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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
A (fish2eod.helpers.dolfin_tools.Equation attribute)
add_boundary_assignement_rules() (fish2eod.models.BaseFishModel method)
add_circle() (fish2eod.mesh.mesh.Mesher method)
(in module fish2eod.mesh.mesh)
add_current_sources() (fish2eod.models.BaseFishModel method)
add_data() (fish2eod.xdmf.save.Saver method)
add_domain() (fish2eod.mesh.model_geometry.ModelGeometry method)
(fish2eod.mesh.model_geometry.QESGeometry method)
add_fenics_data() (fish2eod.xdmf.save.Saver method)
add_geometry() (fish2eod.models.BaseFishModel method)
add_line() (fish2eod.mesh.mesh.Mesher method)
add_line_loop() (fish2eod.mesh.mesh.Mesher method)
add_misc_data() (fish2eod.xdmf.save.Saver method)
add_parameter_set() (fish2eod.sweep.EODPhase method)
(fish2eod.sweep.ParameterSet method)
add_poly() (in module fish2eod.mesh.mesh)
add_polygon() (fish2eod.mesh.mesh.Mesher method)
add_surface() (fish2eod.mesh.mesh.Mesher method)
add_voltage_sources() (fish2eod.models.BaseFishModel method)
align_contour_head_tail() (in module fish2eod.geometry.fish)
arc_length (fish2eod.helpers.type_helpers.ComputatableSideInformation attribute)
assign_left_right() (in module fish2eod.geometry.fish)
B
b (fish2eod.helpers.dolfin_tools.Equation attribute)
BACKGROUND_LABEL (fish2eod.mesh.model_geometry.ModelGeometry attribute)
BaseFishModel (class in fish2eod.models)
body (fish2eod.data.species_registry.SpeciesData attribute)
BODY_CONDUCTIVITY (fish2eod.models.BaseFishModel attribute)
boundary_iterator() (in module fish2eod.mesh.boundary)
BoundaryCondition (class in fish2eod.math)
build_equations() (fish2eod.models.Model method)
(fish2eod.models.QESModel method)
C
center (fish2eod.geometry.primitives.Polygon property)
check_intersection() (fish2eod.mesh.model_geometry.ModelGeometry method)
Circle (class in fish2eod.geometry.primitives)
clean_linestring() (in module fish2eod.geometry.fish)
clear() (fish2eod.mesh.model_geometry.ModelGeometry method)
compile() (fish2eod.models.Model method)
ComputatableSideInformation (class in fish2eod.helpers.type_helpers)
compute_transdermal_potential() (in module fish2eod.analysis.transdermal)
convert_fenics_data() (in module fish2eod.helpers.dolfin_tools)
coordinates (fish2eod.helpers.type_helpers.ComputatableSideInformation attribute)
create_dolfin_mesh() (in module fish2eod.mesh.mesh)
create_geometry() (fish2eod.models.BaseFishModel method)
(fish2eod.models.Model method)
create_mesh() (in module fish2eod.mesh.mesh)
create_mesh_function() (in module fish2eod.mesh.mesh)
create_minimal_xdmf() (in module fish2eod.xdmf.xml_tools)
create_next_grid() (fish2eod.xdmf.save.Saver method)
create_timestep_grid() (in module fish2eod.xdmf.xml_tools)
create_timestep_grid_misc() (in module fish2eod.xdmf.xml_tools)
cut_line_between_fractions() (in module fish2eod.geometry.operations)
D
data (fish2eod.helpers.type_helpers.DataSet attribute)
DataSet (class in fish2eod.helpers.type_helpers)
DataSolution (class in fish2eod.xdmf.load)
determine_right() (in module fish2eod.geometry.fish)
domain_map (fish2eod.helpers.type_helpers.DataSet attribute)
domain_map_from_data() (in module fish2eod.xdmf.load)
domains (fish2eod.helpers.type_helpers.ElectricImageParameters attribute)
