From 3b68cf3e48bd3449b321d46be4e045478ecfaa9c Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Mon, 30 Dec 2024 10:49:04 +0100
Subject: [PATCH] Set the default logger to a stdout stream, and add option to
 manually specify an output directory for file loggers

---
 micro_manager/adaptivity/adaptivity.py        | 13 +++++++++---
 micro_manager/config.py                       | 20 ++++++++++++++++++-
 micro_manager/micro_manager.py                |  4 +---
 micro_manager/tools/logging_wrapper.py        | 12 ++++++++---
 ...ger-config-global-adaptivity-parallel.json |  1 +
 5 files changed, 40 insertions(+), 10 deletions(-)

diff --git a/micro_manager/adaptivity/adaptivity.py b/micro_manager/adaptivity/adaptivity.py
index 4feb63b..b61e008 100644
--- a/micro_manager/adaptivity/adaptivity.py
+++ b/micro_manager/adaptivity/adaptivity.py
@@ -37,9 +37,16 @@ def __init__(self, configurator, rank) -> None:
             configurator.get_adaptivity_similarity_measure()
         )
 
-        self._metrics_logger = Logger(
-            "Adaptivity", "adaptivity-metrics.csv", rank, csv_logger=True
-        )
+        output_dir = configurator.get_output_dir()
+
+        if output_dir is not None:
+            self._metrics_logger = Logger(
+                __name__, output_dir + "adaptivity-metrics.csv", rank, csv_logger=True
+            )
+        else:
+            self._metrics_logger = Logger(
+                __name__, "adaptivity-metrics.csv", rank=rank, csv_logger=True
+            )
 
         self._metrics_logger.log_info_one_rank(
             "Time Window,Avg Active Sims,Avg Inactive Sims,Max Active,Max Inactive"
diff --git a/micro_manager/config.py b/micro_manager/config.py
index 4e2cc32..deb0729 100644
--- a/micro_manager/config.py
+++ b/micro_manager/config.py
@@ -58,7 +58,7 @@ def __init__(self, config_file_name):
         self._postprocessing_file_name = None
         self._initialize_once = False
 
-        self._output_micro_sim_time = False
+        self._output_dir = None
 
     def set_logger(self, logger):
         """
@@ -93,6 +93,13 @@ def _read_json(self, config_file_name):
             .replace(".py", "")
         )
 
+        try:
+            self._output_dir = self._data["output_dir"]
+        except BaseException:
+            self._logger.log_info_one_rank(
+                "No output directory provided. Output (including logging) will be saved in the current working directory."
+            )
+
         try:
             self._write_data_names = self._data["coupling_params"]["write_data_names"]
             assert isinstance(
@@ -642,3 +649,14 @@ def create_single_sim_object(self):
             True if initialization is done only once, False otherwise.
         """
         return self._initialize_once
+
+    def get_output_dir_name(self):
+        """
+        Get the name of the output directory.
+
+        Returns
+        -------
+        output_dir : string
+            Name of the output folder.
+        """
+        return self._output_dir
diff --git a/micro_manager/micro_manager.py b/micro_manager/micro_manager.py
index 9636b83..3b54f98 100644
--- a/micro_manager/micro_manager.py
+++ b/micro_manager/micro_manager.py
@@ -57,9 +57,7 @@ def __init__(self, config_file: str) -> None:
         """
         super().__init__(config_file)
 
-        self._logger = Logger(
-            "MicroManagerCoupling", "micro-manager-coupling.log", self._rank
-        )
+        self._logger = Logger(__name__, self._rank)
 
         self._config.set_logger(self._logger)
         self._config.read_json_micro_manager()
diff --git a/micro_manager/tools/logging_wrapper.py b/micro_manager/tools/logging_wrapper.py
index 8ef7c6b..b1671bc 100644
--- a/micro_manager/tools/logging_wrapper.py
+++ b/micro_manager/tools/logging_wrapper.py
@@ -10,7 +10,9 @@ class Logger:
     Provides a logging wrapper for the Micro Manager classes.
     """
 
-    def __init__(self, name, log_file, rank=0, level=logging.INFO, csv_logger=False):
+    def __init__(
+        self, name, log_file=None, rank=0, level=logging.INFO, csv_logger=False
+    ):
         """
         Set up a logger.
 
@@ -19,7 +21,7 @@ def __init__(self, name, log_file, rank=0, level=logging.INFO, csv_logger=False)
         name : string
             Name of the logger.
         log_file : string
-            Name of the log file.
+            Name of the log file (default is "micro-manager.log").
         rank : int, optional
             Rank of the logger (default is 0).
         level : int, optional
@@ -30,7 +32,11 @@ def __init__(self, name, log_file, rank=0, level=logging.INFO, csv_logger=False)
 
         self._rank = rank
 
-        handler = logging.FileHandler(log_file)
+        if log_file is None:
+            handler = logging.StreamHandler()
+        else:
+            handler = logging.FileHandler(log_file)
+
         handler.setLevel(level)
 
         if csv_logger:
diff --git a/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json b/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json
index bd2c738..cc2cd67 100644
--- a/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json
+++ b/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json
@@ -1,5 +1,6 @@
 {
     "micro_file_name": "micro_dummy",
+    "output_dir": "adaptivity_output",
     "coupling_params": {
         "precice_config_file_name": "precice-config.xml",
         "macro_mesh_name": "macro-cube-mesh",