def test_visualization_omit_empty_datasets(
data_file_Fujita_nanData,
condition_file_Fujita
):
observable_num_list = [[0, 1]]
plot_data_and_simulation(data_file_Fujita_nanData, condition_file_Fujita,
observable_num_list=observable_num_list)
def test_save_plots_to_file(data_file_Isensee, condition_file_Isensee,
vis_spec_file_Isensee, simulation_file_Isensee):
with TemporaryDirectory() as temp_dir:
plot_data_and_simulation(data_file_Isensee,
condition_file_Isensee,
vis_spec_file_Isensee,
simulation_file_Isensee,
subplot_file_path=temp_dir)
def test_visualization_empty_visu_file(data_file_Fujita, condition_file_Fujita,
visu_file_Fujita_empty):
"""
Test: Empty visualization spezification file should default to routine
for no file at all
"""
plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
visu_file_Fujita_empty)
def test_visualization_with_vis(
data_file_Isensee,
condition_file_Isensee,
vis_spec_file_Isensee
):
plot_data_and_simulation(data_file_Isensee,
condition_file_Isensee,
vis_spec_file_Isensee)
def test_visualization_minimal_data_file(data_file_Fujita_minimal,
condition_file_Fujita,
visu_file_Fujita_small):
"""
Test visualization, with the case: data file only with mandatory columns
(optional columns are optional)
"""
plot_data_and_simulation(data_file_Fujita_minimal, condition_file_Fujita,
visu_file_Fujita_small)
def test_visualization_minimal_visu_file(data_file_Fujita,
condition_file_Fujita,
visu_file_Fujita_minimal):
"""
Test: visualization spezification file only with mandatory column plotId
(optional columns are optional)
"""
plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
visu_file_Fujita_minimal)
def test_visualization_small_visu_file_w_datasetid(data_file_Fujita,
condition_file_Fujita,
visu_file_Fujita_small):
"""
Test: visualization spezification file only with few columns in
particular datasetId
(optional columns are optional)
"""
plot_data_and_simulation(data_file_Fujita, condition_file_Fujita,
visu_file_Fujita_small)
def test_visualization_with_dataset_list(data_file_Isensee,
condition_file_Isensee):
datasets = [[
'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl',
'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk'
],
[
'JI09_160201_Drg453-452_CycNuc__ctrl',
'JI09_160201_Drg453-452_CycNuc__Fsk',
'JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM'
]]
plot_data_and_simulation(data_file_Isensee,
condition_file_Isensee,
dataset_id_list=datasets)
def test_visualization_warnings(data_file_Isensee, condition_file_Isensee):
datasets = [[
'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl',
'JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk'
],
[
'JI09_160201_Drg453-452_CycNuc__ctrl',
'JI09_160201_Drg453-452_CycNuc__Fsk',
'JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM'
]]
sim_cond_num_list = [[0, 1, 2], [0, 2, 3], [0, 3, 4], [0, 4, 5]]
observable_num_list = [[0], [1], [2], [0, 2], [1, 2]]
# close open figures to avoid runtime warnings
plt.close("all")
with warnings.catch_warnings(record=True) as warnMsg:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# plotting with datasetIds and sim conditions should issue a warning
plot_data_and_simulation(data_file_Isensee,
condition_file_Isensee,
dataset_id_list=datasets,
sim_cond_num_list=sim_cond_num_list)
# plotting with datasetIds and observables should issue a warning
plot_data_and_simulation(data_file_Isensee,
condition_file_Isensee,
dataset_id_list=datasets,
observable_num_list=observable_num_list)
# plotting with datasetIds and observables and sim conditions should
# issue a warning
plot_data_and_simulation(data_file_Isensee,
condition_file_Isensee,
dataset_id_list=datasets,
observable_num_list=observable_num_list,
sim_cond_num_list=sim_cond_num_list)
# plotting grouped by something else than datasetIds should issue a
# warning if datasetsIDs would have been available
plot_data_and_simulation(data_file_Isensee,
condition_file_Isensee,
sim_cond_num_list=sim_cond_num_list)
# test correct number of warnings
assert len(warnMsg) == 4
# test that all warnings were indeed UserWarnings
for i_warn in warnMsg:
assert issubclass(i_warn.category, UserWarning)
def test_visualization_without_datasets(data_file_Fujita,
condition_file_Fujita):
sim_cond_num_list = [[0, 1, 2], [0, 2, 3], [0, 3, 4], [0, 4, 5]]