draw() (fish2eod.geometry.fish.Fish method)
(fish2eod.geometry.primitives.Polygon method)
(fish2eod.mesh.model_geometry.ModelGeometry method)
E
ElectricImageParameters (class in fish2eod.helpers.type_helpers)
eod (fish2eod.data.species_registry.SpeciesData attribute)
eod() (fish2eod.geometry.fish.Fish method)
eod_boundary_condition() (fish2eod.geometry.fish.Fish method)
EODPhase (class in fish2eod.sweep)
Equation (class in fish2eod.helpers.dolfin_tools)
eval() (fish2eod.properties.SplineExpression method)
eval_cell() (fish2eod.properties.Property method)
expand() (fish2eod.geometry.primitives.Polygon method)
extend_line() (in module fish2eod.geometry.operations)
External (class in fish2eod.mesh.boundary)
extract() (in module fish2eod.analysis.plotting)
extract_all_data() (in module fish2eod.xdmf.load)
extract_edges() (in module fish2eod.analysis.plotting)
extract_path_from_grid() (in module fish2eod.xdmf.load)
extract_unique_from_grid() (in module fish2eod.xdmf.load)
F
field_norm() (in module fish2eod.analysis.plotting)
filter_line_length() (in module fish2eod.geometry.operations)
filter_parameters() (fish2eod.xdmf.load.H5Solution method)
filter_variables() (fish2eod.xdmf.load.Solution method)
find_manifest() (in module fish2eod.xdmf.load)
Fish (class in fish2eod.geometry.fish)
fish2eod
module
fish2eod.analysis
module
fish2eod.analysis.plotting
module
fish2eod.analysis.transdermal
module
fish2eod.data
module
fish2eod.data.load_data
module
fish2eod.data.settings
module
fish2eod.data.species_registry
module
fish2eod.geometry
module
fish2eod.geometry.fish
module
fish2eod.geometry.operations
module
fish2eod.geometry.primitives
module
fish2eod.helpers
module
fish2eod.helpers.dolfin_tools
module
fish2eod.helpers.type_helpers
module
fish2eod.math
module
fish2eod.mesh
module
fish2eod.mesh.boundary
module
fish2eod.mesh.domain
module
fish2eod.mesh.mesh
module
fish2eod.mesh.model_geometry
module
fish2eod.models
module
fish2eod.properties
module
fish2eod.sweep
module
fish2eod.xdmf
module
fish2eod.xdmf.load
module
fish2eod.xdmf.save
module
fish2eod.xdmf.xml_tools
module
fish_rotation_matrix() (in module fish2eod.geometry.fish)
FishContainer (class in fish2eod.geometry.fish)
FishPosition (class in fish2eod.sweep)
FishSettings (class in fish2eod.data.settings)
from_center() (fish2eod.geometry.primitives.Rectangle class method)
G
generate_mask() (in module fish2eod.analysis.plotting)
generate_save_data() (fish2eod.models.BaseFishModel method)
(fish2eod.models.Model method)
(fish2eod.models.QESModel method)
generate_triangles() (in module fish2eod.analysis.plotting)
generate_triangles_for_1d() (in module fish2eod.analysis.plotting)
generate_triangles_for_2d() (in module fish2eod.analysis.plotting)
geometry (fish2eod.helpers.type_helpers.DataSet attribute)
geometry_path (fish2eod.xdmf.save.Saver property)
get_body_coordinates() (fish2eod.geometry.fish.Fish method)
get_body_data() (in module fish2eod.data.load_data)
get_boundary_markers() (fish2eod.models.BaseFishModel method)
(fish2eod.models.Model method)
get_data() (in module fish2eod.helpers.dolfin_tools)
get_dimension() (in module fish2eod.helpers.dolfin_tools)
get_dirichlet_conditions() (fish2eod.models.BaseFishModel method)
(fish2eod.models.QESModel method)
get_eod_data() (in module fish2eod.data.load_data)
