CMGUI Commands

For other help see http://www.cmiss.org/cmgui

For examples see http://cmiss.bioeng.auckland.ac.nz/development/examples/a

Tue Sep 30 11:30:56 2014


General notes:

  1. The commands are case insensitive apart from names.
  2. Command options may be abreviated.

Commands:

   assert blocks closed
   set
   gfx
   open
   quit
   list_memory
   read
   set
   system

set

   echo
   debug
   directory

set echo

   <on>
   <off>
   <prompt PROMPT_STRING>

set debug

   <on>
   <off>

set directory

   <example>
   <NAME>

gfx

   change_identifier
   convert
   create
   data_tool
   define
   destroy
   draw
   edit
   element_creator
   element_point_tool
   element_tool
   evaluate
   export
   list
   minimise
   modify
   node_tool
   print
   read
   select
   set
   #
   mesh
   smooth
   timekeeper
   transform_toolERROR: execute_command_gfx_transform_tool.  Invalid argument(s)
   unselect
   update
   write

gfx change_identifier

   <data_offset #[NOT SET]>
   <element_offset #[NOT SET]>
   <face_offset #[NOT SET]>
   <group REGION_PATH/GROUP>
   <line_offset #[NOT SET]>
   <node_offset #[NOT SET]>
   <sort_by FIELD_NAME>
   <time #[0]>

gfx convert

   elements
   graphics

gfx convert elements

Convert element fields to specified bases on a new mesh in destination_region. Modes 'convert_trilinear' and 'convert_triquadratic' ONLY: converts element fields on 3-D elements to specified basis. The first field specified must be a 3-component coordinate field; nodes with values of this field within the specified tolerance are merged on the resulting mesh. Note: field value versions of non-coordinate fields are not handled - the first processed element's versions are assumed. Mode 'convert_hermite_2D_product_elements' ONLY: converts element fields on 2-D elements into bicubic hermite basis WITHOUT merging nearby nodes.

   <destination_region PATH_TO_REGION>
   <fields NAME[""]>
   <number_of_fields #[1]{>0,integer}>
   <convert_hermite_2D_product_elements|convert_trilinear|convert_triquadratic>
   <refinement #*#*#[1*1*1]{integer*integer*integer}>
   <source_region PATH_TO_REGION[/]>
   <tolerance #[1e-06]{>=0}>

gfx convert graphics

Create finite elements or a point cloud of nodes from lines and surfaces graphics, or create nodes from points graphics. With mode 'render_linear_product_elements' linear finite elements are made from lines and surfaces. With mode 'render_surface_node_cloud', nodes are created at points in the lines and surfaces sampled according to a Poisson distribution with the supplied densities. The surface_density gives the base expected number of points per unit area, and if the graphics has a data field, the value of its first component scaled by surface_density_scale_factor is added to the expected number. Separate values for lines control the expected number per unit length. With mode 'render_nodes', nodes are created at points.

   <coordinate FIELD_NAME>
   <line_density #[1]>
   <line_density_scale_factor #[0]>
   <render_linear_product_elements[render_linear_product_elements]|render_surface_node_cloud|render_nodes>
   <filter GRAPHICS_FILTER_NAME|none[default]>
   <region REGION_PATH/GROUP>
   <scene SCENE_NAME[/REGION_PATH][.GRAPHIC_NAME]{default}>
   <surface_density #[1]>
   <surface_density_scale_factor #[0]>

gfx create

   axes
   colour_bar
   data_viewer
   dgroup NAME
   egroup NAME
   element_creator
   element_point_viewer
   flow_particles The flow particles feature has been removed.
   graphical_material_editor
   gauss_points
   light
   lmodel
   material
   more_flow_particles The flow particles feature has been removed.
   ngroup NAME
   node_viewer
   region
   snake
   spectrum
   texture
   window

gfx create colour_bar

   <as NAME[colour_bar]>
   <axis # # #[0 1 0]>
   <centre # # #[-0.9 0 0.5]>
   <divisions #[10]{>=0,integer}>
   <extend_length #[0.06]>
   <fontNAME>
   <label_material MATERIAL_NAME|none[default]>
   <length #[1.6]>
   <number_format NAME[%+.4e]>
   <material MATERIAL_NAME|none[none]>
   <radius #[0.06]>
   <spectrum SPECTRUM_NAME|none[default]>
   <tick_direction # # #[1 0 0]>
   <tick_length #[0.04]>

gfx create dgroup NAME

   <add_ranges #|#..#[,#|#..#[,etc.]]>
   <from GROUP_NAME>
   <manage_subobjects[manage_subobjects]|no_manage_subobjects>
   <region PATH_TO_REGION[/]>

gfx create egroup NAME

   <add_ranges #|#..#[,#|#..#[,etc.]]>
   <from GROUP_NAME>
   <manage_subobjects[manage_subobjects]|no_manage_subobjects>
   <region PATH_TO_REGION[/]>

gfx create gauss_points

Creates points at Gauss point locations in the elements of the mesh. Nodes are created in the gauss_point_nodeset starting from first_identifier, and setting the element_xi gauss_location and real gauss_weight fields. Supports all main element shapes, with polynomial order up to 4. Order gives the number of Gauss points per element dimension for line/square/cube shapes.

   <first_identifier #[1]{>=0,integer}>
   <gauss_location_field FIELD_NAME>
   <gauss_point_nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints|none>
   <gauss_weight_field FIELD_NAME>
   <mesh ELEMENT_GROUP_FIELD_NAME|[GROUP_REGION_NAME.]mesh_1d|mesh_2d|mesh_3d>
   <order #[4]{>0,integer}>
   <region PATH_TO_REGION[/]>

gfx create light LIGHT_NAME

   <colour RED#[0.9]{>=0,<=1} GREEN#[0.9]{>=0,<=1} BLUE#[0.9]{>=0,<=1}>
   <constant_attenuation #[1]{>=0}>
   <cut_off #[90]>
   <direction # # #[0 -0.5 -1]>
   <exponent #[0]{>=0}>
   <infinite[infinite]|point|spot>
   <linear_attenuation #[0]{>=0}>
   <position # # #[0 0 0]>
   <quadratic_attenuation #[0]{>=0}>

gfx create lmodel LIGHT_MODEL_NAME

   <ambient_colour RED#[0.1]{>=0,<=1} GREEN#[0.1]{>=0,<=1} BLUE#[0.1]{>=0,<=1}>
   <disable|enable>
   <infinite_viewer|local_viewer>
   <one_sided|two_sided>

gfx create material MATERIAL_NAME

The material controls how pixels will be rendered on the screen. The initial mode of operation reflects the standard gouraud shading model usual within OpenGL, this is called <normal_mode>. This has rgb colour values for <diffuse>, <ambient> <emission> and <specular> colours. The <ambient> colour is the unlit colour, the <diffuse> colour interacts with the light and is the lit surface, the <specular> colour is used for the glossy highlights, the spread of which is specified by the<shininess>. The <alpha> controls the transparency of the material. See a/a1.If a <texture> is specified then this is combined with the calculated gouraud colour according to the textures rendering mode and the texture coordinates. Additional support is provided for more accurate rendering using phong shading calculated at every pixel, called <per_pixel_lighting>. This is implemented using the ARB_vertex_program and ARB_fragment_program OpenGL extensions. The program only implements a single point light so you should set the default light to a point light at the position you want. See a/per_pixel_lighting. <bump_mapping> uses a <secondary_texture> to specify a perturbation to the normal, giving a smooth model a much more detailed surface appearance. Also demonstrated in a/per_pixel_lighting. A <colour_lookup_spectrum> takes the calculated colour values and further modifies them by using the specified subset of colour values specified by <colour_lookup_red>, <colour_lookup_green>, <colour_lookup_blue> and <colour_lookup_alpha>, as inputs to a 1, 2 or 3 component spectrum. Depending on the spectrum this will override either the rgb colour, the alpha value or both rgb and alpha. If the number of input components used in the spectrum matches the number of components specified then a texture of this dimension will be used and evaluated for each tensor product combination. If only a 1 component spectrum is specified then it will be applied independently to each input component specified. This spectrum can be modified to quickly change the appearance of a large volume dataset, see example a/indexed_volume. A lit volume uses a per voxel normal to calculate the phong lighting model at each pixel. The normal can be specified by encoding it into the blue, green and alpha channels of an input texture (the red channel being the intensity) <lit_volume_intensity_normal_texture>.Alternatively it can be estimated on the fly by applying a finite difference operator to the pixel intensities. <lit_volume_finite_difference_normal>.A <lit_volume_normal_scaling> can be applied, modifying the estimated normal by scaling it. The normal is used as if it is a coordinate normal and so the texture coordinates must line up with the geometrical coordinates. The <lit_volume_normal_scaling> can be used to account for when the texture coordinates are not equally matched to the geometrical coordinates. The magnitude of the <lit_volume_normal_scaling> will only affect the optional following parameter, <lit_volume_scale_alpha>, scaling the alpha attenuation. Optionally with either normal, the magnitude of that normalcan multiply the calculated alpha value, <lit_volume_scale_alpha> making those pixels with small gradients more transparent. See a/volume_render. <secondary_texture>, <third_texture> and <fourth_texture> will be blended with the first <texture> according to the multitexture rules controlled by each textures combine mode (such as modulate or add). Specifying a <vertex_program_string> and <fragment_program_string> allows any arbitrary program to be loaded, overriding the one that is generated automatically, no checks for consistency with textures or inputs are made. Both must be specified together. Optional <geometry_program_string> is also available, which is only available on relatively newer hardware, it must be used with <vertex_program_string> and <fragment_program_string> and only works with surface at the moment. Specifying a <uniform_name> and <uniform_value> allows any uniform qualified variables inany arbitrary program to be set. At the moment only float type is supported.

   <alpha #[1]{>=0,<=1}>
   <ambient RED#[1]{>=0,<=1} GREEN#[1]{>=0,<=1} BLUE#[1]{>=0,<=1}>
   <bump_mapping>
   <colour_lookup_alpha>
   <colour_lookup_blue>
   <colour_lookup_green>
   <colour_lookup_red>
   <colour_lookup_spectrum SPECTRUM_NAME|none[none]>
   <diffuse RED#[1]{>=0,<=1} GREEN#[1]{>=0,<=1} BLUE#[1]{>=0,<=1}>
   <emission RED#[0]{>=0,<=1} GREEN#[0]{>=0,<=1} BLUE#[0]{>=0,<=1}>
   <fourth_texture IMAGE_NAME|none[none]>
   <fragment_program_stringNAME>
   <lit_volume_intensity_normal_texture>
   <lit_volume_finite_difference_normal>
   <lit_volume_normal_scaling # # #[1 1 1]>
   <lit_volume_scale_alpha>
   <normal_mode|per_pixel_mode>
   <secondary_texture IMAGE_NAME|none[none]>
   <shininess #[0]{>=0,<=1}>
   <specular RED#[0]{>=0,<=1} GREEN#[0]{>=0,<=1} BLUE#[0]{>=0,<=1}>
   <texture IMAGE_NAME|none[none]>
   <third_texture IMAGE_NAME|none[none]>
   <vertex_program_stringNAME>
   <geometry_program_stringNAME>
   <uniform_nameNAME>
   <uniform_values #..#>

gfx create ngroup NAME

   <add_ranges #|#..#[,#|#..#[,etc.]]>
   <from GROUP_NAME>
   <manage_subobjects[manage_subobjects]|no_manage_subobjects>
   <region PATH_TO_REGION[/]>

gfx create region

Create a region at the supplied path, with names in the path separated by slash '/' characters. Use the 'no_error_if_exists' option to avoid errors if region exists already.

