diff --git a/photon_mosaic/dataset_discovery.py b/photon_mosaic/dataset_discovery.py index 2a2c6bb..bab2272 100644 --- a/photon_mosaic/dataset_discovery.py +++ b/photon_mosaic/dataset_discovery.py @@ -142,9 +142,9 @@ def get_session_name(self, dataset_idx: int, session_idx: int) -> str: # session_idx here is actually the original session ID from the # folder name if session_meta: - return f"ses-{session_idx:03d}_{session_meta}" + return f"ses-{session_idx}_{session_meta}" else: - return f"ses-{session_idx:03d}" + return f"ses-{session_idx}" @staticmethod def _extract_session_id_from_folder_name(folder_name: str) -> str: @@ -640,8 +640,8 @@ def _extract_neuroblueprint_files( ) # Use the actual session ID as key, not enumerate index - tiff_files_by_session[int(session_id)] = files_in_session - session_meta_by_session[int(session_id)] = session_meta + tiff_files_by_session[session_id] = files_in_session + session_meta_by_session[session_id] = session_meta self._all_tiff_files.extend(files_in_session) logging.debug( @@ -724,10 +724,10 @@ def _extract_custom_files( ) # Use the actual session ID as key - tiff_files_by_session[int(session_id)] = ( + tiff_files_by_session[session_id] = ( files_in_session ) - session_meta_by_session[int(session_id)] = session_meta + session_meta_by_session[session_id] = session_meta self._all_tiff_files.extend(files_in_session) logging.debug( @@ -772,7 +772,7 @@ def _extract_custom_files( r"session-(\d+)", session_folder.name ) if session_id_match: - custom_session_id = int(session_id_match.group(1)) + custom_session_id = session_id_match.group(1) else: # If no session-XXX pattern, use enumerate starting # from 1 diff --git a/photon_mosaic/workflow/Snakefile b/photon_mosaic/workflow/Snakefile index 201bddb..fea25e7 100644 --- a/photon_mosaic/workflow/Snakefile +++ b/photon_mosaic/workflow/Snakefile @@ -26,6 +26,9 @@ logger = logging.getLogger("snakemake.workflow") onstart: log_cuda_availability() +envvars: + "PYTHONUNBUFFERED" + raw_data_base = Path(config["raw_data_base"]).resolve() processed_data_base = Path(config["processed_data_base"]).resolve() slurm_config = config.get("slurm", {}) diff --git a/photon_mosaic/workflow/preprocessing.smk b/photon_mosaic/workflow/preprocessing.smk index 53e4363..f5b3a73 100644 --- a/photon_mosaic/workflow/preprocessing.smk +++ b/photon_mosaic/workflow/preprocessing.smk @@ -45,7 +45,7 @@ rule preprocessing: / wildcards.session_name / "funcimg" ), - ses_idx=lambda wildcards: int(wildcards.session_name.split("_")[0].replace("ses-", "")), + ses_idx=lambda wildcards: wildcards.session_name.split("_")[0].replace("ses-", ""), wildcard_constraints: tiff="|".join(sorted(discoverer.tiff_files_flat)) if discoverer.tiff_files_flat else "dummy", subject_name="|".join(discoverer.transformed_datasets), @@ -59,6 +59,6 @@ rule preprocessing: Path(params.output_folder), config["preprocessing"], Path(params.dataset_folder), - ses_idx=int(params.ses_idx), + ses_idx=params.ses_idx, tiff_name=wildcards.tiff, ) diff --git a/photon_mosaic/workflow/suite2p.smk b/photon_mosaic/workflow/suite2p.smk index bc22dd6..4df1634 100644 --- a/photon_mosaic/workflow/suite2p.smk +++ b/photon_mosaic/workflow/suite2p.smk @@ -28,7 +28,7 @@ rule suite2p: / f"{output_pattern}{tiff_name}" ) for tiff_name in discoverer.tiff_files[discoverer.original_datasets[discoverer.transformed_datasets.index(wildcards.subject_name)]][ - int(wildcards.session_name.split("_")[0].replace("ses-", "")) + wildcards.session_name.split("_")[0].replace("ses-", "") ] ], output: