physicool
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physicool
Index
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Index
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A
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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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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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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
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X
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Y
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Z
_
__post_init__() (physicool.optimization.MultiLevelSweep method)
(physicool.optimization.PhysiCellBlackBox method)
(physicool.plotting.SweeperPlot method)
(physicool.updaters.ParamsUpdater method)
__repr__() (physicool.config.ConfigFileParser method)
_create_project_command() (in module physicool.optimization)
A
add_bounds_to_ax() (physicool.plotting.SweeperPlot method)
APOPTOSIS (physicool.datatypes.DeathCode attribute)
ax (physicool.plotting.SweeperPlot attribute)
B
black_box (physicool.optimization.MultiLevelSweep attribute)
C
calcification_rate (physicool.datatypes.Death attribute)
(physicool.datatypes.Volume attribute)
calcified_fraction (physicool.datatypes.Volume attribute)
cell_cell_adhesion_strength (physicool.datatypes.Mechanics attribute)
cell_cell_repulsion_strength (physicool.datatypes.Mechanics attribute)
cell_definition_name (physicool.updaters.CellUpdater attribute)
cell_definitions_list (physicool.config.ConfigFileParser property)
CELL_OUTPUT_LABELS (in module physicool.processing)
CellParameters (class in physicool.datatypes)
CellUpdater (class in physicool.updaters)
CellUpdaterFunction (in module physicool.updaters)
check_version_status() (in module physicool.processing)
chemotaxis_direction (physicool.datatypes.Motility attribute)
chemotaxis_enabled (physicool.datatypes.Motility attribute)
chemotaxis_substrate (physicool.datatypes.Motility attribute)
clean_outputs() (in module physicool.optimization)
clean_tmp_files() (in module physicool.optimization)
code (physicool.datatypes.Cycle attribute)
(physicool.datatypes.Death attribute)
compile_project() (in module physicool.optimization)
compute_mean_squared_error() (in module physicool.processing)
compute_objective() (physicool.optimization.MultiLevelSweep method)
config_path (physicool.updaters.ParamsUpdater attribute)
ConfigFileParser (class in physicool.config)
convert_version_str_to_tuple() (in module physicool.processing)
current_level (physicool.optimization.MultiLevelSweep attribute)
current_opt_point (physicool.optimization.MultiLevelSweep attribute)
custom (physicool.datatypes.CellParameters attribute)
CustomData (class in physicool.datatypes)
Cycle (class in physicool.datatypes)
cycle (physicool.datatypes.CellParameters attribute)
Cycle.Config (class in physicool.datatypes)
CycleCode (class in physicool.datatypes)
cytoplasmic_biomass_change_rate (physicool.datatypes.Death attribute)
(physicool.datatypes.Volume attribute)
D
Death (class in physicool.datatypes)
death (physicool.datatypes.CellParameters attribute)
Death.Config (class in physicool.datatypes)
death_rate (physicool.datatypes.Death attribute)
DeathCode (class in physicool.datatypes)
decay_rate (physicool.datatypes.Substance attribute)
diffusion_coefficient (physicool.datatypes.Substance attribute)
dirichlet_boundary_condition (physicool.datatypes.Substance attribute)
Domain (class in physicool.datatypes)
draw() (physicool.plotting.SweeperPlot method)
dt_diffusion (physicool.datatypes.Overall attribute)
dt_mechanics (physicool.datatypes.Overall attribute)
dt_phenotype (physicool.datatypes.Overall attribute)
dx (physicool.datatypes.Domain attribute)
dy (physicool.datatypes.Domain attribute)
dz (physicool.datatypes.Domain attribute)
E
error_estimator (physicool.optimization.MultiLevelSweep attribute)
ErrorQuantification (in module physicool.processing)
F
fig (physicool.plotting.SweeperPlot attribute)
FLOW_CYTOMETRY_SEPARATED (physicool.datatypes.CycleCode attribute)
fluid_change_rate (physicool.datatypes.Volume attribute)
fluid_fraction (physicool.datatypes.Volume attribute)
G
get_cell_data() (in module physicool.processing)
get_cell_file_name() (in module physicool.processing)
get_cell_file_num() (in module physicool.processing)
get_cell_numbers_over_time() (in module physicool.processing)
get_cell_trajectories() (in module physicool.processing)
get_cells_in_z_slice() (in module physicool.processing)
get_colormap() (physicool.plotting.SweeperPlot static method)
