Index

A

AbcModel (class in deeprootgen.calibration.model_versioning) add_child_node() (deeprootgen.model.hgraph.RootNode method) (deeprootgen.model.root.RootOrgan method) add_edge() (deeprootgen.model.hgraph.RootSystemGraph method) add_node() (deeprootgen.model.hgraph.RootSystemGraph method) as_df() (deeprootgen.model.hgraph.RootSystemGraph method) as_dict() (deeprootgen.model.hgraph.RootEdge method) (deeprootgen.model.hgraph.RootNode method) (deeprootgen.model.hgraph.RootSystemGraph method)

as_networkx() (deeprootgen.model.hgraph.RootSystemGraph method) as_torch() (deeprootgen.model.hgraph.RootSystemGraph method) AverageDiameter (class in deeprootgen.statistics.summary_statistics) AverageLength (class in deeprootgen.statistics.summary_statistics) AverageSpecificRootLength (class in deeprootgen.statistics.summary_statistics) AverageVolume (class in deeprootgen.statistics.summary_statistics) AverageWeight (class in deeprootgen.statistics.summary_statistics)

B

build_calibration_parameters() (in module deeprootgen.form.components) build_collapsible() (in module deeprootgen.form.components)

build_common_components() (in module deeprootgen.form.components) build_common_layout() (in module deeprootgen.form.components)

C

calculate() (deeprootgen.statistics.distance_metrics.DistanceMetricBase method) (deeprootgen.statistics.distance_metrics.L1Norm method) (deeprootgen.statistics.distance_metrics.MeanAbsoluteError method) (deeprootgen.statistics.distance_metrics.MeanAbsolutePercentageError method) (deeprootgen.statistics.distance_metrics.MeanPinballLoss method) (deeprootgen.statistics.distance_metrics.MeanSquaredError method) (deeprootgen.statistics.distance_metrics.MedianAbsoluteError method) (deeprootgen.statistics.distance_metrics.RootMeanSquaredError method) (deeprootgen.statistics.summary_statistics.AverageDiameter method) (deeprootgen.statistics.summary_statistics.AverageLength method) (deeprootgen.statistics.summary_statistics.AverageSpecificRootLength method) (deeprootgen.statistics.summary_statistics.AverageVolume method) (deeprootgen.statistics.summary_statistics.AverageWeight method) (deeprootgen.statistics.summary_statistics.ConvexHullArea method) (deeprootgen.statistics.summary_statistics.ConvexHullVolume method) (deeprootgen.statistics.summary_statistics.DepthDistribution method) (deeprootgen.statistics.summary_statistics.RadialDistribution method) (deeprootgen.statistics.summary_statistics.SummaryStatisticBase method) (deeprootgen.statistics.summary_statistics.TotalDiameter method) (deeprootgen.statistics.summary_statistics.TotalLength method) (deeprootgen.statistics.summary_statistics.TotalSpecificRootLength method) (deeprootgen.statistics.summary_statistics.TotalVolume method) (deeprootgen.statistics.summary_statistics.TotalWeight method)

calculate_mass() (deeprootgen.model.root.RootOrgan method) calculate_statistic_per_layer() (deeprootgen.statistics.summary_statistics.SummaryStatisticBase method) calculate_summary_statistic_discrepancy() (in module deeprootgen.calibration.summary_statistics) calculate_summary_statistics() (in module deeprootgen.calibration.summary_statistics) cascading_set_invalid_root() (deeprootgen.model.root.RootOrgan method) cascading_to_world_origin() (deeprootgen.model.root.RootOrgan method) cascading_transform() (deeprootgen.model.root.RootOrgan method) cascading_update_transform() (deeprootgen.model.root.RootOrgan method) construct_root() (deeprootgen.model.root.RootOrgan method) construct_root_from_parent() (deeprootgen.model.root.RootOrgan method) ConvexHullArea (class in deeprootgen.statistics.summary_statistics) ConvexHullVolume (class in deeprootgen.statistics.summary_statistics) create_soil_fig() (deeprootgen.model.soil.Soil method) create_soil_grid() (deeprootgen.model.soil.Soil method)

