Adding working root sim

JBris · Sep 9, 2024 · 650b006 · 650b006
1 parent 745eff4
commit 650b006
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Showing 8 changed files with 1,050 additions and 350 deletions.
diff --git a/app/conf/form/common.yaml b/app/conf/form/common.yaml
@@ -25,16 +25,18 @@ components:
           max: 1
           step: 0.1
           value: 0.5
+          persistence: true
       - id: fine-root-threshold-input
         param: fine_root_threshold
-        label: Fine root threshold ratio
-        help: Threshold for classifying a root as a fine root, rather than a structural root (mm)
+        label: Fine root threshold
+        help: Threshold for classifying a root as a fine root, rather than a structural root (cm)
         class_name: dash_bootstrap_components.Input 
         kwargs:
           type: number
           min: 0
-          step: 0.1
-          value: 1.5
+          step: 0.01
+          value: 0.06
+          persistence: true
       - id: outer-primary-root-num-input
         param: outer_root_num
         label: Number of outer roots
@@ -46,6 +48,7 @@ components:
           max: 20
           step: 1
           value: 10
+          persistence: true
       - id: inner-primary-root-num-input
         param: inner_root_num
         label: Number of inner roots
@@ -57,6 +60,7 @@ components:
           max: 20
           step: 1
           value: 8
+          persistence: true
       - id: min-length-primary-root-input
         param: min_primary_length
         label: Primary root minimum length
@@ -68,6 +72,7 @@ components:
           max: 50
           step: 1
           value: 20
+          persistence: true
       - id: max-length-primary-root-input
         param: max_primary_length
         label: Primary root maximum length
@@ -79,6 +84,7 @@ components:
           max: 50
           step: 1
           value: 30
+          persistence: true
       - id: base-diameter-root-input
         param: base_diameter
         label: Base root diameter
@@ -87,31 +93,34 @@ components:
         kwargs:
           type: number
           min: 0.001
-          max: 10
-          step: 0.1
+          max: 1
+          step: 0.01
           value: 0.11
+          persistence: true
       - id: root-apex-input
         param: apex_diameter
         label: Apex diameter
         help: The diameter of the root apex (cm)
         class_name: dash_bootstrap_components.Input 
         kwargs:
           type: number
-          min: 0.001
+          min: 0.01
           max: 1
-          step: 0.1
-          value: 0.1
+          step: 0.01
+          value: 0.02
+          persistence: true
       - id: diameter-reduction-factor-input
         param: diameter_reduction
         label: Diameter reduction
         help: The diameter reduction factor for subsequent root segments.
         class_name: dash_bootstrap_components.Input 
         kwargs:
           type: number
-          min: 0.001
+          min: 0
           max: 1
           step: 0.1
-          value: 0.7
+          value: 0.2
+          persistence: true
       - id: min-num-secondary-roots-input
         param: min_sec_root_num
         label: Minimum number of secondary roots
@@ -120,9 +129,9 @@ components:
         kwargs:
           type: number
           min: 0
-          max: 10
           step: 1
-          value: 3
+          value: 1
+          persistence: true
       - id: max-num-secondary-roots-input
         param: max_sec_root_num
         label: Maximum number of secondary roots
@@ -131,9 +140,10 @@ components:
         kwargs:
           type: number
           min: 0
-          max: 10
+          max: 20
           step: 1
-          value: 4
+          value: 3
+          persistence: true
       - id: secondary-root-growth-input
         param: growth_sec_root
         label: Secondary root growth rate
@@ -143,7 +153,8 @@ components:
           type: number
           min: 0
           step: 0.1
-          value: 0.5
+          value: 0.2
+          persistence: true
       - id: min-length-secondary-root-input
         param: min_sec_root_length
         label: Secondary root minimum length
@@ -155,6 +166,7 @@ components:
           max: 250
           step: 1
           value: 100
+          persistence: true
       - id: max-length-secondary-root-input
         param: max_sec_root_length
         label: Secondary root maximum length
@@ -166,6 +178,7 @@ components:
           max: 500
           step: 1
           value: 220
+          persistence: true
       - id: segments-per-root-input
         param: segments_per_root
         label: Segments per root
@@ -176,7 +189,8 @@ components:
           min: 1
           max: 500
           step: 1
-          value: 10
+          value: 50
+          persistence: true
       - id: root-length-reduction-input
         param: length_reduction
         label: Length reduction
@@ -188,6 +202,7 @@ components:
           max: 1
           step: 0.1
           value: 0.5
+          persistence: true
       - id: root-vary-input
         param: root_vary
         label: Root segment variance
@@ -199,28 +214,7 @@ components:
           max: 360
           step: 1
           value: 30
-      - id: origin-min-input
-        param: origin_min
-        label: Origin minimum
-        help: The minimum distance of the initial primary root from the origin (cm)
-        class_name: dash_bootstrap_components.Input 
-        kwargs:
-          type: number
-          min: 0.001
-          max: 1
-          step: 0.01
-          value: 0.01
-      - id: origin-max-input
-        param: origin_max
-        label: Origin maximum
-        help: The maximum distance of the initial primary root from the origin (cm)
-        class_name: dash_bootstrap_components.Input 
-        kwargs:
-          type: number
-          min: 0.01
-          max: 1
-          step: 0.01
-          value: 0.1
+          persistence: true
       - id: enable-soil-input
         param: enable_soil
         label: Enable soil
@@ -238,6 +232,7 @@ components:
           max: 100
           step: 10
           value: 10
+          persistence: true
       - id: soil-layer-width-input
         param: soil_layer_width
         label: Soil layer width
@@ -249,6 +244,7 @@ components:
           max: 100
           step: 10
           value: 10
+          persistence: true
       - id: soil-n-layers
         param: soil_n_layers
         label: Number soil layers
@@ -260,6 +256,7 @@ components:
           max: 20
           step: 1
           value: 1
+          persistence: true
       - id: soil-n-cols
         param: soil_n_cols
         label: Number soil columns
@@ -271,6 +268,7 @@ components:
           max: 20
           step: 1
           value: 1
+          persistence: true
       - id: random-seed-input
         param: random_seed
         label: Random seed
@@ -279,6 +277,19 @@ components:
         kwargs:
           type: number
           step: 1
+          persistence: true
+      - id: max-val-attempts-input
+        param: max_val_attempts
+        label: Maximum validation attempts
+        help: The maximum number of attempts to validate each root (for plausibility) within the root system.
+        class_name: dash_bootstrap_components.Input 
+        kwargs:
+          type: number
+          min: 0
+          max: 1000
+          step: 1
+          value: 50
+          persistence: true
       - id: simulation-tag-input
         param: simulation_tag
         label: Simulation tag
@@ -287,6 +298,7 @@ components:
         kwargs:
           type: text
           value: default
+          persistence: true
   simulation:
     collapsible: true
     children:
@@ -298,6 +310,11 @@ components:
           children: Run model
           color: primary
           className: me-1
+      - id: download-sim-data-input
+        label: Download
+        help: Download the simulation output data
+        class_name: dash_daq.BooleanSwitch.BooleanSwitch 
+        kwargs: {}
       - id: save-param-button
         label: Save
         help: Save current parameter configuration to file