get_data() (physicool.processing.Microenvironment method)
get_final_y_position() (in module physicool.processing)
get_mesh() (physicool.processing.Microenvironment method)
get_optimal_idx() (physicool.optimization.MultiLevelSweep method)
get_parameter_range() (physicool.optimization.MultiLevelSweep method)
get_parameter_space() (physicool.optimization.MultiLevelSweep method)
get_substance_data() (physicool.processing.Microenvironment method)
get_substances() (physicool.processing.Microenvironment method)
I
initial_condition (physicool.datatypes.Substance attribute)
L
LIVE (physicool.datatypes.CycleCode attribute)
LOG_FILE (in module physicool.optimization)
lysed_fluid_change_rate (physicool.datatypes.Death attribute)
M
max_time (physicool.datatypes.Overall attribute)
me_substance_list (physicool.config.ConfigFileParser property)
Mechanics (class in physicool.datatypes)
mechanics (physicool.datatypes.CellParameters attribute)
Mechanics.Config (class in physicool.datatypes)
Microenvironment (class in physicool.processing)
MicroenvironmentUpdater (class in physicool.updaters)
migration_bias (physicool.datatypes.Motility attribute)
module
physicool
physicool.config
physicool.datatypes
physicool.optimization
physicool.pcxml
physicool.plotting
physicool.processing
physicool.updaters
Motility (class in physicool.datatypes)
motility (physicool.datatypes.CellParameters attribute)
Motility.Config (class in physicool.datatypes)
motility_enabled (physicool.datatypes.Motility attribute)
MultiLevelSweep (class in physicool.optimization)
N
n_levels (physicool.optimization.MultiLevelSweep attribute)
name (physicool.datatypes.CellParameters attribute)
(physicool.datatypes.CustomData attribute)
(physicool.datatypes.Death attribute)
(physicool.datatypes.Secretion attribute)
(physicool.datatypes.Substance attribute)
NECROSIS (physicool.datatypes.DeathCode attribute)
net_export_rate (physicool.datatypes.Secretion attribute)
NEW_OUTPUTS_VERSION (in module physicool.processing)
nuclear (physicool.datatypes.Volume attribute)
nuclear_biomass_change_rate (physicool.datatypes.Death attribute)
(physicool.datatypes.Volume attribute)
O
OutputProcessor (in module physicool.processing)
Overall (class in physicool.datatypes)
P
param_bounds (physicool.optimization.MultiLevelSweep attribute)
parameters (physicool.optimization.MultiLevelSweep attribute)
ParamsUpdater (class in physicool.updaters)
parse_custom() (in module physicool.pcxml)
parse_cycle() (in module physicool.pcxml)
parse_death() (in module physicool.pcxml)
parse_death_model() (in module physicool.pcxml)
parse_domain() (in module physicool.pcxml)
parse_mechanics() (in module physicool.pcxml)
parse_microenvironment() (in module physicool.pcxml)
parse_motility() (in module physicool.pcxml)
parse_overall() (in module physicool.pcxml)
parse_secretion() (in module physicool.pcxml)
parse_secretion_substance() (in module physicool.pcxml)
parse_substance() (in module physicool.pcxml)
parse_volume() (in module physicool.pcxml)
parser (physicool.updaters.ParamsUpdater attribute)
percentage_dir (physicool.optimization.MultiLevelSweep attribute)
persistence_time (physicool.datatypes.Motility attribute)
phase_durations (physicool.datatypes.Cycle attribute)
(physicool.datatypes.Death attribute)
phase_transition_rates (physicool.datatypes.Cycle attribute)
(physicool.datatypes.Death attribute)
PhysiCellBlackBox (class in physicool.optimization)
physicool
module
physicool.config
module
physicool.datatypes
module
physicool.optimization
module
physicool.pcxml
module
physicool.plotting
module
physicool.processing
module
physicool.updaters
module
plot_level_results() (physicool.plotting.SweeperPlot method)
plot_trajectories_2d() (in module physicool.plotting)
plot_trajectories_3d() (in module physicool.plotting)
plotter (physicool.optimization.MultiLevelSweep attribute)
points_dir (physicool.optimization.MultiLevelSweep attribute)
processor (physicool.optimization.PhysiCellBlackBox attribute)
project_command (physicool.optimization.PhysiCellBlackBox attribute)
project_name (physicool.optimization.PhysiCellBlackBox attribute)
R
read_cell_data() (physicool.config.ConfigFileParser method)
read_custom_data() (physicool.config.ConfigFileParser method)
read_cycle_params() (physicool.config.ConfigFileParser method)
read_death_params() (physicool.config.ConfigFileParser method)
read_domain_params() (physicool.config.ConfigFileParser method)
read_mat_file_cells() (in module physicool.processing)
read_me_params() (physicool.config.ConfigFileParser method)
read_mechanics_params() (physicool.config.ConfigFileParser method)
read_motility_params() (physicool.config.ConfigFileParser method)
