diff --git a/_modules/deeprootgen/data_model/simulation_data_models.html b/_modules/deeprootgen/data_model/simulation_data_models.html index 0f65216..6e6e6f0 100644 --- a/_modules/deeprootgen/data_model/simulation_data_models.html +++ b/_modules/deeprootgen/data_model/simulation_data_models.html @@ -258,7 +258,8 @@

Source code for deeprootgen.data_model.simulation_data_models

summary_statistics: Optional[List[str]] = None distance_metric: Optional[str] = "" stat_by_soil_layer: Optional[bool] = False - stat_by_soil_column: Optional[bool] = False
+ stat_by_soil_column: Optional[bool] = False + use_summary_statistics: Optional[bool] = True @@ -315,6 +316,7 @@

Source code for deeprootgen.data_model.simulation_data_models

summary_statistics: Optional[List[SummaryStatisticsModel]] = None observed_data: Optional[List[RootNodeModel]] = None observed_data_content: Optional[str] = "" + raw_edge_content: Optional[str] = "" statistics_comparison: Optional[StatisticsComparisonModel] = None origin_min: Optional[float] = 1e-3 origin_max: Optional[float] = 1e-2 diff --git a/_modules/deeprootgen/form/components.html b/_modules/deeprootgen/form/components.html index 217a7c8..5b3c865 100644 --- a/_modules/deeprootgen/form/components.html +++ b/_modules/deeprootgen/form/components.html @@ -622,8 +622,10 @@

Source code for deeprootgen.form.components

     observed_data: list[dict] | None = None,
     summary_statistics: list[dict] | None = None,
     observed_data_content: str = "",
+    raw_edge_content: str = "",
     stat_by_layer: bool = False,
     stat_by_col: bool = False,
+    use_summary_statistics: bool = True,
 ) -> dict | None:
     """Build calibration parameters for workflow submission from form inputs.
 
@@ -642,10 +644,14 @@ 
Source code for deeprootgen.form.components
             The list of observed summary statistic data. Defaults to None.
         observed_data_content (str, optional):
             The raw content string for the observed root data. Defaults to "".
+        raw_edge_content (str, optional):
+            The raw content string for the simulated edge data. Defaults to "".
         stat_by_layer (bool, optional):
             Whether to calculate statistics by soil layer. Defaults to False.
-        stat_by_col (bool, optional ):
+        stat_by_col (bool, optional):
             Whether to calculate statistics by soil column. Defaults to False.
+        use_summary_statistics (bool, optional):
+            Whether to use summary statistics rather than graph data. Defaults to True.
 
     Returns:
         dict | None:
@@ -674,7 +680,11 @@ 
Source code for deeprootgen.form.components
         k = input["param"]
         calibration_value = calibration_values[i]
         if k == "summary_statistics" or k == "distance_metric":
-            if calibration_value is None or len(calibration_value) == 0:
+            if (
+                calibration_value is None
+                or len(calibration_value) == 0
+                and use_summary_statistics
+            ):
                 return None
 
         if input.get("statistic_parameter"):
@@ -684,9 +694,18 @@ 
Source code for deeprootgen.form.components
 
     form_inputs["statistics_comparison"]["stat_by_soil_layer"] = stat_by_layer
     form_inputs["statistics_comparison"]["stat_by_soil_column"] = stat_by_col
+    form_inputs["statistics_comparison"][
+        "use_summary_statistics"
+    ] = use_summary_statistics
+
+    if use_summary_statistics:
+        observed_data_content = ""
+        raw_edge_content = ""
+
     form_inputs["observed_data"] = observed_data
     form_inputs["summary_statistics"] = summary_statistics
     form_inputs["observed_data_content"] = observed_data_content
+    form_inputs["raw_edge_content"] = raw_edge_content
 
     return form_inputs

 
diff --git a/api_reference/data_model.html b/api_reference/data_model.html
index 776da7a..2ca5309 100644
--- a/api_reference/data_model.html
+++ b/api_reference/data_model.html
@@ -322,7 +322,7 @@ 
Data Model
 

-class deeprootgen.data_model.simulation_data_models.RootCalibrationModel(*, random_seed: int | None, parameter_intervals: RootCalibrationIntervals, calibration_parameters: Dict[str, bool | float | int | str], summary_statistics: List[SummaryStatisticsModel] | None = None, observed_data: List[RootNodeModel] | None = None, observed_data_content: str | None = '', statistics_comparison: StatisticsComparisonModel | None = None, origin_min: float | None = 0.001, origin_max: float | None = 0.01, enable_soil: bool | None = False, soil_layer_height: float | None = 0, soil_layer_width: float | None = 0, soil_n_layers: int | None = 0, soil_n_cols: int | None = 0, max_val_attempts: int | None = 50, simulation_tag: str | None = 'default', no_root_zone: float | None = 0.0001, floor_threshold: float | None = 0.4, ceiling_threshold: float | None = 0.9)[source]

+class deeprootgen.data_model.simulation_data_models.RootCalibrationModel(*, random_seed: int | None, parameter_intervals: RootCalibrationIntervals, calibration_parameters: Dict[str, bool | float | int | str], summary_statistics: List[SummaryStatisticsModel] | None = None, observed_data: List[RootNodeModel] | None = None, observed_data_content: str | None = '', raw_edge_content: str | None = '', statistics_comparison: StatisticsComparisonModel | None = None, origin_min: float | None = 0.001, origin_max: float | None = 0.01, enable_soil: bool | None = False, soil_layer_height: float | None = 0, soil_layer_width: float | None = 0, soil_n_layers: int | None = 0, soil_n_cols: int | None = 0, max_val_attempts: int | None = 50, simulation_tag: str | None = 'default', no_root_zone: float | None = 0.0001, floor_threshold: float | None = 0.4, ceiling_threshold: float | None = 0.9)[source]
 
The root system architecture calibration data model.

 

 
Args:

@@ -345,7 +345,7 @@ 
Data Model
 

-model_fields: ClassVar[dict[str, FieldInfo]] = {'calibration_parameters': FieldInfo(annotation=Dict[str, Union[bool, float, int, str]], required=True), 'ceiling_threshold': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.9), 'enable_soil': FieldInfo(annotation=Union[bool, NoneType], required=False, default=False), 'floor_threshold': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.4), 'max_val_attempts': FieldInfo(annotation=Union[int, NoneType], required=False, default=50), 'no_root_zone': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.0001), 'observed_data': FieldInfo(annotation=Union[List[RootNodeModel], NoneType], required=False, default=None), 'observed_data_content': FieldInfo(annotation=Union[str, NoneType], required=False, default=''), 'origin_max': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.01), 'origin_min': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.001), 'parameter_intervals': FieldInfo(annotation=RootCalibrationIntervals, required=True), 'random_seed': FieldInfo(annotation=Union[int, NoneType], required=True), 'simulation_tag': FieldInfo(annotation=Union[str, NoneType], required=False, default='default'), 'soil_layer_height': FieldInfo(annotation=Union[float, NoneType], required=False, default=0), 'soil_layer_width': FieldInfo(annotation=Union[float, NoneType], required=False, default=0), 'soil_n_cols': FieldInfo(annotation=Union[int, NoneType], required=False, default=0), 'soil_n_layers': FieldInfo(annotation=Union[int, NoneType], required=False, default=0), 'statistics_comparison': FieldInfo(annotation=Union[StatisticsComparisonModel, NoneType], required=False, default=None), 'summary_statistics': FieldInfo(annotation=Union[List[SummaryStatisticsModel], NoneType], required=False, default=None)}

+model_fields: ClassVar[dict[str, FieldInfo]] = {'calibration_parameters': FieldInfo(annotation=Dict[str, Union[bool, float, int, str]], required=True), 'ceiling_threshold': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.9), 'enable_soil': FieldInfo(annotation=Union[bool, NoneType], required=False, default=False), 'floor_threshold': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.4), 'max_val_attempts': FieldInfo(annotation=Union[int, NoneType], required=False, default=50), 'no_root_zone': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.0001), 'observed_data': FieldInfo(annotation=Union[List[RootNodeModel], NoneType], required=False, default=None), 'observed_data_content': FieldInfo(annotation=Union[str, NoneType], required=False, default=''), 'origin_max': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.01), 'origin_min': FieldInfo(annotation=Union[float, NoneType], required=False, default=0.001), 'parameter_intervals': FieldInfo(annotation=RootCalibrationIntervals, required=True), 'random_seed': FieldInfo(annotation=Union[int, NoneType], required=True), 'raw_edge_content': FieldInfo(annotation=Union[str, NoneType], required=False, default=''), 'simulation_tag': FieldInfo(annotation=Union[str, NoneType], required=False, default='default'), 'soil_layer_height': FieldInfo(annotation=Union[float, NoneType], required=False, default=0), 'soil_layer_width': FieldInfo(annotation=Union[float, NoneType], required=False, default=0), 'soil_n_cols': FieldInfo(annotation=Union[int, NoneType], required=False, default=0), 'soil_n_layers': FieldInfo(annotation=Union[int, NoneType], required=False, default=0), 'statistics_comparison': FieldInfo(annotation=Union[StatisticsComparisonModel, NoneType], required=False, default=None), 'summary_statistics': FieldInfo(annotation=Union[List[SummaryStatisticsModel], NoneType], required=False, default=None)}
 
Metadata about the fields defined on the model,
 mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

 
This replaces Model.__fields__ from Pydantic V1.

@@ -493,7 +493,7 @@ 
Data Model
 

-class deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel(*, summary_statistics: List[str] | None = None, distance_metric: str | None = '', stat_by_soil_layer: bool | None = False, stat_by_soil_column: bool | None = False)[source]

+class deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel(*, summary_statistics: List[str] | None = None, distance_metric: str | None = '', stat_by_soil_layer: bool | None = False, stat_by_soil_column: bool | None = False, use_summary_statistics: bool | None = True)[source]
 
The data model for comparing synthetic and observed data.

 

 
Args:

@@ -516,7 +516,7 @@ 
Data Model
 

-model_fields: ClassVar[dict[str, FieldInfo]] = {'distance_metric': FieldInfo(annotation=Union[str, NoneType], required=False, default=''), 'stat_by_soil_column': FieldInfo(annotation=Union[bool, NoneType], required=False, default=False), 'stat_by_soil_layer': FieldInfo(annotation=Union[bool, NoneType], required=False, default=False), 'summary_statistics': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None)}

+model_fields: ClassVar[dict[str, FieldInfo]] = {'distance_metric': FieldInfo(annotation=Union[str, NoneType], required=False, default=''), 'stat_by_soil_column': FieldInfo(annotation=Union[bool, NoneType], required=False, default=False), 'stat_by_soil_layer': FieldInfo(annotation=Union[bool, NoneType], required=False, default=False), 'summary_statistics': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None), 'use_summary_statistics': FieldInfo(annotation=Union[bool, NoneType], required=False, default=True)}
 
Metadata about the fields defined on the model,
 mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

 
This replaces Model.__fields__ from Pydantic V1.

diff --git a/api_reference/form.html b/api_reference/form.html
index 70d7811..931f7c5 100644
--- a/api_reference/form.html
+++ b/api_reference/form.html
@@ -108,7 +108,7 @@ 
Form<
 components that are specific to a given page.

 

 

-deeprootgen.form.components.build_calibration_parameters(form_name: str, task: str, parameter_values: list, calibration_values: list, observed_data: list[dict] | None = None, summary_statistics: list[dict] | None = None, observed_data_content: str = '', stat_by_layer: bool = False, stat_by_col: bool = False) → dict | None[source]

+deeprootgen.form.components.build_calibration_parameters(form_name: str, task: str, parameter_values: list, calibration_values: list, observed_data: list[dict] | None = None, summary_statistics: list[dict] | None = None, observed_data_content: str = '', raw_edge_content: str = '', stat_by_layer: bool = False, stat_by_col: bool = False, use_summary_statistics: bool = True) → dict | None[source]
 
Build calibration parameters for workflow submission from form inputs.

 

 
Args:

@@ -126,9 +126,13 @@ 
Form<
 

 
observed_data_content (str, optional):
The raw content string for the observed root data. Defaults to “”.

 

+
raw_edge_content (str, optional):
The raw content string for the simulated edge data. Defaults to “”.

+

 
stat_by_layer (bool, optional):
Whether to calculate statistics by soil layer. Defaults to False.

 

-
stat_by_col (bool, optional ):
Whether to calculate statistics by soil column. Defaults to False.

+
stat_by_col (bool, optional):
Whether to calculate statistics by soil column. Defaults to False.

+

+
use_summary_statistics (bool, optional):
Whether to use summary statistics rather than graph data. Defaults to True.

