[feature] The polar transport coefficient is now a function of time.

controlpanel.py

@@ -79,7 +79,7 @@ class JSONCodec():
             if json_obj["__class__"] == "ControlPanel":
                 del json_obj["__class__"]
                 return json_obj
-            # the two following elif blocks are for backward campatibility
+            # the following elif blocks are here for backward campatibility
             elif json_obj["__class__"] == "DiffusiveSignal":
                 del json_obj["__class__"]
                 D = json_obj["d_intracell"]
@@ -104,6 +104,15 @@ class JSONCodec():
                 obj.set(**json_obj)
                 obj.d_function = Constant(constant_value=d)
                 return obj
+            elif json_obj["__class__"] == \
+                    "SimpleUnidirectionalActiveTransport" and "p" in json_obj:
+                del json_obj["__class__"]
+                p = json_obj["p"]
+                del json_obj["p"]
+                obj = SimpleUnidirectionalActiveTransport()
+                obj.set(**json_obj)
+                obj.p_function = Constant(constant_value=p)
+                return obj
             for key, value in self.class_dict.items():
                 if json_obj["__class__"] == value:
                     del json_obj["__class__"]
@@ -179,8 +188,6 @@ def growth(simu):
             simu.start_time + (nb_input_samples - 1) *
                 simu.input_time_step / time_units["day"],
             nb_input_samples)
-#     activation_time_for_simu = \
-#         (simu.activation_time - simu.start_time) * time_units["day"]
     simu.cell_file = CellFile(
         nb_cells=simu.nb_cells,
         initial_CRD=simu.cell_diameter,

evolution_function.py

@@ -191,3 +191,11 @@ class FunctionHandler(Handler):
                                         info.object.d_evolution,
                                         info.object.d_function,
                                         "d_function")
+
+    def object_p_evolution_changed(self, info):
+        if not hasattr(info.object, "p_evolution"):
+            return None
+        self.replace_evolution_function(info.object,
+                                        info.object.p_evolution,
+                                        info.object.p_function,
+                                        "p_function")

transport.py

@@ -58,12 +58,12 @@ class UniformDiffusion(Transport):
 
     Of course, this medium is growing nonuniformly.
     """
-    time = 0
+    time = 0  # necessary for time-varying parameters
 
     D = Float(0.1,
               label="Diffusion coefficient (µm.s¯²)",
               desc="diffusion coefficient of the signal, in µm.s¯², "
-                   "constant along the whole file.")
+                   "uniform along the whole file.")
 
     # type of evolution function for the decay rate
     d_evolution = Enum(
@@ -130,6 +130,7 @@ class UniformDiffusion(Transport):
 
     def set_values(self, start, stop, num):
         """
+        Set the values of the time-varying parameters.
         """
         self.set_d_values(start, stop, num)
 
@@ -171,10 +172,62 @@ class SimpleUnidirectionalActiveTransport(Transport):
     Transport mechanism described in Grieneisen et al., 2012,
     doi: 10.1186/1752-0509-6-37
     """
-    p = Float(19,
-              label="Polar transport (µm.s¯¹)",
-              desc="coefficient accounting for the action of polar efflux "
-                   "carriers, in µm.s¯¹.")
+    time = 0  # necessary for time-varying parameters
+
+    # type of evolution function for the polar transport coefficient p
+    p_evolution = Enum(
+        "constant",
+        "exponential decay",
+        "log-normal",
+        "user-defined",
+        label="Evolution of the polar transport",
+        desc="type of evolution function for the polar transport coefficient"
+             "of the signal, coefficient accounting for the action of polar"
+             "efflux carriers, in µm.s¯¹.")
+
+    _function_dict = {
+        "constant": Constant,
+        "log-normal": LogNormal,
+        "exponential decay": Exponential,
+        "user-defined": UserDefined}
+
+    p_function = Instance(EvolutionFunction)
+
+    def _p_function_default(self):
+        return self._function_dict[self.p_evolution]()
+
+    # This dictionary is intended to the FunctionHandler instance assigned to
+    # the traits_view's handler attribute.
+    _dict_for_functionhandler = {
+        "evolution": "p_evolution",
+        "function": "p_function"}
+
+    # polar transport coefficient values
+    p_values = None
+
+    def compute_p_values(self, start, stop, num):
+        """
+        Compute the values taken by the polar transport coefficient during the
+        simulation.
+        """
+        X = np.linspace(start, stop, num)
+        return self.p_function.f(X)
+
+    def set_p_values(self, start, stop, num):
+        """
+        Set the values taken by the polar transport coefficient during the
+        simulation.
+        """
+        self.p_values = self.compute_p_values(start, stop, num)
+
+    @property
+    def p(self):
+        return self.p_values[self.time]
+
+    @p.setter
+    def p(self):
+        raise AttributeError("Sorry, the decay rate can not assigned that way."
+                             "Use the p_function trait instead.")
 
     q = Float(1,
               label="Permeability rate (µm.s¯¹)",
@@ -193,21 +246,51 @@ class SimpleUnidirectionalActiveTransport(Transport):
     carrier_orientation = Enum(
         "toward the cambium",
         "toward the xylem",
-        label="Corrier orientation",
+        label="Carrier orientation",
         desc="in which direction the carriers are oriented.")
 
     only_in_cambial_cells = Bool(
         label="Polar transport only in cambial cells",
         desc="if polar transport is limited to cambial cells.")
 
+    def set_values(self, start, stop, num):
+        """
+        Set the values of the time-varying parameters.
+        """
+        self.set_p_values(start, stop, num)
+
+    general_group = Group(Item('d'),
+                          Item('q'),
+                          Item('p_evolution'),
+                          springy=True)
+
+    function_group = Group(
+        Group(
+            Item('p_function',
+                 style='custom',
+                 springy=True,
+                 show_label=False
+                 ),
+            show_labels=False
+            ),
+        label="Definition of the evolution function",
+        springy=True,
+        show_border=True
+        )
+
     traits_view = View(
-        Item('p'),
-        Item('q'),
-        Item('d'),
-        # Item('s'),
-        Item('carrier_orientation'),
-        Item('only_in_cambial_cells'),
-        resizable=True)
+        Group(
+            general_group,
+            function_group,
+            # Item('plot_function', show_label = False),
+            # Item('s'),
+            Item('carrier_orientation'),
+            Item('only_in_cambial_cells'),
+            springy=True
+            ),
+        handler=FunctionHandler(),
+        resizable=True
+        )
 
 # end of the SimpleUnidirectionalActiveTransport class