strawberry
stable
Installation
Developer Install - Ubuntu (linux)
1. Miniconda installation
2. Create virtual environment and activate it
3. Install dependencies with conda
4. Install the strawberry package
5. Optional packages
Developer Install - Windows 10
1. Miniconda installation
2. Create virtual environment and activate it
3. Install dependencies with conda
4. Install the strawberry package
5. 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 analysis function
Strawberry geometry function
2D-visualisation function
3D-visualisation function
strawberry
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Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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G
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I
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L
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M
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N
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O
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P
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S
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T
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U
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V
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W
A
apparent_axis() (in module openalea.strawberry.analysis)
B
branching_type() (in module openalea.strawberry.analysis)
bud() (in module openalea.strawberry.geometry)
bud2d() (in module openalea.strawberry.geometry)
C
color_code() (in module openalea.strawberry.visu2d)
(in module openalea.strawberry.visu3d)
colors_turtle() (in module openalea.strawberry.geometry)
complete() (in module openalea.strawberry.analysis)
complete_module() (in module openalea.strawberry.analysis)
(in module openalea.strawberry.visu2d)
compute_leaf_area() (in module openalea.strawberry.analysis)
crown_status() (in module openalea.strawberry.analysis)
crowntype_distribution() (in module openalea.strawberry.analysis)
D
date() (in module openalea.strawberry.analysis)
df2waffle() (in module openalea.strawberry.analysis)
drawable() (in module openalea.strawberry.visu2d)
E
extract_at_module_scale() (in module openalea.strawberry.analysis)
extract_at_node_scale() (in module openalea.strawberry.analysis)
extract_at_plant_scale() (in module openalea.strawberry.analysis)
G
genotype() (in module openalea.strawberry.analysis)
get_symbols() (in module openalea.strawberry.geometry)
get_symbols2d() (in module openalea.strawberry.geometry)
graph_layout() (in module openalea.strawberry.visu2d)
I
inflo_primordia() (in module openalea.strawberry.geometry)
inflo_primordia2d() (in module openalea.strawberry.geometry)
inflorescence() (in module openalea.strawberry.geometry)
inflorescence2d() (in module openalea.strawberry.geometry)
is_axis_root() (in module openalea.strawberry.analysis)
is_visible() (in module openalea.strawberry.visu2d)
L
leaflet() (in module openalea.strawberry.geometry)
leaflet2d() (in module openalea.strawberry.geometry)
M
mean_leaf_area() (in module openalea.strawberry.analysis)
median_individuals() (in module openalea.strawberry.analysis)
missing_leaves() (in module openalea.strawberry.analysis)
modality() (in module openalea.strawberry.analysis)
module
openalea.strawberry.analysis
openalea.strawberry.geometry
openalea.strawberry.visu2d
openalea.strawberry.visu3d
module_tree() (in module openalea.strawberry.analysis)
my_bt() (in module openalea.strawberry.analysis)
my_complete() (in module openalea.strawberry.analysis)
my_visitor() (in module openalea.strawberry.visu2d)
N
nb_aborted_flowers() (in module openalea.strawberry.analysis)
nb_branching_tree() (in module openalea.strawberry.analysis)
nb_branching_tree_weight() (in module openalea.strawberry.analysis)
nb_extension_tree() (in module openalea.strawberry.analysis)
nb_floral_buds() (in module openalea.strawberry.analysis)
nb_foliar_primordia() (in module openalea.strawberry.analysis)
nb_inflorescence() (in module openalea.strawberry.analysis)
nb_initiated_buds() (in module openalea.strawberry.analysis)
nb_open_flowers() (in module openalea.strawberry.analysis)
nb_stolons() (in module openalea.strawberry.analysis)
nb_total_flowers() (in module openalea.strawberry.analysis)
nb_total_leaves() (in module openalea.strawberry.analysis)
nb_total_module_tree() (in module openalea.strawberry.analysis)
nb_vegetative_buds() (in module openalea.strawberry.analysis)
nb_visible_leaves() (in module openalea.strawberry.analysis)
nb_visible_leaves_tree() (in module openalea.strawberry.analysis)
O
occurence_module_order_along_time() (in module openalea.strawberry.analysis)
openalea.strawberry.analysis
module
openalea.strawberry.geometry
module
openalea.strawberry.visu2d
module
openalea.strawberry.visu3d
module
P
phytomer() (in module openalea.strawberry.geometry)
phytomer2d() (in module openalea.strawberry.geometry)
phytomer_primordia() (in module openalea.strawberry.geometry)
plant() (in module openalea.strawberry.analysis)
plant_positions() (in module openalea.strawberry.visu3d)
plot2d() (in module openalea.strawberry.visu2d)
plot3d() (in module openalea.strawberry.visu3d)
plot_pie() (in module openalea.strawberry.analysis)
plot_waffle() (in module openalea.strawberry.analysis)
plot_waffle_matplotlib() (in module openalea.strawberry.analysis)
plot_waffle_plotly_heatmap() (in module openalea.strawberry.analysis)
plot_waffle_plotly_imshow() (in module openalea.strawberry.analysis)
pointwisemean_plot() (in module openalea.strawberry.analysis)
prob_axillary_production() (in module openalea.strawberry.analysis)
property() (in module openalea.strawberry.analysis)
S
stage() (in module openalea.strawberry.analysis)
stage_tree() (in module openalea.strawberry.analysis)
stolon() (in module openalea.strawberry.geometry)
stolon2d() (in module openalea.strawberry.geometry)
stolon_curve() (in module openalea.strawberry.geometry)
strawberry_dataframe() (in module openalea.strawberry.analysis)
strawberry_visitor() (in module openalea.strawberry.visu3d)
T
to_dataframe() (in module openalea.strawberry.analysis)
trifoliate() (in module openalea.strawberry.geometry)
trileaflet() (in module openalea.strawberry.geometry)
type_of_crown() (in module openalea.strawberry.analysis)
(in module openalea.strawberry.visu2d)
U
unifoliate() (in module openalea.strawberry.geometry)
unileaflet() (in module openalea.strawberry.geometry)
V
visible_modules() (in module openalea.strawberry.analysis)
(in module openalea.strawberry.visu2d)
visualise_plants() (in module openalea.strawberry.visu3d)
W
write_sequences() (in module openalea.strawberry.analysis)
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