physioblocks 1.0.0__py3-none-any.whl

physioblocks/launcher/series.py

@@ -0,0 +1,165 @@
+# SPDX-FileCopyrightText: Copyright INRIA
+#
+# SPDX-License-Identifier: LGPL-3.0-only
+#
+# Copyright INRIA
+#
+# This file is part of PhysioBlocks, a library mostly developed by the
+# [Ananke project-team](https://team.inria.fr/ananke) at INRIA.
+#
+# Authors:
+# - Colin Drieu
+# - Dominique Chapelle
+# - François Kimmig
+# - Philippe Moireau
+#
+# PhysioBlocks is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free Software
+# Foundation, version 3 of the License.
+#
+# PhysioBlocks is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License along with
+# PhysioBlocks. If not, see <https://www.gnu.org/licenses/>.
+
+"""
+Defines function to handles series and simulation results
+"""
+
+import socket
+from dataclasses import dataclass
+from datetime import datetime
+from importlib.metadata import version
+from pathlib import Path
+
+import pandas as pd
+
+import physioblocks
+from physioblocks.launcher.constants import (
+    LAUNCHER_DATE_TIME_FORMAT,
+    LAUNCHER_HOSTNAME_SEPARATOR,
+    LAUNCHER_LOG_COLUMNS,
+    LAUNCHER_LOG_FILE_SEPARATOR,
+    LAUNCHER_REFERENCE_SEPARATOR,
+)
+
+
+@dataclass
+class SimulationInfo:
+    machine_name: str
+    "the mane of the machine running the simulation"
+    date_time: str
+    "the time stamp of the simulation run"
+    series: str
+    "the simulation serie"
+    number: str
+    "the simulation number"
+    version: str
+    "the PhysioBlocks version used"
+    message: str = ""
+    "a note associated with the simulation"
+
+    @property
+    def reference(self) -> str:
+        return str.join(
+            LAUNCHER_REFERENCE_SEPARATOR, [self.machine_name, self.series, self.number]
+        )
+
+    @property
+    def data_frame(self) -> pd.DataFrame:
+        return pd.DataFrame(
+            [
+                [
+                    self.date_time,
+                    self.machine_name,
+                    self.reference,
+                    self.version,
+                    self.message,
+                ]
+            ],
+            columns=LAUNCHER_LOG_COLUMNS,
+        )
+
+    def __str__(self) -> str:
+        return str.join(
+            LAUNCHER_LOG_FILE_SEPARATOR,
+            (
+                self.date_time,
+                self.machine_name,
+                self.reference,
+                self.version,
+                self.message,
+            ),
+        )
+
+
+def is_valid_reference_name(reference: str) -> bool:
+    dir_name_split = reference.split(LAUNCHER_REFERENCE_SEPARATOR)
+    return len(dir_name_split) >= 3 and str.isdigit(dir_name_split[-1])
+
+
+def is_valid_reference_dir_name(dir_name: str, series_name: str) -> bool:
+    dir_name_split = dir_name.split(LAUNCHER_REFERENCE_SEPARATOR)
+    dir_series_name = LAUNCHER_REFERENCE_SEPARATOR.join(dir_name_split[1:-1])
+    return is_valid_reference_name(dir_name) and dir_series_name == series_name
+
+
+def parse_reference_number(reference: str) -> tuple[str, str, int]:
+    split_ref = reference.split(LAUNCHER_REFERENCE_SEPARATOR)
+
+    if is_valid_reference_name(reference) is False:
+        raise ValueError(
+            str.format(
+                "{0} is not a valid simulation reference name.",
+                reference,
+            )
+        )
+
+    number = split_ref[-1]
+    serie = split_ref[-2]
+    machine = str.join(LAUNCHER_REFERENCE_SEPARATOR, split_ref[0:-2])
+
+    return machine, serie, int(number)
+
+
+def reference_follows(tested_reference: str, base_reference: str) -> bool:
+    # Return true if the base reference comes after (or is the same as)
+    # the tested reference
+    parsed_tested = parse_reference_number(tested_reference)
+    parsed_base = parse_reference_number(base_reference)
+    return parsed_tested[1] == parsed_base[1] and parsed_tested[2] >= parsed_base[2]
+
+
+def get_reference_number(serie_path: Path) -> str:
+    serie_name = serie_path.name
+    if serie_path.exists() is False:
+        raise FileNotFoundError(str.format("No series directory at {0}", serie_path))
+    numbers = [
+        int(d.name.split(LAUNCHER_REFERENCE_SEPARATOR)[-1])
+        for d in serie_path.iterdir()
+        if is_valid_reference_dir_name(d.name, serie_name) is True
+    ]
+    if len(numbers) > 0:
+        return str(max(numbers) + 1)
+
+    return str(1)
+
+
+def get_simulation_info(serie_path: Path, message: str) -> SimulationInfo:
+    number = get_reference_number(serie_path)
+
+    # get the machine name
+    host_name = socket.gethostname()
+    machine_name = host_name.split(LAUNCHER_HOSTNAME_SEPARATOR, 2)[0]
+
+    # get the current time stamp
+    time_stamp = datetime.now().strftime(LAUNCHER_DATE_TIME_FORMAT)
+
+    # get the PhysioBlocks version
+    lib_version = version(physioblocks.__name__)
+
+    return SimulationInfo(
+        machine_name, time_stamp, serie_path.name, number, lib_version, message
+    )

