simul.simul
¶
Module Contents¶
-
class
simul.simul.
Simul
[source]¶ Generic simulator.
-
sim
(model, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)[source]¶ Time course simulator.
Parameters: - model – the model to process
- inputdir – the directory containing the model
- outputdir – the directory containing the output files
- cluster – local, lsf for Load Sharing Facility, sge for Sun Grid Engine.
- local_cpus – the number of CPU.
- runs – the number of model simulation
- output_msg – print the output messages on screen (available for cluster=’local’ only)
-
ps1
(model, scanned_par, simulate_intervals, single_param_scan_intervals, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)[source]¶ Single parameter scan.
Parameters: - model – the model to process
- scanned_par – the scanned parameter
- simulate_intervals – the time step of each simulation
- single_param_scan_intervals – the number of scans to perform
- inputdir – the directory containing the model
- outputdir – the directory to store the results
- cluster – local, lsf for Load Sharing Facility, sge for Sun Grid Engine.
- local_cpus – the number of CPU used.
- runs – the number of model simulation
- output_msg – print the output messages on screen (available for cluster=’local’ only)
-
ps2
(model, sim_length, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)[source]¶ Double paramter scan.
Parameters: - model – the model to process
- sim_length – the length of the simulation
- inputdir – the directory containing the model
- outputdir – the directory to store the results
- cluster – local, lsf for Load Sharing Facility, sge for Sun Grid Engine.
- local_cpus – the number of CPU.
- runs – the number of model simulation
- output_msg – print the output messages on screen (available for cluster=’local’ only)
-
pe
(model, inputdir, cluster, local_cpus, runs, outputdir, sim_data_dir, output_msg=False)[source]¶ parameter estimation.
Parameters: - model – the model to process
- inputdir – the directory containing the model
- cluster – local, lsf for load sharing facility, sge for sun grid engine
- local_cpus – the number of cpu
- runs – the number of fits to perform
- outputdir – the directory to store the results
- sim_data_dir – the directory containing the simulation data sets
- output_msg – print the output messages on screen (available for cluster=’local’ only)
-
get_sim_columns
(path_in=".")[source]¶ Return the columns to analyse (sim task)
Parameters: path_in – the path to the input files
-
get_best_fits
(path_in=".", path_out=".", filename_out="final_estimates.csv")[source]¶ Collect the final parameter estimates. Results are stored in filename_out.
Parameters: - path_in – the path to the input files
- path_out – the path to the output files
- filename_out – a global file containing the best fits from independent parameter estimations.
Returns: the number of retrieved files
-
get_all_fits
(path_in=".", path_out=".", filename_out="all_estimates.csv")[source]¶ Collect all the parameter estimates. Results are stored in filename_out.
Parameters: - path_in – the path to the input files
- path_out – the path to the output files
- filename_out – a global file containing all fits from independent parameter estimations.
Returns: the number of retrieved files
-
_run_par_comput
(model, inputdir, outputdir, cluster="local", local_cpus=1, runs=1, output_msg=False)[source]¶ Run generic parallel computation.
Parameters: - model – the model to process
- inputdir – the directory containing the model
- outputdir – the directory to store the results
- cluster – local, lsf for load sharing facility, sge for sun grid engine
- local_cpus – the number of cpus
- runs – the number of runs to perform
- output_msg – print the output messages on screen (available for cluster=’local’ only)
Returns: (groupid, group_model)
-
_get_model_group
(model)[source]¶ Return the model without extension concatenated with the groupid string :param model: the model name :return: the concatenated string
-
_move_reports
(inputdir, outputdir, model, groupid)[source]¶ Move the report files
Parameters: - inputdir – the directory containing the model
- outputdir – the directory containing the output files
- model – the model to process
- groupid – a string identifier in the file name characterising the batch of simulated models.
-
replace_str_in_report
(report)[source]¶ Replaces strings in a report file.
Parameters: report – a report file with its absolute path
-
_get_input_files
(path)[source]¶ Retrieve the input files in a path.
Parameters: path – the path containing the input files to retrieve Returns: the list of input files
-
_get_params_list
(filein)[source]¶ Return the list of parameter names from filein
Parameters: filein – a report file Returns: the list of parameter names
-
_write_params
(col_names, path_out, filename_out)[source]¶ Write the list of parameter names to filename_out
Parameters: - col_names – the list of parameter names
- path_out – the path to store filename_out
- filename_out – the output file to store the parameter names
-
_write_best_fits
(files, path_out, filename_out)[source]¶ Write the final estimates to filename_out
Parameters: - files – the list of parameter estimation reports
- path_out – the path to store the file combining the final (best) estimates (filename_out)
- filename_out – the file containing the final (best) estimates
-
_write_all_fits
(files, path_out, filename_out)[source]¶ Write all the estimates to filename_out
Parameters: - files – the list of parameter estimation reports
- path_out – the path to store the file combining all the estimates
- filename_out – the file containing all the estimates
-
_ps1_header_init
(report, scanned_par)[source]¶ Header report initialisation for single parameter scan pipeline.
Parameters: - report – a report
- scanned_par – the scanned parameter
:return a list containing the header or an empty list if no header was created.
-
ps1_postproc
(model, scanned_par, simulate_intervals, single_param_scan_intervals, outputdir)[source]¶ Perform post processing organisation to single parameter scan report files.
Parameters: - model – the model to process
- scanned_par – the scanned parameter
- simulate_intervals – the time step of each simulation
- single_param_scan_intervals – the number of scans to perform
- outputdir – the directory to store the results
-