get_eod_functions() (fish2eod.models.BaseFishModel method)
get_neumann_conditions() (fish2eod.models.BaseFishModel method)
(fish2eod.models.QESModel method)
get_outer_grid() (in module fish2eod.xdmf.xml_tools)
get_property() (fish2eod.models.Model method)
get_side_information() (in module fish2eod.analysis.transdermal)
get_skin_arc_length() (in module fish2eod.analysis.transdermal)
get_skin_coordinates() (in module fish2eod.analysis.transdermal)
get_valid_nodes() (in module fish2eod.analysis.plotting)
gradient() (in module fish2eod.analysis.plotting)
GROUND_CONDUCTIVITY (fish2eod.models.BaseFishModel attribute)
H
H5Solution (class in fish2eod.xdmf.load)
head_conductance (fish2eod.data.settings.FishSettings attribute)
head_distance (fish2eod.data.settings.FishSettings attribute)
I
init_fish() (fish2eod.geometry.fish.FishContainer method)
inner_skin_rule() (fish2eod.models.BaseFishModel method)
inside() (fish2eod.geometry.primitives.Circle method)
(fish2eod.geometry.primitives.Polygon method)
(fish2eod.geometry.primitives.Rectangle method)
(fish2eod.mesh.boundary.External static method)
intersects() (fish2eod.geometry.primitives.Polygon method)
intersects_background() (fish2eod.mesh.model_geometry.ModelGeometry method)
is_background() (fish2eod.mesh.model_geometry.ModelGeometry method)
iterate_domains() (in module fish2eod.mesh.domain)
IterativeSolver (class in fish2eod.sweep)
L
label (fish2eod.geometry.primitives.PreDomain attribute)
(fish2eod.math.BoundaryCondition attribute)
left (fish2eod.geometry.fish.SideStruct attribute)
left_arc_length (fish2eod.helpers.type_helpers.SkinStructure attribute)
left_inner (fish2eod.helpers.type_helpers.SkinStructure attribute)
left_outer (fish2eod.helpers.type_helpers.SkinStructure attribute)
left_tdp (fish2eod.helpers.type_helpers.TDP attribute)
load_data() (fish2eod.xdmf.load.DataSolution method)
(fish2eod.xdmf.load.H5Solution method)
(fish2eod.xdmf.load.Solution method)
load_fem_data() (in module fish2eod.xdmf.load)
load_from_file() (in module fish2eod.xdmf.load)
load_from_h5() (in module fish2eod.xdmf.load)
load_misc_data() (in module fish2eod.xdmf.load)
load_xdmf() (in module fish2eod.xdmf.load)
M
make_eod_fcn() (in module fish2eod.geometry.fish)
make_geometry() (in module fish2eod.xdmf.xml_tools)
make_manifest_file() (in module fish2eod.xdmf.xml_tools)
make_mesh() (fish2eod.mesh.mesh.Mesher method)
make_topology() (in module fish2eod.xdmf.xml_tools)
mark_boundaries() (in module fish2eod.mesh.boundary)
mark_boundary() (in module fish2eod.mesh.boundary)
mark_domains() (in module fish2eod.mesh.domain)
mark_edge_by_rules() (in module fish2eod.mesh.boundary)
mark_polygon() (in module fish2eod.mesh.domain)
mark_primitives() (in module fish2eod.mesh.domain)
measure_and_interpolate() (in module fish2eod.geometry.operations)
mesh_add() (in module fish2eod.mesh.mesh)
mesh_plot_1d() (in module fish2eod.analysis.plotting)
mesh_plot_2d() (in module fish2eod.analysis.plotting)
mesh_representation (fish2eod.geometry.primitives.Polygon property)
Mesher (class in fish2eod.mesh.mesh)
middle_conductance() (fish2eod.data.settings.FishSettings method)
misc_attribute_to_data_set() (in module fish2eod.xdmf.load)
Model (class in fish2eod.models)
ModelGeometry (class in fish2eod.mesh.model_geometry)
module
fish2eod
fish2eod.analysis
fish2eod.analysis.plotting