physioblocks/library/__init__.py

@@ -0,0 +1,27 @@
+# SPDX-FileCopyrightText: Copyright INRIA
+#
+# SPDX-License-Identifier: LGPL-3.0-only
+#
+# Copyright INRIA
+#
+# This file is part of PhysioBlocks, a library mostly developed by the
+# [Ananke project-team](https://team.inria.fr/ananke) at INRIA.
+#
+# Authors:
+# - Colin Drieu
+# - Dominique Chapelle
+# - François Kimmig
+# - Philippe Moireau
+#
+# PhysioBlocks is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free Software
+# Foundation, version 3 of the License.
+#
+# PhysioBlocks is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License along with
+# PhysioBlocks. If not, see <https://www.gnu.org/licenses/>.
+
+"""Define objects (blocks, function, etc) usable in PhysioBlocks configurations"""

physioblocks/library/aliases/blocks/c_block.json

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+{
+    "type": "block_description",
+    "model_type": "c_block",
+    "time": "time"
+}

physioblocks/library/aliases/blocks/rc_block.json

@@ -0,0 +1,5 @@
+{
+    "type": "block_description",
+    "model_type": "rc_block",
+    "time": "time"
+}

physioblocks/library/aliases/blocks/rcr_block.json

@@ -0,0 +1,5 @@
+{
+    "type": "block_description",
+    "model_type": "rcr_block",
+    "time": "time"
+}

physioblocks/library/aliases/blocks/spherical_cavity_block.json

@@ -0,0 +1,5 @@
+{
+    "type": "block_description",
+    "model_type": "spherical_cavity_block",
+    "time": "time"
+}

physioblocks/library/aliases/blocks/valve_rl_block.json

@@ -0,0 +1,5 @@
+{
+    "type": "block_description",
+    "model_type": "valve_rl_block",
+    "time": "time"
+}

physioblocks/library/aliases/flux/heart_flux_dof_couples.jsonc

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+// Define available flux - dof types couples
+{
+    "blood_flow": "blood_pressure"
+}

physioblocks/library/aliases/model_components/active_law_macro_huxley_two_moments.json

@@ -0,0 +1,5 @@
+{
+    "type": "model_description",
+    "model_type": "active_law_macro_huxley_two_moments",
+    "time": "time"
+}

physioblocks/library/aliases/model_components/rheology_fiber_additive.json

@@ -0,0 +1,5 @@
+{
+    "type": "model_description",
+    "model_type": "rheology_fiber_additive",
+    "time": "time"
+}

physioblocks/library/aliases/model_components/spherical_dynamics.json

@@ -0,0 +1,5 @@
+{
+    "type": "model_description",
+    "model_type": "spherical_dynamics",
+    "time": "time"
+}

physioblocks/library/aliases/model_components/velocity_law_hht.json

@@ -0,0 +1,5 @@
+{
+    "type": "model_description",
+    "model_type": "velocity_law_hht",
+    "time": "time"
+}

physioblocks/library/aliases/nets/circulation_alone_net.json

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+{
+    "type": "net",
+    "flux_dof_definitions": {"type": "heart_flux_dof_couples"},
+    "nodes": [
+        "aorta_proximal",
+        "aorta_distal",
+        "venous"
+    ],
+    "blocks": {
+        "circulation_aorta_proximal": {
+            "type": "rc_block",
+            "flux_type": "blood_flow",
+            "resistance": "aorta_proximal.resistance",
+            "capacitance": "aorta_proximal.capacitance",
+            "nodes": {
+                "1": "aorta_distal",
+                "2": "aorta_proximal"
+            }
+        },
+        "circulation_aorta_distal": {
+            "type": "rc_block",
+            "flux_type": "blood_flow",
+            "resistance": "aorta_distal.resistance",
+            "capacitance": "aorta_distal.capacitance",
+            "nodes": {
+                "1": "venous",
+                "2": "aorta_distal"
+            }
+        }
+    }
+}