 

 

 

diff --git a/searchindex.js b/searchindex.js
index 40d969f..3b3df64 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"0.1.0 - 2024/08/17": [[9, "id1"]], "API Reference": [[3, null]], "Calibration": [[0, null]], "Changelog": [[9, null]], "Components": [[2, "module-deeprootgen.form.components"]], "Config": [[1, "module-deeprootgen.data_model.config_data_models"]], "Contacts": [[11, "contacts"]], "Contents:": [[10, null]], "Data Model": [[1, null]], "DeepRootGen": [[10, null]], "Distance Metrics": [[8, "module-deeprootgen.statistics.distance_metrics"]], "Experiment": [[6, "module-deeprootgen.pipeline.experiment"]], "Form": [[2, null]], "Graph": [[5, "module-deeprootgen.model.hgraph"]], "Indices and tables": [[10, "indices-and-tables"]], "Input/Output": [[4, null]], "Introduction": [[11, null]], "Model": [[5, null]], "Model Versioning": [[0, "module-deeprootgen.calibration.model_versioning"]], "Pipeline": [[6, null]], "Root": [[5, "module-deeprootgen.model.root"]], "Simulation": [[1, "module-deeprootgen.data_model.simulation_data_models"]], "Simulation Data": [[4, "module-deeprootgen.io.simulation_data"]], "Soil": [[5, "module-deeprootgen.model.soil"]], "Spatial": [[7, null]], "Statistics": [[8, null]], "Summary Statistics": [[0, "module-deeprootgen.calibration.summary_statistics"], [8, "module-deeprootgen.statistics.summary_statistics"]], "Transform": [[7, "module-deeprootgen.spatial.transform"]], "Workflow": [[6, "module-deeprootgen.pipeline.workflow"]]}, "docnames": ["api_reference/calibration", "api_reference/data_model", "api_reference/form", "api_reference/index", "api_reference/io", "api_reference/model", "api_reference/pipeline", "api_reference/spatial", "api_reference/statistics", "changelogs/changelog", "index", "introduction/index"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["api_reference/calibration.rst", "api_reference/data_model.rst", "api_reference/form.rst", "api_reference/index.rst", "api_reference/io.rst", "api_reference/model.rst", "api_reference/pipeline.rst", "api_reference/spatial.rst", "api_reference/statistics.rst", "changelogs/changelog.rst", "index.rst", "introduction/index.rst"], "indexentries": {"abcmodel (class in deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.AbcModel", false]], "add_child_node() (deeprootgen.model.hgraph.rootnode method)": [[5, "deeprootgen.model.hgraph.RootNode.add_child_node", false]], "add_child_node() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.add_child_node", false]], "add_edge() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.add_edge", false]], "add_node() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.add_node", false]], "as_df() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_df", false]], "as_dict() (deeprootgen.model.hgraph.rootedge method)": [[5, "deeprootgen.model.hgraph.RootEdge.as_dict", false]], "as_dict() (deeprootgen.model.hgraph.rootnode method)": [[5, "deeprootgen.model.hgraph.RootNode.as_dict", false]], "as_dict() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_dict", false]], "as_networkx() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_networkx", false]], "as_torch() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_torch", false]], "averagediameter (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageDiameter", false]], "averagelength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageLength", false]], "averagespecificrootlength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageSpecificRootLength", false]], "averagevolume (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageVolume", false]], "averageweight (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageWeight", false]], "build_calibration_parameters() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_calibration_parameters", false]], "build_collapsible() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_collapsible", false]], "build_common_components() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_common_components", false]], "build_common_layout() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_common_layout", false]], "calculate() (deeprootgen.statistics.distance_metrics.distancemetricbase method)": [[8, "deeprootgen.statistics.distance_metrics.DistanceMetricBase.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.l1norm method)": [[8, "deeprootgen.statistics.distance_metrics.L1Norm.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meanabsoluteerror method)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsoluteError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meanabsolutepercentageerror method)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsolutePercentageError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meanpinballloss method)": [[8, "deeprootgen.statistics.distance_metrics.MeanPinballLoss.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meansquarederror method)": [[8, "deeprootgen.statistics.distance_metrics.MeanSquaredError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.medianabsoluteerror method)": [[8, "deeprootgen.statistics.distance_metrics.MedianAbsoluteError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.rootmeansquarederror method)": [[8, "deeprootgen.statistics.distance_metrics.RootMeanSquaredError.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagediameter method)": [[8, "deeprootgen.statistics.summary_statistics.AverageDiameter.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagelength method)": [[8, "deeprootgen.statistics.summary_statistics.AverageLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagespecificrootlength method)": [[8, "deeprootgen.statistics.summary_statistics.AverageSpecificRootLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagevolume method)": [[8, "deeprootgen.statistics.summary_statistics.AverageVolume.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averageweight method)": [[8, "deeprootgen.statistics.summary_statistics.AverageWeight.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.convexhullarea method)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullArea.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.convexhullvolume method)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullVolume.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.depthdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.radialdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totaldiameter method)": [[8, "deeprootgen.statistics.summary_statistics.TotalDiameter.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totallength method)": [[8, "deeprootgen.statistics.summary_statistics.TotalLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totalspecificrootlength method)": [[8, "deeprootgen.statistics.summary_statistics.TotalSpecificRootLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totalvolume method)": [[8, "deeprootgen.statistics.summary_statistics.TotalVolume.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totalweight method)": [[8, "deeprootgen.statistics.summary_statistics.TotalWeight.calculate", false]], "calculate_statistic_per_layer() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.calculate_statistic_per_layer", false]], "calculate_summary_statistic_discrepancy() (in module deeprootgen.calibration.summary_statistics)": [[0, "deeprootgen.calibration.summary_statistics.calculate_summary_statistic_discrepancy", false]], "cascading_set_invalid_root() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_set_invalid_root", false]], "cascading_to_world_origin() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_to_world_origin", false]], "cascading_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_transform", false]], "cascading_update_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_update_transform", false]], "construct_root() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.construct_root", false]], "construct_root_from_parent() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.construct_root_from_parent", false]], "convexhullarea (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullArea", false]], "convexhullvolume (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullVolume", false]], "create_soil_fig() (deeprootgen.model.soil.soil method)": [[5, "deeprootgen.model.soil.Soil.create_soil_fig", false]], "create_soil_grid() (deeprootgen.model.soil.soil method)": [[5, "deeprootgen.model.soil.Soil.create_soil_grid", false]], "deeprootgen.calibration.model_versioning": [[0, "module-deeprootgen.calibration.model_versioning", false]], "deeprootgen.calibration.summary_statistics": [[0, "module-deeprootgen.calibration.summary_statistics", false]], "deeprootgen.data_model.config_data_models": [[1, "module-deeprootgen.data_model.config_data_models", false]], "deeprootgen.data_model.simulation_data_models": [[1, "module-deeprootgen.data_model.simulation_data_models", false]], "deeprootgen.form.components": [[2, "module-deeprootgen.form.components", false]], "deeprootgen.io.simulation_data": [[4, "module-deeprootgen.io.simulation_data", false]], "deeprootgen.model.hgraph": [[5, "module-deeprootgen.model.hgraph", false]], "deeprootgen.model.root": [[5, "module-deeprootgen.model.root", false]], "deeprootgen.model.soil": [[5, "module-deeprootgen.model.soil", false]], "deeprootgen.pipeline.experiment": [[6, "module-deeprootgen.pipeline.experiment", false]], "deeprootgen.pipeline.workflow": [[6, "module-deeprootgen.pipeline.workflow", false]], "deeprootgen.spatial.transform": [[7, "module-deeprootgen.spatial.transform", false]], "deeprootgen.statistics.distance_metrics": [[8, "module-deeprootgen.statistics.distance_metrics", false]], "deeprootgen.statistics.summary_statistics": [[8, "module-deeprootgen.statistics.summary_statistics", false]], "depthdistribution (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution", false]], "dispatch_new_run() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.dispatch_new_run", false]], "distancemetricbase (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.DistanceMetricBase", false]], "experimentmodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel", false]], "formmodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.FormModel", false]], "get_apex_coordinates() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_apex_coordinates", false]], "get_calibration_summary_stats() (in module deeprootgen.calibration.summary_statistics)": [[0, "deeprootgen.calibration.summary_statistics.get_calibration_summary_stats", false]], "get_common_layout() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.get_common_layout", false]], "get_coordinates() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_coordinates", false]], "get_datetime_now() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.get_datetime_now", false]], "get_distance_metric_func() (in module deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.get_distance_metric_func", false]], "get_distance_metrics() (in module deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.get_distance_metrics", false]], "get_external_links() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.get_external_links", false]], "get_local_origin() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_local_origin", false]], "get_number_of_roots() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.get_number_of_roots", false]], "get_out_table_df() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.get_out_table_df", false]], "get_outdir() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.get_outdir", false]], "get_parent_origin() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_parent_origin", false]], "get_simulation_uuid() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.get_simulation_uuid", false]], "get_summary_statistic_func() (in module deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.get_summary_statistic_func", false]], "get_summary_statistics() (in module deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.get_summary_statistics", false]], "get_transform_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_transform_matrix", false]], "get_x_rotation_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_x_rotation_matrix", false]], "get_xy_comparison_data() (deeprootgen.statistics.summary_statistics.depthdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution.get_xy_comparison_data", false]], "get_xy_comparison_data() (deeprootgen.statistics.summary_statistics.radialdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution.get_xy_comparison_data", false]], "get_xy_comparison_data() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.get_xy_comparison_data", false]], "get_y_rotation_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_y_rotation_matrix", false]], "get_yaw() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.get_yaw", false]], "get_z_rotation_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_z_rotation_matrix", false]], "increment_node_id() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.increment_node_id", false]], "increment_organ_id() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.increment_organ_id", false]], "init_diameters() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.init_diameters", false]], "init_fig() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.init_fig", false]], "init_lengths() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.init_lengths", false]], "init_organs() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.init_organs", false]], "init_segment_coordinates() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.init_segment_coordinates", false]], "l1norm (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.L1Norm", false]], "load_context() (deeprootgen.calibration.model_versioning.abcmodel method)": [[0, "deeprootgen.calibration.model_versioning.AbcModel.load_context", false]], "load_context() (deeprootgen.calibration.model_versioning.optimisationmodel method)": [[0, "deeprootgen.calibration.model_versioning.OptimisationModel.load_context", false]], "load_context() (deeprootgen.calibration.model_versioning.sensitivityanalysismodel method)": [[0, "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel.load_context", false]], "load_data_from_file() (in module deeprootgen.io.simulation_data)": [[4, "deeprootgen.io.simulation_data.load_data_from_file", false]], "load_form_parameters() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.load_form_parameters", false]], "log_model() (in module deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.log_model", false]], "make_homogenous() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.make_homogenous", false]], "meanabsoluteerror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsoluteError", false]], "meanabsolutepercentageerror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsolutePercentageError", false]], "meanpinballloss (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanPinballLoss", false]], "meansquarederror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanSquaredError", false]], "medianabsoluteerror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MedianAbsoluteError", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.experimentmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.formmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.FormModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.objectstoragemodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.orchestrationmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.parameterintervalmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationintervals attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootedgemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootnodemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootsimulationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.roottypemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.statisticscomparisonmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.summarystatisticsmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel.model_computed_fields", false]], "model_config (deeprootgen.data_model.config_data_models.experimentmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel.model_config", false]], "model_config (deeprootgen.data_model.config_data_models.formmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.FormModel.model_config", false]], "model_config (deeprootgen.data_model.config_data_models.objectstoragemodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel.model_config", false]], "model_config (deeprootgen.data_model.config_data_models.orchestrationmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.parameterintervalmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootcalibrationintervals attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootcalibrationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootedgemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootnodemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootsimulationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.roottypemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.statisticscomparisonmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.summarystatisticsmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel.model_config", false]], "model_fields (deeprootgen.data_model.config_data_models.experimentmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel.model_fields", false]], "model_fields (deeprootgen.data_model.config_data_models.formmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.FormModel.model_fields", false]], "model_fields (deeprootgen.data_model.config_data_models.objectstoragemodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel.model_fields", false]], "model_fields (deeprootgen.data_model.config_data_models.orchestrationmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.parameterintervalmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationintervals attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootedgemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootnodemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootsimulationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.roottypemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.statisticscomparisonmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.summarystatisticsmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel.model_fields", false]], "module": [[0, "module-deeprootgen.calibration.model_versioning", false], [0, "module-deeprootgen.calibration.summary_statistics", false], [1, "module-deeprootgen.data_model.config_data_models", false], [1, "module-deeprootgen.data_model.simulation_data_models", false], [2, "module-deeprootgen.form.components", false], [4, "module-deeprootgen.io.simulation_data", false], [5, "module-deeprootgen.model.hgraph", false], [5, "module-deeprootgen.model.root", false], [5, "module-deeprootgen.model.soil", false], [6, "module-deeprootgen.pipeline.experiment", false], [6, "module-deeprootgen.pipeline.workflow", false], [7, "module-deeprootgen.spatial.transform", false], [8, "module-deeprootgen.statistics.distance_metrics", false], [8, "module-deeprootgen.statistics.summary_statistics", false]], "objectstoragemodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel", false]], "optimisationmodel (class in deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.OptimisationModel", false]], "orchestrationmodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel", false]], "parameterintervalmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel", false]], "plot_hierarchical_graph() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.plot_hierarchical_graph", false]], "plot_root_system() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.plot_root_system", false]], "position_primary_roots() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.position_primary_roots", false]], "position_secondary_roots() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.position_secondary_roots", false]], "predict() (deeprootgen.calibration.model_versioning.abcmodel method)": [[0, "deeprootgen.calibration.model_versioning.AbcModel.predict", false]], "predict() (deeprootgen.calibration.model_versioning.optimisationmodel method)": [[0, "deeprootgen.calibration.model_versioning.OptimisationModel.predict", false]], "predict() (deeprootgen.calibration.model_versioning.sensitivityanalysismodel method)": [[0, "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel.predict", false]], "radialdistribution (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution", false]], "reset_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.reset_transform", false]], "rootcalibrationintervals (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals", false]], "rootcalibrationmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel", false]], "rootedge (class in deeprootgen.model.hgraph)": [[5, "deeprootgen.model.hgraph.RootEdge", false]], "rootedgemodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel", false]], "rootmeansquarederror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.RootMeanSquaredError", false]], "rootnode (class in deeprootgen.model.hgraph)": [[5, "deeprootgen.model.hgraph.RootNode", false]], "rootnodemodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel", false]], "rootorgan (class in deeprootgen.model.root)": [[5, "deeprootgen.model.root.RootOrgan", false]], "rootsimulationmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel", false]], "rootsystemgraph (class in deeprootgen.model.hgraph)": [[5, "deeprootgen.model.hgraph.RootSystemGraph", false]], "rootsystemsimulation (class in deeprootgen.model.root)": [[5, "deeprootgen.model.root.RootSystemSimulation", false]], "roottype (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootType", false]], "roottypemodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel", false]], "run() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.run", false]], "run_calibration_simulation() (in module deeprootgen.calibration.summary_statistics)": [[0, "deeprootgen.calibration.summary_statistics.run_calibration_simulation", false]], "s3_upload_file() (in module deeprootgen.io.simulation_data)": [[4, "deeprootgen.io.simulation_data.s3_upload_file", false]], "save_form_parameters() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.save_form_parameters", false]], "save_simulation_runs() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.save_simulation_runs", false]], "sensitivityanalysismodel (class in deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel", false]], "set_invalid_root() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.set_invalid_root", false]], "soil (class in deeprootgen.model.soil)": [[5, "deeprootgen.model.soil.Soil", false]], "statisticscomparisonmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel", false]], "summarystatisticbase (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase", false]], "summarystatisticsmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel", false]], "totaldiameter (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalDiameter", false]], "totallength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalLength", false]], "totalspecificrootlength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalSpecificRootLength", false]], "totalvolume (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalVolume", false]], "totalweight (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalWeight", false]], "transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.transform", false]], "update_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.update_transform", false]], "validate() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.validate", false]], "validate() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.validate", false]], "visualise() (deeprootgen.statistics.summary_statistics.depthdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution.visualise", false]], "visualise() (deeprootgen.statistics.summary_statistics.radialdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution.visualise", false]], "visualise() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.visualise", false]]}, "objects": {"deeprootgen.calibration": [[0, 0, 0, "-", "model_versioning"], [0, 0, 0, "-", "summary_statistics"]], "deeprootgen.calibration.model_versioning": [[0, 1, 1, "", "AbcModel"], [0, 1, 1, "", "OptimisationModel"], [0, 1, 1, "", "SensitivityAnalysisModel"], [0, 3, 1, "", "log_model"]], "deeprootgen.calibration.model_versioning.AbcModel": [[0, 2, 1, "", "load_context"], [0, 2, 1, "", "predict"]], "deeprootgen.calibration.model_versioning.OptimisationModel": [[0, 2, 1, "", "load_context"], [0, 2, 1, "", "predict"]], "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel": [[0, 2, 1, "", "load_context"], [0, 2, 1, "", "predict"]], "deeprootgen.calibration.summary_statistics": [[0, 3, 1, "", "calculate_summary_statistic_discrepancy"], [0, 3, 1, "", "get_calibration_summary_stats"], [0, 3, 1, "", "run_calibration_simulation"]], "deeprootgen.data_model": [[1, 0, 0, "-", "config_data_models"], [1, 0, 0, "-", "simulation_data_models"]], "deeprootgen.data_model.config_data_models": [[1, 1, 1, "", "ExperimentModel"], [1, 1, 1, "", "FormModel"], [1, 1, 1, "", "ObjectStorageModel"], [1, 1, 1, "", "OrchestrationModel"]], "deeprootgen.data_model.config_data_models.ExperimentModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.config_data_models.FormModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.config_data_models.ObjectStorageModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.config_data_models.OrchestrationModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models": [[1, 1, 1, "", "ParameterIntervalModel"], [1, 1, 1, "", "RootCalibrationIntervals"], [1, 1, 1, "", "RootCalibrationModel"], [1, 1, 1, "", "RootEdgeModel"], [1, 1, 1, "", "RootNodeModel"], [1, 1, 1, "", "RootSimulationModel"], [1, 1, 1, "", "RootType"], [1, 1, 1, "", "RootTypeModel"], [1, 1, 1, "", "StatisticsComparisonModel"], [1, 1, 