   <error_if_exists[error_if_exists]|no_error_if_exists>
   <PATH_TO_REGION>

gfx create snake

   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <density_factor #[0]{>=0,<=1}>
   <source_group PATH_TO_REGION>
   <destination_group REGION_PATH/GROUP>
   <fitting_fields FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <number_of_fitting_fields #[1]{>0,integer}>
   <number_of_elements #[1]{>0,integer}>
   <stiffness #[0]{>=0}>
   <weight_field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx create spectrum SPECTRUM_NAME

   <autorange>
   <blue_to_red>
   <blue_white_red>
   <clear>
   <field
   <linear
   <lg_red_to_blue>
   <maximum MAXIMUM_VALUE#[0]>
   <minimum MINIMUM_VALUE#[0]>
   <overlay_colour>
   <overwrite_colour>
   <scene_for_autorange PATH_TO_SCENE[/]>
   <red_to_blue>

gfx create texture TEXTURE_NAME

   <alpha #[0]{>=0,<=1}>
   <blend|decal[decal]|modulate|add|signed_add|scale_4_modulate|scale_4_blend|subtract|scale_4_add|scale_4_subtract|invert_scale_4_add|invert_scale_4_subtract>
   <clamp_wrap|repeat_wrap[repeat_wrap]|edge_clamp_wrap|border_clamp_wrap|mirrored_repeat_wrap>
   <colour RED#[0]{>=0,<=1} GREEN#[0]{>=0,<=1} BLUE#[0]{>=0,<=1}>
   <uncompressed[uncompressed]|compressed_unspecified>
   <depth #[1]{>=0}>
   <distortion DISTORTION_CENTRE_X DISTORTION_CENTRE_Y DISTORTION_FACTOR_K1>
   <height #[1]{>0}>
   <image <crop LEFT_MARGIN#[0] BOTTOM_MARGIN#[0] WIDTH#[0] HEIGHT#[0]>
   <nearest_filter[nearest_filter]|linear_filter|filter_nearest_mipmap_nearest|filter_linear_mipmap_nearest|filter_linear_mipmap_linear>
   <mipmap_level_of_detail_bias #[0]>
   <number_pattern NAME>
   <number_series START STOP INCREMENT>
   <raw_interleaved_rgb|raw_planar_rgb[raw_planar_rgb]>
   <resize_linear_filter|resize_nearest_filter[resize_nearest_filter]>
   <specify_depth #[0]{>=0,integer}>
   <specify_format i|ia|rgb[rgb]|rgba|abgr>
   <specify_height #[0]{>=0,integer}>
   <specify_number_of_bytes_per_component #[0]{>=0,integer}>
   <specify_width #[0]{>=0,integer}>
   <texture_tiling>
   <no_texture_tiling>
   <width #[1]{>0}>
   <evaluate_image

gfx create window

   <accumulation_buffer_depth #[8]{>=0,integer}>
   <any_buffer_mode|double_buffer|single_buffer>
   <any_stereo_mode|mono_buffer|stereo_buffer>
   <colour_buffer_depth #[8]{>=0,integer}>
   <depth_buffer_depth #[8]{>=0,integer}>
   <name NAME[1]>
   <NAME[1]>

gfx data_tool

   <coordinate_fieldNAME>
   <constrain_to_surfaces|no_constrain_to_surfaces[no_constrain_to_surfaces]>
   <create|no_create[no_create]>
   <define|no_define[no_define]>
   <edit|no_edit[no_edit]>
   <element_xi_fieldNAME>
   <group REGION_PATH/GROUP>
   <motion_update|no_motion_update[no_motion_update]>
   <select[select]|no_select>
   <streaming_create|no_streaming_create[no_streaming_create]>
   <command_fieldNAME>

gfx define

   curve
   faces
   field
   font FONT_NAME FONT_STRING
   sceneWARNING: To define a filter and light on a graphics window please see gfx modify window command
   graphics_filter
   tessellation

gfx define curve CURVE_NAME <c.Hermite|c.Lagrange|l.Lagrange|q.Lagrange>


gfx define faces <egroup REGION_PATH/GROUP>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME]

   2d_strain
   abs
   acos
   add
   alias
   and
   asin
   atan
   atan2
   basis_derivative
   binary_dilate_filter
   binary_erode_filter
   binary_threshold_filter
   canny_edge_detection_filter
   clamp_maximum
   clamp_minimum
   cmiss_number
   component
   compose
   composite
   connected_threshold_filter
   constant
   coordinate_transformation
   cos
   cross_product
   cubic_texture_coordinates
   curl
   curvature_anisotropic_diffusion_filter
   curve_lookup
   derivative
   derivative_filter
   determinant
   discrete_gaussian_filter
   divergence
   divide_components
   dot_product
   edge_discontinuity
   edit_mask
   eigenvalues
   eigenvectors
   embedded
   equal_to
   exp
   fast_marching_filter
   fibre_axes
   find_mesh_location
   finite_element
   format_output
   function
   gradient
   gradient_magnitude_recursive_gaussian_filter
   greater_than
   histogram_filter
   if
   image
   image_resample
   integration
   is_defined
   is_exterior
   is_on_face
   less_than
   log
   magnitude
   matrix_invert
   matrix_multiply
   matrix_to_quaternion
   mean_filter
   mesh_integral
   mesh_integral_squares
   multiply_components
   nodal_lookup
   node_value
   nodeset_maximum
   nodeset_mean
   nodeset_mean_squares
   nodeset_minimum
   nodeset_sum
   nodeset_sum_squares
   normalise
   not
   offset
   or
   power
   projection
   quaternion_SLERP
   quaternion_to_matrix
   rescale_intensity_filter
   sample_texture
   scale
   sigmoid_filter
   sin
   sqrt
   string_constant
   sum_components
   tan
   threshold_filter
   time_lookup
   time_value
   transpose
   vector_coordinate_transformation
   window_projection
   xi_coordinates
   xi_texture_coordinates
   xor

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] 2d_strain

   <deformed_coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <undeformed_coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <fibre_angle FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] abs <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] acos <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] add

   <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <scale_factors # #[1 1]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] alias <field [[/]REGION_PATH/]FIELD_NAME>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] and <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] asin <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] atan <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] atan2 <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] basis_derivative

The basis_derivative calculates a monomial derivative on element based fields. It is not defined for nodes. It allows you to calculate an arbitrary derivative by specifying an <order> and a list of <xi_indices> of length order. This derivative then becomes the "value" for the field.

   <fe_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <order #[1]{>0,integer}>
   <xi_indices #[1]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] binary_dilate_filter

The binary_dilate_filter field uses the itk::BinaryDilateImageFilter code to produce an output field which is a dilation of a binary image (an image where each pixel has 1 of 2 values). The region identified by the pixels with intensity <dilate_value> is dilate (enlarged), by replacing each pixel with a ball. The size of the ball is set by specifying the <radius>. The <field> it operates on is usually a thresholded or segmented field. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <radius #[1]{>=0,integer}>
   <dilate_value #[1]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] binary_erode_filter

The binary_erode_filter field uses the itk::BinaryErodeImageFilter code to produce an output field which is a erosion of a binary image (an image where each pixel has 1 of 2 values). The region identified by the pixels with intensity <erode_value> is eroded (decreased). The erosion effect can be increase by inreasing the <radius> value. The <field> it operates on is usually a thresholded or segmented field. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <radius #[1]{>=0,integer}>
   <erode_value #[1]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] binary_threshold_filter

The binary_threshold_filter field uses the itk::BinaryThresholdImageFilter code to produce an output field where each pixel has one of two values (either 0 or 1). It is useful for separating out regions of interest. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). Pixels with an intensity range between <lower_threshold> and the <upper_threshold> are set to 1, the rest are set to 0. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <lower_threshold #[0]>
   <upper_threshold #[1]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] canny_edge_detection_filter

The canny_edge_detection field uses the itk::CannyEdgeDetectionImageFilter code to detect edges in a field. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). Increasing the <variance> smooths the input image more, which reduces sensitivity to image noise at the expense of losing some detail. Decreasing the <maximum_error> also reduces edges detected as the result of noise. The <upper_threshold> sets the level which a point must be above to use it as the start of the edge. The edge will then grow from that point until the level drops below the <lower_threshold>. Increasing the <upper_threshold> will decrease the number of edges detected. Increasing the <lower_threshold> will reduce the length of edges. See a/testing/image_processing_2D for an example of using this field.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <variance #[0]>
   <maximum_error #[0.01]>
   <upper_threshold #[0]>
   <lower_threshold #[0]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] clamp_maximum

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <maximums VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] clamp_minimum

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <minimums VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] component < #|FIELD[.COMPONENT_NAME] #|FIELD[.COMPONENT_NAME] #|FIELD[.COMPONENT_NAME] ... >


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] compose

The value of a compose field is found by evaluating the <texture_coordinates_field>, then searching for matching values of the <find_element_xi_field> in the elements of the <mesh> (alternatively specified by <group> and <element_dimension>) and then finally evaluating the <calculate_values_field> at this found location. You can specify the outcome if the matching values cannot be found in the mesh with <use_point_five_when_out_of_bounds> or <fail_when_out_of_bounds>. See examples a/resample_texture or a/create_slices where the compose field is used to find the equivalent coordinate in another element to evaluate a texture.

