From 8ad8c99bc37d1f7c3bf84a1929d9b71d0cfc4381 Mon Sep 17 00:00:00 2001 From: baugetfa Date: Wed, 4 Feb 2026 14:01:39 +0100 Subject: [PATCH] removed example directory symlink to doc. copied example directory into doc --- README.md | 4 +- doc/example | 1 - .../Boursiac2022/adjustment_K_and_k.py | 0 .../example}/Boursiac2022/boursiac2022.ipynb | 28 ++-- .../Boursiac2022/data/10-arabido-plants.csv | 0 .../data/15012020-1045-cut-n-flow-archi2.txt | 0 .../data/160316#2-cut-n-flow-archi2.txt | 0 .../data/20-06-09-FB-180719-e15ch1-1.txt | 0 .../data/20-07-02-SD-150218-esk11-7.txt | 0 .../200219-YBFB-Col-cut-n-flow-archi2.txt | 0 .../200619-YBFB-Col-1-cut-n-flow-archi2.txt | 0 .../200619-YBFB-Col-2-cut-n-flow-archi2.txt | 0 .../200619-YBFB-e11-2-cut-n-flow-archi0.txt | 0 .../200619-YBFB-e15-1-cut-n-flow-archi0.txt | 0 .../200619-YBFB-e15-2-cut-n-flow-archi2.txt | 0 .../200702-YBFB-Col-1-cut-n-flow-archi2.txt | 0 .../200703-YBFB-Col-2-cut-n-flow-archi2.txt | 0 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.../example}/example_archi_from_file.ipynb | 34 +--- .../example}/example_archi_from_rsml.ipynb | 0 .../example_cut_and_flow_analysis.ipynb | 0 .../example_cut_and_flow_pure_water.py | 0 .../example_cut_and_flow_water_solute.py | 0 .../example}/example_generated_archi.ipynb | 0 .../example}/example_k_adjustment.ipynb | 0 .../example}/example_parameter_class.ipynb | 0 .../example}/example_rsml_export.rsml | 0 {example => doc/example}/example_rsml_io.py | 0 .../example_solute_water_transport.ipynb | 0 .../example}/examples_cut_and_flow.ipynb | 0 .../example}/generated_architectures.csv | 0 .../example}/millet/CR_diameters.csv | 0 .../example}/millet/LR_diameters.csv | 0 .../millet/Old/Millet_Root_Model.ipynb | 4 +- .../millet/Old/Water_flux-Copy1.ipynb | 0 .../example}/millet/Old/Water_flux.ipynb | 0 .../example}/millet/SR_diameters.csv | 0 .../example}/millet/WIP_notebook.ipynb | 0 .../example}/millet/lr_length_law_data.csv | 0 .../example}/millet/seminal_growth_109.csv | 0 .../example}/millet/seminal_growth_57.csv | 0 {example => doc/example}/notebook_list.ipynb | 0 {example => doc/example}/parameters.yml | 0 doc/example/parameters_10LP08.yml | 150 ++++++++++++++++++ .../example}/parameters_150-5P13.yml | 0 .../example}/parameters_Ctr-3P2.yml | 0 .../parameters_architecture_generation.yml | 0 .../example}/parameters_example_rsml_io.yml | 0 .../example}/parameters_plant_01.yml | 0 133 files changed, 170 insertions(+), 51 deletions(-) delete mode 120000 doc/example rename {example => doc/example}/Boursiac2022/adjustment_K_and_k.py (100%) rename {example => doc/example}/Boursiac2022/boursiac2022.ipynb (99%) rename {example => doc/example}/Boursiac2022/data/10-arabido-plants.csv (100%) rename {example => doc/example}/Boursiac2022/data/15012020-1045-cut-n-flow-archi2.txt (100%) rename {example => doc/example}/Boursiac2022/data/160316#2-cut-n-flow-archi2.txt (100%) rename {example => doc/example}/Boursiac2022/data/20-06-09-FB-180719-e15ch1-1.txt (100%) rename 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doc/example}/example_generated_archi.ipynb (100%) rename {example => doc/example}/example_k_adjustment.ipynb (100%) rename {example => doc/example}/example_parameter_class.ipynb (100%) rename {example => doc/example}/example_rsml_export.rsml (100%) rename {example => doc/example}/example_rsml_io.py (100%) rename {example => doc/example}/example_solute_water_transport.ipynb (100%) rename {example => doc/example}/examples_cut_and_flow.ipynb (100%) rename {example => doc/example}/generated_architectures.csv (100%) rename {example => doc/example}/millet/CR_diameters.csv (100%) rename {example => doc/example}/millet/LR_diameters.csv (100%) rename {example => doc/example}/millet/Old/Millet_Root_Model.ipynb (99%) rename {example => doc/example}/millet/Old/Water_flux-Copy1.ipynb (100%) rename {example => doc/example}/millet/Old/Water_flux.ipynb (100%) rename {example => doc/example}/millet/SR_diameters.csv (100%) rename {example => doc/example}/millet/WIP_notebook.ipynb (100%) rename {example => doc/example}/millet/lr_length_law_data.csv (100%) rename {example => doc/example}/millet/seminal_growth_109.csv (100%) rename {example => doc/example}/millet/seminal_growth_57.csv (100%) rename {example => doc/example}/notebook_list.ipynb (100%) rename {example => doc/example}/parameters.yml (100%) create mode 100644 doc/example/parameters_10LP08.yml rename {example => doc/example}/parameters_150-5P13.yml (100%) rename {example => doc/example}/parameters_Ctr-3P2.yml (100%) rename {example => doc/example}/parameters_architecture_generation.yml (100%) rename {example => doc/example}/parameters_example_rsml_io.yml (100%) rename {example => doc/example}/parameters_plant_01.yml (100%) diff --git a/README.md b/README.md index eda7a283..9a6f3ca3 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root architecture system generator package.
- Alt text + Alt text
Heat map representation of the incoming local radial flows on an arabidopsis root.
@@ -76,7 +76,7 @@ mamba env create -f ./conda/environment.yml #### Usage -See notebooks in example directory, they are listed [here](example/notebook_list.ipynb) and can be played following [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/openalea/hydroroot/HEAD?urlpath=%2Fdoc%2Ftree%2Fexample%2Fnotebook_list.ipynb) +See notebooks in example directory, they are listed [here](doc/example/notebook_list.ipynb) and can be played following [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/openalea/hydroroot/HEAD?urlpath=%2Fdoc%2Ftree%2Fexample%2Fnotebook_list.ipynb) ## Documentation diff --git a/doc/example b/doc/example deleted file mode 120000 index 3cfc163b..00000000 --- a/doc/example +++ /dev/null @@ -1 +0,0 @@ -../example \ No newline at end of file diff --git a/example/Boursiac2022/adjustment_K_and_k.py b/doc/example/Boursiac2022/adjustment_K_and_k.py similarity index 100% rename from example/Boursiac2022/adjustment_K_and_k.py rename to doc/example/Boursiac2022/adjustment_K_and_k.py diff --git a/example/Boursiac2022/boursiac2022.ipynb b/doc/example/Boursiac2022/boursiac2022.ipynb similarity index 99% rename from example/Boursiac2022/boursiac2022.ipynb rename to doc/example/Boursiac2022/boursiac2022.ipynb index 4dfd1198..40859d8b 100644 --- a/example/Boursiac2022/boursiac2022.ipynb +++ b/doc/example/Boursiac2022/boursiac2022.ipynb @@ -107,7 +107,7 @@ } ], "source": [ - "draw = pd.read_csv(\"data_figures/fig_2-A.csv\", sep = ';')\n", + "draw = pd.read_csv(\"data_figures/fig_2-A.csv\", sep =';')\n", "fig = {}\n", "ax5 = {}\n", "ax6 = {}\n", @@ -276,7 +276,7 @@ } ], "source": [ - "draw = pd.read_csv(\"data_figures/fig_2-C.csv\", sep = ',', dtype = 'float')\n", + "draw = pd.read_csv(\"data_figures/fig_2-C.csv\", sep =',', dtype ='float')\n", "ax = draw.plot('x K median', 'mediancurve from cut and flow measurements',color='m')\n", "draw.plot('x K median', 'median -t*SE', color='m', ax=ax, style='--')\n", "draw.plot('x K median', 'median + t*SE', color='m', ax=ax, style='--')\n", @@ -435,7 +435,7 @@ } ], "source": [ - "df3a = pd.read_csv(\"data_figures/fig-3-A.csv\", sep = ',', dtype = 'float')\n", + "df3a = pd.read_csv(\"data_figures/fig-3-A.csv\", sep =',', dtype ='float')\n", "df3a.iloc[:,range(0,43,2)]=df3a.iloc[:,range(0,43,2)]/1000\n", "ax = df3a.plot.scatter(0,1,marker='o',color='black',edgecolor ='black')\n", "for i in range(2,26,2):\n", @@ -447,7 +447,7 @@ "ax.set_ylabel('Number of lateral roots')\n", "ax.set_xlabel('distance to tip (m)')\n", "ax.set_title('fig-3-A')\n", - "df3b = pd.read_csv(\"data_figures/fig-3-B.csv\", sep = ',', dtype = 'float')\n", + "df3b = pd.read_csv(\"data_figures/fig-3-B.csv\", sep =',', dtype ='float')\n", "df3b.iloc[:,[0,2]]=df3b.iloc[:,[0,2]]/1000\n", "ax = df3b.plot.scatter(1,0,marker='o',color='black',edgecolor ='black')\n", "df3b.plot.scatter(3,2,marker='o',color='white',edgecolor ='black',ax=ax)\n", @@ -574,7 +574,7 @@ } ], "source": [ - "df4a = pd.read_csv(\"data_figures/fig-4-A.csv\", sep = ',', dtype = 'float')\n", + "df4a = pd.read_csv(\"data_figures/fig-4-A.csv\", sep =',', dtype ='float')\n", "df4a.iloc[:,[0,3,6]]=df4a.iloc[:,[0,3,6]]/1e3\n", "ax=df4a.plot(0,'all intercepts 1',color='orange')\n", "df4a.plot(0,'all intercepts 2',color='blue',ax=ax)\n", @@ -622,7 +622,7 @@ } ], "source": [ - "df4b = pd.read_csv(\"data_figures/fig-4-B.csv\", sep = ',')\n", + "df4b = pd.read_csv(\"data_figures/fig-4-B.csv\", sep =',')\n", "df4b.iloc[:,[0]]/=1e3\n", "ax=df4b.plot(0,'all intercepts',color='orange')\n", "df4b.plot(0,'intercepts order 2',color='purple',ax=ax)\n", @@ -668,7 +668,7 @@ } ], "source": [ - "df4c = pd.read_csv(\"data_figures/fig-4-C.csv\", sep = ',')\n", + "df4c = pd.read_csv(\"data_figures/fig-4-C.csv\", sep =',')\n", "ax=df4c.plot.scatter('simulated plant id','total length simulated (m)',color='grey')\n", "df4c.plot.scatter('plant id','total length (m)',color='pink',marker='s',edgecolor='pink',ax=ax)\n", "ax.set_title('fig-4-C')" @@ -1051,7 +1051,7 @@ } ], "source": [ - "df7a = pd.read_csv(\"data_figures/fig-7-A.csv\", sep = ',')\n", + "df7a = pd.read_csv(\"data_figures/fig-7-A.csv\", sep =',')\n", "ax=df7a.plot('dist to base (m)','n Col0',color='black')\n", "df7a.plot('dist to base (m)','95 - Col',color='black',ax=ax)\n", "df7a.plot('dist to base (m)','95 + Col',color='black',ax=ax)\n", @@ -1185,12 +1185,12 @@ ], "source": [ "ax = draw.plot('x K median', 'mediancurve from cut and flow measurements',color='grey')\n", - "draw2 = pd.read_csv(\"data_figures/fig_7-C-e11.csv\", sep = ',', dtype = float)\n", + "draw2 = pd.read_csv(\"data_figures/fig_7-C-e11.csv\", sep =',', dtype = float)\n", "draw2.plot('x', 'median-esk1-1',color = 'green',ax=ax)\n", "for i in range(0,10,2):\n", " color = (0.25,1.0-float(i)/10.0,0.25)\n", " draw2.plot.scatter(i,i+1, ax = ax, color = color, edgecolor = color)\n", - "draw3 = pd.read_csv(\"data_figures/fig_7-C-e15.csv\", sep = ',', dtype = float)\n", + "draw3 = pd.read_csv(\"data_figures/fig_7-C-e15.csv\", sep =',', dtype = float)\n", "draw3.plot('x', 'median esk1-5',color ='blue',ax=ax)\n", "for i in range(0,14,2):\n", " color = (0.,1.0-float(i)/14.0,1.)