1, "", "SummaryStatisticsModel"]], "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootCalibrationModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootEdgeModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootNodeModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootSimulationModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootTypeModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.form": [[2, 0, 0, "-", "components"]], "deeprootgen.form.components": [[2, 3, 1, "", "build_calibration_parameters"], [2, 3, 1, "", "build_collapsible"], [2, 3, 1, "", "build_common_components"], [2, 3, 1, "", "build_common_layout"], [2, 3, 1, "", "get_common_layout"], [2, 3, 1, "", "get_external_links"], [2, 3, 1, "", "get_out_table_df"]], "deeprootgen.io": [[4, 0, 0, "-", "simulation_data"]], "deeprootgen.io.simulation_data": [[4, 3, 1, "", "load_data_from_file"], [4, 3, 1, "", "s3_upload_file"]], "deeprootgen.model": [[5, 0, 0, "-", "hgraph"], [5, 0, 0, "-", "root"], [5, 0, 0, "-", "soil"]], "deeprootgen.model.hgraph": [[5, 1, 1, "", "RootEdge"], [5, 1, 1, "", "RootNode"], [5, 1, 1, "", "RootSystemGraph"]], "deeprootgen.model.hgraph.RootEdge": [[5, 2, 1, "", "as_dict"]], "deeprootgen.model.hgraph.RootNode": [[5, 2, 1, "", "add_child_node"], [5, 2, 1, "", "as_dict"]], "deeprootgen.model.hgraph.RootSystemGraph": [[5, 2, 1, "", "add_edge"], [5, 2, 1, "", "add_node"], [5, 2, 1, "", "as_df"], [5, 2, 1, "", "as_dict"], [5, 2, 1, "", "as_networkx"], [5, 2, 1, "", "as_torch"], [5, 2, 1, "", "increment_node_id"], [5, 2, 1, "", "increment_organ_id"]], "deeprootgen.model.root": [[5, 1, 1, "", "RootOrgan"], [5, 1, 1, "", "RootSystemSimulation"]], "deeprootgen.model.root.RootOrgan": [[5, 2, 1, "", "add_child_node"], [5, 2, 1, "", "cascading_set_invalid_root"], [5, 2, 1, "", "cascading_to_world_origin"], [5, 2, 1, "", "cascading_transform"], [5, 2, 1, "", "cascading_update_transform"], [5, 2, 1, "", "construct_root"], [5, 2, 1, "", "construct_root_from_parent"], [5, 2, 1, "", "get_apex_coordinates"], [5, 2, 1, "", "get_coordinates"], [5, 2, 1, "", "get_local_origin"], [5, 2, 1, "", "get_parent_origin"], [5, 2, 1, "", "init_diameters"], [5, 2, 1, "", "init_lengths"], [5, 2, 1, "", "init_segment_coordinates"], [5, 2, 1, "", "reset_transform"], [5, 2, 1, "", "set_invalid_root"], [5, 2, 1, "", "transform"], [5, 2, 1, "", "update_transform"], [5, 2, 1, "", "validate"]], "deeprootgen.model.root.RootSystemSimulation": [[5, 2, 1, "", "get_yaw"], [5, 2, 1, "", "init_fig"], [5, 2, 1, "", "init_organs"], [5, 2, 1, "", "plot_hierarchical_graph"], [5, 2, 1, "", "plot_root_system"], [5, 2, 1, "", "position_primary_roots"], [5, 2, 1, "", "position_secondary_roots"], [5, 2, 1, "", "run"], [5, 2, 1, "", "validate"]], "deeprootgen.model.soil": [[5, 1, 1, "", "Soil"]], "deeprootgen.model.soil.Soil": [[5, 2, 1, "", "create_soil_fig"], [5, 2, 1, "", "create_soil_grid"]], "deeprootgen.pipeline": [[6, 0, 0, "-", "experiment"], [6, 0, 0, "-", "workflow"]], "deeprootgen.pipeline.experiment": [[6, 3, 1, "", "dispatch_new_run"], [6, 3, 1, "", "get_datetime_now"], [6, 3, 1, "", "get_outdir"], [6, 3, 1, "", "get_simulation_uuid"], [6, 3, 1, "", "load_form_parameters"], [6, 3, 1, "", "save_form_parameters"], [6, 3, 1, "", "save_simulation_runs"]], "deeprootgen.spatial": [[7, 0, 0, "-", "transform"]], "deeprootgen.spatial.transform": [[7, 3, 1, "", "get_transform_matrix"], [7, 3, 1, "", "get_x_rotation_matrix"], [7, 3, 1, "", "get_y_rotation_matrix"], [7, 3, 1, "", "get_z_rotation_matrix"], [7, 3, 1, "", "make_homogenous"]], "deeprootgen.statistics": [[8, 0, 0, "-", "distance_metrics"], [8, 0, 0, "-", "summary_statistics"]], "deeprootgen.statistics.distance_metrics": [[8, 1, 1, "", "DistanceMetricBase"], [8, 1, 1, "", "L1Norm"], [8, 1, 1, "", "MeanAbsoluteError"], [8, 1, 1, "", "MeanAbsolutePercentageError"], [8, 1, 1, "", "MeanPinballLoss"], [8, 1, 1, "", "MeanSquaredError"], [8, 1, 1, "", "MedianAbsoluteError"], [8, 1, 1, "", "RootMeanSquaredError"], [8, 3, 1, "", "get_distance_metric_func"], [8, 3, 1, "", "get_distance_metrics"]], "deeprootgen.statistics.distance_metrics.DistanceMetricBase": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.L1Norm": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanAbsoluteError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanAbsolutePercentageError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanPinballLoss": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanSquaredError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MedianAbsoluteError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.RootMeanSquaredError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics": [[8, 1, 1, "", "AverageDiameter"], [8, 1, 1, "", "AverageLength"], [8, 1, 1, "", "AverageSpecificRootLength"], [8, 1, 1, "", "AverageVolume"], [8, 1, 1, "", "AverageWeight"], [8, 1, 1, "", "ConvexHullArea"], [8, 1, 1, "", "ConvexHullVolume"], [8, 1, 1, "", "DepthDistribution"], [8, 1, 1, "", "RadialDistribution"], [8, 1, 1, "", "SummaryStatisticBase"], [8, 1, 1, "", "TotalDiameter"], [8, 1, 1, "", "TotalLength"], [8, 1, 1, "", "TotalSpecificRootLength"], [8, 1, 1, "", "TotalVolume"], [8, 1, 1, "", "TotalWeight"], [8, 3, 1, "", "get_summary_statistic_func"], [8, 3, 1, "", "get_summary_statistics"]], "deeprootgen.statistics.summary_statistics.AverageDiameter": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageSpecificRootLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageVolume": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageWeight": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.ConvexHullArea": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.ConvexHullVolume": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.DepthDistribution": [[8, 2, 1, "", "calculate"], [8, 2, 1, "", "get_xy_comparison_data"], [8, 2, 1, "", "visualise"]], "deeprootgen.statistics.summary_statistics.RadialDistribution": [[8, 2, 1, "", "calculate"], [8, 2, 1, "", "get_xy_comparison_data"], [8, 2, 1, "", "visualise"]], "deeprootgen.statistics.summary_statistics.SummaryStatisticBase": [[8, 2, 1, "", "calculate"], [8, 2, 1, "", "calculate_statistic_per_layer"], [8, 2, 1, "", "get_number_of_roots"], [8, 2, 1, "", "get_xy_comparison_data"], [8, 2, 1, "", "visualise"]], "deeprootgen.statistics.summary_statistics.TotalDiameter": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalSpecificRootLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalVolume": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalWeight": [[8, 2, 1, "", "calculate"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "function", "Python function"], "4": ["py", "attribute", "Python attribute"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:function", "4": "py:attribute"}, "terms": {"0": [1, 5, 7], "0001": 1, "001": 1, "01": 1, "1": [1, 5, 7], "10": 8, "3d": [5, 11], "4": 1, "45": 5, "50": [1, 5], "9": 1, "90": 5, "A": [0, 1, 2, 5, 8, 11], "The": [0, 1, 2, 4, 5, 6, 7, 8], "These": 2, "_": 8, "__fields__": 1, "_description_": 5, "abcmodel": 0, "about": [1, 5, 7], "absolut": 8, "abstract": 8, "across": 2, "add": [2, 5, 7], "add_child_nod": 5, "add_edg": 5, "add_nod": 5, "addit": 7, "afflin": 7, "against": 8, "all": 5, "an": [0, 1, 4, 5, 7, 11], "analysi": 0, "angl": 7, "annot": 1, "anoth": 8, "apex": 5, "apex_diamet": [1, 5], "api": 10, "api_enable_http2": 1, "api_tls_insecure_skip_verifi": 1, "api_url": 1, "appli": 5, "approxim": 0, "ar": [1, 2, 5], "architectur": [1, 5, 11], "area": 8, "arg": [0, 1, 2, 4, 5, 6, 7, 8], "arr": 7, "arrai": [5, 7], "artifact": 0, "as_df": 5, "as_dict": 5, "as_networkx": 5, "as_torch": 5, "attempt": 5, "avail": 8, "averag": 8, "averagediamet": 8, "averagelength": 8, "averagespecificrootlength": 8, "averagevolum": 8, "averageweight": 8, "aws_access_key_id": 1, "aws_secret_access_kei": 1, "axi": 7, "base": [1, 5, 11], "base_diamet": 1, "basemodel": 1, "bayesian": 0, "been": [0, 1], "belong": 5, "between": [0, 8], "bin": 8, "bool": [1, 2, 4, 5], "bristow": 11, "bucket": 4, "bucket_nam": 4, "build": 2, "build_calibration_paramet": 2, "build_collaps": 2, "build_common_compon": 2, "build_common_layout": 2, "cacul": 8, "calcul": [0, 2, 8], "calculate_statistic_per_lay": 8, "calculate_summary_statistic_discrep": 0, "calibr": [1, 2, 3, 6], "calibration_input": 6, "calibration_model": 0, "calibration_paramet": 1, "calibration_valu": 2, "callabl": 8, "can": 8, "cartesian": 7, "cascading_set_invalid_root": 5, "cascading_to_world_origin": 5, "cascading_transform": 5, "cascading_update_transform": 5, "ceiling_threshold": 1, "changelog": 10, "child": 5, "child_data": 5, "child_id": 1, "children": 5, "class": [0, 1, 5, 8], "classifi": 1, "classvar": 1, "client": 4, "cm3": 5, "collaps": 2, "collect": 11, "column": [2, 5], "common": 2, "compar": [1, 8], "comparison": 8, "compat": 0, "compon": [1, 4, 5, 6], "component_data": 2, "component_spec": 2, "component_typ": 2, "compos": [1, 2], "comput": [0, 1], "computedfieldinfo": 1, "config_data_model": 1, "configdict": 1, "configur": 1, "conform": 1, "construct": [5, 7], "construct_root": 5, "construct_root_from_par": 5, "contain": [0, 1, 2, 4, 5, 6, 7, 8, 11], "content": [2, 4, 6], "context": 0, "convers": 7, "convex": 8, "convexhullarea": 8, "convexhullvolum": 8, "coordin": [5, 7], "core": 1, "correspond": 1, "creat": 5, "create_soil_fig": 5, "create_soil_grid": 5, "crop": 11, "csv": 4, "cumul": 8, "current": [0, 2, 5, 6], "dashboard": 2, "data": [0, 2, 3, 5, 6, 8, 11], "data_kei": 2, "data_model": 1, "data_typ": 1, "datafram": [0, 2, 5, 8], "dataset": 5, "datetim": 6, "dbc": 2, "decrement": 8, "deep": 11, "deeprootgen": [0, 1, 2, 4, 5, 6, 7, 8, 11], "default": [0, 1, 2, 4, 5, 6, 8], "defin": [0, 1, 4, 5, 6, 7, 8], "definit": 6, "degre": [5, 7], "densiti": 5, "deploy": 0, "depth": [5, 8], "depthdistribut": 8, "descript": 2, "develop": 11, "df": 8, "diamet": [1, 5, 8], "diameter_reduct": 1, "dict": [0, 1, 2, 5, 6, 8], "dictionari": [1, 2, 5, 6], "differ": 1, "digit": 11, "dimens": 7, "directori": 6, "discrep": 0, "dispatch": 6, "dispatch_new_run": 6, "distanc": 0, "distance_metr": [1, 8], "distancemetricbas": [0, 8], "distribut": 8, "div": 2, "each": [5, 8], "edg": [1, 5], "edge_data": 5, "element": [2, 8], "empti": 0, "enabl": 1, "enable_soil": 1, "enumer": 1, "error": [0, 8], "estim": 11, "experi": [0, 1], "experimentmodel": 1, "extern": 2, "extract": 0, "fals": [1, 2, 5], "featur": 5, "feature_kei": 5, "field": [1, 11], "fieldinfo": 1, "fig": 5, "figur": [5, 8], "file": [4, 6], "file_nam": 4, "fine_root_threshold": 1, "float": [0, 1, 5, 7, 8], "floor_threshold": 1, "form": [1, 3, 6], "form_input": 6, "form_nam": [2, 6], "format": 5, "formmodel": 1, "from": [0, 1, 2, 4, 5, 6, 7, 11], "function": [0, 4, 6, 8], "g": 5, "gener": [5, 11], "geometr": 5, "get": [2, 5, 6, 8], "get_apex_coordin": 5, "get_calibration_summary_stat": 0, "get_common_layout": 2, "get_coordin": 5, "get_datetime_now": 6, "get_distance_metr": 8, "get_distance_metric_func": 8, "get_external_link": 2, "get_local_origin": 5, "get_number_of_root": 8, "get_out_table_df": 2, "get_outdir": 6, "get_parent_origin": 5, "get_simulation_uuid": 6, "get_summary_statist": 8, "get_summary_statistic_func": 8, "get_transform_matrix": 7, "get_x_rotation_matrix": 7, "get_xy_comparison_data": 8, "get_y_rotation_matrix": 7, "get_yaw": 5, "get_z_rotation_matrix": 7, "given": 2, "go": [5, 8], "graph": 1, "gravitrop": 1, "grid": 5, "group": 2, "growth": 5, "growth_sec_root": 1, "ha": 0, "have": 1, "height": 5, "hgraph": 5, "hierarch": [1, 5], "histogram": 8, "histori": 4, "homogen": 7, "horizont": [5, 8], "html": 2, "hull": 8, "hydra": 1, "i": [0, 2, 5], "id": [2, 5, 6], "implement": 11, "includ": [2, 5], "increment": 5, "increment_node_id": 5, "increment_organ_id": 5, "index": [5, 10], "infer": 11, "inform": 11, "inherit": 5, "init_diamet": 5, "init_fig": 5, "init_length": 5, "init_organ": 5, "init_segment_coordin": 5, "initialis": 5, "inner_root_num": 1, "input": [0, 2, 3, 6], "input_compon": 2, "input_paramet": [0, 5], "insecure_tl": 1, "int": [1, 5, 8], "integr": [1, 5, 11], "interact": 2, "interbranch_dist": 1, "interv": 1, "introduct": 10, "invalid": 5, "invalid_root": 1, "io": 4, "its": [0, 5], "jame": 11, "junqi": 11, "kei": [2, 5], "l1": 8, "l1norm": 8, "label": [2, 8], "last": 2, "layer": [2, 5, 8], "layer_decr": 8, "layout": 2, "layout_descript": 2, "learn": 11, "left": 2, "left_sticki": 2, "length": [1, 5, 8], "length_rang": 5, "length_reduct": 1, "link": 2, "list": [0, 1, 2, 4, 5, 6, 7, 8], "list_of_cont": [4, 6], "list_of_nam": [4, 6], "load": [0, 4, 6], "load_context": 0, "load_data_from_fil": 4, "load_form_paramet": 6, "local": 5, "log": 0, "log_model": 0, "loss": 8, "lower_bound": 1, "make": 0, "make_homogen": 7, "manag": [4, 6], "manipul": 7, "map": 1, "matric": 7, "matrix": [5, 7], "max_attempt": 5, "max_ord": 1, "max_primary_length": 1, "max_sec_root_length": 1, "max_sec_root_num": 1, "max_val_attempt": 1, "maximum": 5, "mean": 8, "meanabsoluteerror": 8, "meanabsolutepercentageerror": 8, "meanpinballloss": 8, "meansquarederror": 8, "mechanical_constraint": 1, "median": 8, "medianabsoluteerror": 8, "messag": [4, 6], "metadata": 1, "method": 8, "metric": 0, "microservic": 0, "min_primary_length": 1, "min_sec_root_length": 1, "min_sec_root_num": 1, "minimum": 5, "mlflow": [0, 6], "model": [2, 3, 11], "model_computed_field": 