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Actin compression plots visualization #26

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merged 6 commits into from
Dec 21, 2023
Merged

Actin compression plots visualization #26

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c5e8027
updating plots to use subcell-analysis for compression metrics
blairlyons Dec 20, 2023
283785d
move visualization out of main actin script for reusability, debugged…
blairlyons Dec 21, 2023
fabad3f
log clock time
blairlyons Dec 21, 2023
bdc7957
a few fixes and tweaks
blairlyons Dec 21, 2023
3d6e9a5
lint
blairlyons Dec 21, 2023
26629d5
try to fix manifest
blairlyons Dec 21, 2023
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106 changes: 9 additions & 97 deletions examples/actin/docker/src/actin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,23 +3,17 @@

import os
import argparse
import time

import numpy as np
import pandas
import psutil

from subcell_analysis.readdy import (
ReaddyLoader,
ReaddyPostProcessor,
)
from simulariumio import BinaryWriter

from simularium_readdy_models.actin import (
FiberData,
ActinSimulation,
ActinGenerator,
ActinTestData,
ActinStructure,
)
from simularium_readdy_models.visualization import ActinVisualization
from simularium_readdy_models import ReaddyUtil
Expand Down Expand Up @@ -114,98 +108,10 @@ def report_hardware_usage():
)


def analyze_results(parameters, save_pickle=False):
# get analysis parameters
plot_actin_compression = parameters.get("plot_actin_compression", False)
visualize_edges = parameters.get("visualize_edges", False)
visualize_normals = parameters.get("visualize_normals", False)
visualize_control_pts = parameters.get("visualize_control_pts", False)

# convert to simularium
traj_data = ActinVisualization.simularium_trajectory(
path_to_readdy_h5=parameters["name"] + ".h5",
box_size=parameters["box_size"],
total_steps=parameters["total_steps"],
time_multiplier=1e-3, # assume 1e3 recorded steps
longitudinal_bonds=bool(parameters.get("longitudinal_bonds", True)),
)

# load different views of ReaDDy data
post_processor = None
fiber_chain_ids = None
axis_positions = None
new_chain_ids = None
if visualize_normals or visualize_control_pts or plot_actin_compression or visualize_edges:
periodic_boundary = parameters.get("periodic_boundary", False)
post_processor = ReaddyPostProcessor(
trajectory=ReaddyLoader(
h5_file_path=parameters["name"] + ".h5",
min_time_ix=0,
max_time_ix=-1,
time_inc=1,
timestep=100.0,
save_pickle_file=save_pickle,
).trajectory(),
box_size=parameters["box_size"],
periodic_boundary=periodic_boundary,
)
if visualize_normals or visualize_control_pts or plot_actin_compression:
fiber_chain_ids = post_processor.linear_fiber_chain_ids(
start_particle_phrases=["pointed"],
other_particle_types=[
"actin#",
"actin#ATP_",
"actin#mid_",
"actin#mid_ATP_",
"actin#fixed_",
"actin#fixed_ATP_",
"actin#mid_fixed_",
"actin#mid_fixed_ATP_",
"actin#barbed_",
"actin#barbed_ATP_",
"actin#fixed_barbed_",
"actin#fixed_barbed_ATP_",
],
polymer_number_range=5,
)
if visualize_normals or visualize_control_pts:
axis_positions, new_chain_ids = post_processor.linear_fiber_axis_positions(
fiber_chain_ids=fiber_chain_ids,
ideal_positions=ActinStructure.mother_positions[2:5],
ideal_vector_to_axis=ActinStructure.vector_to_axis(),
)

# create plots
if plot_actin_compression:
print("plot actin compression")
traj_data.plots = ActinVisualization.generate_actin_compression_plots(
post_processor,
fiber_chain_ids,
temperature_c=parameters["temperature_C"],
)

# add annotation objects to the spatial data
traj_data = ActinVisualization.add_spatial_annotations(
traj_data,
post_processor,
visualize_edges,
visualize_normals,
visualize_control_pts,
new_chain_ids,
axis_positions,
)

# save simularium file
BinaryWriter.save(
trajectory_data=traj_data,
output_path=parameters["name"] + ".h5",
validate_ids=False,
)


def main():
args = parse_args()
parameters = setup_parameters(args)
start_time = time.time()
actin_simulation = ActinSimulation(
parameters=parameters,
record=True,
Expand All @@ -217,8 +123,14 @@ def main():
timestep=actin_simulation.parameters.get("internal_timestep", 0.1),
show_summary=False,
)
print("Run time: %s seconds " % (time.time() - start_time))
report_hardware_usage()
analyze_results(actin_simulation.parameters, args.save_pickle)
ActinVisualization.analyze_and_visualize_trajectory(
actin_simulation.parameters["name"],
actin_simulation.parameters["total_steps"],
actin_simulation.parameters,
args.save_pickle,
)


if __name__ == "__main__":
Expand Down
Binary file modified examples/actin/template.xlsx
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3 changes: 1 addition & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -144,10 +144,9 @@ ignore = [
".cookiecutter.yaml",
"*docs/*",
"*.ipynb",
"*examples/*",
"*examples/**",
"*tests/**",
"environment.yml",
"examples/*",
]

[tool.mypy]
Expand Down
52 changes: 24 additions & 28 deletions simularium_readdy_models/actin/actin_analyzer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1149,7 +1149,7 @@ def analyze_filament_length(
return np.array(filament_length)