read_overall_params() (physicool.config.ConfigFileParser method)
read_physicell_version() (in module physicool.processing)
read_secretion_params() (physicool.config.ConfigFileParser method)
read_user_params() (physicool.config.ConfigFileParser method)
read_volume_params() (physicool.config.ConfigFileParser method)
relative_maximum_adhesion_distance (physicool.datatypes.Mechanics attribute)
relative_rupture_volume (physicool.datatypes.Death attribute)
(physicool.datatypes.Volume attribute)
results (physicool.optimization.MultiLevelSweep attribute)
run() (physicool.optimization.PhysiCellBlackBox method)
run_level() (physicool.optimization.MultiLevelSweep method)
run_sweep() (in module physicool.optimization)
(physicool.optimization.MultiLevelSweep method)
S
Secretion (class in physicool.datatypes)
secretion (physicool.datatypes.CellParameters attribute)
Secretion.Config (class in physicool.datatypes)
secretion_rate (physicool.datatypes.Secretion attribute)
secretion_target (physicool.datatypes.Secretion attribute)
set_absolute_equilibrium_distance (physicool.datatypes.Mechanics attribute)
set_param_bounds() (physicool.optimization.MultiLevelSweep method)
set_relative_equilibrium_distance (physicool.datatypes.Mechanics attribute)
set_up_plotter() (physicool.plotting.SweeperPlot method)
speed (physicool.datatypes.Motility attribute)
Substance (class in physicool.datatypes)
substance_name (physicool.updaters.MicroenvironmentUpdater attribute)
SweeperPlot (class in physicool.plotting)
T
target_data (physicool.optimization.MultiLevelSweep attribute)
total (physicool.datatypes.Volume attribute)
U
unlysed_fluid_change_rate (physicool.datatypes.Death attribute)
update() (physicool.updaters.CellUpdater method)
(physicool.updaters.MicroenvironmentUpdater method)
(physicool.updaters.ParamsUpdater class method)
update_cycle_values() (in module physicool.updaters)
update_mechanics_values() (in module physicool.updaters)
update_motility_values() (in module physicool.updaters)
update_substance_values() (in module physicool.updaters)
update_volume_values() (in module physicool.updaters)
updater (physicool.optimization.PhysiCellBlackBox attribute)
updater_function (physicool.updaters.CellUpdater attribute)
uptake_rate (physicool.datatypes.Secretion attribute)
use_2d (physicool.datatypes.Domain attribute)
(physicool.datatypes.Motility attribute)
V
validate_assignment (physicool.datatypes.Cycle.Config attribute)
(physicool.datatypes.Death.Config attribute)
(physicool.datatypes.Mechanics.Config attribute)
(physicool.datatypes.Motility.Config attribute)
(physicool.datatypes.Secretion.Config attribute)
(physicool.datatypes.Volume.Config attribute)
value (physicool.datatypes.CustomData attribute)
version (physicool.optimization.PhysiCellBlackBox attribute)
Volume (class in physicool.datatypes)
volume (physicool.datatypes.CellParameters attribute)
Volume.Config (class in physicool.datatypes)
W
write_cell_params() (physicool.config.ConfigFileParser method)
write_custom_data() (in module physicool.pcxml)
write_custom_params() (physicool.config.ConfigFileParser method)
write_cycle() (in module physicool.pcxml)
write_cycle_params() (physicool.config.ConfigFileParser method)
write_death_model() (in module physicool.pcxml)
write_death_model_params() (physicool.config.ConfigFileParser method)
write_death_params() (physicool.config.ConfigFileParser method)
write_domain() (in module physicool.pcxml)
write_domain_params() (physicool.config.ConfigFileParser method)
write_mechanics() (in module physicool.pcxml)
write_mechanics_params() (physicool.config.ConfigFileParser method)
write_motility() (in module physicool.pcxml)
write_motility_params() (physicool.config.ConfigFileParser method)
write_overall() (in module physicool.pcxml)
write_overall_params() (physicool.config.ConfigFileParser method)
write_secretion_params() (physicool.config.ConfigFileParser method)
write_secretion_substance() (in module physicool.pcxml)
write_secretion_substance_params() (physicool.config.ConfigFileParser method)
write_substance() (in module physicool.pcxml)
write_substance_params() (physicool.config.ConfigFileParser method)
write_user_params() (physicool.config.ConfigFileParser method)
write_volume() (in module physicool.pcxml)
write_volume_params() (physicool.config.ConfigFileParser method)
X
x_max (physicool.datatypes.Domain attribute)
x_min (physicool.datatypes.Domain attribute)
Y
y_max (physicool.datatypes.Domain attribute)
y_min (physicool.datatypes.Domain attribute)
Z
z_max (physicool.datatypes.Domain attribute)
z_min (physicool.datatypes.Domain attribute)
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