1, "model_config": 1, "model_field": 1, "model_input": 0, "model_vers": 0, "modul": [0, 1, 2, 4, 5, 6, 7, 8, 10], "multipl": 2, "n_element": 8, "name": [0, 1, 2, 4, 6, 8], "name_prefix": 1, "nav": 2, "navig": 2, "ndarrai": [0, 5, 7, 8], "need": [0, 7], "networkx": 5, "new": [5, 6], "new_organ": 5, "no_root_zon": [1, 5], "node": [1, 5], "node_data": 5, "node_df": 5, "node_id": 1, "none": [0, 1, 2, 5, 6], "nonetyp": 1, "norm": 8, "notimplementederror": 8, "now": 6, "np": [0, 5, 7, 8], "number": [5, 8], "number_of_root": 5, "nx": 5, "object": [0, 1, 4], "object_nam": 4, "objectstoragemodel": 1, "observ": [0, 1, 2, 8, 11], "observed_data": [1, 2], "observed_data_cont": [1, 2], "omegaconf": 1, "ones": 7, "optimis": 0, "optimisationmodel": 0, "option": [0, 2, 4, 5, 6, 8], "orchestr": [1, 6], "orchestrationmodel": 1, "order": 1, "order_typ": 1, "organ": 5, "organ_id": 1, "origin": 5, "origin_max": 1, "origin_min": 1, "outer_root_num": 1, "output": [0, 2, 3, 6], "output_compon": 2, "page": [2, 6, 10], "page_descript": 2, "page_id": [2, 6], "param": 0, "param_input": 6, "paramet": [0, 1, 2, 6, 11], "parameter_form_nam": 2, "parameter_interv": 1, "parameter_spec": 0, "parameter_valu": 2, "parameterintervalmodel": 1, "parent": 5, "parent_id": 1, "parent_nod": 5, "pass": 6, "pd": [0, 2, 5, 8], "per": [5, 8], "percentag": 8, "perform": [6, 7], "pinbal": 8, "pipelin": 3, "pitch": [5, 7], "plant": 5, "plant_id": 1, "plausibl": 5, "plot_hierarchical_graph": 5, "plot_root_system": 5, "plotli": 5, "posit": 5, "position_primary_root": 5, "position_secondary_root": 5, "position_typ": 1, "predict": 0, "prefect": 6, "primari": 5, "prior": 5, "procedur": [1, 2], "produc": 8, "project": 11, "properti": 5, "purpos": 0, "pydant": 1, "pyfunc": 0, "pythonmodel": 0, "pytorch": 5, "radialdistribut": 8, "rais": [0, 8], "random_se": [1, 5], "raw": 2, "reconstruct": 11, "refer": 10, "reflect": [5, 7], "registri": 0, "render": 2, "replac": 1, "repositori": 11, "represent": [1, 5], "requir": 1, "reset": 5, "reset_transform": 5, "resiz": 2, "resize_compon": 2, "respons": 4, "result": 5, "return": [0, 2, 4, 5, 6, 7, 8], "right": 2, "right_sticki": 2, "rng": 5, "roll": [5, 7], "root": [0, 1, 2, 7, 8, 11], "root_ratio": 1, "root_tissue_dens": [1, 5, 8], "root_typ": [1, 5], "root_vari": 1, "rootcalibrationinterv": 1, "rootcalibrationmodel": [0, 1], "rootedg": 5, "rootedgemodel": [1, 5], "rootmeansquarederror": 8, "rootnod": 5, "rootnodemodel": [1, 5], "rootorgan": 5, "rootsimulationmodel": [1, 5], "rootsystemgraph": 5, "rootsystemsimul": 5, "roottyp": 1, "roottypemodel": [1, 5], "rotat": [5, 7], "row": 2, "run": [0, 4, 5, 6], "run_calibration_simul": 0, "s3": 4, "s3_endpoint_url": 1, "s3_ignore_tl": 1, "s3_upload_fil": 4, "save": 6, "save_form_paramet": 6, "save_simulation_run": 6, "scale": [5, 7], "search": 10, "secondari": 5, "segment": 5, "segment_rank": 1, "segments_per_root": [1, 5], "sensit": 0, "sensitivityanalysismodel": 0, "set_invalid_root": 5, "sever": 1, "should": [1, 2], "side": 2, "signatur": 0, "signature_i": 0, "signature_x": 0, "simul": [0, 2, 5, 6, 8, 11], "simulation_data": 4, "simulation_data_model": 1, "simulation_form": 2, "simulation_form_nam": 2, "simulation_run": 6, "simulation_tag": [1, 5], "simulation_uuid": 0, "singl": 5, "soil": [2, 8], "soil_df": 5, "soil_layer_height": [1, 5], "soil_layer_width": [1, 5], "soil_n_col": [1, 5], "soil_n_lay": [1, 5], "sourc": [0, 1, 2, 4, 5, 6, 7, 8], "spatial": 3, "specif": [0, 1, 2, 8], "specifi": 5, "squar": 8, "stat_by_col": 2, "stat_by_lay": 2, "stat_by_soil_column": 1, "stat_by_soil_lay": 1, "statist": [1, 2, 3], "statistic_nam": 1, "statistic_valu": 1, "statistics_comparison": 1, "statistics_list": 0, "statisticscomparisonmodel": 1, "sticki": 2, "storag": 1, "str": [0, 1, 2, 4, 5, 6, 8], "string": 2, "stub": 9, "submiss": 2, "summari": [1, 2], "summary_data": 2, "summary_statist": [0, 1, 2, 8], "summarystatisticbas": 8, "summarystatisticsmodel": [0, 1], "supervisor": 11, "surround": 5, "synthet": 1, "system": [1, 5, 7, 8, 11], "tabl": 2, "task": [0, 2, 6], "theta": 7, "thi": [0, 1, 2, 4, 5, 6, 7, 8, 11], "threshold": 5, "thrown": 0, "tissu": 5, "titl": 2, "toast": [4, 6], "tooltip": 2, "total": 8, "totaldiamet": 8, "totallength": 8, "totalspecificrootlength": 8, "totalvolum": 8, "totalweight": 8, "track": 6, "tracking_uri": 1, "transform": 5, "translat": [5, 7], "true": [1, 2], "tupl": [0, 4, 5, 6, 8], "type": [1, 2, 5], "underli": 5, "unimpl": 8, "union": 1, "updat": [5, 7], "update_transform": 5, "upload": [4, 6], "upper_bound": 1, "us": [2, 7, 8], "util": [0, 2, 4, 6, 8], "uuid": [0, 6], "v1": 1, "valid": 5, "valu": [1, 5, 8], "valueerror": 0, "variou": 2, "vertic": 5, "visualis": [5, 8], "volum": 8, "voxel": 5, "w": 7, "weight": 8, "when": 0, "whether": [2, 5], "width": 5, "within": [1, 2, 5], "workflow": 2, "world": 5, "write": 6, "x": [1, 5, 7], "x_kei": 5, "xiumei": 11, "y": [1, 5, 7], "y_kei": 5, "yang": 11, "yaw": [5, 7], "z": [1, 5, 7], "z_kei": 5, "z_lower_bound": 1, "z_upper_bound": 1, "zhu": 11}, "titles": ["Calibration", "Data Model", "Form", "API Reference", "Input/Output", "Model", "Pipeline", "Spatial", "Statistics", "Changelog", "DeepRootGen", "Introduction"], "titleterms": {"0": 9, "08": 9, "1": 9, "17": 9, "2024": 9, "api": 3, "calibr": 0, "changelog": 9, "compon": 2, "config": 1, "contact": 11, "content": 10, "data": [1, 4], "deeprootgen": 10, "distanc": 8, "experi": 6, "form": 2, "graph": 5, "indic": 10, "input": 4, "introduct": 11, "metric": 8, "model": [0, 1, 5], "output": 4, "pipelin": 6, "refer": 3, "root": 5, "simul": [1, 4], "soil": 5, "spatial": 7, "statist": [0, 8], "summari": [0, 8], "tabl": 10, "transform": 7, "version": 0, "workflow": 6}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"0.1.0 - 2024/08/17": [[9, "id1"]], "API Reference": [[3, null]], "Calibration": [[0, null]], "Changelog": [[9, null]], "Components": [[2, "module-deeprootgen.form.components"]], "Config": [[1, "module-deeprootgen.data_model.config_data_models"]], "Contacts": [[11, "contacts"]], "Contents:": [[10, null]], "Data Model": [[1, null]], "DeepRootGen": [[10, null]], "Distance Metrics": [[8, "module-deeprootgen.statistics.distance_metrics"]], "Experiment": [[6, "module-deeprootgen.pipeline.experiment"]], "Form": [[2, null]], "Graph": [[5, "module-deeprootgen.model.hgraph"]], "Indices and tables": [[10, "indices-and-tables"]], "Input/Output": [[4, null]], "Introduction": [[11, null]], "Model": [[5, null]], "Model Versioning": [[0, "module-deeprootgen.calibration.model_versioning"]], "Pipeline": [[6, null]], "Root": [[5, "module-deeprootgen.model.root"]], "Simulation": [[1, "module-deeprootgen.data_model.simulation_data_models"]], "Simulation Data": [[4, "module-deeprootgen.io.simulation_data"]], "Soil": [[5, "module-deeprootgen.model.soil"]], "Spatial": [[7, null]], "Statistics": [[8, null]], "Summary Statistics": [[0, "module-deeprootgen.calibration.summary_statistics"], [8, "module-deeprootgen.statistics.summary_statistics"]], "Transform": [[7, "module-deeprootgen.spatial.transform"]], "Workflow": [[6, "module-deeprootgen.pipeline.workflow"]]}, "docnames": ["api_reference/calibration", "api_reference/data_model", "api_reference/form", "api_reference/index", "api_reference/io", "api_reference/model", "api_reference/pipeline", "api_reference/spatial", "api_reference/statistics", "changelogs/changelog", "index", "introduction/index"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["api_reference/calibration.rst", "api_reference/data_model.rst", "api_reference/form.rst", "api_reference/index.rst", "api_reference/io.rst", "api_reference/model.rst", "api_reference/pipeline.rst", "api_reference/spatial.rst", "api_reference/statistics.rst", "changelogs/changelog.rst", "index.rst", "introduction/index.rst"], "indexentries": {"abcmodel (class in deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.AbcModel", false]], "add_child_node() (deeprootgen.model.hgraph.rootnode method)": [[5, "deeprootgen.model.hgraph.RootNode.add_child_node", false]], "add_child_node() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.add_child_node", false]], "add_edge() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.add_edge", false]], "add_node() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.add_node", false]], "as_df() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_df", false]], "as_dict() (deeprootgen.model.hgraph.rootedge method)": [[5, "deeprootgen.model.hgraph.RootEdge.as_dict", false]], "as_dict() (deeprootgen.model.hgraph.rootnode method)": [[5, "deeprootgen.model.hgraph.RootNode.as_dict", false]], "as_dict() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_dict", false]], "as_networkx() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_networkx", false]], "as_torch() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.as_torch", false]], "averagediameter (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageDiameter", false]], "averagelength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageLength", false]], "averagespecificrootlength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageSpecificRootLength", false]], "averagevolume (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageVolume", false]], "averageweight (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.AverageWeight", false]], "build_calibration_parameters() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_calibration_parameters", false]], "build_collapsible() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_collapsible", false]], "build_common_components() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_common_components", false]], "build_common_layout() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.build_common_layout", false]], "calculate() (deeprootgen.statistics.distance_metrics.distancemetricbase method)": [[8, "deeprootgen.statistics.distance_metrics.DistanceMetricBase.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.l1norm method)": [[8, "deeprootgen.statistics.distance_metrics.L1Norm.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meanabsoluteerror method)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsoluteError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meanabsolutepercentageerror method)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsolutePercentageError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meanpinballloss method)": [[8, "deeprootgen.statistics.distance_metrics.MeanPinballLoss.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.meansquarederror method)": [[8, "deeprootgen.statistics.distance_metrics.MeanSquaredError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.medianabsoluteerror method)": [[8, "deeprootgen.statistics.distance_metrics.MedianAbsoluteError.calculate", false]], "calculate() (deeprootgen.statistics.distance_metrics.rootmeansquarederror method)": [[8, "deeprootgen.statistics.distance_metrics.RootMeanSquaredError.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagediameter method)": [[8, "deeprootgen.statistics.summary_statistics.AverageDiameter.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagelength method)": [[8, "deeprootgen.statistics.summary_statistics.AverageLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagespecificrootlength method)": [[8, "deeprootgen.statistics.summary_statistics.AverageSpecificRootLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averagevolume method)": [[8, "deeprootgen.statistics.summary_statistics.AverageVolume.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.averageweight method)": [[8, "deeprootgen.statistics.summary_statistics.AverageWeight.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.convexhullarea method)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullArea.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.convexhullvolume method)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullVolume.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.depthdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.radialdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totaldiameter method)": [[8, "deeprootgen.statistics.summary_statistics.TotalDiameter.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totallength method)": [[8, "deeprootgen.statistics.summary_statistics.TotalLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totalspecificrootlength method)": [[8, "deeprootgen.statistics.summary_statistics.TotalSpecificRootLength.