diff --git a/app/pages/generate_root_system.py b/app/pages/generate_root_system.py
@@ -4,10 +4,13 @@
 # Imports
 ######################################
 
+import base64
 import os.path as osp
+from datetime import datetime
 
 import dash_bootstrap_components as dbc
 import pandas as pd
+import yaml
 from dash import ALL, Input, Output, State, callback, dcc, get_app, html, register_page
 
 from deeprootgen.data_model import RootSimulationModel
@@ -117,10 +120,6 @@ def save_param(n_clicks: int, param_inputs: list) -> None:
         k = input["param"]
         inputs[k] = param_inputs[i]
 
-    from datetime import datetime
-
-    import yaml
-
     outfile = osp.join(
         "outputs", f"{datetime.today().strftime('%Y-%m-%d-%H-%M')}-{PAGE_ID}.yaml"
     )
@@ -138,10 +137,6 @@ def save_param(n_clicks: int, param_inputs: list) -> None:
     prevent_initial_call=True,
 )
 def update_output(list_of_contents: list, list_of_names: list) -> tuple:
-    import base64
-
-    import yaml
-
     _, content_string = list_of_contents[0].split(",")
     decoded = base64.b64decode(content_string)
     input_dict = yaml.safe_load(decoded.decode("utf-8"))
@@ -156,17 +151,23 @@ def update_output(list_of_contents: list, list_of_names: list) -> tuple:
     Input({"index": f"{PAGE_ID}-run-sim-button", "type": ALL}, "n_clicks"),
     State({"type": f"{PAGE_ID}-parameters", "index": ALL}, "value"),
     State({"index": f"{PAGE_ID}-enable-soil-input", "type": ALL}, "on"),
+    State({"index": f"{PAGE_ID}-download-sim-data-input", "type": ALL}, "on"),
     prevent_initial_call=True,
 )
-def run_root_model(n_clicks: list, form_values: list, enable_soils: list) -> dcc.Graph:
+def run_root_model(
+    n_clicks: list, form_values: list, enable_soils: list, download_data: list
+) -> dcc.Graph:
     """Run and plot the root model.
 
     Args:
         n_clicks (list):
             Number of times the button has been clicked.
         form_values (list):
             The form input data.
-
+        enable_soils (list):
+            Enable visualisation of soil data.
+        download_data (list):
+            Whether to download the simulation results data.
     Returns:
         dcc.Graph: The visualised root model.
     """
@@ -186,18 +187,25 @@ def run_root_model(n_clicks: list, form_values: list, enable_soils: list) -> dcc
 
     input_params = RootSimulationModel.parse_obj(form_inputs)
     simulation = RootSystemSimulation(
-        simulation_tag=input_params.simulation_tag, random_seed=input_params.random_seed
+        simulation_tag=input_params.simulation_tag,
+        random_seed=input_params.random_seed,
+        visualise=True,
     )
     results = simulation.run(input_params)
 
-    from datetime import datetime
+    download_data = download_data[0]
+    if download_data:
+        from datetime import datetime
 
-    now = datetime.today().strftime("%Y-%m-%d-%H-%M")
-    outfile = osp.join("outputs", f"{now}-nodes.csv")
-    df = pd.DataFrame(results.nodes)
-    df.to_csv(outfile, index=False)
+        now = datetime.today().strftime("%Y-%m-%d-%H-%M")
+        outfile = osp.join("outputs", f"{now}-nodes.csv")
+        df = pd.DataFrame(results.nodes)
+        df.to_csv(outfile, index=False)
+        download_file = dcc.send_file(outfile)
+    else:
+        download_file = None
 
-    return results.figure, dcc.send_file(outfile)
+    return results.figure, download_file
 
 
 ######################################

diff --git a/deeprootgen/data_model/__init__.py b/deeprootgen/data_model/__init__.py
@@ -8,5 +8,7 @@
     RootEdgeModel,
     RootNodeModel,
     RootSimulationModel,
-    RootSimulationResults,
+    RootSimulationResultModel,
+    RootType,
+    RootTypeModel,
 )