Allow setting log level in run()

mesmerize_core/algorithms/_utils.py

@@ -0,0 +1,10 @@
+import logging
+from typing import Union
+
+def setup_logging(log_level: Union[int, str] = logging.INFO):
+    if isinstance(log_level, str):
+        log_level = getattr(logging, log_level)
+    logging.basicConfig(
+        format="{asctime} - {levelname} - [{filename} {funcName}() {lineno}] - pid {process} - {message}",
+        filename=None, force=True,
+        level=log_level, style="{") # logging level can be DEBUG, INFO, WARNING, ERROR, CRITICAL

mesmerize_core/algorithms/cnmf.py

@@ -16,12 +16,16 @@
 if __name__ in ["__main__", "__mp_main__"]:  # when running in subprocess
     from mesmerize_core import set_parent_raw_data_path, load_batch
     from mesmerize_core.utils import IS_WINDOWS
+    from mesmerize_core.algorithms._utils import setup_logging
 else:  # when running with local backend
     from ..batch_utils import set_parent_raw_data_path, load_batch
     from ..utils import IS_WINDOWS
+    from ._utils import setup_logging
 
 
-def run_algo(batch_path, uuid, data_path: str = None):
+def run_algo(batch_path, uuid, data_path: str = None, log_level=None):
+    if log_level is not None:
+        setup_logging(log_level)
     algo_start = time.time()
     set_parent_raw_data_path(data_path)
 
@@ -147,9 +151,10 @@ def run_algo(batch_path, uuid, data_path: str = None):
 @click.command()
 @click.option("--batch-path", type=str)
 @click.option("--uuid", type=str)
-@click.option("--data-path")
-def main(batch_path, uuid, data_path: str = None):
-    run_algo(batch_path, uuid, data_path)
+@click.option("--data-path", default=None)
+@click.option("--log-level", type=int, default=None)
+def main(batch_path, uuid, data_path, log_level):
+    run_algo(batch_path, uuid, data_path, log_level=log_level)
 
 
 if __name__ == "__main__":

mesmerize_core/algorithms/cnmfe.py

@@ -13,12 +13,16 @@
 if __name__ in ["__main__", "__mp_main__"]:  # when running in subprocess
     from mesmerize_core import set_parent_raw_data_path, load_batch
     from mesmerize_core.utils import IS_WINDOWS
+    from mesmerize_core.algorithms._utils import setup_logging
 else:  # when running with local backend
     from ..batch_utils import set_parent_raw_data_path, load_batch
     from ..utils import IS_WINDOWS
+    from ._utils import setup_logging
 
 
-def run_algo(batch_path, uuid, data_path: str = None):
+def run_algo(batch_path, uuid, data_path: str = None, log_level=None):
+    if log_level is not None:
+        setup_logging(log_level)
     algo_start = time.time()
     set_parent_raw_data_path(data_path)
 
@@ -128,9 +132,10 @@ def run_algo(batch_path, uuid, data_path: str = None):
 @click.command()
 @click.option("--batch-path", type=str)
 @click.option("--uuid", type=str)
-@click.option("--data-path")
-def main(batch_path, uuid, data_path: str = None):
-    run_algo(batch_path, uuid, data_path)
+@click.option("--data-path", default=None)
+@click.option("--log-level", type=int, default=None)
+def main(batch_path, uuid, data_path, log_level):
+    run_algo(batch_path, uuid, data_path, log_level=log_level)
 
 
 if __name__ == "__main__":

mesmerize_core/algorithms/mcorr.py

@@ -14,11 +14,15 @@
 # prevent circular import
 if __name__ in ["__main__", "__mp_main__"]:  # when running in subprocess
     from mesmerize_core import set_parent_raw_data_path, load_batch
+    from mesmerize_core.algorithms._utils import setup_logging
 else:  # when running with local backend
     from ..batch_utils import set_parent_raw_data_path, load_batch
+    from ._utils import setup_logging
 
 
-def run_algo(batch_path, uuid, data_path: str = None):
+def run_algo(batch_path, uuid, data_path: str = None, log_level=None):
+    if log_level is not None:
+        setup_logging(log_level)
     algo_start = time.time()
     set_parent_raw_data_path(data_path)
 
@@ -156,9 +160,10 @@ def run_algo(batch_path, uuid, data_path: str = None):
 @click.command()
 @click.option("--batch-path", type=str)
 @click.option("--uuid", type=str)
-@click.option("--data-path", type=str)
-def main(batch_path, uuid, data_path: str = None):
-    run_algo(batch_path, uuid, data_path)
+@click.option("--data-path", default=None)
+@click.option("--log-level", type=int, default=None)
+def main(batch_path, uuid, data_path, log_level):
+    run_algo(batch_path, uuid, data_path, log_level=log_level)
 
 
 if __name__ == "__main__":

mesmerize_core/caiman_extensions/common.py

@@ -9,6 +9,7 @@
 from datetime import datetime
 import time
 from copy import deepcopy
+import logging
 
 import numpy as np
 import pandas as pd
@@ -536,10 +537,14 @@ def _run_local(
         batch_path: Path,
         uuid: UUID,
         data_path: Union[Path, None],
+        log_level=None,
     ):
         algo_module = getattr(algorithms, algo)
         algo_module.run_algo(
-            batch_path=str(batch_path), uuid=str(uuid), data_path=str(data_path)
+            batch_path=str(batch_path),
+            uuid=str(uuid),
+            data_path=str(data_path),
+            log_level=log_level
         )
 
         return DummyProcess()
@@ -643,6 +648,7 @@ def run(self, backend: Optional[str] = None, wait: bool = True, **kwargs):
                 batch_path=batch_path,
                 uuid=self._series["uuid"],
                 data_path=get_parent_raw_data_path(),
+                log_level=kwargs.get("log_level")
             )
 
         # Create the runfile in the batch dir using this Series' UUID as the filename
@@ -660,6 +666,15 @@ def run(self, backend: Optional[str] = None, wait: bool = True, **kwargs):
         if get_parent_raw_data_path() is not None:
             args_str += f" --data-path {lex.quote(str(get_parent_raw_data_path()))}"
 
+        # set log level
+        if 'log_level' in kwargs:
+            level = kwargs['log_level']
+            if isinstance(level, str):
+                level = getattr(logging, level)
+        else:
+            level = logging.getLogger().getEffectiveLevel()
+        args_str += f" --log-level {level}"
+
         # make the runfile
         runfile_path = make_runfile(
             module_path=os.path.abspath(