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totalvolume method)": [[8, "deeprootgen.statistics.summary_statistics.TotalVolume.calculate", false]], "calculate() (deeprootgen.statistics.summary_statistics.totalweight method)": [[8, "deeprootgen.statistics.summary_statistics.TotalWeight.calculate", false]], "calculate_statistic_per_layer() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.calculate_statistic_per_layer", false]], "calculate_summary_statistic_discrepancy() (in module deeprootgen.calibration.summary_statistics)": [[0, "deeprootgen.calibration.summary_statistics.calculate_summary_statistic_discrepancy", false]], "cascading_set_invalid_root() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_set_invalid_root", false]], "cascading_to_world_origin() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_to_world_origin", false]], "cascading_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_transform", false]], "cascading_update_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.cascading_update_transform", false]], "construct_root() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.construct_root", false]], "construct_root_from_parent() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.construct_root_from_parent", false]], "convexhullarea (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullArea", false]], "convexhullvolume (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.ConvexHullVolume", false]], "create_soil_fig() (deeprootgen.model.soil.soil method)": [[5, "deeprootgen.model.soil.Soil.create_soil_fig", false]], "create_soil_grid() (deeprootgen.model.soil.soil method)": [[5, "deeprootgen.model.soil.Soil.create_soil_grid", false]], "deeprootgen.calibration.model_versioning": [[0, "module-deeprootgen.calibration.model_versioning", false]], "deeprootgen.calibration.summary_statistics": [[0, "module-deeprootgen.calibration.summary_statistics", false]], "deeprootgen.data_model.config_data_models": [[1, "module-deeprootgen.data_model.config_data_models", false]], "deeprootgen.data_model.simulation_data_models": [[1, "module-deeprootgen.data_model.simulation_data_models", false]], "deeprootgen.form.components": [[2, "module-deeprootgen.form.components", false]], "deeprootgen.io.simulation_data": [[4, "module-deeprootgen.io.simulation_data", false]], "deeprootgen.model.hgraph": [[5, "module-deeprootgen.model.hgraph", false]], "deeprootgen.model.root": [[5, "module-deeprootgen.model.root", false]], "deeprootgen.model.soil": [[5, "module-deeprootgen.model.soil", false]], "deeprootgen.pipeline.experiment": [[6, "module-deeprootgen.pipeline.experiment", false]], "deeprootgen.pipeline.workflow": [[6, "module-deeprootgen.pipeline.workflow", false]], "deeprootgen.spatial.transform": [[7, "module-deeprootgen.spatial.transform", false]], "deeprootgen.statistics.distance_metrics": [[8, "module-deeprootgen.statistics.distance_metrics", false]], "deeprootgen.statistics.summary_statistics": [[8, "module-deeprootgen.statistics.summary_statistics", false]], "depthdistribution (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution", false]], "dispatch_new_run() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.dispatch_new_run", false]], "distancemetricbase (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.DistanceMetricBase", false]], "experimentmodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel", false]], "formmodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.FormModel", false]], "get_apex_coordinates() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_apex_coordinates", false]], "get_calibration_summary_stats() (in module deeprootgen.calibration.summary_statistics)": [[0, "deeprootgen.calibration.summary_statistics.get_calibration_summary_stats", false]], "get_common_layout() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.get_common_layout", false]], "get_coordinates() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_coordinates", false]], "get_datetime_now() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.get_datetime_now", false]], "get_distance_metric_func() (in module deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.get_distance_metric_func", false]], "get_distance_metrics() (in module deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.get_distance_metrics", false]], "get_external_links() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.get_external_links", false]], "get_local_origin() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_local_origin", false]], "get_number_of_roots() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.get_number_of_roots", false]], "get_out_table_df() (in module deeprootgen.form.components)": [[2, "deeprootgen.form.components.get_out_table_df", false]], "get_outdir() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.get_outdir", false]], "get_parent_origin() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.get_parent_origin", false]], "get_simulation_uuid() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.get_simulation_uuid", false]], "get_summary_statistic_func() (in module deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.get_summary_statistic_func", false]], "get_summary_statistics() (in module deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.get_summary_statistics", false]], "get_transform_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_transform_matrix", false]], "get_x_rotation_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_x_rotation_matrix", false]], "get_xy_comparison_data() (deeprootgen.statistics.summary_statistics.depthdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution.get_xy_comparison_data", false]], "get_xy_comparison_data() (deeprootgen.statistics.summary_statistics.radialdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution.get_xy_comparison_data", false]], "get_xy_comparison_data() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.get_xy_comparison_data", false]], "get_y_rotation_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_y_rotation_matrix", false]], "get_yaw() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.get_yaw", false]], "get_z_rotation_matrix() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.get_z_rotation_matrix", false]], "increment_node_id() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.increment_node_id", false]], "increment_organ_id() (deeprootgen.model.hgraph.rootsystemgraph method)": [[5, "deeprootgen.model.hgraph.RootSystemGraph.increment_organ_id", false]], "init_diameters() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.init_diameters", false]], "init_fig() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.init_fig", false]], "init_lengths() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.init_lengths", false]], "init_organs() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.init_organs", false]], "init_segment_coordinates() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.init_segment_coordinates", false]], "l1norm (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.L1Norm", false]], "load_context() (deeprootgen.calibration.model_versioning.abcmodel method)": [[0, "deeprootgen.calibration.model_versioning.AbcModel.load_context", false]], "load_context() (deeprootgen.calibration.model_versioning.optimisationmodel method)": [[0, "deeprootgen.calibration.model_versioning.OptimisationModel.load_context", false]], "load_context() (deeprootgen.calibration.model_versioning.sensitivityanalysismodel method)": [[0, "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel.load_context", false]], "load_data_from_file() (in module deeprootgen.io.simulation_data)": [[4, "deeprootgen.io.simulation_data.load_data_from_file", false]], "load_form_parameters() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.load_form_parameters", false]], "log_model() (in module deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.log_model", false]], "make_homogenous() (in module deeprootgen.spatial.transform)": [[7, "deeprootgen.spatial.transform.make_homogenous", false]], "meanabsoluteerror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsoluteError", false]], "meanabsolutepercentageerror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanAbsolutePercentageError", false]], "meanpinballloss (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanPinballLoss", false]], "meansquarederror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MeanSquaredError", false]], "medianabsoluteerror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.MedianAbsoluteError", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.experimentmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.formmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.FormModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.objectstoragemodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.config_data_models.orchestrationmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.parameterintervalmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationintervals attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootedgemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootnodemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.rootsimulationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.roottypemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.statisticscomparisonmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel.model_computed_fields", false]], "model_computed_fields (deeprootgen.data_model.simulation_data_models.summarystatisticsmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel.model_computed_fields", false]], "model_config (deeprootgen.data_model.config_data_models.experimentmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel.model_config", false]], "model_config (deeprootgen.data_model.config_data_models.formmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.FormModel.model_config", false]], "model_config (deeprootgen.data_model.config_data_models.objectstoragemodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel.model_config", false]], "model_config (deeprootgen.data_model.config_data_models.orchestrationmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.parameterintervalmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootcalibrationintervals attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootcalibrationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootedgemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootnodemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.rootsimulationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.roottypemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.statisticscomparisonmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel.model_config", false]], "model_config (deeprootgen.data_model.simulation_data_models.summarystatisticsmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel.model_config", false]], "model_fields (deeprootgen.data_model.config_data_models.experimentmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ExperimentModel.model_fields", false]], "model_fields (deeprootgen.data_model.config_data_models.formmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.FormModel.model_fields", false]], "model_fields (deeprootgen.data_model.config_data_models.objectstoragemodel attribute)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel.model_fields", false]], "model_fields (deeprootgen.data_model.config_data_models.orchestrationmodel attribute)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.parameterintervalmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationintervals attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootcalibrationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootedgemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootnodemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.rootsimulationmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.roottypemodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.statisticscomparisonmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel.model_fields", false]], "model_fields (deeprootgen.data_model.simulation_data_models.summarystatisticsmodel attribute)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel.model_fields", false]], "module": [[0, "module-deeprootgen.calibration.model_versioning", false], [0, "module-deeprootgen.calibration.summary_statistics", false], [1, "module-deeprootgen.data_model.config_data_models", false], [1, "module-deeprootgen.data_model.simulation_data_models", false], [2, "module-deeprootgen.form.components", false], [4, "module-deeprootgen.io.simulation_data", false], [5, "module-deeprootgen.model.hgraph", false], [5, "module-deeprootgen.model.root", false], [5, "module-deeprootgen.model.soil", false], [6, "module-deeprootgen.pipeline.experiment", false], [6, "module-deeprootgen.pipeline.workflow", false], [7, "module-deeprootgen.spatial.transform", false], [8, "module-deeprootgen.statistics.distance_metrics", false], [8, "module-deeprootgen.statistics.summary_statistics", false]], "objectstoragemodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.ObjectStorageModel", false]], "optimisationmodel (class in deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.OptimisationModel", false]], "orchestrationmodel (class in deeprootgen.data_model.config_data_models)": [[1, "deeprootgen.data_model.config_data_models.OrchestrationModel", false]], "parameterintervalmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel", false]], "plot_hierarchical_graph() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.plot_hierarchical_graph", false]], "plot_root_system() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.plot_root_system", false]], "position_primary_roots() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.position_primary_roots", false]], "position_secondary_roots() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.position_secondary_roots", false]], "predict() (deeprootgen.calibration.model_versioning.abcmodel