ImageSubdomainGenerator

Samples an image at the coordinates of each element centroid, using the resulting pixel color value as each element's subdomain ID

Example Syntax

Normal usage of ImageSubdomainGenerator involves creation of a standard mesh (in the example, GeneratedMeshGenerator), using that mesh as the input for ImageSubdomainGenerator, and providing an image to sample. See an example below:

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 41
    ny = 41
  []
  [./image]
    input = gen
    type = ImageSubdomainGenerator
    file = kitten.png
    threshold = 100
  [../]
[]

note

In this example, the parameter threshold is used. This sets a color value above which the subdomain ID is set to upper_value (default = 1) and below which the subdomain ID is set to lower_value (default = 0). More information about these and other extended parameters can be seen below in the Input Parameters section.

Input Image (kitten.png)

Mesh Subdomain ID Output

Input Parameters

inputThe mesh we want to modify
C++ Type:MeshGeneratorName
Controllable:No
Description:The mesh we want to modify

Required Parameters

componentThe image RGB-component to return, leaving this blank will result in a greyscale value for the image to be created. The component number is zero based, i.e. 0 returns the first (RED) component of the image.
C++ Type:unsigned int
Controllable:No
Description:The image RGB-component to return, leaving this blank will result in a greyscale value for the image to be created. The component number is zero based, i.e. 0 returns the first (RED) component of the image.
dimensionsx,y,z dimensions of the image (defaults to mesh dimensions)
C++ Type:libMesh::Point
Controllable:No
Description:x,y,z dimensions of the image (defaults to mesh dimensions)
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'
originOrigin of the image (defaults to mesh origin)
C++ Type:libMesh::Point
Controllable:No
Description:Origin of the image (defaults to mesh origin)

Optional Parameters

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.
save_with_nameKeep the mesh from this mesh generator in memory with the name specified
C++ Type:std::string
Controllable:No
Description:Keep the mesh from this mesh generator in memory with the name specified

Advanced Parameters

flip_xFalseFlip the image along the x-axis
Default:False
C++ Type:bool
Controllable:No
Description:Flip the image along the x-axis
flip_yFalseFlip the image along the y-axis
Default:False
C++ Type:bool
Controllable:No
Description:Flip the image along the y-axis
flip_zFalseFlip the image along the z-axis
Default:False
C++ Type:bool
Controllable:No
Description:Flip the image along the z-axis

Flip Parameters

lower_value0The value to set for data less than the threshold value
Default:0
C++ Type:double
Controllable:No
Description:The value to set for data less than the threshold value
thresholdThe threshold value
C++ Type:double
Controllable:No
Description:The threshold value
upper_value1The value to set for data greater than the threshold value
Default:1
C++ Type:double
Controllable:No
Description:The value to set for data greater than the threshold value

Threshold Parameters

nemesisFalseWhether or not to output the mesh file in the nemesisformat (only if output = true)
Default:False
C++ Type:bool
Controllable:No
Description:Whether or not to output the mesh file in the nemesisformat (only if output = true)
outputFalseWhether or not to output the mesh file after generating the mesh
Default:False
C++ Type:bool
Controllable:No
Description:Whether or not to output the mesh file after generating the mesh
show_infoFalseWhether or not to show mesh info after generating the mesh (bounding box, element types, sidesets, nodesets, subdomains, etc)
Default:False
C++ Type:bool
Controllable:No
Description:Whether or not to show mesh info after generating the mesh (bounding box, element types, sidesets, nodesets, subdomains, etc)

Debugging Parameters

scale1Multiplier to apply to all pixel values; occurs after shifting
Default:1
C++ Type:double
Controllable:No
Description:Multiplier to apply to all pixel values; occurs after shifting
shift0Value to add to all pixels; occurs prior to scaling
Default:0
C++ Type:double
Controllable:No
Description:Value to add to all pixels; occurs prior to scaling

Rescale Parameters

Input Files

(test/tests/meshgenerators/image_mesh_generator/image_2d.i)
(test/tests/preconditioners/fsp/fsp_test_image.i)
(test/tests/meshgenerators/image_mesh_generator/image_3d.i)

(test/tests/preconditioners/fsp/fsp_test_image.i)

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 41
    ny = 41
  []
  [./image]
    input = gen
    type = ImageSubdomainGenerator
    file = kitten.png
    threshold = 100
  [../]
[]

[Variables]
  [./u]
    order = FIRST
    family = LAGRANGE
    block = 1
  [../]
  [./v]
    order = FIRST
    family = LAGRANGE
    block = 1
  [../]
[]

[Kernels]
  [./diff_u]
    type = Diffusion
    variable = u
  [../]
  [./conv_v]
    type = CoupledForce
    variable = v
    v = u
  [../]
  [./diff_v]
    type = Diffusion
    variable = v
  [../]
[]

[BCs]
  active = 'left_u left_v right_u'
  [./left_u]
    type = DirichletBC
    variable = u
    boundary = left
    value = 0
  [../]
  [./right_u]
    type = DirichletBC
    variable = u
    boundary = right
    value = 100
  [../]
  [./left_v]
    type = DirichletBC
    variable = v
    boundary = left
    value = 0
  [../]
  [./right_v]
    type = DirichletBC
    variable = v
    boundary = right
    value = 0
  [../]
[]

[Problem]
  type = FEProblem
  material_coverage_check = false
  kernel_coverage_check = false
[]

[Executioner]
  # This is setup automatically in MOOSE (SetupPBPAction.C)
  # petsc_options = '-snes_mf_operator'
  # petsc_options_iname = '-pc_type'
  # petsc_options_value =  'asm'
  type = Steady
[]

