Module wtracker.sim.config
View Source
from __future__ import annotations
from dataclasses import dataclass, field
import math
from wtracker.utils.config_base import ConfigBase
from wtracker.utils.frame_reader import FrameReader
@dataclass
class TimingConfig(ConfigBase):
"""
Configuration for timing parameters of the experiment.
These parameters should not change between different experiments.
This class affects the timings of the simulation.
"""
experiment_config: ExperimentConfig = field(repr=False)
"""The configuration of the experiment parameters."""
px_per_mm: int = field(init=False)
mm_per_px: float = field(init=False)
frames_per_sec: int = field(init=False)
ms_per_frame: float = field(init=False)
imaging_time_ms: float
imaging_frame_num: int = field(init=False)
pred_time_ms: float
pred_frame_num: int = field(init=False)
moving_time_ms: float
moving_frame_num: int = field(init=False)
camera_size_mm: tuple[float, float]
camera_size_px: tuple[int, int] = field(init=False)
micro_size_mm: tuple[float, float]
micro_size_px: tuple[int, int] = field(init=False)
def __post_init__(self):
self.frames_per_sec = self.experiment_config.frames_per_sec
self.ms_per_frame = self.experiment_config.ms_per_frame
self.imaging_frame_num = math.ceil(self.imaging_time_ms / self.ms_per_frame)
self.pred_frame_num = math.ceil(self.pred_time_ms / self.ms_per_frame)
self.moving_frame_num = math.ceil(self.moving_time_ms / self.ms_per_frame)
self.mm_per_px = self.experiment_config.mm_per_px
self.px_per_mm = self.experiment_config.px_per_mm
self.camera_size_px = (
round(self.px_per_mm * self.camera_size_mm[0]),
round(self.px_per_mm * self.camera_size_mm[1]),
)
self.micro_size_px = (
round(self.px_per_mm * self.micro_size_mm[0]),
round(self.px_per_mm * self.micro_size_mm[1]),
)
del self.experiment_config # experiment_config was temporary, only for the constructor
@property
def cycle_frame_num(self) -> int:
return self.imaging_frame_num + self.moving_frame_num
@property
def cycle_time_ms(self) -> float:
return self.cycle_frame_num * self.ms_per_frame
@dataclass
class ExperimentConfig(ConfigBase):
"""
Configuration for the experiment parameters.
These parameters can change between different experiments.
"""
name: str
"""Experiment name"""
num_frames: int
"""total number of frames of the experiment"""
frames_per_sec: float
"""Number of frames per second that the experiment was recorded at"""
orig_resolution: tuple[int, int]
"""Original resolution of the frames in pixels, in format (h, w)"""
px_per_mm: float
"""Number of pixels in a single millimeter"""
init_position: tuple[int, int]
"""The initial position of the center of the platform, in pixels (x, y) format.
Platform's initial position should point to the worm, or close to it."""
comments: str = ""
"""Additional comments about the experiment"""
mm_per_px: float = field(init=False)
"""Number of millimeters in a single pixel"""
ms_per_frame: float = field(init=False)
"""Number of milliseconds per frame"""
def __post_init__(self):
self.ms_per_frame = 1000 / self.frames_per_sec
self.mm_per_px = 1 / self.px_per_mm
@classmethod
def from_frame_reader(
cls,
reader: FrameReader,
name: str,
frames_per_sec: int,
px_per_mm: float,
init_position: tuple[int, int],
) -> ExperimentConfig:
return ExperimentConfig(
name=name,
num_frames=len(reader),
frames_per_sec=frames_per_sec,
orig_resolution=reader.frame_size,
px_per_mm=px_per_mm,
init_position=init_position,
)
Classes
ExperimentConfig
class ExperimentConfig(
name: 'str',
num_frames: 'int',
frames_per_sec: 'float',
orig_resolution: 'tuple[int, int]',
px_per_mm: 'float',
init_position: 'tuple[int, int]',
comments: 'str' = ''
)
Configuration for the experiment parameters.
These parameters can change between different experiments.
View Source
@dataclass
class ExperimentConfig(ConfigBase):
"""
Configuration for the experiment parameters.
These parameters can change between different experiments.
"""
name: str
"""Experiment name"""
num_frames: int
"""total number of frames of the experiment"""
frames_per_sec: float
"""Number of frames per second that the experiment was recorded at"""
orig_resolution: tuple[int, int]
"""Original resolution of the frames in pixels, in format (h, w)"""
px_per_mm: float
"""Number of pixels in a single millimeter"""
init_position: tuple[int, int]
"""The initial position of the center of the platform, in pixels (x, y) format.