method)": [[0, "deeprootgen.calibration.model_versioning.AbcModel.predict", false]], "predict() (deeprootgen.calibration.model_versioning.optimisationmodel method)": [[0, "deeprootgen.calibration.model_versioning.OptimisationModel.predict", false]], "predict() (deeprootgen.calibration.model_versioning.sensitivityanalysismodel method)": [[0, "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel.predict", false]], "radialdistribution (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution", false]], "reset_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.reset_transform", false]], "rootcalibrationintervals (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals", false]], "rootcalibrationmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootCalibrationModel", false]], "rootedge (class in deeprootgen.model.hgraph)": [[5, "deeprootgen.model.hgraph.RootEdge", false]], "rootedgemodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootEdgeModel", false]], "rootmeansquarederror (class in deeprootgen.statistics.distance_metrics)": [[8, "deeprootgen.statistics.distance_metrics.RootMeanSquaredError", false]], "rootnode (class in deeprootgen.model.hgraph)": [[5, "deeprootgen.model.hgraph.RootNode", false]], "rootnodemodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootNodeModel", false]], "rootorgan (class in deeprootgen.model.root)": [[5, "deeprootgen.model.root.RootOrgan", false]], "rootsimulationmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootSimulationModel", false]], "rootsystemgraph (class in deeprootgen.model.hgraph)": [[5, "deeprootgen.model.hgraph.RootSystemGraph", false]], "rootsystemsimulation (class in deeprootgen.model.root)": [[5, "deeprootgen.model.root.RootSystemSimulation", false]], "roottype (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootType", false]], "roottypemodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.RootTypeModel", false]], "run() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.run", false]], "run_calibration_simulation() (in module deeprootgen.calibration.summary_statistics)": [[0, "deeprootgen.calibration.summary_statistics.run_calibration_simulation", false]], "s3_upload_file() (in module deeprootgen.io.simulation_data)": [[4, "deeprootgen.io.simulation_data.s3_upload_file", false]], "save_form_parameters() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.save_form_parameters", false]], "save_simulation_runs() (in module deeprootgen.pipeline.experiment)": [[6, "deeprootgen.pipeline.experiment.save_simulation_runs", false]], "sensitivityanalysismodel (class in deeprootgen.calibration.model_versioning)": [[0, "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel", false]], "set_invalid_root() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.set_invalid_root", false]], "soil (class in deeprootgen.model.soil)": [[5, "deeprootgen.model.soil.Soil", false]], "statisticscomparisonmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel", false]], "summarystatisticbase (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase", false]], "summarystatisticsmodel (class in deeprootgen.data_model.simulation_data_models)": [[1, "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel", false]], "totaldiameter (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalDiameter", false]], "totallength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalLength", false]], "totalspecificrootlength (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalSpecificRootLength", false]], "totalvolume (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalVolume", false]], "totalweight (class in deeprootgen.statistics.summary_statistics)": [[8, "deeprootgen.statistics.summary_statistics.TotalWeight", false]], "transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.transform", false]], "update_transform() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.update_transform", false]], "validate() (deeprootgen.model.root.rootorgan method)": [[5, "deeprootgen.model.root.RootOrgan.validate", false]], "validate() (deeprootgen.model.root.rootsystemsimulation method)": [[5, "deeprootgen.model.root.RootSystemSimulation.validate", false]], "visualise() (deeprootgen.statistics.summary_statistics.depthdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.DepthDistribution.visualise", false]], "visualise() (deeprootgen.statistics.summary_statistics.radialdistribution method)": [[8, "deeprootgen.statistics.summary_statistics.RadialDistribution.visualise", false]], "visualise() (deeprootgen.statistics.summary_statistics.summarystatisticbase method)": [[8, "deeprootgen.statistics.summary_statistics.SummaryStatisticBase.visualise", false]]}, "objects": {"deeprootgen.calibration": [[0, 0, 0, "-", "model_versioning"], [0, 0, 0, "-", "summary_statistics"]], "deeprootgen.calibration.model_versioning": [[0, 1, 1, "", "AbcModel"], [0, 1, 1, "", "OptimisationModel"], [0, 1, 1, "", "SensitivityAnalysisModel"], [0, 3, 1, "", "log_model"]], "deeprootgen.calibration.model_versioning.AbcModel": [[0, 2, 1, "", "load_context"], [0, 2, 1, "", "predict"]], "deeprootgen.calibration.model_versioning.OptimisationModel": [[0, 2, 1, "", "load_context"], [0, 2, 1, "", "predict"]], "deeprootgen.calibration.model_versioning.SensitivityAnalysisModel": [[0, 2, 1, "", "load_context"], [0, 2, 1, "", "predict"]], "deeprootgen.calibration.summary_statistics": [[0, 3, 1, "", "calculate_summary_statistic_discrepancy"], [0, 3, 1, "", "get_calibration_summary_stats"], [0, 3, 1, "", "run_calibration_simulation"]], "deeprootgen.data_model": [[1, 0, 0, "-", "config_data_models"], [1, 0, 0, "-", "simulation_data_models"]], "deeprootgen.data_model.config_data_models": [[1, 1, 1, "", "ExperimentModel"], [1, 1, 1, "", "FormModel"], [1, 1, 1, "", "ObjectStorageModel"], [1, 1, 1, "", "OrchestrationModel"]], "deeprootgen.data_model.config_data_models.ExperimentModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.config_data_models.FormModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.config_data_models.ObjectStorageModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.config_data_models.OrchestrationModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models": [[1, 1, 1, "", "ParameterIntervalModel"], [1, 1, 1, "", "RootCalibrationIntervals"], [1, 1, 1, "", "RootCalibrationModel"], [1, 1, 1, "", "RootEdgeModel"], [1, 1, 1, "", "RootNodeModel"], [1, 1, 1, "", "RootSimulationModel"], [1, 1, 1, "", "RootType"], [1, 1, 1, "", "RootTypeModel"], [1, 1, 1, "", "StatisticsComparisonModel"], [1, 1, 1, "", "SummaryStatisticsModel"]], "deeprootgen.data_model.simulation_data_models.ParameterIntervalModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootCalibrationIntervals": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootCalibrationModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootEdgeModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootNodeModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootSimulationModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.RootTypeModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.StatisticsComparisonModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.data_model.simulation_data_models.SummaryStatisticsModel": [[1, 4, 1, "", "model_computed_fields"], [1, 4, 1, "", "model_config"], [1, 4, 1, "", "model_fields"]], "deeprootgen.form": [[2, 0, 0, "-", "components"]], "deeprootgen.form.components": [[2, 3, 1, "", "build_calibration_parameters"], [2, 3, 1, "", "build_collapsible"], [2, 3, 1, "", "build_common_components"], [2, 3, 1, "", "build_common_layout"], [2, 3, 1, "", "get_common_layout"], [2, 3, 1, "", "get_external_links"], [2, 3, 1, "", "get_out_table_df"]], "deeprootgen.io": [[4, 0, 0, "-", "simulation_data"]], "deeprootgen.io.simulation_data": [[4, 3, 1, "", "load_data_from_file"], [4, 3, 1, "", "s3_upload_file"]], "deeprootgen.model": [[5, 0, 0, "-", "hgraph"], [5, 0, 0, "-", "root"], [5, 0, 0, "-", "soil"]], "deeprootgen.model.hgraph": [[5, 1, 1, "", "RootEdge"], [5, 1, 1, "", "RootNode"], [5, 1, 1, "", "RootSystemGraph"]], "deeprootgen.model.hgraph.RootEdge": [[5, 2, 1, "", "as_dict"]], "deeprootgen.model.hgraph.RootNode": [[5, 2, 1, "", "add_child_node"], [5, 2, 1, "", "as_dict"]], "deeprootgen.model.hgraph.RootSystemGraph": [[5, 2, 1, "", "add_edge"], [5, 2, 1, "", "add_node"], [5, 2, 1, "", "as_df"], [5, 2, 1, "", "as_dict"], [5, 2, 1, "", "as_networkx"], [5, 2, 1, "", "as_torch"], [5, 2, 1, "", "increment_node_id"], [5, 2, 1, "", "increment_organ_id"]], "deeprootgen.model.root": [[5, 1, 1, "", "RootOrgan"], [5, 1, 1, "", "RootSystemSimulation"]], "deeprootgen.model.root.RootOrgan": [[5, 2, 1, "", "add_child_node"], [5, 2, 1, "", "cascading_set_invalid_root"], [5, 2, 1, "", "cascading_to_world_origin"], [5, 2, 1, "", "cascading_transform"], [5, 2, 1, "", "cascading_update_transform"], [5, 2, 1, "", "construct_root"], [5, 2, 1, "", "construct_root_from_parent"], [5, 2, 1, "", "get_apex_coordinates"], [5, 2, 1, "", "get_coordinates"], [5, 2, 1, "", "get_local_origin"], [5, 2, 1, "", "get_parent_origin"], [5, 2, 1, "", "init_diameters"], [5, 2, 1, "", "init_lengths"], [5, 2, 1, "", "init_segment_coordinates"], [5, 2, 1, "", "reset_transform"], [5, 2, 1, "", "set_invalid_root"], [5, 2, 1, "", "transform"], [5, 2, 1, "", "update_transform"], [5, 2, 1, "", "validate"]], "deeprootgen.model.root.RootSystemSimulation": [[5, 2, 1, "", "get_yaw"], [5, 2, 1, "", "init_fig"], [5, 2, 1, "", "init_organs"], [5, 2, 1, "", "plot_hierarchical_graph"], [5, 2, 1, "", "plot_root_system"], [5, 2, 1, "", "position_primary_roots"], [5, 2, 1, "", "position_secondary_roots"], [5, 2, 1, "", "run"], [5, 2, 1, "", "validate"]], "deeprootgen.model.soil": [[5, 1, 1, "", "Soil"]], "deeprootgen.model.soil.Soil": [[5, 2, 1, "", "create_soil_fig"], [5, 2, 1, "", "create_soil_grid"]], "deeprootgen.pipeline": [[6, 0, 0, "-", "experiment"], [6, 0, 0, "-", "workflow"]], "deeprootgen.pipeline.experiment": [[6, 3, 1, "", "dispatch_new_run"], [6, 3, 1, "", "get_datetime_now"], [6, 3, 1, "", "get_outdir"], [6, 3, 1, "", "get_simulation_uuid"], [6, 3, 1, "", "load_form_parameters"], [6, 3, 1, "", "save_form_parameters"], [6, 3, 1, "", "save_simulation_runs"]], "deeprootgen.spatial": [[7, 0, 0, "-", "transform"]], "deeprootgen.spatial.transform": [[7, 3, 1, "", "get_transform_matrix"], [7, 3, 1, "", "get_x_rotation_matrix"], [7, 3, 1, "", "get_y_rotation_matrix"], [7, 3, 1, "", "get_z_rotation_matrix"], [7, 3, 1, "", "make_homogenous"]], "deeprootgen.statistics": [[8, 0, 0, "-", "distance_metrics"], [8, 0, 0, "-", "summary_statistics"]], "deeprootgen.statistics.distance_metrics": [[8, 1, 1, "", "DistanceMetricBase"], [8, 1, 1, "", "L1Norm"], [8, 1, 1, "", "MeanAbsoluteError"], [8, 1, 1, "", "MeanAbsolutePercentageError"], [8, 1, 1, "", "MeanPinballLoss"], [8, 1, 1, "", "MeanSquaredError"], [8, 1, 1, "", "MedianAbsoluteError"], [8, 1, 1, "", "RootMeanSquaredError"], [8, 3, 1, "", "get_distance_metric_func"], [8, 3, 1, "", "get_distance_metrics"]], "deeprootgen.statistics.distance_metrics.DistanceMetricBase": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.L1Norm": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanAbsoluteError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanAbsolutePercentageError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanPinballLoss": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MeanSquaredError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.MedianAbsoluteError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.distance_metrics.RootMeanSquaredError": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics": [[8, 1, 1, "", "AverageDiameter"], [8, 1, 1, "", "AverageLength"], [8, 1, 1, "", "AverageSpecificRootLength"], [8, 1, 1, "", "AverageVolume"], [8, 1, 1, "", "AverageWeight"], [8, 1, 1, "", "ConvexHullArea"], [8, 1, 1, "", "ConvexHullVolume"], [8, 1, 1, "", "DepthDistribution"], [8, 1, 1, "", "RadialDistribution"], [8, 1, 1, "", "SummaryStatisticBase"], [8, 1, 1, "", "TotalDiameter"], [8, 1, 1, "", "TotalLength"], [8, 1, 1, "", "TotalSpecificRootLength"], [8, 1, 1, "", "TotalVolume"], [8, 1, 1, "", "TotalWeight"], [8, 3, 1, "", "get_summary_statistic_func"], [8, 3, 1, "", "get_summary_statistics"]], "deeprootgen.statistics.summary_statistics.AverageDiameter": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageSpecificRootLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageVolume": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.AverageWeight": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.ConvexHullArea": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.ConvexHullVolume": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.DepthDistribution": [[8, 2, 1, "", "calculate"], [8, 2, 1, "", "get_xy_comparison_data"], [8, 2, 1, "", "visualise"]], "deeprootgen.statistics.summary_statistics.RadialDistribution": [[8, 2, 1, "", "calculate"], [8, 2, 1, "", "get_xy_comparison_data"], [8, 2, 