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Cellfinder config + path change #64

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merged 17 commits into from
Jan 10, 2024
Merged

Cellfinder config + path change #64

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5ef149b
pass all parameters to cellfinder_run
sfmig Dec 20, 2023
cb0d506
changed required, optional and internal fields. read_config passes. a…
sfmig Dec 20, 2023
974140b
add signal and background data from local
sfmig Dec 20, 2023
b41d743
add missing data config fixtures
sfmig Dec 20, 2023
574733c
mark GIN download data test as slow
sfmig Dec 20, 2023
075cc50
refactor config class methods and remove setup_workflow
sfmig Dec 22, 2023
40a658d
tests pass with default config
sfmig Dec 22, 2023
45c118d
remove unused fixtures
sfmig Dec 22, 2023
b911ef3
update entry point
sfmig Dec 22, 2023
a00177d
Merge branch 'main' into smg/cellfinder-config
sfmig Jan 9, 2024
e96a883
change cellfinder-core to cellfinder in pyproject
sfmig Jan 9, 2024
a511c36
update cellfinder to cellfinder_core
sfmig Jan 9, 2024
c15b09f
renaming cellfinder script workflow to cellfinder_core. fix entrypoin…
sfmig Jan 9, 2024
f8f2af6
docstrings for class config
sfmig Jan 9, 2024
7022785
fix entry point
sfmig Jan 9, 2024
bedd3ba
skip add input paths test
sfmig Jan 9, 2024
a1fab20
feedback from code review
sfmig Jan 10, 2024
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26 changes: 13 additions & 13 deletions benchmarks/cellfinder_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,11 @@
from cellfinder.core.main import main as cellfinder_run
from cellfinder.core.tools.IO import read_with_dask

from brainglobe_workflows.cellfinder_core.cellfinder import (
from brainglobe_workflows.cellfinder_core.cellfinder_core import (
CellfinderConfig,
run_workflow_from_cellfinder_run,
)
from brainglobe_workflows.cellfinder_core.cellfinder import (
from brainglobe_workflows.cellfinder_core.cellfinder_core import (
setup as setup_cellfinder_workflow,
)
from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER
Expand Down Expand Up @@ -112,14 +112,14 @@ def setup_cache(
_ = pooch.retrieve(
url=config.data_url,
known_hash=config.data_hash,
path=config.install_path,
path=config._install_path,
progressbar=True,
processor=pooch.Unzip(extract_dir=config.data_dir_relative),
)

# Check paths to input data should now exist in config
assert Path(config.signal_dir_path).exists()
assert Path(config.background_dir_path).exists()
assert Path(config._signal_dir_path).exists()
assert Path(config._background_dir_path).exists()

def setup(self):
"""
Expand All @@ -146,7 +146,7 @@ def teardown(self):
The input data is kept for all repeats of the same benchmark,
to avoid repeated downloads from GIN.
"""
shutil.rmtree(Path(self.cfg.output_path).resolve())
shutil.rmtree(Path(self.cfg._output_path).resolve())


class TimeFullWorkflow(TimeBenchmarkPrepGIN):
Expand Down Expand Up @@ -177,10 +177,10 @@ class TimeReadInputDask(TimeBenchmarkPrepGIN):
"""

def time_read_signal_with_dask(self):
read_with_dask(self.cfg.signal_dir_path)
read_with_dask(self.cfg._signal_dir_path)

def time_read_background_with_dask(self):
read_with_dask(self.cfg.background_dir_path)
read_with_dask(self.cfg._background_dir_path)


class TimeDetectCells(TimeBenchmarkPrepGIN):
Expand All @@ -199,8 +199,8 @@ def setup(self):
TimeBenchmarkPrepGIN.setup(self)

# add input data as arrays to config
self.signal_array = read_with_dask(self.cfg.signal_dir_path)
self.background_array = read_with_dask(self.cfg.background_dir_path)
self.signal_array = read_with_dask(self.cfg._signal_dir_path)
self.background_array = read_with_dask(self.cfg._background_dir_path)

def time_cellfinder_run(self):
cellfinder_run(
Expand All @@ -215,13 +215,13 @@ def setup(self):
TimeBenchmarkPrepGIN.setup(self)

# add input data as arrays to config
self.signal_array = read_with_dask(self.cfg.signal_dir_path)
self.background_array = read_with_dask(self.cfg.background_dir_path)
self.signal_array = read_with_dask(self.cfg._signal_dir_path)
self.background_array = read_with_dask(self.cfg._background_dir_path)

# detect cells
self.detected_cells = cellfinder_run(
self.signal_array, self.background_array, self.cfg.voxel_sizes
)

def time_save_cells(self):
save_cells(self.detected_cells, self.cfg.detected_cells_path)
save_cells(self.detected_cells, self.cfg._detected_cells_path)
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