Platform's initial position should point to the worm, or close to it."""
comments: str = ""
"""Additional comments about the experiment"""
mm_per_px: float = field(init=False)
"""Number of millimeters in a single pixel"""
ms_per_frame: float = field(init=False)
"""Number of milliseconds per frame"""
def __post_init__(self):
self.ms_per_frame = 1000 / self.frames_per_sec
self.mm_per_px = 1 / self.px_per_mm
@classmethod
def from_frame_reader(
cls,
reader: FrameReader,
name: str,
frames_per_sec: int,
px_per_mm: float,
init_position: tuple[int, int],
) -> ExperimentConfig:
return ExperimentConfig(
name=name,
num_frames=len(reader),
frames_per_sec=frames_per_sec,
orig_resolution=reader.frame_size,
px_per_mm=px_per_mm,
init_position=init_position,
)
Ancestors (in MRO)
- wtracker.utils.config_base.ConfigBase
Class variables
comments
Static methods
from_frame_reader
def from_frame_reader(
reader: 'FrameReader',
name: 'str',
frames_per_sec: 'int',
px_per_mm: 'float',
init_position: 'tuple[int, int]'
) -> 'ExperimentConfig'
View Source
@classmethod
def from_frame_reader(
cls,
reader: FrameReader,
name: str,
frames_per_sec: int,
px_per_mm: float,
init_position: tuple[int, int],
) -> ExperimentConfig:
return ExperimentConfig(
name=name,
num_frames=len(reader),
frames_per_sec=frames_per_sec,
orig_resolution=reader.frame_size,
px_per_mm=px_per_mm,
init_position=init_position,
)
load_json
def load_json(
path: 'str' = None
) -> 'T'
Load the class from a JSON file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the JSON file. | None |
Returns:
| Type | Description |
|---|---|
| ConfigBase | The class loaded from the JSON file. |
View Source
@classmethod
def load_json(cls: type[T], path: str = None) -> T:
"""
Load the class from a JSON file.
Args:
path (str): The path to the JSON file.
Returns:
ConfigBase: The class loaded from the JSON file.
"""
if path is None:
path = UserPrompt.open_file(
title=f"Open {cls.__name__} File",
file_types=[("json", ".json")],
)
with open(path, "r") as f:
data = json.load(f)
obj = cls.__new__(cls)
obj.__dict__.update(data)
return obj
load_pickle
def load_pickle(
path: 'str' = None
) -> 'T'
Load the class from a pickle file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the pickle file. | None |
Returns:
| Type | Description |
|---|---|
| None | The class loaded from the pickle file. |
View Source
@classmethod
def load_pickle(cls: type[T], path: str = None) -> T:
"""
Load the class from a pickle file.
Args:
path (str): The path to the pickle file.
Returns:
The class loaded from the pickle file.
"""
if path is None:
path = UserPrompt.open_file(
title=f"Open {cls.__name__} File",
file_types=[("pickle", ".pkl")],
)
return pickle_load_object(path)
Methods
save_json
def save_json(
self,
path: 'str' = None
)
Saves the class as JSON file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the output JSON file. | None |
View Source
def save_json(self, path: str = None):
"""
Saves the class as JSON file.
Args:
path (str): The path to the output JSON file.
"""
if path is None:
path = UserPrompt.save_file(
title=f"Save {type(self).__name__} As",
file_types=[("json", ".json")],
defaultextension=".json",
)
with open(path, "w") as f:
json.dump(self.__dict__, f, indent=4)
save_pickle
def save_pickle(
self,
path: 'str' = None
) -> 'None'
Saves the class as a pickle file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the output pickle file. | None |
View Source
def save_pickle(self, path: str = None) -> None:
"""
Saves the class as a pickle file.
Args:
path (str): The path to the output pickle file.
"""
if path is None:
path = UserPrompt.save_file(
title=f"Save {type(self).__name__} As",
file_types=[("pickle", ".pkl")],
defaultextension=".pkl",
)
pickle_save_object(self, path)
TimingConfig
class TimingConfig(
experiment_config: 'ExperimentConfig',
imaging_time_ms: 'float',
pred_time_ms: 'float',
moving_time_ms: 'float',
camera_size_mm: 'tuple[float, float]',
micro_size_mm: 'tuple[float, float]'
)
Configuration for timing parameters of the experiment.
These parameters should not change between different experiments. This class affects the timings of the simulation.
View Source
@dataclass
class TimingConfig(ConfigBase):
"""
Configuration for timing parameters of the experiment.
These parameters should not change between different experiments.
This class affects the timings of the simulation.
"""
experiment_config: ExperimentConfig = field(repr=False)
"""The configuration of the experiment parameters."""
px_per_mm: int = field(init=False)
mm_per_px: float = field(init=False)
frames_per_sec: int = field(init=False)
ms_per_frame: float = field(init=False)
imaging_time_ms: float
imaging_frame_num: int = field(init=False)
pred_time_ms: float
pred_frame_num: int = field(init=False)
moving_time_ms: float
moving_frame_num: int = field(init=False)
camera_size_mm: tuple[float, float]
camera_size_px: tuple[int, int] = field(init=False)
micro_size_mm: tuple[float, float]
micro_size_px: tuple[int, int] = field(init=False)
def __post_init__(self):
self.frames_per_sec = self.experiment_config.frames_per_sec
self.ms_per_frame = self.experiment_config.ms_per_frame
self.imaging_frame_num = math.ceil(self.imaging_time_ms / self.ms_per_frame)
self.pred_frame_num = math.ceil(self.pred_time_ms / self.ms_per_frame)
self.moving_frame_num = math.ceil(self.moving_time_ms / self.ms_per_frame)
self.mm_per_px = self.experiment_config.mm_per_px
self.px_per_mm = self.experiment_config.px_per_mm
self.camera_size_px = (
round(self.px_per_mm * self.camera_size_mm[0]),
round(self.px_per_mm * self.camera_size_mm[1]),
)
self.micro_size_px = (
round(self.px_per_mm * self.micro_size_mm[0]),
round(self.px_per_mm * self.micro_size_mm[1]),
)
del self.experiment_config # experiment_config was temporary, only for the constructor
@property
def cycle_frame_num(self) -> int:
return self.imaging_frame_num + self.moving_frame_num
@property
def cycle_time_ms(self) -> float:
return self.cycle_frame_num * self.ms_per_frame
Ancestors (in MRO)
- wtracker.utils.config_base.ConfigBase
Static methods
load_json
def load_json(
path: 'str' = None
) -> 'T'
Load the class from a JSON file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the JSON file. | None |
Returns:
| Type | Description |
|---|---|
| ConfigBase | The class loaded from the JSON file. |
View Source
@classmethod
def load_json(cls: type[T], path: str = None) -> T:
"""
Load the class from a JSON file.
Args:
path (str): The path to the JSON file.
Returns:
ConfigBase: The class loaded from the JSON file.
"""
if path is None:
path = UserPrompt.open_file(
title=f"Open {cls.__name__} File",
file_types=[("json", ".json")],
)
with open(path, "r") as f:
data = json.load(f)
obj = cls.__new__(cls)
obj.__dict__.update(data)
return obj
load_pickle
def load_pickle(
path: 'str' = None
) -> 'T'
Load the class from a pickle file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the pickle file. | None |
Returns:
| Type | Description |
|---|---|
| None | The class loaded from the pickle file. |
View Source
@classmethod
def load_pickle(cls: type[T], path: str = None) -> T:
"""
Load the class from a pickle file.
Args:
path (str): The path to the pickle file.
Returns:
The class loaded from the pickle file.
"""
if path is None:
path = UserPrompt.open_file(
title=f"Open {cls.__name__} File",
file_types=[("pickle", ".pkl")],
)
return pickle_load_object(path)
Instance variables
cycle_frame_num
cycle_time_ms
Methods
save_json
def save_json(
self,
path: 'str' = None
)
Saves the class as JSON file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the output JSON file. | None |
View Source
def save_json(self, path: str = None):
"""
Saves the class as JSON file.
Args:
path (str): The path to the output JSON file.
"""
if path is None:
path = UserPrompt.save_file(
title=f"Save {type(self).__name__} As",
file_types=[("json", ".json")],
defaultextension=".json",
)
with open(path, "w") as f:
json.dump(self.__dict__, f, indent=4)
save_pickle
def save_pickle(
self,
path: 'str' = None
) -> 'None'
Saves the class as a pickle file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| path | str | The path to the output pickle file. | None |
View Source
def save_pickle(self, path: str = None) -> None:
"""
Saves the class as a pickle file.
Args:
path (str): The path to the output pickle file.
"""
if path is None:
path = UserPrompt.save_file(
title=f"Save {type(self).__name__} As",
file_types=[("pickle", ".pkl")],
defaultextension=".pkl",
)
pickle_save_object(self, path)