Welcome to strawberry’s documentation!

The Strawberry package is an amazing tools for strawberry architectural analysis. It enables the construction & vizualisation of 2D/3D architecture. It is an extension of the software OpenAlea.

Contents

• Welcome to strawberry’s documentation!

  • Installation

  • Quick start

  • Gallery

  • Documentation

    • Strawberry User Guide

  • References

  • Authors

  • License

Installation

• 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

• Quick start to use Strawberry

Gallery

• Gallery

Documentation

Strawberry User Guide

• 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
        • 2.5.2.1. Extraction of data at plant scale using ariable.extract_at_plant_scale function
        • 2.5.2.2. Calcul of the most central individual for each date using analysis.median_individuals function from extraction_at_plant_scale
        • 2.5.2.3. Vizualisation of the most central plant along time
  • 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
        • 3.4.2.1. Pointwise mean no. leaves by module order and génotype
        • 3.4.2.2. Pointwise mean of no. total flowers by genotype and orders
      • 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

References

• 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()

Authors

• Marc Labadie

• Christophe Pradal

• Gaetan Heidsieck

License

Strawberry is released under a Cecill-C license.

Note

Cecill-C license is a LGPL compatible license.