D

deeprootgen.calibration.model_versioning module deeprootgen.calibration.parameters module deeprootgen.calibration.summary_statistics module deeprootgen.calibration.surrogates module deeprootgen.data_model.config_data_models module deeprootgen.data_model.simulation_data_models module deeprootgen.form.components module deeprootgen.io.simulation_data module deeprootgen.model.hgraph module

deeprootgen.model.root module deeprootgen.model.soil module deeprootgen.pipeline.experiment module deeprootgen.pipeline.workflow module deeprootgen.spatial.transform module deeprootgen.statistics.distance_metrics module deeprootgen.statistics.summary_statistics module DepthDistribution (class in deeprootgen.statistics.summary_statistics) dispatch_new_run() (in module deeprootgen.pipeline.experiment) DistanceMetricBase (class in deeprootgen.statistics.distance_metrics)

E

EarlyStopper (class in deeprootgen.calibration.surrogates)

encode() (deeprootgen.calibration.model_versioning.GraphFlowFeatureExtractor method) ExperimentModel (class in deeprootgen.data_model.config_data_models)

F

flow() (deeprootgen.calibration.model_versioning.GraphFlowFeatureExtractor method) FormModel (class in deeprootgen.data_model.config_data_models)

forward() (deeprootgen.calibration.model_versioning.GraphFlowFeatureExtractor method) (deeprootgen.calibration.surrogates.SingleTaskVariationalGPModel method) from_content_string() (deeprootgen.model.hgraph.RootSystemGraph method)

G

get_apex_coordinates() (deeprootgen.model.root.RootOrgan method) get_calibration_summary_stats() (in module deeprootgen.calibration.summary_statistics) get_common_layout() (in module deeprootgen.form.components) get_coordinates() (deeprootgen.model.root.RootOrgan method) get_datetime_now() (in module deeprootgen.pipeline.experiment) get_deployment_links() (in module deeprootgen.form.components) get_diameters() (deeprootgen.model.root.RootOrgan method) get_distance_metric_func() (in module deeprootgen.statistics.distance_metrics) get_distance_metrics() (in module deeprootgen.statistics.distance_metrics) get_external_links() (in module deeprootgen.form.components) get_lengths() (deeprootgen.model.root.RootOrgan method) get_local_origin() (deeprootgen.model.root.RootOrgan method) get_number_of_roots() (deeprootgen.statistics.summary_statistics.SummaryStatisticBase method) get_out_table_df() (in module deeprootgen.form.components) get_outdir() (in module deeprootgen.pipeline.experiment)

get_parent_origin() (deeprootgen.model.root.RootOrgan method) get_simulation_parameters() (in module deeprootgen.calibration.parameters) get_simulation_uuid() (in module deeprootgen.pipeline.experiment) get_summary_statistic_func() (in module deeprootgen.statistics.summary_statistics) get_summary_statistics() (in module deeprootgen.statistics.summary_statistics) get_transform_matrix() (in module deeprootgen.spatial.transform) get_x_rotation_matrix() (in module deeprootgen.spatial.transform) get_xy_comparison_data() (deeprootgen.statistics.summary_statistics.DepthDistribution method) (deeprootgen.statistics.summary_statistics.RadialDistribution method) (deeprootgen.statistics.summary_statistics.SummaryStatisticBase method) get_y_rotation_matrix() (in module deeprootgen.spatial.transform) get_yaw() (deeprootgen.model.root.RootSystemSimulation method) get_z_rotation_matrix() (in module deeprootgen.spatial.transform) GraphFlowFeatureExtractor (class in deeprootgen.calibration.model_versioning) grow() (deeprootgen.model.root.RootOrgan method) (deeprootgen.model.root.RootSystemSimulation method)

I

increment_node_id() (deeprootgen.model.hgraph.RootSystemGraph method) increment_organ_id() (deeprootgen.model.hgraph.RootSystemGraph method) init_diameters() (deeprootgen.model.root.RootOrgan method)

init_fig() (deeprootgen.model.root.RootSystemSimulation method) init_lengths() (deeprootgen.model.root.RootOrgan method) init_organs() (deeprootgen.model.root.RootSystemSimulation method) init_segment_coordinates() (deeprootgen.model.root.RootOrgan method)