   <calculate_values_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <element_dimension #[0]{>0,integer}>
   <find_element_xi_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <find_nearest|find_exact>
   <group GROUP_NAME>
   <mesh ELEMENT_GROUP_FIELD_NAME|[GROUP_NAME.]mesh1d|mesh2d|mesh3d[none]>
   <texture_coordinates_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <use_point_five_when_out_of_bounds|fail_when_out_of_bounds>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] composite < #|FIELD[.COMPONENT_NAME] #|FIELD[.COMPONENT_NAME] #|FIELD[.COMPONENT_NAME] ... >


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] connected_threshold_filter

The connected_threshold_filter field uses the itk::ConnectedThresholdImageFilter code to segment a field. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). The segmentation is based on a region growing algorithm which requires at least one seed point. To specify the seed points first set the <num_seed_points> and the <dimension> of the image. The <seed_points> are a list of the coordinates for the first and any subsequent seed points. Starting from the seed points any neighbouring pixels with an intensity between <lower_threshold> and the <upper_threshold> are added to the region. Pixels within the region have their pixel intensity set to <replace_value> while the remaining pixels are set to 0. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <lower_threshold #[0]>
   <upper_threshold #[1]>
   <replace_value #[1]>
   <num_seed_points #[0]{>0,integer}>
   <dimension #[2]{>0,integer}>
   <seed_points VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] constant < VALUES>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] coordinate_transformation <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] cos <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] cross_product

   <dimension #[3]{>0,integer}>
   <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] cubic_texture_coordinates <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] curl

   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <vector FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] curvature_anisotropic_diffusion_filter

The curvature_anisotropic_filter field uses the itk::CurvatureAnisotropicImageFilter code to smooth a field to reduce noise (or unwanted detail) while preserving edges. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). The smoothing is accomplished by numerically solving a modified curvature diffusion equation. The accuracy of the numerical solution can be adjusted by varying the <time_step> and <num_iterations> used. The <conductance> is a parameter used by the diffusion equation. A high value of conductance causes the image to diffuse (smooth) more, while a low value puts more emphasis on preserving features. Typical conductance values are often in the range 0.5 to 2. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <time_step #[0.125]>
   <conductance #[3]>
   <num_iterations #[5]{>=0,integer}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] curve_lookup

   <curve CURVE_NAME|none[none]>
   <source FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] derivative

The derivative field has two modes of operation. For normal finite element fields it simply promotes the derivative values corresponding to <xi_index> calculated by the input <field> to be the field values. These derivatives are with respect to xi. If the input <field> cannot cannot calculate element based derivatives then if the input field has a native resolution then this field uses the ITK DerivativeImageFilter to calculate a pixel based derivative at that same resolution. The derivative filter will use the image pixel physical spacing if that is defined for ITK. Note that as the derivative is a signed value you may want to offset and scale the resultant values if you intend to store them in an unsigned pixel format.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <xi_index #[1]{>0,integer}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] derivative_filter

The derivative_filter field uses the itk::DerivativeImageFilter code to calculate the derivative of a field in a particular direction. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). The <order> paramater sets the order of the derivative and the <direction> parameter is an integer value that specifies the direction to evaluate the derivative in. 0 corresponds to the x direction. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <order #[1]{>=0,integer}>
   <direction #[1]{>=0,integer}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] determinant <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] discrete_gaussian_filter

The discrete_gaussian_filter field uses the itk::DiscreteGaussianImageFilter code to smooth a field. It is useful for removing noise or unwanted detail. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). The effect of applying a discrete gaussian image filter is that a pixel value is based on a weighted average of surrounding pixel values, where the closer the pixel the more weight its value is given. Increasing the <variance> increases the width of the gaussian distribution used and hence the number of pixels used to calculate the weighted average. This smooths the image more. A limit is set on the <max_kernel_width> used to approximate the guassian to ensure the calculation completes. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <variance #[1]>
   <max_kernel_width #[4]{>0,integer}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] divergence

   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <vector FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] divide_components <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] dot_product <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] edge_discontinuity

An edge_discontinuity field produces a value on 1-D line elements with as many components as the source field, which gives the discontinuity of that field between two adjacent surfaces by a chosen measure. An optional conditional field restricts which adjacent surfaces qualify to those where the conditional field is true (non-zero). The first two qualifying surfaces are always used. The field values are zero when the surfaces are continuous by the chosen measure, and when there are fewer than two qualifying adjacent surfaces. Supported measures of discontinuity are C1 (the default, giving the difference in transverse xi derivatives), G1 (difference in transverse xi derivatives, normalised so only direction matters) and SURFACE_NORMAL (difference in unit surface normals, for 3-component coordinate source field only). In optimisation problems, adding an objective field consisting of the integral of [squares of] this field over a 1-D mesh will favour high-continuity solutions.

   <conditional_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <measure_c1[measure_c1]|measure_g1|measure_surface_normal>
   <source_field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] edit_mask

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <edit_mask VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] eigenvalues <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] eigenvectors <eigenvalues FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] embedded

An embedded field returns the value of a source field at the location given by the element_xi field - a field whose value is a location in a mesh.

   <element_xi FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] equal_to <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] exp <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] fast_marching_filter

The fast_marching_filter field uses the itk::FastMarchingImageFilter code to segment a field. The segmentation is based on a level set algorithm. The <field> it operates on is used as a speed term, to govern where the level set curve grows quickly. The speed term is usually some function (eg a sigmoid) of an image gradient field. The output field is a time crossing map, where the value at is each pixel is the time take to reach that location from the specified seed points. Values typically range from 0 through to extremely large (10 to the 38). To convert the time cross map into a segmented region use a binary threshold filter. To specify the seed points first set the <num_seed_points> and the <dimension> of the image. The <seed_points> are a list of the coordinates for the first and any subsequent seed points. It is also possible to specify non-zero initial <seed_values> if desired and to set the <output_size> of the time crossing map. See a/segmentation for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <stopping_value #[100]>
   <num_seed_points #[1]{>0,integer}>
   <dimension #[2]{>0,integer}>
   <seed_points # #[0.5 0.5]>
   <seed_values #[0]>
   <output_size # #[128 128]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] fibre_axes

   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <fibre FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] find_mesh_location

A find_mesh_location field calculates the source_field then finds and returns the location in the mesh where the mesh_field has the same value. Use an embedded field to evaluate other fields on the mesh at the found location. Option find_nearest returns the location with the nearest value of the mesh_field if no exact match is found.

   <find_nearest|find_exact[find_exact]>
   <mesh ELEMENT_GROUP_FIELD_NAME|[GROUP_NAME.]mesh1d|mesh2d|mesh3d[none]>
   <mesh_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <source_field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] finite_element

   <anatomical|coordinate|field[field]>
   <component_names NAME[1]>
   <double|element_xi|real[real]|float|integer|short|string|unsigned|url>
   <number_of_components #[1]{>0,integer}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] format_output

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <format_stringC style formatting string>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] function

The value of a function field is found by evaluating the <source_field> values, and then evaluating the <result_field> with respect to the <reference_field> using the values from the source field. The sequence of operations <reference_field> to <result_field> become a function operating on the input <source_field> values. Either the number of components in the <source_field> and <reference_field> should be the same, and then the number of components of this <field> will be the same as the number of components in the <result_field>, or if the <reference_field> and <result_field> are scalar then the function operation will be applied as many times as required for each component in the <source_field> and then this <field> will have as many components as the <source_field>.

   <reference_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <result_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <source_field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] gradient

The gradient field calculates the partial derivatives of each of the source field components with respect to each of the coordinate field components. The first values are each of the source field components with respect to the first coordinate component and then each of the source field components wrt to the second coordinate component and so on. This field can now be used at both element_xi and nodal locations. At element_xi locations the basis function supplied xi derivative is multiplied by the basis function coordinate field jacobian. For nodal locations a finite difference approximation is calculated by perturbing each of the coordinate field values and reevaluating the source field. See a/graph_axes for an example of using the gradient field to calculate the number of pixels per ndc coordinate.

   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] gradient_magnitude_recursive_gaussian_filter

The gradient_magnitude_recursive_filter field uses the itk::GradientMagnitudeRecursiveImageFilter code to compute the magnitude of the image gradient at each location in the field. It is useful for identifying regions where the pixel intensities change rapidly. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). The filter first smooths the image using a discrete gaussian image subfilter before calculating the gradient and magnitudes. Increasing <sigma> increases the width of the gaussian distribution used during the smoothing and hence the number of pixels used to calculate the weighted average. This smooths the image more. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <sigma #[2]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] greater_than <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] histogram_filter

The histogram_filter field uses the itk::ImageToHistogramGenerator code to generate binned values representing the relative frequency of the various pixel intensities. There should be a number_of_bins for each component direction, and so the total number of bins will be a product of these, so that for a 3 component image you would get a volume histogram. If you wanted a histogram for a single component then set the number_of_bins for the other components to 1. If you do not set the optional histogram_minimums or histogram_maximums (which is a vector of values, 1 for each source component) then the histogram will automatically range the values to the minimum and maximum values in the source image.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <histogram_minimums #[0]>
   <histogram_maximums #[1]>
   <number_of_bins #[64]{>0,integer}>
   <marginal_scale #[10]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] if <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] image

The image field allows you to look up the values of a <texture>. This sample_texture interface wraps an existing texture in a image field. The resulting field will have the same number of components as the texture it was created from. If <field> is specified, it will be used as the source and the image field will create a texture using the field values either when <coordinates> is provided or source field has a texture coordinates defined already; the format of texture it creates depends on the number of components of the provided field. 1 component field creates a LUMINANCE texture, 2 component field creates a LUMINANCE_ALPHA texture, 3 component field creates a RGB texture, 4 component field creates a RGBA texture. The native_texture, maximum and minimum setting does not affect image field generated from another field. The <number_of_bytes_per_pixel> values only works with image field based on a field, it will affect the number of bytes of the generated image. The <coordinates> field is used as the texel location, with values from 0..texture_width, 0..texture_height and 0..texture_depth valid coordinates within the image. Normally the resulting colour values are real values for 0 to 1. The <minimum> and <maximum> values can be used to rerange the colour values. The <texture_coordinates_sizes> will set the texture_width,texture_height and texture_depth used by the coordinates field to determinedthe texel location.

   <coordinates FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <number_of_bytes_per_component #[1]{>=0,integer}>
   <maximum #[1]{>=0}>
   <minimum #[0]{>=0}>
   <texture_coordinates_sizes # # #[1 1 1]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] image_resample

The image_resample field resamples the field to a new user specified size. It is especially useful for resizing image based fields. The new size of the field is specified by using the <sizes> option with a list of values for the new size in each dimension. See a/testing/image_processing_2D for an example of using this field.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <sizes VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] integration

   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <integrand FIELD_NAME[.COMPONENT_NAME]|none[constant_1.0]>
   <magnitude_coordinates|no_magnitude_coordinates[no_magnitude_coordinates]>
   <mesh ELEMENT_GROUP_FIELD_NAME|[GROUP_NAME.]mesh1d|mesh2d|mesh3d[none]>
   <region GROUP_NAME(DEPRECATED)>
   <seed_element #[0]{>=0,integer}>
   <update_time_integration #[0]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] is_defined <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] is_on_face <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] less_than <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] log <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] magnitude <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] matrix_invert <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] matrix_multiply

A matrix_mutliply field calculates the product of two matrices, giving a new m by n matrix. The product is represented as a field with a list of (m * n) components. The components of the matrix are listed row by row. The <number_of_rows> m is used to infer the dimensions of the source matrices. The two source <fields> are multiplied, with the components of the first interpreted as a matrix with dimensions m by s and the second as a matrix with dimensions s by n. If the matrix dimensions are not consistent then an error is returned. See a/curvature for an example of using the matrix_multiply field.

