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@blairlyons
blairlyons committed Dec 21, 2023
1 parent bdc7957 commit 3d6e9a5
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Showing 2 changed files with 83 additions and 74 deletions.
21 changes: 3 additions & 18 deletions simularium_readdy_models/actin/actin_analyzer.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1149,12 +1149,7 @@ def analyze_filament_length(
return np.array(filament_length)

@staticmethod
def analyze_bond_stretch(
trajectory,
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 Down Expand Up @@ -1209,12 +1204,7 @@ def analyze_bond_stretch(
return np.array(stretch_lat), np.array(stretch_long)

@staticmethod
def analyze_angle_stretch(
trajectory,
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 Down Expand Up @@ -1293,12 +1283,7 @@ def analyze_angle_stretch(
)

@staticmethod
def analyze_dihedral_stretch(
trajectory,
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 Down
136 changes: 80 additions & 56 deletions simularium_readdy_models/visualization/actin_visualization.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -263,10 +263,10 @@ def ACTIN_DISPLAY_DATA(longitudinal_bonds: bool) -> Dict[str, DisplayData]:

@staticmethod
def get_bond_stretch_plot(
trajectory: List[FrameData],
box_size: np.ndarray,
periodic_boundary: bool,
stride: int,
trajectory: List[FrameData],
box_size: np.ndarray,
periodic_boundary: bool,
stride: int,
times: np.ndarray,
) -> ScatterPlotData:
"""
Expand Down Expand Up @@ -296,10 +296,10 @@ def get_bond_stretch_plot(

@staticmethod
def get_angle_stretch_plot(
trajectory: List[FrameData],
box_size: np.ndarray,
periodic_boundary: bool,
stride: int,
trajectory: List[FrameData],
box_size: np.ndarray,
periodic_boundary: bool,
stride: int,
times: np.ndarray,
) -> ScatterPlotData:
"""
Expand Down Expand Up @@ -333,10 +333,10 @@ def get_angle_stretch_plot(

@staticmethod
def get_dihedral_stretch_plot(
trajectory: List[FrameData],
box_size: np.ndarray,
periodic_boundary: bool,
stride: int,
trajectory: List[FrameData],
box_size: np.ndarray,
periodic_boundary: bool,
stride: int,
times: np.ndarray,
) -> ScatterPlotData:
"""
Expand Down Expand Up @@ -417,23 +417,36 @@ def generate_actin_compression_plots(
peak_asym = []
contour_length = []
total_steps = len(axis_positions)
control_pts = ReaddyPostProcessor.linear_fiber_control_points(axis_positions, 10.)
control_pts = ReaddyPostProcessor.linear_fiber_control_points(
axis_positions, 10.0
)
for time_ix in range(total_steps):
perp_dist.append(CompressionAnalyzer.get_average_distance_from_end_to_end_axis(
polymer_trace=control_pts[time_ix][0],
))
bending_energy.append(1000. * CompressionAnalyzer.get_bending_energy_from_trace(
polymer_trace=control_pts[time_ix][0],
))
non_coplanarity.append(CompressionAnalyzer.get_third_component_variance(
polymer_trace=control_pts[time_ix][0],
))
peak_asym.append(CompressionAnalyzer.get_asymmetry_of_peak(
polymer_trace=control_pts[time_ix][0],
))
contour_length.append(CompressionAnalyzer.get_contour_length_from_trace(
polymer_trace=control_pts[time_ix][0],
))
perp_dist.append(
CompressionAnalyzer.get_average_distance_from_end_to_end_axis(
polymer_trace=control_pts[time_ix][0],
)
)
bending_energy.append(
1000.0
* CompressionAnalyzer.get_bending_energy_from_trace(
polymer_trace=control_pts[time_ix][0],
)
)
non_coplanarity.append(
CompressionAnalyzer.get_third_component_variance(
polymer_trace=control_pts[time_ix][0],
)
)
peak_asym.append(
CompressionAnalyzer.get_asymmetry_of_peak(
polymer_trace=control_pts[time_ix][0],
)
)
contour_length.append(
CompressionAnalyzer.get_contour_length_from_trace(
polymer_trace=control_pts[time_ix][0],
)
)
times = timestep * np.arange(total_steps)
plots["scatter"] += [
ScatterPlotData(
Expand All @@ -444,9 +457,9 @@ def generate_actin_compression_plots(
ytraces={
"<<<": np.zeros(times.shape),
">>>": 85.0 * np.ones(times.shape),
"filament" : np.array(perp_dist),
"filament": np.array(perp_dist),
},
render_mode="lines"
render_mode="lines",
),
ScatterPlotData(
title="Bending Energy",
Expand All @@ -456,9 +469,9 @@ def generate_actin_compression_plots(
ytraces={
"<<<": np.zeros(times.shape),
">>>": 10.0 * np.ones(times.shape),
"filament" : np.array(bending_energy),
"filament": np.array(bending_energy),
},
render_mode="lines"
render_mode="lines",
),
ScatterPlotData(
title="Non-coplanarity",
Expand All @@ -468,9 +481,9 @@ def generate_actin_compression_plots(
ytraces={
"<<<": np.zeros(times.shape),
">>>": 0.03 * np.ones(times.shape),
"filament" : np.array(non_coplanarity),
"filament": np.array(non_coplanarity),
},
render_mode="lines"
render_mode="lines",
),
ScatterPlotData(
title="Peak Asymmetry",
Expand All @@ -480,9 +493,9 @@ def generate_actin_compression_plots(
ytraces={
"<<<": np.zeros(times.shape),
">>>": 0.5 * np.ones(times.shape),
"filament" : np.array(peak_asym),
"filament": np.array(peak_asym),
},
render_mode="lines"
render_mode="lines",
),
ScatterPlotData(
title="Contour Length",
Expand All @@ -492,17 +505,17 @@ def generate_actin_compression_plots(
ytraces={
"<<<": 480 * np.ones(times.shape),
">>>": 505 * np.ones(times.shape),
"filament" : np.array(contour_length),
"filament": np.array(contour_length),
},
render_mode="lines"
render_mode="lines",
),
]
return plots

