fix issue #102

README.md

@@ -11,7 +11,7 @@ OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root
 architecture system generator package.
 
 <figure>
-    <img src="example/data/fig-6E.png" alt="Alt text" />
+    <img src="doc/example/data/fig-6E.png" alt="Alt text" />
     <figcaption>Heat map representation of the incoming local radial flows on an
 arabidopsis root.</figcaption>
 </figure>
@@ -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

example/Boursiac2022/boursiac2022.ipynb → 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')"
    ]
   },

example/example_archi_from_file.ipynb → 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": {

example/millet/Old/Millet_Root_Model.ipynb → doc/example/millet/Old/Millet_Root_Model.ipynb

@@ -336,9 +336,7 @@
      "output_type": "execute_result"
     }
    ],
-   "source": [
-    "FileLinks('.')"
-   ]
+   "source": "FileLinks('')"
   },
   {
    "cell_type": "code",

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
+
+