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Feature/simple readdy example #25

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Feature/simple readdy example #25

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c9ed173
initial ReaddySimpleProcess runs, todo viz and test output
blairlyons May 4, 2023
17477e8
added radius to monomer ports schema
blairlyons May 5, 2023
ac22236
viz simple readdy output and fixed issues
blairlyons May 5, 2023
63bf439
turn ReaddySimpleProcess into a test that uses Vivarium-ReaDDy's Read…
blairlyons May 17, 2023
ac65c76
clean up and lint
blairlyons May 17, 2023
81c7687
Merge branch 'maintenance' into feature/simple-readdy-example
blairlyons May 17, 2023
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4 changes: 2 additions & 2 deletions env.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ name: vivarium-models
channels:
- conda-forge
dependencies:
- python=3.8
- conda-forge::readdy
- python=3.9
- readdy==2.0.9
- pip
- pip:
- "vivarium_models @ git+https://github.com/simularium/vivarium-models.git"
1 change: 1 addition & 0 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
"vivarium-core",
"vivarium_medyan @ git+https://github.com/vivarium-collective/vivarium-MEDYAN.git",
"vivarium_cytosim @ git+https://github.com/vivarium-collective/vivarium-cytosim.git",
"vivarium_readdy @ git+https://github.com/vivarium-collective/vivarium-ReaDDy.git@monomers-ports",
"simularium_readdy_models @ git+https://github.com/simularium/readdy-models.git",
"simulariumio",
]
Expand Down
51 changes: 3 additions & 48 deletions vivarium_models/processes/readdy_actin_process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@
ActinAnalyzer,
)
from simularium_readdy_models import ReaddyUtil
from vivarium_models.util import create_monomer_update, format_monomer_results
from vivarium_readdy import create_monomer_update, monomer_ports_schema
from ..util import format_monomer_results
from vivarium_models.library.scan import Scan

NAME = "ReaDDy_actin"
Expand Down Expand Up @@ -69,53 +70,7 @@ def __init__(self, parameters=None):
self.readdy_simulation = actin_simulation.simulation

def ports_schema(self):
return {
"monomers": {
"box_center": {
"_default": np.array([1000.0, 0.0, 0.0]),
"_updater": "set",
"_emit": True,
},
"box_size": {
"_default": 500.0,
"_updater": "set",
"_emit": True,
},
"topologies": {
"*": {
"type_name": {
"_default": "",
"_updater": "set",
"_emit": True,
},
"particle_ids": {
"_default": [],
"_updater": "set",
"_emit": True,
},
}
},
"particles": {
"*": {
"type_name": {
"_default": "",
"_updater": "set",
"_emit": True,
},
"position": {
"_default": np.zeros(3),
"_updater": "set",
"_emit": True,
},
"neighbor_ids": {
"_default": [],
"_updater": "set",
"_emit": True,
},
}
},
}
}
return monomer_ports_schema

def initial_state(self, config=None):
# TODO: make this more general
Expand Down
134 changes: 39 additions & 95 deletions vivarium_models/processes/simularium_emitter.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
from typing import Any, Dict
from typing import Any, Dict, List

from vivarium.core.emitter import Emitter

Expand All @@ -10,14 +10,16 @@
AgentData,
MetaData,
UnitData,
DisplayData,
DISPLAY_TYPE,
)


class SimulariumEmitter(Emitter):
def __init__(self, config: Dict[str, str]) -> None:
super().__init__(config)
self.configuration_data = None
self.saved_data: Dict[float, Dict[str, Any]] = {}
self.saved_data: List[Dict[str, Any]] = []

def emit(self, data: Dict[str, Any]) -> None:
"""
Expand All @@ -29,17 +31,14 @@ def emit(self, data: Dict[str, Any]) -> None:
self.configuration_data = data["data"]
assert "processes" in self.configuration_data, "please emit processes"
if data["table"] == "history":
emit_data = data["data"]
time = emit_data["time"]
self.saved_data[time] = {
key: value for key, value in emit_data.items() if key not in ["time"]
}
self.saved_data.append(data["data"])