L

L1Norm (class in deeprootgen.statistics.distance_metrics) lhc_sample() (in module deeprootgen.calibration.parameters) load_context() (deeprootgen.calibration.model_versioning.AbcModel method) (deeprootgen.calibration.model_versioning.OptimisationModel method) (deeprootgen.calibration.model_versioning.SensitivityAnalysisModel method) (deeprootgen.calibration.model_versioning.SnpeModel method) (deeprootgen.calibration.model_versioning.SurrogateModel method)

load_data_from_file() (in module deeprootgen.io.simulation_data) load_form_parameters() (in module deeprootgen.pipeline.experiment) log_model() (in module deeprootgen.calibration.model_versioning)

M

make_homogenous() (in module deeprootgen.spatial.transform) MeanAbsoluteError (class in deeprootgen.statistics.distance_metrics) MeanAbsolutePercentageError (class in deeprootgen.statistics.distance_metrics) MeanPinballLoss (class in deeprootgen.statistics.distance_metrics) MeanSquaredError (class in deeprootgen.statistics.distance_metrics) MedianAbsoluteError (class in deeprootgen.statistics.distance_metrics) model_computed_fields (deeprootgen.data_model.config_data_models.ExperimentModel attribute) (deeprootgen.data_model.config_data_models.FormModel attribute) (deeprootgen.data_model.config_data_models.ObjectStorageModel attribute) (deeprootgen.data_model.config_data_models.OrchestrationModel attribute) (deeprootgen.data_model.simulation_data_models.ParameterIntervalModel attribute) (deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals attribute) (deeprootgen.data_model.simulation_data_models.RootCalibrationModel attribute) (deeprootgen.data_model.simulation_data_models.RootEdgeModel attribute) (deeprootgen.data_model.simulation_data_models.RootNodeModel attribute) (deeprootgen.data_model.simulation_data_models.RootSimulationModel attribute) (deeprootgen.data_model.simulation_data_models.RootTypeModel attribute) (deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel attribute) (deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel attribute) model_config (deeprootgen.data_model.config_data_models.ExperimentModel attribute) (deeprootgen.data_model.config_data_models.FormModel attribute) (deeprootgen.data_model.config_data_models.ObjectStorageModel attribute) (deeprootgen.data_model.config_data_models.OrchestrationModel attribute) (deeprootgen.data_model.simulation_data_models.ParameterIntervalModel attribute) (deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals attribute) (deeprootgen.data_model.simulation_data_models.RootCalibrationModel attribute) (deeprootgen.data_model.simulation_data_models.RootEdgeModel attribute) (deeprootgen.data_model.simulation_data_models.RootNodeModel attribute) (deeprootgen.data_model.simulation_data_models.RootSimulationModel attribute) (deeprootgen.data_model.simulation_data_models.RootTypeModel attribute) (deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel attribute) (deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel attribute)

model_fields (deeprootgen.data_model.config_data_models.ExperimentModel attribute) (deeprootgen.data_model.config_data_models.FormModel attribute) (deeprootgen.data_model.config_data_models.ObjectStorageModel attribute) (deeprootgen.data_model.config_data_models.OrchestrationModel attribute) (deeprootgen.data_model.simulation_data_models.ParameterIntervalModel attribute) (deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals attribute) (deeprootgen.data_model.simulation_data_models.RootCalibrationModel attribute) (deeprootgen.data_model.simulation_data_models.RootEdgeModel attribute) (deeprootgen.data_model.simulation_data_models.RootNodeModel attribute) (deeprootgen.data_model.simulation_data_models.RootSimulationModel attribute) (deeprootgen.data_model.simulation_data_models.RootTypeModel attribute) (deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel attribute) (deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel attribute) module deeprootgen.calibration.model_versioning deeprootgen.calibration.parameters deeprootgen.calibration.summary_statistics deeprootgen.calibration.surrogates deeprootgen.data_model.config_data_models deeprootgen.data_model.simulation_data_models deeprootgen.form.components deeprootgen.io.simulation_data deeprootgen.model.hgraph deeprootgen.model.root deeprootgen.model.soil deeprootgen.pipeline.experiment deeprootgen.pipeline.workflow deeprootgen.spatial.transform deeprootgen.statistics.distance_metrics deeprootgen.statistics.summary_statistics