\n", @@ -1289,7 +1289,7 @@ } ], "source": [ - "df1c = pd.read_csv(\"data_figures/sup-fig-1-C.csv\", sep = ',', dtype = float)\n", + "df1c = pd.read_csv(\"data_figures/sup-fig-1-C.csv\", sep =',', dtype = float)\n", "marker = ['o','s','^','d','s','d','v']\n", "colors = ['green','green','green','green','purple','purple','purple']\n", "ax = df1c.plot('X lowess','K lowess', color='black')\n", @@ -1359,13 +1359,13 @@ } ], "source": [ - "dsf2a = pd.read_csv(\"data_figures/sup-fig-3-A.csv\", sep = ',', dtype = float)\n", + "dsf2a = pd.read_csv(\"data_figures/sup-fig-3-A.csv\", sep =',', dtype = float)\n", "ax = dsf2a.plot.scatter(0,1,color='black')\n", "for i in range(1,6):\n", " dsf2a.plot(0,i, ax=ax)\n", "ax.set_ylim(0.03,0.045)\n", "ax.set_title('supplemental figure 3-A')\n", - "dsf2b = pd.read_csv(\"data_figures/sup-fig-3-B.csv\", sep = ',', dtype = float)\n", + "dsf2b = pd.read_csv(\"data_figures/sup-fig-3-B.csv\", sep =',', dtype = float)\n", "ax2 = dsf2b.iloc[:,range(1,10,2)].plot(style='--')\n", "dsf2b.iloc[:,range(2,11,2)].plot(ax=ax2)\n", "ax2.legend(bbox_to_anchor=(1.05, 1), loc='upper left')\n", @@ -1472,7 +1472,7 @@ } ], "source": [ - "dfs3a = pd.read_csv(\"data_figures/sup-fig-5-A.csv\", sep = ',')\n", + "dfs3a = pd.read_csv(\"data_figures/sup-fig-5-A.csv\", sep =',')\n", "ax=dfs3a.plot.scatter('totals length (m)','integral6pointSum',color='black')" ] }, diff --git a/example/Boursiac2022/data/10-arabido-plants.csv b/doc/example/Boursiac2022/data/10-arabido-plants.csv similarity index 100% rename from example/Boursiac2022/data/10-arabido-plants.csv rename to doc/example/Boursiac2022/data/10-arabido-plants.csv diff --git a/example/Boursiac2022/data/15012020-1045-cut-n-flow-archi2.txt b/doc/example/Boursiac2022/data/15012020-1045-cut-n-flow-archi2.txt 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example/Boursiac2022/simulation_table-1.py rename to doc/example/Boursiac2022/simulation_table-1.py diff --git a/example/Visualea_workflow/data/Exp01_P1.txt b/doc/example/Visualea_workflow/data/Exp01_P1.txt similarity index 100% rename from example/Visualea_workflow/data/Exp01_P1.txt rename to doc/example/Visualea_workflow/data/Exp01_P1.txt diff --git a/example/Visualea_workflow/data/maize-K.csv b/doc/example/Visualea_workflow/data/maize-K.csv similarity index 100% rename from example/Visualea_workflow/data/maize-K.csv rename to doc/example/Visualea_workflow/data/maize-K.csv diff --git a/example/adjustment_K_and_k.py b/doc/example/adjustment_K_and_k.py similarity index 100% rename from example/adjustment_K_and_k.py rename to doc/example/adjustment_K_and_k.py diff --git a/example/architectures_generation.py b/doc/example/architectures_generation.py similarity index 100% rename from example/architectures_generation.py rename to doc/example/architectures_generation.py diff --git a/example/data/Exp03_P2.txt b/doc/example/data/Exp03_P2.txt similarity index 100% rename from example/data/Exp03_P2.txt rename to doc/example/data/Exp03_P2.txt diff --git a/example/data/Exp05_P13.txt b/doc/example/data/Exp05_P13.txt similarity index 100% rename from example/data/Exp05_P13.txt rename to doc/example/data/Exp05_P13.txt diff --git a/example/data/arabidopsis-simple.rsml b/doc/example/data/arabidopsis-simple.rsml similarity index 100% rename from example/data/arabidopsis-simple.rsml rename to doc/example/data/arabidopsis-simple.rsml diff --git a/example/data/fig-6E.png