[Preconditioning]
  [./FSP]
    # It is the starting point of splitting
    type = FSP
    topsplit = 'uv' # 'uv'
    [./uv]
      # Generally speaking, there are four types of splitting we could choose
      # <additive,multiplicative,symmetric_multiplicative,schur>
      # An approximate solution to the original system
      # | A_uu  A_uv | | u | _ |f_u|
      # |  0    A_vv | | v | - |f_v|
      # is obtained by solving the following subsystems
      # A_uu u = f_u and A_vv v = f_v
      # If splitting type is specified as schur, we may also want to set more options to
      # control how schur works using PETSc options
      # petsc_options_iname = '-pc_fieldsplit_schur_fact_type -pc_fieldsplit_schur_precondition'
      # petsc_options_value = 'full selfp'
      splitting = 'u v' # 'u' and 'v'
      splitting_type = additive
    [../]
    [./u]
      # PETSc options for this subsolver
      # A prefix will be applied, so just put the options for this subsolver only
      vars = u
      petsc_options_iname = '-pc_type -ksp_type'
      petsc_options_value = '     hypre preonly'
    [../]
    [./v]
      # PETSc options for this subsolver
      vars = v
      petsc_options_iname = '-pc_type -ksp_type'
      petsc_options_value = '     hypre  preonly'
    [../]
  [../]
[]

[Outputs]
  file_base = kitten_out
  exodus = true
[]

(test/tests/meshgenerators/image_mesh_generator/image_2d.i)

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 176
    ny = 287
  []
  [image]
    type = ImageSubdomainGenerator
    input = gen
    file = kitten.png #../../functions/image_function/stack/test
    threshold = 100
  []
[]

[Variables]
  [u]
  []
[]

[Problem]
  type = FEProblem
  solve = false
[]

[Executioner]
  type = Steady
[]

[Outputs]
  execute_on = 'timestep_end'
  exodus = true
[]

(test/tests/preconditioners/fsp/fsp_test_image.i)

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 41
    ny = 41
  []
  [./image]
    input = gen
    type = ImageSubdomainGenerator
    file = kitten.png
    threshold = 100
  [../]
[]

[Variables]
  [./u]
    order = FIRST
    family = LAGRANGE
    block = 1
  [../]
  [./v]
    order = FIRST
    family = LAGRANGE
    block = 1
  [../]
[]

[Kernels]
  [./diff_u]
    type = Diffusion
    variable = u
  [../]
  [./conv_v]
    type = CoupledForce
    variable = v
    v = u
  [../]
  [./diff_v]
    type = Diffusion
    variable = v
  [../]
[]

[BCs]
  active = 'left_u left_v right_u'
  [./left_u]
    type = DirichletBC
    variable = u
    boundary = left
    value = 0
  [../]
  [./right_u]
    type = DirichletBC
    variable = u
    boundary = right
    value = 100
  [../]
  [./left_v]
    type = DirichletBC
    variable = v
    boundary = left
    value = 0
  [../]
  [./right_v]
    type = DirichletBC
    variable = v
    boundary = right
    value = 0
  [../]
[]

[Problem]
  type = FEProblem
  material_coverage_check = false
  kernel_coverage_check = false
[]

[Executioner]
  # This is setup automatically in MOOSE (SetupPBPAction.C)
  # petsc_options = '-snes_mf_operator'
  # petsc_options_iname = '-pc_type'
  # petsc_options_value =  'asm'
  type = Steady
[]

[Preconditioning]
  [./FSP]
    # It is the starting point of splitting
    type = FSP
    topsplit = 'uv' # 'uv'
    [./uv]
      # Generally speaking, there are four types of splitting we could choose
      # <additive,multiplicative,symmetric_multiplicative,schur>
      # An approximate solution to the original system
      # | A_uu  A_uv | | u | _ |f_u|
      # |  0    A_vv | | v | - |f_v|
      # is obtained by solving the following subsystems
      # A_uu u = f_u and A_vv v = f_v
      # If splitting type is specified as schur, we may also want to set more options to
      # control how schur works using PETSc options
      # petsc_options_iname = '-pc_fieldsplit_schur_fact_type -pc_fieldsplit_schur_precondition'
      # petsc_options_value = 'full selfp'
      splitting = 'u v' # 'u' and 'v'
      splitting_type = additive
    [../]
    [./u]
      # PETSc options for this subsolver
      # A prefix will be applied, so just put the options for this subsolver only
      vars = u
      petsc_options_iname = '-pc_type -ksp_type'
      petsc_options_value = '     hypre preonly'
    [../]
    [./v]
      # PETSc options for this subsolver
      vars = v
      petsc_options_iname = '-pc_type -ksp_type'
      petsc_options_value = '     hypre  preonly'
    [../]
  [../]
[]

[Outputs]
  file_base = kitten_out
  exodus = true
[]

(test/tests/meshgenerators/image_mesh_generator/image_3d.i)

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 3
    nx = 20
    ny = 20
    nz = 20
  []
  [image]
    type = ImageSubdomainGenerator
    input = gen
    file_base = stack/test
    file_suffix = png
    threshold = 2.7e4
  []
[]

[Variables]
  [u]
  []
[]

[Problem]
  type = FEProblem
  solve = false
[]

[Executioner]
  type = Steady
[]

[Outputs]
  execute_on = 'timestep_end'
  exodus = true
[]

Example Syntax
Input Parameters
Input Files