1, "", "visualise"]], "deeprootgen.statistics.summary_statistics.SummaryStatisticBase": [[8, 2, 1, "", "calculate"], [8, 2, 1, "", "calculate_statistic_per_layer"], [8, 2, 1, "", "get_number_of_roots"], [8, 2, 1, "", "get_xy_comparison_data"], [8, 2, 1, "", "visualise"]], "deeprootgen.statistics.summary_statistics.TotalDiameter": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalSpecificRootLength": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalVolume": [[8, 2, 1, "", "calculate"]], "deeprootgen.statistics.summary_statistics.TotalWeight": [[8, 2, 1, "", "calculate"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "function", "Python function"], "4": ["py", "attribute", "Python attribute"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:function", "4": "py:attribute"}, "terms": {"0": [1, 5, 7], "0001": 1, "001": 1, "01": 1, "1": [1, 5, 7], "10": 8, "3d": [5, 11], "4": 1, "45": 5, "50": [1, 5], "9": 1, "90": 5, "A": [0, 1, 2, 5, 8, 11], "The": [0, 1, 2, 4, 5, 6, 7, 8], "These": 2, "_": 8, "__fields__": 1, "_description_": 5, "abcmodel": 0, "about": [1, 5, 7], "absolut": 8, "abstract": 8, "across": 2, "add": [2, 5, 7], "add_child_nod": 5, "add_edg": 5, "add_nod": 5, "addit": 7, "afflin": 7, "against": 8, "all": 5, "an": [0, 1, 4, 5, 7, 11], "analysi": 0, "angl": 7, "annot": 1, "anoth": 8, "apex": 5, "apex_diamet": [1, 5], "api": 10, "api_enable_http2": 1, "api_tls_insecure_skip_verifi": 1, "api_url": 1, "appli": 5, "approxim": 0, "ar": [1, 2, 5], "architectur": [1, 5, 11], "area": 8, "arg": [0, 1, 2, 4, 5, 6, 7, 8], "arr": 7, "arrai": [5, 7], "artifact": 0, "as_df": 5, "as_dict": 5, "as_networkx": 5, "as_torch": 5, "attempt": 5, "avail": 8, "averag": 8, "averagediamet": 8, "averagelength": 8, "averagespecificrootlength": 8, "averagevolum": 8, "averageweight": 8, "aws_access_key_id": 1, "aws_secret_access_kei": 1, "axi": 7, "base": [1, 5, 11], "base_diamet": 1, "basemodel": 1, "bayesian": 0, "been": [0, 1], "belong": 5, "between": [0, 8], "bin": 8, "bool": [1, 2, 4, 5], "bristow": 11, "bucket": 4, "bucket_nam": 4, "build": 2, "build_calibration_paramet": 2, "build_collaps": 2, "build_common_compon": 2, "build_common_layout": 2, "cacul": 8, "calcul": [0, 2, 8], "calculate_statistic_per_lay": 8, "calculate_summary_statistic_discrep": 0, "calibr": [1, 2, 3, 6], "calibration_input": 6, "calibration_model": 0, "calibration_paramet": 1, "calibration_valu": 2, "callabl": 8, "can": 8, "cartesian": 7, "cascading_set_invalid_root": 5, "cascading_to_world_origin": 5, "cascading_transform": 5, "cascading_update_transform": 5, "ceiling_threshold": 1, "changelog": 10, "child": 5, "child_data": 5, "child_id": 1, "children": 5, "class": [0, 1, 5, 8], "classifi": 1, "classvar": 1, "client": 4, "cm3": 5, "collaps": 2, "collect": 11, "column": [2, 5], "common": 2, "compar": [1, 8], "comparison": 8, "compat": 0, "compon": [1, 4, 5, 6], "component_data": 2, "component_spec": 2, "component_typ": 2, "compos": [1, 2], "comput": [0, 1], "computedfieldinfo": 1, "config_data_model": 1, "configdict": 1, "configur": 1, "conform": 1, "construct": [5, 7], "construct_root": 5, "construct_root_from_par": 5, "contain": [0, 1, 2, 4, 5, 6, 7, 8, 11], "content": [2, 4, 6], "context": 0, "convers": 7, "convex": 8, "convexhullarea": 8, "convexhullvolum": 8, "coordin": [5, 7], "core": 1, "correspond": 1, "creat": 5, "create_soil_fig": 5, "create_soil_grid": 5, "crop": 11, "csv": 4, "cumul": 8, "current": [0, 2, 5, 6], "dashboard": 2, "data": [0, 2, 3, 5, 6, 8, 11], "data_kei": 2, "data_model": 1, "data_typ": 1, "datafram": [0, 2, 5, 8], "dataset": 5, "datetim": 6, "dbc": 2, "decrement": 8, "deep": 11, "deeprootgen": [0, 1, 2, 4, 5, 6, 7, 8, 11], "default": [0, 1, 2, 4, 5, 6, 8], "defin": [0, 1, 4, 5, 6, 7, 8], "definit": 6, "degre": [5, 7], "densiti": 5, "deploy": 0, "depth": [5, 8], "depthdistribut": 8, "descript": 2, "develop": 11, "df": 8, "diamet": [1, 5, 8], "diameter_reduct": 1, "dict": [0, 1, 2, 5, 6, 8], "dictionari": [1, 2, 5, 6], "differ": 1, "digit": 11, "dimens": 7, "directori": 6, "discrep": 0, "dispatch": 6, "dispatch_new_run": 6, "distanc": 0, "distance_metr": [1, 8], "distancemetricbas": [0, 8], "distribut": 8, "div": 2, "each": [5, 8], "edg": [1, 2, 5], "edge_data": 5, "element": [2, 8], "empti": 0, "enabl": 1, "enable_soil": 1, "enumer": 1, "error": [0, 8], "estim": 11, "experi": [0, 1], "experimentmodel": 1, "extern": 2, "extract": 0, "fals": [1, 2, 5], "featur": 5, "feature_kei": 5, "field": [1, 11], "fieldinfo": 1, "fig": 5, "figur": [5, 8], "file": [4, 6], "file_nam": 4, "fine_root_threshold": 1, "float": [0, 1, 5, 7, 8], "floor_threshold": 1, "form": [1, 3, 6], "form_input": 6, "form_nam": [2, 6], "format": 5, "formmodel": 1, "from": [0, 1, 2, 4, 5, 6, 7, 11], "function": [0, 4, 6, 8], "g": 5, "gener": [5, 11], "geometr": 5, "get": [2, 5, 6, 8], "get_apex_coordin": 5, "get_calibration_summary_stat": 0, "get_common_layout": 2, "get_coordin": 5, "get_datetime_now": 6, "get_distance_metr": 8, "get_distance_metric_func": 8, "get_external_link": 2, "get_local_origin": 5, "get_number_of_root": 8, "get_out_table_df": 2, "get_outdir": 6, "get_parent_origin": 5, "get_simulation_uuid": 6, "get_summary_statist": 8, "get_summary_statistic_func": 8, "get_transform_matrix": 7, "get_x_rotation_matrix": 7, "get_xy_comparison_data": 8, "get_y_rotation_matrix": 7, "get_yaw": 5, "get_z_rotation_matrix": 7, "given": 2, "go": [5, 8], "graph": [1, 2], "gravitrop": 1, "grid": 5, "group": 2, "growth": 5, "growth_sec_root": 1, "ha": 0, "have": 1, "height": 5, "hgraph": 5, "hierarch": [1, 5], "histogram": 8, "histori": 4, "homogen": 7, "horizont": [5, 8], "html": 2, "hull": 8, "hydra": 1, "i": [0, 2, 5], "id": [2, 5, 6], "implement": 11, "includ": [2, 5], "increment": 5, "increment_node_id": 5, "increment_organ_id": 5, "index": [5, 10], "infer": 11, "inform": 11, "inherit": 5, "init_diamet": 5, "init_fig": 5, "init_length": 5, "init_organ": 5, "init_segment_coordin": 5, "initialis": 5, "inner_root_num": 1, "input": [0, 2, 3, 6], "input_compon": 2, "input_paramet": [0, 5], "insecure_tl": 1, "int": [1, 5, 8], "integr": [1, 5, 11], "interact": 2, "interbranch_dist": 1, "interv": 1, "introduct": 10, "invalid": 5, "invalid_root": 1, "io": 4, "its": [0, 5], "jame": 11, "junqi": 11, "kei": [2, 5], "l1": 8, "l1norm": 8, "label": [2, 8], "last": 2, "layer": [2, 5, 8], "layer_decr": 8, "layout": 2, "layout_descript": 2, "learn": 11, "left": 2, "left_sticki": 2, "length": [1, 5, 8], "length_rang": 5, "length_reduct": 1, "link": 2, "list": [0, 1, 2, 4, 5, 6, 7, 8], "list_of_cont": [4, 6], "list_of_nam": [4, 6], "load": [0, 4, 6], "load_context": 0, "load_data_from_fil": 4, "load_form_paramet": 6, "local": 5, "log": 0, "log_model": 0, "loss": 8, "lower_bound": 1, "make": 0, "make_homogen": 7, "manag": [4, 6], "manipul": 7, "map": 1, "matric": 7, "matrix": [5, 7], "max_attempt": 5, "max_ord": 1, "max_primary_length": 1, "max_sec_root_length": 1, "max_sec_root_num": 1, "max_val_attempt": 1, "maximum": 5, "mean": 8, "meanabsoluteerror": 8, "meanabsolutepercentageerror": 8, "meanpinballloss": 8, "meansquarederror": 8, "mechanical_constraint": 1, "median": 8, "medianabsoluteerror": 8, "messag": [4, 6], "metadata": 1, "method": 8, "metric": 0, "microservic": 0, "min_primary_length": 1, "min_sec_root_length": 1, "min_sec_root_num": 1, "minimum": 5, "mlflow": [0, 6], "model": [2, 3, 11], "model_computed_field": 1, "model_config": 1, "model_field": 1, "model_input": 0, "model_vers": 0, "modul": [0, 1, 2, 4, 5, 6, 7, 8, 10], "multipl": 2, "n_element": 8, "name": [0, 1, 2, 4, 6, 8], "name_prefix": 1, "nav": 2, "navig": 2, "ndarrai": [0, 5, 7, 8], "need": [0, 7], "networkx": 5, "new": [5, 6], "new_organ": 5, "no_root_zon": [1, 5], "node": [1, 5], "node_data": 5, "node_df": 5, "node_id": 1, "none": [0, 1, 2, 5, 6], "nonetyp": 1, "norm": 8, "notimplementederror": 8, "now": 6, "np": [0, 5, 7, 8], "number": [5, 8], "number_of_root": 5, "nx": 5, "object": [0, 1, 4], "object_nam": 4, "objectstoragemodel": 1, "observ": [0, 1, 2, 8, 11], "observed_data": [1, 2], "observed_data_cont": [1, 2], "omegaconf": 1, "ones": 7, "optimis": 0, "optimisationmodel": 0, "option": [0, 2, 4, 5, 6, 8], "orchestr": [1, 6], "orchestrationmodel": 1, "order": 1, "order_typ": 1, "organ": 5, "organ_id": 1, "origin": 5, "origin_max": 1, "origin_min": 1, "outer_root_num": 1, "output": [0, 2, 3, 6], "output_compon": 2, "page": [2, 6, 10], "page_descript": 2, "page_id": [2, 6], "param": 0, "param_input": 6, "paramet": [0, 1, 2, 6, 11], "parameter_form_nam": 2, "parameter_interv": 1, "parameter_spec": 0, "parameter_valu": 2, "parameterintervalmodel": 1, "parent": 5, "parent_id": 1, "parent_nod": 5, "pass": 6, "pd": [0, 2, 5, 8], "per": [5, 8], "percentag": 8, "perform": [6, 7], "pinbal": 8, "pipelin": 3, "pitch": [5, 7], "plant": 5, "plant_id": 1, "plausibl": 5, "plot_hierarchical_graph": 5, "plot_root_system": 5, "plotli": 5, "posit": 5, "position_primary_root": 5, "position_secondary_root": 5, "position_typ": 1, "predict": 0, "prefect": 6, "primari": 5, "prior": 5, "procedur": [1, 2], "produc": 8, "project": 11, "properti": 5, "purpos": 0, "pydant": 1, "pyfunc": 0, "pythonmodel": 0, "pytorch": 5, "radialdistribut": 8, "rais": [0, 8], "random_se": [1, 5], "rather": 2, "raw": 2, "raw_edge_cont": [1, 2], "reconstruct": 11, "refer": 10, "reflect": [5, 7], "registri": 0, "render": 2, "replac": 1, "repositori": 11, "represent": [1, 5], "requir": 1, "reset": 5, "reset_transform": 5, "resiz": 2, "resize_compon": 2, "respons": 4, "result": 5, "return": [0, 2, 4, 5, 6, 7, 8], "right": 2, "right_sticki": 2, "rng": 5, "roll": [5, 7], "root": [0, 1, 2, 7, 8, 11], "root_ratio": 1, "root_tissue_dens": [1, 5, 8], "root_typ": [1, 5], "root_vari": 1, "rootcalibrationinterv": 1, "rootcalibrationmodel": [0, 1], "rootedg": 5, "rootedgemodel": [1, 5], "rootmeansquarederror": 8, "rootnod": 5, "rootnodemodel": [1, 5], "rootorgan": 5, "rootsimulationmodel": [1, 5], "rootsystemgraph": 5, "rootsystemsimul": 5, "roottyp": 1, "roottypemodel": [1, 5], "rotat": [5, 7], "row": 2, "run": [0, 4, 5, 6], "run_calibration_simul": 0, "s3": 4, "s3_endpoint_url": 1, "s3_ignore_tl": 1, "s3_upload_fil": 4, "save": 6, "save_form_paramet": 6, "save_simulation_run": 6, "scale": [5, 7], "search": 10, "secondari": 5, "segment": 5, "segment_rank": 1, "segments_per_root": [1, 5], "sensit": 0, "sensitivityanalysismodel": 0, "set_invalid_root": 5, "sever": 1, "should": [1, 2], "side": 2, "signatur": 0, "signature_i": 0, "signature_x": 0, "simul": [0, 2, 5, 6, 8, 11], "simulation_data": 4, "simulation_data_model": 1, "simulation_form": 2, "simulation_form_nam": 2, "simulation_run": 6, "simulation_tag": [1, 5], "simulation_uuid": 0, "singl": 5, "soil": [2, 8], "soil_df": 5, "soil_layer_height": [1, 5], "soil_layer_width": [1, 5], "soil_n_col": [1, 5], "soil_n_lay": [1, 5], "sourc": [0, 1, 2, 4, 5, 6, 7, 8], "spatial": 3, "specif": [0, 1, 2, 8], "specifi": 5, "squar": 8, "stat_by_col": 2, "stat_by_lay": 2, "stat_by_soil_column": 1, "stat_by_soil_lay": 1, "statist": [1, 2, 3], "statistic_nam": 1, "statistic_valu": 1, "statistics_comparison": 1, "statistics_list": 0, "statisticscomparisonmodel": 1, "sticki": 2, "storag": 1, "str": [0, 1, 2, 4, 5, 6, 8], "string": 2, "stub": 9, "submiss": 2, "summari": [1, 2], "summary_data": 2, "summary_statist": [0, 1, 2, 8], "summarystatisticbas": 8, "summarystatisticsmodel": [0, 1], "supervisor": 11, "surround": 5, "synthet": 1, "system": [1, 5, 7, 8, 11], "tabl": 2, "task": [0, 2, 6], "than": 2, "theta": 7, "thi": [0, 1, 2, 4, 5, 6, 7, 8, 11], "threshold": 5, "thrown": 0, "tissu": 5, "titl": 2, "toast": [4, 6], "tooltip": 2, "total": 8, "totaldiamet": 8, "totallength": 8, "totalspecificrootlength": 8, "totalvolum": 8, "totalweight": 8, "track": 6, "tracking_uri": 1, "transform": 5, "translat": [5, 7], "true": [1, 2], "tupl": [0, 4, 5, 6, 8], "type": [1, 2, 5], "underli": 5, "unimpl": 8, "union": 1, "updat": [5, 7], "update_transform": 5, "upload": [4, 6], "upper_bound": 1, "us": [2, 7, 8], "use_summary_statist": [1, 2], "util": [0, 2, 4, 6, 8], "uuid": [0, 6], "v1": 1, "valid": 5, "valu": [1, 5, 8], "valueerror": 0, "variou": 2, "vertic": 5, "visualis": [5, 8], "volum": 8, "voxel": 5, "w": 7, "weight": 8, "when": 0, "whether": [2, 5], "width": 5, "within": [1, 2, 5], "workflow": 2, "world": 5, "write": 6, "x": [1, 5, 7], "x_kei": 5, "xiumei": 11, "y": [1, 5, 7], "y_kei": 5, "yang": 11, "yaw": [5, 7], "z": [1, 5, 7], "z_kei": 5, "z_lower_bound": 1, "z_upper_bound": 1, "zhu": 11}, "titles": ["Calibration", "Data Model", "Form", "API Reference", "Input/Output", "Model", "Pipeline", "Spatial", "Statistics", "Changelog", "DeepRootGen", "Introduction"], "titleterms": {"0": 9, "08": 9, "1": 9, "17": 9, "2024": 9, "api": 3, "calibr": 0, "changelog": 9, "compon": 2, "config": 1, "contact": 11, "content": 10, "data": [1, 4], "deeprootgen": 10, "distanc": 8, "experi": 6, "form": 2, "graph": 5, "indic": 10, "input": 4, "introduct": 11, "metric": 8, "model": [0, 1, 5], "output": 4, "pipelin": 6, "refer": 3, "root": 5, "simul": [1, 4], "soil": 5, "spatial": 7, "statist": [0, 8], "summari": [0, 8], "tabl": 10, "transform": 7, "version": 0, "workflow": 6}})
\ No newline at end of file