Mask entries in simulated SFS out if they are negative and return None

when all values are masked during evaluation of ll

gadma/code_generator/dadi_generator.py

@@ -227,6 +227,8 @@ def _print_dadi_simulation():
     ret_str = f"func_ex = dadi.Numerics.make_extrap_log_func"\
               f"({FUNCTION_NAME})\n"
     ret_str += "model = func_ex(p0, ns, pts)\n"
+    # check if some entries are negative - mask them out
+    ret_str += f"model.mask[np.where(model < 0)] = True\n"
     return ret_str
 
 

gadma/code_generator/moments_generator.py

@@ -176,6 +176,8 @@ def _print_moments_load_data(data_holder):
 
 def _print_moments_simulation():
     ret_str = f"model = {FUNCTION_NAME}(p0, ns)\n"
+    # check if some entries are negative - mask them out
+    ret_str += f"model.mask[np.where(model < 0)] = True\n"
     return ret_str
 
 

gadma/engines/dadi_engine.py

@@ -3,6 +3,7 @@
 from ..models import CustomDemographicModel, Epoch, Split
 from ..utils import DynamicVariable
 from .. import SFSDataHolder, dadi_available
+import numpy as np
 
 
 class DadiEngine(DadiOrMomentsEngine):
@@ -162,6 +163,8 @@ def simulate(self, values, ns, sequence_length, population_labels, pts):
         model = func_ex(values, ns, pts)
         if population_labels is not None:
             model.pop_ids = population_labels
+        # check if some entries are negative - mask them out
+        model.mask[np.where(model < 0)] = True
         # TODO: Nref
         return model
 

gadma/engines/dadi_moments_common.py

@@ -236,6 +236,12 @@ def evaluate(self, values, grid_sizes):
             raise ValueError(f"{self.id} engine could not process constrains "
                              "on demographic model parameters (bounds of time "
                              "splits) in not-multinom mode.")
+        # Check if masks intersection gives any values to work with
+        if np.all(np.logical_or(self.data.mask, model_sfs.mask)):
+            key = self._get_key(values, grid_sizes)
+            self.saved_add_info[key] = None
+            return None
+
         if not self.multinom:
             theta0_inv = self.get_N_ancestral_from_theta(1)
             if theta0_inv is None:

gadma/engines/moments_engine.py

@@ -231,6 +231,8 @@ def simulate(self, values, ns, sequence_length, population_labels,
         model = self._inner_func(values, ns, dt_fac)
         if population_labels is not None:
             model.pop_ids = population_labels
+        # check if some entries are negative - mask them out
+        model.mask[np.where(model < 0)] = True
         return model
 
     def get_N_ancestral(self, values, dt_fac=default_dt_fac):

gadma/optimizers/optimizer.py

@@ -629,4 +629,3 @@ def check_variables(self, variables):
                 print(var.domain)
             assert (isinstance(var, DiscreteVariable)
                     or np.all(var.domain != np.array([-np.inf, np.inf])))
-