O

ObjectStorageModel (class in deeprootgen.data_model.config_data_models)

OptimisationModel (class in deeprootgen.calibration.model_versioning) OrchestrationModel (class in deeprootgen.data_model.config_data_models)

P

ParameterIntervalModel (class in deeprootgen.data_model.simulation_data_models) plot_hierarchical_graph() (deeprootgen.model.root.RootSystemSimulation method) plot_root_system() (deeprootgen.model.root.RootSystemSimulation method) position_primary_roots() (deeprootgen.model.root.RootSystemSimulation method) position_secondary_roots() (deeprootgen.model.root.RootSystemSimulation method) predict() (deeprootgen.calibration.model_versioning.AbcModel method) (deeprootgen.calibration.model_versioning.OptimisationModel method) (deeprootgen.calibration.model_versioning.SensitivityAnalysisModel method) (deeprootgen.calibration.model_versioning.SnpeModel method) (deeprootgen.calibration.model_versioning.SurrogateModel method)

prepare_surrogate_data() (in module deeprootgen.calibration.surrogates) PriorCollection (class in deeprootgen.calibration.parameters) process_graph() (in module deeprootgen.model.hgraph)

R

RadialDistribution (class in deeprootgen.statistics.summary_statistics) reset_transform() (deeprootgen.model.root.RootOrgan method) RootCalibrationIntervals (class in deeprootgen.data_model.simulation_data_models) RootCalibrationModel (class in deeprootgen.data_model.simulation_data_models) RootEdge (class in deeprootgen.model.hgraph) RootEdgeModel (class in deeprootgen.data_model.simulation_data_models) RootMeanSquaredError (class in deeprootgen.statistics.distance_metrics) RootNode (class in deeprootgen.model.hgraph)

RootNodeModel (class in deeprootgen.data_model.simulation_data_models) RootOrgan (class in deeprootgen.model.root) RootSimulationModel (class in deeprootgen.data_model.simulation_data_models) RootSystemGraph (class in deeprootgen.model.hgraph) RootSystemSimulation (class in deeprootgen.model.root) RootType (class in deeprootgen.data_model.simulation_data_models) RootTypeModel (class in deeprootgen.data_model.simulation_data_models) run() (deeprootgen.model.root.RootSystemSimulation method) run_calibration_simulation() (in module deeprootgen.calibration.summary_statistics)

S

s3_upload_file() (in module deeprootgen.io.simulation_data) sample() (deeprootgen.calibration.parameters.PriorCollection method) save_form_parameters() (in module deeprootgen.pipeline.experiment) save_simulation_runs() (in module deeprootgen.pipeline.experiment) SensitivityAnalysisModel (class in deeprootgen.calibration.model_versioning) set_coordinates() (deeprootgen.model.root.RootOrgan method) set_invalid_root() (deeprootgen.model.root.RootOrgan method)

SingleTaskVariationalGPModel (class in deeprootgen.calibration.surrogates) SnpeModel (class in deeprootgen.calibration.model_versioning) Soil (class in deeprootgen.model.soil) StatisticsComparisonModel (class in deeprootgen.data_model.simulation_data_models) SummaryStatisticBase (class in deeprootgen.statistics.summary_statistics) SummaryStatisticsModel (class in deeprootgen.data_model.simulation_data_models) SurrogateModel (class in deeprootgen.calibration.model_versioning)

T

TotalDiameter (class in deeprootgen.statistics.summary_statistics) TotalLength (class in deeprootgen.statistics.summary_statistics) TotalSpecificRootLength (class in deeprootgen.statistics.summary_statistics)

TotalVolume (class in deeprootgen.statistics.summary_statistics) TotalWeight (class in deeprootgen.statistics.summary_statistics) transform() (deeprootgen.model.root.RootOrgan method)

U

update_transform() (deeprootgen.model.root.RootOrgan method)

V

validate() (deeprootgen.model.root.RootOrgan method) (deeprootgen.model.root.RootSystemSimulation method)

visualise() (deeprootgen.statistics.summary_statistics.DepthDistribution method) (deeprootgen.statistics.summary_statistics.RadialDistribution method) (deeprootgen.statistics.summary_statistics.SummaryStatisticBase method)