@staticmethod
def add_plots_to_trajectory(
trajectory: TrajectoryData,
plots: Dict[str,List[ScatterPlotData or HistogramPlotData]]
trajectory: TrajectoryData,
plots: Dict[str, List[ScatterPlotData or HistogramPlotData]],
) -> TrajectoryData:
reader = ScatterPlotReader()
for plot in plots["scatter"]:
Expand Down Expand Up @@ -609,25 +622,25 @@ def simularium_trajectory(
spatial_units=UnitData("nm"),
)
return ReaddyConverter(data)._data

@staticmethod
def analyze_and_visualize_trajectory(
output_name: str,
total_steps: float,
parameters: Dict[str, Any],
save_pickle: bool = False
parameters: Dict[str, Any],
save_pickle: bool = False,
) -> TrajectoryData:
"""
Do all visualization, annotation, and metric calculation on an actin trajectory
and save it as a simularium file.
"""
# get analysis parameters
plot_actin_structure = parameters.get("plot_actin_structure", False)
plot_actin_compression = parameters.get("plot_actin_compression", False)
visualize_edges = parameters.get("visualize_edges", False)
visualize_normals = parameters.get("visualize_normals", False)
plot_actin_structure = parameters.get("plot_actin_structure", False)
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=output_name + ".h5",
Expand All @@ -636,15 +649,23 @@ def analyze_and_visualize_trajectory(
saved_frames=1e3,
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
time_step = max(1, total_steps * 1E-3) * parameters.get("internal_timestep", 0.1) * 1E-6 # ms
if visualize_normals or visualize_control_pts or visualize_edges or plot_actin_structure or plot_actin_compression:
periodic_boundary = parameters.get("periodic_boundary", False)
time_step = (
max(1, total_steps * 1e-3) * parameters.get("internal_timestep", 0.1) * 1e-6
) # ms
if (
visualize_normals
or visualize_control_pts
or visualize_edges
or plot_actin_structure
or plot_actin_compression
):
periodic_boundary = parameters.get("periodic_boundary", False)
post_processor = ReaddyPostProcessor(
trajectory=ReaddyLoader(
h5_file_path=output_name + ".h5",
Expand Down Expand Up @@ -676,12 +697,15 @@ def analyze_and_visualize_trajectory(
],
polymer_number_range=5,
)
axis_positions, new_chain_ids = post_processor.linear_fiber_axis_positions(
(
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
plots = None
if plot_actin_compression:
Expand Down Expand Up @@ -711,7 +735,7 @@ def analyze_and_visualize_trajectory(
new_chain_ids,
axis_positions,
)

# save simularium file
BinaryWriter.save(
trajectory_data=traj_data,
Expand Down

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