from shutil import rmtree
import pandas as pd
from pandas.testing import assert_frame_equal
from neuralactivitycubic.view import WidgetsInterface
test_filepath = Path('../test_data/00')
example_results_dir = Path('../test_data/00/example_test_results_for_spiking_neuron')
results_filepath = Path('../test_data/00/results_directory')
def test_correct_model_run():
correct_config = WidgetsInterface().export_user_settings()
correct_config.data_source_path = test_filepath / 'spiking_neuron.avi'
correct_config.save_single_trace_results = True
model = Model(correct_config)
model.create_analysis_jobs()
model.run_analysis()
# evil hacks
return model.analysis_job_queue[0].results_dir_path
def test_correct_model_run_with_custom_results_dir():
correct_config = WidgetsInterface().export_user_settings()
correct_config.data_source_path = test_filepath / 'spiking_neuron.avi'
correct_config.results_filepath = results_filepath
model = Model(correct_config)
model.create_analysis_jobs()
model.run_analysis()
return correct_config.results_filepathmodel
Defines data and processing structures.
Logger
Logger ()
Initialize self. See help(type(self)) for accurate signature.
Model
Model (config:neuralactivitycubic.datamodels.Config|str)
Initialize self. See help(type(self)) for accurate signature.
Setup for testing:
def _test_csv_files(relative_filepath_to_csv: str, results_dir: Path) -> bool:
filepath = results_dir / relative_filepath_to_csv
# confirm results have been created:
if not filepath.is_file():
return False
# confirm computational consistency of results, while allowing minor numerical tolerance
df_test = pd.read_csv(filepath)
df_validation = pd.read_csv(example_results_dir / relative_filepath_to_csv)
if assert_frame_equal(df_test, df_validation) is not None:
return False
else:
return True
def test_all_peak_results(results_dir):
return _test_csv_files('all_peak_results.csv', results_dir)
def test_amplitude_and_df_over_f_results(results_dir):
return _test_csv_files('Amplitude_and_dF_over_F_results.csv', results_dir)
def test_auc_results(results_dir):
return _test_csv_files('AUC_results.csv', results_dir)
def test_variance_area_results(results_dir):
return _test_csv_files('Variance_area_results.csv', results_dir)
def test_representative_single_trace_results(results_dir):
return _test_csv_files('single_traces/data_of_ROI_7-10.csv', results_dir)def test_activity_overview_png(results_dir):
filepath = results_dir / 'activity_overview.png'
return filepath.is_file()
def test_roi_label_ids_overview_png(results_dir):
filepath = results_dir / 'ROI_label_IDs_overview.png'
return filepath.is_file()
def test_individual_traces_with_identified_events_pdf(results_dir):
filepath = results_dir / 'Individual_traces_with_identified_events.pdf'
return filepath.is_file()
def test_logs_txt(results_dir):
filepath = results_dir / 'logs.txt'
return filepath.is_file()
def test_user_settings_json(results_dir):
filepath = results_dir / 'user_settings.json'
return filepath.is_file()
def test_nwb_export(results_dir):
filepath = results_dir / 'autogenerated_nwb_file.nwb'Run tests:
# confirm that model can be executed:
results_directory = test_correct_model_run()
assert results_directory.exists()
# confirm all csv files have been created and are correct:
assert test_all_peak_results(results_directory), 'There is an issue with the "all_peak_results.csv" file!'
assert test_amplitude_and_df_over_f_results(results_directory)
assert test_auc_results(results_directory)
assert test_variance_area_results(results_directory)
assert test_representative_single_trace_results(results_directory)
# confirm all other result files have been created:
assert test_activity_overview_png(results_directory)
assert test_roi_label_ids_overview_png(results_directory)
assert test_individual_traces_with_identified_events_pdf(results_directory)
assert test_logs_txt(results_directory)
assert test_user_settings_json(results_directory)
# cleanup
rmtree(results_directory)02-07-25 12:00:54.655666 (UTC): Basic configurations for data import validated. Starting creation of analysis job(s)...
02-07-25 12:00:54.655714 (UTC): Starting with Job creation(s) for ../test_data/00/spiking_neuron.avi
02-07-25 12:00:54.655767 (UTC): Found recording file of supported type at: ../test_data/00/spiking_neuron.avi.
02-07-25 12:00:54.655823 (UTC): Successfully created a single job for ../test_data/00/spiking_neuron.avi at queue position: #1.
02-07-25 12:00:54.655838 (UTC): Finished Job creation(s) for ../test_data/00/spiking_neuron.avi!
02-07-25 12:00:54.655845 (UTC): All job creation(s) completed.
02-07-25 12:00:54.655853 (UTC): Configurations for Analysis Settings and Result Creation validated successfully.
02-07-25 12:00:54.655861 (UTC): Analysis Settings are:
02-07-25 12:00:54.655918 (UTC): batch_mode: False
02-07-25 12:00:54.655927 (UTC): baseline_estimation_method: asls
02-07-25 12:00:54.655933 (UTC): customize_octave_filtering: False
02-07-25 12:00:54.655940 (UTC): data_source_path: ../test_data/00/spiking_neuron.avi
02-07-25 12:00:54.655946 (UTC): end_frame_idx: 500
02-07-25 12:00:54.655953 (UTC): focus_area_enabled: False
02-07-25 12:00:54.655959 (UTC): focus_area_filepath: None
02-07-25 12:00:54.655966 (UTC): grid_size: 10
02-07-25 12:00:54.655972 (UTC): include_variance: False
02-07-25 12:00:54.655979 (UTC): mean_signal_threshold: 10.0
02-07-25 12:00:54.655985 (UTC): min_octave_span: 1.0
02-07-25 12:00:54.655991 (UTC): min_peak_count: 2
02-07-25 12:00:54.655998 (UTC): noise_window_size: 200
02-07-25 12:00:54.656004 (UTC): recording_filepath: None
02-07-25 12:00:54.656011 (UTC): results_filepath: None
02-07-25 12:00:54.656017 (UTC): roi_filepath: None
02-07-25 12:00:54.656023 (UTC): roi_mode: grid
02-07-25 12:00:54.656029 (UTC): save_overview_png: True
02-07-25 12:00:54.656035 (UTC): save_single_trace_results: True
02-07-25 12:00:54.656044 (UTC): save_summary_results: True
02-07-25 12:00:54.656050 (UTC): signal_to_noise_ratio: 3.0
02-07-25 12:00:54.656056 (UTC): start_frame_idx: 0
02-07-25 12:00:54.656062 (UTC): use_frame_range: False
02-07-25 12:00:54.656068 (UTC): variance_window_size: 15
02-07-25 12:00:54.656075 (UTC): Starting analysis...
