ImageMesh

Generated mesh with the aspect ratio of a given image stack.

Description

The ImageMesh object is a convenience tool for setting up a mesh to match the pixel structure of a two or three dimensional image. It is generally used in union with the ImageFunction object to perform simulations that rely on image data, such as setting up an initial condition of a grain structure. By default the generated mesh is sized to the dimensions of the images and creates one element per pixel.

Example Syntax

[Mesh]
  type = ImageMesh
  dim = 3
  file_base = stack/test
  file_suffix = png
[]
(../moose/test/tests/functions/image_function/image_mesh_3d.i)

Input Parameters

  • add_subdomain_idsThe listed subdomains will be assumed valid for the mesh. This permits setting up subdomain restrictions for subdomains initially containing no elements, which can occur, for example, in additive manufacturing simulations which dynamically add and remove elements.

    C++ Type:std::vector<unsigned short>

    Controllable:No

    Description:The listed subdomains will be assumed valid for the mesh. This permits setting up subdomain restrictions for subdomains initially containing no elements, which can occur, for example, in additive manufacturing simulations which dynamically add and remove elements.

  • allow_renumberingTrueIf allow_renumbering=false, node and element numbers are kept fixed until deletion

    Default:True

    C++ Type:bool

    Controllable:No

    Description:If allow_renumbering=false, node and element numbers are kept fixed until deletion

  • bias_x1The amount by which to grow (or shrink) the cells in the x-direction.

    Default:1

    C++ Type:double

    Controllable:No

    Description:The amount by which to grow (or shrink) the cells in the x-direction.

  • bias_y1The amount by which to grow (or shrink) the cells in the y-direction.

    Default:1

    C++ Type:double

    Controllable:No

    Description:The amount by which to grow (or shrink) the cells in the y-direction.

  • bias_z1The amount by which to grow (or shrink) the cells in the z-direction.

    Default:1

    C++ Type:double

    Controllable:No

    Description:The amount by which to grow (or shrink) the cells in the z-direction.

  • build_all_side_lowerd_meshFalseTrue to build the lower-dimensional mesh for all sides.

    Default:False

    C++ Type:bool

    Controllable:No

    Description:True to build the lower-dimensional mesh for all sides.

  • cells_per_pixel1The number of mesh cells per pixel, must be <=1

    Default:1

    C++ Type:double

    Controllable:No

    Description:The number of mesh cells per pixel, must be <=1

  • coord_blockBlock IDs for the coordinate systems. If this parameter is specified, then it must encompass all the subdomains on the mesh.

    C++ Type:std::vector<SubdomainName>

    Controllable:No

    Description:Block IDs for the coordinate systems. If this parameter is specified, then it must encompass all the subdomains on the mesh.

  • elem_typeThe type of element from libMesh to generate (default: linear element for requested dimension)

    C++ Type:MooseEnum

    Options:EDGE, EDGE2, EDGE3, EDGE4, QUAD, QUAD4, QUAD8, QUAD9, TRI3, TRI6, HEX, HEX8, HEX20, HEX27, TET4, TET10, PRISM6, PRISM15, PRISM18, PYRAMID5, PYRAMID13, PYRAMID14

    Controllable:No

    Description:The type of element from libMesh to generate (default: linear element for requested dimension)

  • fileName of single image file to extract mesh parameters from. If provided, a 2D mesh is created.

    C++ Type:FileName

    Controllable:No

    Description:Name of single image file to extract mesh parameters from. If provided, a 2D mesh is created.

  • file_baseImage file base to open, use this option when a stack of images must be read (ignored if 'file' is given)

    C++ Type:FileNameNoExtension

    Controllable:No

    Description:Image file base to open, use this option when a stack of images must be read (ignored if 'file' is given)

  • file_rangeRange of images to analyze, used with 'file_base' (ignored if 'file' is given)

    C++ Type:std::vector<unsigned int>

    Controllable:No

    Description:Range of images to analyze, used with 'file_base' (ignored if 'file' is given)

  • file_suffixSuffix of the file to open, e.g. 'png'

    C++ Type:std::string

    Controllable:No

    Description:Suffix of the file to open, e.g. 'png'

  • gauss_lobatto_gridFalseGrade mesh into boundaries according to Gauss-Lobatto quadrature spacing.

    Default:False

    C++ Type:bool

    Controllable:No

    Description:Grade mesh into boundaries according to Gauss-Lobatto quadrature spacing.

  • ghosting_patch_sizeThe number of nearest neighbors considered for ghosting purposes when 'iteration' patch update strategy is used. Default is 5 * patch_size.

    C++ Type:unsigned int

    Controllable:No

    Description:The number of nearest neighbors considered for ghosting purposes when 'iteration' patch update strategy is used. Default is 5 * patch_size.

  • max_leaf_size10The maximum number of points in each leaf of the KDTree used in the nearest neighbor search. As the leaf size becomes larger,KDTree construction becomes faster but the nearest neighbor searchbecomes slower.

    Default:10

    C++ Type:unsigned int

    Controllable:No

    Description:The maximum number of points in each leaf of the KDTree used in the nearest neighbor search. As the leaf size becomes larger,KDTree construction becomes faster but the nearest neighbor searchbecomes slower.

