def update_btn_single():
genotype = genotypes_selection_single_genotype.v_model
if genotype:
vids = get_vid_of_genotype(misc.all_mtg, [genotype])
df = extract_at_module_scale(misc.all_mtg, vids=vids)
geno_frequency = occurence_module_order_along_time(
data=df, frequency_type="cdf")
update_btn_export(link_export_t11, geno_frequency)
if genotype:
vids = get_vid_of_genotype(misc.all_mtg, [genotype])
df = extract_at_module_scale(misc.all_mtg, vids=vids)
res = pd.crosstab(index=df["order"],
columns=df["complete_module"],
normalize="index")
res.columns = ["incomplete", "complete"]
update_btn_export(link_export_t12, res)
if genotype:
vids = get_vid_of_genotype(misc.all_mtg, [genotype])
df = extract_at_module_scale(misc.all_mtg, vids=vids)
res = pd.crosstab(index=df["date"],
columns=df["complete_module"],
normalize="index")
res.columns = ["incomplete", "complete"]
update_btn_export(link_export_t13, res)
def update_btn_multiple():
if misc.all_mtg:
df = extract_at_module_scale(misc.all_mtg)
Mean = df.groupby(["Genotype", "order"]).mean()
update_btn_export(link_export_t21, Mean)
if misc.all_mtg:
df = extract_at_module_scale(misc.all_mtg)
Mean = df.groupby(["Genotype", "order"]).mean()
update_btn_export(link_export_t22, Mean)
if misc.all_mtg:
df = extract_at_module_scale(misc.all_mtg)
Mean = df.groupby(["Genotype", "order"]).mean()
update_btn_export(link_export_t23, Mean)
if misc.all_mtg:
df = extract_at_module_scale(misc.all_mtg)
ctd = crowntype_distribution(data=df, crown_type="branch_crown")
ctd = ctd[ctd.index.get_level_values('order') != 0]
update_btn_export(link_export_t24, ctd)
if misc.all_mtg:
df = extract_at_module_scale(misc.all_mtg)
ctd = crowntype_distribution(data=df, crown_type="extension_crown")
ctd = ctd[ctd.index.get_level_values('order') != 0]
update_btn_export(link_export_t25, ctd)
def on_change_module_plot_type(widget, event, data):
if date_selection_waffle.v_model and parameter_selection_waffle.v_model:
with waffle:
waffle.clear_output()
genotype = genotypes_selection_waffle.v_model
vids = get_vid_of_genotype(misc.all_mtg, [genotype])
df = extract_at_module_scale(misc.all_mtg, vids=vids)
if aggfunc_selection_waffle.v_model == 'concat_string':
tmp = df2waffle(df,
index='order',
date=date_selection_waffle.v_model,
variable=parameter_selection_waffle.v_model,
aggfunc=lambda x: ' '.join(x),
crosstab=False)
else:
tmp = df2waffle(df,
index='order',
date=date_selection_waffle.v_model,
variable=parameter_selection_waffle.v_model,
aggfunc=aggfunc_selection_waffle.v_model,
crosstab=False)
fig = plot_waffle(
tmp,
# layout=layout,
plot_func=data)
display(fig)
def on_change_module_waffle_genotype(widget, event, data):
genotype = genotypes_selection_waffle.v_model
vids = get_vid_of_genotype(misc.all_mtg, [genotype])
df = extract_at_module_scale(misc.all_mtg, vids=vids)
param = list(df.columns)
param.remove("Genotype")
param.remove('date')
param.remove('order')
param.remove('plant')
date_selection_waffle.items = list(df.date.unique())
date_selection_waffle.v_model = ""
parameter_selection_waffle.items = param
def on_change_genotype_p4(widget, event, data):
# update table
df = pd.DataFrame()
if misc.all_mtg:
vids = get_vid_of_genotype(misc.all_mtg, genotypes=data)
df = extract_at_module_scale(misc.all_mtg, vids=vids)
update_grid(df, df_modulescale)
# update descriptors
update_grid(df.describe(), df_description)
# update the extraction button
update_btn_extract()
def test_extract_at_module_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette_extraction_at_module_scale = extract_at_module_scale(gariguette)
