xopto.mcml.mclayer.layer module

class Layer(d: float, n: float, mua: float, mus: float, pf: xopto.mcbase.mcpf.pfbase.PfBase)[source]

Bases: xopto.mcbase.mcobject.McObject

Class that represents a single sample layer.

Layer object constructor.

Parameters

  • d (float) – Layer thickness (m).

  • n (float) – Index of refraction.

  • mua (float) – Absorption coefficient (1/m).

  • mus (float) – Scattering (NOT reduced) coefficient (1/m).

  • pf (mcpf.PfBase) – Scattering phase function object that is derived from PhBase class.

The physical properties of the layer can be read or changed through member properties:

  • d: float - Layer thickness (m).

  • n: float - Index of refraction.

  • mua: float - Absorption coefficient (1/m).

  • mus: float - Scattering (NOT reduced) coefficient (1/m).

  • pf: mcpf.PfBase - Scattering phase function object that is derived from PhBase class.

Note

The layer boundaries in the z direction are increasing in the direction of the layer stack. Z coordinate 0.0 belongs to the top surface of the first sample layer!

static cl_declaration(mc: xopto.mcbase.mcobject.McObject) → str[source]

Structure and related API that defines a layer in the Monte Carlo simulator.

cl_type(mc: xopto.mcbase.mcobject.McObject) → xopto.cl.cltypes.Structure[source]

Returns a structure data type that is used to represent one Layer instance in the OpenCL kernel of the Monte Carlo simulator.

Parameters

mc (mcobject.McObject) – Monte Carlo simulator instance.

Returns

opencl_t – OpenCL Structure that represents a layer.

Return type

ClLayer

property d: float

Layer thickens (m).

classmethod fromdict(data: dict) → xopto.mcml.mclayer.layer.Layer[source]

Create a new object from dict. The dict keys must match the parameter names defined by the constructor.

property mua: float

Absorption coefficient of the layer (1/m).

property mus: float

Scattering coefficient of the layer (1/m).

property n: float

Refractive index of the layer.

property pf: xopto.mcbase.mcpf.pfbase.PfBase

Phase function object.

todict() → dict[source]

Export object to a dict.

class Layers(layers: List[xopto.mcml.mclayer.layer.Layer])[source]

Bases: xopto.mcbase.mcobject.McObject

Class that represents a stack of layers forming the sample.

Note

The topmost and bottommost layers of the stack are used to describe the medium that surrounds the sample top and bottom surfaces, respectively. Therefore, at least three layers must be always specified, namely two layers of the surrounding medium and one sample layer! The thicknesses of the topmost and bottommost layers will be automatically set to infinity regardless of the layer thickness set by the user.

Constructs a managed sample layer stack from a list of sample layers.

Note

The topmost and bottommost layers of the stack are used to describe the medium that surrounds the sample top and bottom surfaces, respectively. Therefore, at least three layers must be always specified, namely two layers of the surrounding medium and one sample layer!

The bottom surface of the topmost layer (the surrounding medium) is located at z=0. The positive direction of the z axis points in the direction of the layer stack.

The thicknesses of the topmost and bottommost layers will be automatically set to infinity when passed to the OpenCL kernel (regardless of the layer thickness set by the user).

Note that all layers must use the same scattering phase function model.

Parameters

layers (list or Layers) – A list of sample layers. Requires at least 3 items!

check()[source]

Check if the layers are consistent and using a single scattering phase function type. Raises exception on error.

cl_pack(mc: xopto.mcbase.mcobject.McObject, target: Optional[_ctypes.Array] = None) → _ctypes.Array[source]

Pack the layers into an OpenCL data type. The OpenCL data type is returned by the Layers.cl_type() method.

Parameters

  • mc (mcobject.McObject) – Monte Carlo simulator instance.

  • target (cltypes.Structure*len(self)) – A structure representing an array of Layers.

Returns

target – Filled structure received as an input argument or a new instance if the input argument target is None.

Return type

cltypes.Structure

cl_type(mc: xopto.mcbase.mcobject.McObject) → _ctypes.Array[source]

Returns an OpenCL array of ClLayer structures that is used to represent one instance of a layer stack.

Parameters

mc (mcobject.McObject) – Monte Carlo simulator instance.

Returns

clarray – Array of ClLayers.

Return type

cltypes.Structure*len(self)

classmethod fromdict(data: dict) → xopto.mcml.mclayer.layer.Layers[source]

Create a new Layers object from a dict. The dict keys must match the parameter names defined by the constructor.

layer(index: int) → xopto.mcml.mclayer.layer.Layer[source]

Returns layer at the specified index. Note that the first layer (index 0) and the last layer (index -1) represent the medium surrounding the top and bottom surfaces of the sample, respectively

layer_index(z: float) → int[source]

Returns the layer index that contains the given z coordinate. Note that the layer includes the top surface boundary but not the bottom surface boundary, i.e. the z extent of the layer is [z_top, z_bottom), where z_bottom > z_top.

Parameters

z (float) – Z coordinate of a point.

Returns

layer_index – Index of the layer that contains the give point z.

Return type

int

thickness() → float[source]

Thickness of the layer stack excluding the topmost and bottommost layers that surround the sample.

Returns

thickness – The sample thickness excluding the topmost and bottommost layers of the surrounding medium.

Return type

float

todict() → dict[source]

Export object to a dict.

tolist() → List[xopto.mcml.mclayer.layer.Layer][source]

Returns a weak copy of the list of managed layers.

Returns

layers – List of managed layers

Return type

List[layers]