b/doc/example/data/fig-6E.png similarity index 100% rename from example/data/fig-6E.png rename to doc/example/data/fig-6E.png diff --git a/example/data/length_LR_order1_160615.csv b/doc/example/data/length_LR_order1_160615.csv similarity index 100% rename from example/data/length_LR_order1_160615.csv rename to doc/example/data/length_LR_order1_160615.csv diff --git a/example/data/length_LR_order1_Exp33_20-10-09.csv b/doc/example/data/length_LR_order1_Exp33_20-10-09.csv similarity index 100% rename from example/data/length_LR_order1_Exp33_20-10-09.csv rename to doc/example/data/length_LR_order1_Exp33_20-10-09.csv diff --git a/example/data/length_LR_order2_160909.csv b/doc/example/data/length_LR_order2_160909.csv similarity index 100% rename from example/data/length_LR_order2_160909.csv rename to doc/example/data/length_LR_order2_160909.csv diff --git a/example/data/maize_JvP_data.csv b/doc/example/data/maize_JvP_data.csv similarity index 100% rename from example/data/maize_JvP_data.csv rename to doc/example/data/maize_JvP_data.csv diff --git a/example/data/maize_cnf_data.csv b/doc/example/data/maize_cnf_data.csv similarity index 100% rename from example/data/maize_cnf_data.csv rename to doc/example/data/maize_cnf_data.csv diff --git a/example/data/plant-01.txt b/doc/example/data/plant-01.txt similarity index 100% rename from example/data/plant-01.txt rename to doc/example/data/plant-01.txt diff --git a/example/data/plant-1.rsml b/doc/example/data/plant-1.rsml similarity index 100% rename from example/data/plant-1.rsml rename to doc/example/data/plant-1.rsml diff --git a/example/data/test.csv b/doc/example/data/test.csv similarity index 100% rename from example/data/test.csv rename to doc/example/data/test.csv diff --git a/example/data/test_fig-5.csv b/doc/example/data/test_fig-5.csv similarity index 100% rename from example/data/test_fig-5.csv rename to doc/example/data/test_fig-5.csv diff --git a/example/data/test_law.csv b/doc/example/data/test_law.csv similarity index 100% rename from example/data/test_law.csv rename to doc/example/data/test_law.csv diff --git a/example/example_archi_from_file.ipynb b/doc/example/example_archi_from_file.ipynb similarity index 99% rename from example/example_archi_from_file.ipynb rename to doc/example/example_archi_from_file.ipynb index 719aebf8..85503e24 100644 --- a/example/example_archi_from_file.ipynb +++ b/doc/example/example_archi_from_file.ipynb @@ -295,38 +295,10 @@ "metadata": {}, "outputs": [], "source": [ - "# from openalea.hydroroot.display import plot\n", - "# %gui qt\n", - "# plot(g, prop_cmap='psi_in')" + "from openalea.hydroroot.display import plot\n", + "%gui qt\n", + "plot(g, prop_cmap='psi_in')" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "56b48ced-dcdc-4425-9fdf-6530e62ade11", - "metadata": {}, - "outputs": [], - "source": [ - "import matplotlib.pyplot as plt" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "254ea21b-1b57-4b63-a9c9-8600a40aa606", - "metadata": {}, - "outputs": [], - "source": [ - "plt.plot(range(2), range(2))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "e1269bf7-3807-4417-a8c7-06cbcd2c6419", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/example/example_archi_from_rsml.ipynb b/doc/example/example_archi_from_rsml.ipynb similarity index 100% rename from example/example_archi_from_rsml.ipynb rename to doc/example/example_archi_from_rsml.ipynb diff --git a/example/example_cut_and_flow_analysis.ipynb b/doc/example/example_cut_and_flow_analysis.ipynb similarity index 100% rename from example/example_cut_and_flow_analysis.ipynb rename to doc/example/example_cut_and_flow_analysis.ipynb diff --git a/example/example_cut_and_flow_pure_water.py b/doc/example/example_cut_and_flow_pure_water.py similarity index 100% rename from example/example_cut_and_flow_pure_water.py rename to doc/example/example_cut_and_flow_pure_water.py diff --git a/example/example_cut_and_flow_water_solute.py b/doc/example/example_cut_and_flow_water_solute.py similarity index 100% rename from example/example_cut_and_flow_water_solute.py rename to doc/example/example_cut_and_flow_water_solute.py diff --git a/example/example_generated_archi.ipynb b/doc/example/example_generated_archi.ipynb similarity index 100% rename from example/example_generated_archi.ipynb rename to doc/example/example_generated_archi.ipynb diff --git a/example/example_k_adjustment.ipynb b/doc/example/example_k_adjustment.ipynb similarity index 100% rename from example/example_k_adjustment.ipynb rename to doc/example/example_k_adjustment.ipynb diff --git a/example/example_parameter_class.ipynb b/doc/example/example_parameter_class.ipynb similarity index 100% rename from example/example_parameter_class.ipynb rename to doc/example/example_parameter_class.ipynb diff --git a/example/example_rsml_export.rsml b/doc/example/example_rsml_export.rsml similarity index 100% rename from example/example_rsml_export.rsml rename to doc/example/example_rsml_export.rsml diff --git a/example/example_rsml_io.py b/doc/example/example_rsml_io.py similarity index 100% rename from example/example_rsml_io.py rename to doc/example/example_rsml_io.py diff --git a/example/example_solute_water_transport.ipynb b/doc/example/example_solute_water_transport.ipynb similarity index 100% rename from example/example_solute_water_transport.ipynb rename to doc/example/example_solute_water_transport.ipynb diff --git a/example/examples_cut_and_flow.ipynb b/doc/example/examples_cut_and_flow.ipynb similarity index 100% rename from example/examples_cut_and_flow.ipynb rename to doc/example/examples_cut_and_flow.ipynb diff --git a/example/generated_architectures.csv b/doc/example/generated_architectures.csv similarity index 100% rename from example/generated_architectures.csv rename to doc/example/generated_architectures.csv diff --git a/example/millet/CR_diameters.csv b/doc/example/millet/CR_diameters.csv similarity index 100% rename from example/millet/CR_diameters.csv rename to doc/example/millet/CR_diameters.csv diff --git a/example/millet/LR_diameters.csv b/doc/example/millet/LR_diameters.csv similarity index 100% rename from example/millet/LR_diameters.csv rename to doc/example/millet/LR_diameters.csv diff --git a/example/millet/Old/Millet_Root_Model.ipynb b/doc/example/millet/Old/Millet_Root_Model.ipynb similarity index 99% rename from example/millet/Old/Millet_Root_Model.ipynb rename to doc/example/millet/Old/Millet_Root_Model.ipynb index d91a71e5..1623311f 100644 --- a/example/millet/Old/Millet_Root_Model.ipynb +++ b/doc/example/millet/Old/Millet_Root_Model.ipynb @@ -336,9 +336,7 @@ "output_type": "execute_result" } ], - "source": [ - "FileLinks('.')" - ] + "source": "FileLinks('')" }, { "cell_type": "code", diff --git a/example/millet/Old/Water_flux-Copy1.ipynb