fish2eod.analysis.transdermal
fish2eod.data
fish2eod.data.load_data
fish2eod.data.settings
fish2eod.data.species_registry
fish2eod.geometry
fish2eod.geometry.fish
fish2eod.geometry.operations
fish2eod.geometry.primitives
fish2eod.helpers
fish2eod.helpers.dolfin_tools
fish2eod.helpers.type_helpers
fish2eod.math
fish2eod.mesh
fish2eod.mesh.boundary
fish2eod.mesh.domain
fish2eod.mesh.mesh
fish2eod.mesh.model_geometry
fish2eod.models
fish2eod.properties
fish2eod.sweep
fish2eod.xdmf
fish2eod.xdmf.load
fish2eod.xdmf.save
fish2eod.xdmf.xml_tools
N
name (fish2eod.data.settings.FishSettings attribute)
(fish2eod.helpers.type_helpers.DataSet attribute)
next_valid_label (fish2eod.mesh.model_geometry.ModelGeometry property)
normal_length (fish2eod.data.settings.FishSettings attribute)
normalize_color() (in module fish2eod.analysis.plotting)
O
objects (fish2eod.geometry.primitives.PreDomain attribute)
offset_skeleton() (fish2eod.geometry.fish.Fish method)
ORGAN_CONDUCTIVITY (fish2eod.models.BaseFishModel attribute)
organ_length (fish2eod.data.settings.FishSettings attribute)
organ_rule() (fish2eod.models.BaseFishModel method)
organ_start (fish2eod.data.settings.FishSettings attribute)
organ_width (fish2eod.data.settings.FishSettings attribute)
P
parallel_curves() (in module fish2eod.geometry.operations)
parameter_levels_from_data() (in module fish2eod.xdmf.load)
parameter_state (fish2eod.helpers.type_helpers.DataSet attribute)
parameters (fish2eod.sweep.ParameterSet property)
(fish2eod.xdmf.load.H5Solution property)
ParameterSet (class in fish2eod.sweep)
ParameterSweep (class in fish2eod.sweep)
parse_manifest() (in module fish2eod.xdmf.load)
plot_domains() (fish2eod.models.Model method)
plot_edges() (in module fish2eod.analysis.plotting)
plot_geometry() (fish2eod.models.Model method)
plot_mesh() (fish2eod.models.Model method)
plot_outline() (in module fish2eod.analysis.plotting)
plot_solution() (fish2eod.models.Model method)
Polygon (class in fish2eod.geometry.primitives)
PreDomain (class in fish2eod.geometry.primitives)
primitive (fish2eod.geometry.primitives.PreDomain attribute)
Property (class in fish2eod.properties)
Q
QESGeometry (class in fish2eod.mesh.model_geometry)
QESModel (class in fish2eod.models)
R
Rectangle (class in fish2eod.geometry.primitives)
refine() (fish2eod.models.Model method)
register_species() (in module fish2eod.data.species_registry)
remesh_index (fish2eod.sweep.ParameterSweep property)
right (fish2eod.geometry.fish.SideStruct attribute)
right_arc_length (fish2eod.helpers.type_helpers.SkinStructure attribute)
right_inner (fish2eod.helpers.type_helpers.SkinStructure attribute)
right_outer (fish2eod.helpers.type_helpers.SkinStructure attribute)
right_tdp (fish2eod.helpers.type_helpers.TDP attribute)
rotate() (fish2eod.geometry.primitives.Polygon method)
run() (fish2eod.sweep.IterativeSolver method)
run_step() (fish2eod.sweep.IterativeSolver method)
S
save() (fish2eod.xdmf.save.Saver method)
save_model() (fish2eod.xdmf.save.Saver method)
Saver (class in fish2eod.xdmf.save)
settings (fish2eod.data.species_registry.SpeciesData attribute)
(fish2eod.geometry.fish.Fish property)
setup_fish() (fish2eod.models.BaseFishModel method)
setup_sides() (fish2eod.geometry.fish.Fish method)
shapely_representation (fish2eod.geometry.primitives.Polygon property)