  • nx1Number of elements in the X direction

    Default:1

    C++ Type:unsigned int

    Controllable:No

    Description:Number of elements in the X direction

  • ny1Number of elements in the Y direction

    Default:1

    C++ Type:unsigned int

    Controllable:No

    Description:Number of elements in the Y direction

  • nz1Number of elements in the Z direction

    Default:1

    C++ Type:unsigned int

    Controllable:No

    Description:Number of elements in the Z direction

  • parallel_typeDEFAULTDEFAULT: Use libMesh::ReplicatedMesh unless --distributed-mesh is specified on the command line REPLICATED: Always use libMesh::ReplicatedMesh DISTRIBUTED: Always use libMesh::DistributedMesh

    Default:DEFAULT

    C++ Type:MooseEnum

    Options:DEFAULT, REPLICATED, DISTRIBUTED

    Controllable:No

    Description:DEFAULT: Use libMesh::ReplicatedMesh unless --distributed-mesh is specified on the command line REPLICATED: Always use libMesh::ReplicatedMesh DISTRIBUTED: Always use libMesh::DistributedMesh

  • scale_to_oneTrueWhether or not to scale the image so its max dimension is 1

    Default:True

    C++ Type:bool

    Controllable:No

    Description:Whether or not to scale the image so its max dimension is 1

  • skip_refine_when_use_splitTrueTrue to skip uniform refinements when using a pre-split mesh.

    Default:True

    C++ Type:bool

    Controllable:No

    Description:True to skip uniform refinements when using a pre-split mesh.

  • xmax1Upper X Coordinate of the generated mesh

    Default:1

    C++ Type:double

    Controllable:No

    Description:Upper X Coordinate of the generated mesh

  • xmin0Lower X Coordinate of the generated mesh

    Default:0

    C++ Type:double

    Controllable:No

    Description:Lower X Coordinate of the generated mesh

  • ymax1Upper Y Coordinate of the generated mesh

    Default:1

    C++ Type:double

    Controllable:No

    Description:Upper Y Coordinate of the generated mesh

  • ymin0Lower Y Coordinate of the generated mesh

    Default:0

    C++ Type:double

    Controllable:No

    Description:Lower Y Coordinate of the generated mesh

  • zmax1Upper Z Coordinate of the generated mesh

    Default:1

    C++ Type:double

    Controllable:No

    Description:Upper Z Coordinate of the generated mesh

  • zmin0Lower Z Coordinate of the generated mesh

    Default:0

    C++ Type:double

    Controllable:No

    Description:Lower Z Coordinate of the generated mesh

Optional Parameters

  • alpha_rotationThe number of degrees that the domain should be alpha-rotated using the Euler angle ZXZ convention from https://en.wikipedia.org/wiki/Euler_angles#Rotation_matrix in order to align with a canonical physical space of your choosing.

    C++ Type:double

    Controllable:No

    Description:The number of degrees that the domain should be alpha-rotated using the Euler angle ZXZ convention from https://en.wikipedia.org/wiki/Euler_angles#Rotation_matrix in order to align with a canonical physical space of your choosing.

  • beta_rotationThe number of degrees that the domain should be beta-rotated using the Euler angle ZXZ convention from https://en.wikipedia.org/wiki/Euler_angles#Rotation_matrix in order to align with a canonical physical space of your choosing.

    C++ Type:double

    Controllable:No

    Description:The number of degrees that the domain should be beta-rotated using the Euler angle ZXZ convention from https://en.wikipedia.org/wiki/Euler_angles#Rotation_matrix in order to align with a canonical physical space of your choosing.

  • gamma_rotationThe number of degrees that the domain should be gamma-rotated using the Euler angle ZXZ convention from https://en.wikipedia.org/wiki/Euler_angles#Rotation_matrix in order to align with a canonical physical space of your choosing.

    C++ Type:double

    Controllable:No

    Description:The number of degrees that the domain should be gamma-rotated using the Euler angle ZXZ convention from https://en.wikipedia.org/wiki/Euler_angles#Rotation_matrix in order to align with a canonical physical space of your choosing.

  • length_unitHow much distance one mesh length unit represents, e.g. 1 cm, 1 nm, 1 ft, 5inches

    C++ Type:std::string

    Controllable:No

    Description:How much distance one mesh length unit represents, e.g. 1 cm, 1 nm, 1 ft, 5inches

  • up_directionSpecify what axis corresponds to the up direction in physical space (the opposite of the gravity vector if you will). If this parameter is provided, we will perform a single 90 degree rotation of the domain--if the provided axis is 'x' or 'z', we will not rotate if the axis is 'y'--such that a point which was on the provided axis will now lie on the y-axis, e.g. the y-axis is our canonical up direction. If you want finer grained control than this, please use the 'alpha_rotation', 'beta_rotation', and 'gamma_rotation' parameters.

