File size: 6,535 Bytes
3a87e2b | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 | #!/usr/bin/env python3
"""
A minimal standalone example for simulating one SBML model with Tellurium.
Examples
--------
Use a model already stored in SysBio-Traj/Data:
python simulate_sbml.py \
--model-id BIOMD0000000013 \
--model-name Poolman2004 \
--start-time 0 \
--end-time 0.4 \
--num-timepoints 512
Use the initial_conditions.json file in the same model directory:
python simulate_sbml.py \
--model-id BIOMD0000000013 \
--model-name Poolman2004 \
--start-time 0 \
--end-time 0.4 \
--num-timepoints 512 \
--use-ic-json \
--output scripts/BIOMD0000000013_Poolman2004_simulated.csv
Use a custom SBML file directly:
python simulate_sbml.py \
--xml-file /path/to/model.xml \
--start-time 0 \
--end-time 100 \
--num-timepoints 512 \
--output /path/to/output.csv
"""
from __future__ import annotations
import argparse
import json
from pathlib import Path
import numpy as np
import pandas as pd
import tellurium as te
ROOT_DIR = Path(__file__).resolve().parents[1]
def parse_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(description="Simulate one SBML model.")
source_group = parser.add_mutually_exclusive_group(required=True)
source_group.add_argument(
"--xml-file",
type=Path,
help="Path to an SBML XML file.",
)
source_group.add_argument(
"--model-id",
help="Model ID under SysBio-Traj/Data, for example BIOMD0000000013.",
)
parser.add_argument(
"--model-name",
help="Model name used to resolve Data/<model_id>/<model_name>.xml.",
)
parser.add_argument("--start-time", type=float, required=True, help="Simulation start time.")
parser.add_argument("--end-time", type=float, required=True, help="Simulation end time.")
parser.add_argument(
"--num-timepoints",
type=int,
default=512,
help="Number of sampled time points.",
)
parser.add_argument(
"--output",
type=Path,
default=None,
help="Output CSV path. If omitted, the file is saved in the scripts directory.",
)
parser.add_argument(
"--ic-json",
type=Path,
default=None,
help="Path to a JSON file containing initial conditions.",
)
parser.add_argument(
"--use-ic-json",
action="store_true",
help="Use Data/<model_id>/initial_conditions.json.",
)
return parser.parse_args()
def resolve_xml_path(args: argparse.Namespace) -> Path:
if args.xml_file is not None:
return args.xml_file.resolve()
if not args.model_name:
raise ValueError("--model-name is required when --model-id is used.")
xml_path = ROOT_DIR / "Data" / args.model_id / f"{args.model_name}.xml"
return xml_path.resolve()
def resolve_output_path(args: argparse.Namespace, xml_path: Path) -> Path:
if args.output is not None:
return args.output.resolve()
if args.model_id and args.model_name:
filename = f"{args.model_id}_{args.model_name}_simulated.csv"
else:
filename = f"{xml_path.stem}_simulated.csv"
return (ROOT_DIR / "scripts" / filename).resolve()
def resolve_ic_json_path(args: argparse.Namespace) -> Path | None:
if args.ic_json is not None:
return args.ic_json.resolve()
if args.use_ic_json:
if not args.model_id:
raise ValueError("--use-ic-json can only be used together with --model-id.")
return (ROOT_DIR / "Data" / args.model_id / "initial_conditions.json").resolve()
return None
def load_initial_conditions(ic_json_path: Path | None) -> dict[str, float]:
if ic_json_path is None:
return {}
with ic_json_path.open("r", encoding="utf-8") as f:
payload = json.load(f)
if isinstance(payload, dict) and "initial_conditions" in payload:
payload = payload["initial_conditions"]
if not isinstance(payload, dict):
raise ValueError(f"Initial-condition JSON must be a dictionary: {ic_json_path}")
ic_map: dict[str, float] = {}
for key, value in payload.items():
if value is None:
continue
ic_map[str(key)] = float(value)
return ic_map
def set_model_value(rr, name: str, value: float) -> bool:
candidates = []
stripped = name.strip()
bare = stripped[1:-1] if stripped.startswith("[") and stripped.endswith("]") else stripped
for candidate in (stripped, bare, f"[{bare}]"):
if candidate not in candidates:
candidates.append(candidate)
for candidate in candidates:
try:
rr[candidate] = float(value)
return True
except Exception:
continue
return False
def apply_initial_conditions(rr, ic_map: dict[str, float]) -> None:
for name, value in ic_map.items():
ok = set_model_value(rr, name, value)
if not ok:
print(f"Warning: cannot set initial condition for '{name}', skipped.")
def normalize_column_name(name: str) -> str:
text = str(name).strip()
if text.startswith("[") and text.endswith("]"):
return text[1:-1]
return text
def simulate_sbml(
xml_path: Path,
output_path: Path,
start_time: float,
end_time: float,
num_timepoints: int,
ic_json_path: Path | None = None,
) -> Path:
rr = te.loadSBMLModel(str(xml_path))
ic_map = load_initial_conditions(ic_json_path)
if ic_map:
apply_initial_conditions(rr, ic_map)
result = rr.simulate(start_time, end_time, num_timepoints)
columns = [normalize_column_name(name) for name in result.colnames]
df = pd.DataFrame(np.asarray(result), columns=columns)
output_path.parent.mkdir(parents=True, exist_ok=True)
df.to_csv(output_path, index=False)
return output_path
def main() -> None:
args = parse_args()
xml_path = resolve_xml_path(args)
output_path = resolve_output_path(args, xml_path)
ic_json_path = resolve_ic_json_path(args)
if not xml_path.is_file():
raise FileNotFoundError(f"Cannot find SBML file: {xml_path}")
if ic_json_path is not None and not ic_json_path.is_file():
raise FileNotFoundError(f"Cannot find IC JSON file: {ic_json_path}")
saved_path = simulate_sbml(
xml_path=xml_path,
output_path=output_path,
start_time=args.start_time,
end_time=args.end_time,
num_timepoints=args.num_timepoints,
ic_json_path=ic_json_path,
)
print(f"Saved to: {saved_path}")
if __name__ == "__main__":
main()
|