Closed dweindl closed 2 years ago
What exactly doesn't work? The old code wasn't removed yet, so they should be fine
---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
/tmp/ipykernel_509298/4631237.py in <module>
----> 1 ax_without_sim = plot_data_and_simulation(
2 data_file_path,
3 condition_file_path,
4 visualization_file_path)
5 plt.show()
~/src/libpetab-python/petab/visualize/plot_data_and_simulation.py in plot_data_and_simulation(exp_data, exp_conditions, vis_spec, sim_data, dataset_id_list, sim_cond_id_list, sim_cond_num_list, observable_id_list, observable_num_list, plotted_noise, subplot_file_path)
179 for _, plot_spec in vis_spec[ind_plot].iterrows():
180 # handle plot of current dataset
--> 181 handle_dataset_plot(plot_spec, ax, exp_data,
182 exp_conditions, sim_data)
183
~/src/libpetab-python/petab/visualize/helper_functions.py in handle_dataset_plot(plot_spec, ax, exp_data, exp_conditions, sim_data)
890 nan_set = all([np.isnan(val) for val in measurement_to_plot['mean']])
891 if not nan_set:
--> 892 plot_lowlevel(plot_spec, ax, conditions, measurement_to_plot, plot_sim)
893
894 # Beautify plots
~/src/libpetab-python/petab/visualize/plotting_config.py in plot_lowlevel(plot_spec, ax, conditions, ms, plot_sim)
158 elif plot_spec[PLOT_TYPE_SIMULATION] == SCATTER_PLOT:
159 if not plot_sim:
--> 160 raise NotImplementedError('Scatter plots do not work without'
161 ' simulation data')
162 ax.scatter(ms['mean'], ms['sim'],
NotImplementedError: Scatter plots do not work without simulation data
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
/tmp/ipykernel_635809/2240385560.py in <module>
6 visualization_files=visualization_file_path)
7
----> 8 ax = petab.visualize.plot_petab_problem(petab_problem=pp)
9
~/src/libpetab-python/petab/visualize/plot_data_and_simulation.py in plot_petab_problem(petab_problem, sim_data, dataset_id_list, sim_cond_id_list, sim_cond_num_list, observable_id_list, observable_num_list, plotted_noise)
229 DeprecationWarning)
230
--> 231 return plot_data_and_simulation(petab_problem.measurement_df,
232 petab_problem.condition_df,
233 petab_problem.visualization_df,
~/src/libpetab-python/petab/visualize/plot_data_and_simulation.py in plot_data_and_simulation(exp_data, exp_conditions, vis_spec, sim_data, dataset_id_list, sim_cond_id_list, sim_cond_num_list, observable_id_list, observable_num_list, plotted_noise, subplot_file_path)
142 vis_spec = core.get_visualization_df(vis_spec)
143
--> 144 exp_data, vis_spec = create_or_update_vis_spec(exp_data,
145 exp_conditions,
146 vis_spec,
~/src/libpetab-python/petab/visualize/helper_functions.py in create_or_update_vis_spec(exp_data, exp_conditions, vis_spec, dataset_id_list, sim_cond_id_list, sim_cond_num_list, observable_id_list, observable_num_list, plotted_noise)
684 # get other settings that could have potentially been there
685 # and expand according to plot_id_column
--> 686 vis_spec = expand_vis_spec_settings(vis_spec, columns_dict)
687
688 # if dataset_id is there, then nothing to expand?
~/src/libpetab-python/petab/visualize/helper_functions.py in expand_vis_spec_settings(vis_spec, columns_dict)
596 vis_spec[Y_VALUES] == columns_dict[Y_VALUES][i])
597 column_entries.append(
--> 598 vis_spec[select_conditions].loc[:, column].values[0])
599 else:
600 # get unique plotIDs from visspecfile
IndexError: index 0 is out of bounds for axis 0 with size 0
The old code wasn't removed yet, so they should be fine
Then they should be revised anyways - we don't want to advertise deprecated functions.
P.S.: I would suggest to use that as an opportunity to kick out the old visualization code in the next release. Any objections?
NotImplementedError: Scatter plots do not work without simulation data
This is because I've added scatter plot to visualization file in Isensee example. So that there are line plots, bar plot and scatter plot. But scatter plot only works if both measurements and simulations are available. In the old notebook Isensee example was used to demonstrate plots without simulations. With the modified visualization file it doesn't work. Fujita example can be used instead or another visualization file for Isensee.
Probably didn't survive the recent visualization refactoring...