@staticmethod
def analyze_bond_stretch(monomer_data, box_size, periodic_boundary, stride=1):
def analyze_bond_stretch(trajectory, box_size, periodic_boundary, stride=1):
"""
Get the difference in bond length from ideal
for lateral and longitudinal actin bonds.
Expand All @@ -1163,22 +1163,18 @@ def analyze_bond_stretch(monomer_data, box_size, periodic_boundary, stride=1):
ActinStructure.mother_positions[2] - ActinStructure.mother_positions[0]
)
print("Analyzing bond stretch...")
for time_index in range(0, len(monomer_data), stride):
for time_index in range(0, len(trajectory), stride):
stretch_lat.append([])
stretch_long.append([])
new_time_index = math.floor(time_index / stride)
filament = monomer_data[time_index]["topologies"][0]["particle_ids"]
filament = trajectory[time_index].topologies[0].particle_ids
for index in range(len(filament) - 2):
particle = monomer_data[time_index]["particles"][filament[index]]
particle_lat = monomer_data[time_index]["particles"][
filament[index + 1]
]
particle_long = monomer_data[time_index]["particles"][
filament[index + 2]
]
type_name = particle["type_name"]
type_name_lat = particle_lat["type_name"]
type_name_long = particle_long["type_name"]
particle = trajectory[time_index].particles[filament[index]]
particle_lat = trajectory[time_index].particles[filament[index + 1]]
particle_long = trajectory[time_index].particles[filament[index + 2]]
type_name = particle.type_name
type_name_lat = particle_lat.type_name
type_name_long = particle_long.type_name
if (
"fixed" in type_name
or "fixed" in type_name_lat
Expand All @@ -1187,9 +1183,9 @@ def analyze_bond_stretch(monomer_data, box_size, periodic_boundary, stride=1):
stretch_lat[new_time_index].append(0.0)
stretch_long[new_time_index].append(0.0)
continue
pos = particle["position"]
pos_lat = particle_lat["position"]
pos_long = particle_long["position"]
pos = particle.position
pos_lat = particle_lat.position
pos_long = particle_long.position
if periodic_boundary:
pos_lat = ReaddyUtil.get_non_periodic_boundary_position(
pos, pos_lat, box_size
Expand All @@ -1208,7 +1204,7 @@ def analyze_bond_stretch(monomer_data, box_size, periodic_boundary, stride=1):
return np.array(stretch_lat), np.array(stretch_long)

@staticmethod
def analyze_angle_stretch(monomer_data, box_size, periodic_boundary, stride=1):
def analyze_angle_stretch(trajectory, box_size, periodic_boundary, stride=1):
"""
Get the difference in angles (degrees) from ideal
for actin angles between:
Expand All @@ -1223,24 +1219,24 @@ def analyze_angle_stretch(monomer_data, box_size, periodic_boundary, stride=1):
ideal_angle_lat_long = ActinStructure.actin_to_actin_angle(True, False, True)
ideal_angle_long_long = ActinStructure.actin_to_actin_angle(False, False, True)
print("Analyzing angle stretch...")
for time_index in range(0, len(monomer_data), stride):
for time_index in range(0, len(trajectory), stride):
result_lat_lat.append([])
result_lat_long.append([])
result_long_long.append([])
new_time_index = math.floor(time_index / stride)
filament = monomer_data[time_index]["topologies"][0]["particle_ids"]
filament = trajectory[time_index].topologies[0].particle_ids
for index in range(len(filament) - 4):
particles = []
positions = []
fixed = False
for d in range(5):
particles.append(
monomer_data[time_index]["particles"][filament[index + d]]
trajectory[time_index].particles[filament[index + d]]
)
if "fixed" in particles[d]["type_name"]:
if "fixed" in particles[d].type_name:
fixed = True
break
positions.append(particles[d]["position"])
positions.append(particles[d].position)
if d > 0 and periodic_boundary:
positions[d] = ReaddyUtil.get_non_periodic_boundary_position(
positions[d - 1], positions[d], box_size
Expand Down Expand Up @@ -1287,7 +1283,7 @@ def analyze_angle_stretch(monomer_data, box_size, periodic_boundary, stride=1):
)

@staticmethod
def analyze_dihedral_stretch(monomer_data, box_size, periodic_boundary, stride=1):
def analyze_dihedral_stretch(trajectory, box_size, periodic_boundary, stride=1):
"""
Get the difference in dihedral angles (degrees) from ideal
for actin angles between:
Expand All @@ -1305,23 +1301,23 @@ def analyze_dihedral_stretch(monomer_data, box_size, periodic_boundary, stride=1
False, False, False, True
)
print("Analyzing dihedral stretch...")
for time_index in range(0, len(monomer_data), stride):
for time_index in range(0, len(trajectory), stride):
result_lat_lat_lat.append([])
result_long_long_long.append([])
new_time_index = math.floor(time_index / stride)
filament = monomer_data[time_index]["topologies"][0]["particle_ids"]
filament = trajectory[time_index].topologies[0].particle_ids
for index in range(len(filament) - 6):
particles = []
positions = []
fixed = False
for d in range(7):
particles.append(
monomer_data[time_index]["particles"][filament[index + d]]
trajectory[time_index].particles[filament[index + d]]
)
if "fixed" in particles[d]["type_name"]:
if "fixed" in particles[d].type_name:
fixed = True
break
positions.append(particles[d]["position"])
positions.append(particles[d].position)
if d > 0 and periodic_boundary:
positions[d] = ReaddyUtil.get_non_periodic_boundary_position(
positions[d - 1], positions[d], box_size
Expand Down
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