assert len(gariguette_extraction_at_module_scale) == 241
gariguette_frequency = occurence_module_order_along_time(data= gariguette_extraction_at_module_scale,frequency_type= "cdf")
assert len(gariguette_frequency) == 6
mean= gariguette_extraction_at_module_scale.groupby(["Genotype", "order"]).mean()
sd= gariguette_extraction_at_module_scale.groupby(["Genotype", "order"]).std()
assert len(mean) == 6
assert len(sd) == 6
def print_multiple_genotypes_plots():
if misc.all_mtg.property('Genotype'):
df = extract_at_module_scale(misc.all_mtg)
# plot pointwisemean leaves
fig = plot_module_pointwisemean(df, "nb_total_leaves")
transfert_figure(fig, plot_pointwisemean_leaves)
# plot pointwisemean flowers
fig = plot_module_pointwisemean(df, "nb_total_flowers")
transfert_figure(fig, plot_pointwisemean_flowers)
# plot pointwisemean stolons
fig = plot_module_pointwisemean(df, "nb_stolons")
transfert_figure(fig, plot_pointwisemean_stolons)
# crowntype branch
fig = plot_module_crown(df, "branch_crown")
transfert_figure(fig, plot_branch_crown)
# crowntype extension
fig = plot_module_crown(df, "extension_crown")
transfert_figure(fig, plot_extension_crown)
def print_single_genotype_plots():
genotype = genotypes_selection_single_genotype.v_model
vids = get_vid_of_genotype(misc.all_mtg, [genotype])
df = extract_at_module_scale(misc.all_mtg, vids=vids)
if genotype:
# plot occurence module order
fig = plot_module_occurence_module_order_along_time(df, genotype)
transfert_figure(fig, plot_occurence)
# plot occurence module order
fig = plot_module_distribution_complete_incomplete_module_order(
df, genotype)
transfert_figure(fig, plot_distribution_module_order)
# plot occurence module order
fig = plot_module_distribution_complete_incomplete_date(df, genotype)
transfert_figure(fig, plot_distribution_date)
else:
with plot_occurence:
plot_occurence.clear_output()
print('Select a Genotype')
def on_change_date_p3(widget, event, data):
genotype = genotypes_selection_analyze.v_model
vids = get_vid_of_genotype(misc.all_mtg, [genotype])
df = extract_at_module_scale(misc.all_mtg, vids=vids)
tmp = df2waffle(df,
index='order',
date=data,
variable='stage',
crosstab=True)
try:
fig = plot_pie(tmp)
fig.update_layout(
title="Percentage representation of each stage at one date")
transfert_figure_pie(fig, pie_plantscale)
except ValueError:
pass
def test_df2waffle():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtg = read_mtg_file(mtg_path['Capriss'])
df = extract_at_node_scale(mtg)
node_scale = df2waffle(df,
index='rank',
date='2015/03/02',
variable='branching_type')
assert node_scale.shape == (20, 9)
df = extract_at_module_scale(mtg)
module_scale = df2waffle(df,
index='order',
date='2015/03/02',
variable='crown_status',
aggfunc='median')
assert module_scale.shape == (3, 9)
def test_extract_at_module_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtg = MTG()
for k, genotype in enumerate(mtg_path):
if (genotype=="Sicile") or (genotype=="Nils") or (genotype=='origine_stolon_gariguetteDV_6novembre2018') \
or (genotype=='friendlyfruit_varieties'):
pass
else:
mtg = union(mtg, read_mtg_file(mtg_path[genotype]))
genotypes = mtg.property('Genotype')
for geno in set(genotypes.values()):
vids = [
vid for vid in mtg.vertices(scale=1) if genotypes.get(vid) == geno
]
df = extract_at_module_scale(mtg, vids)
assert not df.empty
assert set(df['Genotype']) == {geno}
def update_btn_extract():
genotype = genotypes_selection_extraction.v_model
if genotype:
vids = get_vid_of_genotype(misc.all_mtg, genotype)
df = extract_at_module_scale(misc.all_mtg, vids=vids)
update_btn_export(export_extraction, df)