physioblocks/library/aliases/nets/spherical_heart_net.json

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+{
+    "type": "net",
+    "flux_dof_definitions": {"type": "heart_flux_dof_couples"},
+    "nodes": [
+        "cavity",
+        "atrial",
+        "aorta_proximal",
+        "aorta_distal",
+        "venous"
+    ],
+    "blocks": {
+        "cavity": {
+            "type": "spherical_cavity_block",
+            "flux_type": "blood_flow",
+            "disp": "cavity.dynamics.disp",
+            "radius": "heart_radius",
+            "thickness": "heart_thickness",
+            "submodels": {
+                "dynamics": {
+                    "type": "spherical_dynamics",
+                    "fib_deform": "cavity.rheology.fib_deform",
+                    "pressure": "cavity.blood_pressure",
+                    "pressure_external": "pleural.pressure",
+                    "vel": "cavity.velocity_law.vel",
+                    "radius": "heart_radius",
+                    "thickness": "heart_thickness",
+                    "series_stiffness": "cavity.rheology.series_stiffness"
+                },
+                "velocity_law": {
+                    "type": "velocity_law_hht",
+                    "disp": "cavity.dynamics.disp"
+                },
+                "rheology": {
+                    "type": "rheology_fiber_additive",
+                    "disp": "cavity.dynamics.disp",
+                    "active_tension_discr": "cavity.rheology.active_law.active_tension_discr",
+                    "radius": "heart_radius",
+                    "submodels": {
+                        "active_law": {
+                            "type": "active_law_macro_huxley_two_moments",
+                            "fib_deform": "cavity.rheology.fib_deform",
+                            "contractility": "heart_contractility"
+                        }
+                    }
+                }
+            },
+            "nodes": {
+                "1": "cavity"
+            }
+        },
+        "valve_atrium": {
+            "type": "valve_rl_block",
+            "flux_type": "blood_flow",
+            "backward_conductance": "conductance_iso",
+            "nodes": {
+                "1": "atrial",
+                "2": "cavity"
+            }
+        },
+        "valve_arterial": {
+            "type": "valve_rl_block",
+            "flux_type": "blood_flow",
+            "backward_conductance": "conductance_iso",
+            "nodes": {
+                "1": "cavity",
+                "2": "aorta_proximal"
+            }
+        },
+        "capacitance_valve": {
+            "type": "c_block",
+            "flux_type": "blood_flow",
+            "nodes": {
+                "1": "cavity"
+            }
+        },
+        "circulation_aorta_proximal": {
+            "type": "rc_block",
+            "flux_type": "blood_flow",
+            "nodes": {
+                "1": "aorta_distal",
+                "2": "aorta_proximal"
+            }
+        },
+        "circulation_aorta_distal": {
+            "type": "rc_block",
+            "flux_type": "blood_flow",
+            "nodes": {
+                "1": "venous",
+                "2": "aorta_distal"
+            }
+        }
+    }
+}

physioblocks/library/aliases/simulations/circulation_alone_forward_simulation.jsonc

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+{
+    "type": "default_forward_simulation",
+    "net": {
+        "type": "circulation_alone_net",
+        "boundaries_conditions": {
+            "aorta_proximal": [
+                {
+                    "type": "condition",
+                    "condition_type": "blood_flow",
+                    "condition_id": "aorta_proximal.blood_flow"
+                }
+            ],
+            "venous": [
+                {
+                    "type": "condition",
+                    "condition_type": "blood_pressure",
+                    "condition_id": "venous.blood_pressure"
+                }
+            ]
+        }
+    },
+    "variables_magnitudes": {
+        "aorta_proximal.blood_pressure":1e5,
+        "aorta_distal.blood_pressure":1e5
+    },
+    "parameters": {
+        "heartbeat_duration": {"type": "product", "factors": [60.0] , "inverses": ["heart_rate"]},
+        "aorta_proximal.capacitance": 2.0e-10,      
+        "aorta_proximal.blood_flow": {
+            "type": "rescale_two_phases_function",
+            "rescaled_period": "heartbeat_duration",
+            "alpha": 0.8,
+            "reference_function": [
+                [0.0, "aorta_proximal.blood_flow.min"],
+                [0.075, "aorta_proximal.blood_flow.min"],
+                [0.134, "aorta_proximal.blood_flow.max"],
+                [0.142, "aorta_proximal.blood_flow.max"],
+                [0.281, "aorta_proximal.blood_flow.min"],
+                [0.9, "aorta_proximal.blood_flow.min"]
+            ],
+            "phases": [0, 0, 1, 1, 0]
+
+        },
+        // initialize the distal capacitance from the distal time constant and resistance (Cc = tc / Rc)
+        // Required parameters initialization is: "aorta_distal.time_constant"
+        "aorta_distal.capacitance": {
+            "type": "product",
+            "factors": ["aorta_distal.time_constant"],
+            "inverses": ["aorta_distal.resistance"]
+        }
+    },
+    "solver": {
+        "iteration_max": 2 // This problem is linear
+    }
+}