b/doc/example/millet/Old/Water_flux-Copy1.ipynb similarity index 100% rename from example/millet/Old/Water_flux-Copy1.ipynb rename to doc/example/millet/Old/Water_flux-Copy1.ipynb diff --git a/example/millet/Old/Water_flux.ipynb b/doc/example/millet/Old/Water_flux.ipynb similarity index 100% rename from example/millet/Old/Water_flux.ipynb rename to doc/example/millet/Old/Water_flux.ipynb diff --git a/example/millet/SR_diameters.csv b/doc/example/millet/SR_diameters.csv similarity index 100% rename from example/millet/SR_diameters.csv rename to doc/example/millet/SR_diameters.csv diff --git a/example/millet/WIP_notebook.ipynb b/doc/example/millet/WIP_notebook.ipynb similarity index 100% rename from example/millet/WIP_notebook.ipynb rename to doc/example/millet/WIP_notebook.ipynb diff --git a/example/millet/lr_length_law_data.csv b/doc/example/millet/lr_length_law_data.csv similarity index 100% rename from example/millet/lr_length_law_data.csv rename to doc/example/millet/lr_length_law_data.csv diff --git a/example/millet/seminal_growth_109.csv b/doc/example/millet/seminal_growth_109.csv similarity index 100% rename from example/millet/seminal_growth_109.csv rename to doc/example/millet/seminal_growth_109.csv diff --git a/example/millet/seminal_growth_57.csv b/doc/example/millet/seminal_growth_57.csv similarity index 100% rename from example/millet/seminal_growth_57.csv rename to doc/example/millet/seminal_growth_57.csv diff --git a/example/notebook_list.ipynb b/doc/example/notebook_list.ipynb similarity index 100% rename from example/notebook_list.ipynb rename to doc/example/notebook_list.ipynb diff --git a/example/parameters.yml b/doc/example/parameters.yml similarity index 100% rename from example/parameters.yml rename to doc/example/parameters.yml diff --git a/doc/example/parameters_10LP08.yml b/doc/example/parameters_10LP08.yml new file mode 100644 index 00000000..0761854b --- /dev/null +++ b/doc/example/parameters_10LP08.yml @@ -0,0 +1,150 @@ +#%YAML + +#All parameters should be in SI units + +#Few parameters may be set to list of float or integer allowing to run successive simulation +# there are two syntaxes: +# [x1, ..., xn] or range(start, end, step) +# eg. range(0.02, 0.09, 0.02) or [0.02, 0.04, 0.06, 0.08] will give the same results +# the parameter will take successively the values 0.02, 0.04, 0.06 and 0.08 + +archi: + #if read_architecture is true then architecture will be constructed from the file(s) given by input_dir and input_file + #otherwise the architecture will be generated according to the parameters + read_architecture: True + + #Input architecture from scanned image (distance_from_base_(mm) \t lateral_root_length_(mm) \t order) + #folder name + input_dir: data/Maize/FB-LR/ + + #File name: + #may be a list of names, eg. [file1, file2, file3] wildcar may be used + input_file: [Exp10_LP08.txt] + + #seed used to generate an MTG, for a same seed we got the same MTG, if no seed is given a seed is generated randomly + #integer, list of integer or nothing + seed: + + #file names with length laws relative path + #file format: "LR_length_mm" ; "relative_distance_to_tip" + #laws used to generate lateral roots of the 1st order (1_order_law), and lateral roots of order above 1 (2_order_law) + length_file: + - data/length_LR_order1_Exp33_20-10-09.csv + - data/length_LR_order1_Exp33_20-10-09.csv + + #length of the primary root + #float or list