Added option to change parameters after compilation

Author: fabriciocravo

for_local_use.py

@@ -1,17 +1,26 @@
+import dateutil.rrule
+
 from mobspy import *
 import numpy as np
 
 if __name__ == '__main__':
 
-    A = BaseSpecies()
-    B, C = New(A)
+    A, B = BaseSpecies()
+    A + B >> Zero [1]
+
+    A(200), B(200)
+    Sim = Simulation(A | B)
+    Sim.level = -1
+    descr = Sim.compile()
+    Sim.plot_data = False
+    Sim.duration = 30 * u.hour
+    Sim.volume = 1*u.m**3
+    Sim.run()
 
-    A.a1, A.a2, A.a3
+    assert Sim._parameters_for_sbml['volume'][0] > 100
+    assert Sim.fres['Time'][-1] > 100
 
-    B + C >> Zero [lambda r1, r2: 100 if A(r1) == A(r2) else 0]
 
-    S = Simulation(B | C)
-    print(S.compile())
 
 
 

mobspy/modules/unit_handler.py

@@ -94,12 +94,13 @@ def convert_counts(quantity, volume, dimension):
     return converted_quantity
 
 
-def check_dimension(dimension, value):
+def check_dimension(dimension, value, error_context=False):
     """
         Checks for dimension consistency. It "stores" the first dimension it was given by returning it
 
         :param dimension: (int) model's dimension (1D, 2D, 3D ...)
         :param value: (int) dimension value being analysed
+        :param error_context: (bool or str) context of the error if dimensions are not consistent
 
         :raise simlog.error: If dimensions are not consistent through the given units (units in 1D with 2D mixed)
 
@@ -109,17 +110,22 @@ def check_dimension(dimension, value):
         dimension = int(value)
     else:
         if dimension != int(value):
-            simlog.error('The dimensions are not consistent. There are at least two units given for different '
-                         'dimension models')
+            message = 'The dimensions are not consistent. There are at least two units given for different ' \
+                      'dimension models.'
+            if error_context:
+                message = message + '\n ' + error_context
+            simlog.error(message)
     return dimension
 
 
-def extract_length_dimension(unit_string, dimension, reaction_order=None):
+def extract_length_dimension(unit_string, dimension, reaction_order=None, context=False):
     """
         Extracts the volume dimension from a Quantity object from Pint
 
         :param unit_string: (str) unit in str format
         :param dimension: (int) model's dimension (1D, 2D, 3D ...)
+        :param reaction_order: (int) number of reactants in a reaction (for dimensional consistency in rates)
+        :param context: (bool or str) context of the error if dimensions are not consistent
     """
     temp_list = unit_string.split()
     try:
@@ -131,12 +137,12 @@ def extract_length_dimension(unit_string, dimension, reaction_order=None):
         return False
     if temp_list[position + 1] == '**':
         if reaction_order is None:
-            dimension = check_dimension(dimension, temp_list[position + 2])
+            dimension = check_dimension(dimension, temp_list[position + 2], context)
         else:
             temp_int = int(int(temp_list[position + 2])/(reaction_order - 1))
-            dimension = check_dimension(dimension, temp_int)
+            dimension = check_dimension(dimension, temp_int, context)
     else:
-        dimension = check_dimension(dimension, 1)
+        dimension = check_dimension(dimension, 1, context)
 
     return dimension
 

mobspy/parameter_scripts/parameter_reader.py

@@ -9,6 +9,8 @@
 import numpy as np
 import mobspy.simulation_logging.log_scripts as simlog
 from pint import Quantity
+import mobspy.modules.unit_handler as uh
+import inspect
 
 
 def read_json(json_file_name):
@@ -84,6 +86,27 @@ def __convert_unit_parameters(params):
                 params[u] = str(params[u])
 