physioblocks/library/aliases/simulations/default_forward_simulation.jsonc

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+{
+    "type": "forward_simulation",
+    "time": {"type": "default_time"},
+    "solver": {
+        "type": "newton_method_solver"
+    }
+}

physioblocks/library/aliases/simulations/default_time.jsonc

@@ -0,0 +1,8 @@
+{
+    "type": "time",
+    // The parameter "start" and "end" must be provided
+    // "start":,
+    // "duration": ,
+    "step_size": 0.001,
+    "min_step": 6.25e-5
+}

physioblocks/library/aliases/simulations/newton_method_solver.json

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+{
+    "type": "newton_solver",
+    "tolerance": 1e-9,
+    "iteration_max": 10
+}

physioblocks/library/aliases/simulations/spherical_heart_forward_simulation.jsonc

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+{
+    "type": "default_forward_simulation",
+    "net": {
+        "type": "spherical_heart_net",
+        "boundaries_conditions": {
+            "atrial": [
+                {
+                    "type": "condition",
+                    "condition_type": "blood_pressure",
+                    "condition_id": "atrial.blood_pressure"
+                }
+            ],
+            "venous": [
+                {
+                    "type": "condition",
+                    "condition_type": "blood_pressure",
+                    "condition_id": "venous.blood_pressure"
+                }
+            ]
+        }
+    },
+    "variables_initialization": {
+        "valve_atrium.flux": 0.0,
+        "valve_arterial.flux": 0.0,
+        "cavity.dynamics.disp": 0.0,
+        "cavity.velocity_law.vel": 0.0,
+        "cavity.velocity_law.accel": 0.0,
+        "cavity.rheology.fib_deform": 0.0,
+        "cavity.rheology.active_law.active_stiffness": 1.0,
+        "cavity.rheology.active_law.active_energy_sqrt": 0.0,
+        "cavity.rheology.active_law.active_tension_discr": 0.0
+    },
+    "variables_magnitudes": {
+        "valve_atrium.flux": 1.0e-3,
+        "valve_arterial.flux": 1.0e-3,
+        "cavity.dynamics.disp": 0.01,
+        "cavity.rheology.fib_deform": 0.1,
+        "cavity.velocity_law.vel": 0.1,
+        "cavity.velocity_law.accel": 1.0,
+        "aorta_proximal.blood_pressure": 1.0e4,
+        "aorta_distal.blood_pressure": 1.0e4,
+        "cavity.blood_pressure": 1.0e4,
+        "cavity.rheology.active_law.active_stiffness": 1.0e5,
+        "cavity.rheology.active_law.active_energy_sqrt": 10.0,
+        "cavity.rheology.active_law.active_tension_discr": 1.0e4
+    },
+    "parameters": {
+
+        // "Inverse the heart_rate to get the heartbeat period in seconds"
+        // Required parameters initialization is:
+        // heart_rate in beat / min
+        "heartbeat_duration": {"type": "product", "factors": [60.0] , "inverses": ["heart_rate"]},
+        "pleural.pressure": 0.0,
+        "diastole_scaling_factor": 0.80,
+
+        // dynamics section
+        "cavity.dynamics.vol_mass": 1000.0,
+        "cavity.dynamics.damping_coef": 70.0,
+        
+        // velocity law section
+        "cavity.velocity_law.scheme_ts_hht": 0.4,
+
+        // rheology section
+        "cavity.rheology.series_stiffness": 100000000.0,
+        "cavity.rheology.damping_parallel": 70.0,
+
+        // active law section
+        "cavity.rheology.active_law.starling_abscissas": [
+            -0.1668,
+            -0.0073,
+            0.0534,
+            0.0969,
+            0.1326,
+            0.2016,
+            0.4663,
+            0.9187,
+            1.1762
+        ],
+        "cavity.rheology.active_law.starling_ordinates": [
+            0.0,
+            0.5614,
+            0.7748,
+            0.8933,
+            0.9618,
+            1.0,
+            1.0,
+            0.1075,
+            0.0
+        ],
+        "cavity.rheology.active_law.destruction_rate": 12.0,
+        "cavity.rheology.active_law.crossbridge_stiffness": 273000.0,
+
+        // Parametrize the active law activation
+        // Required parameters initialization are:
+        // heartbeat_duration
+        // active_law.activation.min
+        // active_law.activation.max
+        "active_law.activation.min": -20.0,
+        "active_law.activation.max": 35.0,
+        "cavity.rheology.active_law.activation": {
+            "type": "rescale_two_phases_function",
+            "rescaled_period": "heartbeat_duration",
+            "alpha": "diastole_scaling_factor",
+            "reference_function": [
+                [0.0, "active_law.activation.min"],
+                [0.027, "active_law.activation.min"],
+                [0.037, 0.0],
+                [0.145, "active_law.activation.max"],
+                [0.309, "active_law.activation.max"],
+                [0.417, 0.0],
+                [0.427, "active_law.activation.min"],
+                [0.9, "active_law.activation.min"]
+            ],
+            "phases": [0, 0, 1, 1, 1, 0, 0]
+        },
+
+        // Section to parametrize the atrial blood pressure
+        // Required parameters initialization are:
+        // heartbeat_duration
+        // atrial.blood_pressure.min
+        // atrial.blood_pressure.max
+        "atrial.blood_pressure": {
+            "type": "rescale_two_phases_function",
+            "rescaled_period": "heartbeat_duration",
+            "alpha": "diastole_scaling_factor",
+            "reference_function": [
+                [0.0, "atrial.blood_pressure.max"],
+                [0.02, "atrial.blood_pressure.max"],
+                [0.07, "atrial.blood_pressure.min"],
+                [0.84, "atrial.blood_pressure.min"],
+                [0.9, "atrial.blood_pressure.max"]
+            ],
+            "phases": [1, 1, 0, 1]
+        },
+
+        // valves section
+        "conductance_iso": 5e-12,
+        "valve_atrium.inductance": 1.0e3,
+        "valve_atrium.conductance": 9e-06,
+        "valve_arterial.inductance": 3.0e4,
+        "valve_arterial.conductance": 1.3e-05,
+        "capacitance_valve.capacitance": 5e-12,
+        "valve_atrium.scheme_ts_flux": 0.25,
+        "valve_arterial.scheme_ts_flux": 0.25,
+
+        // circulation section
+        "circulation_aorta_proximal.capacitance": 2.0e-10,
+        
+        // initialize the distal capacitance from the distal time constant and resistance (Cc = tc / Rc)
+        // Required parameters initialization is: "circulation_aorta_distal.time_constant"
+        "circulation_aorta_distal.capacitance": {
+            "type": "product",
+            "factors": ["circulation_aorta_distal.time_constant"],
+            "inverses": ["circulation_aorta_distal.resistance"]
+        }
+    }
+}

