bluepymm package

Subpackages

• bluepymm.prepare_combos package
  • Submodules
  • bluepymm.prepare_combos.create_mm_sqlite module
    • check_morphology_existence()
    • create_exemplar_rows()
    • create_mm_sqlite()
    • create_mm_sqlite_circuitmvd3()
    • remove_morph_regex_failures()
  • bluepymm.prepare_combos.main module
    • add_parser()
    • prepare_combos()
    • prepare_emodels()
  • bluepymm.prepare_combos.parse_files module
    • convert_emodel_etype_map()
    • fullmatch()
    • read_circuitmvd3()
    • read_mm_recipe()
    • read_mm_recipe_xml()
    • read_mm_recipe_yaml()
    • read_morph_records()
    • read_mtype_morph_map()
    • read_recipe_records()
    • verify_no_zero_percentage()
  • bluepymm.prepare_combos.prepare_emodel_dirs module
    • check_emodels_in_repo()
    • convert_emodel_input()
    • create_and_write_hoc_file()
    • get_emodel_dicts()
    • prepare_emodel_dir()
    • prepare_emodel_dirs()
  • Module contents
• bluepymm.run_combos package
  • Submodules
  • bluepymm.run_combos.calculate_scores module
    • calculate_scores()
    • create_arg_list()
    • expand_scores_to_score_values_table()
    • read_apical_point()
    • run_emodel_morph()
    • run_emodel_morph_isolated()
    • save_scores()
  • bluepymm.run_combos.main module
    • add_parser()
    • run_combos()
    • run_combos_from_conf()
  • Module contents
• bluepymm.select_combos package
  • Submodules
  • bluepymm.select_combos.main module
    • add_parser()
    • select_combos()
    • select_combos_from_conf()
  • bluepymm.select_combos.megate_output module
    • save_megate_results()
    • write_mecomboreleasejson()
  • bluepymm.select_combos.process_megate_config module
    • join_regex()
    • read_megate_thresholds()
    • read_to_skip_features()
  • bluepymm.select_combos.reporting module
    • add_plot_to_report()
    • create_final_db_and_write_report()
    • create_metype()
    • create_morphology_label()
    • pdf_file()
    • plot_dict()
    • plot_emodels_per_metype()
    • plot_emodels_per_morphology()
    • plot_median_per_metype()
    • plot_morphs_per_feature_for_emodel()
    • plot_morphs_per_mtype_for_emodel()
    • plot_stacked_bars()
  • bluepymm.select_combos.sqlite_io module
    • read_and_process_sqlite_score_tables()
  • bluepymm.select_combos.table_processing module
    • calc_median_scores()
    • check_opt_scores()
    • convert_extra_values()
    • process_combo_name()
    • process_emodel()
    • process_emodels()
    • row_threshold_transform()
    • select_passed_combos()
  • Module contents

Submodules

bluepymm.main module

Main

bluepymm.main.get_parser()[source]

Return the argument parser

bluepymm.main.main()[source]

Main

bluepymm.main.run(arg_list)[source]

Run BluePyMM

bluepymm.tools module

BluePyMM tools

class bluepymm.tools.NestedPool(processes=None, initializer=None, initargs=(), maxtasksperchild=None, context=None)[source]

Bases: Pool

Class that represents a MultiProcessing nested pool

Process(*args, **kwds)[source]

bluepymm.tools.cd(dir_name)[source]

Change directory

bluepymm.tools.check_all_combos_have_run(database, description)[source]

Verify that all entries of a given database have run.

Parameters:

• database – a pandas.DataFrame with a column ‘to_run’

• description – string that contains description of database

Returns:

True if the value of ‘to_run’ is False for all rows.

Raises:

• Exception, if the database contains at least one entry where the value –

• of 'to_run' is True. –

bluepymm.tools.check_compliance_with_neuron(template_name)[source]

Verify that a given name is compliant with the rules for a NEURON template name: a name should be a non-empty alphanumeric string, and start with a letter. Underscores are allowed. The length should not exceed 50 characters.

Returns:

True if compliant, false otherwise.

bluepymm.tools.check_no_null_nan_values(data, description)[source]

Check whether a pandas.DataFrame contains neither None nor NaN values.

Returns:

True if successful.

Return type:

bool

Raises:

Exception – if data contains at least one None or NaN value.

bluepymm.tools.decode_bstring(bstr_obj)[source]

Decodes and returns the str object from bytes.

Parameters:

bstr_obj – the bytes string object

Returns:

string object if conversion is successful, input object otherwise.

bluepymm.tools.get_neuron_compliant_template_name(name)[source]

Get template name that is compliant with NEURON based on given name.

Parameters:

name – string

Returns:

If name is NEURON-compliant, the same string is return. Otherwise, hyphens are replaced by underscores and if appropriate, the string is shortened. Leading numbers are removed.

bluepymm.tools.load_json(path)[source]

Load json file

bluepymm.tools.load_module(name, path)[source]

Try and load module name but only in path

from https://docs.python.org/2/library/imp.html#examples

bluepymm.tools.makedirs(path)[source]

mkdir but don’t fail when dir exists

bluepymm.tools.shorten_and_hash_string(label, keep_length=40, hash_length=9)[source]

Convert string to a shorter string if required.

Parameters:

• label – a string to be converted

• keep_length – length of the original string to keep. Default is 40 characters.

• hash_length – length of the hash to generate, should not be more then 20. Default is 9 characters.

Returns:

If the length of the original label is shorter than the sum of ‘keep_length’ and ‘hash_length’ plus one the original string is returned. Otherwise, a string with structure <partial>_<hash> is returned, where <partial> is the first part of the original string with length equal to <keep_length> and the last part is a hash of ‘hash_length’ characters, based on the original string.

Raises:

ValueError, if 'hash_length' exceeds 20. –

bluepymm.tools.write_json(output_dir, output_name, config)[source]

Write json file

Module contents

Init