of float + #unit: m + primary_length: 0.3 + + #branching delay + #float or list of float + #unit: m + branching_delay: 1.07e-3 + + #branching variability + #float between [0 ; 1], 0.25 means 25% + branching_variability: 0.25 + + #maximum roots order + order_max: 1 + + #vertices length + #unit: m + segment_length: 1.0e-3 + + #part of roots without any lateral root, distance from tip + #float or list of float + #unit: m + nude_length: 0.021 + + #reference radius of the primary root + #float + #unit: m + ref_radius: 0.54e-3 + + #radius decrease factor applied when increasing order + #float + #radius lateral order n: r = order_decrease_factor^n * ref_radius + order_decrease_factor: 0.25 + +hydro: + #radial conductivity + #float + #unit: microL/(s.MPa.m2) + k0: 225 + + #axial_conductance_data + # - [x1, ......, xn] + # - [K1, ....., Kn] + #list of float + #unit: microL.m/(s.Mpa) + axial_conductance_data: + - [0, 0.0335, 0.0579, 0.0713, 0.0854, 0.13] +# - [2.0e-2, 2.0e-2, 2.0e-2, 2.0e-2, 2.0e-2, 0.2] +# - [ 0.00125315, 0.00100948, 0.0161021 , 0.0155661 , 0.02511466, +# 0.03140052 ] + - [7.393e-04, 5.955e-04, 1.597e-02, 1.578e-02, 2.607e-02, 3.284e-02] + + +solute: + #J_s: active pumping rate + #float + #unit: mol/(m2.s) + J_s: 2.0e-4 + + #P_s: permeability coefficient + #float + #unit: m/s + P_s: 4.9e-6 + + #Cse: concentration of permeating solutes + #float + #unit: mol/m3 or mM + Cse: 13.96 #13.96 -> pi CTR = -0.034 MPa + + #Ce: concentration of non-permeating solutes + #float + #unit: mol/m3 or mM + Ce: 0. + + #sigma: reflexion coefficient + #float + #dimensionless + Sigma: 0.85 # + +experimental: + #water flux at the root base + #float + #unit: microL/s + Jv: 0.0 + + #hydric potential outside the roots (pressure chamber) + #float + #unit: MPa + psi_e: 0.201325 + + #hydric potential at the root base (e.g. atmospheric pressure for decapitated plant) + #float + #unit: MPa + psi_base: .101325 + +output: + #distance from the base for intercepts calculation + # float or list of float + #unit: m + intercepts: [] + + #factor to explore a k0 range + # float or list of float + radfold: 1.0 + + #like radfold but apply to axial_conductance_data + axfold: 1.0 + + #number of run with the same set of parameters i.e. number of different seeds + #integer + #enable only if read_architecture is false + run_nb: 1 + + diff --git a/example/parameters_150-5P13.yml b/doc/example/parameters_150-5P13.yml similarity index 100% rename from example/parameters_150-5P13.yml rename to doc/example/parameters_150-5P13.yml diff --git a/example/parameters_Ctr-3P2.yml b/doc/example/parameters_Ctr-3P2.yml similarity index 100% rename from example/parameters_Ctr-3P2.yml rename to doc/example/parameters_Ctr-3P2.yml diff --git a/example/parameters_architecture_generation.yml b/doc/example/parameters_architecture_generation.yml similarity index 100% rename from example/parameters_architecture_generation.yml rename to doc/example/parameters_architecture_generation.yml diff --git a/example/parameters_example_rsml_io.yml b/doc/example/parameters_example_rsml_io.yml similarity index 100% rename from example/parameters_example_rsml_io.yml rename to doc/example/parameters_example_rsml_io.yml diff --git a/example/parameters_plant_01.yml b/doc/example/parameters_plant_01.yml similarity index 100% rename from example/parameters_plant_01.yml rename to doc/example/parameters_plant_01.yml