physioblocks/library/aliases/simulations/spherical_heart_with_respiration_forward_simulation.jsonc

@@ -0,0 +1,45 @@
+{
+    // Define a varying pleural pressure from a respiratory period
+    // on top of a default spherical heart forward simulation
+    // The required parameter in parent configuration are:
+    // pleural.pressure.min
+    // pleural.pressure.max
+    // respiration.period
+    "type": "spherical_heart_forward_simulation",
+    "parameters":{
+        // pleural.pressure.offset = (pleural.pressure.min + pleural.pressure.max) / 2
+        "pleural.pressure.offset": {
+            "type": "product",
+            "factors": [
+                {
+                    "type": "sum",
+                    "add" : ["pleural.pressure.min", "pleural.pressure.max"]
+                },
+                0.5
+            ]
+        },
+        // pleural.pressure.amplitude = pleural.pressure.max - pleural.pressure.offset
+        "pleural.pressure.amplitude": {
+            "type": "sum",
+            "add": [
+                "pleural.pressure.max"
+            ],
+            "subtract": [
+                "pleural.pressure.offset"
+            ]
+        },
+        // pleural.pressure.frequency = 1 / "respiration.period"
+        "pleural.pressure.frequency": {
+            "type": "product", 
+            "factors": [1.0], 
+            "inverses": ["respiration.period"]
+        },
+        "pleural.pressure": {
+            "type": "sinus_offset",
+            "offset_value": "pleural.pressure.offset",
+            "amplitude": "pleural.pressure.amplitude",
+            "frequency": "pleural.pressure.frequency",
+            "phase_shift": 0.0
+        }
+    }
+}