   <number_of_rows #[1]{>0,integer}>
   <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] matrix_to_quaternion <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] mean_filter

The mean_filter field uses the itk::MeanImageFilter code to replace each pixel with the mean intensity of the pixel and its surrounding neighbours. It is useful for reducing the level of noise. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). The size of the neighbourhood of pixels used to calculate the mean is determined be a list of <radius_sizes>, one value for each dimension. Each radius size sets how many pixels to include either side of the central pixel for the corresponding dimension. If radius values are increased, more neighbouring pixels are included and the image becomes smoother. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <radius_sizes VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] mesh_integral

A mesh_integral field calculates the integral of each of the integrand field's component values over the mesh multiplied by differential volume/area/length, depending on the mesh dimension, calculated from the coordinate field which is assumed to be rectangular Cartesian; use a coordinate_transformation field if it is not. Different quadrature rules are supported. The numbers of quadrature points are applied on the top-level element with the appropriate values inherited on faces and lines; this is only important if different numbers are used in each element axis. Simplex elements use the maximum number set on on any linked dimension. For 1-D Gaussian quadrature, N points exactly integrates a polynomial of degree 2N - 1, however 1 more point than the degree is often needed to avoid spurious modes in many numerical solutions. Simplex elements use specialised point arrangements that are sufficient for integrating a polynomial with the same degree as the number of points. The maximum number of Gauss points on each element axis is currently 4; if a higher number is supplied, only 4 are used. There is no upper limit on the numbers of points with midpoint quadrature. Note: assumes all elements of the mesh have a right-handed coordinate system; if this is not the case the integral will be incorrect.

   <coordinate_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <gaussian_quadrature[gaussian_quadrature]|midpoint_quadrature>
   <integrand_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <mesh ELEMENT_GROUP_FIELD_NAME|[GROUP_NAME.]mesh1d|mesh2d|mesh3d>
   <numbers_of_points "#*#*..."["1"]{>=0}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] mesh_integral_squares

A mesh_integral_squares field is a specialisation of the mesh_integral field type that integrates the squares of the components of the integrand field. Note that the volume/area/length and weights are not squared in the integral. This field type supports least-squares optimisation by giving individual terms being squared and summed.

   <coordinate_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <gaussian_quadrature[gaussian_quadrature]|midpoint_quadrature>
   <integrand_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <mesh ELEMENT_GROUP_FIELD_NAME|[GROUP_NAME.]mesh1d|mesh2d|mesh3d>
   <numbers_of_points "#*#*..."["1"]{>=0}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] multiply_components <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] nodal_lookup

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <node #[NOT SET]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints[nodes][nodes]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] node_value

   <fe_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <value[value]|d/ds1|d/ds2|d/ds3|d2/ds1ds2|d2/ds1ds3|d2/ds2ds3|d3/ds1ds2ds3>
   <version #[1]{>0,integer}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] nodeset_maximum

A nodeset_maximum field returns the maximum value of each component of the source field over the nodeset.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] nodeset_mean

A nodeset_mean field calculates the means of each of the supplied field's component values over all nodes in the nodeset over which it is defined.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] nodeset_mean_squares

A nodeset_mean_squares field calculates the means of the squares of each of the supplied field's component values over all nodes in the nodeset over which it is defined. This field supplies individual terms to least-squares optimisation methods. See 'gfx minimise' command.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] nodeset_minimum

A nodeset_minimum field returns the minimum value of each component of the source field over the nodeset.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] nodeset_sum

A nodeset_sum field calculates the sums of each of the supplied field's component values over all nodes in the nodeset over which it is defined.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] nodeset_sum_squares

A nodeset_sum_squares field calculates the sums of the squares of each of the supplied field's component values over all nodes in the nodeset over which it is defined. This field supplies individual terms to least-squares optimisation methods. See 'gfx minimise' command.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] normalise <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] not <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] offset

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <offsets VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] or <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] power <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] projection

Creates a projection field returning the result of a matrix multiplication with perspective division on the source field vector. The source_field vector is expanded to a homogeneous coordinate by appending a component of value 1, which is multiplied by the projection_matrix field, and the extra calculated value resulting from the unit component is used to divide through each of the other components to give a perspective projection in the resulting field. The projection_matrix field must have have a multiple of (source_field->number_of_components + 1) components forming a matrix with that many columns and the resulting (number_of_components + 1) rows. The first values in the projection_matrix are across the first row, followed by the next row and so on. Hence a 4x4 matrix transforms a 3-component vector to a 3-component vector.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <projection_matrix FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] quaternion_SLERP

A 4 components quaternion field. The components of the quaternion field are expected to be the w, x, y, z componentsof a quaternion (4 components in total). The quaternion field isevaluated and interpolated using SLERP at a normalised time between twoquaternions (read in from the exnode generally). This quaternion fieldcan be convert to a matrix with quaternion_to_matrix field, the resultingmatrix can be used to create a smooth time dependent rotation for an objectusing the quaternion_to_matrix field. This field must be define directly fromexnode file or from a matrix_to_quaternion field

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <node #[NOT SET]>
   <nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints[nodes][nodes]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] quaternion_to_matrix <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] rescale_intensity_filter

The rescale_intensity_filter field uses the itk::RescaleIntensityImageFilter code to linearly scale the pixel intensity to vary between the specified minimum and maximum intensity values. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). Set the <output_min> and <output_max> values to define the new range to scale to. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <output_min #[0]>
   <output_max #[255]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] sample_texture

The image field allows you to look up the values of a <texture>. This sample_texture interface wraps an existing texture in a image field. The resulting field will have the same number of components as the texture it was created from. If <field> is specified, it will be used as the source and the image field will create a texture using the field values either when <coordinates> is provided or source field has a texture coordinates defined already; the format of texture it creates depends on the number of components of the provided field. 1 component field creates a LUMINANCE texture, 2 component field creates a LUMINANCE_ALPHA texture, 3 component field creates a RGB texture, 4 component field creates a RGBA texture. The native_texture, maximum and minimum setting does not affect image field generated from another field. The <number_of_bytes_per_pixel> values only works with image field based on a field, it will affect the number of bytes of the generated image. The <coordinates> field is used as the texel location, with values from 0..texture_width, 0..texture_height and 0..texture_depth valid coordinates within the image. Normally the resulting colour values are real values for 0 to 1. The <minimum> and <maximum> values can be used to rerange the colour values. The <texture_coordinates_sizes> will set the texture_width,texture_height and texture_depth used by the coordinates field to determinedthe texel location.

   <coordinates FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <number_of_bytes_per_component #[1]{>=0,integer}>
   <maximum #[1]{>=0}>
   <minimum #[0]{>=0}>
   <texture_coordinates_sizes # # #[1 1 1]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] scale

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <scale_factors VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] sigmoid_filter

The sigmoid_filter field uses the itk::SigmoidImageFilter code to nonlinearly scale the pixel intensity to vary between the specified minimum and maximum intensity values according to a sigmoid curve. It is useful for focusing attention on a particular set of values while providing a smooth transition at the borders of the range. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). Intensity values are rescaled to vary from the <minimum> to the <maximum> value using a sigmoid curve which has a width and centre defined by <alpha> and <beta>. Increasing the <alpha> parameter widens the curve while increasing the <beta> parameter moves the centre of the curve to the right. See a/testing/image_processing_2D for an example of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <minimum #[0]>
   <maximum #[1]>
   <alpha #[0.25]>
   <beta #[0.5]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] sin <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] sqrt <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] string_constant <STRING>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] sum_components

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <weights VALUES>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] tan <field FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] threshold_filter

The threshold_filter field uses the itk::ThresholdImageFilter code to change or identify pixels based on whether they are above or below a particular intensity value. The <field> it operates on is usually a sample_texture field, based on a texture that has been created from image file(s). To specify an intensity range to change use one of the three threshold modes: <below>, <above> or <outside>. Pixels within the specified range are changed to the <outside_value> intensity, the other pixels are left unchanged. For the <below> mode all pixels are changed that are below the <below_value>. For the <above> mode all pixels are changed that are above the <above_value>. For the <outside> mode all pixels are changed that are oustide the range <below_value> to <above_value> . See a/testing/image_processing_2D for examples of using this field. For more information see the itk software guide.

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <above|below[below]|outside>
   <outside_value #[0]>
   <below_value #[0.5]>
   <above_value #[0.5]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] time_lookup

   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <time_field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] transpose

A transpose field returns the transpose of a source matrix field. If the source <field> has (m * n) components where m is specified by <source_number_of_rows> (with the first n components being the first row), the result is its (n * m) transpose. See a/current_density for an example of using the matrix_invert field.

   <source_number_of_rows #[1]{>0,integer}>
   <field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] vector_coordinate_transformation

   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <vector FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] window_projection

A 16 component computed field which continuously update the transformation between 'from' and 'to' graphics_coordinate systems in the give pane of window.

   <pane_number #[1]{>0,integer}>
   <window WINDOW_NUMBER>
   <from_coordinate_system LOCAL|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <to_coordinate_system LOCAL|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] xi_texture_coordinates

   <mesh ELEMENT_GROUP_FIELD_NAME|[GROUP_NAME.]mesh1d|mesh2d|mesh3d[none]>
   <region GROUP_NAME(OBSOLETE)>
   <seed_element #[0]{>=0,integer}>

gfx define field [REGION_PATH/]FIELD_NAME [coordinate_system NAME] xor <fields FIELD_NAME[.COMPONENT_NAME]|none[none] FIELD_NAME[.COMPONENT_NAME]|none[none]>


gfx define graphics_filter GRAPHICS_FILTER_NAME

Filter to set up what will be and what will not be included in a scene. The optional inverse_match flag will invert the filter's match criterion. The behaviour is to show matching graphics with the matching criteria. <match_graphics_name> filters graphics with the matching name. <match_visibility_flags> filters graphics with the setting on the visibility flag. <match_region_path> filters graphics in the specified region or its subregion. <operator_or> filters the scene using the logical operation 'or' on a collective of filters. <operator_and> filters the scene using the logical operation 'and' on a collective of filters. Filters created earlier can be added or removed from the <operator_or> and <operator_and> filter.

   <operator_or
   <match_graphics_name MATCH_NAME>
   <match_visibility_flags>
   <match_region_path REGION_PATH>
   <inverse_match|normal_match[normal_match]>

gfx define tessellation TESSELLATION_NAME

Defines tessellation objects which control how finite elements are subdivided into graphics. The minimum_divisions option gives the minimum number of linear segments approximating geometry in each xi dimension of the element. If the coordinate field of a graphics uses non-linear basis functions the minimum_divisions is multiplied by the refinement_factors to give the refined number of segments. Both minimum_divisions and refinement_factors use the last supplied number for all higher dimensions, so "4" = "4*4" and so on. The circle_divisions sets the number of line segments used to approximate circles in cylinders, spheres etc.

