add entry_noise option (#41)

Enable/Disable noise on entry nodes

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+### v0.1.6
+* New parameter `entry_noise` to enable or disable the endfeet activity on entry nodes. (#41)
+* Add helper script to load archngv graphs and convert them in pickle binary format. (#40)
+
 ### v0.1.5
 * Lazy import of mpi4py module (#27)
 

astrovascpy/bloodflow.py

@@ -547,6 +547,11 @@ def simulate_ou_process(
         - np.ndarray: (nb_iteration, n_edges) radius values at each time-step for each edge.
     """
 
+    if "entry_noise" not in params:
+        raise BloodFlowError("Missing boolean parameter: entry_noise")
+    if not isinstance(params["entry_noise"], bool):
+        raise BloodFlowError("The parameter entry_noise must be true or false")
+
     nb_iteration = round(simulation_time / time_step)
     # nb_iteration_noise = number of time_steps before relaxation starts:
     nb_iteration_noise = round(relaxation_start / time_step)
@@ -587,6 +592,13 @@ def simulate_ou_process(
             if radii is not None:
                 graph.edge_properties.loc[end_df.index, "radius"] = radii[:, time_it]
 
+            if params["entry_noise"]:
+                radii_at_entry_edges = graph.edge_properties["radius"].iloc[input_edge].to_numpy()
+            else:
+                radii_at_entry_edges = (
+                    graph.edge_properties["radius_origin"].iloc[input_edge].to_numpy()
+                )
+
             radii_at_entry_edges = graph.edge_properties["radius"].iloc[input_edge].to_numpy()
             input_flows = entry_speed[time_it] * np.pi * radii_at_entry_edges**2
         else:

astrovascpy/typing.py

@@ -38,6 +38,8 @@ class VasculatureParams(TypedDict):
 
     Args:
 
+        entry_noise: Boolean value to enable or disable the endfeet activity on entry nodes.
+
         threshold_r: radius (µm) threshold. A radius smaller than the threshold is considered a capillary. A radius bigger than the threshold is considered an artery.
 
         c_cap: constant used in the ROU parameter calibration for capillaries
@@ -62,6 +64,7 @@ class VasculatureParams(TypedDict):
     blood_viscosity: float
     base_pressure: float
 
+    entry_noise: NotRequired[bool]
     c_cap: NotRequired[float]
     c_art: NotRequired[float]
     threshold_r: NotRequired[float]

astrovascpy/version.py

@@ -9,5 +9,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-VERSION = "0.1.5"
+VERSION = "0.1.6"
 version = VERSION

examples/data/params.yaml

@@ -11,6 +11,8 @@ max_nb_inputs: 3 # maximum number of inputs to inject flow/pressure into vascula
 
 base_pressure: 1.33e-3  # reference pressure in g * um^{-1} * s^{-2}. At resting state equal to the external pressure
 
+# Enable/Disable endfeet activity on entry nodes.
+entry_noise: true
 
 ### OU calibration parameters
 

tests/test_bloodflow.py

@@ -36,6 +36,7 @@ def params():
         "max_nb_inputs": 3,
         "depth_ratio": 0.05,
         "vasc_axis": 1,
+        "entry_noise": True,
         "threshold_r": 3,
         "max_r_capill": 1.38,
         "t_2_max_capill": 2.7,