02-07-25 12:00:54.656083 (UTC): Starting to process analysis job with index #0.
02-07-25 12:00:55.381320 (UTC): Analysis successfully completed. Continue with creation of results..
02-07-25 12:00:58.072123 (UTC): Results successfully created at: ../test_data/00/2025_07_02_14-00-54_results_for_spiking_neuron
Logs saved to ../test_data/00/2025_07_02_14-00-54_results_for_spiking_neuron/logs.txt
02-07-25 12:00:58.072675 (UTC): Updating all log files to contain all logs as final step. All valid logs files will end with this message.
Logs saved to ../test_data/00/2025_07_02_14-00-54_results_for_spiking_neuron/logs.txt
# confirm that model can be executed with custom results directory:
results_directory = test_correct_model_run_with_custom_results_dir()
assert results_directory.exists()
# confirm all csv files have been created and are correct:
assert test_all_peak_results(results_directory), 'There is an issue with the "all_peak_results.csv" file!'
assert test_amplitude_and_df_over_f_results(results_directory)
assert test_auc_results(results_directory)
assert test_variance_area_results(results_directory)
# confirm all other result files have been created:
assert test_activity_overview_png(results_directory)
assert test_roi_label_ids_overview_png(results_directory)
assert test_logs_txt(results_directory)
assert test_user_settings_json(results_directory)
# cleanup
rmtree(results_directory)02-07-25 12:00:58.375384 (UTC): Basic configurations for data import validated. Starting creation of analysis job(s)...
02-07-25 12:00:58.375449 (UTC): Starting with Job creation(s) for ../test_data/00/spiking_neuron.avi
02-07-25 12:00:58.375495 (UTC): Found recording file of supported type at: ../test_data/00/spiking_neuron.avi.
02-07-25 12:00:58.375540 (UTC): Successfully created a single job for ../test_data/00/spiking_neuron.avi at queue position: #1.
02-07-25 12:00:58.375549 (UTC): Finished Job creation(s) for ../test_data/00/spiking_neuron.avi!
02-07-25 12:00:58.375556 (UTC): All job creation(s) completed.
02-07-25 12:00:58.375563 (UTC): Configurations for Analysis Settings and Result Creation validated successfully.
02-07-25 12:00:58.375571 (UTC): Analysis Settings are:
02-07-25 12:00:58.375635 (UTC): batch_mode: False
02-07-25 12:00:58.375645 (UTC): baseline_estimation_method: asls
02-07-25 12:00:58.375652 (UTC): customize_octave_filtering: False
02-07-25 12:00:58.375659 (UTC): data_source_path: ../test_data/00/spiking_neuron.avi
02-07-25 12:00:58.375666 (UTC): end_frame_idx: 500
02-07-25 12:00:58.375673 (UTC): focus_area_enabled: False
02-07-25 12:00:58.375680 (UTC): focus_area_filepath: None
02-07-25 12:00:58.375686 (UTC): grid_size: 10
02-07-25 12:00:58.375693 (UTC): include_variance: False
02-07-25 12:00:58.375699 (UTC): mean_signal_threshold: 10.0
02-07-25 12:00:58.375706 (UTC): min_octave_span: 1.0
02-07-25 12:00:58.375712 (UTC): min_peak_count: 2
02-07-25 12:00:58.375718 (UTC): noise_window_size: 200
02-07-25 12:00:58.375725 (UTC): recording_filepath: None
02-07-25 12:00:58.375731 (UTC): results_filepath: ../test_data/00/results_directory
02-07-25 12:00:58.375738 (UTC): roi_filepath: None
02-07-25 12:00:58.375744 (UTC): roi_mode: grid
02-07-25 12:00:58.375751 (UTC): save_overview_png: True
02-07-25 12:00:58.375758 (UTC): save_single_trace_results: False
02-07-25 12:00:58.375765 (UTC): save_summary_results: True
02-07-25 12:00:58.375772 (UTC): signal_to_noise_ratio: 3.0
02-07-25 12:00:58.375778 (UTC): start_frame_idx: 0
02-07-25 12:00:58.375784 (UTC): use_frame_range: False
02-07-25 12:00:58.375791 (UTC): variance_window_size: 15
02-07-25 12:00:58.375798 (UTC): Starting analysis...
02-07-25 12:00:58.375806 (UTC): Starting to process analysis job with index #0.
02-07-25 12:00:59.002000 (UTC): Analysis successfully completed. Continue with creation of results..
02-07-25 12:01:01.558814 (UTC): Results successfully created at: ../test_data/00/results_directory
Logs saved to ../test_data/00/results_directory/logs.txt
02-07-25 12:01:01.559384 (UTC): Updating all log files to contain all logs as final step. All valid logs files will end with this message.
Logs saved to ../test_data/00/results_directory/logs.txt