   <circle_divisions #{integer>=3}>
   <minimum_divisions "#*#*..."["1"]{>=0}>
   <refinement_factors "#*#*..."["1"]{>=0}>

gfx destroy

   curve CURVE_NAME
   data
   dgroup REGION_PATH/GROUP
   egroup REGION_PATH/GROUP
   elements
   faces
   field [REGION_PATH/]FIELD_NAME
   graphics_object GRAPHICS_OBJECT_NAME
   lines
   material MATERIAL_NAME
   ngroup REGION_PATH/GROUP
   nodes
   region REGION_PATH
   scene Scene is now the 1 to 1  graphics properties of a region and cannot be destroyed
   spectrum SPECTRUM_NAME
   tessellation
   vtextures <NAME[all]>

gfx destroy data

   <all>
   <conditional_field FIELD_NAME>
   <group REGION_PATH/GROUP>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx destroy elements

   <all>
   <conditional_field FIELD_NAME>
   <group REGION_PATH/GROUP>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx destroy faces

   <all>
   <conditional_field FIELD_NAME>
   <group REGION_PATH/GROUP>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx destroy lines

   <all>
   <conditional_field FIELD_NAME>
   <group REGION_PATH/GROUP>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx destroy nodes

   <all>
   <conditional_field FIELD_NAME>
   <group REGION_PATH/GROUP>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx destroy tessellation < TESSELLATION_NAME|none[none]>


gfx draw

   <as NAME>
   <glyph GLYPH_NAME|none[none]>
   <group PATH_TO_REGION>
   <scene PATH_TO_SCENE[/]>
   < GLYPH_NAME|none[none]>

gfx edit

   graphics_object
   scene
   spectrum

gfx edit graphics_object

   <apply_transformation>
   <name NAME>
   <NAME>

gfx edit scene <close>


gfx edit spectrum < SPECTRUM_NAME|none[none]>


gfx element_point_tool

   <open_dialog|close_dialog>
   <command_field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx element_tool

   <open_dialog|close_dialog>
   <select_elements[select_elements]|no_select_elements>
   <select_faces[select_faces]|no_select_faces>
   <select_lines[select_lines]|no_select_lines>
   <command_field FIELD_NAME[.COMPONENT_NAME]|none[none]>

gfx evaluate

   <destination FIELD_NAME>
   <dgroup REGION_PATH/GROUP_NAME>
   <egroup REGION_PATH/GROUP_NAME>
   <ngroup REGION_PATH/GROUP_NAME>
   <selected>
   <source FIELD_NAME>

gfx export

   alias
   cm
   iges
   stl
   threejs
   vrml
   wavefront
   webgl

gfx export alias <sceneERROR: set_Scene. Missing state


gfx export cm

   <field FIELD_NAME|none[none]>
   <ipcoor_filenameNAME>
   <ipbase_filenameNAME>
   <ipmap_filenameNAME>
   <ipnode_filenameNAME>
   <ipelem_filenameNAME>
   <region PATH_TO_REGION>

gfx export iges

   <coordinate_field NAME>
   <group PATH_TO_REGION[/]>
   <FILE_NAME>

gfx export stl

   <file NAME>
   <scene PATH_TO_SCENE[/]>
   <filter GRAPHICS_FILTER_NAME|none[default]>

gfx export threejs

Creates a json file containing data of primitives readable using ThreeJS for web browser rendering of 3D surfaces. [file_prefix] dictates the export file's name, name of the export will be in the following format - [file_prefix]_[region]_[graphicsname].json. [start_time], [end_time] and [number_of_time_steps] must be used together; when specified animated mesh will be generated. [data_export_colour] will export the data on per vertices basis as spectrum colours when data and spectrum are specified for surface graphics. [data_export_per_vertex_value] will export the data for each vertex as hex when data is specified on graphics. [data_export_per_face_value] will export the data for each face as hex when data is specified on graphics, this should be used with per element constant field (e.g ID). must be used together; when specified animated mesh will be generated. [scene] generates the exports for this scene and its children. [filter] applies the filter the provided scene.

   <file_prefix NAME>
   <start_time #[0]>
   <end_time #[0]>
   <number_of_time_steps #[0]{>=0,integer}>
   <data_export_colour[data_export_colour]|data_export_per_vertex_value|data_export_per_face_value>
   <scene PATH_TO_SCENE[/]>
   <filter GRAPHICS_FILTER_NAME|none[default]>

gfx export vrml

   <file NAME>
   <scene PATH_TO_SCENE[/]>
   <filter GRAPHICS_FILTER_NAME|none[default]>

gfx export wavefront

   <file NAME>
   <frame_number #[0]{>=0,integer}>
   <full_comments>
   <number_of_frames #[100]{>0,integer}>
   <sceneERROR: set_Scene.  Missing state
   <version #[3]{>0,integer}>
   <filter>

gfx export webgl

   <file NAME>
   <scene PATH_TO_SCENE[/]>
   <filter GRAPHICS_FILTER_NAME|none[default]>

gfx list

   all_commands [ALL]
   btree_statistics
   curve
   data
   elements
   environment_map ENVIRONMENT_MAP_NAME
   faces
   field
   g_element
   glyph OBJECT_NAME[ALL]
   graphics_filter
   grid_points
   group PATH_TO_REGION[/]
   light LIGHT_NAME
   lines
   lmodel LIGHT_MODEL_NAME
   material
   nodes
   region REGION_PATH
   sceneWARNING: gfx list scene:  Scene is now the direct graphical representation of a region, please use gfx list g_element instead.
   spectrum
   tessellation
   texture
   transformation
   window

gfx list btree_statistics <region PATH_TO_REGION[/]>


gfx list curve < CURVE_NAME|none[none]>


gfx list data

   <all>
   <region PATH_TO_REGION[/]>
   <selected>
   <conditional FIELD_NAME>
   <verbose>
   < #|#..#[,#|#..#[,etc.]]>

gfx list elements

   <all>
   <region PATH_TO_REGION[/]>
   <selected>
   <conditional FIELD_NAME>
   <verbose>
   < #|#..#[,#|#..#[,etc.]]>

gfx list faces

   <all>
   <region PATH_TO_REGION[/]>
   <selected>
   <conditional FIELD_NAME>
   <verbose>
   < #|#..#[,#|#..#[,etc.]]>

gfx list field

   <commands>
   < REGION_PATH|REGION_PATH/FIELD_NAME|FIELD_NAME>

gfx list g_element

   <commands[commands]|description>
   <recursive[recursive]|non_recursive>
   < PATH_TO_REGION[/]>

gfx list graphics_filter <GRAPHICS_FILTER_NAME[all]>


gfx list grid_points

   <all>
   <grid_field FIELD_NAME|none[none]>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx list lines

   <all>
   <region PATH_TO_REGION[/]>
   <selected>
   <conditional FIELD_NAME>
   <verbose>
   < #|#..#[,#|#..#[,etc.]]>

gfx list material

   <commands>
   <name MATERIAL_NAME|none[none]>
   < MATERIAL_NAME|none[none]>

gfx list nodes

   <all>
   <region PATH_TO_REGION[/]>
   <selected>
   <conditional FIELD_NAME>
   <verbose>
   < #|#..#[,#|#..#[,etc.]]>

gfx list spectrum

   <commands>
   < SPECTRUM_NAME|none[none]>

gfx list tessellation < TESSELLATION_NAME|none[none]>


gfx list texture

   <region NAME>
   <commands>
   <field NAME>

gfx list transformation

   <commands>
   <region NAME>

gfx list window

   <commands>
   <name WINDOW_NUMBER>
   < WINDOW_NUMBER>

gfx minimise

Optimise the parameters of the independent_fields (actually dependent fields as far as the optimisation is concerned) to give the minimum values of the objective_fields' components, equally weighted if more than one. The conditional_fields control which parameters of the independent fields to use and must be listed in the same order. Parameters are used only at nodes where the conditional is non-zero; if the conditional field has an equal number of components as the corresponding independent field, the condition is applied per-component. Field types 'nodeset_sum_squares' and 'mesh_integral_squares' have special behaviour with the LEAST_SQUARES_QUASI_NEWTON solution method, supplying individual terms for the least squares solution, useful for least squares fitting problems.

   <conditional_fields FIELD_NAME|none [& FIELD_NAME|none [& ...]]>
   <independent_fields FIELD_NAME [& FIELD_NAME [& ...]]>
   <maximum_iterations #[100]{>0,integer}>
   <QUASI_NEWTON[QUASI_NEWTON]|LEAST_SQUARES_QUASI_NEWTON>
   <objective_fields FIELD_NAME [& FIELD_NAME [& ...]]>
   <region PATH_TO_REGION[/]>
   <show_output[show_output]|hide_output>

gfx modify

   data
   dgroup REGION_PATH/GROUP
   egroup REGION_PATH/GROUP
   environment_map
   field
   flow_particles The flow particles feature has been removed.
   g_element
   glyph
   GRAPHICS_OBJECT_NAME
   graphics_objectERROR: gfx_modify_graphics_object.  This function is no longer supported, please use gfx modify glyph instead
   light
   lmodel
   material
   ngroup REGION_PATH/GROUP
   nodes
   sceneWARNING: To define a filter and light on a graphics window please see gfx modify window command
   spectrum
   texture

gfx modify data

   <all>
   <conditional_field FIELD_NAME>
   <define FIELD_NAME>
   <derivatives DERIVATIVE_NAMES(D_DS1 D2_DS1DS2 etc.)|none[none]>
   <group REGION_PATH/GROUP>
   <selected>
   <undefine FIELD_NAME>
   <versions #[1]{>0,integer}>
   < #|#..#[,#|#..#[,etc.]]>

gfx modify dgroup REGION_PATH/GROUP

   <add>
   <all>
   <conditional_field FIELD_NAME>
   <group GROUP_NAME>
   <remove>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx modify egroup REGION_PATH/GROUP

   <add>
   <all>
   <conditional_field FIELD_NAME>
   <elements[elements]|faces|lines>
   <group GROUP_NAME>
   <manage_subobjects[manage_subobjects]|no_manage_subobjects>
   <remove>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx modify environment_map ENVIRONMENT_MAP_NAME <face_materials MAT_1[none] MAT_2[none] MAT_3[none] MAT_4[none] MAT_5[none] MAT_6[none]>


gfx modify field [REGION_PATH/]FIELD_NAME rename NEW_FIELD_NAME


gfx modify g_element REGION_PATH

   contours
   cylinders
   data_points
   element_points
   general
   iso_surfaces
   lines
   node_points
   point
   points
   streamlines
   surfaces

gfx modify g_element REGION_PATH contours

Create contours i.e. isosurfaces in volume elements <domain_elements_3d> or isolines in face or surface elements <domain_elements_2d>. The isosurface will be generated at the values in the elements where <iso_scalar> equals the iso values specified. The iso values can be specified either as a list with the <iso_values> option or by specifying <range_number_of_iso_values>, <first_iso_value> and <last_iso_value>. The <as> parameter allows a name to be specified for this setting. The <coordinate> parameter optionally overrides the groups default coordinate field. If a <data> field is specified then the <spectrum> is used to render the data values as colour on the generated isosurface. If a <decimation_threshold> is specified then the resulting iso_surface will be decimated according to the threshold. If <delete> is specified then if the graphics matches an existing setting (either by parameters or name) then it will be removed. If <exterior> is specified then only faces with one parent will be selected when <use_faces> is specified. If <face> is specified then only that face will be selected when <use_faces> is specified. The <material> is used to render the surface. You can specify the <position> the graphics has in the graphics list. You can specify the <line_width>, this option only applies when <use_faces> is specified. You can render a mesh as solid <render_shaded> or as a wireframe <render_wireframe>. If <select_on> is active then the element tool will select the elements the iso_surface was generated from. If <no_select> is active then the iso_surface cannot be selected. If <draw_selected> is active then iso_surfaces will only be generated in elements that are selected. Conversely, if <draw_unselected> is active then iso_surfaces will only be generated in elements that are not selected. The <texture_coordinates> are used to lay out a texture if the <material> contains a texture. A graphics can be made <visible> or <invisible>.

