Module nlisim.modules.geometry

Expand source code 
from enum import Enum
from pathlib import Path

import attr
import h5py
import numpy as np

from nlisim.module import ModuleModel, ModuleState
from nlisim.state import State, grid_variable
from nlisim.validation import ValidationError


# I am not quite sure if we should put the definition of the lung tissue types here
class TissueTypes(Enum):
    AIR = 0
    BLOOD = 1
    OTHER = 2
    EPITHELIUM = 3
    SURFACTANT = 4
    PORE = 5

    @classmethod
    def validate(cls, value: np.ndarray):
        return np.logical_and(value >= 0, value <= 5).all() and np.issubclass_(
            value.dtype.type, np.integer
        )


@attr.s(kw_only=True, repr=False)
class GeometryState(ModuleState):
    lung_tissue = grid_variable(np.dtype('int'))

    # noinspection PyUnusedLocal
    @lung_tissue.validator  # type: ignore
    def _validate_lung_tissue(self, attribute: attr.Attribute, value: np.ndarray) -> None:
        if not TissueTypes.validate(value):
            raise ValidationError('input illegal')

    def __repr__(self):
        return 'GeometryState(lung_tissue)'


class Geometry(ModuleModel):
    name = 'geometry'
    StateClass = GeometryState

    def initialize(self, state: State):
        geometry: GeometryState = state.geometry
        # The geometry data file is included next to this one
        path = Path(__file__).parent / 'geometry.hdf5'
        try:
            with h5py.File(path, 'r') as f:
                if f['geometry'][:].shape != state.grid.shape:
                    raise ValidationError("shape doesn't match")
                geometry.lung_tissue[:] = f['geometry'][:]
        except Exception:
            print(f'Error loading geometry file at {path}.')
            raise

        return state

Classes

class Geometry (config: SimulationConfig)
Expand source code 
class Geometry(ModuleModel):
    name = 'geometry'
    StateClass = GeometryState

    def initialize(self, state: State):
        geometry: GeometryState = state.geometry
        # The geometry data file is included next to this one
        path = Path(__file__).parent / 'geometry.hdf5'
        try:
            with h5py.File(path, 'r') as f:
                if f['geometry'][:].shape != state.grid.shape:
                    raise ValidationError("shape doesn't match")
                geometry.lung_tissue[:] = f['geometry'][:]
        except Exception:
            print(f'Error loading geometry file at {path}.')
            raise

        return state

Ancestors

Inherited members

class GeometryState (*, global_state: State, lung_tissue=NOTHING)

Base type intended to store the state for simulation modules.

This class contains serialization support for basic types (float, int, str, bool) and numpy arrays of those types. Modules containing more complicated state must override the serialization mechanism with custom behavior.

Method generated by attrs for class GeometryState.

Expand source code 
class GeometryState(ModuleState):
    lung_tissue = grid_variable(np.dtype('int'))

    # noinspection PyUnusedLocal
    @lung_tissue.validator  # type: ignore
    def _validate_lung_tissue(self, attribute: attr.Attribute, value: np.ndarray) -> None:
        if not TissueTypes.validate(value):
            raise ValidationError('input illegal')

    def __repr__(self):
        return 'GeometryState(lung_tissue)'

Ancestors

Class variables

var global_state : State

Inherited members

class TissueTypes (value, names=None, *, module=None, qualname=None, type=None, start=1)

An enumeration.

Expand source code 
class TissueTypes(Enum):
    AIR = 0
    BLOOD = 1
    OTHER = 2
    EPITHELIUM = 3
    SURFACTANT = 4
    PORE = 5

    @classmethod
    def validate(cls, value: np.ndarray):
        return np.logical_and(value >= 0, value <= 5).all() and np.issubclass_(
            value.dtype.type, np.integer
        )

Ancestors

  • enum.Enum

Class variables

var AIR
var BLOOD
var EPITHELIUM
var OTHER
var PORE
var SURFACTANT

Static methods

def validate(value: numpy.ndarray)
Expand source code 
@classmethod
def validate(cls, value: np.ndarray):
    return np.logical_and(value >= 0, value <= 5).all() and np.issubclass_(
        value.dtype.type, np.integer
    )