Fixed bug with PointEvaluator (no sign argument in constructor).

ModelEngineering · Mar 25, 2024 · a8e9787 · a8e9787
1 parent eed9a92
commit a8e9787
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Showing 5 changed files with 60 additions and 38 deletions.
diff --git a/examples/Controlling-Glucose-Metabolis-in-Yeast.ipynb b/examples/Controlling-Glucose-Metabolis-in-Yeast.ipynb
diff --git a/src/controlSBML/control_sbml.py b/src/controlSBML/control_sbml.py
@@ -786,9 +786,17 @@ def setValue(val):
                 input_name=self.input_name,
                 output_name=self.output_name,
                 save_path=self.save_path)
-        designs = designer.design(kP_spec=kP_spec, kI_spec=kI_spec, kF_spec=kF_spec,
-            num_restart=num_restart, min_value=min_parameter_value, max_value=max_parameter_value,
-            num_coordinate=num_coordinate, is_greedy=is_greedy, is_report=is_report, num_process=num_process)   # type: ignore
+        designs = designer.design(
+            kP_spec=kP_spec,
+            kI_spec=kI_spec,
+            kF_spec=kF_spec,
+            num_restart=num_restart,
+            min_value=min_parameter_value,
+            max_value=max_parameter_value,
+            num_coordinate=num_coordinate,
+            is_greedy=is_greedy,
+            is_report=is_report,
+            num_process=num_process)   # type: ignore
         if designer.residual_mse is None:
             msgs.warn("No design found!")
             return DesignResult(timeseries=None, antimony_builder=None, designs=designs)

diff --git a/src/controlSBML/point_evaluator.py b/src/controlSBML/point_evaluator.py
@@ -9,10 +9,11 @@
 
 
 ##################################################################
+# FIXME: Need to specify the sign 
 class PointEvaluator(Evaluator):
     # Evaluates a point in the design space
-    def __init__(self, sbml_system:SBMLSystem, input_name:str, output_name:str, setpoint:float, times:np.array,
-                 is_greedy:bool=False):
+    def __init__(self, sbml_system:SBMLSystem, input_name:str, output_name:str, setpoint:float, 
+                 sign:float, times:np.array, is_greedy:bool=False):
         """
         Args:
             sbml_system (SBMLSystem): Should be a copy of the original system so it is light weight
@@ -28,6 +29,7 @@ def __init__(self, sbml_system:SBMLSystem, input_name:str, output_name:str, setp
         self.input_name = input_name
         self.output_name = output_name
         self.setpoint = setpoint
+        self.sign = sign
         self.times = times
         self.siso_evaluator = None
         self.is_greedy = is_greedy
@@ -77,9 +79,9 @@ def _calculateMse(self, **parameter_dct:dict)->Tuple[str, object]:
         max_output = SIZE_MARGIN*self.sbml_system._max_value_dct[self.output_name]
         min_output = self.sbml_system._min_value_dct[self.output_name]/SIZE_MARGIN
         try:
-            response_ts, _ = self.sbml_system.simulateSISOClosedLoop(setpoint=self.setpoint,
+            response_ts, builder = self.sbml_system.simulateSISOClosedLoop(setpoint=self.setpoint,
                         input_name=self.input_name, output_name=self.output_name,
-                        times=self.times,
+                        times=self.times, sign=self.sign,
                         is_steady_state=self.sbml_system.is_steady_state, inplace=False,
                         **parameter_dct)  # type: ignore
         except Exception as error:

diff --git a/src/controlSBML/siso_closed_loop_designer.py b/src/controlSBML/siso_closed_loop_designer.py
@@ -296,16 +296,14 @@ def getValue(val):
             else:
                 return float(val)
         #
-        point_evaluator = PointEvaluator(self.system.copy(), self.input_name, self.output_name, 
-                                            self.setpoint, self.times, is_greedy=is_greedy)
+        point_evaluator = PointEvaluator(self.system.copy(), self.input_name, self.output_name,
+                                            self.setpoint, self.sign, self.times, is_greedy=is_greedy)
         parallel_search = ParallelSearch(point_evaluator, grid.points, num_process=num_process, is_report=is_report) # type: ignore
         search_results = []
         for _ in range(num_restart):
             parallel_search.search()
             search_results.append(parallel_search.getSearchResults())
         if len(search_results) == 0:
-            # Why no results?
-            import pdb; pdb.set_trace()
             df = pd.DataFrame([[None, None, None, None, cn.DESIGN_RESULT_CANNOT_SIMULATE]],
                               columns=[CP_kP, CP_kI, CP_kF, cn.SCORE, cn.REASON])
             return DesignResult(dataframe=df)

diff --git a/tests/test_control_sbml.py b/tests/test_control_sbml.py
@@ -404,6 +404,9 @@ def testBug10(self):
         INPUT_NAME = "Mlc"
         OUTPUT_NAME = "EI_P"
         CTLSB.setSystem(input_name=INPUT_NAME, output_name=OUTPUT_NAME)
+        result = CTLSB.plotDesign(setpoint=0.0000003, kP_spec=1, kI_spec=1, times=TIMES, num_restart=1, sign=1,
+                                  is_plot=IS_PLOT)
+        self.assertEqual(result.designs.dataframe.loc[0, cn.REASON], cn.DESIGN_RESULT_CANNOT_SIMULATE)
         result = CTLSB.plotDesign(setpoint=0.0000003, kP_spec=0.1, times=TIMES, num_restart=1, sign=1,
                                   is_plot=IS_PLOT)
         self.assertEqual(result.designs.dataframe.loc[0, cn.REASON], cn.DESIGN_RESULT_CANNOT_SIMULATE)