Generator): Random number generator instance
+            correlation_iterations (int): Number of permutations performed
+            on samples after Iman-Conover in an attempt to match observed
+            correlation to desired correlation as well as possible.
         """
         if back_dict is None:
             self.backgroundvalues = None
         elif "extern" in back_dict:
             self.backgroundvalues = _parameters_from_extern(back_dict["extern"])
         elif "parameters" in back_dict:
-            self._add_dist_background(back_dict, max_values, rng)
+            self._add_dist_background(
+                back_dict,
+                max_values,
+                rng,
+                correlation_iterations=correlation_iterations,
+            )
 
     def background_to_excel(
         self, filename: str, backgroundsheet: str = "Background"
@@ -442,7 +456,11 @@ def _fill_with_defaultvalues(self) -> None:
                 raise LookupError(f"No defaultvalues given for parameter {key} ")
 
     def _add_dist_background(
-        self, back_dict: Mapping[str, Any], numreal: int, rng: np.random.Generator
+        self,
+        back_dict: Mapping[str, Any],
+        numreal: int,
+        rng: np.random.Generator,
+        correlation_iterations: int,
     ) -> None:
         """Drawing background values from distributions
         specified in dictionary
@@ -462,7 +480,7 @@ def _add_dist_background(
             seedvalues=None,
             corrdict=back_dict["correlations"],
             rng=rng,
-            correlation_iterations=0,
+            correlation_iterations=correlation_iterations,
         )
 
         mc_backgroundvalues = mc_background.sensvalues

tests/fmudesign/test_designmatrix.py

@@ -86,18 +86,18 @@ def test_endpoint(tmpdir, monkeypatch):
 Generating sensitivity : contacts
 Added sensitivity : contacts
 Generating sensitivity : multz
-Wrote 10 samples from 'MULTZ_ILE' Distribution("loguniform", a=0.0001, b=1.0)
+Wrote 10 samples from 'MULTZ_ILE'
 Added sensitivity : multz
 Generating sensitivity : sens6
-Wrote 10 samples from 'PARAM5' Distribution("truncnorm", a=-2.0, b=2.0, loc=3.0, scale=1.0)
-Wrote 10 samples from 'PARAM6' Distribution("uniform", loc=0.0, scale=1.0)
-Wrote 10 samples from 'PARAM7' Distribution("triang", loc=1.0, scale=4.0, c=0.5)
-Wrote 10 samples from 'FAULT_SEAL' Distribution("uniform")
+Wrote 10 samples from 'PARAM5'
+Wrote 10 samples from 'PARAM6'
+Wrote 10 samples from 'PARAM7'
+Wrote 10 samples from 'FAULT_SEAL'
 Added sensitivity : sens6
 Generating sensitivity : sens7
 Sampling parameters in 'corr1': ['PARAM9', 'PARAM10', 'PARAM11', 'PARAM12']
 
-Warning: Correlation matrix 'corr1' is not consistent
+Warning: Correlation matrix 'corr1' is invalid
 Requirements:
   - Ones on the diagonal
   - Positive semi-definite matrix
@@ -117,10 +117,10 @@ def test_endpoint(tmpdir, monkeypatch):
 | PARAM10 |     0.74 | 1.00      |           |           |
 | PARAM11 |     0.11 | 0.74      | 1.00      |           |
 | PARAM12 |     0.00 | 0.00      | 0.00      | 1.00      |
-Wrote 30 samples from 'PARAM9' Distribution("lognorm", s=1.0, scale=Exp(Constant(0.0)))
-Wrote 30 samples from 'PARAM10' Distribution("uniform", loc=0.0, scale=1.0)
-Wrote 30 samples from 'PARAM11' Distribution("triang", loc=1.0, scale=4.0, c=0.5)
-Wrote 30 samples from 'PARAM12' Distribution("loguniform", a=1.0, b=10.0)
+Wrote 30 samples from 'PARAM9'
+Wrote 30 samples from 'PARAM10'
+Wrote 30 samples from 'PARAM11'
+Wrote 30 samples from 'PARAM12'
 Added sensitivity : sens7
 Generating sensitivity : sens8
 Added sensitivity : sens8
@@ -129,7 +129,8 @@ def test_endpoint(tmpdir, monkeypatch):
 Provided number of background values (11) is smaller than number of realisations for sensitivity ('sens7', 'p10_p90') and parameter PARAM15. Will be filled with default values.
 Provided number of background values (11) is smaller than number of realisations for sensitivity ('sens7', 'p10_p90') and parameter PARAM16. Will be filled with default values.
 A total of 91 realizations were generated
-Designmatrix written to generateddesignmatrix.xlsx"""
+Designmatrix written to generateddesignmatrix.xlsx
+"""
 
     assert result.stdout.split() == expected_output.split()
     assert Path("generateddesignmatrix.xlsx").exists  # Default output file