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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

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", {})

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,
         )

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: