sarcasm.core

Classes

SarcAsM

Base class for sarcomere structural and functional analysis.

Module Contents

class sarcasm.core.SarcAsM(filepath: str | os.PathLike, restart: bool = False, channel: int | None | Literal['RGB'] = None, auto_save: bool = True, use_gui: bool = False, device: torch.device | Literal['auto', 'mps', 'cuda', 'cpu'] = 'auto', **info: Dict[str, Any])[source]

Base class for sarcomere structural and functional analysis.

Parameters:

filepath (str | os.PathLike) – Path to the TIFF file for analysis.
restart (bool, optional) – If True, deletes existing analysis and starts fresh (default: False).
channel (int, None or Literal['RGB'], optional) – Specifies the channel with sarcomeres in multicolor stacks (default: None).
auto_save (bool, optional) – Automatically saves analysis results when True (default: True).
use_gui (bool, optional) – Indicates GUI mode operation (default: False).
device (Union[torch.device, Literal['auto']], optional) – Device for PyTorch computations. ‘auto’ selects CUDA/MPS if available (default: ‘auto’).
**info (Any) – Additional metadata as keyword arguments (e.g. cell_line=’wt’).

filepath

Absolute path to the input TIFF file.

Type:: str

base_dir

Base directory for analysis of the TIFF file.

Type:: str

data_dir

Directory for processed data storage.

Type:: str

analysis_dir

Directory for analysis results.

Type:: str

device

Active computation device for PyTorch operations.

Type:: torch.device

Dynamic Attributes (loaded on demand)

zbands

Z-band mask

Type:: ndarray

zbands_fast_movie

High-temporal resolution Z-band mask

Type:: ndarray

mbands

Sarcomere M-band mask

Type:: ndarray

orientation

Sarcomere orientation map

Type:: ndarray

cell_mask

Binary cell mask

Type:: ndarray

sarcomere_mask

Binary sarcomere mask

Type:: ndarray

meta_data_handler: sarcasm.meta_data_handler.MetaDataHandler

metadata: dict[str, Any]

filepath = b'.'

auto_save = True

channel = None

use_gui = False

restart = False

info

base_dir

data_dir

analysis_dir

file_zbands

file_zbands_fast_movie

file_mbands

file_orientation

file_cell_mask

file_sarcomere_mask

__getattr__(name: str) → Any[source]: Dynamic loading of analysis result TIFFs

__dir__() → list[str][source]: Augment autocomplete with dynamic attributes

__str__()[source]: Returns a pretty, concise string representation of the SarcAsM object.

open_base_dir()[source]: Opens the base directory of the tiff file in the file explorer.

property model_dir: str: Returns the path to the model directory.

read_imgs(frames: str | int | List[int] = None)[source]: Load tif file, and optionally select channel

remove_intermediate_tiffs() → None[source]: Removes intermediate TIFF files while preserving the original input.