def get_simularium_fibers(self, time, fibers, actin_radius, trajectory):
def get_simularium_fibers(self, time, fibers, trajectory):
"""
Shape fiber state data into Simularium fiber agents
"""
n_agents = 0
actin_radius = 3.0
time_index = len(trajectory["times"])
trajectory["times"].append(time)
trajectory["unique_ids"].append([])
Expand All @@ -59,7 +58,7 @@ def get_simularium_fibers(self, time, fibers, actin_radius, trajectory):
trajectory["radii"].append(n_agents * [actin_radius])
return trajectory

def get_simularium_monomers(self, time, monomers, actin_radius, trajectory):
def get_simularium_monomers(self, time, monomers, trajectory):
"""
Shape monomer state data into Simularium agents
"""
Expand All @@ -68,13 +67,21 @@ def get_simularium_monomers(self, time, monomers, actin_radius, trajectory):
trajectory["unique_ids"].append([])
trajectory["type_names"].append([])
trajectory["positions"].append([])
trajectory["radii"].append([])
edge_ids = []
edge_positions = []
for particle_id in monomers["particles"]:
particle = monomers["particles"][particle_id]
trajectory["unique_ids"][time_index].append(int(particle_id))
trajectory["type_names"][time_index].append(particle["type_name"])
# HACK needed until simulariumio default display data fix
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@ascibisz ascibisz May 24, 2023 •
edited
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I thought the default display data fix got merged in simulariumio, unless there's another default display data bug then the one I'm thinking of?

if particle["type_name"] not in trajectory["display_data"]:
trajectory["display_data"][particle["type_name"]] = DisplayData(
name=particle["type_name"],
display_type=DISPLAY_TYPE.SPHERE,
)
trajectory["positions"][time_index].append(np.array(particle["position"]))
trajectory["radii"][time_index].append(particle["radius"])
# visualize edges between particles
for neighbor_id in particle["neighbor_ids"]:
neighbor_id_str = str(neighbor_id)
Expand All @@ -101,7 +108,6 @@ def get_simularium_monomers(self, time, monomers, actin_radius, trajectory):
trajectory["unique_ids"][time_index] += [1000 + i for i in range(n_edges)]
trajectory["type_names"][time_index] += ["edge" for edge in range(n_edges)]
trajectory["positions"][time_index] += n_edges * [[0.0, 0.0, 0.0]]
trajectory["radii"].append(n_agents * [actin_radius])
trajectory["radii"][time_index] += n_edges * [1.0]
trajectory["n_subpoints"].append(n_agents * [0])
trajectory["n_subpoints"][time_index] += n_edges * [2]
Expand Down Expand Up @@ -167,7 +173,7 @@ def get_agent_data_from_jagged_lists(trajectory, scale_factor) -> AgentData:
Shape a dictionary of jagged lists into a Simularium AgentData object
"""
return AgentData(
times=np.arange(len(trajectory["times"])),
times=trajectory["times"],
n_agents=np.array(trajectory["n_agents"]),
viz_types=SimulariumEmitter.fill_df(
pd.DataFrame(trajectory["viz_types"]), 1000.0
Expand All @@ -187,17 +193,17 @@ def get_agent_data_from_jagged_lists(trajectory, scale_factor) -> AgentData:
).to_numpy(dtype=int),
subpoints=scale_factor
* SimulariumEmitter.get_subpoints_numpy_array(trajectory),
display_data=trajectory["display_data"],
)

@staticmethod
def get_simularium_converter(
trajectory, box_dimensions, scale_factor
trajectory, box_dimensions, scale_factor, time_units, spatial_units
) -> TrajectoryConverter:
"""
Shape a dictionary of jagged lists into a Simularium TrajectoryData object
and provide it to a TrajectoryConverter for conversion
"""
spatial_units = UnitData("nm")
spatial_units.multiply(1 / scale_factor)
return TrajectoryConverter(
TrajectoryData(
Expand All @@ -207,36 +213,18 @@ def get_simularium_converter(
agent_data=SimulariumEmitter.get_agent_data_from_jagged_lists(
trajectory, scale_factor
),
time_units=UnitData("count"),
time_units=time_units,
spatial_units=spatial_units,
)
)