should_remesh() (fish2eod.sweep.ParameterSweep method)
side (fish2eod.helpers.type_helpers.ComputatableSideInformation attribute)
SideStruct (class in fish2eod.geometry.fish)
simplify() (fish2eod.geometry.primitives.Polygon method)
skin_conductance() (fish2eod.geometry.fish.Fish method)
skin_potential() (in module fish2eod.analysis.transdermal)
skin_type (fish2eod.helpers.type_helpers.ComputatableSideInformation attribute)
SkinStructure (class in fish2eod.helpers.type_helpers)
Solution (class in fish2eod.xdmf.load)
solution (fish2eod.models.Model property)
solve() (fish2eod.models.BaseFishModel method)
(fish2eod.models.Model method)
(fish2eod.models.QESModel method)
sort_parameter_sets() (in module fish2eod.sweep)
SpatialFunction (class in fish2eod.properties)
spawn_from_variable() (fish2eod.xdmf.load.DataSolution method)
(fish2eod.xdmf.load.H5Solution method)
(fish2eod.xdmf.load.Solution method)
SpeciesData (class in fish2eod.data.species_registry)
SpeciesRegistry (class in fish2eod.data.species_registry)
SplineExpression (class in fish2eod.properties)
split_body() (in module fish2eod.geometry.fish)
split_mpl_kwargs() (in module fish2eod.analysis.plotting)
structural_compilation() (fish2eod.models.Model method)
structure_to_dataset() (fish2eod.models.Model method)
T
tail_conductance (fish2eod.data.settings.FishSettings attribute)
tail_distance (fish2eod.data.settings.FishSettings attribute)
TDP (class in fish2eod.helpers.type_helpers)
time_step (fish2eod.helpers.type_helpers.DataSet attribute)
to_dirichlet_condition() (fish2eod.math.BoundaryCondition method)
to_fenics_representation() (fish2eod.math.BoundaryCondition method)
to_neumann_condition() (fish2eod.math.BoundaryCondition method)
to_sweep() (fish2eod.sweep.ParameterSet method)
topology (fish2eod.helpers.type_helpers.DataSet attribute)
topology_0d (fish2eod.models.Model property)
topology_1d (fish2eod.models.Model property)
topology_2d (fish2eod.models.Model property)
topology_path_1d (fish2eod.xdmf.save.Saver property)
topology_path_2d (fish2eod.xdmf.save.Saver property)
translate() (fish2eod.geometry.primitives.Polygon method)
U
u (fish2eod.helpers.dolfin_tools.Equation attribute)
uniform_spline_interpolation() (in module fish2eod.geometry.operations)
update_for_image() (fish2eod.models.BaseFishModel method)
update_parameter() (fish2eod.models.Model method)
upscale_parameter_name() (in module fish2eod.analysis.plotting)
V
validate() (fish2eod.sweep.EODPhase method)
(fish2eod.sweep.FishPosition method)
(fish2eod.sweep.ParameterSet method)
validate_intersections() (fish2eod.mesh.model_geometry.ModelGeometry method)
value (fish2eod.helpers.type_helpers.ElectricImageParameters attribute)
(fish2eod.math.BoundaryCondition attribute)
value_shape() (fish2eod.properties.Property static method)
(fish2eod.properties.SplineExpression static method)
variables_from_data() (in module fish2eod.xdmf.load)
verboseness (fish2eod.models.Model property)
W
WATER_CONDUCTIVITY (fish2eod.models.BaseFishModel attribute)
write() (fish2eod.mesh.mesh.Mesher method)
write_geometry() (fish2eod.xdmf.save.Saver method)
write_h5() (fish2eod.xdmf.save.Saver method)
write_topology() (fish2eod.xdmf.save.Saver method)
write_xml() (in module fish2eod.xdmf.xml_tools)
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