Index

B

build_snakemake_command() (in module photon_mosaic.cli)

C

configure_slurm_execution() (in module photon_mosaic.cli)

create_argument_parser() (in module photon_mosaic.cli) cross_platform_path() (in module photon_mosaic.snakemake_utils)

D

DatasetDiscoverer (class in photon_mosaic.dataset_discovery)

DatasetInfo (class in photon_mosaic.dataset_discovery) discover() (photon_mosaic.dataset_discovery.DatasetDiscoverer method)

E

ensure_default_config() (in module photon_mosaic.cli)

execute_pipeline_with_retry() (in module photon_mosaic.cli)

G

get_edited_options() (in module photon_mosaic.rules.suite2p_run)

get_session_name() (photon_mosaic.dataset_discovery.DatasetDiscoverer method) get_snakefile_path() (in module photon_mosaic.snakemake_utils)

L

load_and_process_config() (in module photon_mosaic.cli)

log_cuda_availability() (in module photon_mosaic.snakemake_utils)

M

main() (in module photon_mosaic.cli) module photon_mosaic.cli photon_mosaic.dataset_discovery photon_mosaic.preprocessing.contrast photon_mosaic.preprocessing.derotation photon_mosaic.preprocessing.noop photon_mosaic.rules.preprocessing photon_mosaic.rules.suite2p_run photon_mosaic.snakemake_utils

O

original_datasets (photon_mosaic.dataset_discovery.DatasetDiscoverer property)

original_name (photon_mosaic.dataset_discovery.DatasetInfo attribute)

P

photon_mosaic.cli module photon_mosaic.dataset_discovery module photon_mosaic.preprocessing.contrast module photon_mosaic.preprocessing.derotation module

photon_mosaic.preprocessing.noop module photon_mosaic.rules.preprocessing module photon_mosaic.rules.suite2p_run module photon_mosaic.snakemake_utils module

R

run() (in module photon_mosaic.preprocessing.contrast) (in module photon_mosaic.preprocessing.derotation) (in module photon_mosaic.preprocessing.noop)

run_preprocessing() (in module photon_mosaic.rules.preprocessing) run_suite2p() (in module photon_mosaic.rules.suite2p_run)

S

save_timestamped_config() (in module photon_mosaic.cli) session_metadata (photon_mosaic.dataset_discovery.DatasetDiscoverer property) (photon_mosaic.dataset_discovery.DatasetInfo attribute)

setup_output_directories() (in module photon_mosaic.cli) subject_metadata (photon_mosaic.dataset_discovery.DatasetDiscoverer property) (photon_mosaic.dataset_discovery.DatasetInfo attribute)

T

tiff_files (photon_mosaic.dataset_discovery.DatasetDiscoverer property) (photon_mosaic.dataset_discovery.DatasetInfo attribute)

tiff_files_flat (photon_mosaic.dataset_discovery.DatasetDiscoverer property) transformed_datasets (photon_mosaic.dataset_discovery.DatasetDiscoverer property) transformed_name (photon_mosaic.dataset_discovery.DatasetInfo attribute)

U

update_default_config() (in module photon_mosaic.cli)