    C++ Type:MooseEnum

    Options:X, Y, Z

    Controllable:No

    Description:Specify what axis corresponds to the up direction in physical space (the opposite of the gravity vector if you will). If this parameter is provided, we will perform a single 90 degree rotation of the domain--if the provided axis is 'x' or 'z', we will not rotate if the axis is 'y'--such that a point which was on the provided axis will now lie on the y-axis, e.g. the y-axis is our canonical up direction. If you want finer grained control than this, please use the 'alpha_rotation', 'beta_rotation', and 'gamma_rotation' parameters.

Transformations Relative To Parent Application Frame Of Reference Parameters

  • coord_typeXYZType of the coordinate system per block param

    Default:XYZ

    C++ Type:MultiMooseEnum

    Options:XYZ, RZ, RSPHERICAL

    Controllable:No

    Description:Type of the coordinate system per block param

  • rz_coord_axisYThe rotation axis (X | Y) for axisymmetric coordinates

    Default:Y

    C++ Type:MooseEnum

    Options:X, Y

    Controllable:No

    Description:The rotation axis (X | Y) for axisymmetric coordinates

  • rz_coord_blocksBlocks using general axisymmetric coordinate systems

    C++ Type:std::vector<SubdomainName>

    Controllable:No

    Description:Blocks using general axisymmetric coordinate systems

  • rz_coord_directionsAxis directions for each block in 'rz_coord_blocks'

    C++ Type:std::vector<libMesh::VectorValue<double>>

    Controllable:No

    Description:Axis directions for each block in 'rz_coord_blocks'

  • rz_coord_originsAxis origin points for each block in 'rz_coord_blocks'

    C++ Type:std::vector<libMesh::Point>

    Controllable:No

    Description:Axis origin points for each block in 'rz_coord_blocks'

Coordinate System Parameters

  • centroid_partitioner_directionSpecifies the sort direction if using the centroid partitioner. Available options: x, y, z, radial

    C++ Type:MooseEnum

    Options:x, y, z, radial

    Controllable:No

    Description:Specifies the sort direction if using the centroid partitioner. Available options: x, y, z, radial

  • partitionerdefaultSpecifies a mesh partitioner to use when splitting the mesh for a parallel computation.

    Default:default

    C++ Type:MooseEnum

    Options:default, metis, parmetis, linear, centroid, hilbert_sfc, morton_sfc

    Controllable:No

    Description:Specifies a mesh partitioner to use when splitting the mesh for a parallel computation.

Partitioning Parameters

  • construct_node_list_from_side_listTrueWhether or not to generate nodesets from the sidesets (usually a good idea).

    Default:True

    C++ Type:bool

    Controllable:No

    Description:Whether or not to generate nodesets from the sidesets (usually a good idea).

  • control_tagsAdds user-defined labels for accessing object parameters via control logic.

    C++ Type:std::vector<std::string>

    Controllable:No

    Description:Adds user-defined labels for accessing object parameters via control logic.

  • enableTrueSet the enabled status of the MooseObject.

    Default:True

    C++ Type:bool

    Controllable:No

    Description:Set the enabled status of the MooseObject.

  • nemesisFalseIf nemesis=true and file=foo.e, actually reads foo.e.N.0, foo.e.N.1, ... foo.e.N.N-1, where N = # CPUs, with NemesisIO.

    Default:False

    C++ Type:bool

    Controllable:No

    Description:If nemesis=true and file=foo.e, actually reads foo.e.N.0, foo.e.N.1, ... foo.e.N.N-1, where N = # CPUs, with NemesisIO.

  • patch_size40The number of nodes to consider in the NearestNode neighborhood.

    Default:40

    C++ Type:unsigned int

    Controllable:No

    Description:The number of nodes to consider in the NearestNode neighborhood.

  • patch_update_strategyneverHow often to update the geometric search 'patch'. The default is to never update it (which is the most efficient but could be a problem with lots of relative motion). 'always' will update the patch for all secondary nodes at the beginning of every timestep which might be time consuming. 'auto' will attempt to determine at the start of which timesteps the patch for all secondary nodes needs to be updated automatically.'iteration' updates the patch at every nonlinear iteration for a subset of secondary nodes for which penetration is not detected. If there can be substantial relative motion between the primary and secondary surfaces during the nonlinear iterations within a timestep, it is advisable to use 'iteration' option to ensure accurate contact detection.

    Default:never

    C++ Type:MooseEnum

    Options:never, always, auto, iteration

    Controllable:No

    Description:How often to update the geometric search 'patch'. The default is to never update it (which is the most efficient but could be a problem with lots of relative motion). 'always' will update the patch for all secondary nodes at the beginning of every timestep which might be time consuming. 'auto' will attempt to determine at the start of which timesteps the patch for all secondary nodes needs to be updated automatically.'iteration' updates the patch at every nonlinear iteration for a subset of secondary nodes for which penetration is not detected. If there can be substantial relative motion between the primary and secondary surfaces during the nonlinear iterations within a timestep, it is advisable to use 'iteration' option to ensure accurate contact detection.

Advanced Parameters

  • dimThe dimension of the mesh to be generated

    C++ Type:MooseEnum

    Options:1, 2, 3

    Controllable:No

    Description:The dimension of the mesh to be generated

Main Parameters