   <as NAME>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <decimation_threshold #[0]>
   <delete>
   <domain_point|domain_nodes|domain_datapoints|domain_mesh1d|domain_mesh2d|domain_mesh3d|domain_mesh_highest_dimension[domain_mesh_highest_dimension]>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <first_iso_value #[0]>
   <iso_scalar FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <iso_values #..#>
   <last_iso_value #[0]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <range_number_of_iso_values #[0]{>0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default]>
   <texture_coordinates FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>

gfx modify g_element REGION_PATH cylinders

   <as NAME>
   <circle_discretization #{integer>=3}>
   <constant_radius #[0]>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <domain_point|domain_nodes|domain_datapoints|domain_mesh1d[domain_mesh1d]|domain_mesh2d|domain_mesh3d|domain_mesh_highest_dimension>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <line|ribbon|circle_extrusion[circle_extrusion]|square_extrusion>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <radius_scalar FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <render_shaded[render_shaded]|render_wireframe>
   <scale_factor #[1]>
   <secondary_material MATERIAL_NAME|none[none]>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default]>
   <texture_coordinates FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>

gfx modify g_element REGION_PATH data_points

Deprecated; use points with domain_data option instead.

   <as NAME>
   <centre # # #[0 0 0]>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <fontNAME>
   <glyph GLYPH_NAME|none[point]>
   <constant|scalar|vector|axes|general>
   <label FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <label_offset # # #[0 0 0]>
   <label_text  LABEL_STRING [& LABEL_STRING [& ...]]>
   <ldensity FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <REPEAT_MODE_NONE[REPEAT_MODE_NONE]|REPEAT_MODE_AXES_2D|REPEAT_MODE_AXES_3D|REPEAT_MODE_MIRROR>
   <orientation FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <scale_factors #*#*#[1*1*1]>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <size #*#*#[1*1*1]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <variable_scale FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>

gfx modify g_element REGION_PATH element_points

Deprecated; use points with domain_elements* option instead.

   <as NAME>
   <cell_centres[cell_centres]|cell_corners|cell_poisson|set_location|gaussian_quadrature>
   <cell_density|cell_random|exact_xi>
   <centre # # #[0 0 0]>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <density FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <discretization "#*#*..."{>=0}>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <fontNAME>
   <glyph GLYPH_NAME|none[point]>
   <constant|scalar|vector|axes|general>
   <label FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <label_offset # # #[0 0 0]>
   <label_text  LABEL_STRING [& LABEL_STRING [& ...]]>
   <ldensity FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <REPEAT_MODE_NONE[REPEAT_MODE_NONE]|REPEAT_MODE_AXES_2D|REPEAT_MODE_AXES_3D|REPEAT_MODE_MIRROR>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <orientation FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <scale_factors #*#*#[1*1*1]>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <size #*#*#[1*1*1]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default_points]>
   <use_elements|use_faces|use_lines>
   <variable_scale FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>
   <xi #..#>

gfx modify g_element REGION_PATH general

The clear option removes all graphics from the scene. Option 'circle_discretization' is deprecated: use tessellation option on individual graphics instead. Option 'default_coordinate' is deprecated: use coordinate option on individual graphics instead. Option 'element_discretization' is deprecated: use tessellation option on individual graphics instead. Option 'native_discretization' is obsolete: use native_discretization option on individual graphics instead.

   <circle_discretization #{integer>=3}>
   <clear>
   <default_coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <element_discretization "#*#*..."{>=0}>
   <native_discretization OBSOLETE>

gfx modify g_element REGION_PATH iso_surfaces

Deprecated; use contours with domain_elements* option instead.

   <as NAME>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <decimation_threshold #[0]>
   <delete>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <first_iso_value #[0]>
   <iso_scalar FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <iso_values #..#>
   <last_iso_value #[0]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <range_number_of_iso_values #[0]{>0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default]>
   <texture_coordinates FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <use_elements|use_faces|use_lines>
   <visible[visible]|invisible>

gfx modify g_element REGION_PATH lines

   <as NAME>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <domain_point|domain_nodes|domain_datapoints|domain_mesh1d[domain_mesh1d]|domain_mesh2d|domain_mesh3d|domain_mesh_highest_dimension>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <line[line]|ribbon|circle_extrusion|square_extrusion>
   <line_base_size #*#[0*0]>
   <line_orientation_scale FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <line_scale_factors #*#[1*1]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <secondary_material MATERIAL_NAME|none[none]>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default]>
   <texture_coordinates FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>

gfx modify g_element REGION_PATH node_points

Deprecated; use points with domain_nodes option instead.

   <as NAME>
   <centre # # #[0 0 0]>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <fontNAME>
   <glyph GLYPH_NAME|none[point]>
   <constant|scalar|vector|axes|general>
   <label FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <label_offset # # #[0 0 0]>
   <label_text  LABEL_STRING [& LABEL_STRING [& ...]]>
   <ldensity FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <REPEAT_MODE_NONE[REPEAT_MODE_NONE]|REPEAT_MODE_AXES_2D|REPEAT_MODE_AXES_3D|REPEAT_MODE_MIRROR>
   <orientation FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <scale_factors #*#*#[1*1*1]>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <size #*#*#[1*1*1]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <variable_scale FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>

gfx modify g_element REGION_PATH point

Deprecated; use points with domain_point option instead.

   <as NAME>
   <centre # # #[0 0 0]>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <fontNAME>
   <glyph GLYPH_NAME|none[point]>
   <constant|scalar|vector|axes|general>
   <label FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <label_offset # # #[0 0 0]>
   <label_text  LABEL_STRING [& LABEL_STRING [& ...]]>
   <ldensity FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <REPEAT_MODE_NONE[REPEAT_MODE_NONE]|REPEAT_MODE_AXES_2D|REPEAT_MODE_AXES_3D|REPEAT_MODE_MIRROR>
   <orientation FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <scale_factors #*#*#[1*1*1]>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <size #*#*#[1*1*1]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <variable_scale FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>

gfx modify g_element REGION_PATH points

   <as NAME>
   <cell_centres[cell_centres]|cell_corners|cell_poisson|set_location|gaussian_quadrature>
   <cell_density|cell_random|exact_xi>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <density FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <domain_point[domain_point]|domain_nodes|domain_datapoints|domain_mesh1d|domain_mesh2d|domain_mesh3d|domain_mesh_highest_dimension>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <fontNAME>
   <glyph GLYPH_NAME|none[point]>
   <label FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <label_offset # # #[0 0 0]>
   <label_text  LABEL_STRING [& LABEL_STRING [& ...]]>
   <ldensity FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <REPEAT_MODE_NONE[REPEAT_MODE_NONE]|REPEAT_MODE_AXES_2D|REPEAT_MODE_AXES_3D|REPEAT_MODE_MIRROR>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <offset # # #[0 0 0]>
   <orientation FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <scale_factors #*#*#[1*1*1]>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <size #*#*#[1*1*1]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default_points]>
   <variable_scale FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>
   <xi #..#>

gfx modify g_element REGION_PATH streamlines

   <as NAME>
   <cell_centres[cell_centres]|cell_corners|cell_poisson|set_location|gaussian_quadrature>
   <cell_density|cell_random|exact_xi>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <density FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <discretization "#*#*..."{>=0}>
   <domain_point|domain_nodes|domain_datapoints|domain_mesh1d|domain_mesh2d|domain_mesh3d|domain_mesh_highest_dimension[domain_mesh_highest_dimension]>
   <ellipse|rectangle|cylinder>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <length #[1]{>=0}>
   <line[line]|ribbon|circle_extrusion|square_extrusion>
   <line_base_size #*#[1*1]>
   <line_orientation_scale FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <line_scale_factors #*#[1*1]>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <no_data[no_data]|field_scalar|magnitude_scalar|travel_scalar>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <forward_track[forward_track]|reverse_track>
   <seed_element ELEMENT_NUMBER>
   <seed_node_mesh_location_field FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <seed_nodeset NODE_GROUP_FIELD_NAME|[GROUP_NAME.]nodes|datapoints|none>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default_points]>
   <vector FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>
   <width #[0]>
   <xi #..#>

gfx modify g_element REGION_PATH surfaces

   <as NAME>
   <coordinate FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <LOCAL[LOCAL]|WORLD|NORMALISED_WINDOW_FILL|NORMALISED_WINDOW_FIT_CENTRE|NORMALISED_WINDOW_FIT_LEFT|NORMALISED_WINDOW_FIT_RIGHT|NORMALISED_WINDOW_FIT_BOTTOM|NORMALISED_WINDOW_FIT_TOP|WINDOW_PIXEL_BOTTOM_LEFT|WINDOW_PIXEL_TOP_LEFT>
   <data FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <delete>
   <domain_point|domain_nodes|domain_datapoints|domain_mesh1d|domain_mesh2d[domain_mesh2d]|domain_mesh3d|domain_mesh_highest_dimension>
   <exterior>
   <face <all|xi1_0|xi1_1|xi2_0|xi2_1|xi3_0|xi3_1>>
   <line_width #[1]{>0}>
   <material MATERIAL_NAME|none[default]>
   <native_discretization FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <point_size #[1]{>0}>
   <position #[-1]{>=0,integer}>
   <render_shaded[render_shaded]|render_wireframe>
   <select_on[select_on]|no_select|draw_selected|draw_unselected>
   <selected_material MATERIAL_NAME|none[default_selected]>
   <spectrum SPECTRUM_NAME|none[none]>
   <subgroup FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <tessellation TESSELLATION_NAME|none[default]>
   <texture_coordinates FIELD_NAME[.COMPONENT_NAME]|none[none]>
   <visible[visible]|invisible>

gfx modify GRAPHICS_OBJECT_NAME

   material MATERIAL_NAME|none[none]
   spectrum SPECTRUM_NAME|none[none]

gfx modify light LIGHT_NAME

   <colour RED#[0.9]{>=0,<=1} GREEN#[0.9]{>=0,<=1} BLUE#[0.9]{>=0,<=1}>
   <constant_attenuation #[1]{>=0}>
   <cut_off #[90]>
   <direction # # #[0 -0.5 -1]>
   <exponent #[0]{>=0}>
   <infinite[infinite]|point|spot>
   <linear_attenuation #[0]{>=0}>
   <position # # #[0 0 0]>
   <quadratic_attenuation #[0]{>=0}>

