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paths

Repo-root data and simulation path helpers.

toric_spines_sim.paths

Path utilities for toric_spines_sim.

Use these helpers instead of ../../data/.... Current morphologies are data/swc/{pixels,microns}/TS{id}_wsink_r{R}um.swc (prefer r10 µm for experiments). Historical TS*_s50_* / TS*_s200_* names live under archive/data/swc/. Pixel and micron trees are the same geometry in different units; pass um_per_px at conversion time (typically 0.005).

PathConfig()

Configuration class for accessing project paths.

Source code in toric_spines_sim/paths.py 
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def __init__(self):
    self.project_root = PROJECT_ROOT
    self.data_dir = DATA_DIR
    self.mesh_dir = MESH_DIR
    self.skeletons_dir = SKELETONS_DIR
    self.swc_pixels_dir = SWC_PIXELS_DIR
    self.swc_microns_dir = SWC_MICRONS_DIR
    self.pointsets_pixels_dir = POINTSETS_PIXELS_DIR
    self.pointsets_microns_dir = POINTSETS_MICRONS_DIR
    self.nff_dir = NFF_DIR
    self.simulations_dir = SIMULATIONS_DIR
    self.notebooks_dir = NOTEBOOKS_DIR

get_data_path(*parts)

Get a path relative to the data directory.

Source code in toric_spines_sim/paths.py 
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def get_data_path(*parts: str) -> Path:
    """Get a path relative to the data directory."""
    return DATA_DIR.joinpath(*parts)

get_mesh_path(filename)

Get path to a mesh file under data/mesh/.

Args: filename: Name of the mesh file (e.g. TS1.obj).

Source code in toric_spines_sim/paths.py 
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def get_mesh_path(filename: str) -> Path:
    """Get path to a mesh file under ``data/mesh/``.

    Args:
        filename: Name of the mesh file (e.g. ``TS1.obj``).
    """
    return MESH_DIR / filename

get_cell_mesh_path()

Path to the full-cell triangle mesh under data/mesh/.

Source code in toric_spines_sim/paths.py 
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def get_cell_mesh_path() -> Path:
    """Path to the full-cell triangle mesh under ``data/mesh/``."""
    return MESH_DIR / CELL_MESH_NAME

get_skeleton_path(filename)

Get path to a skeleton / polylines file under data/skeletons/.

Args: filename: Name of the file (e.g. TS1.polylines.txt).

Source code in toric_spines_sim/paths.py 
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def get_skeleton_path(filename: str) -> Path:
    """Get path to a skeleton / polylines file under ``data/skeletons/``.

    Args:
        filename: Name of the file (e.g. ``TS1.polylines.txt``).
    """
    return SKELETONS_DIR / filename

get_swc_path(filename, units='microns')

Get path to an SWC file.

Args: filename: Name of the SWC file. units: Either 'pixels' or 'microns'.

Source code in toric_spines_sim/paths.py 
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def get_swc_path(filename: str, units: str = "microns") -> Path:
    """Get path to an SWC file.

    Args:
        filename: Name of the SWC file.
        units: Either 'pixels' or 'microns'.
    """
    if units == "pixels":
        return SWC_PIXELS_DIR / filename
    elif units == "microns":
        return SWC_MICRONS_DIR / filename
    else:
        raise ValueError(f"units must be 'pixels' or 'microns', got {units}")

get_pointset_path(filename, units='microns')

Get path to a pointset file.

Args: filename: Name of the pointset file. units: Either 'pixels' or 'microns'.

Source code in toric_spines_sim/paths.py 
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def get_pointset_path(filename: str, units: str = "microns") -> Path:
    """Get path to a pointset file.

    Args:
        filename: Name of the pointset file.
        units: Either 'pixels' or 'microns'.
    """
    if units == "pixels":
        return POINTSETS_PIXELS_DIR / filename
    elif units == "microns":
        return POINTSETS_MICRONS_DIR / filename
    else:
        raise ValueError(f"units must be 'pixels' or 'microns', got {units}")

get_simulation_path(simulation_name, *parts)

Get a path within a specific simulation directory.

Source code in toric_spines_sim/paths.py 
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def get_simulation_path(simulation_name: str, *parts: str) -> Path:
    """Get a path within a specific simulation directory."""
    path = SIMULATIONS_DIR / simulation_name
    if parts:
        path = path.joinpath(*parts)
    return path