 
+def convert_time_parameters_after_compilation(value):
+    """
+        This function converts the duration if the model was already compiled
+    """
+    if isinstance(value, Quantity):
+        if str(value.dimensionality) == '[time]':
+            value = value.convert('second').magnitude
+    return value
+
+def convert_volume_after_compilation(dimension, parameters_for_sbml, value):
+    if isinstance(value, Quantity):
+        message = 'Error at '
+        context = inspect.stack()[2].code_context[0][:-1]
+        message += context + '\n The dimension is set to tree at the moment of the compilation if not specified' \
+                             ' beforehand \n Please set a volume in the correct dimension before compilation'
+        uh.extract_length_dimension(str(value.dimensionality), dimension, context=message)
+
+    value = uh.convert_volume(value, dimension)
+    parameters_for_sbml['volume'] = (value, f'dimensionless')
+    return value
+
 def parameter_process(params):
     __convert_unit_parameters(params)
     __name_output_file(params)

mobspy/simulation.py

@@ -150,6 +150,8 @@ def __init__(self, model, names=None, parameters=None, plot_parameters=None):
         self.model_parameters = {}
         self.sbml_data_list = []
         self._parameter_list_of_dic = []
+        self._is_compiled = False
+        self.dimension = None
 
         # Must copy to avoid reference assignment
         self.model = List_Species(model)
@@ -197,6 +199,9 @@ def compile(self, verbose=True):
 
             :param verbose: (bool) = print or not the results of the compilation
         """
+        if self.dimension is None:
+            self.dimension = 3
+
         simlog.global_simlog_level = self.parameters['level']
         simlog.debug('Compiling model')
 
@@ -253,6 +258,8 @@ def compile(self, verbose=True):
 
         self._list_of_parameters = [self.parameters]
 
+        self._is_compiled = True
+
         if self.model_string != '':
             return self.model_string
 
@@ -409,7 +416,7 @@ def __setattr__(self, name, value):
                       'initial_duration', '_reactions_set', '_list_of_models', '_list_of_parameters',
                       '_context_not_active', '_species_counts', '_assigned_species_list', '_conditional_event',
                       '_end_condition', 'orthogonal_vector_structure', 'model_parameters', 'fres',
-                      'sbml_data_list', '_parameter_list_of_dic']
+                      'sbml_data_list', '_parameter_list_of_dic', '_is_compiled', 'dimension']
 
         plotted_flag = False
         if name in white_list:
@@ -423,6 +430,12 @@ def __setattr__(self, name, value):
         if not plotted_flag:
             example_parameters = get_example_parameters()
             if name in example_parameters.keys():
+                # If the model is already compiled, the change in parameters should be faster
+                if self._is_compiled:
+                    value = pr.convert_time_parameters_after_compilation(value)
+                if self._is_compiled and name == 'volume':
+                    value = pr.convert_volume_after_compilation(self.dimension, self._parameters_for_sbml, value)
+
                 if name == 'duration':
                     if type(value) == bool:
                         simlog.error(f'MobsPy has received an invalid trigger type: {type(value)} \n' +
@@ -640,7 +653,6 @@ def __init__(self, S1, S2):
     def __add__(self, other):
         return SimulationComposition(self, other)
 
-    # FIX THIS
     def __setattr__(self, name, value):
         white_list = ['list_of_simulations', 'results', 'base_sim', 'fres']
         broad_cast_parameters = ['level', 'method', 'volume']

test_plot_images/deterministic_tree.png

@@ -1237,6 +1237,23 @@ def test_matching_characteristic_rate():
     assert compare_model(S.compile(), 'test_tools/model_43.txt')
 
 
+def test_changes_after_compilation():
+    A, B = BaseSpecies()
+    A + B >> Zero [1]
+
+    A(200), B(200)
+    Sim = Simulation(A | B)
+    Sim.level = -1
+    descr = Sim.compile()
+    Sim.plot_data = False
+    Sim.duration = 30 * u.hour
+    Sim.volume = 1*u.m**3
+    Sim.run()
+
+    assert Sim._parameters_for_sbml['volume'][0] > 100
+    assert Sim.fres['Time'][-1] > 100
+
+
 
 # This is here because pytest is slow - but this script works fine with pytest. Just make sure that the
 # python version in terminal is above 3.10
@@ -1256,7 +1273,7 @@ def test_matching_characteristic_rate():
              test_conversion_outside, test_first_characteristic_in_reacting_species, test_model_reference,
              test_sbml_generation, test_multi_sim_sbml, test_inline_comment,
              test_with_statement_any_and_species_characteristics, test_with_statement_on_any_and_event,
-             test_matching_characteristic_rate]
+             test_matching_characteristic_rate, test_changes_after_compilation]
 
 sub_test = test_list