diff --git a/benchmarks/cellfinder_core.py b/benchmarks/cellfinder_core.py index a929a211..14a3e358 100644 --- a/benchmarks/cellfinder_core.py +++ b/benchmarks/cellfinder_core.py @@ -17,7 +17,7 @@ from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER -class TimeBenchmarkPrepGIN: +class TimeBenchmark: """ A base class for timing benchmarks for the cellfinder workflow. @@ -142,7 +142,7 @@ def teardown(self): shutil.rmtree(Path(self.cfg._output_path).resolve()) -class TimeFullWorkflow(TimeBenchmarkPrepGIN): +class TimeFullWorkflow(TimeBenchmark): """ Time the full cellfinder workflow. @@ -151,7 +151,7 @@ class TimeFullWorkflow(TimeBenchmarkPrepGIN): Parameters ---------- - TimeBenchmarkPrepGIN : _type_ + TimeBenchmark : _type_ A base class for timing benchmarks for the cellfinder workflow. """ @@ -159,13 +159,13 @@ def time_workflow(self): run_workflow_from_cellfinder_run(self.cfg) -class TimeReadInputDask(TimeBenchmarkPrepGIN): +class TimeReadInputDask(TimeBenchmark): """ Time the reading input data operations with dask Parameters ---------- - TimeBenchmarkPrepGIN : _type_ + TimeBenchmark : _type_ A base class for timing benchmarks for the cellfinder workflow. """ @@ -176,20 +176,20 @@ def time_read_background_with_dask(self): read_with_dask(str(self.cfg._background_dir_path)) -class TimeDetectCells(TimeBenchmarkPrepGIN): +class TimeDetectAndClassifyCells(TimeBenchmark): """ Time the cell detection main pipeline (`cellfinder_run`) Parameters ---------- - TimeBenchmarkPrepGIN : _type_ + TimeBenchmark : _type_ A base class for timing benchmarks for the cellfinder workflow. """ # extend basic setup function def setup(self): # basic setup - TimeBenchmarkPrepGIN.setup(self) + TimeBenchmark.setup(self) # add input data as arrays to the config self.signal_array = read_with_dask(str(self.cfg._signal_dir_path)) @@ -225,11 +225,11 @@ def time_cellfinder_run(self): ) -class TimeSaveCells(TimeBenchmarkPrepGIN): +class TimeSaveCells(TimeBenchmark): # extend basic setup function def setup(self): # basic setup - TimeBenchmarkPrepGIN.setup(self) + TimeBenchmark.setup(self) # add input data as arrays to config self.signal_array = read_with_dask(str(self.cfg._signal_dir_path))