gfx modify lmodel LIGHT_MODEL_NAME

   <ambient_colour RED#[0.1]{>=0,<=1} GREEN#[0.1]{>=0,<=1} BLUE#[0.1]{>=0,<=1}>
   <disable|enable>
   <infinite_viewer|local_viewer>
   <one_sided|two_sided>

gfx modify material MATERIAL_NAME

The material controls how pixels will be rendered on the screen. The initial mode of operation reflects the standard gouraud shading model usual within OpenGL, this is called <normal_mode>. This has rgb colour values for <diffuse>, <ambient> <emission> and <specular> colours. The <ambient> colour is the unlit colour, the <diffuse> colour interacts with the light and is the lit surface, the <specular> colour is used for the glossy highlights, the spread of which is specified by the<shininess>. The <alpha> controls the transparency of the material. See a/a1.If a <texture> is specified then this is combined with the calculated gouraud colour according to the textures rendering mode and the texture coordinates. Additional support is provided for more accurate rendering using phong shading calculated at every pixel, called <per_pixel_lighting>. This is implemented using the ARB_vertex_program and ARB_fragment_program OpenGL extensions. The program only implements a single point light so you should set the default light to a point light at the position you want. See a/per_pixel_lighting. <bump_mapping> uses a <secondary_texture> to specify a perturbation to the normal, giving a smooth model a much more detailed surface appearance. Also demonstrated in a/per_pixel_lighting. A <colour_lookup_spectrum> takes the calculated colour values and further modifies them by using the specified subset of colour values specified by <colour_lookup_red>, <colour_lookup_green>, <colour_lookup_blue> and <colour_lookup_alpha>, as inputs to a 1, 2 or 3 component spectrum. Depending on the spectrum this will override either the rgb colour, the alpha value or both rgb and alpha. If the number of input components used in the spectrum matches the number of components specified then a texture of this dimension will be used and evaluated for each tensor product combination. If only a 1 component spectrum is specified then it will be applied independently to each input component specified. This spectrum can be modified to quickly change the appearance of a large volume dataset, see example a/indexed_volume. A lit volume uses a per voxel normal to calculate the phong lighting model at each pixel. The normal can be specified by encoding it into the blue, green and alpha channels of an input texture (the red channel being the intensity) <lit_volume_intensity_normal_texture>.Alternatively it can be estimated on the fly by applying a finite difference operator to the pixel intensities. <lit_volume_finite_difference_normal>.A <lit_volume_normal_scaling> can be applied, modifying the estimated normal by scaling it. The normal is used as if it is a coordinate normal and so the texture coordinates must line up with the geometrical coordinates. The <lit_volume_normal_scaling> can be used to account for when the texture coordinates are not equally matched to the geometrical coordinates. The magnitude of the <lit_volume_normal_scaling> will only affect the optional following parameter, <lit_volume_scale_alpha>, scaling the alpha attenuation. Optionally with either normal, the magnitude of that normalcan multiply the calculated alpha value, <lit_volume_scale_alpha> making those pixels with small gradients more transparent. See a/volume_render. <secondary_texture>, <third_texture> and <fourth_texture> will be blended with the first <texture> according to the multitexture rules controlled by each textures combine mode (such as modulate or add). Specifying a <vertex_program_string> and <fragment_program_string> allows any arbitrary program to be loaded, overriding the one that is generated automatically, no checks for consistency with textures or inputs are made. Both must be specified together. Optional <geometry_program_string> is also available, which is only available on relatively newer hardware, it must be used with <vertex_program_string> and <fragment_program_string> and only works with surface at the moment. Specifying a <uniform_name> and <uniform_value> allows any uniform qualified variables inany arbitrary program to be set. At the moment only float type is supported.

   <alpha #[1]{>=0,<=1}>
   <ambient RED#[1]{>=0,<=1} GREEN#[1]{>=0,<=1} BLUE#[1]{>=0,<=1}>
   <bump_mapping>
   <colour_lookup_alpha>
   <colour_lookup_blue>
   <colour_lookup_green>
   <colour_lookup_red>
   <colour_lookup_spectrum SPECTRUM_NAME|none[none]>
   <diffuse RED#[1]{>=0,<=1} GREEN#[1]{>=0,<=1} BLUE#[1]{>=0,<=1}>
   <emission RED#[0]{>=0,<=1} GREEN#[0]{>=0,<=1} BLUE#[0]{>=0,<=1}>
   <fourth_texture IMAGE_NAME|none[none]>
   <fragment_program_stringNAME>
   <lit_volume_intensity_normal_texture>
   <lit_volume_finite_difference_normal>
   <lit_volume_normal_scaling # # #[1 1 1]>
   <lit_volume_scale_alpha>
   <normal_mode|per_pixel_mode>
   <secondary_texture IMAGE_NAME|none[none]>
   <shininess #[0]{>=0,<=1}>
   <specular RED#[0]{>=0,<=1} GREEN#[0]{>=0,<=1} BLUE#[0]{>=0,<=1}>
   <texture IMAGE_NAME|none[none]>
   <third_texture IMAGE_NAME|none[none]>
   <vertex_program_stringNAME>
   <geometry_program_stringNAME>
   <uniform_nameNAME>
   <uniform_values #..#>

gfx modify ngroup REGION_PATH/GROUP

   <add>
   <all>
   <conditional_field FIELD_NAME>
   <group GROUP_NAME>
   <remove>
   <selected>
   < #|#..#[,#|#..#[,etc.]]>

gfx modify nodes

   <all>
   <conditional_field FIELD_NAME>
   <define FIELD_NAME>
   <derivatives DERIVATIVE_NAMES(D_DS1 D2_DS1DS2 etc.)|none[none]>
   <group REGION_PATH/GROUP>
   <selected>
   <undefine FIELD_NAME>
   <versions #[1]{>0,integer}>
   < #|#..#[,#|#..#[,etc.]]>

gfx modify spectrum SPECTRUM_NAME

   <autorange>
   <blue_to_red>
   <blue_white_red>
   <clear>
   <field
   <linear
   <lg_red_to_blue>
   <maximum MAXIMUM_VALUE#[0]>
   <minimum MINIMUM_VALUE#[0]>
   <overlay_colour>
   <overwrite_colour>
   <scene_for_autorange PATH_TO_SCENE[/]>
   <red_to_blue>

gfx modify texture

   TEXTURE_NAME
   GRAPHICS_WINDOW_NAME

gfx modify texture TEXTURE_NAME

   <alpha #[0]{>=0,<=1}>
   <blend|decal[decal]|modulate|add|signed_add|scale_4_modulate|scale_4_blend|subtract|scale_4_add|scale_4_subtract|invert_scale_4_add|invert_scale_4_subtract>
   <clamp_wrap|repeat_wrap[repeat_wrap]|edge_clamp_wrap|border_clamp_wrap|mirrored_repeat_wrap>
   <colour RED#[0]{>=0,<=1} GREEN#[0]{>=0,<=1} BLUE#[0]{>=0,<=1}>
   <uncompressed[uncompressed]|compressed_unspecified>
   <depth #[1]{>=0}>
   <distortion DISTORTION_CENTRE_X DISTORTION_CENTRE_Y DISTORTION_FACTOR_K1>
   <height #[1]{>0}>
   <image <crop LEFT_MARGIN#[0] BOTTOM_MARGIN#[0] WIDTH#[0] HEIGHT#[0]>
   <nearest_filter[nearest_filter]|linear_filter|filter_nearest_mipmap_nearest|filter_linear_mipmap_nearest|filter_linear_mipmap_linear>
   <mipmap_level_of_detail_bias #[0]>
   <number_pattern NAME>
   <number_series START STOP INCREMENT>
   <raw_interleaved_rgb|raw_planar_rgb[raw_planar_rgb]>
   <resize_linear_filter|resize_nearest_filter[resize_nearest_filter]>
   <specify_depth #[0]{>=0,integer}>
   <specify_format i|ia|rgb[rgb]|rgba|abgr>
   <specify_height #[0]{>=0,integer}>
   <specify_number_of_bytes_per_component #[0]{>=0,integer}>
   <specify_width #[0]{>=0,integer}>
   <texture_tiling>
   <no_texture_tiling>
   <width #[1]{>0}>
   <evaluate_image

gfx modify texture GRAPHICS_WINDOW_NAME

   background
   image
   layout
   node_tool
   overlayGraphics window overlay scene is no longer supported. Individual graphics are now drawn in overlay by choosing a window-relative coordinate system.
   set
   view

gfx modify texture GRAPHICS_WINDOW_NAME background

   <all_panes>
   <colour RED#[0]{>=0,<=1} GREEN#[0]{>=0,<=1} BLUE#[0]{>=0,<=1}>
   <max_pixels_per_polygon #[0]>
   <texture IMAGE_NAME|none[none]>
   <tex_placement TEXTURE_LEFT TEXTURE_TOP TEXTURE_WIDTH TEXTURE_HEIGHT>
   <undistort_texture|no_undistort_texture>

gfx modify texture GRAPHICS_WINDOW_NAME image

   <add_light LIGHT_NAME|none[none]>
   <light_model LIGHT_MODEL_NAME[none]>
   <remove_light LIGHT_NAME|none[none]>
   <rotate AXIS_X AXIS_Y AXIS_Z ANGLE>
   <scene PATH_TO_SCENE>
   <filter GRAPHICS_FILTER_NAME|none[none]>
   <update>
   <view_all>

gfx modify texture GRAPHICS_WINDOW_NAME layout

   <2d|free_ortho|front_back|front_side|orthographic|pseudo_3d|simple[simple]|two_free>
   <eye_spacing #[0]>
   <height #[0]{>=0,integer}>
   <ortho_axes ORTHO_UP{X/Y/Z/-X/-Y/-Z} ORTHO_FRONT{X/Y/Z/-X/-Y/-Z}>
   <width #[0]{>=0,integer}>

gfx modify texture GRAPHICS_WINDOW_NAME node_tool

   <coordinate_fieldNAME>
   <constrain_to_surfaces|no_constrain_to_surfaces[no_constrain_to_surfaces]>
   <create|no_create[no_create]>
   <define|no_define[no_define]>
   <edit|no_edit[no_edit]>
   <element_xi_fieldNAME>
   <group REGION_PATH/GROUP>
   <motion_update|no_motion_update[no_motion_update]>
   <select[select]|no_select>
   <streaming_create|no_streaming_create[no_streaming_create]>
   <command_fieldNAME>