sim_cond_id_list = [['model1_data1'], ['model1_data2', 'model1_data3'],
['model1_data4', 'model1_data5'], ['model1_data6']]
observable_num_list = [[0], [1], [2], [0, 2], [1, 2]]
observable_id_list = [['pS6_tot'], ['pEGFR_tot'], ['pAkt_tot']]
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
sim_cond_num_list=sim_cond_num_list,
plotted_noise='provided')
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
sim_cond_id_list=sim_cond_id_list)
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
observable_num_list=observable_num_list)
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
observable_id_list=observable_id_list,
plotted_noise='provided')
def test_visualization_raises(data_file_Fujita, condition_file_Fujita,
data_file_Fujita_wrongNoise):
sim_cond_num_list = [[0, 1, 2], [0, 2, 3], [0, 3, 4], [0, 4, 5]]
sim_cond_id_list = [['model1_data1'], ['model1_data2', 'model1_data3'],
['model1_data4', 'model1_data5'], ['model1_data6']]
observable_num_list = [[0], [1], [2], [0, 2], [1, 2]]
observable_id_list = [['pS6_tot'], ['pEGFR_tot'], ['pAkt_tot']]
error_counter = 0
# Combining simulation condition numbers and IDs should not be allowed
try:
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
sim_cond_num_list=sim_cond_num_list,
sim_cond_id_list=sim_cond_id_list)
except NotImplementedError as ErrMsg:
assert (ErrMsg.args[0] == 'Either specify a list of simulation '
'condition IDs or a list of simulation '
'condition numbers, but not both. '
'Stopping.')
error_counter += 1
assert (error_counter == 1)
# Combining observable numbers and IDs should not be allowed
try:
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
observable_num_list=observable_num_list,
observable_id_list=observable_id_list)
except NotImplementedError as ErrMsg:
assert (ErrMsg.args[0] == 'Either specify a list of observable IDs or '
'a list of observable numbers, but not both. '
'Stopping.')
error_counter += 1
assert (error_counter == 2)
# Combining observable and simulation conditions numbers or IDs should not
# be allowed
try:
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
sim_cond_num_list=observable_num_list,
observable_num_list=observable_num_list)
except NotImplementedError as ErrMsg:
assert (
ErrMsg.args[0] == 'Plotting without visualization specification'
' file and datasetId can be performed via '
'grouping by simulation conditions OR '
'observables, but not both. Stopping.')
error_counter += 1
assert (error_counter == 3)
try:
plot_data_and_simulation(data_file_Fujita,
condition_file_Fujita,
sim_cond_id_list=observable_id_list,
observable_id_list=observable_id_list)
except NotImplementedError as ErrMsg:
assert (
ErrMsg.args[0] == 'Plotting without visualization specification'
' file and datasetId can be performed via '
'grouping by simulation conditions OR '
'observables, but not both. Stopping.')
error_counter += 1
assert (error_counter == 4)
# If no numerical noise is provided, it should not work to plot it
try:
plot_measurements_by_observable(data_file_Fujita_wrongNoise,
condition_file_Fujita,
plotted_noise='provided')
except NotImplementedError as ErrMsg:
assert (ErrMsg.args[0] == "No numerical noise values provided in the "
"measurement table. Stopping.")
error_counter += 1
assert (error_counter == 5)
'time', 'time', 'time', 'time', 'concentration', 'concentration',
'concentration', 'concentration'
],
'xScale': ['lin', 'lin', 'lin', 'lin', 'log10', 'log10', 'log10', 'log10'],
'xLabel': [
'time [h]', 'time [h]', 'time [h]', 'time [h]',
r'concentration [$\mu$M]', r'concentration [$\mu$M]',
r'concentration [$\mu$M]', r'concentration [$\mu$M]'
],
'yValues': [
'D_obs', 'S_obs', 'G1_obs', 'G2_plus_M_obs', 'D_obs', 'S_obs',
'G1_obs', 'G2_plus_M_obs'
],
'yLabel': [
'cell count', 'cell count', 'cell count', 'cell count', 'cell count',
'cell count', 'cell count', 'cell count'
],
'yScale':
['log10', 'log10', 'log10', 'log10', 'log10', 'log10', 'log10', 'log10'],
'legendEntry': ['D', 'S', 'G1', 'G2_plus_M', 'D', 'S', 'G1', 'G2_plus_M'],
'xOffset': [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
})
plot_data_and_simulation(
exp_data=petab_problem.measurement_df,
exp_conditions=petab_problem.condition_df,
sim_data=simu_meas_df,
vis_spec=vis_spec,
)
plt.savefig(os.path.join(resultdir, f'simulation_and_data__{setting}.pdf'))
