HOTFIX: Un-Assigned Typing with StochSS Live!

spatialpy/core/boundarycondition.py

@@ -87,6 +87,8 @@ def __init__(self, xmin=None, xmax=None, ymin=None, ymax=None, zmin=None, zmax=N
         if type_id is not None and not isinstance(type_id, (int, str)):
             raise BoundaryConditionError("Type-ID must be of type int.")
         elif type_id is not None:
+            if "UnAssigned" in type_id:
+                raise BoundaryConditionError("'UnAssigned' is not a valid type_id")
             type_id = f"type_{type_id}"
         if target is None or not (isinstance(target, (str, Species)) or
                 type(target).__name__ == 'Species' or property in ('nu', 'rho', 'v')):

spatialpy/core/domain.py

@@ -68,13 +68,13 @@ def __init__(self, numpoints, xlim, ylim, zlim, rho0=1.0, c0=10, P0=None, gravit
 
         self.vol = numpy.zeros((numpoints), dtype=float)
         self.mass = numpy.zeros((numpoints), dtype=float)
-        self.type_id = numpy.array([None] * numpoints, dtype=object)
+        self.type_id = numpy.array(["type_UnAssigned"] * numpoints, dtype=object)
         self.nu = numpy.zeros((numpoints), dtype=float)
         self.c = numpy.zeros((numpoints), dtype=float)
         self.rho = numpy.zeros((numpoints), dtype=float)
         self.fixed = numpy.zeros((numpoints), dtype=bool)
         self.listOfTypeIDs = []
-        self.typeNdxMapping = OrderedDict()
+        self.typeNdxMapping = OrderedDict({"type_UnAssigned": 0})
         self.typeNameMapping = None
 
         self.rho0 = rho0
@@ -136,7 +136,7 @@ def compile_prep(self):
 
         :raises DomainError: If a type_id is not set or rho=0 for a particle.
         """
-        if self.type_id.tolist().count(None) > 0:
+        if self.type_id.tolist().count("type_UnAssigned") > 0:
             raise DomainError(f"Particles must be assigned a type_id.")
         if numpy.count_nonzero(self.rho) < len(self.rho):
             raise DomainError(f"Rho must be a positive value.")
@@ -184,7 +184,10 @@ def add_point(self, point, vol=0, mass=0, type_id=1, nu=0, fixed=False, rho=None
             if (char in string.punctuation and char != "_") or char == " ":
                 raise DomainError(f"Type_id cannot contain {char}")
         if type_id not in self.typeNdxMapping:
-            self.typeNdxMapping[type_id] = len(self.typeNdxMapping) + 1
+            if "UnAssigned" in type_id:
+                self.typeNdxMapping[type_id] = 0
+            else:
+                self.typeNdxMapping[type_id] = len(self.typeNdxMapping)
 
         if rho is None:
             rho = mass / vol
@@ -240,7 +243,10 @@ def set_properties(self, geometry_ivar, type_id, vol=None, mass=None, nu=None, r
             if (char in string.punctuation and char != "_") or char == " ":
                 raise DomainError(f"Type_id cannot contain '{char}'")
         if type_id not in self.typeNdxMapping:
-            self.typeNdxMapping[type_id] = len(self.typeNdxMapping) + 1
+            if "UnAssigned" in type_id:
+                self.typeNdxMapping[type_id] = 0
+            else:
+                self.typeNdxMapping[type_id] = len(self.typeNdxMapping)
         # apply the type to all points, set type for any points that match
         count = 0
         on_boundary = self.find_boundary_points()
@@ -807,7 +813,10 @@ def read_stochss_subdomain_file(self, filename, type_ids=None):
                         if (char in string.punctuation and char != "_") or char == " ":
                             raise DomainError(f"Type_id cannot contain {char}")
                     if type_id not in self.typeNdxMapping:
-                        self.typeNdxMapping[type_id] = len(self.typeNdxMapping) + 1
+                        if "UnAssigned" in type_id:
+                            self.typeNdxMapping[type_id] = 0
+                        else:
+                            self.typeNdxMapping[type_id] = len(self.typeNdxMapping)
 
                     self.type_id[int(ndx)] = type_id
 
@@ -834,13 +843,15 @@ def read_stochss_domain(cls, filename):
             obj = Domain(0, tuple(domain['x_lim']), tuple(domain['y_lim']), tuple(domain['z_lim']),
                         rho0=domain['rho_0'], c0=domain['c_0'], P0=domain['p_0'], gravity=domain['gravity'])
 
-            for particle in domain['particles']:
+            for i, particle in enumerate(domain['particles']):
                 try:
                     type_id = list(filter(
                         lambda d_type, t_ndx=particle['type']: d_type['typeID'] == t_ndx, domain['types']
                     ))[0]['name']
                 except IndexError:
                     type_id = particle['type']
+                if type_id == "Un-Assigned" or type_id == 0:
+                    type_id = "UnAssigned"
                 # StochSS backward compatability check for rho
                 rho = None if "rho" not in particle.keys() else particle['rho']
                 # StochSS backward compatability check for c

spatialpy/core/reaction.py

@@ -623,6 +623,8 @@ def validate(self, coverage="build", reactants=None, products=None, propensity_f
                         raise ReactionError("Type ids in restrict_to must be of type int or str.")
                     if type_id == "":
                         raise ReactionError("Type ids in restrict_to can't be an empty string.")
+                    if isinstance(type_id, str) and "UnAssigned" in type_id:
+                        raise ReactionError("'UnAssigned' is not a valid type_id.")
                     if coverage in ("all", "initialized"):
                         if not isinstance(type_id, str):
                             raise ReactionError("Type ids in restrict_to must be of type str.")

spatialpy/solvers/solver.py

@@ -312,9 +312,9 @@ def __get_param_defs(self):
     def __get_particle_inits(self, num_chem_species):
         init_particles = ""
         if self.model.domain.type_id is None:
-            self.model.domain.type_id = ["type 1"] * self.model.domain.get_num_voxels()
+            self.model.domain.type_id = ["type_1"] * self.model.domain.get_num_voxels()
         for i, type_id in enumerate(self.model.domain.type_id):
-            if type_id is None:
+            if "UnAssigned" in type_id:
                 errmsg = "Not all particles have been defined in a type. Mass and other properties must be defined"
                 raise SimulationError(errmsg)
             x = self.model.domain.coordinates()[i, 0]

spatialpy/stochss/stochss_export.py

@@ -173,12 +173,13 @@ def __build_element(stoich_species):
 def __get_particles(domain):
     s_particles = []
     for i, point in enumerate(domain.vertices):
+        type_id = domain.typeNdxMapping[domain.type_id[i]]
         s_particle = {"fixed":bool(domain.fixed[i]),
                       "mass":domain.mass[i],
                       "nu":domain.nu[i],
                       "particle_id":i,
                       "point":list(point),
-                      "type":int(domain.type_id[i]),
+                      "type":type_id,
                       "volume":domain.vol[i]}
 
         s_particles.append(s_particle)