gfx modify texture GRAPHICS_WINDOW_NAME set

   <antialias #[0]{>0,integer}|no_antialias[CURRENT]>
   <blend_normal[blend_normal]|blend_none|blend_true_alpha>
   <current_pane #[1]{integer}>
   <depth_of_field #[0]>
   <focal_depth #[0]>
   <perturb_lines|normal_lines[normal_lines]>
   <std_view_angle #[40]>
   <show_time_editor|hide_time_editor>
   <fast_transparency|layered_transparency #[0]{>0,integer}|order_independent_transparency #[0]{>0,integer}|slow_transparency>

gfx modify texture GRAPHICS_WINDOW_NAME view

   <allow_skew>
   <clip_plane_add A B C D>
   <clip_plane_remove A B C D>
   <eye_point # # #[0 0 0]>
   <far_clipping_plane #[0]>
   <interest_point # # #[0 0 0]>
   <modelview_matrix M11 M12 M13 M14 M21 M22 M23 M24 M31 M32 M33 M34 M41 M42 M43 M44>
   <ndc_placement NDC_LEFT NDC_TOP NDC_WIDTH NDC_HEIGHT>
   <near_clipping_plane #[0]>
   <photogrammetry_matrix T11 T12 T13 T21 T22 T23 T31 T32 T33 T41 T42 T43>
   <projection_matrix M11 M12 M13 M14 M21 M22 M23 M24 M31 M32 M33 M34 M41 M42 M43 M44>
   <custom|parallel|perspective>
   <up_vector # # #[0 0 0]>
   <viewport_coordinates VIEWPORT_LEFT VIEWPORT_TOP PIXELS_PER_UNIT_X PIXELS_PER_UNIT_Y>
   <view_angle #[0]>
   <absolute_viewport|relative_viewport|distorting_relative_viewport>

gfx node_tool

   <coordinate_fieldNAME>
   <constrain_to_surfaces|no_constrain_to_surfaces[no_constrain_to_surfaces]>
   <create|no_create[no_create]>
   <define|no_define[no_define]>
   <edit|no_edit[no_edit]>
   <element_xi_fieldNAME>
   <group REGION_PATH/GROUP>
   <motion_update|no_motion_update[no_motion_update]>
   <select[select]|no_select>
   <streaming_create|no_streaming_create[no_streaming_create]>
   <command_fieldNAME>

gfx print

   <antialias #[-1]{>0,integer}>
   <bmp|dcm|jpg|gif|postscript|png|raw|rgb|tiff|yuv|analyze>
   <file NAME>
   <force_onscreen>
   <format i|ia|rgb|rgba[rgba]|abgr>
   <height #[0]{>=0,integer}>
   <transparency_layers #[0]{>0,integer}>
   <width #[0]{>=0,integer}>
   <window WINDOW_NUMBER>

gfx read

   curve
   data
   elements
   nodes
   objects
   region
   wavefront_obj

gfx read curve

   <example FILE_NAME>
   < FILE_NAME>

gfx read data

   <example FILE_NAME>
   <data_offset #[NOT SET]>
   <region NAME>
   <time #[0]>
   < FILE_NAME>

gfx read elements

   <element_offset #[NOT SET]>
   <example FILE_NAME>
   <face_offset #[NOT SET]>
   <line_offset #[NOT SET]>
   <node_offset #[NOT SET]>
   <region NAME>
   < FILE_NAME>

gfx read nodes

   <example FILE_NAME>
   <node_offset #[NOT SET]>
   <region NAME>
   <time #[0]>
   < FILE_NAME>

gfx read objects

   <example FILE_NAME>
   < FILE_NAME>

gfx read region

   <fields FIELD_NAMES|all|none[all]>
   <region PATH_TO_REGION[/]>
   <FILE_NAME>

gfx read wavefront_obj

   <example FILE_NAME>
   <as NAME>
   <render_shaded[render_shaded]|render_wireframe>
   <time #[0]>
   < FILE_NAME>

gfx select

   <all>
   <conditional_field FIELD_NAME>
   <data>
   <elements>
   <faces>
   <grid_field FIELD_NAME|none[none]>
   <grid_points>
   <group PATH_TO_REGION[/]>
   <lines>
   <nodes>
   <points element|face|line # {cell_centres|cell_corners #xi1 #xi2.. #xiN #,#..#,# etc. | exact_xi xi1 xi2...}>
   <verbose>
   < #|#..#[,#|#..#[,etc.]]>

gfx set

   node_value NODE_NUMBER FIELD_NAME.COMPONENT_NAME
   order
   point_size #[0]{>0}
   transformation
   time
   visibility

gfx set node_value NODE_NUMBER FIELD_NAME.COMPONENT_NAME

   value
   d/ds1
   d/ds2
   d/ds3
   d2/ds1ds2
   d2/ds1ds3
   d2/ds2ds3
   d3/ds1ds2ds3

gfx set order

Change the order of regions in the region hierarchy. The 'region' option specifies the current path of the region to be moved. The 'before' option gives the name of an existing sibling region which the region will be re-inserted before.

   <before SIBLING_REGION_NAME>
   <region REGION_PATH/GROUP>

gfx set transformation

   <name PATH_TO_REGION[/]>
   <field FIELD_NAME>
   <# # # # # # # # # # # # # # # # [1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1]>

gfx set time

   <timekeeperNAME[default]>
   < #[0]>

gfx set visibility

Set the visibility of a whole region's scene or individual graphics in it. Specify visibility as 'on', 'off' or omit both to toggle. If name option is specified, sets visibility for all graphics in region whose name contains the string.

   <off>
   <on>
   <name PART_GRAPHIC_NAME>
   < REGION_PATH>

gfx mesh graphics

   tetrahedral
   triangle

gfx mesh graphics tetrahedral

   <region PATH_TO_REGION[/]>
   <scene PATH_TO_SCENE[/]>
   <filter GRAPHICS_FILTER_NAME|none[default]>
   <clear_region>
   <mesh_global_size #[100000]>
   <fineness #[0.5]>
   <secondorder #[0]{integer}>
   <meshsize_file FILENAME>

gfx mesh graphics triangle

   <scene PATH_TO_SCENE[/]>
   <filter GRAPHICS_FILTER_NAME|none[default]>
   <target_region PATH_TO_REGION[/]>
   <clear_region>

gfx smooth

   <field FINITE ELEMENT FIELD NAME>
   <region PATH_TO_REGION[/]>
   <time #[0]>

gfx timekeeper

   TIMEKEEPER_NAME
   <every_frame>
   <loop>
   <maximum #[0]>
   <minimum #[0]>
   <once>
   <play>
   <set_time #[0]>
   <skip_frames>
   <speed #[1]>
   <stop>
   <swing>

gfx unselect

   <all>
   <conditional_field FIELD_NAME>
   <data>
   <elements>
   <faces>
   <grid_field FIELD_NAME|none[none]>
   <grid_points>
   <group PATH_TO_REGION[/]>
   <lines>
   <nodes>
   <points element|face|line # {cell_centres|cell_corners #xi1 #xi2.. #xiN #,#..#,# etc. | exact_xi xi1 xi2...}>
   <verbose>
   < #|#..#[,#|#..#[,etc.]]>

gfx update <window WINDOW_NUMBER>


gfx write

   all
   curve
   data
   elements
   nodes
   texture

gfx write all

   <complete_group[complete_group]|with_all_listed_fields|with_any_listed_fields>
   <fields FIELD_NAME [& FIELD_NAME [& ...]]|all|none|[all]>
   <group RELATIVE_PATH_TO_REGION>
   <recursive[recursive]|recurse_subgroups|non_recursive>
   <root PATH_TO_REGION[/]>
   <time #[0]>
   <FILE_NAME>

gfx write curve

   <all>
   < CURVE_NAME|none[none]>

gfx write data

Write data nodes and data node fields in EX format to FILE_NAME. Output is restricted to the specified <root> region which forms the root region in the EX file, and optionally a region or sub-group specified by the relative path with the <group> option. Output can be restricted to just <fields> listed in required order, or 'none' to list just object identifiers. Recursion options control whether sub-regions are output with the chosen root region or group. Time option allow user to specify at which time of nodes and node fields to be output if there nodes/node fields are time dependent. If time is outof range then the nodal values at the nearest valid time will be output. Time is ignored if node is not time dependent.

   <complete_group[complete_group]|with_all_listed_fields|with_any_listed_fields>
   <fields FIELD_NAME [& FIELD_NAME [& ...]]|all|none|[all]>
   <group RELATIVE_PATH_TO_REGION/GROUP>
   <recursive[recursive]|recurse_subgroups|non_recursive>
   <root PATH_TO_REGION[/]>
   <time #[0]>
   <FILE_NAME>

gfx write elements

Write elements and element fields in EX format to FILE_NAME. Output is restricted to the specified <root> region which forms the root region in the EX file, and optionally a sub-group or region specified with the relative <group> path. Output can be restricted to just <fields> listed in required order, or 'none' to list just object identifiers. Recursion options control whether sub-groups and sub-regions are output with the chosen root region or group. Specify <nodes> to include nodes and node fields in the same file. with the chosen root region or group. Time option specifies nodes and node fields at time to be output if nodes or node fields are time dependent. If time is out of range then the nodal values at the nearest valid time will be output. Time is ignored if node is not time dependent.

   <complete_group[complete_group]|with_all_listed_fields|with_any_listed_fields>
   <fields FIELD_NAME [& FIELD_NAME [& ...]]|all|none|[all]>
   <group RELATIVE_PATH_TO_REGION/GROUP>
   <nodes>
   <data>
   <recursive[recursive]|recurse_subgroups|non_recursive>
   <root PATH_TO_REGION[/]>
   <time #[0]>
   <FILE_NAME>

gfx write nodes

Write nodes and node fields in EX format to FILE_NAME. Output is restricted to the specified <root> region which forms the root region in the EX file, and optionally a region or sub-group specified by the relative path with the <group> option. Output can be restricted to just <fields> listed in required order, or 'none' to list just object identifiers. Recursion options control whether sub-regions are output with the chosen root region or group. Time option allow user to specify at which time of nodes and node fields to be output if there nodes/node fields are time dependent. If time is outof range then the nodal values at the nearest valid time will be output. Time is ignored if node is not time dependent.

   <complete_group[complete_group]|with_all_listed_fields|with_any_listed_fields>
   <fields FIELD_NAME [& FIELD_NAME [& ...]]|all|none|[all]>
   <group RELATIVE_PATH_TO_REGION/GROUP>
   <recursive[recursive]|recurse_subgroups|non_recursive>
   <root PATH_TO_REGION[/]>
   <time #[0]>
   <FILE_NAME>

open

   comfile
   example

open comfile

   <example>
   <execute <#>[1]{integer}>
   <name NAME>
   <NAME>

open example

   <example NAME>
   <execute>
   <NAME>

list_memory

   <increment_counter>
   <suppress_pointers>
   < #[0]{integer}>

read comfile

   <example>
   <execute <#>[1]{integer}>
   <name NAME>
   <NAME>

set

   echo
   debug
   directory

set echo

   <on>
   <off>
   <prompt PROMPT_STRING>

set debug

   <on>
   <off>

set directory

   <example>
   <NAME>

http://www.cmiss.org/cmgui