@staticmethod
def get_active_simulator(choices) -> str:
"""
Use choices from state to determine which simulator ran
"""
medyan_active = "medyan_active" in choices and choices["medyan_active"]
readdy_active = "readdy_active" in choices and choices["readdy_active"]
cytosim_active = "cytosim_active" in choices and choices["cytosim_active"]

if medyan_active and not readdy_active and not cytosim_active:
return "medyan"
elif readdy_active and not medyan_active and not cytosim_active:
return "readdy"
elif cytosim_active and not medyan_active and not readdy_active:
return "cytosim"

def get_data(self) -> dict:
"""
Save the accumulated timeseries history of "emitted" data to file
"""
if "readdy_actin" in self.configuration_data:
actin_radius = self.configuration_data["readdy_actin"]["actin_radius"]
else:
actin_radius = 3.0 # TODO add to MEDYAN config
box_dimensions = None
box_size = None
time_units = None
spatial_units = None
trajectory = {
"times": [],
"n_agents": [],
Expand All @@ -247,66 +235,22 @@ def get_data(self) -> dict:
"radii": [],
"n_subpoints": [],
"subpoints": [],
"display_data": {},
}
times = list(self.saved_data.keys())
times.sort()
vizualize_time_index = 0
for time, state in self.saved_data.items():
print(f"time = {time}")
index = times.index(time)
prev_simulator = "none"
if index > 0:
prev_simulator = SimulariumEmitter.get_active_simulator(
self.saved_data[times[index - 1]]["choices"]
)
current_simulator = SimulariumEmitter.get_active_simulator(state["choices"])
print(f"prev_simulator = {prev_simulator}")
print(f"current_simulator = {current_simulator}")
"""visualize the first frame in the simulator that started first
then subsequent frames according the the simulator that ran
right before that time point"""
if prev_simulator == "none":
if current_simulator == "medyan" or current_simulator == "cytosim":
print(f" visualize current {current_simulator}")
if box_dimensions is None:
box_dimensions = np.array(state["fibers_box_extent"])
trajectory = self.get_simularium_fibers(
vizualize_time_index,
state["fibers"],
actin_radius,
trajectory,
)
vizualize_time_index += 1
if current_simulator == "readdy":
print(" visualize current readdy")
trajectory = self.get_simularium_monomers(
vizualize_time_index,
state["monomers"],
actin_radius,
trajectory,
)
vizualize_time_index += 1
elif prev_simulator == "medyan" or prev_simulator == "cytosim":
print(f" visualize previous {prev_simulator}")
if box_dimensions is None:
box_dimensions = np.array(state["fibers_box_extent"])
trajectory = self.get_simularium_fibers(
vizualize_time_index,
state["fibers"],
actin_radius,
trajectory,
)
vizualize_time_index += 1
elif prev_simulator == "readdy":
print(" visualize readdy")
trajectory = self.get_simularium_monomers(
vizualize_time_index,
state["monomers"],
actin_radius,
trajectory,
)
vizualize_time_index += 1
for state in self.saved_data:
if box_size is None:
box_size = state["monomers"]["box_size"]
if time_units is None:
time_units = state["time_units"]
if spatial_units is None:
spatial_units = state["spatial_units"]
trajectory = self.get_simularium_monomers(
state["time"],
state["monomers"],
trajectory,
)
simularium_converter = SimulariumEmitter.get_simularium_converter(
trajectory, box_dimensions, 0.1
trajectory, box_size, 0.1, UnitData(time_units), UnitData(spatial_units)
)
simularium_converter.save("out/actin_test")
simularium_converter.save("out/test")
return {"simularium_converter": simularium_converter}
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