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  • Installation
    • Developer Install - Ubuntu (linux)
      • 1. Miniconda installation
      • 2. Create virtual environment and activate it
      • 3. Install the strawberry package
      • 5. Optional packages
    • Developer Install - Windows 10
      • 1. Miniconda installation
      • 2. Create virtual environment and activate it
      • 3. Install the strawberry package
      • 4. Optional packages
    • Install with docker
      • 1. Docker installation
      • 2. Download and run the strawberry docker image
  • Quick start to use Strawberry
  • Gallery
  • Strawberry User Guide
    • 1. Import and read mtg file
      • 1.1. Modules requierement
        • 1.1.1. Import openalea module
        • 1.1.2. Import oawidget module
        • 1.1.3. Import strawberry modules
      • 1.2. Import mtg and read
      • 1.3. Somes functions to check if mtg are correctly read
        • 1.3.1. Display mtg
        • 1.3.2. Check properties contains in mtg
        • 1.3.3. Check varieties and the number of plant contain in mtg files
    • 2. Architecture visualisation
      • 2.1. Module requierement
      • 2.2. Import and load mtg file
      • 2.3. Visualisations
      • 2.4. 3D Visualizations
      • 2.5. 2D visualization
        • 2.5.1. 2D-Visualization plant by plant
        • 2.5.2. Visualization of the most central individuals
    • 3. Architecture analysis at module scale
      • 3.1. Module Requierement
        • 3.1.1. import standard python modules
        • 3.1.2. Import strawberry modules
      • 3.2. Import and read mtg files
      • 3.3. Extraction of data at module scale
      • 3.4. Exploratory data analysis at module scale
        • 3.4.1. Occurence of the successive module orders along time
        • 3.4.2. Pointwise mean no. Leaves, Flowers, Stolon by module order
        • 3.4.3. Number of stolons by module orders
        • 3.4.4. Type of Crowns (Extension crown vs Branch crowns)
        • 3.4.5. Distribution of complete vs complete module as function of module order
        • 3.4.6. As fonction of module orders
        • 3.4.7. As fonction of date
    • 4. Architecture analysis at node scale
      • 4.1. Module requierement
        • 4.1.1. Import standard module python
        • 4.1.2. Import strawberry modules
      • 4.2. Import and read mtg files
      • 4.3. Extraction of data at node scale
      • 4.4. Analysis at node scale
    • 5. Represent extracted variables into waffle plots
      • 5.1. Modules requirement
        • 5.1.1. Import external modules
        • 5.1.2. Import openalea modules
        • 5.1.3. Import strawberry modules
      • 5.2. Import MTG
      • 5.3. Waffle plot at node scale
        • 5.3.1. Create the waffle dataframe
        • 5.3.2. Plot the waffle
      • 5.4. 3. Waffle at module scale
        • 5.4.1. 3.1 Create waffle dataframe
        • 5.4.2. 3.2 plot the waffle
        • 5.4.3. 3.3 Crosstab
    • 6. Interactive usage through widgets
      • 6.1. Import & read MTG
        • 6.1.1. Display MTG informations
        • 6.1.2. Display MTG
      • 6.2. 2D & 3D visualization
        • 6.2.1. 2D
        • 6.2.2. 3D
      • 6.3. Analyses at plant scale
        • 6.3.1. Extract data
        • 6.3.2. Analyses
      • 6.4. Module scale
        • 6.4.1. Analyse single genotypes
        • 6.4.2. Multiple genotype analyses
        • 6.4.3. Waffle plot
      • 6.5. Node Scale analyses
        • 6.5.1. Waffle plot
  • API References
    • Strawberry import MTG function
      • add_axis_scale()
      • add_properties()
      • filter_none()
      • import_mtg_from_csv()
      • import_mtgfile()
      • name()
      • plant_number_by_varieties()
      • read_file()
      • strawberry_reader_csv()
      • topology()
      • union()
    • Strawberry analysis function
      • apparent_axis()
      • branching_type()
      • complete()
      • complete_module()
      • compute_leaf_area()
      • crown_status()
      • crowntype_distribution()
      • date()
      • df2waffle()
      • extract_at_module_scale()
      • extract_at_node_scale()
      • extract_at_plant_scale()
      • genotype()
      • is_axis_root()
      • mean_leaf_area()
      • median_individuals()
      • missing_leaves()
      • modality()
      • module_tree()
      • my_bt()
      • my_complete()
      • nb_aborted_flowers()
      • nb_branching_tree()
      • nb_branching_tree_weight()
      • nb_close_flowers()
      • nb_extension_tree()
      • nb_floral_buds()
      • nb_foliar_primordia()
      • nb_inflorescence()
      • nb_initiated_buds()
      • nb_open_flowers()
      • nb_stolons()
      • nb_total_flowers()
      • nb_total_leaves()
      • nb_total_module_tree()
      • nb_vegetative_buds()
      • nb_visible_leaves()
      • nb_visible_leaves_tree()
      • no_fruits()
      • occurence_module_order_along_time()
      • plant()
      • plot_pie()
      • plot_waffle()
      • plot_waffle_matplotlib()
      • plot_waffle_plotly_heatmap()
      • plot_waffle_plotly_imshow()
      • pointwisemean_plot()
      • prob_axillary_production()
      • property()
      • stage()
      • stage_tree()
      • strawberry_dataframe()
      • to_dataframe()
      • type_of_crown()
      • visible_modules()
      • write_sequences()
    • Strawberry geometry function
      • bud()
      • bud2d()
      • colors_turtle()
      • get_symbols()
      • get_symbols2d()
      • inflo_primordia()
      • inflo_primordia2d()
      • inflorescence()
      • inflorescence2d()
      • leaflet()
      • leaflet2d()
      • phytomer()
      • phytomer2d()
      • phytomer_primordia()
      • stolon()
      • stolon2d()
      • stolon_curve()
      • trifoliate()
      • trileaflet()
      • unifoliate()
      • unileaflet()
    • 2D-visualisation function
      • color_code()
      • complete_module()
      • drawable()
      • graph_layout()
      • is_visible()
      • my_visitor()
      • plot2d()
      • type_of_crown()
      • visible_modules()
    • 3D-visualisation function
      • color_code()
      • plant_positions()
      • plot3d()
      • strawberry_visitor()
      • visualise_plants()
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Gallery

../_images/mtg_graph.png

MTG Graph

../_images/capriss_3d.png

Visualization 3D

../_images/multi_modulescale.png

Module scale analysis: pointwisemean of total number of leaves

../_images/waffle_modulescale.png

Waffle representation: number of visible leaves at module scale

../_images/single_modulescale.png

Module scale analysis: occurence of successive module order

../_images/single_plantscale.png

Plant scale analysis: number of stolon accross time

../_images/occurence_plantscale.png

Pie plot representation: count the representation of each stage at plant scale

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© Copyright 2021, Marc Labadie, Christophe Pradal, Gaetan Heidsieck. Revision 9106ba85.

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